diff --git a/docs/contents/related_projects.rst b/docs/contents/related_projects.rst index f0f32fc..d2a0961 100644 --- a/docs/contents/related_projects.rst +++ b/docs/contents/related_projects.rst @@ -4,5 +4,6 @@ Related projects - `BrainCoordinator `_ - `BrainCoord `_ - `VVASP `_ -- `Li2013 <10.1016/j.jneumeth.2013.08.017>`_ - `AtlasGuide: Software for stereotaxic guidance using 3D CT/MRI hybrid atlases of developing mouse brains` -- `Tokuno2009 <10.1016/j.neures.2009.08.004>`_ - Stereo Navi 2.0: Software for stereotaxic surgery of the common marmoset (Callithrix jacchus) \ No newline at end of file +- `Li2013 `_ - `AtlasGuide: Software for stereotaxic guidance using 3D CT/MRI hybrid atlases of developing mouse brains` +- `Tokuno2009 `_ - `Stereo Navi 2.0: Software for stereotaxic surgery of the common marmoset (Callithrix jacchus)` +- `Brainsight Vet `_ \ No newline at end of file diff --git a/joss_paper/neustim.bib b/joss_paper/neustim.bib new file mode 100644 index 0000000..c31363d --- /dev/null +++ b/joss_paper/neustim.bib @@ -0,0 +1,6379 @@ +@article{Abbott1999, + title = {Rationale and Derivation of {{MI}} and {{TI}}---a Review}, + author = {Abbott, John G.}, + year = {1999}, + month = mar, + journal = {Ultrasound in Medicine \& Biology}, + volume = {25}, + number = {3}, + pages = {431--441}, + issn = {03015629}, + doi = {10.1016/S0301-5629(98)00172-0}, + urldate = {2023-12-05}, + abstract = {This review article provides a summary rationale and derivation for the mechanical index (MI) and thermal index (TI) formulas presented in the body of the ``Standard for real-time display of thermal and mechanical acoustic output indices on diagnostic ultrasound equipment'' (AIUM/NEMA 1998).1 For purposes of simplicity, this standard is referred to in this article by its colloquial ``nickname,'' the ``output display standard'' or ODS. This review expands on the summary information provided in Appendix A of the ODS. Numerous references are made to the root publications from which the formulas were derived. As will be discussed in the derivation notes that follow, key parts of the MI and TI models rely heavily on experimental data. This document does not attempt to do any more than describe the relevant results of the experiments. A general overview is provided in the Introduction and Rationale for the nontechnical reader and the more rigorous Models and Derivation Notes provides a detailed mathematical review of the MI and TI models. A complete set of defined terms is provided in Appendix 1. {\copyright} 1999 World Federation for Ultrasound in Medicine \& Biology.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Abbott1999.pdf} +} + +@misc{Ahlers2023, + title = {Napari: A Multi-Dimensional Image Viewer for {{Python}}}, + shorttitle = {Napari}, + author = {Ahlers, Jannis and Althviz Mor{\'e}, Daniel and Amsalem, Oren and Anderson, Ashley and Bokota, Grzegorz and Boone, Peter and Bragantini, Jord{\~a}o and Buckley, Genevieve and Burt, Alister and Bussonnier, Matthias and Can Solak, Ahmet and Caporal, Cl{\'e}ment and Doncila Pop, Draga and Evans, Kira and Freeman, Jeremy and Gaifas, Lorenzo and Gohlke, Christoph and Gunalan, Kabilar and {Har-Gil}, Hagai and Harfouche, Mark and Harrington, Kyle I. S. and Hilsenstein, Volker and Hutchings, Katherine and Lambert, Talley and Lauer, Jessy and Lichtner, Gregor and Liu, Ziyang and Liu, Lucy and Lowe, Alan and Marconato, Luca and Martin, Sean and McGovern, Abigail and Migas, Lukasz and Miller, Nadalyn and Mu{\~n}oz, Hector and M{\"u}ller, Jan-Hendrik and {Nauroth-Kre{\ss}}, Christopher and {Nunez-Iglesias}, Juan and Pape, Constantin and Pevey, Kim and {Pe{\~n}a-Castellanos}, Gonzalo and Pierr{\'e}, Andrea and {Rodr{\'i}guez-Guerra}, Jaime and Ross, David and Royer, Loic and Russell, Craig T. and Selzer, Gabriel and Smith, Paul and Sobolewski, Peter and Sofiiuk, Konstantin and Sofroniew, Nicholas and Stansby, David and Sweet, Andrew and Vierdag, Wouter-Michiel and Wadhwa, Pam and Weber Mendon{\c c}a, Melissa and Windhager, Jonas and Winston, Philip and Yamauchi, Kevin}, + year = {2023}, + month = jul, + doi = {10.5281/ZENODO.3555620}, + urldate = {2023-10-31}, + abstract = {napari 0.4.18 We're happy to announce the release of napari 0.4.18! napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images. It's built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy). This is primarily a bug-fix release, addressing many issues from 0.4.17 (see "Bug Fixes", below). However, it also contains some performance improvements and several exciting new features (see "Highlights"), so read on below! For more information, examples, and documentation, please visit our website: https://napari.org Highlights Drawing polygons in the Shapes layer can now be done much faster with the new lasso tool (napari/napari/\#5555) Surface layers now support textures and vertex colors, allowing a whole new type of dataset to be visualised in napari. Have a look at {$<$}code{$>$}surface\_multi\_texture.py{$<$}/code{$>$} and {$<$}code{$>$}surface\_texture\_and\_colors.py{$<$}/code{$>$} in the {$<$}code{$>$}examples{$<$}/code{$>$} directory for some pretty demos! (napari/napari/\#5642) Previously, navigating an image required switching out of whatever drawing mode you might have been using and going back to pan/zoom mode. Now you can use the mouse wheel to zoom in and out in any mode. (napari/napari/\#5701) Painting labels is now much, much faster (achieving 60fps even on an 8k x 8k image) (napari/napari/\#5723 and napari/napari/\#5732) Vectors layers can now be displayed with two different styles of arrowheads, instead of just plain lines. This removes a longstanding limitation of the vectors layer! (napari/napari/\#5740) New Features Overlays 2.0 (napari/napari/\#4894) expose custom image interpolation kernels (napari/napari/\#5130) Add user agent environment variable for pip installations (napari/napari/\#5135) Add option to check if plugin try to set viewer attr outside main thread (napari/napari/\#5195) Set selection color for QListView item. (napari/napari/\#5202) Add warning about set private attr when using proxy (napari/napari/\#5209) Shapes interpolation (napari/napari/\#5334) Add dask settings to preferences (napari/napari/\#5490) Add lasso tool for faster drawing of polygonal Shapes (napari/napari/\#5555) Feature: support for textures and vertex colors on Surface layers (napari/napari/\#5642) Back point selection with a psygnal Selection (napari/napari/\#5691) Zooming with the mouse wheel in any mode (napari/napari/\#5701) Add cancellation functionality to progress (napari/napari/\#5728) Add arrow display styles to Vectors layer (napari/napari/\#5740) Improvements Set keyboard focus on console when opened (napari/napari/\#5208) Push variables to console when instantiated (napari/napari/\#5210) Tracks layer creation performance improvement (napari/napari/\#5303) PERF: Event emissions and perf regression. (napari/napari/\#5307) Much faster FormatStringEncoding (napari/napari/\#5315) Add parent when creating layer context menu to inherit application theme and add style entry for disabled widgets and menus (napari/napari/\#5381) Add correct {$<$}code{$>$}enablement{$<$}/code{$>$} kwarg to {$<$}code{$>$}Split Stack{$<$}/code{$>$} action, {$<$}code{$>$}Convert data type{$<$}/code{$>$} submenu and {$<$}code{$>$}Projections{$<$}/code{$>$} submenu (napari/napari/\#5437) Apply disabled widgets style only for menus and set menus styles for {$<$}code{$>$}QModelMenu{$<$}/code{$>$} and {$<$}code{$>$}QMenu{$<$}/code{$>$} instances (napari/napari/\#5446) Add disabled style rule for {$<$}code{$>$}QComboBox{$<$}/code{$>$} following the one for {$<$}code{$>$}QPushButton{$<$}/code{$>$} (napari/napari/\#5469) Allow layers control section to resize to contents (napari/napari/\#5474) Allow to use {$<$}code{$>$}Optional{$<$}/code{$>$} annotation in function return type for magicgui functions (napari/napari/\#5595) Skip equality comparisons in EventedModel when unnecessary (napari/napari/\#5615) Bugfix: improve layout of Preferences \> Shortcuts tables (napari/napari/\#5679) Improve preferences genration (napari/napari/\#5696) Add dev example for adding custom overlays. (napari/napari/\#5719) Disable buffer swapping (napari/napari/\#5741) Remove max brush size from increase brush size keybinding (napari/napari/\#5761) Explicitly list valid layer names in types (napari/napari/\#5823) Sort npe1 widget contributions (napari/napari/\#5865) feat: add {$<$}code{$>$}since\_version{$<$}/code{$>$} argument of {$<$}code{$>$}rename\_argument{$<$}/code{$>$} decorator (napari/napari/\#5910) Emit extra information with layer.events.data (napari/napari/\#5967) Performance Return early when no slicing needed (napari/napari/\#5239) Tracks layer creation performance improvement (napari/napari/\#5303) PERF: Event emissions and perf regression. (napari/napari/\#5307) Much faster FormatStringEncoding (napari/napari/\#5315) Fix inefficient label mapping in direct color mode (10-20x speedup) (napari/napari/\#5723) Efficient labels mapping for drawing in Labels (60 FPS even with 8000x8000 images) (napari/napari/\#5732) Disable buffer swapping (napari/napari/\#5741) Bug Fixes Warn instead of failing on empty or invalid alt-text (napari/napari/\#4505) Fix display of order and scale combinations (napari/napari/\#5004) Enforce that contrast limits must be increasing (napari/napari/\#5036) Bugfix: Move Window menu to be before Help (napari/napari/\#5093) Add extra garbage collection for some viewer tests (napari/napari/\#5108) Connect image to plane events and expose them (napari/napari/\#5131) Workaround for discover themes from plugins (napari/napari/\#5150) Add missed dialogs to {$<$}code{$>$}qtbot{$<$}/code{$>$} in {$<$}code{$>$}test\_qt\_notifications{$<$}/code{$>$} to prevent segfaults (napari/napari/\#5171) DOC Update docstring of {$<$}code{$>$}add\_dock\_widget{$<$}/code{$>$} \& {$<$}code{$>\_$}add\_viewer\_dock\_widget{$<$}/code{$>$} (napari/napari/\#5173) Fix unsortable features (napari/napari/\#5186) Avoid possible divide-by-zero in Vectors layer thumbnail update (napari/napari/\#5192) Disable napari-console button when launched from jupyter (napari/napari/\#5213) Volume rendering updates for isosurface and attenuated MIP (napari/napari/\#5215) Return early when no slicing needed (napari/napari/\#5239) Check strictly increasing values when clipping contrast limits to a new range (napari/napari/\#5258) UI Bugfix: Make disabled QPushButton more distinct (napari/napari/\#5262) Respect background color when calculating scale bar color (napari/napari/\#5270) Fix circular import in \_vispy module (napari/napari/\#5276) Use only data dimensions for cord in status bar (napari/napari/\#5283) Prevent obsolete reports about failure of cleaning viewer instances (napari/napari/\#5317) Add scikit-image[data] to install\_requires, because it's required by builtins (napari/napari/\#5329) Fix repeating close dialog on macOS and qt 5.12 (napari/napari/\#5337) Disable napari-console if napari launched from vanilla python REPL (napari/napari/\#5350) For npe2 plugin, use manifest display\_name for File \> Open Samples (napari/napari/\#5351) Bugfix plugin display\_name use (File \> Open Sample, Plugin menus) (napari/napari/\#5366) Fix editing shape data above 2 dimensions (napari/napari/\#5383) Fix test keybinding for layer actions (napari/napari/\#5406) fix theme id not being used correctly (napari/napari/\#5412) Clarify layer's editable property and separate interaction with visible property (napari/napari/\#5413) Fix theme reference to get image for {$<$}code{$>$}success\_label{$<$}/code{$>$} style (napari/napari/\#5447) Bugfix: Ensure layer.\_fixed\_vertex is set when rotating (napari/napari/\#5449) Fix {$<$}code{$>\_$}n\_selected\_points{$<$}/code{$>$} in \_layerlist\_context.py (napari/napari/\#5450) Refactor Main Window status bar to improve information presentation (napari/napari/\#5451) Bugfix: Fix test\_get\_system\_theme test for {$<$}code{$>$}name{$<$}/code{$>$} to {$<$}code{$>$}id{$<$}/code{$>$} change (napari/napari/\#5456) Bugfix: POLL\_INTERVAL\_MS used in QTimer needs to be an int on python 3.10 (napari/napari/\#5467) Bugfix: Add missing Enums and Flags required by PySide6 \> 6.4 (napari/napari/\#5480) BugFix: napari does not start with Python v3.11.1: "ValueError: A distribution name is required." (napari/napari/\#5482) Fix inverted LUT and blending (napari/napari/\#5487) Fix opening file dialogs in PySide (napari/napari/\#5492) Handle case when QtDims play thread is partially deleted (napari/napari/\#5499) Ensure surface normals and wireframes are using Models internally (napari/napari/\#5501) Recursively check for dependent property to fire events. (napari/napari/\#5528) Set PYTHONEXECUTABLE as part of macos fixes on (re)startup (napari/napari/\#5531) Un-set unified title and tool bar on mac (Qt property) (napari/napari/\#5533) Fix key error issue of action manager (napari/napari/\#5539) Bugfix: ensure Checkbox state comparisons are correct by using Qt.CheckState(state) (napari/napari/\#5541) Clean dangling widget in test (napari/napari/\#5544) Fix {$<$}code{$>$}test\_worker\_with\_progress{$<$}/code{$>$} by wait on worker end (napari/napari/\#5548) Fix min req (napari/napari/\#5560) Fix vispy axes labels (napari/napari/\#5565) Fix colormap utils error suggestion code and add a test (napari/napari/\#5571) Fix problem of missing plugin widgets after minimize napari (napari/napari/\#5577) Make point size isotropic (napari/napari/\#5582) Fix guard of qt import in {$<$}code{$>$}napari.utils.theme{$<$}/code{$>$} (napari/napari/\#5593) Fix empty shapes layer duplication and {$<$}code{$>$}Convert to Labels{$<$}/code{$>$} enablement logic for selected empty shapes layers (napari/napari/\#5594) Stop using removed multichannel= kwarg to skimage functions (napari/napari/\#5596) Add information about {$<$}code{$>$}syntax\_style{$<$}/code{$>$} value in error message for theme validation (napari/napari/\#5602) Remove catch\_warnings in slicing (napari/napari/\#5603) Incorret theme should not prevent napari from start (napari/napari/\#5605) Unblock axis labels event to be emitted when slider label changes (napari/napari/\#5631) Bugfix: IndexError slicing Surface with higher-dimensional vertex\_values (napari/napari/\#5635) Bugfix: Convert Viewer Delete button to QtViewerPushButton with action and shortcut (napari/napari/\#5636) Change dim {$<$}code{$>$}axis\_label{$<$}/code{$>$} resize logic to set width using only displayed labels width (napari/napari/\#5640) Feature: support for textures and vertex colors on Surface layers (napari/napari/\#5642) Fix features issues with init param and property setter (napari/napari/\#5646) Bugfix: Don't double toggle visibility for linked layers (napari/napari/\#5656) Bugfix: ensure pan/zoom buttons work, along with spacebar keybinding (napari/napari/\#5669) Bugfix: Add Tracks to qt\_keyboard\_settings (napari/napari/\#5678) Fix automatic naming and GUI exposure of multiple unnamed colormaps (napari/napari/\#5682) Fix mouse movement handling for {$<$}code{$>$}TransformBoxOverlay{$<$}/code{$>$} (napari/napari/\#5692) Update environment.yml (napari/napari/\#5693) Resolve symlinks from path to environment for setting path (napari/napari/\#5704) Fix tracks color-by when properties change (napari/napari/\#5708) Fix Sphinx warnings (napari/napari/\#5717) Do not use depth for canvas overlays; allow setting blending mode for overlays (napari/napari/\#5720) Unify event behaviour for points and its qt controls (napari/napari/\#5722) Fix camera 3D absolute rotation bug (napari/napari/\#5726) Maint: Bump mypy (napari/napari/\#5727) Style {$<$}code{$>$}QGroupBox{$<$}/code{$>$} indicator (napari/napari/\#5729) Fix centering of non-displayed dimensions (napari/napari/\#5736) Don't attempt to use npe1 readers in napari.plugins.\_npe2.read (napari/napari/\#5739) Prevent canvas micro-panning on point add (}, + copyright = {BSD 3-Clause "New" or "Revised" License, Open Access}, + howpublished = {Zenodo} +} + +@article{Airan2018, + title = {Hearing out {{Ultrasound Neuromodulation}}}, + author = {Airan, Raag D. and Butts Pauly, Kim}, + year = {2018}, + month = jun, + journal = {Neuron}, + volume = {98}, + number = {5}, + pages = {875--877}, + issn = {08966273}, + doi = {10.1016/j.neuron.2018.05.031}, + urldate = {2023-06-01}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Airan2018.pdf} +} + +@article{Akerboom2012, + title = {Optimization of a {{GCaMP Calcium Indicator}} for {{Neural Activity Imaging}}}, + author = {Akerboom, Jasper and Chen, Tsai-Wen and Wardill, Trevor J. and Tian, Lin and Marvin, Jonathan S. and Mutlu, Sevin{\c c} and Calder{\'o}n, Nicole Carreras and Esposti, Federico and Borghuis, Bart G. and Sun, Xiaonan Richard and Gordus, Andrew and Orger, Michael B. and Portugues, Ruben and Engert, Florian and Macklin, John J. and Filosa, Alessandro and Aggarwal, Aman and Kerr, Rex A. and Takagi, Ryousuke and Kracun, Sebastian and Shigetomi, Eiji and Khakh, Baljit S. and Baier, Herwig and Lagnado, Leon and Wang, Samuel S.-H. and Bargmann, Cornelia I. and Kimmel, Bruce E. and Jayaraman, Vivek and Svoboda, Karel and Kim, Douglas S. and Schreiter, Eric R. and Looger, Loren L.}, + year = {2012}, + month = oct, + journal = {The Journal of Neuroscience}, + volume = {32}, + number = {40}, + pages = {13819--13840}, + issn = {0270-6474, 1529-2401}, + doi = {10.1523/JNEUROSCI.2601-12.2012}, + urldate = {2023-03-14}, + abstract = {Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been deployed in a number of model organisms and can reliably detect three or more action potentials in short bursts in several systems in vivo . Through protein structure determination, targeted mutagenesis, high-throughput screening, and a battery of in vitro assays, we have increased the dynamic range of GCaMP3 by severalfold, creating a family of ``GCaMP5'' sensors. We tested GCaMP5s in several systems: cultured neurons and astrocytes, mouse retina, and in vivo in Caenorhabditis chemosensory neurons, Drosophila larval neuromuscular junction and adult antennal lobe, zebrafish retina and tectum, and mouse visual cortex. Signal-to-noise ratio was improved by at least 2- to 3-fold. In the visual cortex, two GCaMP5 variants detected twice as many visual stimulus-responsive cells as GCaMP3. By combining in vivo imaging with electrophysiology we show that GCaMP5 fluorescence provides a more reliable measure of neuronal activity than its predecessor GCaMP3. GCaMP5 allows more sensitive detection of neural activity in vivo and may find widespread applications for cellular imaging in general.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Akerboom2012.pdf} +} + +@article{Alexander2021, + title = {{{THE CONCISE GUIDE TO PHARMACOLOGY}} 2021/22: {{Transporters}}}, + shorttitle = {{{THE CONCISE GUIDE TO PHARMACOLOGY}} 2021/22}, + author = {Alexander, Stephen P H and Kelly, Eamonn and Mathie, Alistair and Peters, John A and Veale, Emma L and Armstrong, Jane F and Faccenda, Elena and Harding, Simon D and Pawson, Adam J and Southan, Christopher and Davies, Jamie A and Amarosi, Laura and Anderson, Catriona M. H. and Beart, Philip Mark and Broer, Stefan and Dawson, Paul A. and Hagenbuch, Bruno and Hammond, James R. and Hancox, Jules C and Inui, Ken-ichi and Kanai, Yoshikatsu and Kemp, Stephan and Stewart, Gavin and Thwaites, David T. and Verri, Tiziano}, + year = {2021}, + month = oct, + journal = {British Journal of Pharmacology}, + volume = {178}, + number = {S1}, + issn = {0007-1188, 1476-5381}, + doi = {10.1111/bph.15543}, + urldate = {2023-07-10}, + abstract = {The Concise Guide to PHARMACOLOGY 2021/22 is the fifth in this series of biennial publications. The Concise Guide provides concise overviews, mostly in tabular format, of the key properties of nearly 1900 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide constitutes over 500 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/ bph.15543. Transporters are one of the six major pharmacological targets into which the Guide is divided, with the others being: G protein-coupled receptors, ion channels, nuclear hormone receptors, catalytic receptors and enzymes. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2021, and supersedes data presented in the 2019/20, 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.}, + langid = {english}, + file = {/Users/tomaubier/Zotero/storage/RH8RLVK2/Alexander et al. - 2021 - THE CONCISE GUIDE TO PHARMACOLOGY 202122 Transpo.pdf} +} + +@article{Apfel1982, + title = {{{ACOUSTIC CAVITATION}}: {{A POSSIBLE CONSEQUENCE OF BIOMEDICAL USES OF ULTRASOUND}}}, + author = {Apfel, R E}, + year = {1982}, + abstract = {Those concerned with acoustic cavitation often use different measures and nomenclature to those who employ ultrasound for medical purposes. After illustrating the connections between the two, acoustic cavitation phenomena are divided into two classes: (1) relatively moderate amplitude changes in the bubble size that occur during each acoustic cycle, as with rectified diffusion and resonant bubble motion, and (2) rather dramatic changes in the bubble radius that occur in one cycle. It is seen that pulse-echo diagnostic equipment can excite the dramatic changes whereas continuous wave therapeutic equipment will excite the slower, but no less important, changes. The ranges of the acoustic variables and material states for which these phenomena are possible are quantified. It is shown that whereas the concept of an ultrasonic (energy) dose may be appropriate for the effects of acoustically induced heating or resonant bubble motion, it is inappropriate when discussing the effects of the transient type of cavitation that can occur from short, high amplitude acoustic pulses.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Apfel1982.pdf} +} + +@article{Apfel1991, + title = {Gauging the Likelihood of Cavitation from Short-Pulse, Low-Duty Cycle Diagnostic Ultrasound.}, + author = {Apfel, Robert E. and Holland, Christy K.}, + year = {1991}, + month = jan, + journal = {Ultrasound in Medicine and Biology}, + volume = {17}, + number = {2}, + pages = {179--185}, + doi = {10.1016/0301-5629(91)90125-g}, + abstract = {Abstract Although no deleterious effects from diagnostic ultrasound have been reported in epidemiologic studies and surveys of widespread clinical usage (Ziskin and Petitti 1988), the conditions for the onset of transient cavitation must be investigated in the total evaluation of potential risks associated with diagnostic ultrasound applications. An extension of the results from the approximate theory developed by Holland and Apfel (1989) is applied in this paper to a population of nuclei to predict the onset of cavitation in host fluids with physical properties similar to those of biological fluids. From this analysis and from results of recent in vitro cavitation experiments, an index is developed which can gauge the likelihood of substantial microbubble growth in the presence of short-pulse, low-duty cycle diagnostic ultrasound.}, + pmid = {2053214}, + annotation = {MAG ID: 2043902038\\ +S2ID: 4aa4c045b00929552c15a181cafede0e30d47292}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Apfel1991.pdf} +} + +@article{Araque2014, + title = {Gliotransmitters {{Travel}} in {{Time}} and {{Space}}}, + author = {Araque, Alfonso and Carmignoto, Giorgio and Haydon, Philip~G. and Oliet, St{\'e}phane~H.R. and Robitaille, Richard and Volterra, Andrea}, + year = {2014}, + month = feb, + journal = {Neuron}, + volume = {81}, + number = {4}, + pages = {728--739}, + issn = {08966273}, + doi = {10.1016/j.neuron.2014.02.007}, + urldate = {2024-03-25}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Araque2014.pdf} +} + +@article{Artusi2018, + title = {Deep Brain Stimulation in Uncommon Tremor Disorders: Indications, Targets, and Programming}, + author = {Artusi, Carlo Alberto and Farooqi, Ashar and Romagnolo, Alberto and Marsili, Luca and Balestrino, Roberta and Sokol, Leonard L. and Wang, Lily L. and Zibetti, Maurizio and Duker, Andrew P. and Mandybur, George T. and Lopiano, Leonardo and Merola, Aristide}, + year = {2018}, + month = mar, + journal = {Journal of Neurology}, + volume = {265}, + number = {11}, + pages = {2473--2493}, + publisher = {{Springer Science and Business Media LLC}}, + doi = {10.1007/s00415-018-8823-x}, + keywords = {DBS,FXTAS,Holmes,Multiple sclerosis,Neuropathy,OT,Tremor}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Artusi2018.pdf} +} + +@article{AStateman2014, + title = {Repetitive {{Transcranial Magnetic Stimulation}} ({{Rtms}}) Increases {{Plasma Calcium}} Both in-Vivo and in-Vitro}, + author = {A Stateman, William}, + year = {2014}, + journal = {Journal of Clinical \& Experimental Pathology}, + volume = {04}, + number = {04}, + issn = {21610681}, + doi = {10.4172/2161-0681.1000187}, + urldate = {2021-09-04} +} + +@inproceedings{Aubier2021, + title = {Mixed {{Focused UltraSound}} ({{FUS}}) / Fluorescence Imaging Platform for Characterization of the Spatial-Temporal Dynamics of {{FUS-evoked}} Calcium Fluxes in an in Vitro Human Cell Model}, + author = {Aubier, Tom and Castellanos, Ivan M. Suarez and Perier, Magali and Carpentier, Alexandre and N'Djin, W. Apoutou}, + year = {2021}, + month = sep, + publisher = {IEEE}, + doi = {10.1109/ius52206.2021.9593676}, + copyright = {All rights reserved}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Aubier2021.pdf} +} + +@phdthesis{Aubier2021a, + title = {Low Energy Focused Ultrasound Stimulation of in Vitro Human Neural Cells}, + author = {Aubier, Tom}, + year = {2021}, + abstract = {Low energy focused ultrasound stimulation of in vitro human neural cells. With the knowledge acquired over the last decades regarding brain function, the use of neurostimulation techniques seems more and more appropriate as a way to improve the quality of life of numerous patients suffering from various neuropathic conditions or neurodegenerative diseases such as Parkinson or Alzheimer. As of today, the available techniques allowing reliable and targeted stimulation of specific regions of the brain are based on an extremely invasive method relying on the implantation of electrodes in the brain tissues directly. Recently, its has been demonstrated that focused ultrasound can affect the activity of neuronal structures. The nature of the mechanisms underlying these effects is however not well understood, which prevents the clinical use of such method. Over the course of this work, the development of a mixed fluorescence / ultrasound stimulation platform is presented as a foundation for future investigation of these mechanisms. The results of a preliminary study are here reported and highlight the relevance of such platform as a tool enabling the exploration of ultrasound evoked responses at a cellular level.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Aubier2021a.pdf} +} + +@article{Aubry, + title = {{{ITRUSST}}\_{{Consensus}}\_on\_{{Biophysical}}\_{{Safety}}\_for\_{{Transcranial}}\_{{Ultrasonic}}\_{{Stimulation}}}, + author = {Aubry, Jean-Francois and Attali, David and Schafer, Mark and Fouragnan, Elsa and Caskey, Charles and Chen, Robert and Darmani, Ghazaleh and Bubrick, Ellen J and Sallet, J{\'e}r{\^o}me and Butler, Christopher and Stagg, Charlotte and {Klein-Fl{\"u}gge}, Miriam and Yoo, Seung-Schik and Treeby, Brad and Verhagen, Lennart and Pauly, Kim Butts}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Aubry.pdf} +} + +@article{Aubry2003, + title = {Experimental Demonstration of Noninvasive Transskull Adaptive Focusing Based on Prior Computed Tomography Scans}, + author = {Aubry, J.-F. and Tanter, M. and Pernot, M. and Thomas, J.-L. and Fink, M.}, + year = {2003}, + month = jan, + journal = {The Journal of the Acoustical Society of America}, + volume = {113}, + number = {1}, + pages = {84--93}, + issn = {0001-4966, 1520-8524}, + doi = {10.1121/1.1529663}, + urldate = {2025-01-28}, + abstract = {Developing minimally invasive brain surgery by high-intensity focused ultrasound beams is of great interest in cancer therapy. However, the skull induces strong aberrations both in phase and amplitude, resulting in a severe degradation of the beam shape. Thus, an efficient brain tumor therapy would require an adaptive focusing, taking into account the effects of the skull. In this paper, we will show that the acoustic properties of the skull can be deduced from high resolution CT scans and used to achieve a noninvasive adaptive focusing. Simulations have been performed with a full 3-D finite differences code, taking into account all the heterogeneities inside the skull. The set of signals to be emitted in order to focus through the skull can thus be computed. The complete adaptive focusing procedure based on prior CT scans has been experimentally validated. This could have promising applications in brain tumor hyperthermia but also in transcranial ultrasonic imaging.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Aubry2003.pdf} +} + +@misc{Aubry2022, + title = {First Evidence of a Drastic and Sustained Reduction of Essential Tremor with Low Energy Transcranial Focused Ultrasound Neurostimulation: {{Clinical}} Report of 98\% Tremor Reduction for More than 25 Minutes}, + author = {Aubry, Jean Francois}, + year = {2022}, + month = oct, + address = {Bethesda, MD, USA}, + urldate = {2023-08-31}, + abstract = {First Evidence of a Drastic and Sustained Reduction of Essential Tremor with Low Energy Transcranial Focused Ultrasound Neurostimulation: Clinical Report of 98\% Tremor Reduction for More than 25 Minutes}, + collaborator = {Bancel, Thomas and B{\'e}ranger, Beno{\^i}t and Didier, M{\'e}lanie and Santin, Mathieu and Rachmilevitch, Itay and Shapira, Yeruham and Tanter, Mickael and Bardinet, Eric and Vidal, Sara Fernandez and Gall{\'e}a, C{\'e}cile and Dizeux, Alexandre and Vidailhet, Marie and Leh{\'e}ricy, St{\'e}phane and Grabli, David and Pyatigorskaya, Nadya and Hainque, Elodie and Karachi, Carine} +} + +@article{Aubry2022a, + title = {Benchmark Problems for Transcranial Ultrasound Simulation: {{Intercomparison}} of Compressional Wave Models}, + shorttitle = {Benchmark Problems for Transcranial Ultrasound Simulation}, + author = {Aubry, Jean-Francois and Bates, Oscar and Boehm, Christian and Butts Pauly, Kim and Christensen, Douglas and Cueto, Carlos and G{\'e}lat, Pierre and Guasch, Lluis and Jaros, Jiri and Jing, Yun and Jones, Rebecca and Li, Ningrui and Marty, Patrick and Montanaro, Hazael and Neufeld, Esra and Pichardo, Samuel and Pinton, Gianmarco and Pulkkinen, Aki and Stanziola, Antonio and Thielscher, Axel and Treeby, Bradley and Van 'T Wout, Elwin}, + year = {2022}, + month = aug, + journal = {The Journal of the Acoustical Society of America}, + volume = {152}, + number = {2}, + pages = {1003--1019}, + issn = {0001-4966, 1520-8524}, + doi = {10.1121/10.0013426}, + urldate = {2023-09-13}, + abstract = {Computational models of acoustic wave propagation are frequently used in transcranial ultrasound therapy, for example, to calculate the intracranial pressure field or to calculate phase delays to correct for skull distortions. To allow intercomparison between the different modeling tools and techniques used by the community, an international working group was convened to formulate a set of numerical benchmarks. Here, these benchmarks are presented, along with intercomparison results. Nine different benchmarks of increasing geometric complexity are defined. These include a single-layer planar bone immersed in water, a multi-layer bone, and a whole skull. Two transducer configurations are considered (a focused bowl and a plane piston operating at 500\,kHz), giving a total of 18 permutations of the benchmarks. Eleven different modeling tools are used to compute the benchmark results. The models span a wide range of numerical techniques, including the finite-difference time-domain method, angular spectrum method, pseudospectral method, boundary-element method, and spectral-element method. Good agreement is found between the models, particularly for the position, size, and magnitude of the acoustic focus within the skull. When comparing results for each model with every other model in a cross-comparison, the median values for each benchmark for the difference in focal pressure and position are less than 10\% and 1\,mm, respectively. The benchmark definitions, model results, and intercomparison codes are freely available to facilitate further comparisons.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Aubry2022a.pdf} +} + +@article{Avins2010, + title = {Placebo {{Adherence}} and {{Its Association}} with {{Morbidity}} and {{Mortality}} in the {{Studies}} of {{Left Ventricular Dysfunction}}}, + author = {Avins, Andrew L. and Pressman, Alice and Ackerson, Lynn and Rudd, Peter and Neuhaus, John and Vittinghoff, Eric}, + year = {2010}, + month = dec, + journal = {Journal of General Internal Medicine}, + volume = {25}, + number = {12}, + pages = {1275--1281}, + issn = {0884-8734, 1525-1497}, + doi = {10.1007/s11606-010-1477-8}, + urldate = {2022-10-14}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Avins2010.pdf} +} + +@article{Badawe2023, + title = {Modeling Ultrasound Modulation of Neural Function in a Single Cell}, + author = {Badawe, Heba M. and El Hassan, Rima H. and Khraiche, Massoud L.}, + year = {2023}, + month = nov, + journal = {Heliyon}, + pages = {e22522}, + issn = {24058440}, + doi = {10.1016/j.heliyon.2023.e22522}, + urldate = {2023-11-21}, + abstract = {Background: Low intensity ultrasound stimulation has been shown to non-invasively modulate neural function in the central nervous system (CNS) and peripheral nervous system (PNS) with high precision. Ultrasound sonication is capable of either excitation or inhibition, depending on the ultrasound parameters used. On the other hand, the mode of interaction of ultrasonic waves with the neural tissue for effective neuromodulation remains ambiguous. New Method: Here within we propose a numerical model that incorporates the mechanical effects of ultrasound stimulation on the Hodgkin-Huxley (HH) neuron by incorporating the relation between increased external pressure and the membrane induced tension, with a stress on the flexoelectric effect on the neural membrane. The external pressure causes an increase in the total tension of the membrane thus affecting the probability of the ion Journal Pre-proof channels being open after the conformational changes that those channels undergo. Results: The interplay between varying the acoustic intensities and frequencies depicts different action potential suppression rates, whereby a combination of low intensity and low frequency ultrasound sonication proved to be the most effective in modulating neural function. Comparison with Existing Methods: Our method solely depends on the HH model of a single neuron and the linear flexoelectric effect of the dielectric neural membrane, when under an ultrasound-induced mechanical strain, while varying the ion-channels conductances based on different sonication frequencies and intensities. We study the effect of ultrasound parameters on the firing rate, latency, and action potential amplitude of a HH neuron for a better understanding of the neuromodulation modality of ultrasound stimulation (in the continuous and pulsed modes). Conclusions: This simulation work confirms the published experimental data that low intensity and low frequency ultrasound sonication has a higher success rate of modulating neural firing.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Badawe2023.pdf} +} + +@article{Bao2024, + title = {Personalized Depth-specific Neuromodulation of the Human Primary Motor Cortex via Ultrasound}, + author = {Bao, Shancheng and Kim, Hakjoo and Shettigar, Nandan B. and Li, Yue and Lei, Yuming}, + year = {2024}, + month = feb, + journal = {The Journal of Physiology}, + pages = {JP285613}, + issn = {0022-3751, 1469-7793}, + doi = {10.1113/JP285613}, + urldate = {2024-02-20}, + abstract = {Non-invasive brain stimulation has the potential to boost neuronal plasticity in the primary motor cortex (M1), but it remains unclear whether the stimulation of both superficial and deep layers of the human motor cortex can effectively promote M1 plasticity. Here, we leveraged transcranial ultrasound stimulation (TUS) to precisely target M1 circuits at depths of approximately 5 mm and 16 mm from the cortical surface. Initially, we generated computed tomography images from each participant's individual anatomical magnetic resonance images (MRI), which allowed for the generation of accurate acoustic simulations. This process ensured that personalized TUS was administered exactly to the targeted depths within M1 for each participant. Using long-term depression and long-term potentiation (LTD/LTP) theta-burst stimulation paradigms, we examined whether TUS over distinct depths of M1 could induce LTD/LTP plasticity. Our findings indicated that continuous theta-burst TUS-induced LTD-like plasticity with both superficial and deep M1 stimulation, persisting for at least 30 min. In comparison, sham TUS did not significantly alter M1 excitability. Moreover, intermittent theta-burst TUS did not result in the induction of LTP- or LTD-like plasticity with either superficial or deep M1 stimulation. These findings suggest that the induction of M1 plasticity can be achieved with ultrasound stimulation targeting distinct depths of M1, which is contingent on the characteristics of TUS.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Bao2024.pdf} +} + +@article{Bazargani2016, + title = {Astrocyte Calcium Signaling: The Third Wave}, + shorttitle = {Astrocyte Calcium Signaling}, + author = {Bazargani, Narges and Attwell, David}, + year = {2016}, + month = feb, + journal = {Nature Neuroscience}, + volume = {19}, + number = {2}, + pages = {182--189}, + issn = {1097-6256, 1546-1726}, + doi = {10.1038/nn.4201}, + urldate = {2022-11-28}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Bazargani2016.pdf} +} + +@book{Bear2016, + title = {Neurosciences: {\`a} La D{\'e}couverte Du Cerveau}, + shorttitle = {Neurosciences}, + author = {Bear, Mark F. and Connors, Barry W. and Paradiso, Michael A.}, + translator = {Nieoullon, Andr{\'e}}, + year = {2016}, + edition = {4e {\'e}dition}, + publisher = {{\'E}ditions Pradel}, + address = {Paris}, + isbn = {978-2-36110-082-7}, + langid = {english}, + annotation = {OCLC: 959617542}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Bear2016.pdf} +} + +@article{Becker2016, + title = {Selective Serotonin 5-{{HT1A}} Receptor Biased Agonists Elicitdistinct Brain Activation Patterns: A {{pharmacoMRI}} Study}, + shorttitle = {Selective Serotonin 5-{{HT1A}} Receptor Biased Agonists Elicitdistinct Brain Activation Patterns}, + author = {Becker, G. and Bolbos, R. and Costes, N. and Redout{\'e}, J. and {Newman-Tancredi}, A. and Zimmer, L.}, + year = {2016}, + month = may, + journal = {Scientific Reports}, + volume = {6}, + number = {1}, + pages = {26633}, + issn = {2045-2322}, + doi = {10.1038/srep26633}, + urldate = {2023-03-14}, + abstract = {Abstract Serotonin 1A (5-HT 1A ) receptors are involved in several physiological and pathological processes and constitute therefore an important therapeutic target. The recent pharmacological concept of biased agonism asserts that highly selective agonists can preferentially direct receptor signaling to specific intracellular responses, opening the possibility of drugs targeting a receptor subtype in specific brain regions. The present study brings additional support to this concept thanks to functional magnetic resonance imaging (7\,Tesla-fMRI) in anaesthetized rats. Three 5-HT 1A receptor agonists (8-OH-DPAT, F13714 and F15599) and one 5-HT 1A receptor antagonist (MPPF) were compared in terms of influence on the brain blood oxygen level-dependent (BOLD) signal. Our study revealed for the first time contrasting BOLD signal patterns of biased agonists in comparison to a classical agonist and a silent antagonist. By providing functional information on the influence of pharmacological activation of 5-HT 1A receptors in specific brain regions, this neuroimaging approach, translatable to the clinic, promises to be useful in exploring the new concept of biased agonism in neuropsychopharmacology.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Becker2016.pdf} +} + +@article{Beissner1982, + title = {On the Plane-Wave Approximation of Acoustic Intensity}, + author = {Beissner, K.}, + year = {1982}, + month = jun, + journal = {The Journal of the Acoustical Society of America}, + volume = {71}, + number = {6}, + pages = {1406--1411}, + issn = {0001-4966, 1520-8524}, + doi = {10.1121/1.387835}, + urldate = {2023-10-31}, + abstract = {The acoustic intensity is given by the product of acoustic pressure p and particle velocity v, but in the literature, expressions like p2/{$\rho$}c or {$\rho$}cv2 are often quoted. These are plane-wave approximations and are not in general valid. Assuming continuous-wave operation, the relations between the approximate formulas and the exact one are discussed in terms of the specific acoustic impedance. Further remarks deal with the vector character of the acoustic intensity and its connection with heat generation in the medium, as considered in a recent paper by Nyborg [J. Acoust. Soc. Am. 70, 310--312 (1981)].}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Beissner1982.pdf} +} + +@article{Beisteiner2020, + title = {Transcranial {{Pulse Stimulation}} with {{Ultrasound}} in {{Alzheimer}}'s {{Disease}}---{{A New Navigated Focal Brain Therapy}}}, + author = {Beisteiner, Roland and Matt, Eva and Fan, Christina and Baldysiak, Heike and Sch{\"o}nfeld, Marleen and Philippi Novak, Tabea and Amini, Ahmad and Aslan, Tuna and Reinecke, Raphael and Lehrner, Johann and Weber, Alexandra and Reime, Ulrike and Goldenstedt, C{\'e}dric and Marlinghaus, Ernst and Hallett, Mark and Lohse-Busch, Henning}, + year = {2020}, + month = feb, + journal = {Advanced Science}, + volume = {7}, + number = {3}, + pages = {1902583}, + issn = {2198-3844, 2198-3844}, + doi = {10.1002/advs.201902583}, + urldate = {2023-08-28}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Beisteiner2020.pdf} +} + +@article{Berridge2000, + title = {The Versatility and Universality of Calcium Signalling}, + author = {Berridge, Michael J. and Lipp, Peter and Bootman, Martin D.}, + year = {2000}, + month = oct, + journal = {Nature Reviews Molecular Cell Biology}, + volume = {1}, + number = {1}, + pages = {11--21}, + publisher = {{Springer Science and Business Media LLC}}, + doi = {10.1038/35036035} +} + +@article{Berridge2003, + title = {Calcium Signalling: Dynamics, Homeostasis and Remodelling}, + shorttitle = {Calcium Signalling}, + author = {Berridge, Michael J. and Bootman, Martin D. and Roderick, H. Llewelyn}, + year = {2003}, + month = jul, + journal = {Nature Reviews Molecular Cell Biology}, + volume = {4}, + number = {7}, + pages = {517--529}, + issn = {1471-0072, 1471-0080}, + doi = {10.1038/nrm1155}, + urldate = {2024-03-30}, + copyright = {http://www.springer.com/tdm}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Berridge2003.pdf} +} + +@article{Bert2002, + title = {In Vivo Temporal Sequence of Rat Striatal Glutamate, Aspartate and Dopamine Efflux during Apomorphine, Nomifensine, {{NMDA}} and {{PDC}} in Situ Administration}, + author = {Bert, L. and Parrot, S. and Robert, F. and Desvignes, C. and Denoroy, L. and {Suaud-Chagny}, M. -F. and Renaud, B.}, + year = {2002}, + month = oct, + journal = {Neuropharmacology}, + volume = {43}, + number = {5}, + pages = {825--835}, + issn = {0028-3908}, + doi = {10.1016/S0028-3908(02)00170-3}, + urldate = {2023-06-26}, + abstract = {In vivo microdialysis was used to investigate the interactions between dopamine (DA), glutamate (Glu) and aspartate (Asp) in anaesthetised-rat striatum. The combination of brain microdialysis and capillary electrophoresis with laser-induced fluorescence detection (CE-LIFD) allows the simultaneous monitoring of the efflux of these neurotransmitters up to every 10 s. DA and Glu reuptake inhibitors, nomifensine and L-trans-pyrrolidine-2,4-dicarboxylic acid (PDC) and, dopaminergic and glutamatergic receptor agonists, apomorphine and NMDA respectively, were administered by reverse dialysis. Reverse dialysis of 20 {$\mu$}M nomifensine induced a rapid and marked increase (+3200\% at 5 min) in extracellular DA, while a decrease in Glu and Asp (--11 and -25\%, respectively) was observed simultaneously. Reverse dialysis of 10 {$\mu$}M apomorphine led to progressive changes: -63\% decrease in DA and +25\% Glu increase at 36 min. Reverse dialysis of 1 mM NMDA induced a simultaneous increase in DA, Glu and Asp which peaked at +2 min (+840\%, +40\% and +150\%, respectively). Surprisingly, a second increase in Glu was observed 5 min after the end of NMDA perfusion. Reverse dialysis of PDC (1 mM and 10 mM) induced a rapid increase in Glu and Asp levels, while DA increased with a 26-s delay. These findings indicate that, in the striatum, endogenous DA and Glu may act in opposition to regulate each other's efflux. These results have been obtained due to unique features offered by microdialysis coupled with CE-LIFD.}, + langid = {english}, + keywords = {Capillary electrophoresis,Dopamine,Glutamate,L--pyrrolidine-34-dicarboxylic acid,Microdialysis,Nomifensine}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Bert2002.pdf} +} + +@article{Blackmore2019, + title = {Ultrasound {{Neuromodulation}}: {{A Review}} of {{Results}}, {{Mechanisms}} and {{Safety}}}, + author = {Blackmore, Joseph and Shrivastava, Shamit and Sallet, Jerome and Butler, Chris R. and Cleveland, Robin O.}, + year = {2019}, + month = jul, + journal = {Ultrasound in Medicine \& Biology}, + volume = {45}, + number = {7}, + pages = {1509--1536}, + publisher = {Elsevier BV}, + doi = {10.1016/j.ultrasmedbio.2018.12.015}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Blackmore2019.pdf} +} + +@article{Blackmore2021, + title = {Low-Intensity Ultrasound Restores Long-Term Potentiation and Memory in Senescent Mice through Pleiotropic Mechanisms Including {{NMDAR}} Signaling}, + author = {Blackmore, Daniel G. and Turpin, Fabrice and Palliyaguru, Tishila and Evans, Harrison T. and Chicoteau, Antony and Lee, Wendy and Pelekanos, Matthew and Nguyen, Nghia and Song, Jae and Sullivan, Robert K. P. and Sah, Pankaj and Bartlett, Perry F. and G{\"o}tz, J{\"u}rgen}, + year = {2021}, + month = may, + journal = {Molecular Psychiatry}, + publisher = {{Springer Science and Business Media LLC}}, + doi = {10.1038/s41380-021-01129-7}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Blackmore2021.pdf} +} + +@article{Bouakaz2007, + title = {{{WFUMB}} Safety Symposium on Echo-Contrast Agents: {{Nature}} and Types of Ultrasound Contrast Agents}, + shorttitle = {{{WFUMB}} Safety Symposium on Echo-Contrast Agents}, + author = {Bouakaz, Ayache and {de Jong}, Nico}, + year = {2007}, + month = feb, + journal = {Ultrasound in Medicine \& Biology}, + volume = {33}, + number = {2}, + pages = {187--196}, + issn = {03015629}, + doi = {10.1016/j.ultrasmedbio.2006.07.008}, + urldate = {2022-10-12}, + langid = {english} +} + +@article{Bove2021, + title = {Long-Term {{Outcomes}} (15 {{Years}}) {{After Subthalamic Nucleus Deep Brain Stimulation}} in {{Patients With Parkinson Disease}}}, + author = {Bove, Francesco and Mulas, Delia and Cavallieri, Francesco and Castrioto, Anna and Chabardes, Stephan and {Sara Meoni} and Meoni, Sara and Schmitt, Emmanuelle and Bichon, Am{\'e}lie and Di Stasio, Enrico and Kistner, Andrea and Pelissier, Pierre and Chevrier, Eric and Seigneuret, Eric and Krack, Paul and Fraix, Val{\'e}rie and Moro, Elena and Moro, Elena}, + year = {2021}, + month = jun, + journal = {Neurology}, + volume = {97}, + number = {3}, + doi = {10.1212/wnl.0000000000012246}, + abstract = {OBJECTIVE To evaluate the effects of deep brain stimulation of the subthalamic nucleus (STN-DBS) in Parkinson disease (PD) patients on motor complications beyond 15 years after surgery. METHODS Data about motor complications, quality of life (QoL), activities of daily living, the UPDRS motor scores, dopaminergic treatment, stimulation parameters, and side effects of STN-DBS were retrospectively retrieved and compared between before surgery, at 1 year and beyond 15 years after bilateral STN-DBS. RESULTS Fifty-one patients with 17.06 {\textpm} 2.18 years STN-DBS follow-up were recruited. Compared to baseline, the time spent with dyskinesia and the time spent in the off state were reduced by 75\% (p{$<$}0.001) and by 58.7\% (p{$<$}0.001), respectively. Moreover, dopaminergic drugs were reduced by 50.6\% (p{$<$}0.001). The PDQL total score, and the emotional function and social function domains improved of 13.8\% (p=0.005), 13.6\% (p=0.01) and 29.9\% (p{$<$}0.001), respectively. Few and mostly manageable device-related adverse events were observed during the follow-up. CONCLUSIONS STN-DBS is still effective beyond 15 years from the intervention, notably with significant improvement in motor complications and stable reduction of dopaminergic drugs. Furthermore, despite the natural continuous progression of PD with worsening of levodopa-resistant motor and non-motor symptoms over the years, STN-DBS patients could maintain an improvement in QoL. CLASSIFICATION OF EVIDENCE This study provides Class IV evidence that, for patients with PD, STN-DBS remains effective at treating motor complications 15 years after surgery.}, + pmid = {34078713}, + annotation = {MAG ID: 3164833447}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Bove2021.pdf} +} + +@article{Bradley2012, + title = {G Protein-Coupled Receptor Signalling in Astrocytes in Health and Disease: {{A}} Focus on Metabotropic Glutamate Receptors}, + shorttitle = {G Protein-Coupled Receptor Signalling in Astrocytes in Health and Disease}, + author = {Bradley, Sophie J. and Challiss, R.A. John}, + year = {2012}, + month = aug, + journal = {Biochemical Pharmacology}, + volume = {84}, + number = {3}, + pages = {249--259}, + issn = {00062952}, + doi = {10.1016/j.bcp.2012.04.009}, + urldate = {2024-03-25}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Bradley2012.pdf} +} + +@article{Braun2020, + title = {Transcranial Ultrasound Stimulation in Humans Is Associated with an Auditory Confound That Can Be Effectively Masked}, + author = {Braun, Verena and Blackmore, Joseph and Cleveland, Robin O. and Butler, Christopher R.}, + year = {2020}, + month = nov, + journal = {Brain Stimulation}, + volume = {13}, + number = {6}, + pages = {1527--1534}, + issn = {1935861X}, + doi = {10.1016/j.brs.2020.08.014}, + urldate = {2023-06-01}, + abstract = {Background: Transcranial ultrasound stimulation (TUS) is emerging as a potentially powerful, noninvasive technique for focal brain stimulation. Recent animal work suggests, however, that TUS effects may be confounded by indirect stimulation of early auditory pathways. Objective: We aimed to investigate in human participants whether TUS elicits audible sounds and if these can be masked by an audio signal. Methods: In 18 healthy participants, T1-weighted magnetic resonance brain imaging was acquired for 3D ultrasound simulations to determine optimal transducer placements and source amplitudes. Thermal simulations ensured that temperature rises were {$<$}0.5 C at the target and {$<$}3 C in the skull. To test for non-specific auditory activation, TUS (500 kHz, 300 ms burst, modulated at 1 kHz with 50\% duty cycle) was applied to primary visual cortex and participants were asked to distinguish stimulation from nonstimulation trials. EEG was recorded throughout the task. Furthermore, ex-vivo skull experiments tested for the presence of skull vibrations during TUS. Results: We found that participants can hear sound during TUS and can distinguish between stimulation and non-stimulation trials. This was corroborated by EEG recordings indicating auditory activation associated with TUS. Delivering an audio waveform to participants through earphones while TUS was applied reduced detection rates to chance level and abolished the TUS-induced auditory EEG signal. Ex vivo skull experiments demonstrated that sound is conducted through the skull at the pulse repetition frequency of the ultrasound. Conclusion: Future studies using TUS in humans need to take this auditory confound into account and mask stimulation appropriately. {\copyright} 2020 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Braun2020.pdf} +} + +@article{Breit2018, + title = {What {{Is Required}} for {{Neuronal Calcium Waves}}? {{A Numerical Parameter Study}}}, + author = {Breit, Markus and Queisser, Gillian}, + year = {2018}, + month = jul, + journal = {The Journal of Mathematical Neuroscience}, + volume = {8}, + number = {1}, + publisher = {{Springer Science and Business Media LLC}}, + doi = {10.1186/s13408-018-0064-x}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Breit2018.pdf} +} + +@article{Breskin2006, + title = {Percolation in {{Living Neural Networks}}}, + author = {Breskin, Ilan and Soriano, Jordi and Moses, Elisha and Tlusty, Tsvi}, + year = {2006}, + month = oct, + journal = {Physical Review Letters}, + volume = {97}, + number = {18}, + pages = {188102}, + issn = {0031-9007, 1079-7114}, + doi = {10.1103/PhysRevLett.97.188102}, + urldate = {2022-05-22}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Breskin2006.pdf} +} + +@article{Bronstein2011, + title = {Deep {{Brain Stimulation}} for {{Parkinson Disease}}: {{An Expert Consensus}} and {{Review}} of {{Key Issues}}}, + author = {Bronstein, Jeff M. and Tagliati, Michele and Tagliati, Michele and Alterman, Ron L. and Lozano, Andres M. and Volkmann, Jens and Stefani, Alessandro and Horak, Fay B. and Okun, Michael S. and Foote, Kelly D. and Krack, Paul and Pahwa, Rajesh and Henderson, Jaimie M. and Hariz, Marwan and Bakay, Roy A.E. and Rezai, Ali R. and Marks, William J. and Moro, Elena and Vitek, Jerrold L. and Weaver, Frances M. and Gross, Robert E. and DeLong, Mahlon R.}, + year = {2011}, + month = feb, + journal = {JAMA Neurology}, + volume = {68}, + number = {2}, + pages = {165--165}, + doi = {10.1001/archneurol.2010.260}, + abstract = {Objective: To provide recommendations to patients, physicians, and other health care providers on several issues involving deep brain stimulation (DBS) for Parkinson disease (PD). Data Sources and Study Selection: An international consortium of experts organized, reviewed the literature, and attended the workshop. Topics were introduced at the workshop, followed by group discussion. Data Extraction and Synthesis: A draft of a consensus statement was presented and further edited after plenary debate. The final statements were agreed on by all members. Conclusions: (1) Patients with PD without significant active cognitive or psychiatric problems who have medically intractable motor fluctuations, intractable tremor, or intolerance of medication adverse effects are good candidates for DBS. (2) Deep brain stimulation surgery is best performed by an experienced neurosurgeon with expertise in stereotactic neurosurgery who is working as part of a interprofessional team. (3) Surgical complication rates are extremely variable, with infection being the most commonly reported complication of DBS. (4) Deep brain stimulation programming is best accomplished by a highly trained clinician and can take 3 to 6 months to obtain optimal results. (5) Deep brain stimulation improves levodopa-responsive symptoms, dyskinesia, and tremor; benefits seem to be long-lasting in many motor domains. (6) Subthalamic nuclei DBS may be complicated by increased depression, apathy, impulsivity, worsened verbal fluency, and executive dysfunction in a subset of patients. (7) Both globus pallidus pars interna and subthalamic nuclei DBS have been shown to be effective in addressing the motor symptoms of PD. (8) Ablative therapy is still an effective alternative and should be considered in a select group of appropriate patients. Arch Neurol. 2011; 68(2):165-171. Published online October 11, 2010. doi:10.1001/archneurol.2010.260}, + pmcid = {4523130}, + pmid = {20937936}, + annotation = {MAG ID: 2105267783\\ +S2ID: 336ee8040691a6202ba366feb34420c0a99fdac3} +} + +@article{Brunelin2012, + title = {Examining {{Transcranial Direct-Current Stimulation}} ({{tDCS}}) as a {{Treatment}} for {{Hallucinations}} in {{Schizophrenia}}}, + author = {Brunelin, Jerome and Mondino, Marine and Gassab, Leila and Haesebaert, Frederic and Gaha, Lofti and {Suaud-Chagny}, Marie-Fran{\c c}oise and Saoud, Mohamed and Mechri, Anwar and Poulet, Emmanuel}, + year = {2012}, + month = jul, + journal = {American Journal of Psychiatry}, + volume = {169}, + number = {7}, + pages = {719--724}, + publisher = {American Psychiatric Association Publishing}, + doi = {10.1176/appi.ajp.2012.11071091} +} + +@phdthesis{Brunet2025, + title = {{Compr{\'e}hension des m{\'e}canismes mol{\'e}culaires et physiques sous-jacents aux stimulations ultrasonores des neurones sensoriels primaires}}, + author = {Brunet, Elena}, + year = {2025}, + abstract = {Dorsal root ganglion (DRG) neurons have a wide range of functions, including touch, pain and itch. These neurons have emerged as promising targets for non-invasive focused ultrasound (FUS) neuromodulation. However, our knowledge of the molecular and physical mechanisms underlying FUS-evoked responses in DRG neurons is limited. This study aims to explore the direct stimulation of individual primary sensory DRG neurons by combining focused US, live-cell calcium imaging and singlecell RNA sequencing. We investigate the neuromodulatory capabilities of FUS in cultured DRG neurons in combination with calcium imaging. We find that a 20-MHz FUS burst of 1-ms duration at an acoustic pressure of 5 MPa elicited calcium responses in 52\% of DRG neurons. Single-cell RNA sequencing reveals that the majority of FUS-sensitive neurons belong to two subsets of DRG neurons: the THexpressing C low-threshold mechanoreceptors (C-LTMRs) and the MRGPRD-expressing C highthreshold mechanoreceptors (C-HTMRs), both of which belonging to the neurons expressing the G{$\alpha$}iinteracting protein (GINIP). This finding was further confirmed by using a ginip mouse model. Ultrasound-sensitive (US+) and -insensitive (US-) DRGs express different gene modules and are associated with specific molecular pathways such as pain response for US+ neurons and collagen fibril organization for US-neurons. FUS excites all the neuronal subtypes by membrane deformation, suggesting a mechanism mediated by mechanosensitive ion channels. Our results identify FUS parameters that activate distinct subsets of DRG neurons and open new avenues for using FUS stimulation to modulate DRG neuron function.}, + langid = {french}, + file = {/Users/tomaubier/Zotero/storage/CSZAHDHY/Brunet - Compréhension des mécanismes moléculaires et physi.pdf} +} + +@article{Brunoni2019, + title = {Noninvasive Brain Stimulation in Psychiatric Disorders: A Primer}, + author = {Brunoni, Andre R. and {Sampaio-Junior}, Bernardo and Moffa, Adriano H. and Apar{\'i}cio, Luana V. and Gordon, Pedro and Klein, Izio and Rios, Rosa M. and Razza, Lais B. and Loo, Colleen and Padberg, Frank and Valiengo, Leandro}, + year = {2019}, + month = feb, + journal = {Brazilian Journal of Psychiatry}, + volume = {41}, + number = {1}, + pages = {70--81}, + publisher = {FapUNIFESP (SciELO)}, + doi = {10.1590/1516-4446-2017-0018}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Brunoni2019.pdf} +} + +@article{Burks2019, + title = {Focused Ultrasound Activates Voltage-Gated Calcium Channels through Depolarizing {{TRPC1}} Sodium Currents in Kidney and Skeletal Muscle}, + author = {Burks, Scott R. and Lorsung, Rebecca M. and Nagle, Matthew E. and Tu, Tsang-Wei and Frank, Joseph A.}, + year = {2019}, + journal = {Theranostics}, + volume = {9}, + number = {19}, + pages = {5517--5531}, + issn = {1838-7640}, + doi = {10.7150/thno.33876}, + urldate = {2023-05-10}, + abstract = {Methods: Murine kidneys and hamstring were given pFUS (1.15 or 1.125 MHz; 4MPa peak rarefactional pressure) under ultrasound or magnetic resonance imaging guidance. Cavitation and tissue displacement were measure by hydrophone and ultrasound radiofrequency data, respectively. Elastic modeling was performed from displacement measurements. COX2 expression and MSC tropism were evaluated in the presence of pharmacological ion channel inhibitors or in transient-receptor-potential-channel-1 (TRPC1)-deficient mice. Immunohistochemistry and co-immunoprecipitation examined physical channel relationships. Fluorescent ionophore imaging of cultured C2C12 muscle cells or TCMK1 kidney cells probed physiological interactions. Results: pFUS induced tissue deformations resulting in kPa-scale forces suggesting mechanical activation of pFUS-induced bioeffects. Inhibiting VGCC or TRPC1 in vivo blocked pFUS-induced COX2 upregulation and MSC tropism to kidneys and muscle. A TRPC1/VGCC complex was observed in plasma membranes. VGCC or TRPC1 suppression blocked pFUS-induced Ca2+ transients in TCMK1 and C2C12 cells. Additionally, Ca2+ transients were blocked by reducing transmembrane Na+ potentials and observed Na+ transients were diminished by genetic TRPC1 suppression. Conclusion: This study suggests that pFUS acoustic radiation forces mechanically activate a Na+-containing TRPC1 current upstream of VGCC rather than directly opening VGCC. The electrogenic function of TRPC1 provides potential mechanistic insight into other pFUS techniques for physiological modulation and optimization strategies for clinical implementation.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Burks2019.pdf} +} + +@article{Burlew1980, + title = {A New Ultrasound Tissue-Equivalent Material.}, + author = {Burlew, M. M. and Madsen, E. L. and Zagzebski, J. A. and Banjavic, R. A. and Sum, S. W.}, + year = {1980}, + month = feb, + journal = {Radiology}, + volume = {134}, + number = {2}, + pages = {517--520}, + publisher = {Radiological Society of North America (RSNA)}, + doi = {10.1148/radiology.134.2.7352242}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Burlew1980.pdf} +} + +@article{Butson2007, + title = {Patient-Specific Analysis of the Volume of Tissue Activated during Deep Brain Stimulation}, + author = {Butson, Christopher R. and Cooper, Scott E. and Henderson, Jaimie M. and McIntyre, Cameron C.}, + year = {2007}, + journal = {NeuroImage}, + volume = {34}, + number = {2}, + pages = {661--670}, + issn = {1053-8119}, + doi = {10.1016/j.neuroimage.2006.09.034}, + abstract = {Despite the clinical success of deep brain stimulation (DBS) for the treatment of movement disorders, many questions remain about its effects on the nervous system. This study presents a methodology to predict the volume of tissue activated (VTA) by DBS on a patient-specific basis. Our goals were to identify the intersection between the VTA and surrounding anatomical structures and to compare activation of these structures with clinical outcomes. The model system consisted of three fundamental components: (1) a 3D anatomical model of the subcortical nuclei and DBS electrode position in the brain, each derived from magnetic resonance imaging (MRI); (2) a finite element model of the DBS electrode and electric field transmitted to the brain, with tissue conductivity properties derived from diffusion tensor MRI; (3) VTA prediction derived from the response of myelinated axons to the applied electric field, which is a function of the stimulation parameters (contact, impedance, voltage, pulse width, frequency). We used this model system to analyze the effects of subthalamic nucleus (STN) DBS in a patient with Parkinson's disease. Quantitative measurements of bradykinesia, rigidity, and corticospinal tract (CST) motor thresholds were evaluated over a range of stimulation parameter settings. Our model predictions showed good agreement with CST thresholds. Additionally, stimulation through electrode contacts that improved bradykinesia and rigidity generated VTAs that overlapped the zona incerta/fields of Forel (ZI/H2). Application of DBS technology to various neurological disorders has preceded scientific characterization of the volume of tissue directly affected by the stimulation. Synergistic integration of clinical analysis, neuroimaging, neuroanatomy, and neurostimulation modeling provides an opportunity to address wide ranging questions on the factors linked with the therapeutic benefits and side effects of DBS.} +} + +@article{Buzsaki2012, + title = {The Origin of Extracellular Fields and Currents --- {{EEG}}, {{ECoG}}, {{LFP}} and Spikes}, + author = {Buzs{\'a}ki, Gy{\"o}rgy and Anastassiou, Costas A. and Koch, Christof}, + year = {2012}, + month = jun, + journal = {Nature Reviews Neuroscience}, + volume = {13}, + number = {6}, + pages = {407--420}, + issn = {1471-003X, 1471-0048}, + doi = {10.1038/nrn3241}, + urldate = {2023-01-20}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Buzsaki2012.pdf} +} + +@article{Bystritsky2011, + title = {A Review of Low-Intensity Focused Ultrasound Pulsation}, + author = {Bystritsky, Alexander and Korb, Alex S. and Douglas, Pamela K. and Cohen, Mark S. and Melega, William P. and Mulgaonkar, Amit P. and DeSalles, Antonio and Min, Byoung-Kyong and Yoo, Seung-Schik}, + year = {2011}, + month = jul, + journal = {Brain Stimulation}, + volume = {4}, + number = {3}, + pages = {125--136}, + issn = {1935861X}, + doi = {10.1016/j.brs.2011.03.007}, + urldate = {2024-02-19}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Bystritsky2011.pdf} +} + +@article{Cadoni2023, + title = {Ectopic Expression of a Mechanosensitive Channel Confers Spatiotemporal Resolution to Ultrasound Stimulations of Neurons for Visual Restoration}, + author = {Cadoni, Sara and Demen{\'e}, Charlie and Alcala, Ignacio and Provansal, Matthieu and Nguyen, Diep and Nelidova, Dasha and Labern{\`e}de, Guillaume and Lubetzki, Jules and Goulet, Ruben and Burban, Emma and D{\'e}gardin, Julie and Simonutti, Manuel and Gauvain, Gregory and Arcizet, Fabrice and Marre, Olivier and Dalkara, Deniz and Roska, Botond and Sahel, Jos{\'e} Alain and Tanter, Mickael and Picaud, Serge}, + year = {2023}, + month = apr, + journal = {Nature Nanotechnology}, + issn = {1748-3387, 1748-3395}, + doi = {10.1038/s41565-023-01359-6}, + urldate = {2023-04-07}, + abstract = {Abstract Remote and precisely controlled activation of the brain is a fundamental challenge in the development of brain--machine interfaces for neurological treatments. Low-frequency ultrasound stimulation can be used to modulate neuronal activity deep in the brain, especially after expressing ultrasound-sensitive proteins. But so far, no study has described an ultrasound-mediated activation strategy whose spatiotemporal resolution and acoustic intensity are compatible with the mandatory needs of brain--machine interfaces, particularly for visual restoration. Here we combined the expression of large-conductance mechanosensitive ion channels with uncustomary high-frequency ultrasonic stimulation to activate retinal or cortical neurons over millisecond durations at a spatiotemporal resolution and acoustic energy deposit compatible with vision restoration. The in vivo sonogenetic activation of the visual cortex generated a behaviour associated with light perception. Our findings demonstrate that sonogenetics can deliver millisecond pattern presentations via an approach less invasive than current brain--machine interfaces for visual restoration.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Cadoni2023.pdf} +} + +@article{Cafarelli2017, + title = {Tuning Acoustic and Mechanical Properties of Materials for Ultrasound Phantoms and Smart Substrates for Cell Cultures}, + author = {Cafarelli, A. and Verbeni, A. and Poliziani, A. and Dario, P. and Menciassi, A. and Ricotti, L.}, + year = {2017}, + month = feb, + journal = {Acta Biomaterialia}, + volume = {49}, + pages = {368--378}, + issn = {17427061}, + doi = {10.1016/j.actbio.2016.11.049}, + urldate = {2024-03-07}, + abstract = {Materials with tailored acoustic properties are of great interest for both the development of tissuemimicking phantoms for ultrasound tests and smart scaffolds for ultrasound mediated tissue engineering and regenerative medicine.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Cafarelli2017.pdf} +} + +@article{Cai2021, + title = {The Neurodevelopmental Role of Dopaminergic Signaling in Neurological Disorders}, + author = {Cai, Yunyun and Xing, Lingyan and Yang, Tuo and Chai, Rui and Wang, Jiaqi and Bao, Jingyin and Shen, Weixing and Ding, Sujun and Chen, Gang}, + year = {2021}, + month = jan, + journal = {Neuroscience Letters}, + volume = {741}, + pages = {135540}, + issn = {03043940}, + doi = {10.1016/j.neulet.2020.135540}, + urldate = {2023-08-29}, + abstract = {Dopamine (DA), a critical neurotransmitter of both the central and peripheral nerve system, plays important roles in a series of biological processes. Dysfunction of dopaminergic signalling may lead to a series of devel\- opmental disorders, including attention deficit/hyperactivity disorder, autism and schizophrenia. However, the exact roles of dopaminergic signalling in these diseases are far from fully understood. We analyse the roles of dopaminergic signalling in multiple physiological and pathological processes, focusing on brain development and related disorders. By summarizing current research in this area, we provide guidance for future studies. This review seeks to deepen our understanding of dopaminergic signalling in developmental disorders, which may offer clues for developing more effective therapeutic drugs.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Cai2021.pdf} +} + +@misc{Calvert, + title = {The {{Buzz Around Brain Stimulation}}}, + author = {Calvert, Anthony} +} + +@article{Cambiaghi2018, + title = {Scribonius {{Largus}} (Probably before {{1CE}}--after {{48CE}})}, + author = {Cambiaghi, Marco and Sconocchia, Sergio}, + year = {2018}, + month = oct, + journal = {Journal of Neurology}, + volume = {265}, + number = {10}, + pages = {2466--2468}, + issn = {0340-5354, 1432-1459}, + doi = {10.1007/s00415-018-8739-5}, + urldate = {2025-02-02}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Cambiaghi2018.pdf} +} + +@article{Carpentier2016, + title = {Clinical Trial of Blood-Brain Barrier Disruption by Pulsed Ultrasound}, + author = {Carpentier, Alexandre and Canney, Michael and Vignot, Alexandre and Reina, Vincent and Beccaria, Kevin and Horodyckid, Catherine and Karachi, Carine and Leclercq, Delphine and Lafon, Cyril and Chapelon, Jean-Yves and Capelle, Laurent and Cornu, Philippe and Sanson, Marc and {Hoang-Xuan}, Kh{\^e} and Delattre, Jean-Yves and Idbaih, Ahmed}, + year = {2016}, + month = jun, + journal = {Science Translational Medicine}, + volume = {8}, + number = {343}, + publisher = {American Association for the Advancement of Science (AAAS)}, + doi = {10.1126/scitranslmed.aaf6086}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Carpentier2016.pdf} +} + +@article{Carpentier2023, + title = {Neurosurgeon at the {{Piti{\'e}-Salp{\^e}tri{\`e}re University Hospital}} ({{AP-HP}}), {{Inventor}} of the {{SonoCloud}} System and {{Founder}} of {{Carthera}}{\textregistered} {{Inc}}.}, + author = {Carpentier, Alexandre}, + year = {2023}, + month = sep, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Carpentier2023.pdf} +} + +@book{Carter2015, + title = {Guide to Research Techniques in Neuroscience}, + author = {Carter, Matt and Shieh, Jennifer C.}, + year = {2015}, + edition = {Second edition}, + publisher = {Elsevier/AP, Academic Press is an imprint of Elsevier}, + address = {Amsterdam}, + isbn = {978-0-12-800511-8}, + lccn = {RC337 .C37 2015}, + keywords = {Neurosciences,Research Methodology}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Carter2015.pdf} +} + +@article{Castellanos2016, + title = {Therapeutic {{Modulation}} of {{Calcium Dynamics Using Ultrasound}} and {{Other Energy-Based Techniques}}}, + author = {Castellanos, Ivan Mauricio Suarez and Balteanu, Bogdan and Singh, Tania and Zderic, Vesna}, + year = {2016}, + journal = {IEEE Reviews in Biomedical Engineering}, + volume = {9}, + pages = {177--191}, + publisher = {{Institute of Electrical and Electronics Engineers (IEEE)}}, + doi = {10.1109/rbme.2016.2555760}, + keywords = {Bioeffects,Biological processes,Ca2+ signaling,Calcium,cell stimulation,Electrical stimulation,energy-based therapy,Microscopy,Noninvasive treatment,therapeutic ultrasound,Ultrasonic imaging}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Castellanos2016.pdf} +} + +@article{Catheline2023, + title = {A Mechanistic Interpretation of Relativistic Rigid Body Rotation}, + author = {Catheline, Stefan}, + year = {2023}, + month = jun, + journal = {Scientific Reports}, + volume = {13}, + number = {1}, + pages = {9047}, + issn = {2045-2322}, + doi = {10.1038/s41598-023-35897-9}, + urldate = {2023-08-11}, + abstract = {Abstract The starting point of this manuscript is classical rigid body rotation. As it is well known, it contradicts basis of relativity since infinite speed is reached at infinite distance from the rotation center O. In order to fix this problem, a phenomenological circle-based construction using Euclidian trigonometry is first described: the relativistic rigid body rotation. The physical Eulerian acceleration implied by this geometrical construction then sketches future links with Maxwell's equation and Lense-Thirring effect. More importantly, relativistic rigid body rotation is shown to be compatible with Lorentz transformation and brings new geometrical interpretations of time and space intervals.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Catheline2023.pdf} +} + +@article{Cathignol1997, + title = {Acoustic {{Field}} of {{Plane}} or {{Spherical Transducers}}}, + author = {Cathignol, Dominique and Faure, Philippe}, + year = {1997}, + volume = {83}, + abstract = {The authors derive a method for calculating the time-dependent Rayleigh integral in the case of plane and spherically focused ultrasonic transducers with uniform distribution of amplitude. The method (line integral method) involves the decomposition of the radiated field into a geometrical wave (either plane or spherical) and a diffracted edge wave. The method has two main advantages. First, it can deal with possibly complex transducer shapes for which an analytical calculation of the diffraction impulse response h(M, t) is not tractable and second, it is considerably faster than the Rayleigh integral method. Comparisons between the transient pressure time waveform obtained with the line integral method and those obtained with conventional methods show an excellent agreement in the two cases of a shell and a spherical sector. In the case of the shell, the computation times of the impulse response with the line integral method are approximately 3 times and 50 times faster than those obtained with the impulse diffraction and the Rayleigh integral methods respectively. In the case of the semi-spherical shell, no analytical expression of h(M, t) exists and the computation time of the impulse response is approximately 15 times faster than with the Rayleigh integral method.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Cathignol1997.pdf} +} + +@article{Chao2014, + title = {Repeated {{BOLD-fMRI Imaging}} of {{Deep Brain Stimulation Responses}} in {{Rats}}}, + author = {Chao, Tzu-Hao Harry and Chen, Jyh-Horng and Yen, Chen-Tung}, + editor = {Antal, Andrea}, + year = {2014}, + month = may, + journal = {PLoS ONE}, + volume = {9}, + number = {5}, + pages = {e97305}, + issn = {1932-6203}, + doi = {10.1371/journal.pone.0097305}, + urldate = {2022-04-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Chao22.pdf} +} + +@article{Charles1991, + title = {Intercellular Signaling in Glial Cells: {{Calcium}} Waves and Oscillations in Response to Mechanical Stimulation and Glutamate}, + author = {Charles, Andrew C. and Merrill, Jean E. and Dirksen, Ellen R. and Sandersont, Michael J.}, + year = {1991}, + month = jun, + journal = {Neuron}, + volume = {6}, + number = {6}, + pages = {983--992}, + publisher = {Elsevier BV}, + doi = {10.1016/0896-6273(91)90238-u}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Charles1991.pdf} +} + +@article{Charles1992, + title = {Intercellular Calcium Signaling via Gap Junctions in Glioma Cells.}, + author = {Charles, A C and Naus, C C and Zhu, D and Kidder, G M and Dirksen, E R and Sanderson, M J}, + year = {1992}, + month = jul, + journal = {Journal of Cell Biology}, + volume = {118}, + number = {1}, + pages = {195--201}, + issn = {0021-9525, 1540-8140}, + doi = {10.1083/jcb.118.1.195}, + urldate = {2023-02-17}, + abstract = {Calcium signaling in C6 glioma cells in culture was examined with digital fluorescence video microscopy. C6 cells express low levels of the gap junction protein connexin43 and have correspondingly weak gap junctional communication as evidenced by dye coupling (Naus, C. C. G., J. F. Bechberger, S. Caveney, and J. X. Wilson. 1991. Neurosci. Lett. 126:33-36). Transfection of C6 cells with the cDNA encoding connexin43 resulted in clones with increased expression of connexin43 mRNA and protein and increased dye coupling, as well as markedly reduced rates of proliferation (Zhu, D., S. Caveney, G. M. Kidder, and C. C. Naus. 1991. Proc. Natl. Acad. Sci. USA. 88:1883-1887; Naus, C. C. G., D. Zhu, S. Todd, and G. M. Kidder. 1992. Cell Mol. Neurobiol. 12:163-175). Mechanical stimulation of a single cell in a culture of non-transfected C6 cells induced a wave of increased intracellular calcium concentration ([Ca2+]i) that showed little or no communication to adjacent cells. By contrast, mechanical stimulation of a single cell in cultures of C6 clones expressing transfected connexin43 cDNA induced a Ca2+ wave that was communicated to multiple surrounding cells, and the extent of communication was proportional to the level of expression of the connexin43 cDNA. These results provide direct evidence that intercellular Ca2+ signaling occurs via gap junctions. Ca2+ signaling through gap junctions may provide a means for the coordinated regulation of cellular function, including cell growth and differentiation.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Charles1992.pdf} +} + +@article{Charles1993, + title = {Mechanisms of Intercellular Calcium Signaling in Glial Cells Studied with Dantrolene and Thapsigargin}, + author = {Charles, Andrew C. and Dirksen, Ellen R. and Merrill, Jean E. and Sanderson, Michael J.}, + year = {1993}, + month = feb, + journal = {Glia}, + volume = {7}, + number = {2}, + pages = {134--145}, + issn = {0894-1491, 1098-1136}, + doi = {10.1002/glia.440070203}, + urldate = {2024-10-09}, + abstract = {Mechanical stimulation of a single cell in a primary mixed glial cell culture induced a wave of increased intracellular calcium concentration ([Ca"'],) that was communicated to surrounding cells. Following propagation of the Ca'+ wave, many cells showed asynchronous oscillations in [Ca2'l,. Dantrolene sodium I10 pM) inhibited the increase in ICa2+Iiassociated with this Ca" wave by 60-80\%, and prevented subsequent Ca"+ oscillations. Despite the markedly decreased magnitude of the increase in [Ca"],, the rate of propagation and the extent of communication ofthe Ca2+wave were similar to those prior to the addition of dantrolene. Thapsigargin (10 nM t o 1pM) induced a n initial increase in LCa" I ji ranging from 100 nM to 500 nM in all cells that was followed by a recovery of LCa2'li to near resting levels in most cells. Transient exposure to thapsigargin for 2 min irreversibly blocked communication of a Ca' ' wave from the stimulated cell to adjacent cells. Glutamate (50 pM) induced a n initial increase in [Ca2+], in most cells that was followed by sustained oscillations in [Ca"li in some cells. Dantrolene (10 pill) inhibited this initial [Ca2+1,increase caused by glutamate by 65-9076 and abolished subsequent oscillations. Thapsigargin (10 nM t o 1 km) abolished the response to glutamate in over 99\% of cells. These results suggest that while both dantrolene and thapsigargin inhibit intracellular Ca2+release, only thapsigargin affects the mechanism that mediates intercellular communication of Ca2- waves. These findings are consistent with the hypothesis that inositol trisphosphate (IP,) mediates the propagation of Ca2 waves whereas Ca" ' -induced Ca'.'- release amplifies Ca" waves and generates subsequent Ca' oscillations. ci: 1993 Wiley-Iiss, Inc.}, + copyright = {http://onlinelibrary.wiley.com/termsAndConditions\#vor}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Charles1993.pdf} +} + +@article{Charles1998, + title = {Intercellular Calcium Waves in Glia}, + author = {Charles, Andrew}, + year = {1998}, + month = sep, + journal = {Glia}, + volume = {24}, + number = {1}, + pages = {39--49}, + issn = {0894-1491, 1098-1136}, + doi = {10.1002/(SICI)1098-1136(199809)24:1<39::AID-GLIA5>3.0.CO;2-W}, + urldate = {2023-07-21}, + abstract = {Glial cells are capable of communicating increases in [Ca2ϩ]i from a single cell to many surrounding cells. These intercellular Ca2ϩ waves have been observed in glia in multiple different preparations, including dissociated brain cell cultures, glial cell lines, organotypic brain slice cultures, and intact retinal preparations. They may occur spontaneously, or in response to a variety of stimuli. Ca2ϩ waves occurring under different conditions in different preparations may have distinctive patterns of initiation and propagation, and distinctive pharmacological characteristics consistent with the involvement of different intracellular and intercellular signaling pathways. This paper presents original data supporting a combination of gap junction and extracellular messenger-mediated signaling in mechanically induced glial Ca2ϩ waves. Additional new observations provide evidence that a rapidly propagated signal may precede the glial Ca2ϩ wave and may mediate rapid glial-neuronal communication. This original data is discussed in the context of a review of the literature and current concepts regarding the potential mechanisms, physiological and pathological roles of this dynamic pattern of glial intercellular signaling. GLIA 24:39--49, 1998. ௠ 1998 Wiley-Liss, Inc.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Charles1998.pdf} +} + +@article{Charles1999, + title = {Nitric Oxide Pumps up Calcium Signalling}, + author = {Charles, Andrew}, + year = {1999}, + month = dec, + journal = {Nature Cell Biology}, + volume = {1}, + number = {8}, + pages = {E193-E195}, + issn = {1465-7392, 1476-4679}, + doi = {10.1038/70221}, + urldate = {2023-07-24}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Charles1999.pdf} +} + +@incollection{Chato1990, + title = {Fundamentals of {{Bioheat Transfer}}}, + booktitle = {Thermal {{Dosimetry}} and {{Treatment Planning}}}, + author = {Chato, J. C.}, + editor = {Gautherie, Michel}, + year = {1990}, + pages = {1--56}, + publisher = {Springer Berlin Heidelberg}, + address = {Berlin, Heidelberg}, + doi = {10.1007/978-3-642-48712-5_1}, + urldate = {2024-06-25}, + isbn = {978-3-642-48714-9 978-3-642-48712-5}, + langid = {english} +} + +@incollection{Chaussy2017, + title = {The {{History}} of {{Shockwave Lithotripsy}}}, + booktitle = {The {{History}} of {{Technologic Advancements}} in {{Urology}}}, + author = {Chaussy, Christian G.}, + year = {2017}, + month = jun, + pages = {109--121}, + publisher = {Springer International Publishing}, + doi = {10.1007/978-3-319-61691-9_11} +} + +@article{Cheng2008, + title = {Calcium {{Sparks}}}, + author = {Cheng, Heping and Lederer, W. J.}, + year = {2008}, + month = oct, + journal = {Physiological Reviews}, + volume = {88}, + number = {4}, + pages = {1491--1545}, + issn = {0031-9333, 1522-1210}, + doi = {10.1152/physrev.00030.2007}, + urldate = {2024-12-05}, + abstract = {The calcium ion (Ca 2+ ) is the simplest and most versatile intracellular messenger known. The discovery of Ca 2+ sparks and a related family of elementary Ca 2+ signaling events has revealed fundamental principles of the Ca 2+ signaling system. A newly appreciated ``digital'' subsystem consisting of brief, high Ca 2+ concentration over short distances (nanometers to microns) comingles with an ``analog'' global Ca 2+ signaling subsystem. Over the past 15 years, much has been learned about the theoretical and practical aspects of spark formation and detection. The quest for the spark mechanisms [the activation, coordination, and termination of Ca 2+ release units (CRUs)] has met unexpected challenges, however, and raised vexing questions about CRU operation in situ. Ample evidence shows that Ca 2+ sparks catalyze many high-threshold Ca 2+ processes involved in cardiac and skeletal muscle excitation-contraction coupling, vascular tone regulation, membrane excitability, and neuronal secretion. Investigation of Ca 2+ sparks in diseases has also begun to provide novel insights into hypertension, cardiac arrhythmias, heart failure, and muscular dystrophy. An emerging view is that spatially and temporally patterned activation of the digital subsystem confers on intracellular Ca 2+ signaling an exquisite architecture in space, time, and intensity, which underpins signaling efficiency, stability, specificity, and diversity. These recent advances in ``sparkology'' thus promise to unify the simplicity and complexity of Ca 2+ signaling in biology.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Cheng2008.pdf} +} + +@article{Cheng2022, + title = {High Resolution Ultrasonic Neural Modulation Observed via in~Vivo Two-Photon Calcium Imaging}, + author = {Cheng, Zongyue and Wang, Chenmao and Wei, Bowen and Gan, Wenbiao and Zhou, Qifa and Cui, Meng}, + year = {2022}, + month = jan, + journal = {Brain Stimulation}, + volume = {15}, + number = {1}, + pages = {190--196}, + issn = {1935-861X}, + doi = {10.1016/j.brs.2021.12.005}, + urldate = {2023-05-17}, + abstract = {Neural modulation plays a major role in delineating the circuit mechanisms and serves as the cornerstone of neural interface technologies. Among the various modulation mechanisms, ultrasound enables noninvasive label-free deep access to mammalian brain tissue. To date, most if not all ultrasonic neural modulation implementations are based on {$\sim$}1~MHz carrier frequency. The long acoustic wavelength results in a spatially coarse modulation zone, often spanning over multiple function regions. The modulation of one function region is inevitably linked with the modulation of its neighboring regions. Moreover, the lack of in~vivo cellular resolution cell-type-specific recording capabilities in most studies prevents the revealing of the genuine cellular response to ultrasound. To significantly increase the spatial resolution, we explored the application of high-frequency ultrasound. To investigate the neuronal response at cellular resolutions, we developed a dual-modality system combining in~vivo two-photon calcium imaging and focused ultrasound modulation. The studies show that the {$\sim$}30~MHz ultrasound can suppress the neuronal activity in awake mice at 100-{$\mu$}m scale spatial resolutions, paving the way for high-resolution ultrasonic neural modulation. The dual-modality in~vivo system validated through this study will serve as a general platform for studying the dynamics of various cell types in response to ultrasound.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Cheng2022.pdf;/Users/tomaubier/Zotero/storage/UZXKMENZ/S1935861X21008408.html} +} + +@article{Chilibon2012, + title = {Ferroelectric Ceramics by Sol--Gel Methods and Applications: A Review}, + shorttitle = {Ferroelectric Ceramics by Sol--Gel Methods and Applications}, + author = {Chilibon, Irinela and {Marat-Mendes}, Jos{\'e} N.}, + year = {2012}, + month = dec, + journal = {Journal of Sol-Gel Science and Technology}, + volume = {64}, + number = {3}, + pages = {571--611}, + issn = {0928-0707, 1573-4846}, + doi = {10.1007/s10971-012-2891-7}, + urldate = {2023-04-02}, + langid = {english} +} + +@article{Church2015, + title = {A {{Theoretical Study}} of {{Inertial Cavitation}} from {{Acoustic Radiation Force Impulse Imaging}} and {{Implications}} for the {{Mechanical Index1}}}, + author = {Church, Charles C. and Labuda, Cecille and Nightingale, Kathryn}, + year = {2015}, + month = feb, + journal = {Ultrasound in Medicine \& Biology}, + volume = {41}, + number = {2}, + pages = {472--485}, + issn = {03015629}, + doi = {10.1016/j.ultrasmedbio.2014.09.012}, + urldate = {2022-06-27}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Church2015.pdf} +} + +@article{Cimrman2019, + title = {Multiscale Finite Element Calculations in {{Python}} Using {{SfePy}}}, + author = {Cimrman, Robert and Luke{\v s}, Vladim{\'i}r and Rohan, Eduard}, + year = {2019}, + month = aug, + journal = {Advances in Computational Mathematics}, + volume = {45}, + number = {4}, + pages = {1897--1921}, + issn = {1019-7168, 1572-9044}, + doi = {10.1007/s10444-019-09666-0}, + urldate = {2023-03-14}, + abstract = {SfePy (simple finite elements in Python) is a software for solving various kinds of problems described by partial differential equations in one, two, or three spatial dimensions by the finite element method. Its source code is mostly (85\%) Python and relies on fast vectorized operations provided by the NumPy package. For a particular problem, two interfaces can be used: a declarative application programming interface (API), where problem description/definition files (Python modules) are used to define a calculation, and an imperative API, that can be used for interactive commands, or in scripts and libraries. After outlining the SfePy package development, the paper introduces its implementation, structure, and general features. The components for defining a partial differential equation are described using an example of a simple heat conduction problem. Specifically, the declarative API of SfePy is presented in the example. To illustrate one of SfePy's main assets, the framework for implementing complex multiscale models based on the theory of homogenization, an example of a two-scale piezoelastic model is presented, showing both the mathematical description of the problem and the corresponding code.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Cimrman2019.pdf} +} + +@article{Cirillo2019, + title = {Transcranial Magnetic Stimulation in Anxiety and Trauma-related Disorders: {{A}} Systematic Review and Meta-analysis}, + shorttitle = {Transcranial Magnetic Stimulation in Anxiety and Trauma-related Disorders}, + author = {Cirillo, Patricia and Gold, Alexandra K. and Nardi, Antonio E. and Ornelas, Ana C. and Nierenberg, Andrew A. and Camprodon, Joan and Kinrys, Gustavo}, + year = {2019}, + month = may, + journal = {Brain and Behavior}, + volume = {9}, + number = {6}, + pages = {e01284}, + issn = {2162-3279}, + doi = {10.1002/brb3.1284}, + urldate = {2023-08-29}, + abstract = {Background Transcranial magnetic stimulation (TMS) has been evaluated as an effective treatment option for patients with major depressive disorder. However, there are limited studies that have evaluated the efficacy of TMS for other neuropsychiatric disorders such as anxiety and trauma-related disorders. We reviewed the literature that has evaluated TMS as a treatment for anxiety and trauma-related disorders. Methods We searched for articles published up to December 2017 in Embase, Medline, and ISI Web of Science databases, following the Preferred Items for Reporting of Systematic Reviews and Meta-Analyses (PRISMA) statement. Articles (n~=~520) evaluating TMS in anxiety and trauma-related disorders were screened and a small subset of these that met the eligibility criteria (n~=~17) were included in the systematic review, of which nine evaluated TMS in posttraumatic stress disorder (PTSD), four in generalized anxiety disorder (GAD), two in specific phobia (SP), and two in panic disorder (PD). The meta-analysis was performed with PTSD and GAD since PD and SP had an insufficient number of studies and sample sizes. Results Among anxiety and trauma-related disorders, TMS has been most widely studied as a treatment for PTSD. TMS demonstrated large overall treatment effect for both PTSD (ES~=~-0.88, 95\% CI: -1.42, -0.34) and GAD (ES~=~-2.06, 95\% CI: -2.64, -1.48), including applying high frequency over the right dorsolateral prefrontal cortex. Since few studies have evaluated TMS for SP and PD, few conclusions can be drawn. Conclusions Our meta-analysis suggests that TMS may be an effective treatment for GAD and PTSD.}, + pmcid = {PMC6576151}, + pmid = {31066227}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Cirillo2019.pdf} +} + +@article{Clapham2007, + title = {Calcium {{Signaling}}}, + author = {Clapham, David E.}, + year = {2007}, + month = dec, + journal = {Cell}, + volume = {131}, + number = {6}, + pages = {1047--1058}, + issn = {00928674}, + doi = {10.1016/j.cell.2007.11.028}, + urldate = {2023-05-11}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Clapham2007.pdf} +} + +@article{Claudi2020a, + title = {{{BrainGlobe Atlas API}}: A Common Interface for Neuroanatomical Atlases}, + shorttitle = {{{BrainGlobe Atlas API}}}, + author = {Claudi, Federico and Petrucco, Luigi and Tyson, Adam and Branco, Tiago and Margrie, Troy and Portugues, Ruben}, + year = {2020}, + month = oct, + journal = {Journal of Open Source Software}, + volume = {5}, + number = {54}, + pages = {2668}, + issn = {2475-9066}, + doi = {10.21105/joss.02668}, + urldate = {2025-01-08}, + abstract = {Neuroscientists routinely perform experiments aimed at recording or manipulating neural activity, uncovering physiological processes underlying brain function or elucidating aspects of brain anatomy. Understanding how the brain generates behaviour ultimately depends on merging the results of these experiments into a unified picture of brain anatomy and function. Brain atlases are crucial in this endeavour: by outlining the organization of brain regions they provide a reference upon which our understanding of brain function can be anchored. More recently, digital high-resolution 3d atlases have been produced for several model organisms providing an invaluable resource for the research community. Effective use of these atlases depends on the availability of an application programming interface (API) that enables researchers to develop software to access and query atlas data. However, while some atlases come with an API, these are generally specific for individual atlases, and this hinders the development and adoption of open-source neuroanatomy software. The BrainGlobe atlas API (BG-Atlas API) overcomes this problem by providing a common interface for programmers to download and process data across a variety of model organisms. By adopting the BG-Atlas API, software can then be developed agnostic to the atlas, increasing adoption and interoperability of packages in neuroscience and enabling direct integration of different experimental modalities and even comparisons across model organisms.}, + copyright = {http://creativecommons.org/licenses/by/4.0/}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Claudi2020a.pdf} +} + +@article{Claudi2021, + title = {Visualizing Anatomically Registered Data with Brainrender}, + author = {Claudi, Federico and Tyson, Adam L and Petrucco, Luigi and Margrie, Troy W and Portugues, Ruben and Branco, Tiago}, + year = {2021}, + month = mar, + journal = {eLife}, + volume = {10}, + pages = {e65751}, + issn = {2050-084X}, + doi = {10.7554/eLife.65751}, + urldate = {2023-06-08}, + abstract = {Three-dimensional (3D) digital brain atlases and high-throughput brain-wide imaging techniques generate large multidimensional datasets that can be registered to a common reference frame. Generating insights from such datasets depends critically on visualization and interactive data exploration, but this a challenging task. Currently available software is dedicated to single atlases, model species or data types, and generating 3D renderings that merge anatomically registered data from diverse sources requires extensive development and programming skills. Here, we present brainrender: an open-source Python package for interactive visualization of multidimensional datasets registered to brain atlases. Brainrender facilitates the creation of complex renderings with different data types in the same visualization and enables seamless use of different atlas sources. High-quality visualizations can be used interactively and exported as highresolution figures and animated videos. By facilitating the visualization of anatomically registered data, brainrender should accelerate the analysis, interpretation, and dissemination of brain-wide multidimensional data.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Claudi2021.pdf} +} + +@article{Clennell2021, + title = {Transient Ultrasound Stimulation Has Lasting Effects on Neuronal Excitability}, + author = {Clennell, Benjamin and Steward, Tom G.J. and Elley, Meg and Shin, Eunju and Weston, Miles and Drinkwater, Bruce W. and Whitcomb, Daniel J.}, + year = {2021}, + month = mar, + journal = {Brain Stimulation}, + volume = {14}, + number = {2}, + pages = {217--225}, + issn = {1935861X}, + doi = {10.1016/j.brs.2021.01.003}, + urldate = {2022-10-17}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Clennell2021.pdf} +} + +@article{Clennell2023, + title = {Ultrasound Modulates Neuronal Potassium Currents via Ionotropic Glutamate Receptors}, + author = {Clennell, Benjamin and Steward, Tom G.J. and Hanman, Kaliya and Needham, Tom and Benachour, Janette and Jepson, Mark and Elley, Meg and Halford, Nathan and Heesom, Kate and Shin, Eunju and Moln{\'a}r, Elek and Drinkwater, Bruce W. and Whitcomb, Daniel J.}, + year = {2023}, + month = mar, + journal = {Brain Stimulation}, + volume = {16}, + number = {2}, + pages = {540--552}, + issn = {1935861X}, + doi = {10.1016/j.brs.2023.01.1674}, + urldate = {2024-02-20}, + abstract = {Background: Focused ultrasound stimulation (FUS) has the potential to provide non-invasive neuromodulation of deep brain regions with unparalleled spatial precision. However, the cellular and molecular consequences of ultrasound stimulation on neurons remains poorly understood. We previously reported that ultrasound stimulation induces increases in neuronal excitability that persist for hours following stimulation in vitro. In the present study we sought to further elucidate the molecular mechanisms by which ultrasound regulates neuronal excitability and synaptic function. Objectives: To determine the effect of ultrasound stimulation on voltage-gated ion channel function and synaptic plasticity. Methods: Primary rat cortical neurons were exposed to a 40 s, 200 kHz pulsed ultrasound stimulus or sham-stimulus. Whole-cell patch clamp electrophysiology, quantitative proteomics and high-resolution confocal microscopy were employed to determine the effects of ultrasound stimulation on molecular regulators of neuronal excitability and synaptic function. Results: We find that ultrasound exposure elicits sustained but reversible increases in whole-cell potassium currents. In addition, we find that ultrasound exposure activates synaptic signalling cascades that result in marked increases in excitatory synaptic transmission. Finally, we demonstrate the requirement of ionotropic glutamate receptor (AMPAR/NMDAR) activation for ultrasound-induced modulation of neuronal potassium currents. Conclusion: These results suggest specific patterns of pulsed ultrasound can induce contemporaneous enhancement of both neuronal excitability and synaptic function, with implications for the application of FUS in experimental and therapeutic settings. Further study is now required to deduce the precise molecular mechanisms through which these changes occur.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Clennell2023.pdf} +} + +@book{Cobbold2007, + title = {Foundations of Biomedical Ultrasound}, + author = {Cobbold, Richard S. C.}, + year = {2007}, + publisher = {Oxford University Press}, + address = {Oxford ; New York}, + isbn = {978-0-19-516831-0}, + lccn = {QM25 .C63 2007}, + keywords = {Ultrasonic imaging,Ultrasonics,Ultrasonography}, + annotation = {OCLC: ocm61351619}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Cobbold2007.pdf} +} + +@article{Codling2008, + title = {Random Walk Models in Biology}, + author = {Codling, Edward A and Plank, Michael J and Benhamou, Simon}, + year = {2008}, + month = aug, + journal = {Journal of The Royal Society Interface}, + volume = {5}, + number = {25}, + pages = {813--834}, + issn = {1742-5689, 1742-5662}, + doi = {10.1098/rsif.2008.0014}, + urldate = {2022-04-15}, + abstract = {Mathematical modelling of the movement of animals, micro-organisms and cells is of great relevance in the fields of biology, ecology and medicine. Movement models can take many different forms, but the most widely used are based on the extensions of simple random walk processes. In this review paper, our aim is twofold: to introduce the mathematics behind random walks in a straightforward manner and to explain how such models can be used to aid our understanding of biological processes. We introduce the mathematical theory behind the simple random walk and explain how this relates to Brownian motion and diffusive processes in general. We demonstrate how these simple models can be extended to include drift and waiting times or be used to calculate first passage times. We discuss biased random walks and show how hyperbolic models can be used to generate correlated random walks. We cover two main applications of the random walk model. Firstly, we review models and results relating to the movement, dispersal and population redistribution of animals and micro-organisms. This includes direct calculation of mean squared displacement, mean dispersal distance, tortuosity measures, as well as possible limitations of these model approaches. Secondly, oriented movement and chemotaxis models are reviewed. General hyperbolic models based on the linear transport equation are introduced and we show how a reinforced random walk can be used to model movement where the individual changes its environment. We discuss the applications of these models in the context of cell migration leading to blood vessel growth (angiogenesis). Finally, we discuss how the various random walk models and approaches are related and the connections that underpin many of the key processes involved.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Codling2008.pdf} +} + +@article{Cole2014, + title = {Marble Game with Optimal Ferroelectric Switching}, + author = {Cole, J and Ahmed, S J and Curiel, L and Pichardo, S and Rubel, O}, + year = {2014}, + month = apr, + journal = {Journal of Physics: Condensed Matter}, + volume = {26}, + number = {13}, + pages = {135901}, + issn = {0953-8984, 1361-648X}, + doi = {10.1088/0953-8984/26/13/135901}, + urldate = {2022-08-16}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Cole2014.pdf} +} + +@article{Collins2020, + title = {Focused {{Ultrasound Neuromodulation}} and the {{Confounds}} of {{Intracellular Electrophysiological Investigation}}}, + author = {Collins, Morgan N. and Mesce, Karen A.}, + year = {2020}, + month = jul, + journal = {eneuro}, + volume = {7}, + number = {4}, + pages = {ENEURO.0213-20.2020}, + issn = {2373-2822}, + doi = {10.1523/ENEURO.0213-20.2020}, + urldate = {2023-08-31}, + abstract = {Focused ultrasound (US) can modulate neuronal activity noninvasively with high spatial specificity. In intact nervous systems, however, efforts to determine its enigmatic mode of efficacy have been confounded by the indirect effects of US on mechanosensitive sensory cells and the inability to target equivalent populations of cells with precision across preparations. Single-cell approaches, either via cultured mammalian neurons or tractable invertebrate neural systems, hold great promise for elucidating the cellular mechanisms underlying the actions of US. Here, we present evidence from the medicinal leech, Hirudo verbana, that researchers should apply caution when using US in conjunction with single-cell electrophysiological recording techniques, including sharp-electrode intracellular recording. Although we found that US could elicit depolarization of the resting membrane potential of single neurons, a finding with precedent, we determined that this effect and others could be reliably mimicked via subtle manual displacement of the recording electrode. Because focused US is known to induce resonance of recording electrodes, we aimed to determine how similarly US-induced depolarizations matched those produced by micro movements of a sharp glass electrode, a phenomenon we believe can account for purported depolarizations measured in this manner. Furthermore, we show that when clonally related homologous neurons, which are essentially isopotential, are impaled before the application of focused US, they show a statistically significant change in their membrane potential as compared with the homologous cells that received US with no initial impalement. Future investigations into US's cellular effects should attempt to control for potential electrode resonance or use alternative recording strategies.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Collins2020.pdf} +} + +@article{Collins2022, + title = {A Review of the Bioeffects of Low-Intensity Focused Ultrasound and the Benefits of a Cellular Approach}, + author = {Collins, Morgan N. and Mesce, Karen A.}, + year = {2022}, + month = nov, + journal = {Frontiers in Physiology}, + volume = {13}, + pages = {1047324}, + issn = {1664-042X}, + doi = {10.3389/fphys.2022.1047324}, + urldate = {2022-11-15}, + abstract = {This review article highlights the historical developments and current state of knowledge of an important neuromodulation technology: low-intensity focused ultrasound. Because compelling studies have shown that focused ultrasound can modulate neuronal activity non-invasively, especially in deep brain structures with high spatial specificity, there has been a renewed interest in attempting to understand the specific bioeffects of focused ultrasound at the cellular level. Such information is needed to facilitate the safe and effective use of focused ultrasound to treat a number of brain and nervous system disorders in humans. Unfortunately, to date, there appears to be no singular biological mechanism to account for the actions of focused ultrasound, and it is becoming increasingly clear that different types of nerve cells will respond to focused ultrasound differentially based on the complement of their ion channels, other membrane biophysical properties, and arrangement of synaptic connections. Furthermore, neurons are apparently not equally susceptible to the mechanical, thermal and cavitation-related consequences of focused ultrasound application---to complicate matters further, many studies often use distinctly different focused ultrasound stimulus parameters to achieve a reliable response in neural activity. In this review, we consider the benefits of studying more experimentally tractable invertebrate preparations, with an emphasis on the medicinal leech, where neurons can be studied as unique individual cells and be synaptically isolated from the indirect effects of focused ultrasound stimulation on mechanosensitive afferents. In the leech, we have concluded that heat is the primary effector of focused ultrasound neuromodulation, especially on motoneurons in which we observed a focused ultrasound-mediated blockade of action potentials. We discuss that the mechanical bioeffects of focused ultrasound, which are frequently described in the literature, are less reliably achieved as compared to thermal ones, and that observations ascribed to mechanical responses may be confounded by activation of synaptically-coupled sensory structures or artifacts associated with electrode resonance. Ultimately, both the mechanical and thermal components of focused ultrasound have significant potential to contribute to the sculpting of specific neural outcomes. Because focused ultrasound can generate significant modulation at a temperature \<5{$^\circ$}C, which is believed to be safe for moderate durations, we support the idea that focused ultrasound should be considered as a thermal neuromodulation technology for clinical use, especially targeting neural pathways in the peripheral nervous system.}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Collins2022.pdf} +} + +@article{Constans2018, + title = {Potential Impact of Thermal Effects during Ultrasonic Neurostimulation: Retrospective Numerical Estimation of Temperature Elevation in Seven Rodent Setups}, + shorttitle = {Potential Impact of Thermal Effects during Ultrasonic Neurostimulation}, + author = {Constans, Charlotte and Mateo, Philippe and Tanter, Micka{\"e}l and Aubry, Jean-Fran{\c c}ois}, + year = {2018}, + month = jan, + journal = {Physics in Medicine \& Biology}, + volume = {63}, + number = {2}, + pages = {025003}, + issn = {1361-6560}, + doi = {10.1088/1361-6560/aaa15c}, + urldate = {2023-08-07}, + abstract = {In the past decade, a handful but growing number of groups have reported worldwide successful low intensity focused ultrasound induced neurostimulation trials on rodents. Its effects range from movement elicitations to reduction of anesthesia time or reduction of the duration of drug induced seizures. The mechanisms underlying ultrasonic neuromodulation are still not fully understood. Given the low intensities used in most of the studies, a mechanical effect is more likely to be responsible for the neuromodulation effect, but a clear description of the thermal and mechanical effects is necessary to optimize clinical applications. Based on five studies settings, we calculated the temperature rise and thermal doses in order to evaluate its implication in the neuromodulation phenomenon. Our retrospective analysis shows thermal rise ranging from 0.002 {$^\circ$}C to 0.8 {$^\circ$}C in the brain for all setups, except for one setup for which the temperature increase is estimated to be as high as 7 {$^\circ$}C. We estimate that in the latter case, temperature rise cannot be neglected as a possible cause of neuromodulation. Simulations results were supported by temperature measurements on a mouse with two different sets of parameters. Although the calculated temperature is compatible with the absence of visible thermal lesions on the skin, it is high enough to impact brain circuits. Our study highlights the usefulness of performing thermal simulations prior to experiment in order to fully take into account not only the impact of the peak intensity but also pulse duration and pulse repetition.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Constans2018.pdf} +} + +@phdthesis{Constans2018a, + title = {{Modulation of brain activity with low intensity focused ultrasound}}, + author = {Constans, Charlotte}, + year = {2018}, + month = sep, + langid = {french}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Constans2018a.pdf} +} + +@article{Cornu2018, + title = {Ultrafast Monitoring and Control of Subharmonic Emissions of an Unseeded Bubble Cloud during Pulsed Sonication}, + author = {Cornu, Corentin and Gu{\'e}dra, Matthieu and B{\'e}ra, Jean-Christophe and Liu, Hao-Li and Chen, Wen-Shiang and Inserra, Claude}, + year = {2018}, + month = apr, + journal = {Ultrasonics Sonochemistry}, + volume = {42}, + pages = {697--703}, + publisher = {Elsevier BV}, + doi = {10.1016/j.ultsonch.2017.12.026}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Cornu2018.pdf} +} + +@article{Crouzet2014, + title = {Whole-Gland {{Ablation}} of {{Localized Prostate Cancer}} with {{High-intensity Focused Ultrasound}}: {{Oncologic Outcomes}} and {{Morbidity}} in 1002 {{Patients}}}, + author = {Crouzet, Sebastien and Chapelon, Jean Yves and Rouvi{\`e}re, Olivier and {Mege-Lechevallier}, Florence and Colombel, Marc and {Tonoli-Catez}, H{\'e}l{\`e}ne and Martin, Xavier and Gelet, Albert}, + year = {2014}, + month = may, + journal = {European Urology}, + volume = {65}, + number = {5}, + pages = {907--914}, + publisher = {Elsevier BV}, + doi = {10.1016/j.eururo.2013.04.039} +} + +@article{Cukiert2017, + title = {Deep Brain Stimulation Targeting in Refractory Epilepsy}, + author = {Cukiert, Arthur and Lehtim{\"a}ki, Kai}, + year = {2017}, + month = apr, + journal = {Epilepsia}, + volume = {58}, + pages = {80--84}, + publisher = {Wiley}, + doi = {10.1111/epi.13686} +} + +@article{Culjat2010, + title = {A {{Review}} of {{Tissue Substitutes}} for {{Ultrasound Imaging}}}, + author = {Culjat, Martin O. and Goldenberg, David and Tewari, Priyamvada and Singh, Rahul S.}, + year = {2010}, + month = jun, + journal = {Ultrasound in Medicine \& Biology}, + volume = {36}, + number = {6}, + pages = {861--873}, + publisher = {Elsevier BV}, + doi = {10.1016/j.ultrasmedbio.2010.02.012}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Culjat2010.pdf} +} + +@article{Curiel2004, + title = {Experimental Evaluation of Lesion Prediction Modelling in the Presence of Cavitation Bubbles: {{Intended}} for High-Intensity Focused Ultrasound Prostate Treatment}, + shorttitle = {Experimental Evaluation of Lesion Prediction Modelling in the Presence of Cavitation Bubbles}, + author = {Curiel, L. and Chavrier, F. and Gignoux, B. and Pichardo, S. and Chesnais, S. and Chapelon, J. Y.}, + year = {2004}, + month = jan, + journal = {Medical \& Biological Engineering \& Computing}, + volume = {42}, + number = {1}, + pages = {44--54}, + issn = {0140-0118, 1741-0444}, + doi = {10.1007/BF02351010}, + urldate = {2023-03-14}, + abstract = {The accuracy of high-intensity focused u/trasound (HIFU) /esion prediction modelling was evaluated for a truncated spherical transducer designed for prostate cancer treatment. The modelling adapted the bio heat transfer equation (BHTE) to take into account the activity of cavitation bubbles generated during HIFU exposure. This modelling was used to predict the lesions produced by three different transducer geometries: fixed-focus, concentric-ring and 1.5D phased-array. Lesions were predicted for different ultrasound exposure conditions close to those used in prostate cancer treatment. Twenty-one in vitro and nine in vitro experiments were performed on pig liver to validate the accuracy of the predictions. A good match was found between the predicted and experimental lesion shapes. Lesion dimensions (maximum depth and length, area at the centre of the lesion or central surface area) were measured on experimental and predicted lesions. The central surface area was predicted by the model with a range of error of O.15-6.5\% for in vitro tests and 0.97-9\% in viva. For comparison, BHTE without bubbles had a range of error of 0.4-55.5\% (in vitro) and 9-25.5\% (in viva). The model should be accurate enough to predict HIFU lesions under ultrasound exposure conditions used in prostate cancer treatment.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Curiel2004.pdf} +} + +@article{Dana2019, + title = {High-Performance Calcium Sensors for Imaging Activity in Neuronal Populations and Microcompartments}, + author = {Dana, Hod and Sun, Yi and Mohar, Boaz and Hulse, Brad K. and Kerlin, Aaron M. and Hasseman, Jeremy P. and Tsegaye, Getahun and Tsang, Arthur and Wong, Allan and Patel, Ronak and Macklin, John J. and Chen, Yang and Konnerth, Arthur and Jayaraman, Vivek and Looger, Loren L. and Schreiter, Eric R. and Svoboda, Karel and Kim, Douglas S.}, + year = {2019}, + month = jul, + journal = {Nature Methods}, + volume = {16}, + number = {7}, + pages = {649--657}, + issn = {1548-7091, 1548-7105}, + doi = {10.1038/s41592-019-0435-6}, + urldate = {2022-04-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Dana2019.pdf} +} + +@phdthesis{Daunizeau2020, + title = {{D{\'e}veloppement de la th{\'e}rapie ultrasonore conformationnelle par voie interstitielle pour le traitement du carcinome h{\'e}patocellulaire}}, + author = {Daunizeau, Lo{\"i}c}, + year = {2020}, + month = aug, + langid = {french}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Daunizeau2020.pdf} +} + +@misc{Dawson-Haggerty2019, + title = {Trimesh}, + author = {{Dawson-Haggerty}}, + year = {2019} +} + +@article{DeCeglia2023, + title = {Specialized Astrocytes Mediate Glutamatergic Gliotransmission in the {{CNS}}}, + author = {De Ceglia, Roberta and Ledonne, Ada and Litvin, David Gregory and Lind, Barbara Lykke and Carriero, Giovanni and Latagliata, Emanuele Claudio and Bindocci, Erika and Di Castro, Maria Amalia and Savtchouk, Iaroslav and Vitali, Ilaria and Ranjak, Anurag and Congiu, Mauro and Canonica, Tara and Wisden, William and Harris, Kenneth and Mameli, Manuel and Mercuri, Nicola and Telley, Ludovic and Volterra, Andrea}, + year = {2023}, + month = sep, + journal = {Nature}, + issn = {0028-0836, 1476-4687}, + doi = {10.1038/s41586-023-06502-w}, + urldate = {2023-10-03}, + abstract = {Abstract Multimodal astrocyte--neuron communications govern brain circuitry assembly and function 1 . For example, through rapid glutamate release, astrocytes can control excitability, plasticity and synchronous activity 2,3 of synaptic networks, while also contributing to their dysregulation in neuropsychiatric conditions 4--7 . For astrocytes to communicate through fast focal glutamate release, they should possess an apparatus for Ca 2+ -dependent exocytosis similar to neurons 8--10 . However, the existence of this mechanism has been questioned 11--13 owing to inconsistent data 14--17 and a lack of direct supporting evidence. Here we revisited the astrocyte glutamate exocytosis hypothesis by considering the emerging molecular heterogeneity of astrocytes 18--21 and using molecular, bioinformatic and imaging approaches, together with cell-specific genetic tools that interfere with glutamate exocytosis in vivo. By analysing existing single-cell RNA-sequencing databases and our patch-seq data, we identified nine molecularly distinct clusters of hippocampal astrocytes, among which we found a notable subpopulation that selectively expressed synaptic-like glutamate-release machinery and localized to discrete hippocampal sites. Using GluSnFR-based glutamate imaging 22 in situ and in vivo, we identified a corresponding astrocyte subgroup that responds reliably to astrocyte-selective stimulations with subsecond glutamate release events at spatially precise hotspots, which were suppressed by astrocyte-targeted deletion of vesicular glutamate transporter~1 (VGLUT1). Furthermore, deletion~of this transporter or its isoform VGLUT2 revealed specific contributions of glutamatergic astrocytes in cortico-hippocampal and nigrostriatal circuits during normal behaviour and pathological processes. By uncovering this atypical subpopulation of specialized astrocytes in the adult brain, we provide insights into the complex roles of astrocytes in central nervous system (CNS) physiology and diseases, and identify a potential therapeutic target.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/DeCeglia2023.pdf} +} + +@book{Deer2013, + title = {Comprehensive {{Treatment}} of {{Chronic Pain}} by {{Medical}}, {{Interventional}}, and {{Integrative Approaches}}: {{The AMERICAN ACADEMY OF PAIN MEDICINE Textbook}} on {{Patient Management}}}, + shorttitle = {Comprehensive {{Treatment}} of {{Chronic Pain}} by {{Medical}}, {{Interventional}}, and {{Integrative Approaches}}}, + editor = {Deer, Timothy R. and Leong, Michael S. and Buvanendran, Asokumar and Gordin, Vitaly and Kim, Philip S. and Panchal, Sunil J. and Ray, Albert L.}, + year = {2013}, + publisher = {Springer New York}, + address = {New York, NY}, + doi = {10.1007/978-1-4614-1560-2}, + urldate = {2023-08-30}, + isbn = {978-1-4614-1559-6 978-1-4614-1560-2}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Deer2013.pdf} +} + +@article{Deffieux2013, + title = {Low-{{Intensity Focused Ultrasound Modulates Monkey Visuomotor Behavior}}}, + author = {Deffieux, Thomas and Younan, Youliana and Wattiez, Nicolas and Tanter, Mickael and Pouget, Pierre and Aubry, Jean-Fran{\c c}ois}, + year = {2013}, + month = dec, + journal = {Current Biology}, + volume = {23}, + number = {23}, + pages = {2430--2433}, + issn = {09609822}, + doi = {10.1016/j.cub.2013.10.029}, + urldate = {2022-12-21}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Deffieux2013.pdf} +} + +@article{DelArco2020, + title = {Unanticipated {{Stressful}} and {{Rewarding Experiences Engage}} the {{Same Prefrontal Cortex}} and {{Ventral Tegmental Area Neuronal Populations}}}, + author = {Del Arco, Alberto and Park, Junchol and Moghaddam, Bita}, + year = {2020}, + month = may, + journal = {eneuro}, + volume = {7}, + number = {3}, + pages = {ENEURO.0029-20.2020}, + issn = {2373-2822}, + doi = {10.1523/ENEURO.0029-20.2020}, + urldate = {2024-03-12}, + abstract = {Brain networks that mediate motivated behavior in the context of aversive and rewarding experiences involve the prefrontal cortex (PFC) and ventral tegmental area (VTA). Neurons in both regions are activated by stress and reward, and by learned cues that predict aversive or appetitive outcomes. Recent studies have proposed that separate neuronal populations and circuits in these regions encode learned aversive versus appetitive contexts. But how about the actual experience? Do the same or different PFC and VTA neurons encode unanticipated aversive and appetitive experiences? To address this, we recorded unit activity and local field potentials (LFPs) in the dorsomedial PFC (dmPFC) and VTA of male rats as they were exposed, in the same recording session, to reward (sucrose) or stress (tail pinch) spaced 1 h apart. As expected, experience-specific neuronal responses were observed. Approximately 15--25\% of single units in each region responded by excitation or inhibition to either stress or reward, and only stress increased LFP theta oscillation power in both regions and coherence between regions. But the largest number of responses (29\% dmPFC and 30\% VTA units) involved dual-valence neurons that responded to both stress and reward exposure. Moreover, the temporal profile of neuronal population activity in dmPFC and VTA as assessed by principal component analysis (PCA) were similar during both types of experiences. These results reveal that aversive and rewarding experiences engage overlapping neuronal populations in the dmPFC and the VTA. These populations may provide a locus of vulnerability for stress-related disorders, which are often associated with anhedonia.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/DelArco2020.pdf} +} + +@inproceedings{Delgado2017, + title = {Optimal Phase on Biaxial Driven Transducers Based Only on Electrical Power Measurements}, + booktitle = {2017 {{IEEE International Ultrasonics Symposium}} ({{IUS}})}, + author = {Delgado, Sagid and Curiel, Laura and Rubel, Oleg and Silva, Geovane Da and Pichardo, Samuel}, + year = {2017}, + month = sep, + publisher = {IEEE}, + doi = {10.1109/ultsym.2017.8092099}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Delgado2017.pdf} +} + +@inproceedings{Delgado2020, + title = {Application of the {{Biaxial Driving Method}} to {{Focus Ultrasound Using Only Two Electric Signals}}}, + author = {Delgado, Sagid and Curiel, Laura and Pichardo, Samuel}, + year = {2020}, + month = sep, + publisher = {IEEE}, + doi = {10.1109/ius46767.2020.9251547}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Delgado2020.pdf} +} + +@phdthesis{Delgado2020a, + title = {Biaxial {{Driving Technique}} for {{Ultrasound Generation}} with {{Ferroelectric Materials}}}, + author = {Delgado, Sagid}, + year = {2020}, + month = dec, + address = {Thunder Bay, Ontario, Canada}, + abstract = {Over the years, ferroelectric materials have been used in a wide variety of applications in the health care field in applications such as thermal therapy, medical imaging and lithotripsy, just to mention some of them. One technical barrier in the transducer industry is that the refocusing or redirection properties of an ultrasound beam depends primarily on the ``classical'' solution of using a large number of independent transducer elements. High-density ultrasound transducer arrays often imply complexity from the electrical driving circuitry, mechanical constraints caused by the ultrasound probe size, and the need to handle heating of the device; all of which translates into high fabrication costs. Commonly used ultrasound transducers are driven by applying an electric field along the poling axis to maximize their mechanical response. More efficient operation of ultrasound transducers translates into less power consumption to obtain the desired effect and less heating into the system. This work is based on an emerging technique called biaxial driving that offers and enhancement of the mechanical response of an ultrasound transducer by using two phase-offset orthogonal electrical fields on the propagation and lateral directions. In addition to the efficiency enhancement, we hypothesize that the biaxial driving technique produces an added vibration mode due tothe application of the second electric field, which will allow a controlled acoustic pressure redistribution that can be exploited to produce a refocusing or steering of the ultrasound beam with a single element, or an array where fewer elements than conventional transducer arrays are needed. The objective of this research work is to demonstrate with numerical and experimental work that controlled steering of the ultrasound beam can be achieved by the application of a biaxial driving in single- element ferroelectric transducers. A finite element analysis has been carried out to simulate and calculate the efficiency and the acoustic field response on different ferroelectric materials biaxially driven. Different transducer shapes and parameters have been tested, demonstrating a change in the efficiency and the steering of the acoustic field using a single-element transducer. Experimental validation was performed for the specific case of the lead zirconate titanate material, using prismatic and ring geometries for the transducers. We demonstrated for the first time the steering capabilities for single-element ultrasound transducers through our simulation and experimental work. Steering angles up to 30{$^\circ$} were reached from our experimental validations for the single-element prismatic transducers while using the biaxial driving technique. It was also demonstrated that a controlled refocusing from 4.5 mm to 9 mm is possible for single-element ring shaped transducers while applying the two orthogonal electric driving signals. In addition to the acoustic efficiency, we also proved that there was an improved response on the axial resolution and the signal-to-noise ratio on a simple ultrasound imaging device. The biaxial driving method has the potential to improve the focusing of phased arrays and open new opportunities for the use of single-element devices that can take advantage of the control of the ultrasound beam directivity.}, + langid = {english}, + school = {Lakehead University}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Delgado_Thesis2020.pdf} +} + +@inproceedings{Delgado2020b, + title = {Improvement of {{Focusing}} for {{Coarse 2D}} Phased {{Arrays Using}} the {{Biaxial Driving Method}}: {{A Numerical Study}}}, + booktitle = {2020 {{IEEE International Ultrasonics Symposium}} ({{IUS}})}, + author = {Delgado, Sagid and Curiel, Laura and Pichardo, Samuel}, + year = {2020}, + month = sep, + publisher = {IEEE}, + doi = {10.1109/ius46767.2020.9251396}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Delgado2020b.pdf} +} + +@article{Delgado2021, + title = {Steering Single-Element Lead Zirconate Titanate Ultrasound Transducers Using Biaxial Driving}, + author = {Delgado, Sagid and Curiel, Laura and Pichardo, Samuel}, + year = {2021}, + month = feb, + journal = {Ultrasonics}, + volume = {110}, + pages = {106241}, + publisher = {Elsevier BV}, + doi = {10.1016/j.ultras.2020.106241}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Delgado2021.pdf} +} + +@inproceedings{Delgado2021a, + title = {Focal {{Size Reduction}} and {{Displacement}} in a {{Single-Element Biaxial Ring Transducer}} at 510 {{kHz}} and 1.66 {{MHz}}}, + booktitle = {2021 {{IEEE UFFC Latin America Ultrasonics Symposium}} ({{LAUS}})}, + author = {Delgado, Sagid and Curiel, Laura and Pichardo, Samuel}, + year = {2021}, + month = oct, + pages = {1--3}, + publisher = {IEEE}, + address = {Gainesville, FL, USA}, + doi = {10.1109/LAUS53676.2021.9639158}, + urldate = {2023-02-17}, + isbn = {978-1-66544-359-3}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Delgado2021a.pdf} +} + +@article{Delgado2023, + title = {Higher Harmonics Dynamic Focalization in Single-Element Ring Transducers Using Biaxial Driving}, + author = {Delgado, Sagid and Curiel, Laura and Li, Siyun and Pichardo, Samuel}, + year = {2023}, + month = aug, + journal = {Ultrasonics}, + volume = {133}, + pages = {107051}, + issn = {0041624X}, + doi = {10.1016/j.ultras.2023.107051}, + urldate = {2023-09-28}, + abstract = {Biaxial driving is a new driving technique that allows the steering of the ultrasound field generated by a singleelement piezoceramic transducer. Because of their natural axisymmetric geometry, ultrasound generation with ring transducers can take advantage of the biaxial driving to change the focus of the beam generated by this type of transducer using only two driving signals. In this study, we applied the biaxial driving technique into a singleelement PZT ring transducer operating at 500 kHz to produce a change in size and position of the focal spot while using the 1st (482 kHz), 3rd (1.362 MHz) and 5th (2.62 MHz) harmonic excitation. The transducer had a thickness of 2.85 mm, an inner diameter of 9.75 mm and a ring width of 2.0 mm, and two pairs of electrodes as required for biaxial driving. Simulation and experimental results showed that both the focal area and the distance at which the focal area centre was located changed as a function of the phase and power difference between the two driving signals. Experimental results showed that the focal area could be reduced from 31.6 mm2 (con\- ventional driving) to 3.4 mm2 (89 \% reduction) when using the first harmonic excitation. For the third harmonic, the focal area could be reduced from 4.0 mm2 (conventional driving) to 3.3 mm2 (17.5 \% reduction). For the fifth harmonic, the focal area could be reduced from 1.7 mm2 (conventional driving) to 1 mm2 (41.7 \% reduction). Results also demonstrated the centre of the focus could be displaced between 3.0 mm and 9.3 mm from the surface of the transducer when using the first harmonic, between 7.3 mm and 8.4 mm at the third harmonic, and between 4.9 mm and 8.2 mm at the fifth harmonic. The reduction in the focus area, as well as the possibility to displace the focus dynamically will be advantageous for preclinical applications of focused ultrasound, especially on drug delivery and neuromodulation studies in small rodents.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Delgado2023.pdf} +} + +@article{DeLima2023, + title = {The {{Implication}} of {{Glial Metabotropic Glutamate Receptors}} in {{Alzheimer}}'{{sDisease}}}, + author = {De Lima, Izabella B.Q. and Ribeiro, Fab{\'i}ola M.}, + year = {2023}, + month = feb, + journal = {Current Neuropharmacology}, + volume = {21}, + number = {2}, + pages = {164--182}, + issn = {1570159X}, + doi = {10.2174/1570159X20666211223140303}, + urldate = {2024-12-10}, + abstract = {Alzheimer's disease (AD) was first identified more than 100 years ago, yet aspects pertaining to its origin and the mechanisms underlying disease progression are not well known. To this date, there is no therapeutic approach or disease-modifying drug that could halt or at least delay disease progression. Until recently, glial cells were seen as secondary actors in brain homeostasis. Although this view was gradually refuted and the relevance of glial cells for the most diverse brain functions such as synaptic plasticity and neurotransmission was vastly proved, many aspects of its functioning, as well as its role in pathological conditions, remain poorly understood. Metabotropic glutamate receptors (mGluRs) in glial cells were shown to be involved in neuroinflammation and neurotoxicity. Besides its relevance for glial function, glutamatergic receptors are also central in the pathology of AD, and recent studies have shown that glial mGluRs play a role in the establishment and progression of AD. AD-related alterations in Ca2+ signalling, APP processing, and A{$\beta$} load, as well as AD-related neurodegeneration, are influenced by glial mGluRs. However, different types of mGluRs play different roles, depending on the cell type and brain region that is being analysed. Therefore, in this review, we focus on the current understanding of glial mGluRs and their implication in AD, providing an insight for future therapeutics and identifying existing research gaps worth investigating.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/DeLima2023.pdf} +} + +@article{DellItalia2022, + title = {Current {{State}} of {{Potential Mechanisms Supporting Low Intensity Focused Ultrasound}} for {{Neuromodulation}}}, + author = {Dell'Italia, John and Sanguinetti, Joseph L. and Monti, Martin M. and Bystritsky, Alexander and Reggente, Nicco}, + year = {2022}, + month = apr, + journal = {Frontiers in Human Neuroscience}, + volume = {16}, + pages = {872639}, + issn = {1662-5161}, + doi = {10.3389/fnhum.2022.872639}, + urldate = {2023-08-07}, + abstract = {Low intensity focused ultrasound (LIFU) has been gaining traction as a non-invasive neuromodulation technology due to its superior spatial specificity relative to transcranial electrical/magnetic stimulation. Despite a growing literature of LIFU-induced behavioral modifications, the mechanisms of action supporting LIFU's parameter-dependent excitatory and suppressive effects are not fully understood. This review provides a comprehensive introduction to the underlying mechanics of both acoustic energy and neuronal membranes, defining the primary variables for a subsequent review of the field's proposed mechanisms supporting LIFU's neuromodulatory effects. An exhaustive review of the empirical literature was also conducted and studies were grouped based on the sonication parameters used and behavioral effects observed, with the goal of linking empirical findings to the proposed theoretical mechanisms and evaluating which model best fits the existing data. A neuronal intramembrane cavitation excitation model, which accounts for differential effects as a function of cell-type, emerged as a possible explanation for the range of excitatory effects found in the literature. The suppressive and other findings need additional theoretical mechanisms and these theoretical mechanisms need to have established relationships to sonication parameters.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/DellItalia2022.pdf} +} + +@article{Demene2021, + title = {Transcranial Ultrafast Ultrasound Localization Microscopy of Brain Vasculature in Patients}, + author = {Demen{\'e}, Charlie and Robin, Justine and Dizeux, Alexandre and Heiles, Baptiste and Pernot, Mathieu and Tanter, Mickael and Perren, Fabienne}, + year = {2021}, + month = mar, + journal = {Nature Biomedical Engineering}, + volume = {5}, + number = {3}, + pages = {219--228}, + issn = {2157-846X}, + doi = {10.1038/s41551-021-00697-x}, + urldate = {2022-10-13}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Demene2021.pdf} +} + +@article{Deschner2016, + title = {Effectiveness and {{Adverse Effects}} of {{Deep Brain Stimulation}}: {{Umbrella Review}} of {{Meta-Analyses}}}, + author = {Deschner, James and Papageorgiou, Spyridon and Papageorgiou, Panagiotis}, + year = {2016}, + month = sep, + journal = {Journal of Neurological Surgery Part A: Central European Neurosurgery}, + volume = {78}, + number = {02}, + pages = {180--190}, + publisher = {Georg Thieme Verlag KG}, + doi = {10.1055/s-0036-1592158} +} + +@article{Deuschl2006, + title = {A {{Randomized Trial}} of {{Deep-Brain Stimulation}} for {{Parkinson}}'s {{Disease}}}, + author = {Deuschl, G{\"u}nther and {Schade-Brittinger}, Carmen and Krack, Paul and Volkmann, Jens and {Helmut Sch{\"a}fer} and Sch{\"a}fer, Helmut and B{\"o}tzel, Kai and Daniels, C. and {Angela Deutschl{\"a}nder} and Deutschl{\"a}nder, Angela and {Ulrich Dillmann} and Dillmann, Ulrich and Eisner, Wilhelm and Gruber, Doreen and Hamel, Wolfgang and Herzog, Jan and Hilker, R{\"u}diger and Klebe, Stephan and Kloss, Manja and Koy, J. and Krause, Martin and Kupsch, Andreas and Lorenz, Delia and Lorenzl, Stefan and {Stefan Lorenzl} and Mehdorn, H. Maximilian and Moringlane, Jean Richard and Oertel, Wolfgang H. and {Wolfgang Oertel} and Pinsker, Marcus O. and Reichmann, Heinz and Reichmann, Heinz and Reuss, Alexander and Schneider, Gerd-Helge and Schneider, Gerd-Helge and Schnitzler, Alfons and {Alfons Schnitzler} and Steude, Ulrich and Sturm, Volker and {Volker Sturm} and Timmermann, Lars and Tronnier, Volker M. and Trottenberg, Thomas and Wojtecki, Lars and Wolf, Elisabeth and Poewe, Werner and Voges, J{\"u}rgen}, + year = {2006}, + month = aug, + journal = {The New England Journal of Medicine}, + volume = {355}, + number = {9}, + pages = {896--908}, + doi = {10.1056/nejmoa060281}, + abstract = {BACKGROUND: Neurostimulation of the subthalamic nucleus reduces levodopa-related motor complications in advanced Parkinson's disease. We compared this treatment plus medication with medical management. METHODS: In this randomized-pairs trial, we enrolled 156 patients with advanced Parkinson's disease and severe motor symptoms. The primary end points were the changes from baseline to six months in the quality of life, as assessed by the Parkinson's Disease Questionnaire (PDQ-39), and the severity of symptoms without medication, according to the Unified Parkinson's Disease Rating Scale, part III (UPDRS-III). RESULTS: Pairwise comparisons showed that neurostimulation, as compared with medication alone, caused greater improvements from baseline to six months in the PDQ-39 (50 of 78 pairs, P=0.02) and the UPDRS-III (55 of 78, P{$<$}0.001), with mean improvements of 9.5 and 19.6 points, respectively. Neurostimulation resulted in improvements of 24 to 38 percent in the PDQ-39 subscales for mobility, activities of daily living, emotional well-being, stigma, and bodily discomfort. Serious adverse events were more common with neurostimulation than with medication alone (13 percent vs. 4 percent, P{$<$}0.04) and included a fatal intracerebral hemorrhage. The overall frequency of adverse events was higher in the medication group (64 percent vs. 50 percent, P=0.08). CONCLUSIONS: In this six-month study of patients under 75 years of age with severe motor complications of Parkinson's disease, neurostimulation of the subthalamic nucleus was more effective than medical management alone. (ClinicalTrials.gov number, NCT00196911 [ClinicalTrials.gov].).}, + pmid = {16943402}, + annotation = {MAG ID: 2149476088} +} + +@article{Dittami2011, + title = {Intracellular Calcium Transients Evoked by Pulsed Infrared Radiation in Neonatal Cardiomyocytes: {{Infrared}} Radiation-Evoked Intracellular Calcium Transients in Cardiomyocytes}, + shorttitle = {Intracellular Calcium Transients Evoked by Pulsed Infrared Radiation in Neonatal Cardiomyocytes}, + author = {Dittami, Gregory M. and Rajguru, Suhrud M. and Lasher, Richard A. and Hitchcock, Robert W. and Rabbitt, Richard D.}, + year = {2011}, + month = mar, + journal = {The Journal of Physiology}, + volume = {589}, + number = {6}, + pages = {1295--1306}, + issn = {00223751}, + doi = {10.1113/jphysiol.2010.198804}, + urldate = {2023-07-08}, + abstract = {Neonatal rat ventricular cardiomyocytes were used to investigate mechanisms underlying transient changes in intracellular free Ca2+ concentration ([Ca2+]i) evoked by pulsed infrared radiation (IR, 1862 nm). Fluorescence confocal microscopy revealed IR-evoked [Ca2+]i events with each IR pulse (3--4 ms pulse-1, 9.1--11.6 J cm-2 pulse-1). IR-evoked [Ca2+]i events were distinct from the relatively large spontaneous [Ca2+]i transients, with IR-evoked events exhibiting smaller amplitudes (0.88 F/F0 vs. 1.99 F/F0) and shorter time constants ({$\tau$} = 0.64 s vs. 1.19 s, respectively). Both IR-evoked [Ca2+]i events and spontaneous [Ca2+]i transients could be entrained by the IR pulse (0.2--1 pulse s-1), provided the IR dose was sufficient and the radiation was applied directly to the cell. Examination of IR-evoked events during peak spontaneous [Ca2+]i periods revealed a rapid drop in [Ca2+]i, often restoring the baseline [Ca2+]i concentration, followed by a transient increase in [Ca2+]i. Cardiomyocytes were challenged with pharmacological agents to examine potential contributors to the IR-evoked [Ca2+]i events. Three compounds proved to be the most potent, reversible inhibitors: (1) CGP-37157 (20 {$\mu$}M, n = 12), an inhibitor of the mitochondrial Na+/Ca2+ exchanger (mNCX), (2) Ruthenium Red (40 {$\mu$}M, n = 13), an inhibitor of the mitochondrial Ca2+ uniporter (mCU), and (3) 2-aminoethoxydiphenylborane (10 {$\mu$}M, n = 6), an IP3 channel antagonist. Ryanodine blocked the spontaneous [Ca2+]i transients but did not alter the IR-evoked events in the same cells. This pharmacological array implicates mitochondria as the major intracellular store of Ca2+ involved in IR-evoked responses reported here. Results support the hypothesis that 1862 nm pulsed IR modulates mitochondrial Ca2+ transport primarily through actions on mCU and mNCX.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Dittami2011.pdf} +} + +@article{Donato2007, + title = {Differential Development of Neuronal Physiological Responsiveness in Two Human Neural Stem Cell Lines}, + author = {Donato, Roberta and Miljan, Erik A and Hines, Susan J and Aouabdi, Sihem and Pollock, Kenneth and Patel, Sara and Edwards, Frances A and Sinden, John D}, + year = {2007}, + month = dec, + journal = {BMC Neuroscience}, + volume = {8}, + number = {1}, + pages = {36}, + issn = {1471-2202}, + doi = {10.1186/1471-2202-8-36}, + urldate = {2022-12-06}, + abstract = {Abstract Background Neural stem cells (NSCs) are powerful research tools for the design and discovery of new approaches to neurodegenerative disease. Overexpression of the myc family transcription factors in human primary cells from developing cortex and mesencephalon has produced two stable multipotential NSC lines (ReNcell VM and CX) that can be continuously expanded in monolayer culture. Results In the undifferentiated state, both ReNcell VM and CX are nestin positive and have resting membrane potentials of around -60 mV but do not display any voltage-activated conductances. As initially hypothesized, using standard methods (stdD) for differentiation, both cell lines can form neurons, astrocytes and oligodendrocytes according to immunohistological characteristics. However it became clear that this was not true for electrophysiological features which designate neurons, such as the firing of action potentials. We have thus developed a new differentiation protocol, designated 'pre-aggregation differentiation' (preD) which appears to favor development of electrophysiologically functional neurons and to lead to an increase in dopaminergic neurons in the ReNcell VM line. In contrast, the protocol used had little effect on the differentiation of ReNcell CX in which dopaminergic differentiation was not observed. Moreover, after a week of differentiation with the preD protocol, 100\% of ReNcell VM featured TTX-sensitive Na + -channels and fired action potentials, compared to 25\% after stdD. Currents via other voltage-gated channels did not appear to depend on the differentiation protocol. ReNcell CX did not display the same electrophysiological properties as the VM line, generating voltage-dependant K + currents but no Na + currents or action potentials under either stdD or preD differentiation. Conclusion These data demonstrate that overexpression of myc in NSCs can be used to generate electrophysiologically active neurons in culture. Development of a functional neuronal phenotype may be dependent on parameters of isolation and differentiation of the cell lines, indicating that not all human NSCs are functionally equivalent.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Donato2007.pdf} +} + +@article{DouglasWahlsten1975, + title = {Implications of Genetic Variation in Mouse Brain Structure for Electrode Placement by Stereotaxic Surgery.}, + author = {{Douglas Wah{\l}sten} and Wahlsten, Douglas and {William J. Hudspeth} and Hudspeth, William J. and {Kathryn Bernhardt} and Bernhardt, Kathryn}, + year = {1975}, + month = aug, + journal = {The Journal of Comparative Neurology}, + volume = {162}, + number = {4}, + pages = {519--531}, + doi = {10.1002/cne.901620408}, + abstract = {The spatial locations of several forebrain and midbrain fibre tracts have been compared across seven commonly used inbred, hybrid and outbred mouse strains using a series of electrolytic lesions of known positions with respect to a stereotaxic instrument. Highly significant genetic variation was found in the positions of lambda, bregma and several major fibre tracts with respect to interaural zero; in the locations of fibre tracts with respect to bregma; and in the location of fibre tracts with respect to each other. It was demonstrated that stereotaxic coordinates of a structure for one strain could not be used for other strains. Errors resulting from improper alignment of the head in the instrument and histological artifact were also determined. These errors showed no significant group differences, but they revealed that within-group variation was substantially affected by such imperfections.}, + pmid = {1097481}, + annotation = {MAG ID: 2161302330\\ +S2ID: d54cee572cb0c17b39e43628d2284efddc3969a7} +} + +@article{Downs2018, + title = {Non-Invasive Peripheral Nerve Stimulation via Focused Ultrasound {\emph{in Vivo}}}, + author = {Downs, Matthew E and Lee, Stephen A and Yang, Georgiana and Kim, Seaok and Wang, Qi and Konofagou, Elisa E}, + year = {2018}, + month = jan, + journal = {Physics in Medicine \& Biology}, + volume = {63}, + number = {3}, + pages = {035011}, + issn = {1361-6560}, + doi = {10.1088/1361-6560/aa9fc2}, + urldate = {2023-09-16}, + abstract = {Focused ultrasound (FUS) has been employed on a wide range of clinical applications to safely and non-invasively achieve desired effects that have previously required invasive and lengthy procedures with conventional methods. Conventional electrical neuromodulation therapies that are applied to the peripheral nervous system (PNS) are invasive and/or non-specific. Recently, focused ultrasound has demonstrated the ability to modulate the central nervous system and ex vivo peripheral neurons. Here, for the first time, noninvasive stimulation of the sciatic nerve eliciting a physiological response in vivo is demonstrated with FUS. FUS was applied on the sciatic nerve in mice with simultaneous electromyography (EMG) on the tibialis anterior muscle. EMG signals were detected during or directly after ultrasound stimulation along with observable muscle contraction of the hind limb. Transecting the sciatic nerve downstream of FUS stimulation eliminated EMG activity during FUS stimulation. Peak-to-peak EMG response amplitudes and latency were found to be comparable to conventional electrical stimulation methods. Histology along with behavioral and thermal testing did not indicate damage to the nerve or surrounding regions. The findings presented herein demonstrate that FUS can serve as a targeted, safe and non-invasive alternative to conventional peripheral nervous system stimulation to treat peripheral neuropathic diseases in the clinic.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Downs2018.pdf} +} + +@article{Drainville2023, + title = {A Simulation Study on the Sensitivity of Transcranial Ray-Tracing Ultrasound Modeling to Skull Properties}, + author = {Drainville, Robert Andrew and Chatillon, Sylvain and Moore, David and Snell, John and Padilla, Frederic and Lafon, Cyril}, + year = {2023}, + month = aug, + journal = {The Journal of the Acoustical Society of America}, + volume = {154}, + number = {2}, + pages = {1211--1225}, + issn = {0001-4966}, + doi = {10.1121/10.0020761}, + urldate = {2023-09-20}, + abstract = {In transcranial focused ultrasound therapies, such as treating essential tremor via thermal ablation in the thalamus, acoustic energy is focused through the skull using a phased-array transducer. Ray tracing is a computationally efficient method that can correct skull-induced phase aberrations via per-element phase delay calculations using patientspecific computed tomography (CT) data. However, recent studies show that variations in CT-derived Hounsfield unit may account for only 50\% of the speed of sound variability in human skull specimens, potentially limiting clinical transcranial ultrasound applications. Therefore, understanding the sensitivity of treatment planning methods to material parameter variations is essential. The present work uses a ray-tracing simulation model to explore how imprecision in model inputs, arising from clinically significant uncertainties in skull properties or considerations of acoustic phenomena, affects acoustic focusing quality through the skull. We propose and validate new methods to optimize ray-tracing skull simulations for clinical treatment planning, relevant for predicting intracranial target's thermal rise, using experimental data from ex-vivo human skulls.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Drainville2023.pdf} +} + +@article{Drukarch2022, + title = {The Thermodynamic Theory of Action Potential Propagation: A Sound Basis for Unification of the Physics of Nerve Impulses}, + shorttitle = {The Thermodynamic Theory of Action Potential Propagation}, + author = {Drukarch, Benjamin and Wilhelmus, Micha M. M. and Shrivastava, Shamit}, + year = {2022}, + month = apr, + journal = {Reviews in the Neurosciences}, + volume = {33}, + number = {3}, + pages = {285--302}, + issn = {0334-1763, 2191-0200}, + doi = {10.1515/revneuro-2021-0094}, + urldate = {2022-07-20}, + abstract = {Abstract The thermodynamic theory of action potential propagation challenges the conventional understanding of the nerve signal as an exclusively electrical phenomenon. Often misunderstood as to its basic tenets and predictions, the thermodynamic theory is virtually ignored in mainstream neuroscience. Addressing a broad audience of neuroscientists, we here attempt to stimulate interest in the theory. We do this by providing a concise overview of its background, discussion of its intimate connection to Albert Einstein's treatment of the thermodynamics of interfaces and outlining its potential contribution to the building of a physical brain theory firmly grounded in first principles and the biophysical reality of individual nerve cells. As such, the paper does not attempt to advocate the superiority of the thermodynamic theory over any other approach to model the nerve impulse, but is meant as an open invitation to~the~neuroscience community to experimentally test the assumptions and predictions of the theory on their validity.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Drukarch2022.pdf} +} + +@article{Dubinsky1993, + title = {Effects of Calcium Chelators on Intracellular Calcium and Excitotoxicity}, + author = {Dubinsky, Janet M.}, + year = {1993}, + month = feb, + journal = {Neuroscience Letters}, + volume = {150}, + number = {2}, + pages = {129--132}, + issn = {0304-3940}, + doi = {10.1016/0304-3940(93)90518-P}, + urldate = {2023-04-05}, + abstract = {In an attempt to probe the relationship between excitotoxicity and increases in intracellular calcium ([Ca2+]i), BAPTA-AM and its analogs were applied to cultured hippocampal neurons. Chelation of [Ca2+]i depressed and prolonged transient responses to glutamate and did not effect elevation of [Ca2+]i by prolonged exposure. This explains the inability of the chelators to prevent glutamate-induced toxicity.}, + langid = {english}, + keywords = {Calcium chelator,Excitotoxicity,Fura-2,Glutamate,Intracellular calcium,Neurotoxicity}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Dubinsky1993.pdf} +} + +@article{Duck2021, + title = {{{ULTRASOUND}} -- {{THE FIRST FIFTY YEARS}}}, + author = {Duck, Francis}, + year = {2021}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Duck2021.pdf} +} + +@article{Dyke2017, + title = {Comparing {{GABA-dependent}} Physiological Measures of Inhibition with Proton Magnetic Resonance Spectroscopy Measurement of {{GABA}} Using Ultra-High-Field {{MRI}}}, + author = {Dyke, Katherine and P{\'e}p{\'e}s, Sophia E. and Chen, Chen and Kim, Soyoung and Sigurdsson, Hilmar P. and Draper, Amelia and Husain, Masud and Nachev, Parashkev and Gowland, Penelope A. and Morris, Peter G. and Jackson, Stephen R.}, + year = {2017}, + month = may, + journal = {NeuroImage}, + volume = {152}, + pages = {360--370}, + issn = {10538119}, + doi = {10.1016/j.neuroimage.2017.03.011}, + urldate = {2025-01-27}, + abstract = {Imbalances in glutamatergic (excitatory) and GABA (inhibitory) signalling within key brain networks are thought to underlie many brain and mental health disorders, and for this reason there is considerable interest in investigating how individual variability in localised concentrations of these molecules relate to brain disorders. Magnetic resonance spectroscopy (MRS) provides a reliable means of measuring, in vivo, concentrations of neurometabolites such as GABA, glutamate and glutamine that can be correlated with brain function and dysfunction. However, an issue of much debate is whether the GABA observed and measured using MRS represents the entire pool of GABA available for measurement (i.e., metabolic, intracellular, and extracellular) or is instead limited to only some portion of it. GABA function can also be investigated indirectly in humans through the use of non-invasive transcranial magnetic stimulation (TMS) techniques that can be used to measure cortical excitability and GABA-mediated physiological inhibition. To investigate this issue further we collected in a single session both types of measurement, i.e., TMS measures of cortical excitability and physiological inhibition and ultra-high-field (7 T) MRS measures of GABA, glutamate and glutamine, from the left sensorimotor cortex of the same group of right-handed individuals. We found that TMS and MRS measures were largely uncorrelated with one another, save for the plateau of the TMS IO curve that was negatively correlated with MRS-Glutamate (Glu) and intra-cortical facilitation (10ms ISI) that was positively associated with MRS-Glutamate concentration. These findings are consistent with the view that the GABA concentrations measured using the MRS largely represent pools of GABA that are linked to tonic rather than phasic inhibition and thus contribute to the inhibitory tone of a brain area rather than GABAergic synaptic transmission.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Dyke2017.pdf} +} + +@article{Eckmann2007, + title = {The Physics of Living Neural Networks}, + author = {Eckmann, J and Feinerman, O and Gruendlinger, L and Moses, E and Soriano, J and Tlusty, T}, + year = {2007}, + month = sep, + journal = {Physics Reports}, + volume = {449}, + number = {1-3}, + pages = {54--76}, + issn = {03701573}, + doi = {10.1016/j.physrep.2007.02.014}, + urldate = {2023-01-10}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Eckmann2007.pdf} +} + +@article{Edwards2017, + title = {Neurostimulation {{Devices}} for the {{Treatment}} of {{Neurologic Disorders}}}, + author = {Edwards, Christine A. and Kouzani, Abbas and Lee, Kendall H. and Ross, Erika K.}, + year = {2017}, + month = sep, + journal = {Mayo Clinic Proceedings}, + volume = {92}, + number = {9}, + pages = {1427--1444}, + publisher = {Elsevier BV}, + doi = {10.1016/j.mayocp.2017.05.005}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Edwards2017.pdf} +} + +@article{Erhardt2004, + title = {Repetitive Transcranial Magnetic Stimulation ({{rTMS}}) Increases the Release of Dopamine in the Nucleus Accumbens of Morphine-Sensitized Rats during Drug-Withdrawal}, + author = {Erhardt, A and Welt, T and Schmidt, W and Sillaber, I and Keck, Me}, + year = {2004}, + month = jun, + journal = {Pharmacopsychiatry}, + volume = {36}, + number = {05}, + pages = {s-2003-825320}, + issn = {0176-3679, 1439-0795}, + doi = {10.1055/s-2003-825320}, + urldate = {2022-09-19}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Erhardt2004.pdf} +} + +@article{Errico2015, + title = {Ultrafast Ultrasound Localization Microscopy for Deep Super-Resolution Vascular Imaging}, + author = {Errico, Claudia and Pierre, Juliette and Pezet, Sophie and Desailly, Yann and Lenkei, Zsolt and Couture, Olivier and Tanter, Mickael}, + year = {2015}, + month = nov, + journal = {Nature}, + volume = {527}, + number = {7579}, + pages = {499--502}, + publisher = {Nature Publishing Group}, + issn = {1476-4687}, + doi = {10.1038/nature16066}, + urldate = {2023-05-12}, + abstract = {Conventional clinical ultrasound imaging has, at best, sub-millimetre-scale resolution, but now a new ultrasound technique is demonstrated that is based on fast tracking of transient signals from a sub-wavelength contrast agent and has sufficiently high resolution to map the microvasculature deep into organs.}, + copyright = {2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.}, + langid = {english}, + keywords = {Biomedical engineering,Imaging techniques,Super-resolution microscopy,Ultrasound} +} + +@article{Estrada2018, + title = {Virtual Craniotomy for High-Resolution Optoacoustic Brain Microscopy}, + author = {Estrada, H{\'e}ctor and Huang, Xiao and Rebling, Johannes and Zwack, Michael and Gottschalk, Sven and Razansky, Daniel}, + year = {2018}, + month = jan, + journal = {Scientific Reports}, + volume = {8}, + number = {1}, + pages = {1459}, + issn = {2045-2322}, + doi = {10.1038/s41598-017-18857-y}, + urldate = {2023-07-21}, + abstract = {Abstract Ultrasound-mediated transcranial images of the brain often suffer from acoustic distortions produced by the skull bone. In high-resolution optoacoustic microscopy, the skull-induced acoustic aberrations are known to impair image resolution and contrast, further skewing the location and intensity of the different absorbing structures. We present a virtual craniotomy deconvolution algorithm based on an ultrasound wave propagation model that corrects for the skull-induced distortions in optically-resolved optoacoustic transcranial microscopy data. The method takes advantage of the geometrical and spectral information of a pulse-echo ultrasound image of the skull simultaneously acquired by our multimodal imaging system. Transcranial mouse brain imaging experiments confirmed the ability to accurately account for the signal amplitude decay, temporal delay and pulse broadening introduced by the rodent's skull. Our study is the first to demonstrate skull-corrected transcranial optoacoustic imaging in vivo .}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Estrada2018.pdf} +} + +@article{Fairbanks1993, + title = {Neurostimulation for {{Obstructive Sleep Apnea}}: {{Investigations}}}, + shorttitle = {Neurostimulation for {{Obstructive Sleep Apnea}}}, + author = {Fairbanks, David W. and Fairbanks, David N.F.}, + year = {1993}, + month = jan, + journal = {Ear, Nose \& Throat Journal}, + volume = {72}, + number = {1}, + pages = {52--57}, + issn = {0145-5613, 1942-7522}, + doi = {10.1177/014556139307200111}, + urldate = {2024-02-19}, + abstract = {Ne urostimulation of the upper airway muscles (acces sory mus cles ofrespiration ) was accompli shed in anesthetized dogs and sleeping human s by electrical stimulation of the hypoglossal nerves. Such stimulations relieved partial airway obstructions in dogs. They also aborted (shortened) obstructive sleep apnea events in humans who suffer with obstruct ive sleep apnea syndrome . In one subject, stimu lations delivered in advance of apneic events (by automa tic cycling) pr evented apneas. Ne urostimulation f or obstructive sleep apnea may be an important concept fo rfuture research and deve lopment.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Fairbanks1993.pdf} +} + +@article{Fauconnier2022, + title = {Nonspherical Dynamics and Microstreaming of a Wall-Attached Microbubble}, + author = {Fauconnier, M. and Mauger, C. and B{\'e}ra, J.-C. and Inserra, C.}, + year = {2022}, + month = mar, + journal = {Journal of Fluid Mechanics}, + volume = {935}, + pages = {A22}, + issn = {0022-1120, 1469-7645}, + doi = {10.1017/jfm.2021.1089}, + urldate = {2023-03-14}, + abstract = {Acoustic microstreaming is a nonlinear response of a fluid that undergoes high-amplitude acoustic stimulation and tends to viscously absorb it. The present experimental study investigates the generation of acoustic microstreaming induced by an oscillating wall-attached bubble undergoing nonspherical shape modes. From a microscope top view, the formation of particular flow signatures is explored for the main classes of spherical harmonics \$Y\_\{nm\}({\textbackslash}theta, {\textbackslash}phi )\$ : zonal ( \$m = 0 {$<$} n\$ ), sectoral ( \$n = m {$>$} 0\$ ) and tesseral ( \$0 {$<$} m {$<$} n\$ ) oscillation. The microstreaming induced by a bubble animated by a sectoral mode alone reveals a pattern characterized by a \$4n\$ -lobe flower shape. Tesseral modes give rise to 4 m -lobe flower-shaped patterns. Finally, when sectoral and zonal modes coexist, two kinds of pattern stand out: \$2n\$ -lobe flower shape and \$n\$ -pointed star shape. The preferential emergence of one or another streaming pattern is discussed on the basis of the amplitude and phase shift between both shape modes.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Fauconnier2022.pdf} +} + +@article{Feigin2020, + title = {The Global Burden of Neurological Disorders: Translating Evidence into Policy}, + shorttitle = {The Global Burden of Neurological Disorders}, + author = {Feigin, Valery L and Vos, Theo and Nichols, Emma and Owolabi, Mayowa O and Carroll, William M and Dichgans, Martin and Deuschl, G{\"u}nther and Parmar, Priya and Brainin, Michael and Murray, Christopher}, + year = {2020}, + month = mar, + journal = {The Lancet Neurology}, + volume = {19}, + number = {3}, + pages = {255--265}, + issn = {14744422}, + doi = {10.1016/S1474-4422(19)30411-9}, + urldate = {2023-08-29}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Feigin2020.pdf} +} + +@article{Fellin2006, + title = {Astrocytic {{Glutamate Is Not Necessary}} for the {{Generation}} of {{Epileptiform Neuronal Activity}} in {{Hippocampal Slices}}}, + author = {Fellin, Tommaso and {Gomez-Gonzalo}, Marta and Gobbo, Sara and Carmignoto, Giorgio and Haydon, Philip G.}, + year = {2006}, + month = sep, + journal = {The Journal of Neuroscience}, + volume = {26}, + number = {36}, + pages = {9312--9322}, + issn = {0270-6474, 1529-2401}, + doi = {10.1523/JNEUROSCI.2836-06.2006}, + urldate = {2023-05-16}, + abstract = {The release of glutamate from astrocytes activates synchronous slow inward currents (SICs) in hippocampal pyramidal neurons, which are mediated by the NMDA receptor and represent a nonsynaptic mechanism to promote the synchronization of neuronal activity. Two recent studies demonstrate that SICs generate neuronal paroxysmal depolarizations resembling those typical of interictal epileptiform activity and proposed that there could be an astrocytic basis of epilepsy (Kang et al., 2005; Tian et al., 2005). We tested this hypothesis using two in vitro models of epileptiform activity in hippocampal slices. Removal of extracellular Mg 2+ and application of picrotoxin or perfusion with 0.5 m m Mg 2+ and 8.5 m m K + -containing saline result mainly in neuronal ictal- and interictal-like epileptiform activity, respectively. Although both models trigger epileptiform activity, astrocytic Ca 2+ oscillations were increased only after slice perfusion with 0 m m Mg 2+ and picrotoxin. The activation of astrocytic Ca 2+ signaling correlates with an increased frequency of SICs, and, when paired neurons were within 100 {$\mu$}m of one another with synchronous neuronal Ca 2+ elevations, the generation of synchronous neuronal depolarizations and action potential discharges. TTX blocked both ictal- and interictal-like epileptiform activity without affecting SICs or SIC-mediated neuronal synchronization. In contrast, NMDA receptor antagonists, which block SICs, did not prevent the generation of either ictal- or interictal-like events. Based on this clear-cut pharmacology, our data demonstrate that nonsynaptic glutamate release from astrocytes is not necessary for the generation of epileptiform activity in vitro , although we cannot exclude the possibility that it may modulate the strength of the ictal (seizure)-like event.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Fellin2006.pdf} +} + +@article{Filkin2021, + title = {Can Ionic Concentration Changes Due to Mechanical Deformation Be Responsible for the Neurostimulation Caused by Focused Ultrasound? {{A}} Simulation Study}, + shorttitle = {Can Ionic Concentration Changes Due to Mechanical Deformation Be Responsible for the Neurostimulation Caused by Focused Ultrasound?}, + author = {Filkin, Vladimir and Kuznetsov, Igor and Antonova, Olga and Tarotin, Ilya and Nemov, Alexander and Aristovich, Kirill}, + year = {2021}, + month = oct, + journal = {Physiological Measurement}, + volume = {42}, + number = {10}, + pages = {105005}, + issn = {0967-3334, 1361-6579}, + doi = {10.1088/1361-6579/ac2790}, + urldate = {2022-05-13}, + abstract = {Abstract Objective. Ultrasound stimulation is an emerging neuromodulation technique, for which the exact mechanism of action is still unknown. Despite the number of hypotheses such as mechanosensitive ion channels and intermembrane cavitation, they fail to explain all of the observed experimental effects. Here we are investigating the ionic concentration change as a prime mechanism for the neurostimulation by the ultrasound. Approach. We derive the direct analytical relationship between the mechanical deformations in the tissue and the electric boundary conditions for the cable theory equations and solve them for two types of neuronal axon models: Hodgkin--Huxley and C-fibre. We detect the activation thresholds for a variety of ultrasound stimulation cases including continuous and pulsed ultrasound and estimate the mechanical deformations required for reaching the thresholds and generating action potentials (APs). Main results. We note that the proposed mechanism strongly depends on the mechanical properties of the neural tissues, which at the moment cannot be located in literature with the required certainty. We conclude that given certain common linear assumptions, this mechanism alone cannot cause significant effects and be responsible for neurostimulation. However, we also conclude that if the lower estimation of mechanical properties of neural tissues in literature is true, or if the normal cavitation occurs during the ultrasound stimulation, the proposed mechanism can be a prime cause for the generation of APs. Significance. The approach allows prediction and modelling of most observed experimental effects, including the probabilistic ones, without the need for any extra physical effects or additional parameters.}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Filkin2021.pdf} +} + +@article{Finkbeiner1992, + title = {Calcium Waves in Astrocytes-Filling in the Gaps}, + author = {Finkbeiner, Steven}, + year = {1992}, + month = jun, + journal = {Neuron}, + volume = {8}, + number = {6}, + pages = {1101--1108}, + issn = {08966273}, + doi = {10.1016/0896-6273(92)90131-V}, + urldate = {2023-07-25}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Finkbeiner1992.pdf} +} + +@article{Foley1987, + title = {Equations for Chromatographic Peak Modeling and Calculation of Peak Area}, + author = {Foley, Joe P.}, + year = {1987}, + month = aug, + journal = {Analytical Chemistry}, + volume = {59}, + number = {15}, + pages = {1984--1987}, + issn = {0003-2700, 1520-6882}, + doi = {10.1021/ac00142a019}, + urldate = {2024-02-02}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Foley1987.pdf} +} + +@article{Folloni2019, + title = {Manipulation of {{Subcortical}} and {{Deep Cortical Activity}} in the {{Primate Brain Using Transcranial Focused Ultrasound Stimulation}}}, + author = {Folloni, Davide and Verhagen, Lennart and Mars, Rogier B. and Fouragnan, Elsa and Constans, Charlotte and Aubry, Jean-Fran{\c c}ois and Rushworth, Matthew F.S. and Sallet, J{\'e}r{\^o}me}, + year = {2019}, + month = mar, + journal = {Neuron}, + volume = {101}, + number = {6}, + pages = {1109-1116.e5}, + issn = {08966273}, + doi = {10.1016/j.neuron.2019.01.019}, + urldate = {2022-04-11}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Folloni2019.pdf} +} + +@article{Foreman1973, + title = {Calcium {{Ionophores}} and {{Movement}} of {{Calcium Ions}} Following the {{Physiological Stimulus}} to a {{Secretory Process}}}, + author = {Foreman, J. C. and Mongar, J. L. and Gomperts, B. D.}, + year = {1973}, + month = oct, + journal = {Nature}, + volume = {245}, + number = {5423}, + pages = {249--251}, + publisher = {{Springer Science and Business Media LLC}}, + doi = {10.1038/245249a0} +} + +@misc{Foundation, + title = {2020 {{State}} of the {{Field Report}}}, + author = {Foundation, F. U. S.} +} + +@article{Franceschetti2004, + title = {A {{Random Walk Model}} of {{Wave Propagation}}}, + author = {Franceschetti, M. and Bruck, J. and Schulman, L. J.}, + year = {2004}, + month = may, + journal = {IEEE Transactions on Antennas and Propagation}, + volume = {52}, + number = {5}, + pages = {1304--1317}, + publisher = {{Institute of Electrical and Electronics Engineers (IEEE)}}, + doi = {10.1109/tap.2004.827540}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Franceschetti2004.pdf} +} + +@article{Fry1950, + title = {Physical {{Factors Involved}} in {{Ultrasonically Induced Changes}} in {{Living Systems}}: {{I}}. {{Identification}} of {{Non}}-{{Temperature Effects}}}, + shorttitle = {Physical {{Factors Involved}} in {{Ultrasonically Induced Changes}} in {{Living Systems}}}, + author = {Fry, W. J. and Wulff, V. J. and Tucker, D. and Fry, F. J.}, + year = {1950}, + month = nov, + journal = {The Journal of the Acoustical Society of America}, + volume = {22}, + number = {6}, + pages = {867--876}, + issn = {0001-4966}, + doi = {10.1121/1.1906707}, + urldate = {2023-06-20}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Fry1950.pdf} +} + +@article{Fry1958, + title = {Production of {{Reversible Changes}} in the {{Central Nervous System}} by {{Ultrasound}}}, + author = {Fry, F. J. and Ades, H. W. and Fry, W. J.}, + year = {1958}, + month = jan, + journal = {Science}, + volume = {127}, + number = {3289}, + pages = {83--84}, + publisher = {American Association for the Advancement of Science (AAAS)}, + doi = {10.1126/science.127.3289.83}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Fry1958.pdf} +} + +@article{Fry1970, + title = {Threshold {{Ultrasonic Dosages}} for {{Structural Changes}} in the {{Mammalian Brain}}}, + author = {Fry, F. J. and Kossoff, G. and Eggleton, R. C. and Dunn, F.}, + year = {1970}, + month = dec, + journal = {Journal of the Acoustical Society of America}, + volume = {48}, + number = {6}, + pages = {1413--1417}, + doi = {10.1121/1.1912301}, + abstract = {The relationship between the acoustic intensity and the time duration of exposure, for a single pulse, necessary to produce a threshold lesion in the cat brain was studied. Focused ultrasound of 1, 3, and 4 MHz was employed with intensities ranging from 102 to 2{\texttimes}104 W/cm2 with the corresponding pulse durations from 7 to 2{\texttimes}10-4 sec, respectively. Three types of lesions were observed attending three regions. At the lower intensities and long time durations of exposure, the lesion is produced by a thermal mechanism. At the highest intensities and shortest time durations, cavitation is believed to be the mechanism responsible for the sometimes randomly appearing lesions. At intermediate dosages, the lesions are formed by a mechanical mechanism which is thus far not well understood. These results exhibit good agreement with that of other investigators on both the cat and the rat brain.}, + pmid = {5489906}, + annotation = {MAG ID: 2041294256\\ +S2ID: 29399fa790d132747d7a5654e80c354eb7a7482b} +} + +@article{G.AllanJohnson2010, + title = {Waxholm Space: An Image-Based Reference for Coordinating Mouse Brain Research.}, + author = {{G. Allan Johnson} and Johnson, G. Allan and {Alexandra Badea} and Badea, Alexandra and {Jeffrey Brandenburg} and Brandenburg, Jeffrey and {Gary P. Cofer} and Cofer, Gary P. and {Boma Fubara} and Fubara, Boma and {Song Liu} and Liu, Song and {Jonathan Nissanov} and Nissanov, Jonathan}, + year = {2010}, + month = nov, + journal = {NeuroImage}, + volume = {53}, + number = {2}, + pages = {365--372}, + doi = {10.1016/j.neuroimage.2010.06.067}, + abstract = {Abstract We describe an atlas of the C57BL/6 mouse brain based on MRI and conventional Nissl histology. Magnetic resonance microscopy was performed on a total of 14 specimens that were actively stained to enhance tissue contrast. Images were acquired with three different MR protocols yielding contrast dependent on spin lattice relaxation (T1), spin spin relaxation (T2), and magnetic susceptibility (T2*). Spatial resolution was 21.5 {$\mu$}m (isotropic). Conventional histology (Nissl) was performed on a limited set of these same specimens and the Nissl images were registered (3D-to-3D) to the MR data. Probabilistic atlases for 37 structures are provided, along with average atlases. The availability of three different MR protocols, the Nissl data, and the labels provides a rich set of options for registration of other atlases to the same coordinate system, thus facilitating data-sharing. All the data is available for download via the web.}, + pmcid = {2930145}, + pmid = {20600960}, + annotation = {MAG ID: 2026527241} +} + +@article{Gafni1997, + title = {Xestospongins: {{Potent Membrane Permeable Blockers}} of the {{Inositol}} 1,4,5-{{Trisphosphate Receptor}}}, + shorttitle = {Xestospongins}, + author = {Gafni, Juliette and Munsch, Julia A and Lam, Tien H and Catlin, Michelle C and Costa, Lucio G and Molinski, Tadeusz F and Pessah, Isaac N}, + year = {1997}, + month = sep, + journal = {Neuron}, + volume = {19}, + number = {3}, + pages = {723--733}, + issn = {08966273}, + doi = {10.1016/S0896-6273(00)80384-0}, + urldate = {2024-10-10}, + abstract = {Xestospongins (Xe's) A, C, D, araguspongine B, and demethylxestospongin B, a group of macrocyclic bis-1-oxaquinolizidines isolated from the Australian sponge, Xestospongia species, are shown to be potent blockers of IP3-mediated Ca2؉ release from endoplasmic reticulum vesicles of rabbit cerebellum. XeC blocks IP3-induced Ca2؉ release (IC50 ϭ 358 nM) without interacting with the IP3-binding site, suggesting a mechanism that is independent of the IP3 effector site. Analysis of Pheochormocytoma cells and primary astrocytes loaded with Ca2؉-sensitive dye reveals that XeC selectively blocks bradykinin- and carbamylcholine-induced Ca2؉ efflux from endoplasmic reticulum stores. Xe's represent a new class of potent, membrane permeable IP3 receptor blockers exhibiting a high selectivity over ryanodine receptors. Xe's are a valuable tool for investigating the structure and function of IP3 receptors and Ca2؉ signaling in neuronal and nonneuronal cells.}, + copyright = {https://www.elsevier.com/tdm/userlicense/1.0/}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Gafni1997.pdf} +} + +@article{Gambardella2021, + title = {The Discovery and Development of {{IP3}} Receptor Modulators: An Update}, + shorttitle = {The Discovery and Development of {{IP3}} Receptor Modulators}, + author = {Gambardella, Jessica and Morelli, Marco B. and Wang, Xujun and Castellanos, Vanessa and Mone, Pasquale and Santulli, Gaetano}, + year = {2021}, + month = jun, + journal = {Expert Opinion on Drug Discovery}, + volume = {16}, + number = {6}, + pages = {709--718}, + issn = {1746-0441, 1746-045X}, + doi = {10.1080/17460441.2021.1858792}, + urldate = {2024-10-07}, + abstract = {Introduction: Inositol 1,4,5-trisphosphate receptors (IP3Rs) are intracellular calcium (Ca2+) release channels located on the endoplasmic/sarcoplasmic reticulum. The availability of the structure of the ligand-binding domain of IP3Rs has enabled the design of compatible ligands, but the limiting step remains their actual effectiveness in a biological context.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Gambardella2021.pdf} +} + +@article{Gaub2020, + title = {Neurons Differentiate Magnitude and Location of Mechanical Stimuli}, + author = {Gaub, Benjamin M. and Kasuba, Krishna Chaitanya and Mace, Emilie and Strittmatter, Tobias and Laskowski, Pawel R. and Geissler, Sydney A. and Hierlemann, Andreas and Fussenegger, Martin and Roska, Botond and M{\"u}ller, Daniel J.}, + year = {2020}, + month = jan, + journal = {Proceedings of the National Academy of Sciences}, + volume = {117}, + number = {2}, + pages = {848--856}, + issn = {0027-8424, 1091-6490}, + doi = {10.1073/pnas.1909933117}, + urldate = {2023-03-15}, + abstract = {Significance Our study provides a quantitative and morphological framework for mechanical neuromodulation. We report that mechanical stimuli at subtraumatic forces and pressures can evoke neuronal calcium responses. Cultured cortex and hippocampus neurons respond to both global and local mechanical forces and pressures delivered by shear stress and indentation, respectively, and show either short-lived or sustained responses, depending on the magnitude and location of the applied stimulus. Chemical perturbation experiments suggest that ion channel activity is modulated by forces and pressures acting on neurons. Our insights contribute to the understanding of how neurons respond to mechanical stimuli and may guide future studies to mechanically control neurons by, for example, electromagnetic forces or ultrasound. , Neuronal activity can be modulated by mechanical stimuli. To study this phenomenon quantitatively, we mechanically stimulated rat cortical neurons by shear stress and local indentation. Neurons show 2 distinct responses, classified as transient and sustained. Transient responses display fast kinetics, similar to spontaneous neuronal activity, whereas sustained responses last several minutes before returning to baseline. Local soma stimulations with micrometer-sized beads evoke transient responses at low forces of {$\sim$}220 nN and pressures of {$\sim$}5.6 kPa and sustained responses at higher forces of {$\sim$}360 nN and pressures of {$\sim$}9.2 kPa. Among the neuronal compartments, axons are highly susceptible to mechanical stimulation and predominantly show sustained responses, whereas the less susceptible dendrites predominantly respond transiently. Chemical perturbation experiments suggest that mechanically evoked responses require the influx of extracellular calcium through ion channels. We propose that subtraumatic forces/pressures applied to neurons evoke neuronal responses via nonspecific gating of ion channels.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Gaub2020.pdf} +} + +@article{Gavrilov1977, + title = {A Study of Reception with the Use of Focused Ultrasound. {{I}}. {{Effects}} on the Skin and Deep Receptor Structures in Man}, + author = {Gavrilov, Leonid R. and Gersuni, Grigoryi V. and Ilyinski, Oleg B. and Tsirulnikov, Efim M. and Shchekanov, Eugenyi E.}, + year = {1977}, + month = oct, + journal = {Brain Research}, + volume = {135}, + number = {2}, + pages = {265--277}, + publisher = {Elsevier BV}, + doi = {10.1016/0006-8993(77)91030-7} +} + +@article{Gavrilov2012, + title = {Focused Ultrasound as a Tool to Input Sensory Information to Humans ({{Review}})}, + author = {Gavrilov, L. R. and Tsirulnikov, E. M.}, + year = {2012}, + month = jan, + journal = {Acoustical Physics}, + volume = {58}, + number = {1}, + pages = {1--21}, + publisher = {Pleiades Publishing Ltd}, + doi = {10.1134/s1063771012010083}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Gavrilov2012.pdf} +} + +@book{Gavrilov2014, + title = {Use of {{Focused Ultrasound}} for {{Stimulation}} of {{Various Neural Structures}}. {{Nova Science Publishers}}. 2014. {{P}}.182}, + author = {Gavrilov, Leonid}, + year = {2014}, + month = jun, + isbn = {978-1-62948-929-2}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Gavrilov2014.pdf} +} + +@incollection{Gees2012, + title = {{{{\textsc{TRP}}}} {{Channels}}}, + booktitle = {Comprehensive {{Physiology}}}, + author = {Gees, Maarten and Owsianik, Grzegorz and Nilius, Bernd and Voets, Thomas}, + editor = {Terjung, Ronald}, + year = {2012}, + month = jan, + edition = {1}, + pages = {563--608}, + publisher = {Wiley}, + doi = {10.1002/cphy.c110026}, + urldate = {2023-08-07}, + abstract = {TRP channels constitute a large superfamily of cation channel forming proteins, all related to the gene product of the transient receptor potential (trp) locus in Drosophila. In mammals, 28 different TRP channel genes have been identified, which exhibit a large variety of functional properties and play diverse cellular and physiological roles. In this article, we provide a brief and systematic summary of expression, function, and (patho)physiological role of the mammalian TRP channels. C 2012 American Physiological Society. Compr Physiol 2:563-608, 2012.}, + isbn = {978-0-470-65071-4}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Gees2012.pdf} +} + +@article{Genoves2023, + title = {Variation in the Viscoelastic Properties of Polydimethylsiloxane ({{PDMS}}) with the Temperature at Ultrasonic Frequencies}, + author = {Genov{\'e}s, V. and Maini, L. and Roman, C. and Hierold, C. and Cesarovic, N.}, + year = {2023}, + month = jul, + journal = {Polymer Testing}, + volume = {124}, + pages = {108067}, + issn = {01429418}, + doi = {10.1016/j.polymertesting.2023.108067}, + urldate = {2024-05-31}, + abstract = {Polydimethylsiloxane (PDMS) is an organic silicone with a viscoelastic behavior suitable for use in engineering. This material presents substantial changes in its properties depending on the temperature and the flow rate: at high temperatures or high flow rates, it behaves as a viscous liquid; whereas, at low temperatures or low flow rates, it behaves as an elastic solid. The lack of accurate information about the modifications in PDMS under thermal changes affects the design of transducers (both sensors and actuators) based on this material and also their calibration. In this study, 10:1 base-agent mixing ratio was analyzed in a 20 {\textopenbullet}C to 50 {\textopenbullet}C temperature range to assess the ultrasonic P-wave properties (velocity, attenuation, and variation of both with the frequency) and hence complex elastic modulii of this material under a temperature dependent environment. P-wave velocity and attenuation were extracted for every temperature step in a 3--7 MHz frequency range which is the typical range for medical applications. Acoustic dispersion of PDMS properties such as velocity and attenuation in a pulse-echo set up were analyzed to also compute attenuation coefficient, temperature and frequency dependent models and complex modulus.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Genoves2023.pdf} +} + +@article{GeorgePaxinos1983, + title = {The {{Rat Brain}} in {{Stereotaxic Coordinates}}}, + author = {{George Paxinos} and Paxinos, George and {Charles Watson} and Watson, Charles}, + year = {1983}, + month = jan, + abstract = {The preceding editions made "The Rat Brain in Stereotaxic Coordinates" the second most cited book in science. This Fifth Edition is the result of years of research providing the user with the drawings of the completely new set of coronal sections, now from one rat, and with significantly improved resolution by adding a third additional section level as compared to earlier editions. Numerous new nuclei and structures also have been identified. The drawings are presented in two color, providing a much better contrast for use, and the accompanying CD-ROM contains all of the drawings from the atlas as well as the corresponding color micrographs (which are not included in the book). Affordable, comprehensive, compact, and convenient, the Fifth Edition continues the legacy of this major neuroscience publication and is a guide to all students and scientists who study the rat brain. It contains 161 coronal diagrams based on a single brain and includes a CD-ROM featuring all of the drawings from the book, plus the accompanying color micrographs that are not in the printed atlas. The delineations are drawn entirely new from a new set of sections. The diagrams are spaced at constant 120 m intervals resulting in the high resolution and convenience of use. The drawings use blue color lines and black labels to facilitate extraction of information. The stereotaxic grid was derived using the same techniques that produced the widely praised stereotaxic grid of the previous editions. Over 1000 structures are identified, a number for the first time in this edition.}, + annotation = {MAG ID: 2163815564} +} + +@article{Ghosh1988, + title = {Competitive, Reversible, and Potent Antagonism of Inositol 1,4,5-Trisphosphate-Activated Calcium Release by Heparin.}, + author = {Ghosh, T K and Eis, P S and Mullaney, J M and Ebert, C L and Gill, D L}, + year = {1988}, + month = aug, + journal = {Journal of Biological Chemistry}, + volume = {263}, + number = {23}, + pages = {11075--11079}, + issn = {00219258}, + doi = {10.1016/S0021-9258(18)37923-7}, + urldate = {2024-10-10}, + copyright = {https://www.elsevier.com/tdm/userlicense/1.0/}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Ghosh1988.pdf} +} + +@article{Giaume1998, + title = {Intercellular Calcium Signaling and Gap Junctional Communication in Astrocytes}, + author = {Giaume, Christian and Venance, Laurent}, + year = {1998}, + journal = {Glia}, + volume = {24}, + number = {1}, + pages = {50--64}, + publisher = {Wiley Online Library}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Giaume1998.pdf} +} + +@article{Gleason1991, + title = {Electrophysiological Fundamentals of Neurostimulation}, + author = {Gleason, C. A.}, + year = {1991}, + month = oct, + journal = {World Journal of Urology}, + volume = {9}, + number = {3}, + publisher = {{Springer Science and Business Media LLC}}, + doi = {10.1007/bf00202502} +} + +@article{Glover2011, + title = {Overview of {{Functional Magnetic Resonance Imaging}}}, + author = {Glover, Gary H.}, + year = {2011}, + month = apr, + journal = {Neurosurgery Clinics of North America}, + volume = {22}, + number = {2}, + pages = {133--139}, + issn = {10423680}, + doi = {10.1016/j.nec.2010.11.001}, + urldate = {2023-03-14}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Glover2011.pdf} +} + +@article{Gomez2018, + title = {Design of Transcranial Magnetic Stimulation Coils with Optimal Trade-off between Depth, Focality, and Energy}, + author = {Gomez, Luis J. and Goetz, Stefan M. and Peterchev, Angel V.}, + year = {2018}, + month = jun, + journal = {Journal of Neural Engineering}, + volume = {15}, + number = {4}, + pages = {046033}, + publisher = {IOP Publishing}, + doi = {10.1088/1741-2552/aac967}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Gomez2018.pdf} +} + +@article{Gonsalvez2021, + title = {Neurostimulation for the Treatment of Functional Neurological Disorder: {{A}} Systematic Review}, + shorttitle = {Neurostimulation for the Treatment of Functional Neurological Disorder}, + author = {Gonsalvez, Irene and Spagnolo, Primavera and Dworetzky, Barbara and Baslet, Gaston}, + year = {2021}, + journal = {Epilepsy \& Behavior Reports}, + volume = {16}, + pages = {100501}, + issn = {25899864}, + doi = {10.1016/j.ebr.2021.100501}, + urldate = {2024-08-06}, + abstract = {Functional Neurological Disorder (FND), also known as conversion disorder, is characterized by neurological symptoms that are incompatible with any known structural disorder and best explained by a biopsychosocial model. Evidence-based treatments for FND are limited, with cognitive behavioral therapy (CBT) and physiotherapy being the most effective interventions [1]. In recent years, functional neuroimaging studies have provided robust evidence of alterations in activity and connectivity in multiple brain networks in FND. This body of evidence suggests that neurocircuitry-based interventions, such as noninvasive brain stimulation techniques (NIBS), may also represent an effective therapeutic option for patients with FND.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Gonsalvez2021.pdf} +} + +@article{Grewal, + title = {Using Focused Ultrasound to Modulate Microglial Structure and Function}, + author = {Grewal, Sarina}, + journal = {Frontiers in Cellular Neuroscience}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Grewal.pdf} +} + +@book{Gruszczak2023, + title = {Routledge {{Handbook}} of the {{Future}} of {{Warfare}}}, + author = {Gruszczak, Artur and Kaempf, Sebastian}, + year = {2023}, + month = jul, + edition = {1}, + publisher = {Routledge}, + address = {London}, + doi = {10.4324/9781003299011}, + urldate = {2024-03-27}, + isbn = {978-1-00-329901-1}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Gruszczak2023.pdf} +} + +@article{Guo2018, + title = {Ultrasound {{Produces Extensive Brain Activation}} via a {{Cochlear Pathway}}}, + author = {Guo, Hongsun and Hamilton, Mark and Offutt, Sarah J. and Gloeckner, Cory D. and Li, Tianqi and Kim, Yohan and Legon, Wynn and Alford, Jamu K. and Lim, Hubert H.}, + year = {2018}, + month = jun, + journal = {Neuron}, + volume = {98}, + number = {5}, + pages = {1020-1030.e4}, + issn = {08966273}, + doi = {10.1016/j.neuron.2018.04.036}, + urldate = {2023-06-01}, + abstract = {Ultrasound (US) can noninvasively activate intact brain circuits, making it a promising neuromodulation technique. However, little is known about the underlying mechanism. Here, we apply transcranial US and perform brain mapping studies in guinea pigs using extracellular electrophysiology. We find that US elicits extensive activation across cortical and subcortical brain regions. However, transection of the auditory nerves or removal of cochlear fluids eliminates the US-induced activity, revealing an indirect auditory mechanism for US neural activation. Our findings indicate that US activates the ascending auditory system through a cochlear pathway, which can activate other non-auditory regions through cross-modal projections. This cochlear pathway mechanism challenges the idea that US can directly activate neurons in the intact brain, suggesting that future US stimulation studies will need to control for this effect to reach reliable conclusions.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Guo2018.pdf} +} + +@techreport{Guo2023, + type = {Preprint}, + title = {Effects of Focused Ultrasound in a ``Clean'' Mouse Model of Ultrasonic Neuromodulation}, + author = {Guo, Hongsun and Salahshoor, Hossein and Wu, Di and Yoo, Sangjin and Sato, Tomokazu and Tsao, Doris Y. and Shapiro, Mikhail G.}, + year = {2023}, + month = may, + institution = {Neuroscience}, + doi = {10.1101/2023.05.22.541780}, + urldate = {2023-06-01}, + abstract = {Recent studies on ultrasonic neuromodulation (UNM) in rodents have shown that focused ultrasound (FUS) can activate peripheral auditory pathways, leading to off-target and brain-wide excitation, which obscures the direct activation of the target area by FUS. To address this issue, we developed a new mouse model, the double transgenic Pou4f3+/DTR {\texttimes} Thy1-GCaMP6s, which allows for inducible deafening using diphtheria toxin and minimizes off-target effects of UNM while allowing effects on neural activity to be visualized with fluorescent calcium imaging. Using this model, we found that the auditory confounds caused by FUS can be significantly reduced or eliminated within a certain pressure range. At higher pressures, FUS can result in focal fluorescence dips at the target, elicit non-auditory sensory confounds, and damage tissue, leading to spreading depolarization. Under the acoustic conditions we tested, we did not observe direct calcium responses in the mouse cortex. Our findings provide a cleaner animal model for UNM and sonogenetics research, establish a parameter range within which off-target effects are confidently avoided, and reveal the non-auditory side effects of higher-pressure stimulation.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Guo2023.pdf} +} + +@article{Gyger2011, + title = {Calcium Imaging in the Optical Stretcher}, + author = {Gyger, Markus and Rose, Daniel and Stange, Roland and Kie{\ss}ling, Tobias and Zink, Mareike and Fabry, Ben and K{\"a}s, Josef A.}, + year = {2011}, + month = sep, + journal = {Optics Express}, + volume = {19}, + number = {20}, + pages = {19212}, + issn = {1094-4087}, + doi = {10.1364/OE.19.019212}, + urldate = {2024-09-04}, + abstract = {The Microfluidic Optical Stretcher (MOS) has previously been shown to be a versatile tool to measure mechanical properties of single suspended cells. In this study we combine optical stretching and fluorescent calcium imaging. A cell line transfected with a heat sensitive cation channel was used as a model system to show the versatility of the setup. The cells were loaded with the Ca2+ dye Fluo-4 and imaged with confocal laser scanning microscopy while being stretched. During optical stretching heat is transferred to the cell causing a pronounced Ca2+ influx through the cation channel. The technique opens new perspectives for investigating the role of Ca2+ in regulating cell mechanical behavior.}, + copyright = {https://doi.org/10.1364/OA\_License\_v1\#VOR-OA}, + langid = {english}, + file = {/Users/tomaubier/Zotero/storage/Q6P2NIB9/Gyger et al. - 2011 - Calcium imaging in the optical stretcher.pdf} +} + +@article{Haak2000, + title = {Mitochondria in Myelinating Cells: Calcium Signaling in Oligodendrocyte Precursor Cells}, + shorttitle = {Mitochondria in Myelinating Cells}, + author = {Haak, L.L. and Grimaldi, M. and Russell, J.T.}, + year = {2000}, + month = nov, + journal = {Cell Calcium}, + volume = {28}, + number = {5-6}, + pages = {297--306}, + issn = {01434160}, + doi = {10.1054/ceca.2000.0176}, + urldate = {2024-04-22}, + copyright = {https://www.elsevier.com/tdm/userlicense/1.0/}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Haak2000.pdf} +} + +@article{Haddadi2017, + title = {Analysis of Nonlinear Acoustic Wave Propagation in {{HIFU}} Treatment Using {{Westervelt}} Equation}, + author = {Haddadi, Samaneh and Ahmadian, Mohammad Taghi}, + year = {2017}, + month = sep, + journal = {Scientia Iranica}, + volume = {0}, + number = {0}, + pages = {0--0}, + issn = {2345-3605}, + doi = {10.24200/sci.2017.4496}, + urldate = {2023-01-18}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Haddadi2017.pdf} +} + +@article{Hamlin2023, + title = {A {{Brief History}} of {{Transcranial Magnetic Stimulation}}}, + author = {Hamlin, Dallas and Garman, John}, + year = {2023}, + month = mar, + journal = {American Journal of Psychiatry Residents' Journal}, + volume = {18}, + number = {3}, + pages = {8--10}, + issn = {2474-4662}, + doi = {10.1176/appi.ajp-rj.2023.180303}, + urldate = {2025-02-02}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Hamlin2023.pdf} +} + +@article{Hangen2018, + title = {Neuronal {{Activity}} and {{Intracellular Calcium Levels Regulate Intracellular Transport}} of {{Newly Synthesized AMPAR}}}, + author = {Hangen, Emilie and Cordeli{\`e}res, Fabrice P. and Petersen, Jennifer D. and Choquet, Daniel and Coussen, Fran{\c c}oise}, + year = {2018}, + month = jul, + journal = {Cell Reports}, + volume = {24}, + number = {4}, + pages = {1001-1012.e3}, + issn = {22111247}, + doi = {10.1016/j.celrep.2018.06.095}, + urldate = {2022-04-12}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Hangen2018.pdf} +} + +@article{Haqshenas2021, + title = {A Fast Full-Wave Solver for Calculating Ultrasound Propagation in the Body}, + author = {Haqshenas, S.R. and G{\'e}lat, P. and Van 'T Wout, E. and Betcke, T. and Saffari, N.}, + year = {2021}, + month = feb, + journal = {Ultrasonics}, + volume = {110}, + pages = {106240}, + issn = {0041624X}, + doi = {10.1016/j.ultras.2020.106240}, + urldate = {2024-02-11}, + abstract = {Therapeutic ultrasound is a promising non-invasive method for inducing various beneficial biological effects in the human body. In cancer treatment applications, high-power ultrasound is focused at a target tissue volume to ablate the malignant tumour. The success of the procedure depends on the ability to accurately focus ultrasound and destroy the target tissue volume through coagulative necrosis whilst preserving the surrounding healthy tissue. Patient-specific treatment planning strategies are therefore being developed to increase the efficacy of such therapies, while reducing any damage to healthy tissue. These strategies require to use high-performance computing methods to solve ultrasound wave propagation in the body quickly and accurately. For realistic clinical scenarios, all numerical methods which employ volumetric meshes require several hours or days to solve the full-wave propagation on a computer cluster. The boundary element method (BEM) is an efficient approach for modelling the wave field because only the boundaries of the hard and soft tissue regions require dis\- cretisation. This paper presents a multiple-domain BEM formulation with a novel preconditioner for solving the Helmholtz transmission problem (HTP). This new formulation is efficient at high-frequencies and where highcontrast materials are present. Numerical experiments are performed to solve the HTP in multiple domains comprising: (i) human ribs, an idealised abdominal fat layer and liver tissue, (ii) a human kidney with a peri\- nephric fat layer, exposed to the acoustic field generated by a high-intensity focused ultrasound (HIFU) array transducer. The time required to solve the equations associated with these problems on a single workstation is of the order of minutes. These results demonstrate the great potential of this new BEM formulation for accurately and quickly solving ultrasound wave propagation problems in large anatomical domains which is essential for developing treatment planning strategies.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Haqshenas2021.pdf} +} + +@article{Hariz2002, + title = {Complications of Deep Brain Stimulation Surgery}, + author = {Hariz, Marwan I.}, + year = {2002}, + month = mar, + journal = {Movement Disorders}, + volume = {17}, + number = {S3}, + pages = {S162--S166}, + publisher = {Wiley}, + doi = {10.1002/mds.10159} +} + +@article{Harris2022, + title = {Hydrophone {{Measurements}} for {{Biomedical Ultrasound Applications}}: {{A Review}}}, + shorttitle = {Hydrophone {{Measurements}} for {{Biomedical Ultrasound Applications}}}, + author = {Harris, Gerald R. and Howard, Samuel and Hurrell, Andrew and Lewin, Peter A. and Schafer, Mark E. and Wear, Keith A. and Wilkens, Volker and Zeqiri, Bajram}, + year = {2022}, + journal = {IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control}, + pages = {1--1}, + issn = {0885-3010, 1525-8955}, + doi = {10.1109/TUFFC.2022.3213185}, + urldate = {2022-11-17} +} + +@article{Harvey1928, + title = {High {{Frequency Sound Waves}} of {{Small Intensity}} and Their {{Biological Effects}}}, + author = {Harvey, E. Newton and Loomis, Alfred L.}, + year = {1928}, + month = apr, + journal = {Nature}, + volume = {121}, + number = {3051}, + pages = {622--624}, + issn = {0028-0836, 1476-4687}, + doi = {10.1038/121622a0}, + urldate = {2024-02-19}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Harvey1928.pdf} +} + +@article{Harvey1929, + title = {The Effect of High Frequency Sound Waves on Heart Muscle and Other Irritable Tissues}, + author = {Harvey, E. Newton}, + year = {1929}, + month = dec, + journal = {American Journal of Physiology-Legacy Content}, + volume = {91}, + number = {1}, + pages = {284--290}, + publisher = {American Physiological Society}, + doi = {10.1152/ajplegacy.1929.91.1.284}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Harvey1929.pdf} +} + +@article{Hay2022, + title = {Functional Magnetic Resonance Imaging ({{fMRI}}) in Design Studies: {{Methodological}} Considerations, Challenges, and Recommendations}, + author = {Hay, Laura and Duffy, Alex H. B. and Gilbert, Sam J. and Grealy, Madeleine}, + year = {2022}, + month = jan, + journal = {Design Studies}, + volume = {78}, + pages = {101078--101078}, + doi = {10.1016/j.destud.2021.101078}, + annotation = {MAG ID: 4200257712} +} + +@book{He2020, + title = {Neural {{Engineering}}}, + editor = {He, Bin}, + year = {2020}, + publisher = {Springer International Publishing}, + address = {Cham}, + doi = {10.1007/978-3-030-43395-6}, + urldate = {2023-09-04}, + isbn = {978-3-030-43394-9 978-3-030-43395-6}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/He2020.pdf} +} + +@article{Heimburg2005, + title = {On Soliton Propagation in Biomembranes and Nerves}, + author = {Heimburg, Thomas and Jackson, Andrew D.}, + year = {2005}, + month = jul, + journal = {Proceedings of the National Academy of Sciences}, + volume = {102}, + number = {28}, + pages = {9790--9795}, + issn = {0027-8424, 1091-6490}, + doi = {10.1073/pnas.0503823102}, + urldate = {2023-03-15}, + abstract = {The lipids of biological membranes and intact biomembranes display chain melting transitions close to temperatures of physiological interest. During this transition the heat capacity, volume and area compressibilities, and relaxation times all reach maxima. Compressibilities are thus nonlinear functions of temperature and pressure in the vicinity of the melting transition, and we show that this feature leads to the possibility of soliton propagation in such membranes. In particular, if the membrane state is above the melting transition solitons will involve changes in lipid state. We discuss solitons in the context of several striking properties of nerve membranes under the influence of the action potential, including mechanical dislocations and temperature changes.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Heimburg2005.pdf} +} + +@book{Herman2020, + title = {Fluorescence {{Microscopy}}}, + author = {Herman, B.}, + year = {2020}, + month = aug, + edition = {2}, + publisher = {Garland Science}, + doi = {10.1201/9781003077060}, + urldate = {2022-04-15}, + isbn = {978-1-00-307706-0}, + langid = {english} +} + +@article{Hodgkin1952, + title = {A Quantitative Description of Membrane Current and Its Application to Conduction and Excitation in Nerve}, + author = {Hodgkin, A. L. and Huxley, A. F.}, + year = {1952}, + month = aug, + journal = {The Journal of Physiology}, + volume = {117}, + number = {4}, + pages = {500--544}, + publisher = {Wiley}, + doi = {10.1113/jphysiol.1952.sp004764} +} + +@article{Hofer2001, + title = {Intercellular {{Ca2}}+ {{Wave Propagation}} through {{Gap-Junctional Ca2}}+ {{Diffusion}}: {{A Theoretical Study}}}, + shorttitle = {Intercellular {{Ca2}}+ {{Wave Propagation}} through {{Gap-Junctional Ca2}}+ {{Diffusion}}}, + author = {H{\"o}fer, Thomas and Politi, Antonio and Heinrich, Reinhart}, + year = {2001}, + month = jan, + journal = {Biophysical Journal}, + volume = {80}, + number = {1}, + pages = {75--87}, + issn = {00063495}, + doi = {10.1016/S0006-3495(01)75996-6}, + urldate = {2023-01-30}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Hofer2001.pdf} +} + +@article{Hofer2002, + title = {Control and {{Plasticity}} of {{Intercellular Calcium Waves}} in {{Astrocytes}}: {{A Modeling Approach}}}, + shorttitle = {Control and {{Plasticity}} of {{Intercellular Calcium Waves}} in {{Astrocytes}}}, + author = {H{\"o}fer, Thomas and Venance, Laurent and Giaume, Christian}, + year = {2002}, + month = jun, + journal = {The Journal of Neuroscience}, + volume = {22}, + number = {12}, + pages = {4850--4859}, + issn = {0270-6474, 1529-2401}, + doi = {10.1523/JNEUROSCI.22-12-04850.2002}, + urldate = {2023-01-30}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Hofer2002.pdf} +} + +@article{Hoffman2022, + title = {Focused Ultrasound Excites Action Potentials in Mammalian Peripheral Neurons in Part through the Mechanically Gated Ion Channel {{PIEZO2}}}, + author = {Hoffman, Benjamin U. and Baba, Yoshichika and Lee, Stephen A. and Tong, Chi-Kun and Konofagou, Elisa E. and Lumpkin, Ellen A.}, + year = {2022}, + month = may, + journal = {Proceedings of the National Academy of Sciences}, + volume = {119}, + number = {21}, + pages = {e2115821119}, + issn = {0027-8424, 1091-6490}, + doi = {10.1073/pnas.2115821119}, + urldate = {2022-06-01}, + abstract = {Significance Modulation of peripheral nervous system (PNS) activity has shown promise in treating a wide range of diseases, from epilepsy to rheumatoid arthritis. Clinically, stimulation of nerves is most commonly delivered through invasive and risk-laden surgical electrode placement. Noninvasive technologies for PNS modulation can both increase safety and expand modulation application to various disease stages. Recent studies have revealed the therapeutic potential of noninvasive neuromodulation of brain circuits with ultrasound. This study identifies reliable protocols and molecular mechanisms for stimulating action potentials from individual peripheral neurons in the mammalian nervous system. These findings reveal the translational potential of ultrasound to effectively modulate the PNS through intrinsic neuronal mechanisms. , Neurons of the peripheral nervous system (PNS) are tasked with diverse roles, from encoding touch, pain, and itch to interoceptive control of inflammation and organ physiology. Thus, technologies that allow precise control of peripheral nerve activity have the potential to regulate a wide range of biological processes. Noninvasive modulation of neuronal activity is an important translational application of focused ultrasound (FUS). Recent studies have identified effective strategies to modulate brain circuits; however, reliable parameters to control the activity of the PNS are lacking. To develop robust noninvasive technologies for peripheral nerve modulation, we employed targeted FUS stimulation and electrophysiology in mouse ex vivo skin-saphenous nerve preparations to record the activity of individual mechanosensory neurons. Parameter space exploration showed that stimulating neuronal receptive fields with high-intensity, millisecond FUS pulses reliably and repeatedly evoked one-to-one action potentials in all peripheral neurons recorded. Interestingly, when neurons were classified based on neurophysiological properties, we identified a discrete range of FUS parameters capable of exciting all neuronal classes, including myelinated A fibers and unmyelinated C fibers. Peripheral neurons were excited by FUS stimulation targeted to either cutaneous receptive fields or peripheral nerves, a key finding that increases the therapeutic range of FUS-based peripheral neuromodulation. FUS elicited action potentials with millisecond latencies compared with electrical stimulation, suggesting ion channel--mediated mechanisms. Indeed, FUS thresholds were elevated in neurons lacking the mechanically gated channel PIEZO2. Together, these results demonstrate that transcutaneous FUS drives peripheral nerve activity by engaging intrinsic mechanotransduction mechanisms in neurons [B. U. Hoffman, PhD thesis, (2019)].}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Hoffman2022.pdf} +} + +@article{Holland1989, + title = {An Improved Theory for the Prediction of Microcavitation Thresholds}, + author = {Holland, C.K. and Apfel, R.E.}, + year = {1989}, + month = mar, + journal = {IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control}, + volume = {36}, + number = {2}, + pages = {204--208}, + issn = {0885-3010}, + doi = {10.1109/58.19152}, + urldate = {2023-12-05}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Holland1989.pdf} +} + +@article{Hsiao2023, + title = {Intercellular {{Calcium Waves}} and {{Permeability Change Induced}} by {{Vertically Deployed Surface Acoustic Waves}} in a {{Human Cerebral Microvascular Endothelial Cell Line}} ({{hCMEC}}/{{D3}}) {{Monolayer}}}, + author = {Hsiao, Ming-Yen and Liao, Defei and Xiang, Gaoming and Zhong, Pei}, + year = {2023}, + month = may, + journal = {Ultrasound in Medicine \& Biology}, + volume = {49}, + number = {5}, + pages = {1153--1163}, + issn = {03015629}, + doi = {10.1016/j.ultrasmedbio.2022.12.019}, + urldate = {2023-05-10}, + abstract = {Objective: The ultrasound-mediated blood-brain barrier (BBB) opening with microbubbles has been widely employed, while recent studies also indicate the possibility that ultrasound alone can open the BBB through a direct mechanical effect. However, the exact mechanisms through which ultrasound interacts with the BBB and whether it can directly trigger intracellular signaling and a permeability change in the BBB endothelium remain unclear. Methods: Vertically deployed surface acoustic waves (VD-SAWs) were applied on a human cerebral microvascular endothelial cell line (hCMEC/D3) monolayer using a 33-MHz interdigital transducer that exerts shear stress-predominant stimulation. The intracellular calcium response was measured by fluorescence imaging, and the permeability of the hCMEC/D3 monolayer was assessed by transendothelial electrical resistance (TEER). Discussion: At a certain intensity threshold, VD-SAWs induced an intracellular calcium surge that propagated to adjacent cells as intercellular calcium waves. VD-SAWs induced a TEER decrease in a pulse repetition frequencydependent manner, thereby suggesting possible involvement of the mechanosensitive ion channels. Conclusion: The unique VD-SAW system enables more physiological mechanical stimulation of the endothelium monolayer. Moreover, it can be easily combined with other measurement devices, providing a useful platform for further mechanistic studies on ultrasound-mediated BBB opening.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Hsiao2023.pdf} +} + +@article{Hu2022, + title = {Implementation of Biohybrid Olfactory Bulb on a High-Density {{CMOS-chip}} to Reveal Large-Scale Spatiotemporal Circuit Information}, + author = {Hu, Xin and Khanzada, Shahrukh and Kl{\"u}tsch, Diana and Calegari, Federico and Amin, Hayder}, + year = {2022}, + month = feb, + journal = {Biosensors and Bioelectronics}, + volume = {198}, + pages = {113834}, + issn = {0956-5663}, + doi = {10.1016/j.bios.2021.113834}, + urldate = {2023-05-22}, + abstract = {Large-scale multi-site biosensors are essential to probe the olfactory bulb (OB) circuitry for understanding the spatiotemporal dynamics of simultaneous discharge patterns. Current ex-vivo biosensing techniques are limited to recording a small set of neurons and cannot provide an adequate resolution, which hinders revealing the fast dynamic underlying the information coding mechanisms in the OB circuit. Here, we demonstrate a novel biohybrid OB-CMOS biosensing platform to decipher the cross-scale dynamics of the OB electrogenesis and quantify the distinct neuronal coding properties. The approach with 4096-microelectrodes offers a non-invasive, label-free, bioelectrical imaging to decode simultaneous firing patterns from thousands of connected neuronal ensembles in acute OB slices. The platform can measure spontaneous and drug-induced extracellular field potential activity with substantially improved spatiotemporal resolution over conventional OB-based biosensors. Also, we employ our OB-CMOS recordings to perform multidimensional analysis to instantiate specific neurophysiological metrics underlying the olfactory spatiotemporal coding that emerged from the OB interconnected layers. Our results delineate the computational implications of large-scale activity patterns in functional olfactory processing. The systematic interplay of the experimental CMOS-base platform architecture and the high-content characterization of the olfactory circuit with various computational analyses endow significant functional interrogations of the OB information processing, high-spatiotemporal connectivity mapping, and global circuit dynamics. Thus, our study can inspire the design of advanced biomimetic olfactory-based biosensors and neuromorphic approaches for diagnostic biomarkers and drug discovery applications.}, + langid = {english}, + keywords = {Bioelectronics nose,CMOS-MEAs,Electrogenesis,Neural circuits,Olfactory bulb-based biosensors,Olfactory spatiotemporal coding}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Hu2022.pdf;/Users/tomaubier/Zotero/storage/XM4KWQMV/S095656632100871X.html} +} + +@article{Huang2015, + title = {Regulation of Neuronal Communication by {{G}} Protein-coupled Receptors}, + author = {Huang, Yunhong and Thathiah, Amantha}, + year = {2015}, + month = jun, + journal = {FEBS Letters}, + volume = {589}, + number = {14}, + pages = {1607--1619}, + issn = {0014-5793, 1873-3468}, + doi = {10.1016/j.febslet.2015.05.007}, + urldate = {2024-10-10}, + abstract = {Neuronal communication plays an essential role in the propagation of information in the brain and requires a precisely orchestrated connectivity between neurons. Synaptic transmission is the mechanism through which neurons communicate with each other. It is a strictly regulated process which involves membrane depolarization, the cellular exocytosis machinery, neurotransmitter release from synaptic vesicles into the synaptic cleft, and the interaction between ion channels, G protein-coupled receptors (GPCRs), and downstream effector molecules. The focus of this review is to explore the role of GPCRs and G protein-signaling in neurotransmission, to highlight the function of GPCRs, which are localized in both presynaptic and postsynaptic membrane terminals, in regulation of intrasynaptic and intersynaptic communication, and to discuss the involvement of astrocytic GPCRs in the regulation of neuronal communication.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Huang2015.pdf} +} + +@misc{IEC-TS-62556-2014, + title = {Ultrasonics - {{Field}} Characterization - {{Specification}} and Measurement of Field Parameters for High Intensity Therapeutic Ultrasound}, + author = {{IEC-TS-62556-}}, + year = {2014}, + number = {IEC TS 62556:2014}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/IEC-TS-62556-2014.pdf} +} + +@article{Inan2010, + title = {The {{Cytoprotective Effects}} of {{Dantrolene}}: {{A Ryanodine Receptor Antagonist}}}, + shorttitle = {The {{Cytoprotective Effects}} of {{Dantrolene}}}, + author = {Inan, Saadet and Wei, Huafeng}, + year = {2010}, + month = dec, + journal = {Anesthesia \& Analgesia}, + volume = {111}, + number = {6}, + pages = {1400--1410}, + issn = {0003-2999}, + doi = {10.1213/ANE.0b013e3181f7181c}, + urldate = {2024-10-09}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Inan2010.pdf} +} + +@article{Innocenti2000, + title = {Imaging {{Extracellular Waves}} of {{Glutamate}} during {{Calcium Signaling}} in {{Cultured Astrocytes}}}, + author = {Innocenti, Barbara and Parpura, Vladimir and Haydon, Philip G.}, + year = {2000}, + month = mar, + journal = {The Journal of Neuroscience}, + volume = {20}, + number = {5}, + pages = {1800--1808}, + publisher = {Society for Neuroscience}, + doi = {10.1523/jneurosci.20-05-01800.2000}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Innocenti2000.pdf} +} + +@misc{ITISFoundation2022, + title = {Tissue {{Properties Database V4}}.1}, + author = {{IT'IS Foundation}}, + year = {2022}, + publisher = {[object Object]}, + doi = {10.13099/VIP21000-04-1}, + urldate = {2024-04-19}, + abstract = {Density, Heat Capacity, Thermal Conductivity, Heat Transfer, T1/T2 Relaxation Times, Acoustic Attenuation, Viscosity, Dielectric Properties, Elemental Composition}, + collaborator = {{IT'IS Foundation}}, + keywords = {Physical and biological properties of living tissues} +} + +@book{Jaffe1971, + title = {Piezoelectric Ceramics}, + author = {Jaffe, Bernard and Cook, William R. and Jaffe, Hans Ludwig}, + year = {1971}, + series = {Non-Metallic Solids}, + number = {v. 3}, + publisher = {Academic Press}, + address = {London, New York}, + isbn = {978-0-12-379550-2}, + lccn = {TK7871.15.C4 J3 1971}, + keywords = {Electronic ceramics,Ferroelectricity,Piezoelectricity}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Jaffe1971.pdf} +} + +@article{Jaffe2010, + title = {Fast Calcium Waves}, + author = {Jaffe, Lionel F.}, + year = {2010}, + month = aug, + journal = {Cell Calcium}, + volume = {48}, + number = {2-3}, + pages = {102--113}, + issn = {01434160}, + doi = {10.1016/j.ceca.2010.08.007}, + urldate = {2024-03-12}, + abstract = {Calcium waves are propagated in five main speed ranges which cover a billion-fold range of speeds. We define the fast speed range as 3--30 ␮m/s after correction to a standard temperature of 20 {\textopenbullet}C. Only waves which are not fertilization waves are considered here. 181 such cases are listed here. These are through organisms in all major taxa from cyanobacteria through mammals including human beings except for those through other bacteria, higher plants and fungi. Nearly two-thirds of these speeds lie between 12 and 24 ␮m/s. We argue that their common mechanism in eukaryotes is a reaction-diffusion one involving calcium-induced calcium release, in which calcium waves are propagated along the endoplasmic reticulum. We propose that the gliding movements of some cyanobacteria are driven by fast calcium waves which are propagated along their plasma membranes. Fast calcium waves may drive materials to one end of developing embryos by cellular peristalsis, help coordinate complex cell movements during development and underlie brain injury waves. Moreover, we continue to argue that such waves greatly increase the likelihood that chronic injuries will initiate tumors and cancers before genetic damage occurs. Finally we propose numerous further studies.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Jaffe2010.pdf} +} + +@article{Jimenez-Gambin2019, + title = {Holograms to {{Focus Arbitrary Ultrasonic Fields}} through the {{Skull}}}, + author = {{Jim{\'e}nez-Gamb{\'i}n}, Sergio and Jim{\'e}nez, No{\'e} and Benlloch, Jos{\'e} Mar{\'i}a and Camarena, Francisco}, + year = {2019}, + month = jul, + journal = {Physical Review Applied}, + volume = {12}, + number = {1}, + pages = {014016}, + issn = {2331-7019}, + doi = {10.1103/PhysRevApplied.12.014016}, + urldate = {2024-02-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Jimenez-Gambin2019.pdf} +} + +@article{Kamimura2020, + title = {Ultrasound {{Neuromodulation}}: {{Mechanisms}} and the {{Potential}} of {{Multimodal Stimulation}} for {{Neuronal Function Assessment}}}, + shorttitle = {Ultrasound {{Neuromodulation}}}, + author = {Kamimura, Hermes A. S. and Conti, Allegra and Toschi, Nicola and Konofagou, Elisa E.}, + year = {2020}, + month = may, + journal = {Frontiers in Physics}, + volume = {8}, + pages = {150}, + issn = {2296-424X}, + doi = {10.3389/fphy.2020.00150}, + urldate = {2023-02-17}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Kamimura2020.pdf} +} + +@article{Kano2018, + title = {Sensory Phenomena and Obsessive-Compulsive Symptoms in {{Tourette}} Syndrome Following Deep Brain Stimulation: {{Two}} Case Reports}, + shorttitle = {Sensory Phenomena and Obsessive-Compulsive Symptoms in {{Tourette}} Syndrome Following Deep Brain Stimulation}, + author = {Kano, Yukiko and Matsuda, Natsumi and Nonaka, Maiko and Fujio, Miyuki and Kono, Toshiaki and Kaido, Takanobu}, + year = {2018}, + month = oct, + journal = {Journal of Clinical Neuroscience}, + volume = {56}, + pages = {199--201}, + issn = {0967-5868}, + doi = {10.1016/j.jocn.2018.06.046}, + urldate = {2023-08-29}, + abstract = {Here, we assess sensory phenomena (SP) and obsessive-compulsive symptoms (OCS) in two patients with refractory Tourette syndrome (TS) before and after deep brain stimulation (DBS) targeting the centromedian-parafascicular complex (CM-Pfc)-ventral oral nuclei of the bilateral thalami. Based on changes in these clinical features, we also aimed to elucidate useful information regarding the use of DBS in TS. We administered the Yale Global Tic Severity Scale (YGTSS) to assess tics, the Premonitory Urge for Tics Scale (PUTS) for premonitory urges, the University of S{\~a}o Paulo Sensory Phenomena Scale (USP-SPS) for broader SP, the Dimensional Yale-Brown Obsessive-Compulsive Scale (DY-BOCS) for OCS, and the Global Assessment of Functioning (GAF) scale for global functioning. We report on two male patients who showed consistent improvement in tics, premonitory urges, and global functioning two years after DBS. In contrast, there were differences between the patients in broader SP, including ``just right'' perceptions, and OCS. Our results suggest that systematic assessment of a wide range of SP and OCS dimensions is necessary to elucidate the usefulness of DBS in TS.}, + keywords = {Deep brain stimulation,Obsessive-compulsive symptoms,Refractory Tourette syndrome,Sensory phenomena,Tics}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Kano2018.pdf;/Users/tomaubier/Zotero/storage/M7UK3379/S096758681830571X.html} +} + +@article{Kaouri2022, + title = {A New Mechanochemical Model for Apical Constriction: {{Coupling}} Calcium Signalling and Viscoelasticity}, + shorttitle = {A New Mechanochemical Model for Apical Constriction}, + author = {Kaouri, Katerina and Christodoulou, Neophytos and Chakraborty, Abhishek and M{\'e}ndez, Paul E. and Skourides, Paris and {Ruiz-Baier}, Ricardo}, + year = {2022}, + month = oct, + journal = {Frontiers in Systems Biology}, + volume = {2}, + pages = {962790}, + issn = {2674-0702}, + doi = {10.3389/fsysb.2022.962790}, + urldate = {2024-12-10}, + abstract = {Embryonic epithelial cells exhibit strong coupling of mechanical responses to chemical signals and most notably to calcium. Recent experiments have shown that the disruption of calcium signals during neurulation strongly correlates with the appearance of neural tube defects. We, thus, develop a multi-dimensional mechanochemical model and use it to reproduce important experimental findings that describe anterior neural plate morphogenetic behaviour during neural tube closure. The governing equations consist of an advection-diffusion-reaction system for calcium concentration which is coupled to a force balance equation for the tissue. The tissue is modelled as a linear viscoelastic material that includes a calcium-dependent contraction stress. We implement a random distribution of calcium sparks that is compatible with experimental findings. A finite element method is employed to generate numerical solutions of the model for an appropriately chosen range of parameter values. We analyse the behaviour of the model as three parameters vary: the level of IP 3 concentration, the strength of the stretch-sensitive activation and the maximum magnitude of the calcium-dependent contraction stress. Importantly, the simulations reproduce important experimental features, such as the spatio-temporal correlation between calcium transients and tissue deformation, the monotonic reduction of the apical surface area and the constant constriction rate, as time progresses. The model could also be employed to gain insights into other biological processes where the coupling of calcium signalling and mechanics is important, such as carcinogenesis and wound healing.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Kaouri2022.pdf} +} + +@article{Karagas2019, + title = {Roles for the {{Endoplasmic Reticulum}} in {{Regulation}} of {{Neuronal Calcium Homeostasis}}}, + author = {Karagas, Nicholas E. and Venkatachalam, Kartik}, + year = {2019}, + month = oct, + journal = {Cells}, + volume = {8}, + number = {10}, + pages = {1232}, + issn = {2073-4409}, + doi = {10.3390/cells8101232}, + urldate = {2023-05-09}, + abstract = {By influencing Ca2+ homeostasis in spatially and architecturally distinct neuronal compartments, the endoplasmic reticulum (ER) illustrates the notion that form and function are intimately related. The contribution of ER to neuronal Ca2+ homeostasis is attributed to the organelle being the largest reservoir of intracellular Ca2+ and having a high density of Ca2+ channels and transporters. As such, ER Ca2+ has incontrovertible roles in the regulation of axodendritic growth and morphology, synaptic vesicle release, and neurotransmission activity dependent gene expression, synaptic plasticity, and mitochondrial bioenergetics. Not surprisingly, many neurological diseases arise from ER Ca2+ dyshomeostasis, either directly due to alterations in ER resident proteins, or indirectly via processes that are coupled to the regulators of ER Ca2+ dynamics. In this review, we describe the mechanisms involved in the establishment of ER Ca2+ homeostasis in neurons. We elaborate upon how changes in the spatiotemporal dynamics of Ca2+ exchange between the ER and other organelles sculpt neuronal function and provide examples that demonstrate the involvement of ER Ca2+ dyshomeostasis in a range of neurological and neurodegenerative diseases.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Karagas22.pdf} +} + +@article{Kasai, + title = {Real-{{Time Two-Dimensional Blood Flow Imaging Using}} an {{Autocorrelation Technique}}}, + author = {Kasai, Chihiro and Namekawa, Koroku and Koyano, Akira and Omoto, Ryozo}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Kasai.pdf} +} + +@article{Kawaguchi1996, + title = {Effect of {{Isoflurane}} on {{Motor-evoked Potentials Induced}} by {{Direct Electrical Stimulation}} of the {{Exposed Motor Cortex}} with {{Single}}, {{Double}}, and {{Triple Stimuli}} in {{Rats}}}, + author = {Kawaguchi, Masahiko and Shimizu, Kiyoshi and Furuya, Hitoshi and Sakamoto, Takanori and Ohnishi, Hideyuki and Karasawa, Jun}, + year = {1996}, + month = nov, + journal = {Anesthesiology}, + volume = {85}, + number = {5}, + pages = {1176--1183}, + issn = {0003-3022}, + doi = {10.1097/00000542-199611000-00027}, + urldate = {2023-02-17}, + abstract = {Background The clinical application of intraoperative motor-evoked potentials (MEPs) has been hampered by their sensitivity to anesthetics. Recently, to overcome anesthetic-induced depression of myogenic MEPs, multiple stimulus setups with a paired or a train of pulses for stimulation of the motor cortex were reported. However, the effects of anesthetics on MEPs induced by these stimulation techniques are unknown. Methods Bipolar electrical stimulation of the left motor cortex was carried out in 15 rats anesthetized with thiopental while the compound muscle action potentials were recorded from the contralateral hind limb. After recording of the MEP in response to the single-shock stimulation of the motor cortex, paired pulses (double pulses) or a train of three pulses (triple pulses) with an interstimulus interval of each pulse at 0.3, 0.5, 1.0, 1.5, and 2.0 ms were applied. After control MEP recording, isoflurane was administered at a concentration of 0.25 minimum alveolar anesthetic concentration (MAC), 0.5 MAC, 0.75 MAC, and 1.0 MAC, and the effects of isoflurane on the MEPs induced by single, double, and triple pulses were evaluated. Results In all animals, distinct baseline MEPs were recorded. During the administration of 0.25 MAC and 0.5 MAC isoflurane, MEPs induced by stimulation with a single pulse could be recorded in 87\% and 33\% of animals, respectively, and MEP amplitude was significantly reduced in a dose-dependent manner. During the administration of 0.75 MAC isoflurane, MEPs after single-pulse stimulation could not be recorded in any animals. By stimulating with paired or triple pulses, the success rate of MEP recording and MEP amplitude significantly increased compared with those after single pulse before and during the administration of isoflurane. Both the success rate of MEP recording and MEP amplitude after double- and triple-pulse stimulation decreased significantly in a dose-dependent manner during the administration of isoflurane. Conclusions Application of double or triple stimulation of the motor cortex increases the success rate of MEP recording and its amplitude during isoflurane anesthesia in rats. However, these responses are suppressed by isoflurane in a dose-dependent manner.}, + langid = {english} +} + +@article{Keck2002, + title = {Repetitive Transcranial Magnetic Stimulation Increases the Release of Dopamine in the Mesolimbic and Mesostriatal System}, + author = {Keck, M. E. and Welt, T. and M{\"u}ller, M. B. and Erhardt, A. and Ohl, F. and Toschi, N. and Holsboer, F. and Sillaber, I.}, + year = {2002}, + month = jul, + volume = {43}, + number = {1}, + pages = {101--109}, + publisher = {Elsevier BV}, + doi = {10.1016/s0028-3908(02)00069-2}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Keck2002.pdf} +} + +@inproceedings{Khraiche2008, + title = {Ultrasound Induced Increase in Excitability of Single Neurons}, + booktitle = {2008 30th {{Annual International Conference}} of the {{IEEE Engineering}} in {{Medicine}} and {{Biology Society}}}, + author = {Khraiche, Massoud L. and Phillips, William B. and Jackson, Nathan and Muthuswamy, Jitendran}, + year = {2008}, + month = aug, + pages = {4246--4249}, + publisher = {IEEE}, + address = {Vancouver, BC}, + doi = {10.1109/IEMBS.2008.4650147}, + urldate = {2023-07-21}, + abstract = {The aim of this study was to carefully assess the level of modulation in electrical excitability of single neurons with the application of high frequency ultrasound. High frequency tone bursts of ultrasound have been shown to dramatically increase the spike frequency of primary hippocampal neurons in culture. In addition, these ultrasonic bursts also induce silent or still developing neurons to fire. Results indicate that the increase in excitability is largely mediated by mechanical effects and not thermal effects of ultrasound. Future studies on culture models exposed to varying ultrasound protocols may provide insight into the feasibility of using ultrasound as a means for neurostimulation studies conducted on brain slice and in vivo models.}, + isbn = {978-1-4244-1814-5}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Khraiche2008.pdf} +} + +@article{Khraiche2017, + title = {Sustained Elevation of Activity of Developing Neurons Grown on Polyimide Microelectrode Arrays ({{MEA}}) in Response to Ultrasound Exposure}, + author = {Khraiche, Massoud L. and Phillips, William B. and Jackson, Nathan and Muthuswamy, Jit}, + year = {2017}, + month = aug, + journal = {Microsystem Technologies}, + volume = {23}, + number = {8}, + pages = {3671--3683}, + issn = {0946-7076, 1432-1858}, + doi = {10.1007/s00542-016-3150-6}, + urldate = {2023-07-21}, + abstract = {High frequency ultrasound (HFUS) is an attractive modality for noninvasive clinical applications such as imaging, diagnostics and more recently for stimulation of the central nervous system. The aim of this study was to investigate the modulation in the electrical activity of developing neurons due to the application of HFUS using polyimide based microelectrode array (MEA) that is acoustically transparent in order to allow ultrasound waves to transmit through the substrate and reach the growing neural layer. High frequency tone bursts of ultrasound were applied to a monolayer of developing primary neurons grown on an acoustical transparent polyimide MEA. HFUS was applied to primary neuronal culture at two frequencies (4.4 and 96 MHz) with spatial peak-temporal average intensities of 100 and 10 mW/cm2. Exposures were found to increase the spike rate of neurons in culture up to 20-fold in some cases and induce silent or still developing neurons to fire at a maximum rate of up to three new units per recording microelectrode. Another new observation reported in this study is that the increase in spike rate was sustained for over 6 min post stimulation. Our results also suggest that mechanical and not thermal effects of ultrasound largely mediate the increase in electrical excitability without any discernible spatial pattern or preference across the monolayer for the US parameters used in this study.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Khraiche2017.pdf} +} + +@article{Kim2021, + title = {Patterned {{Interference Radiation Force}} for {{Transcranial Neuromodulation}}.}, + author = {Kim, Young Hun and {Young Hun Kim} and {Ki Chang Kang} and Kim, Jeongyeon and {Chi Nan Pai} and {Yichi Zhang} and {Pejman Ghanouni} and Park, Kwan Kyu and {Kwan Kyu Park} and Firouzi, Kamyar and {Burtus T Khuri-Yakub}}, + year = {2021}, + journal = {Ultrasound in Medicine and Biology}, + doi = {10.1016/j.ultrasmedbio.2021.11.006}, + abstract = {Compared with the conventional method of transcranial focused ultrasound stimulation using a single transducer or a focused beam, the compression and tensile forces are generated from the high-pressure gradient of a standing wave that can generate increased stimulation. We experimentally verified a neuromodulation system using patterned interference radiation force (PIRF) and propose a method for obtaining the magnitude of the radiation force, which is considered the main factor influencing ultrasound neuromodulation. The radiation forces generated using a single focused transducer and a standing wave created via two focused transducers were compared using simulations. Radiation force was calculated based on the relationship between the acoustic pressure, radiation force and time-averaged second-order pressure obtained using an acoustic streaming simulation. The presence of the radiation force was verified by measuring the time-averaged second-order pressure generated due to the radiation force, by using a glass tube.}, + pmid = {34955292}, + annotation = {MAG ID: 4200522550} +} + +@article{Kim2021a, + title = {Transcranial Focused Ultrasound Stimulation with High Spatial Resolution}, + author = {Kim, Seongyeon and Jo, Yehhyun and Kook, Geon and Pasquinelli, Cristina and Kim, Hyunggug and Kim, Kipom and Hoe, Hyang-Sook and Choe, Youngshik and Rhim, Hyewhon and Thielscher, Axel and Kim, Jeongyeon and Lee, Hyunjoo Jenny}, + year = {2021}, + month = mar, + journal = {Brain Stimulation}, + volume = {14}, + number = {2}, + pages = {290--300}, + issn = {1935861X}, + doi = {10.1016/j.brs.2021.01.002}, + urldate = {2022-04-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Kim2021a.pdf} +} + +@article{Kim2023, + title = {Acoustic Radiation Force for Analyzing the Mechanical Stress in Ultrasound Neuromodulation}, + author = {Kim, Young Hun and Lee, Chang Hoon and Firouzi, Kamyar and Park, Beom Hoon and Pyun, Joo Young and Kim, Jeong Nyeon and Park, Kwan Kyu and {Khuri-Yakub}, Butrus T}, + year = {2023}, + month = jul, + journal = {Physics in Medicine \& Biology}, + volume = {68}, + number = {13}, + pages = {135008}, + issn = {0031-9155, 1361-6560}, + doi = {10.1088/1361-6560/acdbb5}, + urldate = {2023-08-07}, + abstract = {Objective. Although recent studies have shown that mechanical stress plays an important role in ultrasound neuromodulation, the magnitude and distribution of the mechanical stress generated in tissues by focused ultrasound transducers have not been adequately examined. Various acoustic radiation force (ARF) equations used in previous studies have been evaluated based on the tissue displacement results and are suitable for estimating the displacement. However, it is unclear whether mechanical stress can be accurately determined. This study evaluates the mechanical stress predicted by various AFR equations and suggests the optimal equation for estimating the mechanical stress in the brain tissue. Approach. In this paper, brain tissue responses are compared through numerical finite element simulations by applying the three most used ARF equations---Reynolds stress force ((RSF)), momentum flux density tensor force, and attenuation force. Three ARF fields obtained from the same pressure field were applied to the linear elastic model to calculate the displacement, mechanical stress, and mean pressure generated inside the tissue. Both the simple pressure field using a single transducer and the complex standing wave pressure field using two transducers were simulated. Main results. For the case using a single transducer, all three ARFs showed similar displacement. However, when comparing the mechanical stress results, only the results using the RSF showed a strong stress tensor at the focal point. For the case of using two transducers, the displacement and stress tensor field of the pattern related to the standing wave were calculated only from the results using the RSF. Significance. The model using RSF equation allows accurate analysis on stress tensor inside the tissue for ultrasound neuromodulation.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Kim2023.pdf} +} + +@article{King2013, + title = {Effective {{Parameters}} for {{Ultrasound-Induced In Vivo Neurostimulation}}}, + author = {King, Randy L. and Brown, Julian R. and Newsome, William T. and Pauly, Kim Butts}, + year = {2013}, + month = feb, + journal = {Ultrasound in Medicine \& Biology}, + volume = {39}, + number = {2}, + pages = {312--331}, + issn = {03015629}, + doi = {10.1016/j.ultrasmedbio.2012.09.009}, + urldate = {2024-02-19}, + abstract = {Ultrasound-induced neurostimulation has recently gained increasing attention, but little is known about the mechanisms by which it affects neural activity or about the range of acoustic parameters and stimulation protocols that elicit responses. We have established conditions for transcranial stimulation of the nervous system in vivo, using the mouse somatomotor response. We report that (1) continuous-wave stimuli are as effective as or more effective than pulsed stimuli in eliciting responses, and responses are elicited with stimulus onset rather than stimulus offset; (2) stimulation success increases as a function of both acoustic intensity and acoustic duration; (3) interactions of intensity and duration suggest that successful stimulation results from the integration of stimulus amplitude over a time interval of 50 to 150 ms; and (4) the motor response elicited appears to be an all-ornothing phenomenon, meaning stronger stimulus intensities and durations increase the probability of a motor response without affecting the duration or strength of the response. (E-mail: rlking@stanford.edu) {\'O} 2013 World Federation for Ultrasound in Medicine \& Biology.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/King2013.pdf} +} + +@article{Kleiner-Fisman2006, + title = {Subthalamic Nucleus Deep Brain Stimulation: {{Summary}} and Meta-Analysis of Outcomes}, + shorttitle = {Subthalamic Nucleus Deep Brain Stimulation}, + author = {{Kleiner-Fisman}, Galit and Herzog, Jan and Fisman, David N. and Tamma, Filippo and Lyons, Kelly E. and Pahwa, Rajesh and Lang, Anthony E. and Deuschl, G{\"u}nther}, + year = {2006}, + month = jun, + journal = {Movement Disorders}, + volume = {21}, + number = {S14}, + pages = {S290-S304}, + issn = {0885-3185, 1531-8257}, + doi = {10.1002/mds.20962}, + urldate = {2023-05-30}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Kleiner-Fisman2006.pdf} +} + +@article{Kleven2023, + title = {Waxholm {{Space}} Atlas of the Rat Brain: A {{3D}} Atlas Supporting Data Analysis and Integration}, + shorttitle = {Waxholm {{Space}} Atlas of the Rat Brain}, + author = {Kleven, Heidi and Bjerke, Ingvild E. and Clasc{\'a}, Francisco and Groenewegen, Henk J. and Bjaalie, Jan G. and Leergaard, Trygve B.}, + year = {2023}, + month = nov, + journal = {Nature Methods}, + volume = {20}, + number = {11}, + pages = {1822--1829}, + publisher = {Nature Publishing Group}, + issn = {1548-7105}, + doi = {10.1038/s41592-023-02034-3}, + urldate = {2025-01-28}, + abstract = {Volumetric brain atlases are increasingly used to integrate and analyze diverse experimental neuroscience data acquired from animal models, but until recently a publicly available digital atlas with complete coverage of the rat brain has been missing. Here we present an update of the Waxholm Space rat brain atlas, a comprehensive open-access volumetric atlas resource. This brain atlas features annotations of 222 structures, of which 112 are new and 57 revised compared to previous versions. It provides a detailed map of the cerebral cortex, hippocampal region, striatopallidal areas, midbrain dopaminergic system, thalamic cell groups, the auditory system and main fiber tracts. We document the criteria underlying the annotations and demonstrate how the atlas with related tools and workflows can be used to support interpretation, integration, analysis and dissemination of experimental rat brain data.}, + copyright = {2023 The Author(s)}, + langid = {english}, + keywords = {Cellular neuroscience,Computational neuroscience,Rat}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Kleven2023.pdf} +} + +@article{Komin2015, + title = {Multiscale {{Modeling Indicates That Temperature Dependent}} [{{Ca}} {\textsuperscript{2+}} ] {\textsubscript{i}} {{Spiking}} in {{Astrocytes Is Quantitatively Consistent}} with {{Modulated SERCA Activity}}}, + author = {Komin, Niko and Moein, Mahsa and Ellisman, Mark H. and Skupin, Alexander}, + year = {2015}, + journal = {Neural Plasticity}, + volume = {2015}, + pages = {1--15}, + issn = {2090-5904, 1687-5443}, + doi = {10.1155/2015/683490}, + urldate = {2024-07-12}, + abstract = {Changes in the cytosolic Ca 2+ concentration ( [ Ca 2 + ] i ) are the most predominant active signaling mechanism in astrocytes that can modulate neuronal activity and is assumed to influence neuronal plasticity. Although Ca 2+ signaling in astrocytes has been intensively studied in the past, our understanding of the signaling mechanism and its impact on tissue level is still incomplete. Here we revisit our previously published data on the strong temperature dependence of Ca 2+ signals in both cultured primary astrocytes and astrocytes in acute brain slices of mice. We apply multiscale modeling to test the hypothesis that the temperature dependent [ Ca 2 + ] i spiking is mainly caused by the increased activity of the sarcoendoplasmic reticulum ATPases (SERCAs) that remove Ca 2+ from the cytosol into the endoplasmic reticulum. Quantitative comparison of experimental data with multiscale simulations supports the SERCA activity hypothesis. Further analysis of multiscale modeling and traditional rate equations indicates that the experimental observations are a spatial phenomenon where increasing pump strength leads to a decoupling of Ca 2+ release sites and subsequently to vanishing [ Ca 2 + ] i spikes.}, + copyright = {http://creativecommons.org/licenses/by/3.0/}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Komin2015.pdf} +} + +@article{Kubanek2016, + title = {Ultrasound Modulates Ion Channel Currents}, + author = {Kubanek, Jan and Shi, Jingyi and Marsh, Jon and Chen, Di and Deng, Cheri and Cui, Jianmin}, + year = {2016}, + month = apr, + journal = {Scientific Reports}, + volume = {6}, + number = {1}, + pages = {24170}, + issn = {2045-2322}, + doi = {10.1038/srep24170}, + urldate = {2024-02-19}, + abstract = {Abstract Transcranial focused ultrasound (US) has been demonstrated to stimulate neurons in animals and humans, but the mechanism of this effect is unknown. It has been hypothesized that US, a mechanical stimulus, may mediate cellular discharge by activating mechanosensitive ion channels embedded within cellular membranes. To test this hypothesis, we expressed potassium and sodium mechanosensitive ion channels (channels of the two-pore-domain potassium family (K2P) including TREK-1, TREK-2, TRAAK; Na V 1.5) in the Xenopus oocyte system. Focused US (10\,MHz, 0.3--4.9\,W/cm 2 ) modulated the currents flowing through the ion channels on average by up to 23\%, depending on channel and stimulus intensity. The effects were reversible upon repeated stimulation and were abolished when a channel blocker (ranolazine to block Na V 1.5, BaCl 2 to block K2P channels) was applied to the solution. These data reveal at the single cell level that focused US modulates the activity of specific ion channels to mediate transmembrane currents. These findings open doors to investigations of the effects of US on ion channels expressed in neurons, retinal cells, or cardiac cells, which may lead to important medical applications. The findings may also pave the way to the development of sonogenetics: a non-invasive, US-based analogue of optogenetics.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Kubanek2016.pdf} +} + +@article{Kuhn2010, + title = {Deep Brain Stimulation for Psychiatric Disorders}, + author = {Kuhn, Jens and Gr{\"u}ndler, Theo O J and Lenartz, Doris and Sturm, Volker and Klosterk{\"o}tter, Joachim and Huff, Wolfgang}, + year = {2010}, + month = feb, + journal = {Deutsches Arzteblatt international}, + volume = {107}, + number = {7}, + pages = {105--113}, + issn = {1866-0452}, + doi = {10.3238/arztebl.2010.0105}, + abstract = {BACKGROUND: Deep brain stimulation (DBS), an established treatment for some movement disorders, is now being used experimentally to treat psychiatric disorders as well. In a number of recently published case series, DBS yielded an impressive therapeutic benefit in patients with medically intractable psychiatric diseases. METHODS: This review of the use of DBS to treat psychiatric disorders is based on literature retrieved from a selective Pubmed search for relevant keywords, reference works on the topic, and the authors' own research. RESULTS: Studies have been performed on the use of DBS to treat medically intractable obsessive-compulsive disorder, depressive disorders, and Tourette syndrome. The case numbers in the cited publications were small, yet at least some of them involved a methodologically sound investigation. Thus, in some studies, the strength of the effect was controlled with a double-blinded interval in which the stimulation was turned off. In general, the primary symptoms were found to improve markedly, by 35\% to 70\%, although not all patients responded to the treatment. Adverse effects of DBS were very rare in most studies and could usually be reversed by changing the stimulation parameters. CONCLUSIONS: The results of DBS for psychiatric disorders that have been published to date are encouraging. They open up a new perspective in the treatment of otherwise intractable disorders. Nonetheless, the efficacy, mechanism of action, and adverse effects of DBS for this indication still need to be further studied in methodologically adequate trials that meet the highest ethical standard.}, + pmid = {20221269}, + keywords = {Biomedical Research/*trends,Deep Brain Stimulation/*adverse effects/*trends,Humans,Mental Disorders/*prevention & control,Nervous System Diseases/*etiology/*prevention & control} +} + +@article{Kumon2009, + title = {Spatiotemporal {{Effects}} of {{Sonoporation Measured}} by {{Real-Time Calcium Imaging}}}, + author = {Kumon, R. E. and Aehle, M. and Sabens, D. and Parikh, P. and Han, Y. W. and Kourennyi, D. and Deng, C. X.}, + year = {2009}, + month = mar, + journal = {Ultrasound in medicine \& biology}, + volume = {35}, + number = {3}, + pages = {494--506}, + issn = {0301-5629}, + doi = {10.1016/j.ultrasmedbio.2008.09.003}, + urldate = {2021-09-04}, + abstract = {To investigate the effects of sonoporation, spatiotemporal evolution of ultrasound-induced changes in intracellular calcium ion concentration ([Ca2+]i) was determined using real time fura-2AM fluorescence imaging. Monolayers of Chinese hamster ovary (CHO) cells were exposed to 1-MHz ultrasound tone burst (0.2 s, 0.45 MPa) in the presence of Optison™ microbubbles. At extracellular [Ca2+]o of 0.9 mM, ultrasound application generated both non-oscillating and oscillating (periods 12--30 s) transients (changes of [Ca2+]i in time) with durations of 100--180 s. Immediate [Ca2+]i transients after ultrasound application were induced by ultrasound-mediated microbubble--cell interactions. In some cases, the immediately-affected cells did not return to pre-ultrasound equilibrium [Ca2+]i levels, thereby indicating irreversible membrane damage. Spatial evolution of [Ca2+]i in different cells formed a calcium wave and was observed to propagate outward from the immediately-affected cells at 7--20 {$\mu$}m/s over a distance greater than 200 {$\mu$}m, causing delayed transients in cells to occur sometimes 60 s or more after ultrasound application. In calcium-free solution, ultrasound-affected cells did not recover, consistent with the requirement of extracellular Ca2+ for cell membrane recovery subsequent to sonoporation. In summary, ultrasound application in the presence of Optison™ microbubbles can generate transient [Ca2+]i changes and oscillations at a focal site and in surrounding cells via calcium waves that last longer than the ultrasound duration and spread beyond the focal site. These results demonstrate the complexity of downstream effects of sonoporation beyond the initial pore formation and subsequent diffusion-related transport through the cellular membrane.}, + pmcid = {PMC2670760}, + pmid = {19010589}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Kumon2009.pdf} +} + +@article{Lachenmayer2021, + title = {Subthalamic and Pallidal Deep Brain Stimulation for {{Parkinson}}'s Disease-Meta-Analysis of Outcomes.}, + author = {Lachenmayer, M. Lenard and M{\"u}rset, Melina and {Nicolas Antih} and Debove, Ines and Muellner, Julia and {Ma{\"e}lys Bompart} and Schlaeppi, Janine-Ai and Nowacki, Andreas and {Hana You} and Michelis, Joan Philipp and Dransart, Alain and Pollo, Claudio and Deuschl, G{\"u}nther and Deuschl, Guenther and Krack, Paul}, + year = {2021}, + month = sep, + journal = {npj Parkinson's disease}, + volume = {7}, + number = {1}, + pages = {77}, + doi = {10.1038/s41531-021-00223-5}, + abstract = {Although deep brain stimulation (DBS) of the globus pallidus internus (GPi) and the subthalamic nucleus (STN) has become an established treatment for Parkinson's disease (PD), a recent meta-analysis of outcomes is lacking. To address this gap, we performed a meta-analysis of bilateral STN- and GPi-DBS studies published from 1990-08/2019. Studies with {$\geq$}10 subjects reporting Unified Parkinson's Disease Rating Scale (UPDRS) III motor scores at baseline and 6--12 months follow-up were included. Several outcome variables were analyzed and adverse events (AE) were summarized. 39 STN studies (2035 subjects) and 5 GPi studies (292 subjects) were eligible. UPDRS-II score after surgery in the stimulation-ON/medication-OFF state compared to preoperative medication-OFF state improved by 47\% with STN-DBS and 18.5\% with GPi-DBS. UPDRS-III score improved by 50.5\% with STN-DBS and 29.8\% with GPi-DBS. STN-DBS improved dyskinesia by 64\%, daily OFF time by 69.1\%, and quality of life measured by PDQ-39 by 22.2\%, while Levodopa Equivalent Daily Dose (LEDD) was reduced by 50.0\%. For GPi-DBS information regarding dyskinesia, OFF time, PDQ-39 and LEDD was insufficient for further analysis. Correlation analysis showed that preoperative L-dopa responsiveness was highly predictive of the STN-DBS motor outcome across all studies. Most common surgery-related AE were infection (5.1\%) and intracranial hemorrhage (3.1\%). Despite a series of technological advances, outcomes of modern surgery are still comparable with those of the early days of DBS. Recent changes in target selection with a preference of GPi in elderly patients with cognitive deficits and more psychiatric comorbidities require more published data for validation.}, + pmcid = {8421387}, + pmid = {34489472}, + annotation = {MAG ID: 3197794658}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lachenmayer2021.pdf} +} + +@article{Lakhssassi2010, + title = {Modifed Pennes' Equation Modelling Bio-Heat Transfer in Living Tissues: Analytical and Numerical Analysis}, + shorttitle = {Modifed Pennes' Equation Modelling Bio-Heat Transfer in Living Tissues}, + author = {Lakhssassi, Ahmed and Kengne, Emmanuel and Semmaoui, Hicham}, + year = {2010}, + journal = {Natural Science}, + volume = {02}, + number = {12}, + pages = {1375--1385}, + issn = {2150-4091, 2150-4105}, + doi = {10.4236/ns.2010.212168}, + urldate = {2024-03-11}, + abstract = {Based on modified version of the Pennes' bio-heat transfer equation, a simplified onedimensional bio-heat transfer model of the living tissues in the steady state has been applied on whole body heat transfer studies, and by using the Weierstrass' elliptic function, its corresponding analytic periodic and non-periodic solutions have been derived in this paper. Using the obtained analytic solutions, the effects of the thermal diffusivity, the temperature-independent perfusion component, and the temperature-dependent perfusion component in living tissues are analyzed numerically. The results show that the derived analytic solution is useful to easily and accurately study the thermal behavior of the biological system, and can be extended to applications such as parameter measurement, temperature field reconstruction and clinical treatment.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lakhssassi2010.pdf} +} + +@article{Lallouette, + title = {{Mod{\'e}lisation des r{\'e}ponses calciques de r{\'e}seaux d'astrocytes: Relations entre topologie et dynamiques}}, + author = {Lallouette, Jules}, + langid = {french}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lallouette.pdf} +} + +@incollection{Lallouette2013, + title = {Topology {{Drives Calcium Wave Propagation}} in {{3D Astrocyte Networks}}}, + booktitle = {Proceedings of the {{European Conference}} on {{Complex Systems}} 2012}, + author = {Lallouette, Jules and Berry, Hugues}, + editor = {Gilbert, Thomas and Kirkilionis, Markus and Nicolis, Gregoire}, + year = {2013}, + pages = {453--463}, + publisher = {Springer International Publishing}, + address = {Cham}, + doi = {10.1007/978-3-319-00395-5_56}, + urldate = {2023-05-11}, + abstract = {Glial cells are non-neuronal cells that constitute the majority of cells in the human brain and significantly modulate information processing via permanent cross-talk with the neurons. Astrocytes are also themselves inter-connected as networks and communicate via chemical wave propagation. How astrocyte wave propagation depends on the local properties of the astrocyte networks is however unknown. In the present work, we investigate the influence of the characteristics of the network topology on wave propagation. Using a model of realistic astrocyte networks ({$>$}1000 cells embedded in a 3D space), we show that the major classes of propagations reported experimentally can be emulated by a mere variation of the topology. Our study indicates that calcium wave propagation is favored when astrocyte connections are limited by the distance between the cells, which means that propagation is better when the mean-shortest path of the network is larger. This unusual property sheds new light on consistent reports that astrocytes in vivo tend to restrict their connections to their nearest neighbors.}, + isbn = {978-3-319-00394-8 978-3-319-00395-5}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lallouette2013.pdf} +} + +@article{Lalonde1995, + title = {Variable Frequency Field Conjugate Lenses for Ultrasound Hyperthermia}, + author = {Lalonde, R. and Hunt, J.W.}, + year = {1995}, + month = sep, + journal = {IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control}, + volume = {42}, + number = {5}, + pages = {825--831}, + issn = {0885-3010}, + doi = {10.1109/58.464838}, + urldate = {2024-02-15}, + abstract = {This paper describes variable frequency focusing with field conjugate lenses designed to mimic the multiplefocusing capabilities of large two-dimensional phased arrays. Simulations, experiments, and Fresnel diffraction analysis are used to show that both the size and the depth of a field conjugate lens focus may vary with frequency. Examples are given for field conjugate lens focusing with planar transducers, focused transducers, and ordinary refracting lenses.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lalonde1995.pdf} +} + +@article{Laloy-Borgna, + title = {Magnetic Micro-Elastography for Evaluation of Ultrasound-Induced Softening of Pancreatic Cancer Spheroids}, + author = {{Laloy-Borgna}, G and Vovard, L and Rohfritsch, A and Wang, L and Ngo, J and Perier, M and Drainville, A and Prat, F and Lafond, M and Lafon, C and Catheline, S}, + abstract = {Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with very low survival rates 5 years after diagnosis. The main reason for this dismal prognosis is the thick stroma which both protects tumor cells from drug penetration and supports tumor development. Ultrasound inertial cavitation is a promising treatment with a potential for stromal disruption, enhancing tumor cells sensitivity to chemical agents and biomodulators. Our goal was to develop a dedicated micro-elastography setup allowing to measure the elasticity of in vitro tumor models called spheroids. In a second step, the impact of cavitation treatment on their mechanical properties was assessed. A transcranial magnetic stimulation (TMS) clinical device was used to induce shear waves in the spheroids containing magnetic nanoparticles. Using an inverted optical microscope, Particle Imaging Velocimetry (PIV) and noise correlation algorithms, the shear wave velocity, indicative of the medium's elasticity, could be measured. Shear waves generated by the magnetic pulse inside the spheroids were detected and their velocity was measured using noise correlation elastography. This allowed to estimate the spheroids elasticity. Cavitation treatment softened them significantly, the impact of the exposure conditions and the spheroids composition have been studied. In the future, such a method could be used to monitor cavitation treatments. In addition, since it is now well established that mechanical constraints and elasticity play an important role in tumor growth, it is of high interest to measure the elasticity of tumor models to better understand the mechanisms of tumor growth.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Laloy-Borgna.pdf} +} + +@article{Laloy-Borgna2023, + title = {Observation of Natural Flexural Pulse Waves in Retinal and Carotid Arteries for Wall Elasticity Estimation}, + author = {{Laloy-Borgna}, Gabrielle and Puyo, L{\'e}o and Nishino, Hidero and Atlan, Michael and Catheline, Stefan}, + year = {2023}, + month = jun, + journal = {Science Advances}, + volume = {9}, + number = {25}, + pages = {eadf1783}, + issn = {2375-2548}, + doi = {10.1126/sciadv.adf1783}, + urldate = {2023-06-24}, + abstract = {The risk of cardiovascular events is linked to arterial elasticity that can be estimated from the pulse wave velocity. This symmetric wave velocity is related to the wall elasticity through the Moens-Korteweg equation. However, ultrasound imaging techniques need improved accuracy, and optical measurements on retinal arteries produce inconsistent results. Here, we report the first observation of an antisymmetric pulse wave: the flexural pulse wave. An optical system performs in vivo wave velocity measurements on retinal arteries and veins. Velocity estimation ranges between 1 and 10 millimeter per second. The theory of guided waves confirms the existence of this wave mode and its low velocity. Natural flexural waves can also be detected at the bigger scale of a carotid artery using ultrafast ultrasound imaging. This second natural pulse wave has great potential of becoming a biomarker of blood vessel aging. , A ``second'' natural pulse wave that could become a biomarker of cardiovascular health has been found.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Laloy-Borgna2023.pdf} +} + +@phdthesis{Laloy-Borgna2023a, + title = {{Micro-{\'e}lastographie: caract{\'e}risation m{\'e}canique de la cellule par ondes {\'e}lastiques}}, + author = {{Laloy-Borgna}, Gabrielle}, + year = {2023}, + langid = {french}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Laloy-Borgna2023a.pdf} +} + +@article{Le2016, + title = {Reflections on the {{Notion}} of {{Culture}} in the {{History}} of {{Mathematics}}: {{The Example}} of ``{{Geometrical Equations}}''}, + shorttitle = {Reflections on the {{Notion}} of {{Culture}} in the {{History}} of {{Mathematics}}}, + author = {L{\^e}, Fran{\c c}ois}, + year = {2016}, + month = sep, + journal = {Science in Context}, + volume = {29}, + number = {3}, + pages = {273--304}, + issn = {0269-8897, 1474-0664}, + doi = {10.1017/S0269889716000089}, + urldate = {2024-04-17}, + abstract = {Argument This paper challenges the use of the notion of ``culture'' to describe a particular organization of mathematical knowledge, shared by a few mathematicians over a short period of time in the second half of the nineteenth century. This knowledge relates to ``geometrical equations,'' objects that proved crucial for the mechanisms of encounters between equation theory, substitution theory, and geometry at that time, although they were not well-defined mathematical objects. The description of the mathematical collective activities linked to ``geometrical equations,'' and especially the technical aspects of these activities, is made on the basis of a sociological definition of ``culture.'' More precisely, after an examination of the social organization of the group of mathematicians, I argue that these activities form an intricate system of patterns, symbols, and values, for which I suggest a characterization as a ``cultural system.''}, + copyright = {https://www.cambridge.org/core/terms}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Le2016.pdf} +} + +@misc{learning, + title = {Cell --- {{Structure}} and {{Functions}}}, + author = {{learning}, Lido} +} + +@article{Lee2004, + title = {Neurotransmitter Release from High-Frequency Stimulation of the Subthalamic Nucleus}, + author = {Lee, Kendall H. and Chang, Su-Youne and Roberts, David W. and Kim, Uhnoh}, + year = {2004}, + month = sep, + journal = {Journal of Neurosurgery}, + volume = {101}, + number = {3}, + pages = {511--517}, + publisher = {Journal of Neurosurgery Publishing Group}, + doi = {10.3171/jns.2004.101.3.0511}, + urldate = {2023-04-05}, + abstract = {Object. High-frequency stimulation (HFS) delivered through implanted electrodes in the subthalamic nucleus (STN) has become an established treatment for Parkinson disease (PD). The precise mechanism of action of deep brain stimulation (DBS) in the STN is unknown, however. In the present study, the authors tested the hypothesis that HFS within the STN changes neuronal action potential firing rates during the stimulation period by modifying neurotransmitter release. Methods. Intracellular electrophysiological recordings were obtained using sharp electrodes in rat STN neurons in an in vitro slice preparation. A concentric bipolar stimulating electrode was placed in the STN slice, and electrical stimulation (pulse width 50--100 {\textmu}sec, duration 100--2000 {\textmu}sec, amplitude 10--500 {\textmu}A, and frequency 10--200 Hz) was delivered while simultaneously obtaining intracellular recordings from an STN neuron. High-frequency stimulation of the STN either generated excitatory postsynaptic potentials (EPSPs) and increased the action potential frequency or it generated inhibitory postsynaptic potentials and decreased the action potential frequency of neurons within the STN. These effects were blocked after antagonists to glutamate and {$\gamma$}-aminobutyric acid were applied to the tissue slice, indicating that HFS resulted in the release of neurotransmitters. Intracellular recordings from substantia nigra pars compacta (SNc) dopaminergic neurons during HFS of the STN revealed increased generation of EPSPs and increased frequency of action potentials in SNc neurons. Conclusions. During HFS of STN neurons the mechanism of DBS may involve the release of neurotransmitters rather than the primary electrogenic inhibition of neurons.}, + chapter = {Journal of Neurosurgery}, + langid = {american}, + keywords = {To Read}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lee2004.pdf} +} + +@article{Lee2005, + title = {Effects of {{Temperature}} on {{Calcium Transients}} and {{Ca}} {\textsuperscript{2+}} -{{Dependent Afterhyperpolarizations}} in {{Neocortical Pyramidal Neurons}}}, + author = {Lee, J. C. F. and Callaway, J. C. and Foehring, R. C.}, + year = {2005}, + month = apr, + journal = {Journal of Neurophysiology}, + volume = {93}, + number = {4}, + pages = {2012--2020}, + issn = {0022-3077, 1522-1598}, + doi = {10.1152/jn.01017.2004}, + urldate = {2023-08-11}, + abstract = {In neocortical pyramidal neurons, the medium (mAHP) and slow AHP (sAHP) have different relationships with intracellular [Ca 2+ ]. To further explore these differences, we varied bath temperature and compared passive and active membrane properties and Ca 2+ transients in response to a single action potential (AP) or trains of APs. We tested whether Ca 2+ -dependent events are more temperature sensitive than voltage-dependent ones, the slow rise time of the sAHP is limited by diffusion, and temperature sensitivity differs between the mAHP and sAHP. The onset and decay kinetics of the sAHP were very temperature sensitive (more so than diffusion). We found that the decay time course of Ca 2+ transients was also very temperature sensitive. In contrast, the mAHP (amplitude, time to peak, and exponential decay) and sAHP peak amplitude were moderately sensitive to temperature. The amplitudes of intracellular Ca 2+ transients evoked either by a single spike or a train of spikes showed modest temperature sensitivities. Pyramidal neuron input resistance was increased by cooling. With the exception of threshold, which remained unchanged between 22 and 35{$^\circ$}C, action potential parameters (amplitude, half-width, maximum rates of rise and fall) were modestly affected by temperature. Collectively, these data suggest that temperature sensitivity was higher for the Ca 2+ -dependent sAHP than for voltage-dependent AP parameters or for the mAHP, diffusion of Ca 2+ over distance cannot explain the slow rise of the sAHP in these cells, and the kinetics of the sAHP and mAHP are affected differently by temperature.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lee2005.pdf} +} + +@article{Lee2018, + title = {Transcranial Focused Ultrasound Stimulation of Motor Cortical Areas in Freely-Moving Awake Rats}, + author = {Lee, Wonhye and Croce, Phillip and Margolin, Ryan W. and Cammalleri, Amanda and Yoon, Kyungho and Yoo, Seung-Schik}, + year = {2018}, + month = dec, + journal = {BMC Neuroscience}, + volume = {19}, + number = {1}, + pages = {57}, + issn = {1471-2202}, + doi = {10.1186/s12868-018-0459-3}, + urldate = {2022-04-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lee2018.pdf} +} + +@article{Lee2022, + title = {Function and Therapeutic Value of Astrocytes in Neurological Diseases}, + author = {Lee, Hong-Gyun and Wheeler, Michael A. and Quintana, Francisco J.}, + year = {2022}, + month = may, + journal = {Nature Reviews Drug Discovery}, + volume = {21}, + number = {5}, + pages = {339--358}, + issn = {1474-1776, 1474-1784}, + doi = {10.1038/s41573-022-00390-x}, + urldate = {2024-03-25}, + abstract = {Astrocytes are abundant glial cells in the central nervous system (CNS) that perform diverse functions in health and disease. Astrocyte dysfunction is found in numerous diseases, including multiple sclerosis, Alzheimer disease, Parkinson disease, Huntington disease and neuropsychiatric disorders. Astrocytes regulate glutamate and ion homeostasis, cholesterol and sphingolipid metabolism and respond to environmental factors, all of which have been implicated in neurological diseases. Astrocytes also exhibit significant heterogeneity, driven by developmental programmes and stimulus-specific cellular responses controlled by CNS location, cell--cell interactions and other mechanisms. In this Review, we highlight general mechanisms of astrocyte regulation and their potential as therapeutic targets, including drugs that alter astrocyte metabolism, and therapies that target transporters and receptors on astrocytes. Emerging ideas, such as engineered probiotics and glia-to-neuron conversion therapies, are also discussed. We further propose a concise nomenclature for astrocyte subsets that we use to highlight the roles of astrocytes and specific subsets in neurological diseases.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lee2022.pdf} +} + +@article{Lee2023, + title = {Ultrasonocoverslip: {{In-vitro}} Platform for High-Throughput Assay of Cell Type-Specific Neuromodulation with Ultra-Low-Intensity Ultrasound Stimulation}, + shorttitle = {Ultrasonocoverslip}, + author = {Lee, Keunhyung and Lee, Jung Moo and Phan, Tien Thuy and Lee, C. Justin and Park, Joo Min and Park, Jinhyoung}, + year = {2023}, + month = aug, + journal = {Brain Stimulation}, + pages = {S1935861X23018740}, + issn = {1935861X}, + doi = {10.1016/j.brs.2023.08.002}, + urldate = {2023-08-30}, + abstract = {Brain stimulation with ultra-low-intensity ultrasound has rarely been investigated due to the lack of a reliable device to measure small neuronal signal changes made by the ultra-low intensity range. We propose Ultra\- sonocoverslip, an ultrasound-transducer-integrated-glass-coverslip that determines the minimum intensity for brain cell activation. Brain cells can be cultured directly on Ultrasonocoverslip to simultaneously deliver uniform ultrasonic pressure to hundreds of cells with real-time monitoring of cellular responses using fluorescence mi\- croscopy and single-cell electrophysiology. The sensitivity for detecting small responses to ultra-low-intensity ultrasound can be improved by averaging simultaneously obtained responses. Acoustic absorbers can be placed under Ultrasonocoverslip, and stimuli distortions are substantially reduced to precisely deliver userintended acoustic stimulations. With the proposed device, we discover the lowest acoustic threshold to induce reliable neuronal excitation releasing glutamate. Furthermore, mechanistic studies on the device show that the ultra-low-intensity ultrasound stimulation induces cell type-specific neuromodulation by activating astrocytemediated neuronal excitation without direct neuronal involvement. The performance of ultra-low-intensity stimulation is validated by in vivo experiments demonstrating improved safety and specificity in motor modu\- lation of tail movement compared to that with supra-watt-intensity.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lee2023.pdf} +} + +@article{Lefebvre2021, + title = {Automated Segmentation and Tracking of Mitochondria in Live-Cell Time-Lapse Images}, + author = {Lefebvre, Austin E. Y. T. and Ma, Dennis and Kessenbrock, Kai and Lawson, Devon A. and Digman, Michelle A.}, + year = {2021}, + month = sep, + journal = {Nature Methods}, + volume = {18}, + number = {9}, + pages = {1091--1102}, + issn = {1548-7091, 1548-7105}, + doi = {10.1038/s41592-021-01234-z}, + urldate = {2022-04-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lefebvre2021.pdf} +} + +@book{Leighton1994, + title = {The Acoustic Bubble}, + author = {Leighton, T. G.}, + year = {1994}, + publisher = {Academic press}, + address = {London San Diego New York [etc.]}, + isbn = {978-0-12-441920-9}, + langid = {english}, + lccn = {534.2}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Leighton1994.pdf} +} + +@article{Leinenga2016, + title = {Ultrasound Treatment of Neurological Diseases --- Current and Emerging Applications}, + author = {Leinenga, Gerhard and Langton, Christian and Nisbet, Rebecca and G{\"o}tz, J{\"u}rgen}, + year = {2016}, + month = feb, + journal = {Nature Reviews Neurology}, + volume = {12}, + number = {3}, + pages = {161--174}, + publisher = {{Springer Science and Business Media LLC}}, + doi = {10.1038/nrneurol.2016.13}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Leinenga2016.pdf} +} + +@article{Leisengang2018, + title = {Effects of Thermal Stimulation on Neurons and Astrocytes Cultured from the Rat Median Preoptic Nucleus}, + author = {Leisengang, Stephan and Ott, Daniela and Gerstberger, R{\"u}diger and Rummel, Christoph and Roth, Joachim}, + year = {2018}, + month = dec, + journal = {NeuroReport}, + volume = {29}, + number = {17}, + pages = {1468--1472}, + issn = {0959-4965}, + doi = {10.1097/WNR.0000000000001134}, + urldate = {2024-07-10}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Leisengang2018.pdf} +} + +@article{Lemaire, + title = {A Modeling Framework to Understand and Optimize Ultrasound Neuromodulation}, + author = {Lemaire, Th{\'e}o}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lemaire.pdf} +} + +@article{Lemaire2021, + title = {{{MorphoSONIC}}: {{A}} Morphologically Structured Intramembrane Cavitation Model Reveals Fiber-Specific Neuromodulation by Ultrasound}, + shorttitle = {{{MorphoSONIC}}}, + author = {Lemaire, Th{\'e}o and Vicari, Elena and Neufeld, Esra and Kuster, Niels and Micera, Silvestro}, + year = {2021}, + month = sep, + journal = {iScience}, + volume = {24}, + number = {9}, + pages = {103085}, + issn = {25890042}, + doi = {10.1016/j.isci.2021.103085}, + urldate = {2024-03-20}, + abstract = {Low-Intensity Focused Ultrasound Stimulation (LIFUS) holds promise for the remote modulation of neural activity, but an incomplete mechanistic characterization hinders its clinical maturation. Here we developed a computational framework to model intramembrane cavitation (a candidate mechanism) in multi-compartment, morphologically structured neuron models, and used it to investigate ultrasound neuromodulation of peripheral nerves. We predict that by engaging membrane mechanoelectrical coupling, LIFUS exploits fiber-specific differences in membrane conductance and capacitance to selectively recruit myelinated and/or unmyelinated axons in distinct parametric subspaces, allowing to modulate their activity concurrently and independently over physiologically relevant spiking frequency ranges. These theoretical results consistently explain recent empirical findings and suggest that LIFUS can simultaneously, yet selectively, engage different neural pathways, opening up opportunities for peripheral neuromodulation currently not addressable by electrical stimulation. More generally, our framework is readily applicable to other neural targets to establish application-specific LIFUS protocols.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lemaire2021.pdf} +} + +@article{Lesslich2022, + title = {Adjusting the Neuron to Astrocyte Ratio with Cytostatics in Hippocampal Cell Cultures from Postnatal Rats: {{A}} Comparison of Cytarabino Furanoside ({{AraC}}) and 5-Fluoro-2'-Deoxyuridine ({{FUdR}})}, + shorttitle = {Adjusting the Neuron to Astrocyte Ratio with Cytostatics in Hippocampal Cell Cultures from Postnatal Rats}, + author = {Lesslich, Heiko M. and Klapal, Lars and Wilke, Justus and Haak, Annika and Dietzel, Irmgard D.}, + editor = {Mongin, Alexander A.}, + year = {2022}, + month = mar, + journal = {PLOS ONE}, + volume = {17}, + number = {3}, + pages = {e0265084}, + issn = {1932-6203}, + doi = {10.1371/journal.pone.0265084}, + urldate = {2023-07-21}, + abstract = {Cell culture studies offer the unique possibility to investigate the influence of pharmacological treatments with quantified dosages applied for defined time durations on survival, morphological maturation, protein expression and function as well as the mutual interaction of various cell types. Cultures obtained from postnatal rat brain contain a substantial number of glial cells that further proliferate with time in culture leading to an overgrowth of neurons with glia, especially astrocytes and microglia. A well-established method to decrease glial proliferation in vitro is to apply low concentrations of cytosine arabinoside (AraC). While AraC primarily effects dividing cells, it has been reported repeatedly that it is also neurotoxic, which is the reason why most protocols limit its application to concentrations of up to 5 {$\mu$}M for a duration of 24 h. Here, we investigated 5-fluoro-2'-deoxyuridine (FUdR) as a possible substitute for AraC. We applied concentrations of both cytostatics ranging from 4 {$\mu$}M to 75 {$\mu$}M and compared cell composition and cell viability in cultures prepared from 0-2- and 3-4-day old rat pups. Using FUdR as proliferation inhibitor, higher ratios of neurons to glia cells were obtained with a maximal neuron to astrocyte ratio of up to 10:1, which could not be obtained using AraC in postnatal cultures. Patch-clamp recordings revealed no difference in the amplitudes of voltage-gated Na+ currents in neurons treated with FUdR compared with untreated control cells suggesting replacement of AraC by FUdR as glia proliferation inhibitor if highly neuron-enriched postnatal cultures are desired.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lesslich2022.pdf} +} + +@article{Li2013, + title = {{{AtlasGuide}}: {{Software}} for Stereotaxic Guidance Using {{3D CT}}/{{MRI}} Hybrid Atlases of Developing Mouse Brains}, + shorttitle = {{{AtlasGuide}}}, + author = {Li, Xin and Aggarwal, Manisha and Hsu, Johnny and Jiang, Hangyi and Mori, Susumu}, + year = {2013}, + month = oct, + journal = {Journal of Neuroscience Methods}, + volume = {220}, + number = {1}, + pages = {75--84}, + issn = {01650270}, + doi = {10.1016/j.jneumeth.2013.08.017}, + urldate = {2025-01-08}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Li2013.pdf} +} + +@book{Li2014, + title = {Functional {{Magnetic Resonance Imaging Processing}}}, + author = {Li, Xingfeng}, + year = {2014}, + edition = {1st ed. 2014}, + publisher = {Springer Netherlands : Imprint: Springer}, + address = {Dordrecht}, + doi = {10.1007/978-94-007-7302-8}, + abstract = {With strong numerical and computational focus, this book serves as an essential resource on the methods for functional neuroimaging analysis, diffusion weighted image analysis, and longitudinal VBM analysis. It includes four MRI image modalities analysis methods. The first covers the PWI methods, which is the basis for understanding cerebral flow in human brain. The second part, the book's core, covers MRI methods in three specific domains: first level analysis, second level analysis, and effective connectivity study. The third part covers the analysis of Diffusion weighted image, id est DTI, QBI and DSI image analysis. Finally, the book covers (longitudinal) VBM methods and its application to Alzheimer's disease study}, + isbn = {978-94-007-7302-8}, + lccn = {612.8}, + keywords = {Cognitive psychology,Cognitive Psychology,Computer Imaging Vision Pattern Recognition and Graphics,Imaging / Radiology,Neurosciences,Numerical and Computational Physics Simulation,Optical data processing,Physics,Radiology,Statistics,Statistics and Computing/Statistics Programs} +} + +@article{Li2014a, + title = {{{NeuroArray}}: {{A Universal Interface}} for {{Patterning}} and {{Interrogating Neural Circuitry}} with {{Single Cell Resolution}}}, + shorttitle = {{{NeuroArray}}}, + author = {Li, Wei and Xu, Zhen and Huang, Junzhe and Lin, Xudong and Luo, Rongcong and Chen, Chia-Hung and Shi, Peng}, + year = {2014}, + month = apr, + journal = {Scientific Reports}, + volume = {4}, + number = {1}, + pages = {4784}, + issn = {2045-2322}, + doi = {10.1038/srep04784}, + urldate = {2023-01-18}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Li2014a.pdf} +} + +@book{Li2014b, + title = {Functional {{Magnetic Resonance Imaging Processing}}}, + author = {Li, Xingfeng}, + year = {2014}, + publisher = {Springer Netherlands}, + address = {Dordrecht}, + doi = {10.1007/978-94-007-7302-8}, + urldate = {2023-03-14}, + isbn = {978-94-007-7301-1 978-94-007-7302-8}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Li2014b.pdf} +} + +@article{Li2016, + title = {Improved {{Anatomical Specificity}} of {{Non-invasive Neuro-stimulation}} by {{High Frequency}} (5 {{MHz}}) {{Ultrasound}}}, + author = {Li, Guo-Feng and Zhao, Hui-Xia and Zhou, Hui and Yan, Fei and Wang, Jing-Yao and Xu, Chang-Xi and Wang, Cong-Zhi and Niu, Li-Li and Meng, Long and Wu, Song and Zhang, Huai-Ling and Qiu, Wei-Bao and Zheng, Hai-Rong}, + year = {2016}, + month = apr, + journal = {Scientific Reports}, + volume = {6}, + number = {1}, + pages = {24738}, + issn = {2045-2322}, + doi = {10.1038/srep24738}, + urldate = {2023-10-20}, + abstract = {Abstract Low frequency ultrasound ({$<$}1\,MHz) has been demonstrated to be a promising approach for non-invasive neuro-stimulation. However, the focal width is limited to be half centimeter scale. Minimizing the stimulation region with higher frequency ultrasound will provide a great opportunity to expand its application. This study first time examines the feasibility of using high frequency (5\,MHz) ultrasound to achieve neuro-stimulation in brain and verifies the anatomical specificity of neuro-stimulation in vivo . 1\,MHz and 5\,MHz ultrasound stimulation were evaluated in the same group of mice. Electromyography (EMG) collected from tail muscles together with the motion response videos were analyzed for evaluating the stimulation effects. Our results indicate that 5\,MHz ultrasound can successfully achieve neuro-stimulation. The equivalent diameter (ED) of the stimulation region with 5\,MHz ultrasound (0.29\,{\textpm}\,0.08\,mm) is significantly smaller than that with 1\,MHz (0.83\,{\textpm}\,0.11\,mm). The response latency of 5\,MHz ultrasound (45\,{\textpm}\,31\,ms) is also shorter than that of 1\,MHz ultrasound (208\,{\textpm}\,111\,ms). Consequently, high frequency (5\,MHz) ultrasound can successfully activate the brain circuits in mice. It provides a smaller stimulation region, which offers improved anatomical specificity for neuro-stimulation in a non-invasive manner.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Li2016.pdf} +} + +@article{Li2018, + title = {Dynamics and Mechanisms of Intracellular Calcium Waves Elicited by Tandem Bubble-Induced Jetting Flow}, + author = {Li, Fenfang and Yang, Chen and Yuan, Fang and Liao, Defei and Li, Thomas and Guilak, Farshid and Zhong, Pei}, + year = {2018}, + month = jan, + journal = {Proceedings of the National Academy of Sciences}, + volume = {115}, + number = {3}, + issn = {0027-8424, 1091-6490}, + doi = {10.1073/pnas.1713905115}, + urldate = {2022-06-08}, + abstract = {Significance Ultrasound-induced microbubble oscillation can lead to cell injury or mechanotransduction via calcium signaling processes such as intracellular calcium waves (ICWs). However, the mechanisms by which microbubbles stimulate ICWs remain unknown. Using a microfluidic system with highly controlled bubble-cell interaction, we identified two distinct types of ICWs: a fast response correlating with significant membrane poration, and a slow response triggered by calcium influx through stretch-activated ion channels. The fast ICWs, distinguished from those under physiological conditions, are associated with cell injuries. We further elicited ICWs without cell injury by displacing integrin-binding beads on the cell membrane under mild cavitation conditions. This study provides mechanistic insights into ICWs for guiding ultrasound therapy in tissue modification, drug delivery, and cell mechanotransduction. , One of the earliest events in cellular mechanotransduction is often an increase in intracellular calcium concentration associated with intracellular calcium waves (ICWs) in various physiologic or pathophysiologic processes. Although cavitation-induced calcium responses are believed to be important for modulating downstream bioeffects such as cell injury and mechanotransduction in ultrasound therapy, the fundamental mechanisms of these responses have not been elucidated. In this study, we investigated mechanistically the ICWs elicited in single HeLa cells by the tandem bubble-induced jetting flow in a microfluidic system. We identified two distinct (fast and slow) types of ICWs at varying degrees of flow shear stress-induced membrane deformation, as determined by different bubble standoff distances. We showed that ICWs were initiated by an extracellular calcium influx across the cell membrane nearest to the jetting flow, either primarily through poration sites for fast ICWs or opening of mechanosensitive ion channels for slow ICWs, which then propagated in the cytosol via a reaction-diffusion process from the endoplasmic reticulum. The speed of ICW ( C ICW ) was found to correlate strongly with the severity of cell injury, with C ICW in the range of 33 {$\mu$}m/s to 93 {$\mu$}m/s for fast ICWs and 1.4 {$\mu$}m/s to 12 {$\mu$}m/s for slow ICWs. Finally, we demonstrated that micrometer-sized beads attached to the cell membrane integrin could trigger ICWs under mild cavitation conditions without collateral injury. The relation between the characteristics of ICW and cell injury, and potential strategies to mitigate cavitation-induced injury while evoking an intracellular calcium response, may be particularly useful for exploiting ultrasound-stimulated mechanotransduction applications in the future.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Li2018.pdf} +} + +@article{Liao2019, + title = {Activation of {{Piezo1}} Mechanosensitive Ion Channel in {{HEK293T}} Cells by 30 {{MHz}} Vertically Deployed Surface Acoustic Waves}, + author = {Liao, Defei and Li, Fenfang and Lu, David and Zhong, Pei}, + year = {2019}, + month = oct, + journal = {Biochemical and Biophysical Research Communications}, + volume = {518}, + number = {3}, + pages = {541--547}, + issn = {0006291X}, + doi = {10.1016/j.bbrc.2019.08.078}, + urldate = {2022-06-08}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Liao2019.pdf} +} + +@misc{Liberzon2020, + title = {{{OpenPIV}}/Openpiv-Python: {{OpenPIV}} - {{Python}} (v0.22.2) with a New Extended Search {{PIV}} Grid Option}, + author = {Liberzon, Alex and Lasagna, Davide and Aubert, Mathias and Bachant, Pete and K{\"a}ufer, Theo and {Jakirkham} and Bauer, Andreas and Vodenicharski, Boyko and Dallas, Cameron and Borg, Joe and {Tomerast} and {Ranleu}}, + year = {2020}, + publisher = {Zenodo}, + doi = {10.5281/ZENODO.3930343}, + copyright = {Open Access} +} + +@article{Lock2015, + title = {A Comparison of Fluorescent {{Ca2}}+ Indicators for Imaging Local {{Ca2}}+ Signals in Cultured Cells}, + author = {Lock, Jeffrey T. and Parker, Ian and Smith, Ian F.}, + year = {2015}, + month = dec, + journal = {Cell Calcium}, + volume = {58}, + number = {6}, + pages = {638--648}, + issn = {01434160}, + doi = {10.1016/j.ceca.2015.10.003}, + urldate = {2023-03-13}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lock2015.pdf} +} + +@article{Logothetis2004, + title = {On the Nature of the {{BOLD fMRI}} Contrast Mechanism}, + author = {Logothetis, Nikos K. and Pfeuffer, Josef}, + year = {2004}, + month = dec, + journal = {Magnetic Resonance Imaging}, + volume = {22}, + number = {10}, + pages = {1517--1531}, + issn = {0730725X}, + doi = {10.1016/j.mri.2004.10.018}, + urldate = {2022-03-23}, + langid = {english} +} + +@article{Long2008, + title = {Using Temperature to Analyse Temporal Dynamics in the Songbird Motor Pathway}, + author = {Long, Michael A. and Fee, Michale S.}, + year = {2008}, + month = nov, + journal = {Nature}, + volume = {456}, + number = {7219}, + pages = {189--194}, + issn = {0028-0836, 1476-4687}, + doi = {10.1038/nature07448}, + urldate = {2023-08-09}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Long2008.pdf} +} + +@inproceedings{Loree-Spacek2020, + title = {Fabrication and {{Validation}} of an {{Acoustic Reflective Casing}} for {{Neurostimulation Studies}} with {{Microscopy}}}, + booktitle = {2020 {{IEEE International Ultrasonics Symposium}} ({{IUS}})}, + author = {{Loree-Spacek}, Jak and {Swytink-Binnema}, Catherine and Kiss, Zelma and Curiel, Laura and Pichardo, Samuel}, + year = {2020}, + month = sep, + pages = {1--4}, + publisher = {IEEE}, + address = {Las Vegas, NV, USA}, + doi = {10.1109/IUS46767.2020.9251625}, + urldate = {2022-05-27}, + isbn = {978-1-72815-448-0}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Loree-Spacek2020.pdf} +} + +@article{Lozano2013, + title = {Probing and {{Regulating Dysfunctional Circuits Using Deep Brain Stimulation}}}, + author = {Lozano, Andres~M. and Lipsman, Nir}, + year = {2013}, + month = feb, + journal = {Neuron}, + volume = {77}, + number = {3}, + pages = {406--424}, + issn = {08966273}, + doi = {10.1016/j.neuron.2013.01.020}, + urldate = {2023-08-29}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Lozano2013.pdf} +} + +@article{Luca, + title = {Statistical {{Analysis Methods}} for {{Physics Models Verification}} and {{Validation}}}, + author = {Luca, Silvia De and Bandieramonte, Marilena and Pokorski, Witold}, + abstract = {The validation and verification process is a fundamental step for any software like Geant4 and GeantV, which aim to perform data simulation using physics models and Monte Carlo techniques. As experimental physicists, we have to face the problem to compare the results obtained using simulations with what the experiments actually observed. One way to solve the problem is to perform a consistency test. Within the Geant group, we developed a C++ compact library which will be added to the automated validation process on the Geant Validation Portal.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Luca.pdf} +} + +@article{Ma2022, + title = {Mechanical and Medical Imaging Properties of {{3D}}-printed Materials as Tissue Equivalent Materials}, + author = {Ma, Depeng and Gao, Ronghui and Li, Minghui and Qiu, Jianfeng}, + year = {2022}, + month = feb, + journal = {Journal of Applied Clinical Medical Physics}, + volume = {23}, + number = {2}, + pages = {e13495}, + issn = {1526-9914, 1526-9914}, + doi = {10.1002/acm2.13495}, + urldate = {2024-03-07}, + abstract = {Three materials of polylactic acid (PLA), polyamide 12 (PA12), and light curing resin (LCR) were used to construct phantom using 3D printing technology. The mechanical and medical imaging properties of the three materials, such as elastic modulus, density, effective atomic number, X-ray attenuation coefficient, computed tomography (CT) number, and acoustic properties, were investigated. The results showed that the elastic modulus for PLA was 1.98 {\texttimes} 103 MPa, for PA12 was 848 MPa, for LCR was 1.18{\texttimes}103 MPa, and that of three materials was close to some bones.In the range of 40{$\sim$}120 kV,the X-ray attenuation coefficient of three materials decreased with increasing tube voltage. The CT number for PLA, PA12, and LCR was 144, -88, and 312 Hounsfield units at 120 kV tube voltage, respectively. The density and the effective atomic number product ({$\rho$}*Zeff ) were computed from three materials and decreased in the order of LCR, PLA, and PA12. The acoustic properties of materials were also studied. The speeds of sound of three materials were similar with those of some soft tissues.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Ma2022.pdf} +} + +@article{Manbachi2011, + title = {Development and {{Application}} of {{Piezoelectric Materials}} for {{Ultrasound Generation}} and {{Detection}}}, + author = {Manbachi, Amir and Cobbold, Richard S. C.}, + year = {2011}, + month = nov, + journal = {Ultrasound}, + volume = {19}, + number = {4}, + pages = {187--196}, + publisher = {SAGE Publications}, + doi = {10.1258/ult.2011.011027}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Manbachi2011.pdf} +} + +@article{Marangell2007, + title = {Neurostimulation Therapies in Depression: A Review of New Modalities}, + shorttitle = {Neurostimulation Therapies in Depression}, + author = {Marangell, L. B. and Martinez, M. and Jurdi, R. A. and Zboyan, H.}, + year = {2007}, + month = sep, + journal = {Acta Psychiatrica Scandinavica}, + volume = {116}, + number = {3}, + pages = {174--181}, + issn = {0001-690X, 1600-0447}, + doi = {10.1111/j.1600-0447.2007.01033.x}, + urldate = {2023-08-29}, + abstract = {Objective: In response to an increased understanding of the neurobiology of severe psychiatric disorders, new therapeutic modalities are entering clinical practice that involve the direct stimulation of the brain. Method: We provide a review of published literature regarding the clinical use of vagus nerve stimulation (VNS) therapy, transcranial magnetic stimulation (TMS) and deep brain stimulation (DBS) in psychiatric disorders, with an emphasis on treatment-resistant depression (TRD). Results: Vagus nerve stimulation is approved for use in both the EU and US for TRD. TMS has been approved for TRD in Canada, Australia, New Zealand, the European Union and Israel, but not yet in the United States. DBS remains in the early stages of investigation. Conclusion: While additional studies are clearly warranted, treatments that directly stimulate the brain appear to hold great therapeutic promise for severe psychiatric disorders.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Marangell2007.pdf} +} + +@article{Marburg2003, + title = {Performance of Iterative Solvers for Acoustic Problems. {{Part I}}. {{Solvers}} and Effect of Diagonal Preconditioning}, + author = {Marburg, Steffen and Schneider, Stefan}, + year = {2003}, + month = jul, + journal = {Engineering Analysis with Boundary Elements}, + volume = {27}, + number = {7}, + pages = {727--750}, + issn = {09557997}, + doi = {10.1016/S0955-7997(03)00025-0}, + urldate = {2024-09-20}, + abstract = {Boundary element discretization of the Kirchhoff-- Helmholtz integral equation gives rise to a linear system of equations. This system may be solved directly or iteratively. Application of direct solvers is quite common but turns out to be inefficient for large scale problem with 10,000 unknowns and more. These systems can be solved on behalf of iterative methods. This paper is dedicated to testing performance of four iterative solvers being the Restarted Bi-Conjugate Gradient Stabilized algorithm, the Conjugate Gradient method applied to the normal equations (CGNR), the Generalized Minimal Residual (GMRes) and the Transpose Free Quasi Minimal Residual. For that, we distinguish between internal and external problems. Performance of iterative solvers with respect to problem size, polynomial degree of interpolation, wave-number, wave-number over problem size, absorption at surface, and smoothness of the surface is investigated. Furthermore, the effect of diagonal preconditioning is illuminated. All examples consist of different meshes of up to more than 100,000 elements. In general, the methods perform well for the internal problems, a duct problem, a sedan cabin compartment and a fictitious small concert hall. GMRes proves to solve the problems most efficiently. External problems appear more challenging due to the hypersingular operator of the Burton and Miller formulation. Scattering of a plane wave at a sphere and at a cat's eye are investigated as well as a tire noise problem. The first two are remarkably efficiently solved in the medium and high frequency range by CGNR whereas the tire noise example is only solved by GMRes. In all examples, at least one or two solution methods turn out to require less operations than a direct solver. The effect of diagonal preconditioning is marginal especially for higher frequencies.}, + copyright = {https://www.elsevier.com/tdm/userlicense/1.0/}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Marburg2003.pdf} +} + +@article{Masson2006, + title = {Mice {{Lacking Brain}}/{{Kidney Phosphate-Activated Glutaminase Have Impaired Glutamatergic Synaptic Transmission}}, {{Altered Breathing}}, {{Disorganized Goal-Directed Behavior}} and {{Die Shortly}} after {{Birth}}}, + author = {Masson, J.}, + year = {2006}, + month = apr, + volume = {26}, + number = {17}, + pages = {4660--4671}, + publisher = {Society for Neuroscience}, + doi = {10.1523/jneurosci.4241-05.2006}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Masson2006.pdf} +} + +@article{Matsushita2024, + title = {Cadmium Inhibits Calcium Activity in Hippocampal {{CA1}} Neurons of Freely Moving Mice}, + author = {Matsushita, Megumi T and Xia, Zhengui}, + year = {2024}, + month = jun, + journal = {Toxicological Sciences}, + volume = {200}, + number = {1}, + pages = {199--212}, + issn = {1096-6080, 1096-0929}, + doi = {10.1093/toxsci/kfae048}, + urldate = {2024-10-16}, + abstract = {Abstract Cadmium (Cd) is a ubiquitous toxic heavy metal and a potential neurotoxicant due to its wide use in industrial manufacturing processes and commercial products, including fertilizers. The general population is exposed to Cd through food and smoking due to high transfer rates of Cd from contaminated soil. Cd has been shown to mimic calcium ions (Ca2+) and interfere with intracellular Ca2+ levels and Ca2+ signaling in in vitro studies. However, nothing is known about Cd's effects on Ca2+ activity in neurons in live animals. This study aimed to determine if Cd disrupts Ca2+ transients of neurons in CA1 region of the hippocampus during an associative learning paradigm. We utilized in vivo Ca2+ imaging in awake, freely moving C57BL/6 mice to measure Ca2+ activity in CA1 excitatory neurons expressing genetically encoded Ca2+ sensor GCaMP6 during an associative learning paradigm. We found that a smaller proportion of neurons are activated in Cd-treated groups compared with control during fear conditioning, suggesting that Cd may contribute to learning and memory deficit by reducing the activity of neurons. We observed these effects at Cd exposure levels that result in blood Cd levels comparable with the general U.S. population levels. This provides a possible molecular mechanism for Cd interference of learning and memory at exposure levels relevant to U.S. adults. To our knowledge, our study is the first to describe Cd effects on brain Ca2+ activity in vivo in freely behaving mice. This study provides evidence for impairment of neuronal calcium activity in hippocampal CA1 excitatory neurons in freely moving mice following cadmium exposure.}, + copyright = {https://academic.oup.com/pages/standard-publication-reuse-rights}, + langid = {english} +} + +@article{Matt2024, + title = {Current State of Clinical Ultrasound Neuromodulation}, + author = {Matt, Eva and Radjenovic, Sonja and Mitterwallner, Michael and Beisteiner, Roland}, + year = {2024}, + month = jun, + journal = {Frontiers in Neuroscience}, + volume = {18}, + pages = {1420255}, + issn = {1662-453X}, + doi = {10.3389/fnins.2024.1420255}, + urldate = {2024-06-21}, + abstract = {Unmatched by other non-invasive brain stimulation techniques, transcranial ultrasound (TUS) offers highly focal stimulation not only on the cortical surface but also in deep brain structures. These unique attributes are invaluable in both basic and clinical research and might open new avenues for treating neurological and psychiatric diseases. Here, we provide a concise overview of the expanding volume of clinical investigations in recent years and upcoming research initiatives concerning focused ultrasound neuromodulation. Currently, clinical TUS research addresses a variety of neuropsychiatric conditions, such as pain, dementia, movement disorders, psychiatric conditions, epilepsy, disorders of consciousness, and developmental disorders. As demonstrated in sham-controlled randomized studies, TUS neuromodulation improved cognitive functions and mood, and alleviated symptoms in schizophrenia and autism. Further, preliminary uncontrolled evidence suggests relieved anxiety, enhanced motor functions in movement disorders, reduced epileptic seizure frequency, improved responsiveness in patients with minimally conscious state, as well as pain reduction after neuromodulatory TUS. While constrained by the relatively modest number of investigations, primarily consisting of uncontrolled feasibility trials with small sample sizes, TUS holds encouraging prospects for treating neuropsychiatric disorders. Larger sham-controlled randomized trials, alongside further basic research into the mechanisms of action and optimal sonication parameters, are inevitably needed to unfold the full potential of TUS neuromodulation.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Matt2024.pdf} +} + +@article{Meijlink2024, + title = {Ultrasound-Activated Microbubbles Mediate {{F-actin}} Disruptions and Endothelial Gap Formation during Sonoporation}, + author = {Meijlink, Bram and Van Der Kooij, H. Rhod{\'e} and Wang, Yuchen and Li, Hongchen and Huveneers, Stephan and Kooiman, Klazina}, + year = {2024}, + month = dec, + journal = {Journal of Controlled Release}, + volume = {376}, + pages = {1176--1189}, + issn = {01683659}, + doi = {10.1016/j.jconrel.2024.10.066}, + urldate = {2024-11-19}, + abstract = {Locally opening up the endothelial barrier in a safe and controlled way is beneficial for drug delivery into the extravascular tissue. Although ultrasound-induced microbubble oscillations can affect the endothelial barrier integrity, the mechanism remains unknown. Here we uncover a new role for F-actin in microbubble-mediated endothelial gap formation. Unique simultaneous high-resolution confocal microscopy and ultra-high-speed camera imaging (10 million frames per second) reveal that single oscillating microbubbles (radius 1.3--3.8 {$\mu$}m; n = 48) induce sonoporation in all cells in which F-actin remodeling occurred. F-actin disruption only mainly resulted in tunnel formation (75 \%), while F-actin stress fiber severing and recoil mainly resulted in cell-cell contact opening within 15 s upon treatment (54 \%) and tunnel formation (15 \%). F-actin stress fiber severing occurred when the fibers were within reach of the microbubble's maximum radius during oscillation, requiring normal forces of {$\geq$}230 nN. In the absence of F-actin stress fibers, oscillating microbubbles induced F-actin remodeling but no cell-cell contact opening. Together, these findings reveal a novel mechanism of microbubblemediated transendothelial drug delivery, which associates with the underlying cytoskeletal F-actin organization.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Meijlink2024.pdf} +} + +@techreport{Menz2017, + type = {Preprint}, + title = {Physical Mechanisms of Ultrasonic Neurostimulation of the Retina}, + author = {Menz, Mike D. and Ye, Patrick and Firouzi, Kamyar and Pauly, Kim Butts and {Khuri-Yakub}, Butrus T. and Baccus, Stephen A.}, + year = {2017}, + month = dec, + institution = {Neuroscience}, + doi = {10.1101/231449}, + urldate = {2022-09-29}, + abstract = {Abstract Focused ultrasound has been shown to be effective at stimulating neurons in vivo, ex vivo and in vitro preparations. Ultrasonic neuromodulation is the only non-invasive method of stimulation that could reach deep in the brain with high spatial-temporal resolution, and thus has potential for use in clinical applications and basic studies of the nervous system. Understanding the physical mechanism by which energy in a high acoustic frequency wave is delivered to stimulate neurons will be important to optimize this technology. Two primary candidates for a physical mechanism are radiation force, the delivery of momentum by the acoustic wave, and cavitation, oscillating gas bubbles. We imaged the isolated salamander retina during ultrasonic stimuli that drive ganglion cell activity and observed micron scale displacements consistent with radiation force. We recorded ganglion cell spiking activity with a planar multielectrode array and changed the acoustic carrier frequency across a broad range (0.5 - 43 MHz), finding that increased stimulation occurs at higher acoustic frequencies, a result that is consistent with radiation force but not cavitation. A quantitative radiation force model can explain retinal responses, and could potentially explain previous in vivo results in the mouse, suggesting a new hypothesis to be tested in vivo. Finally, we found that neural activity was strongly modulated by the distance between the transducer and the electrode array showing the influence of standing waves on the response. We conclude that radiation force is the physical mechanism underlying ultrasonic neurostimulation in the ex vivo retina, and that the control of standing waves is a new potential method to modulate these effects.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Menz2017.pdf} +} + +@article{Menz2019, + title = {Radiation {{Force}} as a {{Physical Mechanism}} for {{Ultrasonic Neurostimulation}} of the {{{\emph{Ex Vivo}}}} {{Retina}}}, + author = {Menz, Mike D. and Ye, Patrick and Firouzi, Kamyar and Nikoozadeh, Amin and Pauly, Kim Butts and {Khuri-Yakub}, Pierre and Baccus, Stephen A.}, + year = {2019}, + month = aug, + journal = {The Journal of Neuroscience}, + volume = {39}, + number = {32}, + pages = {6251--6264}, + issn = {0270-6474, 1529-2401}, + doi = {10.1523/JNEUROSCI.2394-18.2019}, + urldate = {2024-02-19}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Menz22.pdf} +} + +@article{Meulenbroek2021, + title = {Multi-{{Axial Transducers}} for {{Passive Point Source Localization}}}, + author = {Meulenbroek, Nathan Earl and Delgado, Sagid and {Sagid Delgado} and Curiel, Laura and Curiel, Laura and Pichardo, Samuel and Pichardo, Samuel}, + year = {2021}, + month = sep, + doi = {10.1109/ius52206.2021.9593667}, + abstract = {Acoustic cavitation is often monitored by single passive cavitation detectors. A single transducer can provide information on the type, intensity, and duration of activity, while being small and relatively inexpensive. However, spatial information about cavitation activity is lacking with these systems. Multi-axial transducers, or transducers with more than one pair of orthogonal electrodes, are hypothesized to provide directivity information about a received signal using a single transducer. Thus, the objective of this study was to demonstrate in-silico that single multi-axial transducers can provide directivity information and two multi-axial transducers can provide accurate source location estimates. Two sets of frequency-domain simulations were performed, one each for two biaxial transducers (two pairs of orthogonal electrodes) and two triaxial transducers (two pairs of orthogonal electrodes). Transducers were placed 2 cm apart along the x axis while acoustic point sources were placed at depths between 10 and 14 cm from the top face of the transducers. Points were a maximum of 4 cm away from the origin in the xy-plane. Signal and amplitude ratio were mapped to source direction using a radial basis function. Trigonometry was then used to calculate two- and three-dimensional positions for biaxial and triaxial cases, respectively. RMS and median localization errors were calculated as a measure of accuracy. Median localization error of less than 1 mm was observer in all cases. Therefore, single multi-axial transducers can estimate the direction of a point source and pairs of multi-axial transducers can estimate the location of a point source.}, + annotation = {MAG ID: 3214240599} +} + +@article{Meyer2002, + title = {{\emph{Ab Initio}} Study of Ferroelectric Domain Walls in {{PbTiO}} 3}, + author = {Meyer, B. and Vanderbilt, David}, + year = {2002}, + month = mar, + journal = {Physical Review B}, + volume = {65}, + number = {10}, + pages = {104111}, + issn = {0163-1829, 1095-3795}, + doi = {10.1103/PhysRevB.65.104111}, + urldate = {2023-04-03}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Meyer22.pdf} +} + +@article{Michelangeli2011, + title = {A Diversity of {{SERCA Ca2}}+ Pump Inhibitors}, + author = {Michelangeli, Francesco and East, J. Malcolm}, + year = {2011}, + month = jun, + journal = {Biochemical Society Transactions}, + volume = {39}, + number = {3}, + pages = {789--797}, + issn = {0300-5127, 1470-8752}, + doi = {10.1042/BST0390789}, + urldate = {2024-10-09}, + abstract = {The SERCA (sarcoplasmic/endoplasmic reticulum Ca2+-ATPase) is probably the most extensively studied membrane protein transporter. There is a vast array of diverse inhibitors for the Ca2+ pump, and many have proved significant in helping to elucidate both the mechanism of transport and gaining conformational structures. Some SERCA inhibitors such as thapsigargin have been used extensively as pharmacological tools to probe the roles of Ca2+ stores in Ca2+ signalling processes. Furthermore, some inhibitors have been implicated in the cause of diseases associated with endocrine disruption by environmental pollutants, whereas others are being developed as potential anticancer agents. The present review therefore aims to highlight some of the wide range of chemically diverse inhibitors that are known, their mechanisms of action and their binding location on the Ca2+ ATPase. Additionally, some ideas for the future development of more useful isoform-specific inhibitors and anticancer drugs are presented.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Michelangeli2011.pdf} +} + +@misc{microsystems, + title = {The {{Patch-Clamp Technique}}}, + author = {{microsystems}, Leica} +} + +@article{Min2011, + title = {Focused Ultrasound Modulates the Level of Cortical Neurotransmitters: {{Potential}} as a New Functional Brain Mapping Technique}, + shorttitle = {Focused Ultrasound Modulates the Level of Cortical Neurotransmitters}, + author = {Min, Byoung-Kyong and Yang, Po Song and Bohlke, Mark and Park, Shinsuk and R.Vago, David and Maher, Timothy J. and Yoo, Seung-Schik}, + year = {2011}, + month = jun, + journal = {International Journal of Imaging Systems and Technology}, + volume = {21}, + number = {2}, + pages = {232--240}, + issn = {08999457}, + doi = {10.1002/ima.20284}, + urldate = {2022-09-19}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Min2011.pdf} +} + +@book{Miniussi2019, + title = {Transcranial Brain Stimulation}, + editor = {Miniussi, Carlo and Paulus, Walter and Rossini, Paolo M}, + year = {2019}, + month = oct, + publisher = {CRC Press}, + address = {London, England}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Miniussi2019.pdf} +} + +@article{Mirzakhalili2020, + title = {Biophysics of {{Temporal Interference Stimulation}}}, + author = {Mirzakhalili, Ehsan and Barra, Beatrice and Capogrosso, Marco and Lempka, Scott F.}, + year = {2020}, + month = dec, + journal = {Cell Systems}, + volume = {11}, + number = {6}, + pages = {557-572.e5}, + issn = {24054712}, + doi = {10.1016/j.cels.2020.10.004}, + urldate = {2023-07-21}, + abstract = {Temporal interference (TI) is a non-invasive neurostimulation technique that utilizes high-frequency external electric fields to stimulate deep neuronal structures without affecting superficial, off-target structures. TI represents a potential breakthrough for treating conditions, such as Parkinson's disease and chronic pain. However, early clinical work on TI stimulation was met with mixed outcomes challenging its fundamental mechanisms and applications. Here, we apply established physics to study the mechanisms of TI with the goal of optimizing it for clinical use. We argue that TI stimulation cannot work via passive membrane filtering, as previously hypothesized. Instead, TI stimulation requires an ion-channel mediated signal rectification process. Unfortunately, this mechanism is also responsible for high-frequency conduction block in off-target tissues, thus challenging clinical applications of TI. In consequence, we propose a set of experimental controls that should be performed in future experiments to refine our understanding and practice of TI stimulation. A record of this paper's transparent peer review process is included in the Supplemental Information.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Mirzakhalili2020.pdf} +} + +@article{Mohammadjavadi2019, + title = {Elimination of Peripheral Auditory Pathway Activation Does Not Affect Motor Responses from Ultrasound Neuromodulation}, + author = {Mohammadjavadi, Morteza and Ye, Patrick Peiyong and Xia, Anping and Brown, Julian and Popelka, Gerald and Pauly, Kim Butts}, + year = {2019}, + month = jul, + journal = {Brain Stimulation}, + volume = {12}, + number = {4}, + pages = {901--910}, + issn = {1935861X}, + doi = {10.1016/j.brs.2019.03.005}, + urldate = {2023-06-01}, + abstract = {Background: Recent studies in a variety of animal models including rodents, monkeys, and humans suggest that transcranial focused ultrasound (tFUS) has considerable promise for non-invasively modulating neural activity with the ability to target deep brain structures. However, concerns have been raised that motor responses evoked by tFUS may be due to indirect activation of the auditory pathway rather than direct activation of motor circuits. Objective: In this study, we sought to examine the involvement of peripheral auditory system activation from tFUS stimulation applied to elicit motor responses. The purpose was to determine to what extent ultrasound induced auditory artifact could be a factor in ultrasound motor neuromodulation. Methods: In this study, tFUS-induced electromyography (EMG) signals were recorded and analyzed in wild-type (WT) normal hearing mice and two strains of genetically deaf mice to examine the involvement of the peripheral auditory system in tFUS-stimulated motor responses. In addition, auditory brainstem responses (ABRs) were measured to elucidate the effect of the tFUS stimulus envelope on auditory and motor responses. We also varied the tFUS stimulation duration to measure its effect on motor response duration. Results: We show, first, that the sharp edges in a tFUS rectangular envelope stimulus activate the peripheral afferent auditory pathway and, second, that smoothing these edges eliminates the auditory responses without affecting the motor responses in normal hearing WT mice. We further show that by eliminating peripheral auditory activity using two different strains of deaf knockout mice, motor responses are the same as in normal hearing WT mice. Finally, we demonstrate a high correlation between tFUS pulse duration and EMG response duration. Conclusion: These results support the concept that tFUS-evoked motor responses are not a result of stimulation of the peripheral auditory system.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Mohammadjavadi2019.pdf} +} + +@article{Moisset2019, + title = {Neurostimulation Methods in the Treatment of Chronic Pain}, + author = {Moisset, X. and {Lanteri-Minet}, M. and Fontaine, D.}, + year = {2019}, + month = oct, + journal = {Journal of Neural Transmission}, + volume = {127}, + number = {4}, + pages = {673--686}, + publisher = {{Springer Science and Business Media LLC}}, + doi = {10.1007/s00702-019-02092-y}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Moisset2019.pdf} +} + +@article{Morgan2013, + title = {Spontaneous {{Calcium Transients}} in {{Human Neural Progenitor Cells Mediated}} by {{Transient Receptor Potential Channels}}}, + author = {Morgan, Peter J. and H{\"u}bner, Rayk and Rolfs, Arndt and Frech, Moritz J.}, + year = {2013}, + month = sep, + journal = {Stem Cells and Development}, + volume = {22}, + number = {18}, + pages = {2477--2486}, + issn = {1547-3287, 1557-8534}, + doi = {10.1089/scd.2013.0061}, + urldate = {2023-05-11}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Morgan2013.pdf} +} + +@article{Mortimer1988, + title = {The Effect of Therapeutic Ultrasound on Calcium Uptake in Fibroblasts}, + author = {Mortimer, A. J. and Dyson, M.}, + year = {1988}, + month = jan, + journal = {Ultrasound in Medicine \& Biology}, + volume = {14}, + number = {6}, + pages = {499--506}, + publisher = {Elsevier BV}, + doi = {10.1016/0301-5629(88)90111-1} +} + +@article{Moustafa2016, + title = {Motor Symptoms in {{Parkinson}}'s Disease: {{A}} Unified Framework}, + author = {Moustafa, Ahmed A. and Chakravarthy, Srinivasa and Phillips, Joseph R. and Gupta, Ankur and Keri, Szabolcs and Polner, Bertalan and Frank, Michael J. and Jahanshahi, Marjan}, + year = {2016}, + journal = {Neuroscience \& Biobehavioral Reviews}, + volume = {68}, + pages = {727--740}, + issn = {0149-7634}, + doi = {10.1016/j.neubiorev.2016.07.010}, + abstract = {Parkinson's disease (PD) is characterized by a range of motor symptoms. Besides the cardinal symptoms (akinesia and bradykinesia, tremor and rigidity), PD patients show additional motor deficits, including: gait disturbance, impaired handwriting, grip force and speech deficits, among others. Some of these motor symptoms (e.g., deficits of gait, speech, and handwriting) have similar clinical profiles, neural substrates, and respond similarly to dopaminergic medication and deep brain stimulation (DBS). Here, we provide an extensive review of the clinical characteristics and neural substrates of each of these motor symptoms, to highlight precisely how PD and its medical and surgical treatments impact motor symptoms. In conclusion, we offer a unified framework for understanding the range of motor symptoms in PD. We argue that various motor symptoms in PD reflect dysfunction of neural structures responsible for action selection, motor sequencing, and coordination and execution of movement.}, + keywords = {Akinesia,Bradykinesia,Freezing of gait,Grip force,Handwriting,Parkinson's disease,Rigidly,Speech,Tremor} +} + +@article{Mueller2014, + title = {A Quantitative Overview of Biophysical Forces Impinging on Neural Function}, + author = {Mueller, Jerel K. and Tyler, William J.}, + year = {2014}, + month = aug, + journal = {Physical Biology}, + volume = {11}, + number = {5}, + pages = {051001}, + publisher = {IOP Publishing}, + doi = {10.1088/1478-3975/11/5/051001}, + abstract = {The fundamentals of neuronal membrane excitability are globally described using the Hodgkin-Huxley (HH) model. The HH model, however, does not account for a number of biophysical phenomena associated with action potentials or propagating nerve impulses. Physical mechanisms underlying these processes, such as reversible heat transfer and axonal swelling, have been compartmentalized and separately investigated to reveal neuronal activity is not solely influenced by electrical or biochemical factors. Instead, mechanical forces and thermodynamics also govern neuronal excitability and signaling. To advance our understanding of neuronal function and dysfunction, compartmentalized analyses of electrical, chemical, and mechanical processes need to be revaluated and integrated into more comprehensive theories. The present perspective is intended to provide a broad overview of biophysical forces that can influence neural function, but which have been traditionally underappreciated in neuroscience. Further, several examples where mechanical forces have been shown to exert their actions on nervous system development, signaling, and plasticity are highlighted to underscore their importance in sculpting neural function. By considering the collective actions of biophysical forces influencing neuronal activity, our working models can be expanded and new paradigms can be applied to the investigation and characterization of brain function and dysfunction.} +} + +@article{Mueller2014a, + title = {Transcranial {{Focused Ultrasound Modulates Intrinsic}} and {{Evoked EEG Dynamics}}}, + author = {Mueller, Jerel and Legon, Wynn and Opitz, Alexander and Sato, Tomokazu F. and Tyler, William J.}, + year = {2014}, + month = nov, + journal = {Brain Stimulation}, + volume = {7}, + number = {6}, + pages = {900--908}, + issn = {1935861X}, + doi = {10.1016/j.brs.2014.08.008}, + urldate = {2022-04-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Mueller2014a.pdf} +} + +@article{Muller2015, + title = {Python in Neuroscience}, + author = {Muller, Eilif and Bednar, James A. and Diesmann, Markus and Gewaltig, Marc-Oliver and Hines, Michael and Davison, Andrew P.}, + year = {2015}, + month = apr, + journal = {Frontiers in Neuroinformatics}, + volume = {9}, + publisher = {Frontiers}, + issn = {1662-5196}, + doi = {10.3389/fninf.2015.00011}, + urldate = {2025-01-08}, + abstract = {This Research Topic of Frontiers in Neuroinformatics is dedicated to the memory of Rolf K\&\#246;tter (1961--2010), who was the Frontiers Associate Editor responsible for this Research Topic, and who gave us considerable support and encouragement during the process of conceiving and launching the Topic, and throughout the reviewing process.Computation is becoming essential across all sciences, for data acquisition and analysis, automation, and hypothesis testing via modeling and simulation. As a consequence, software development is becoming a critical scientific activity. Training of scientists in programming, software development, and computational thinking (Wilson, 2006), choice of tools, community-building and interoperability are all issues that should be addressed, if we wish to accelerate scientific progress while maintaining standards of correctness and reproducibility.The Python programming language in particular has seen a surge in popularity across the sciences, for reasons which include its readability, modularity, and large standard library (also see Figure 1). The use of Python as a scientific programming language began to increase with the development of numerical libraries for optimized operations on large arrays in the late 1990s, in which an important development was the merging of the competing Numeric and Numarray packages in 2006 to form NumPy (Oliphant, 2007). As Python and NumPy have gained traction in a given scientific domain, we have seen the emergence of domain-specific ecosystems of open-source Python software developed by scientists. It became clear to us in 2007 that we were on the cusp of an emerging Python in neuroscience ecosystem, particularly in computational neuroscience and neuroimaging, but also in electrophysiological data analysis and in psychophysics. Two major strengths of Python are its modularity and ability to easily ``glue'' together different programming languages, which together facilitate the interaction of modular components and their composition into larger systems. This focus on reusable components, which has proven its value in commercial and open-source software development (Brooks, 1987), is, we contend, essential for scientific computing in neuroscience, if we are to cope with the increasingly large amounts of data being produced in experimental labs, and if we wish to understand and model the brain in all its complexity, We therefore felt that it was timely and important to raise awareness of the emerging Python in Neuroscience software ecosystem amongst researchers developing Python-based tools, but also in the larger neuroscience community. Our goals were several-fold:- establish a critical mass for Python use and development in the eyes of the community;- encourage interoperability and collaboration between developers;- expose neuroscientists to the new Python-based tools now available.From this was born the idea for a Research Topic in Frontiers in Neuroinformatics on ``Python in Neuroscience'' to showcase those projects we were aware of, and to give exposure to projects of which we were not aware. Although it may seem strange at first glance to centre a Research Topic around a tool, rather than around a scientific problem, we feel it is justified by the increasingly critical role of scientific programming in neuroscience research, and by the particular strengths of the Python language and the broader Python scientific computing ecosystem.Collected in this Research Topic are 24 articles describing some ways in which neuroscience researchers around the world are turning to the Python programming language to get their job done faster and more efficiently.[Figure 1 around here]Figure 1. Beginning to use Python for scientific computing can be a liberating, even exhilarating experience. Comic by Randall Munroe, available from http://xkcd.com/353/. Reproduced under the terms of the Creative Commons Attribution-NonCommercial 2.5 License (see http://xkcd.com/license.html)Overview of the Research TopicWe will now briefly summarize the 24 articles in the Research Topic, drawing out common themes.Both Southey et al. (2008) and Yanashima et al. (2009) use Python for bioinformatics applications, but in very different areas. Yanashima et al. have developed a Python package for graph-theoretical analysis of biomolecular networks, BioNetpy, and employed it to investigate protein networks associated with Alzheimer's disease. Southey et al.'s study demonstrates the wide breadth of application of Python, and the large number of high quality scientific libraries available, combining existing tools for bioinformatics, machine learning and web development to build an integrated pipeline for identification of prohormone precursors and prediction of prohormone cleavage sites.Jurica and van Leeuwen (2009) address the needs of scientists who already have significant amounts of code written in MATLAB\&\#174; and who wish to transfer this to Python. They present OMPC, which uses syntax adaptation and emulation to allow transparent import of existing MATLAB\&\#174; functions into Python programs. Three articles reported on new tools in the domain of neuroimaging. Hanke et al. (2009) report on PyMVPA, a Python framework for machine learning-based data analysis, and its application to analysis of fMRI, EEG, MEG, and extracellular electrophysiology recordings. Gouws et al. (2009) describe DataViewer3D, a Python application for displaying and integrating data from multiple neuroimaging modalities, showcasing Python's abilities to easily interface with libraries written in other languages, such as C++, and to integrate them into user-friendly systems. Strangman et al. (2009) emphasize the advantages of Python for ``swift prototyping followed by efficient transition to stable production systems'' in their description of NinPy, a toolkit for near-infrared neuroimaging.Zito et al. (2009) and Ince et al. (2009) both report on the use of Python for general purpose data analysis, with a focus on machine learning and information theory respectively. Zito et al. have developed MDP, the Modular toolkit for Data Processing, a collection of computationally efficient data analysis modules that can be combined into complex pipelines. MDP was originally developed for theoretical research in neuroscience, but has broad application in general scientific data analysis and in teaching. Ince et al. (2009) describe the use of Python for information-theoretic analysis of neuroscience data, outlining algorithmic, statistical and numerical challenges in the application of information theory in neuroscience, and explaining how the use of Python has significantly improved the speed and domain of applicability of the algorithms, allowing more ambitious analyses of more complex data sets. Their code is available as an open-source package, pyEntropy.Three articles report on tools for visual stimulus generation, for use in visual neurophysiology and psychophysics experiments. Straw (2008) describes VisionEgg, while Peirce (2009) presents PsychoPy, both of which are easy-to-use and easy-to-install applications that make use of OpenGL to generate temporally and spatially precise, arbitrarily complex visual stimulation protocols. Python is used to provide a simple, intuitive interface to the underlying graphics libraries, to provide a graphical user interface, and to interface with external hardware. PsychoPy can also generate and deliver auditory stimuli. Spacek et al. (2009) also report on a Python library for visual stimulus generation, as part of a toolkit for the acquisition and analysis of highly parallel electrophysiological recordings from cat and rat visual cortex. The other two components in the toolkit are for electrophysiological waveform visualization and spike sorting; and for spike train and stimulus analysis. The authors note ``The requirements and solutions for these projects differed greatly, yet we found Python to be well suited for all three.'' Also in the domain of electrophysiology, Garcia and Fourcaud-Trocm\&\#233; (2009) describe OpenElectrophy, an application for efficient storage and analysis of large electrophysiology datasets, which includes a graphical user interface for interactive visualization and exploration and a library of analysis routines, including several spike-sorting methods.By far the largest contribution to the Research Topic came from the field of modelling and simulation, with 12 articles on the topic. Nine of these articles present neuroscience simulation environments with Python scripting interfaces. In most cases, the Python interface was added to an existing simulator written in a compiled language such as C++. This was the case for NEURON (Hines et al., 2009), NEST (Eppler et al., 2009), PCSIM (Pecevski et al., 2009), Nengo (Stewart et al., 2009), MOOSE (Ray and Bhalla, 2008), STEPS (Wils and De Schutter, 2009) and NCS (Drewes et al., 2009). However, as the articles by Goodman and Brette (2008) on the Brian simulator and Bednar (2009) on the Topographica simulator demonstrate, it is also possible to develop new simulation environments purely in Python, making use of the vectorization techniques available in the underlying NumPy package to obtain computational efficiency. The range of modelling domains of these simulators is wide, from stochastic simulation of coupled reaction-diffusion systems (STEPS), through simulation of morphologically detailed neurons and networks (NEURON, MOOSE), highly-efficient large-scale networks of spiking point neurons (NEST, PCSIM, NCS, Brian) to population coding or point-neuron models of large brain regions (Nengo, Topographica). Note that although we have categorized each simulator by its main area of application, most of these tools support modelling at a range of scales and levels of detail: Bednar (2009), for example, describes the integration of a spiking NEST simulation as one component in a Topographica simulation.The addition of Python interfaces to such a large number of widely used simulation environments suggested a huge opportunity to enhance interoperability between different simulators, making use of the common scripting language, which in turn has the potential to enhance the transfer of technology, knowledge and models between users of the different simulators, and to promote model reuse. Davison et al. (2009) describe PyNN, a common Python interface to multiple simulators, which enables the same modelling and simulation script to be run on any supported simulator without modification. At the time of writing, PyNN supports NEURON, NEST, PCSIM and Brian, with MOOSE support under development. The existence of such a common ``meta-simulator'' then makes it much easier for scientists developing new, hardware-based approaches to neural simulation to engage with the computational neuroscience community, as evidenced by the article by Br\&\#252;derle et al. (2009) on interfacing a novel neuromorphic hardware system with PyNN.Finally, Fox et al. (2009) describe the possibilities when one is not limited to a single simulator, but can use Python to integrate multiple models into a brain-wide system. In their development of an integrated basal ganglia-hippocampal formation model for spatial navigation and its embodiment in a simulated robotic environment, Fox et al. found that Python offers ``a significant reduction in development time, without a corresponding significant increase in execution time''.It is important to note that most or all of the Python tools and libraries described in the Research Topic are open source and hence free to download, use and extend.DiscussionThis editorial is being written six years after the first articles in the Research Topic were published. It is with the benefit of considerable hindsight, therefore, that we can confidently say that our goals in launching this Research Topic -- to establish a critical mass for Python use and development in the eyes of the community and to encourage interoperability and collaboration between developers -- have been met or exceeded.The average number of citations per article for the Research Topic as a whole is 54, or approximately 9 per year, using figures from Google Scholar. Although citation counts from Google Scholar tend to be higher than those from Journal Citation Reports so the numbers are not directly comparable, this compares favourably with the impact factors of well respected journals such as Journal of Neuroscience or PLoS Computational Biology. Some of the articles were much more highly cited, with three of them being cited more than 20 times per year, on average, over the period. Four of the articles were chosen to ``climb the tier'' in the Frontiers system, and were followed up by Focused Review articles in Frontiers in Neuroscience (Davison, Hines and Muller, 2009; Goodman and Brette, 2009; Hanke et al., 2010; Ince et al., 2010), another was the subject of a commentary (Einevoll, 2009). Concerning the goals of interoperability and collaboration, several articles in a follow-up volume Python in Neuroscience II attest to the degree to which the developers of different tools have worked together, and prioritized interoperability in recent years. For example, the developers of OpenElectrophy (Garcia and Fourcaud-Trocm\&\#233;, 2009) and the community around PyNN (Davison et al., 2009) formed the nucleus of an effort to develop a baseline Python representation for electrophysiology data, which resulted in the Neo project, reported in the Python in Neuroscience II Research Topic (Garcia et al., 2014) together with two of the several projects which build on Neo (Pr\&\#246;pper and Obermayer, 2013; Sobolev et al., 2014). A new workflow system for computational neuroscience, Mozaik (Antol\&\#237;k and Davison, 2014) builds on both PyNN and Topographica (Bednar, 2009). PyNEST (Eppler et al., 2009) and PyNN developers collaborated with the INCF to improve the interoperability between these tools (Djurfeldt et al., 2014) when using the Connection Set Algebra (Djurfeldt, 2010). Finally, a number of tools have been built on the Python interface to NEURON (Hines et al., 2009), including morphforge (Hull and Willshaw, 2014) and LFPy (Lind\&\#233;n et al., 2014).Observing the rapid growth in adoption of Python in neuroscience over the last six years, which appears to continue to accelerate, it is clear that Python is here to stay, which augurs well for the growth, productivity, and rigour of computational methods in neuroscience.}, + langid = {english}, + keywords = {collaboration,interoperability,python language,scientific computing,Software Development}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Muller2015.pdf} +} + +@article{Muratore2009, + title = {Bioeffective {{Ultrasound}} at {{Very Low Doses}}: {{Reversible Manipulation}} of {{Neuronal Cell Morphology}} and {{Function}} in {{Vitro}}}, + shorttitle = {Bioeffective {{Ultrasound}} at {{Very Low Doses}}}, + author = {Muratore, Robert and LaManna, Justine and Szulman, Erin and Kalisz, M. S. Andrew and Lamprecht, Michael and Simon, M. S. Melissa and Yu, M. S. Zhe and Xu, Nina and Morrison, Barclay}, + year = {2009}, + month = apr, + journal = {AIP Conference Proceedings}, + volume = {1113}, + number = {1}, + pages = {25}, + publisher = {American Institute of PhysicsAIP}, + issn = {0094-243X}, + doi = {10.1063/1.3131426}, + urldate = {2023-03-15}, + abstract = {Direct and safe manipulation of neurons by external means is an increasingly studied therapeutic modality with the potential to treat many neurological diseases. Anticipating such future applications, we investigated reversible bioeffects of very low dose focused ultrasound on neuronal cell morphology and function in vitro. To test morphological changes, undifferentiated PC12 cells were serum-cultured. The culture plates were placed on an inverted optical microscope. An f/1.1 ultrasound transducer with a water-filled coupling cone was focused on the culture and excited with 30-ms 4.67-MHz 100-kPa pulses. To test functional changes, rat hippocampal slices were cultured and individually transferred to the well of a 60-channel multi electrode array. An f/2.1 ultrasound transducer with a water-filled coupling cone was focused on a culture and excited with 100-{$\mu$}s 4.04-MHz 77-kPa pulses. The culture was stimulated before and after the ultrasonic stimulus with a 100-{$\mu$}s 100-{$\mu$}A biphasic electrical stimulus. Optical microscopy of PC12 cultures under insonification revealed that cells that were clustered near the ultrasound focal region elongated by approximately 2 {$\mu$}m during insonification and returned to approximately their original shapes following insonification. We conclude that the acoustic radiation force is capable of reversibly deforming cultured cells. In the rat hippocampal cultures, the ultrasonically and electrically evoked responses exhibited similar biphasic waveforms. In addition, robust electrically evoked responses following insonification indicated that the insonified cultures remained viable. We conclude that low-dose ultrasound can stimulate neurons; the mechanism is currently under investigation.}, + copyright = {{\copyright} 2009 American Institute of Physics.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Muratore2009.pdf} +} + +@article{Murphy2022, + title = {A Tool for Monitoring Cell Type--Specific Focused Ultrasound Neuromodulation and Control of Chronic Epilepsy}, + author = {Murphy, Keith R. and Farrell, Jordan S. and Gomez, Juan L. and Stedman, Quintin G. and Li, Ningrui and Leung, Steven A. and Good, Cameron H. and Qiu, Zhihai and Firouzi, Kamyar and Butts Pauly, Kim and {Khuri-Yakub}, Butrus Pierre T. and Michaelides, Michael and Soltesz, Ivan and {de Lecea}, Luis}, + year = {2022}, + month = nov, + journal = {Proceedings of the National Academy of Sciences}, + volume = {119}, + number = {46}, + pages = {e2206828119}, + issn = {0027-8424, 1091-6490}, + doi = {10.1073/pnas.2206828119}, + urldate = {2023-03-06}, + abstract = {Focused ultrasound (FUS) is a powerful tool for noninvasive modulation of deep brain activity with promising therapeutic potential for refractory epilepsy; however, tools for examining FUS effects on specific cell types within the deep brain do not yet exist. Consequently, how cell types within heterogeneous networks can be modulated and whether parameters can be identified to bias these networks in the context of complex behaviors remains unknown. To address this, we developed a fiber Photometry Coupled focused Ultrasound System (PhoCUS) for simultaneously monitoring FUS effects on neural activity of subcortical genetically targeted cell types in freely behaving animals. We identified a parameter set that selectively increases activity of parvalbumin interneurons while suppressing excitatory neurons in the hippocampus. A net inhibitory effect localized to the hippocampus was further confirmed through whole brain metabolic imaging. Finally, these inhibitory selective parameters achieved significant spike suppression in the kainate model of chronic temporal lobe epilepsy, opening the door for future noninvasive therapies.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Murphy2022.pdf} +} + +@article{Murphy2024, + title = {Cell Type Specific Focused Ultrasound Neuromodulation in Preclinical Models of Sleep and Psychiatric Disorders}, + author = {Murphy, Keith R. and De Lecea, Luis}, + year = {2024}, + month = jan, + journal = {Neuropsychopharmacology}, + volume = {49}, + number = {1}, + pages = {299--300}, + issn = {0893-133X, 1740-634X}, + doi = {10.1038/s41386-023-01662-9}, + urldate = {2024-03-20}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Murphy2024.pdf} +} + +@article{Murphy2024a, + title = {Optimized Ultrasound Neuromodulation for Non-Invasive Control of Behavior and Physiology}, + author = {Murphy, Keith R. and Farrell, Jordan S. and Bendig, Jonas and Mitra, Anish and Luff, Charlotte and Stelzer, Ina A. and Yamaguchi, Hiroshi and Angelakos, Christopher C. and Choi, Mihyun and Bian, Wenjie and DiIanni, Tommaso and Pujol, Esther Martinez and Matosevich, Noa and Airan, Raag and Gaudilli{\`e}re, Brice and Konofagou, Elisa E. and {Butts-Pauly}, Kim and Soltesz, Ivan and De Lecea, Luis}, + year = {2024}, + month = jul, + journal = {Neuron}, + pages = {S0896627324004938}, + issn = {08966273}, + doi = {10.1016/j.neuron.2024.07.002}, + urldate = {2024-07-30}, + abstract = {Focused ultrasound can non-invasively modulate neural activity, but whether effective stimulation parameters generalize across brain regions and cell types remains unknown. We used focused ultrasound coupled with fiber photometry to identify optimal neuromodulation parameters for four different arousal centers of the brain in an effort to yield overt changes in behavior. Applying coordinate descent, we found that optimal parameters for excitation or inhibition are highly distinct, the effects of which are generally conserved across brain regions and cell types. Optimized stimulations induced clear, target-specific behavioral effects, whereas non-optimized protocols of equivalent energy resulted in substantially less or no change in behavior. These outcomes were independent of auditory confounds and, contrary to expectation, accompanied by a cyclooxygenase-dependent and prolonged reduction in local blood flow and temperature with brain-region-specific scaling. These findings demonstrate that carefully tuned and targeted ultrasound can exhibit powerful effects on complex behavior and physiology.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Murphy2024a.pdf} +} + +@article{Nande2015, + title = {Ultrasound-Mediated Oncolytic Virus Delivery and Uptake for Increased Therapeutic Efficacy: State of Art}, + shorttitle = {Ultrasound-Mediated Oncolytic Virus Delivery and Uptake for Increased Therapeutic Efficacy}, + author = {Nande, Rounak and Howard, Candace and Claudio, Pier Paolo}, + year = {2015}, + month = nov, + journal = {Oncolytic Virotherapy}, + pages = {193}, + issn = {2253-1572}, + doi = {10.2147/OV.S66097}, + urldate = {2022-07-18}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Nande2015.pdf} +} + +@article{Nandi, + title = {The Relationship between Parameters and Effects in Transcranial Ultrasonic Stimulation.}, + author = {Nandi, Tulika and Pauly, Kim Butts and Kop, Benjamin R and Stagg, Charlotte J}, + abstract = {Transcranial ultrasonic stimulation (TUS) is rapidly gaining traction for non-invasive human neuromodulation, with a pressing need to establish protocols that maximise neuromodulatory efficacy. In this review, we aggregate and examine empirical evidence for the relationship between tunable TUS parameters and in vitro and in vivo outcomes. Based on this multiscale approach, TUS researchers can make better informed decisions about optimal parameter settings. Importantly, we also discuss the challenges involved in extrapolating results from prior empirical work to future interventions, including the translation of protocols between models and the complex interaction between TUS protocols and the brain. A synthesis of the empirical evidence suggests that larger effects will be observed at lower frequencies within the sub-MHz range, higher intensities and pressures than commonly administered thus far, and longer pulses and pulse train durations. Nevertheless, we emphasise the need for cautious interpretation of empirical data from different experimental paradigms when basing protocols on prior work as we advance towards refined TUS parameters for human neuromodulation.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Nandi.pdf} +} + +@article{Naor2016, + title = {Ultrasonic Neuromodulation}, + author = {Naor, Omer and Krupa, Steve and Shoham, Shy}, + year = {2016}, + month = jun, + journal = {Journal of Neural Engineering}, + volume = {13}, + number = {3}, + pages = {031003}, + issn = {1741-2560, 1741-2552}, + doi = {10.1088/1741-2560/13/3/031003}, + urldate = {2023-08-31}, + abstract = {Ultrasonic waves can be non-invasively steered and focused into mm-scale regions across the human body and brain, and their application in generating controlled artificial modulation of neuronal activity could therefore potentially have profound implications for neural science and engineering. Ultrasonic neuro-modulation phenomena were experimentally observed and studied for nearly a century, with recent discoveries on direct neural excitation and suppression sparking a new wave of investigations in models ranging from rodents to humans. In this paper we review the physics, engineering and scientific aspects of ultrasonic fields, their control in both space and time, and their effect on neuronal activity, including a survey of both the field's foundational history and of recent findings. We describe key constraints encountered in this field, as well as key engineering systems developed to surmount them. In closing, the state of the art is discussed, with an emphasis on emerging research and clinical directions.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Naor2016.pdf} +} + +@article{Nardone2015, + title = {Neurostimulation in {{Alzheimer}}'s Disease: From Basic Research to Clinical Applications}, + shorttitle = {Neurostimulation in {{Alzheimer}}'s Disease}, + author = {Nardone, Raffaele and H{\"o}ller, Yvonne and Tezzon, Frediano and Christova, Monica and Schwenker, Kerstin and Golaszewski, Stefan and Trinka, Eugen and Brigo, Francesco}, + year = {2015}, + month = may, + journal = {Neurological Sciences}, + volume = {36}, + number = {5}, + pages = {689--700}, + issn = {1590-1874, 1590-3478}, + doi = {10.1007/s10072-015-2120-6}, + urldate = {2023-08-11}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Nardone2015.pdf} +} + +@article{NDjin2023, + title = {Causal Neurostimulation by Focused Ultrasound: Down to the Effect of a Single-Pulse}, + shorttitle = {Causal Neurostimulation by Focused Ultrasound}, + author = {N'Djin, W. Apoutou}, + year = {2023}, + month = jan, + journal = {Brain Stimulation}, + volume = {16}, + number = {1}, + pages = {152--153}, + issn = {1935861X}, + doi = {10.1016/j.brs.2023.01.117}, + urldate = {2023-03-01}, + langid = {english} +} + +@article{Newman2023, + title = {Ultrasound {{Modulates Calcium Activity}} in {{Cultured Neurons}}, {{Glial Cells}}, {{Endothelial Cells}} and {{Pericytes}}}, + author = {Newman, Malachy and Rasiah, Pratheepa Kumari and Kusunose, Jiro and Rex, Tonia S. and {Mahadevan-Jansen}, Anita and Hardenburger, Jacob and Jansen, E. Duco and Millis, Bryan and Caskey, Charles F.}, + year = {2023}, + month = dec, + journal = {Ultrasound in Medicine \& Biology}, + pages = {S0301562923003642}, + issn = {03015629}, + doi = {10.1016/j.ultrasmedbio.2023.11.004}, + urldate = {2023-12-17}, + abstract = {Objective: Ultrasound is being researched as a method to modulate the brain. Studies of the interaction of sound with neurons support the hypothesis that mechanosensitive ion channels play an important role in ultrasound neuromodulation. The response of cells other than neurons (e.g., astrocytes, pericytes and endothelial cells) have not been fully characterized, despite playing an important role in brain function. Methods: To address this gap in knowledge, we examined cultured murine primary cortical neurons, astrocytes, endothelial cells and pericytes in an in vitro widefield microscopy setup during application of a 500 ms burst of 250 kHz focused ultrasound over a pressure range known to elicit neuromodulation. We examined cell membrane health in response to a range of pulses and used optical calcium indicators in conjunction with pharmacological antagonists to selectively block different groups of thermo- and mechanosensitive ion channels known to be responsive to ultrasound. Results: All cell types experienced an increase in calcium fluorescence in response to ultrasound. Gadolinium (Gad), 2-aminoethoxydiphenyl borate (2-APB) and ruthenium red (RR) reduced the percentage of responding neurons and magnitude of response. The percentage of astrocytes responding was significantly lowered only by Gad, whereas both 2-APB and Gad decreased the amplitude of the fluorescence response. 2-APB decreased the percentage of responding endothelial cells, whereas only Gad reduced the magnitude of responses. Pericytes exposed to RR or Gad were less likely to respond to stimulation. RR had no detectable effect on the magnitude of the pericyte responses while 2-APB and Gad significantly decreased the fluorescence intensity, despite not affecting the percentage responding. Conclusion: Our study highlights the role of non-neuronal cells during FUS neuromodulation. All of the investigated cell types are sensitive to mechanical ultrasound stimulation and rely on mechanosensitive ion channels to undergo ultrasound neuromodulation.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Newman2023.pdf} +} + +@article{Nguyen2022, + title = {Neuronal Responses to Focused Ultrasound Are Gated by Pre-Stimulation Brain Rhythms}, + author = {Nguyen, Duc T. and Berisha, Destiny E. and Konofagou, Elisa E. and Dmochowski, Jacek P.}, + year = {2022}, + month = jan, + journal = {Brain Stimulation}, + volume = {15}, + number = {1}, + pages = {233--243}, + issn = {1935861X}, + doi = {10.1016/j.brs.2022.01.002}, + urldate = {2022-04-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Nguyen2022.pdf} +} + +@article{Niu2022, + title = {Transcranial Focused Ultrasound Induces Sustained Synaptic Plasticity in Rat Hippocampus}, + author = {Niu, Xiaodan and Yu, Kai and He, Bin}, + year = {2022}, + month = mar, + journal = {Brain Stimulation}, + volume = {15}, + number = {2}, + pages = {352--359}, + issn = {1935861X}, + doi = {10.1016/j.brs.2022.01.015}, + urldate = {2022-04-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Niu2022.pdf} +} + +@article{Nizar2013, + title = {{\emph{In Vivo}} {{Stimulus-Induced Vasodilation Occurs}} without {{IP}} {\textsubscript{3}} {{Receptor Activation}} and {{May Precede Astrocytic Calcium Increase}}}, + author = {Nizar, Krystal and Uhlirova, Hana and Tian, Peifang and Saisan, Payam A. and Cheng, Qun and Reznichenko, Lidia and Weldy, Kimberly L. and Steed, Tyler C. and Sridhar, Vishnu B. and MacDonald, Christopher L. and Cui, Jianxia and Gratiy, Sergey L. and Sakad{\v z}i{\'c}, Sava and Boas, David A. and Beka, Thomas I. and Einevoll, Gaute T. and Chen, Ju and Masliah, Eliezer and Dale, Anders M. and Silva, Gabriel A. and Devor, Anna}, + year = {2013}, + month = may, + journal = {The Journal of Neuroscience}, + volume = {33}, + number = {19}, + pages = {8411--8422}, + issn = {0270-6474, 1529-2401}, + doi = {10.1523/JNEUROSCI.3285-12.2013}, + urldate = {2024-09-26}, + abstract = {Calcium-dependent release of vasoactive gliotransmitters is widely assumed to trigger vasodilation associated with rapid increases in neuronal activity. Inconsistent with this hypothesis, intact stimulus-induced vasodilation was observed in inositol 1,4,5-triphosphate (IP 3 ) type-2 receptor (R2) knock-out (KO) mice, in which the primary mechanism of astrocytic calcium increase---the release of calcium from intracellular stores following activation of an IP 3 -dependent pathway---is lacking. Further, our results in wild-type (WT) mice indicate that in vivo onset of astrocytic calcium increase in response to sensory stimulus could be considerably delayed relative to the simultaneously measured onset of arteriolar dilation. Delayed calcium increases in WT mice were observed in both astrocytic cell bodies and perivascular endfeet. Thus, astrocytes may not play a role in the initiation of blood flow response, at least not via calcium-dependent mechanisms. Moreover, an increase in astrocytic intracellular calcium was not required for normal vasodilation in the IP 3 R 2 -KO animals.}, + copyright = {https://creativecommons.org/licenses/by-nc-sa/4.0/}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Nizar2013.pdf} +} + +@article{Novell2020, + title = {A New Safety Index Based on Intrapulse Monitoring of Ultra-Harmonic Cavitation during Ultrasound-Induced Blood-Brain Barrier Opening Procedures}, + author = {Novell, A. and Kamimura, H. A. S. and Cafarelli, A. and Gerstenmayer, M. and Flament, J. and Valette, J. and Agou, P. and Conti, A. and Selingue, E. and Aron Badin, R. and Hantraye, P. and Larrat, B.}, + year = {2020}, + month = jun, + journal = {Scientific Reports}, + volume = {10}, + number = {1}, + pages = {10088}, + issn = {2045-2322}, + doi = {10.1038/s41598-020-66994-8}, + urldate = {2024-03-16}, + abstract = {Abstract Ultrasound-induced blood-brain barrier (BBB) opening using microbubbles is a promising technique for local delivery of therapeutic molecules into the brain. The real-time control of the ultrasound dose delivered through the skull is necessary as the range of pressure for efficient and safe BBB opening is very narrow. Passive cavitation detection (PCD) is a method proposed to monitor the microbubble activity during ultrasound exposure. However, there is still no consensus on a reliable safety indicator able to predict potential damage in the brain. Current approaches for the control of the beam intensity based on~PCD~employ a full-pulse analysis~and may suffer from a lack of sensitivity and poor reaction time. To overcome these limitations, we propose an intra-pulse analysis to monitor the evolution of the frequency content during ultrasound bursts. We hypothesized that the destabilization of microbubbles exposed to a critical level of ultrasound would result in the instantaneous generation of subharmonic and ultra-harmonic components. This specific signature was exploited to define a new sensitive indicator of the safety of the ultrasound protocol. The approach was validated in vivo in rats and non-human primates using a retrospective analysis. Our results demonstrate that intra-pulse monitoring was able to exhibit a sudden appearance of ultra-harmonics during the ultrasound excitation pulse. The repeated detection of such a signature within the excitation pulse was highly correlated with the occurrence of side effects such as hemorrhage and edema. Keeping the acoustic pressure at levels where no such sign of microbubble destabilization occurred resulted in safe BBB openings, as shown by MR images and gross pathology. This new indicator~should be more sensitive than conventional full-pulse analysis and can be used to distinguish between potentially harmful and safe ultrasound conditions in the brain with very short reaction time.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Novell2020.pdf} +} + +@incollection{Nyborg1983, + title = {Physical {{Mechanisms}} for {{Biological Effects}} of {{Ultrasound}} at {{Low-Intensity Levels}}}, + booktitle = {Ultrasound {{Interactions}} in {{Biology}} and {{Medicine}}}, + author = {Nyborg, W. L. and Miller, D. L.}, + editor = {Millner, R. and Rosenfeld, E. and Cobet, U.}, + year = {1983}, + pages = {131--138}, + publisher = {Springer US}, + address = {Boston, MA}, + doi = {10.1007/978-1-4684-8384-0_18}, + urldate = {2024-02-19}, + isbn = {978-1-4684-8386-4 978-1-4684-8384-0}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Nyborg1983.pdf} +} + +@article{OBrien2007, + title = {Ultrasound--Biophysics Mechanisms}, + author = {O'Brien, William D.}, + year = {2007}, + month = jan, + journal = {Progress in Biophysics and Molecular Biology}, + volume = {93}, + number = {1-3}, + pages = {212--255}, + issn = {00796107}, + doi = {10.1016/j.pbiomolbio.2006.07.010}, + urldate = {2024-02-19}, + abstract = {Ultrasonic biophysics is the study of mechanisms responsible for how ultrasound and biological materials interact. Ultrasound-induced bioeffect or risk studies focus on issues related to the effects of ultrasound on biological materials. On the other hand, when biological materials affect the ultrasonic wave, this can be viewed as the basis for diagnostic ultrasound. Thus, an understanding of the interaction of ultrasound with tissue provides the scientific basis for image production and risk assessment. Relative to the bioeffect or risk studies, that is, the biophysical mechanisms by which ultrasound affects biological materials, ultrasound-induced bioeffects are generally separated into thermal and nonthermal mechanisms. Ultrasonic dosimetry is concerned with the quantitative determination of ultrasonic energy interaction with biological materials.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/OBrien2007.pdf} +} + +@article{Oh2019, + title = {Ultrasonic {{Neuromodulation}} via {{Astrocytic TRPA1}}}, + author = {Oh, Soo-Jin and Lee, Jung Moo and Kim, Hyun-Bum and Lee, Jungpyo and Han, Sungmin and Bae, Jin Young and Hong, Gyu-Sang and Koh, Wuhyun and Kwon, Jea and Hwang, Eun-Sang and Woo, Dong Ho and Youn, Inchan and Cho, Il-Joo and Bae, Yong Chul and Lee, Sungon and Shim, Jae Wan and Park, Ji-Ho and Lee, C. Justin}, + year = {2019}, + month = oct, + journal = {Current Biology}, + volume = {29}, + number = {20}, + pages = {3386--3401.e8}, + publisher = {Elsevier BV}, + doi = {10.1016/j.cub.2019.08.021}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Oh2019.pdf} +} + +@article{Ohl2006, + title = {Sonoporation from {{Jetting Cavitation Bubbles}}}, + author = {Ohl, Claus-Dieter and Arora, Manish and Ikink, Roy and {de Jong}, Nico and Versluis, Michel and Delius, Michael and Lohse, Detlef}, + year = {2006}, + month = dec, + journal = {Biophysical Journal}, + volume = {91}, + number = {11}, + pages = {4285--4295}, + issn = {00063495}, + doi = {10.1529/biophysj.105.075366}, + urldate = {2023-01-18}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Ohl2006.pdf} +} + +@article{Okun2012, + title = {Deep-{{Brain Stimulation}} for {{Parkinson}}'s {{Disease}}}, + author = {Okun, Michael S.}, + year = {2012}, + month = oct, + journal = {The New England Journal of Medicine}, + volume = {367}, + number = {16}, + pages = {1529--1538}, + doi = {10.1056/nejmct1208070}, + abstract = {A 72-year-old right-handed man with a 12-year history of Parkinson's disease pre sents with a diminished response to medication and right-sided dyskinesia (involuntary movements). During the past several years, he has been taking multiple drugs for Parkinson's disease, including a monoamine oxidase inhibitor, amantadine, a dopa mine agonist, and carbidopa--levodopa. He reports that with his current regimen, which includes 1.5 tablets of 25/100 carbidopa--levodopa taken every 2 hours, he has marked reductions in tremor, rigidity, and bradykinesia and substantial improvement in his walking. Despite multiple interval and dose adjustments, however, he also reports 6 hours per day of ``off'' time, when his symptoms are unresponsive to his current medication regimen. In addition, he has severe, disabling right-sided dyskinesia 4 hours per day. Symptoms affecting his left side are mild and not bothersome. His cognition is excellent, his neurologic examination is otherwise normal, and he has no other coexisting medical conditions. His neurologist refers him to a neurosurgeon for consideration of deep-brain stimulation. T h e C l i nic a l Probl e m Parkinson's disease typically develops between the ages of 55 and 65 years and oc curs in 1 to 2\% of persons over the age of 60 years. 1 Approximately 0.3\% of the general population is affected, and the prevalence is higher among men than women, with a ratio of 1.6 to 1.0. 2 Motor manifestations of the disorder commonly include a resting tremor, a soft voice, small handwriting (micrographia), stiffness (rigidity), slowness of movements (bradykinesia), shuffling steps, and difficulties with balance. 3 A classic symptom is resting tremor, although 20\% of patients do not have it. 4 Parkinson's disease also has a multitude of nonmotor manifestations, including disturbances of mood (e.g., depression, anxiety, and apathy), cognition (e.g., frontal-lobe dysfunction, memory difficulties, and dementia), and sleep (e.g., apnea and sleep disorders), as well as autonomic dysfunction (e.g., sexual dysfunction, digestive problems, and orthostasis). 5 One third of patients with Parkinson's disease lose employment within a year after diagnosis, and within 5 years, a majority are not employed full time. 6 Estimated costs of drug treatment range from \$1,000 to \$6,000 per patient per year. The annual health care cost per patient ranges from \$2,000 to more than \$20,000 per year. 7-10 The risk of death from any cause is nearly doubled for patients with Parkinson's disease, regardless of the duration of the disease. 11 Referral to a neu}, + pmid = {23075179}, + annotation = {MAG ID: 1981841610\\ +S2ID: 71e05a602e95f5641d940a773f9b5a7c9cef04ce}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Okun2012.pdf} +} + +@misc{Olaitan2024, + title = {Focused {{Ultrasound Modulates Dopamine}} in a {{Mesolimbic Reward Circuit}}}, + author = {Olaitan, Greatness O. and Ganesana, Mallikarjunarao and Strohman, Andrew and Lynch, Wendy J. and Legon, Wynn and Jill Venton, B.}, + year = {2024}, + month = feb, + doi = {10.1101/2024.02.13.580202}, + urldate = {2025-01-10}, + abstract = {Dopamine is a neurotransmitter that plays a significant role in reward and motivation. Dysfunction in the mesolimbic dopamine pathway has been linked to a variety of psychiatric disorders, including addiction. Low-intensity focused ultrasound (LIFU) has demonstrated effects on brain activity, but how LIFU affects dopamine neurotransmission is not known. Here, we applied three different intensities (6.5, 13, and 26 W/cm2 Isppa) of 2-minute LIFU to the prelimbic region (PLC) and measured dopamine in the nucleus accumbens (NAc) core using fast-scan cyclic voltammetry. Two minutes of LIFU sonication at 13 W/cm2 to the PLC significantly reduced dopamine release by {\textasciitilde} 50\% for up to 2 hours. However, double the intensity (26 W/cm2) resulted in less inhibition ({\textasciitilde}30\%), and half the intensity (6.5 W/cm2) did not result in any inhibition of dopamine. Anatomical controls applying LIFU to the primary somatosensory cortex did not change NAc core dopamine, and applying LIFU to the PLC did not affect dopamine release in the caudate or NAc shell. Histological evaluations showed no evidence of cell damage or death. Modeling of temperature rise demonstrates a maximum temperature change of 0.5{$^\circ$}C with 13 W/cm2, suggesting that modulation is not due to thermal mechanisms. These studies show that LIFU at a moderate intensity provides a noninvasive, high spatial resolution means to modulate specific mesolimbic circuits that could be used in future studies to target and repair pathways that are dysfunctional in addiction and other psychiatric diseases.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Olaitan2024.pdf} +} + +@article{ONeil1949, + title = {Theory of {{Focusing Radiators}}}, + author = {O'Neil, H. T.}, + year = {1949}, + month = sep, + journal = {The Journal of the Acoustical Society of America}, + volume = {21}, + number = {5}, + pages = {516--526}, + issn = {0001-4966, 1520-8524}, + doi = {10.1121/1.1906542}, + urldate = {2024-05-02}, + abstract = {An approximate theory has been derived describing part of the sound field due to a concave spherical radiator, vibrating with uniform normal velocity; the radius a of the circular boundary is assumed to be large relative to the wave-length and large relative to the depth of the concave surface. The theory describes the distribution of pressure, particle velocity, and intensity along the axis of symmetry and in the vicinity of the focal plane, perpendicular to the axis at the center of curvature. It is shown that the ratio of the intensity at the center of curvature to the average intensity at the radiating surface is nearly equal to (2{$\pi$}h/{$\lambda$})2 where h is the depth of the concave surface and {$\lambda$} is the wave-length. This ratio can be made very large by suitable choice of dimensions, and the focusing is then very sharp. The point of greatest intensity is not at the center of curvature but approaches it with increasing kh = 2{$\pi$}h/{$\lambda$}, and the greatest intensity is not much greater than the intensity at the center of curvature except when kh is small. In the central part of the focal plane, at angle {\texttheta} from the axis, the pressure is approximately proportional to (2/ka sin{\texttheta})J1(ka sin{\texttheta}), which is equivalent to the directivity function of a flat circular piston of radius a, for the region at large distance from the piston. The calculations are in reasonable agreement with G. W. Willard's experimental data for a 5-mc concave quartz crystal, when allowance is made for the non-uniform normal velocity of the crystal.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/ONeil1949.pdf} +} + +@article{OpenScienceCollaboration2015, + title = {Estimating the Reproducibility of Psychological Science}, + author = {{Open Science Collaboration}}, + year = {2015}, + month = aug, + journal = {Science}, + volume = {349}, + number = {6251}, + pages = {aac4716}, + issn = {0036-8075, 1095-9203}, + doi = {10.1126/science.aac4716}, + urldate = {2024-03-13}, + abstract = {Empirically analyzing empirical evidence One of the central goals in any scientific endeavor is to understand causality. Experiments that seek to demonstrate a cause/effect relation most often manipulate the postulated causal factor. Aarts et al. describe the replication of 100 experiments reported in papers published in 2008 in three high-ranking psychology journals. Assessing whether the replication and the original experiment yielded the same result according to several criteria, they find that about one-third to one-half of the original findings were also observed in the replication study. Science , this issue 10.1126/science.aac4716 , A large-scale assessment suggests that experimental reproducibility in psychology leaves a lot to be desired. , INTRODUCTION Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. Scientific claims should not gain credence because of the status or authority of their originator but by the replicability of their supporting evidence. Even research of exemplary quality may have irreproducible empirical findings because of random or systematic error. RATIONALE There is concern about the rate and predictors of reproducibility, but limited evidence. Potentially problematic practices include selective reporting, selective analysis, and insufficient specification of the conditions necessary or sufficient to obtain the results. Direct replication is the attempt to recreate the conditions believed sufficient for obtaining a previously observed finding and is the means of establishing reproducibility of a finding with new data. We conducted a large-scale, collaborative effort to obtain an initial estimate of the reproducibility of psychological science. RESULTS We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. There is no single standard for evaluating replication success. Here, we evaluated reproducibility using significance and P values, effect sizes, subjective assessments of replication teams, and meta-analysis of effect sizes. The mean effect size (r) of the replication effects ( M r = 0.197, SD = 0.257) was half the magnitude of the mean effect size of the original effects ( M r = 0.403, SD = 0.188), representing a substantial decline. Ninety-seven percent of original studies had significant results ( P {$<$} .05). Thirty-six percent of replications had significant results; 47\% of original effect sizes were in the 95\% confidence interval of the replication effect size; 39\% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68\% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams. CONCLUSION No single indicator sufficiently describes replication success, and the five indicators examined here are not the only ways to evaluate reproducibility. Nonetheless, collectively these results offer a clear conclusion: A large portion of replications produced weaker evidence for the original findings despite using materials provided by the original authors, review in advance for methodological fidelity, and high statistical power to detect the original effect sizes. Moreover, correlational evidence is consistent with the conclusion that variation in the strength of initial evidence (such as original P value) was more predictive of replication success than variation in the characteristics of the teams conducting the research (such as experience and expertise). The latter factors certainly can influence replication success, but they did not appear to do so here. Reproducibility is not well understood because the incentives for individual scientists prioritize novelty over replication. Innovation is the engine of discovery and is vital for a productive, effective scientific enterprise. However, innovative ideas become old news fast. Journal reviewers and editors may dismiss a new test of a published idea as unoriginal. The claim that ``we already know this'' belies the uncertainty of scientific evidence. Innovation points out paths that are possible; replication points out paths that are likely; progress relies on both. Replication can increase certainty when findings are reproduced and promote innovation when they are not. This project provides accumulating evidence for many findings in psychological research and suggests that there is still more work to do to verify whether we know what we think we know. Original study effect size versus replication effect size (correlation coefficients). Diagonal line represents replication effect size equal to original effect size. Dotted line represents replication effect size of 0. Points below the dotted line were effects in the opposite direction of the original. Density plots are separated by significant (blue) and nonsignificant (red) effects. , Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47\% of original effect sizes were in the 95\% confidence interval of the replication effect size; 39\% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68\% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/OpenScienceCollaboration2015.pdf} +} + +@misc{optimuslib, + title = {{{OptimUS}}}, + author = {G{\'e}lat, Pierre and Haqshenas, Reza and {van 't Wout}, Elwin} +} + +@article{Padilla2022, + title = {Recommendations for {{Reporting Therapeutic Ultrasound Treatment Parameters}}}, + author = {Padilla, Frederic and {ter Haar}, Gail}, + year = {2022}, + month = jul, + journal = {Ultrasound in Medicine \& Biology}, + volume = {48}, + number = {7}, + pages = {1299--1308}, + issn = {0301-5629}, + doi = {10.1016/j.ultrasmedbio.2022.03.001}, + urldate = {2023-03-24}, + abstract = {These recommendations are intended to provide guidance and to encourage best practice in reporting therapeutic ultrasound treatment parameters. Detailed uniform reporting will allow testing of therapy ultrasound systems and protocols, cross-comparison of studies between different teams using different systems and validation of therapeutic bio-effects. These recommendations have been divided into two sets, one for clinical and one for preclinical studies, each with stratified reporting categories, to account for the disparities in expertise and access to equipment between sites. The recommendations are intended to be useful for clinicians and researchers, for ethical and funding review boards and for the editors and reviewers of scientific journals.}, + langid = {english}, + keywords = {Acoustic cavitation,Acoustic pressure,Exposure parameters,Focused ultrasound,High-intensity focused ultrasound,Histotripsy,Intensity,Therapy ultrasound}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Padilla2022.pdf} +} + +@article{Palmeri2005, + title = {A Finite-Element Method Model of Soft Tissue Response to Impulsive Acoustic Radiation Force}, + author = {Palmeri, M.L. and Sharma, A.C. and Bouchard, R.R. and Nightingale, R.W. and Nightingale, K.R.}, + year = {2005}, + month = oct, + journal = {IEEE Transactions on Ultrasonics, Ferroelectrics and Frequency Control}, + volume = {52}, + number = {10}, + pages = {1699--1712}, + issn = {0885-3010}, + doi = {10.1109/TUFFC.2005.1561624}, + urldate = {2023-01-12}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Palmeri2005.pdf} +} + +@article{Papp2014, + title = {Waxholm {{Space}} Atlas of the {{Sprague Dawley}} Rat Brain}, + author = {Papp, Eszter A. and Leergaard, Trygve B. and Calabrese, Evan and Johnson, G. Allan and Bjaalie, Jan G.}, + year = {2014}, + month = aug, + journal = {NeuroImage}, + volume = {97}, + pages = {374--386}, + issn = {10538119}, + doi = {10.1016/j.neuroimage.2014.04.001}, + urldate = {2023-06-16}, + abstract = {Three-dimensional digital brain atlases represent an important new generation of neuroinformatics tools for understanding complex brain anatomy, assigning location to experimental data, and planning of experiments. We have acquired a microscopic resolution isotropic MRI and DTI atlasing template for the Sprague Dawley rat brain with 39 {$\mu$}m isotropic voxels for the MRI volume and 78 {$\mu$}m isotropic voxels for the DTI. Building on this template, we have delineated 76 major anatomical structures in the brain. Delineation criteria are provided for each structure. We have applied a spatial reference system based on internal brain landmarks according to the Waxholm Space standard, previously developed for the mouse brain, and furthermore connected this spatial reference system to the widely used stereotaxic coordinate system by identifying cranial sutures and related stereotaxic landmarks in the template using contrast given by the active staining technique applied to the tissue. With the release of the present atlasing template and anatomical delineations, we provide a new tool for spatial orientationanalysis of neuroanatomical location, and planning and guidance of experimental procedures in the rat brain. The use of Waxholm Space and related infrastructures will connect the atlas to interoperable resources and services for multi-level data integration and analysis across reference spaces.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Papp2014.pdf} +} + +@article{Parent2004, + title = {Giovanni {{Aldini}}: {{From Animal Electricity}} to {{Human Brain Stimulation}}}, + shorttitle = {Giovanni {{Aldini}}}, + author = {Parent, Andr{\'e}}, + year = {2004}, + month = nov, + journal = {Canadian Journal of Neurological Sciences / Journal Canadien des Sciences Neurologiques}, + volume = {31}, + number = {4}, + pages = {576--584}, + issn = {0317-1671, 2057-0155}, + doi = {10.1017/S0317167100003851}, + urldate = {2025-02-03}, + abstract = {Two hundred years ago, Giovanni Aldini published a highly influential book that reported experiments in which the principles of Luigi Galvani (animal electricity) and Alessandro Volta (bimetallic electricity) were used together for the first time. Aldini was born in Bologna in 1762 and graduated in physics at the University of his native town in 1782. As nephew and assistant of Galvani, he actively participated in a series of crucial experiments with frog's muscles that led to the idea that electricity was the long-sought vital force coursing from brain to muscles. Aldini became professor of experimental physics at the University of Bologna in 1798. He traveled extensively throughout Europe, spending much time defending the concept of his discreet uncle against the incessant attacks of Volta, who did not believe in animal electricity. Aldini used Volta's bimetallic pile to apply electric current to dismembered bodies of animals and humans; these spectacular galvanic reanimation experiments made a strong and enduring impression on his contemporaries. Aldini also treated patients with personality disorders and reported complete rehabilitation following transcranial administration of electric current. Aldini's work laid the ground for the development of various forms of electrotherapy that were heavily used later in the 19th century. Even today, deep brain stimulation, a procedure currently employed to relieve patients with motor or behavioral disorders, owes much to Aldini and galvanism. In recognition of his merits, Aldini was made a knight of the Iron Crown and a councillor of state at Milan, where he died in 1834.}, + copyright = {https://www.cambridge.org/core/terms}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Parent2004.pdf} +} + +@article{Park2021, + title = {Implication of Auditory Confounding in Interpreting Somatosensory and Motor Responses in Low-Intensity Focused Transcranial Ultrasound Stimulation}, + author = {Park, Christine and Chen, Mengyue and Kim, Taewon}, + year = {2021}, + month = jun, + journal = {Journal of Neurophysiology}, + volume = {125}, + number = {6}, + pages = {2356--2360}, + issn = {0022-3077, 1522-1598}, + doi = {10.1152/jn.00701.2020}, + urldate = {2023-06-01}, + abstract = {Low-intensity transcranial focused ultrasound (LI-tFUS) stimulation is a noninvasive neuromodulation tool that demonstrates high target localization accuracy and depth penetration. It has been shown to modulate activities in the primary motor and somatosensory cortex. Previous studies in animals as well as in humans, illustrated in the recently published paper in Brain Stimulation by Braun et al. [Braun V, Blackmore J, Cleveland RO, Butler CR. Brain Stimul 13: 1527--1534, 2020], acknowledged the possibility of indirect stimulation of the peripheral auditory pathway that could confound the somatosensory and motor responses observed with LI-tFUS stimulation. Here, we discuss the implications and interpretations of auditory confounding in the context of neuromodulation.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Park2021.pdf} +} + +@article{Parpura1994, + title = {Glutamate-Mediated Astrocyte--Neuron Signalling}, + author = {Parpura, Vladimir and Basarsky, Trent A. and Liu, Fang and Jeftinija, Ksenija and Jeftinija, Srdija and Haydon, Philip G.}, + year = {1994}, + month = jun, + journal = {Nature}, + volume = {369}, + number = {6483}, + pages = {744--747}, + issn = {0028-0836, 1476-4687}, + doi = {10.1038/369744a0}, + urldate = {2023-05-16}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Parpura1994.pdf} +} + +@article{Parpura2000, + title = {Physiological Astrocytic Calcium Levels Stimulate Glutamate Release to Modulate Adjacent Neurons}, + author = {Parpura, Vladimir and Haydon, Philip G.}, + year = {2000}, + month = jul, + journal = {Proceedings of the National Academy of Sciences}, + volume = {97}, + number = {15}, + pages = {8629--8634}, + issn = {0027-8424, 1091-6490}, + doi = {10.1073/pnas.97.15.8629}, + urldate = {2023-05-16}, + abstract = {Astrocytes can release glutamate in a calcium-dependent manner and consequently signal to adjacent neurons. Whether this glutamate release pathway is used during physiological signaling or is recruited only under pathophysiological conditions is not well defined. One reason for this lack of understanding is the limited knowledge about the levels of calcium necessary to stimulate glutamate release from astrocytes and about how they compare with the range of physiological calcium levels in these cells. We used flash photolysis to raise internal calcium in astrocytes, while monitoring astrocytic calcium levels and glutamate, which evoked slow inward currents that were recorded electrophysiologically from single neurons grown on microislands of astrocytes. With this approach, we demonstrate that modest changes of astrocytic calcium, from 84 to 140 nM, evoke substantial glutamatergic currents in neighboring neurons (-391 pA), with a Hill coefficient of 2.1 to 2.7. Because the agonists glutamate, norepinephrine, and dopamine all raise calcium in astrocytes to levels exceeding 1.8 {$\mu$}M, these quantitative studies demonstrate that the astrocytic glutamate release pathway is engaged at physiological levels of internal calcium. Consequently, the calcium-dependent release of glutamate from astrocytes functions within an appropriate range of astrocytic calcium levels to be used as a signaling pathway within the functional nervous system.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Parpura2000.pdf} +} + +@article{Parrot2011, + title = {A Rapid and Sensitive Method for the Analysis of Brain Monoamine Neurotransmitters Using Ultra-Fast Liquid Chromatography Coupled to Electrochemical Detection}, + author = {Parrot, Sandrine and Neuzeret, Pierre-Charles and Denoroy, Luc}, + year = {2011}, + month = dec, + volume = {879}, + number = {32}, + pages = {3871--3878}, + publisher = {Elsevier BV}, + doi = {10.1016/j.jchromb.2011.10.038}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Parrot2011.pdf} +} + +@article{Parrot2011a, + title = {Microdialyse Intrac{\'e}r{\'e}brale : Une Technique d'{\'e}chantillonnage in Vivo Pour {\'E}tudier La Neurochimie}, + author = {Parrot, Sandrine}, + year = {2011}, + journal = {STAL}, + volume = {37}, + pages = {40--49} +} + +@article{Pascual-Leone2000, + title = {Transcranial Magnetic Stimulation in Cognitive Neuroscience -- Virtual Lesion, Chronometry, and Functional Connectivity}, + author = {{Pascual-Leone}, Alvaro and Walsh, Vincent and Rothwell, John}, + year = {2000}, + journal = {Current Opinion in Neurobiology}, + volume = {10}, + number = {2}, + pages = {232--237}, + issn = {0959-4388}, + doi = {10.1016/S0959-4388(00)00081-7}, + abstract = {Fifteen years after its introduction by Anthony Barker, transcranial magnetic stimulation (TMS) appears to be `coming of age' in cognitive neuroscience and promises to reshape the way we investigate brain--behavior relations. Among the many methods now available for imaging the activity of the human brain, magnetic stimulation is the only technique that allows us to interfere actively with brain function. As illustrated by several experiments over the past couple of years, this property of TMS allows us to investigate the relationship between focal cortical activity and behavior, to trace the timing at which activity in a particular cortical region contributes to a given task, and to map the functional connectivity between brain regions.} +} + +@article{Paulus2016, + title = {Application of {{Transcranial Electric Stimulation}} ({{tDCS}},{{tACS}},{{tRNS}})}, + author = {Paulus, Walter and Nitsche, Michael A. and Antal, Andrea}, + year = {2016}, + month = jan, + journal = {European Psychologist}, + volume = {21}, + number = {1}, + pages = {4--14}, + publisher = {Hogrefe Publishing Group}, + doi = {10.1027/1016-9040/a000242}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Paulus2016.pdf} +} + +@article{Perera2016, + title = {The {{Clinical TMS Society Consensus Review}} and {{Treatment Recommendations}} for {{TMS Therapy}} for {{Major Depressive Disorder}}}, + author = {Perera, Tarique and George, Mark S. and Grammer, Geoffrey and Janicak, Philip G. and {Pascual-Leone}, Alvaro and Wirecki, Theodore S.}, + year = {2016}, + month = may, + journal = {Brain Stimulation}, + volume = {9}, + number = {3}, + pages = {336--346}, + issn = {1935-861X}, + doi = {10.1016/j.brs.2016.03.010}, + urldate = {2023-08-29}, + abstract = {Background Prefrontal Transcranial Magnetic Stimulation (TMS) therapy repeated daily over 4--6 weeks (20--30 sessions) is US Food and Drug Administration (FDA) approved for treating Major Depressive Disorder in adults who have not responded to prior antidepressant medications. In 2011, leading TMS clinical providers and researchers created the Clinical TMS Society (cTMSs) (www.clinicaltmssociety.org, Greenwich, CT, USA), incorporated in 2013. Methods This consensus review was written by cTMSs leaders, informed by membership polls, and approved by the governing board. It summarizes current evidence for the safety and efficacy of the use of TMS therapy for treating depression in routine clinical practice. Authors systematically reviewed the published TMS antidepressant therapy clinical trials. Studies were then assessed and graded on their strength of evidence using the Levels of Evidence framework published by the University of Oxford Centre for Evidence Based Medicine. The authors then summarize essentials for using TMS therapy in routine clinical practice settings derived from discussions and polls of cTMSs members. Finally, each summary clinical recommendation is presented with the substantiating peer-reviewed, published evidence supporting that recommendation. When the current published clinical trial evidence was insufficient or incomplete, expert opinion was included when sufficient consensus was available from experienced clinician users among the membership of the cTMSs, who were polled at the Annual Meetings in 2014 and 2015. Conclusions Daily left prefrontal TMS has substantial evidence of efficacy and safety for treating the acute phase of depression in patients who are treatment resistant or intolerant. Following the clinical recommendations in this document should result in continued safe and effective use of this exciting new treatment modality.}, + keywords = {Depression,Guidelines,Review,TMS}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Perera2016.pdf;/Users/tomaubier/Zotero/storage/6G3E5WV7/S1935861X16300389.html} +} + +@article{Pessina2001, + title = {Pulsed Electromagnetic Fields Affect the Intracellular Calcium Concentrations in Human Astrocytoma Cells}, + author = {Pessina, G.P. and Aldinucci, C. and Palmi, M. and Sgaragli, G. and Benocci, A. and Meini, A and Pessina, F.}, + year = {2001}, + month = oct, + journal = {Bioelectromagnetics}, + volume = {22}, + number = {7}, + pages = {503--510}, + issn = {0197-8462, 1521-186X}, + doi = {10.1002/bem.79}, + urldate = {2021-09-04}, + langid = {english} +} + +@article{Petrov1993, + title = {Flexoelectric Effects in Model and Native Membranes Containing Ion Channels}, + author = {Petrov, {\relax AlexanderG}. and Miller, {\relax BarbaraA}. and Hristova, Kalina and Usherwood, {\relax PeterN.R}.}, + year = {1993}, + month = oct, + journal = {European Biophysics Journal}, + volume = {22}, + number = {4}, + issn = {0175-7571, 1432-1017}, + doi = {10.1007/BF00180263}, + urldate = {2023-03-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Petrov1993.pdf} +} + +@article{Pichardo2015, + title = {Efficient {{Driving}} of {{Piezoelectric Transducers Using}} a {{Biaxial Driving Technique}}}, + author = {Pichardo, Samuel and Silva, Rafael R. C. and Rubel, Oleg and Curiel, Laura}, + editor = {Gruverman, Alexei}, + year = {2015}, + month = sep, + journal = {PLOS ONE}, + volume = {10}, + number = {9}, + pages = {e0139178}, + issn = {1932-6203}, + doi = {10.1371/journal.pone.0139178}, + urldate = {2022-08-16}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Pichardo2015.pdf} +} + +@article{Pichardo2017, + title = {A Viscoelastic Model for the Prediction of Transcranial Ultrasound Propagation: Application for the Estimation of Shear Acoustic Properties in the Human Skull}, + shorttitle = {A Viscoelastic Model for the Prediction of Transcranial Ultrasound Propagation}, + author = {Pichardo, Samuel and {Moreno-Hern{\'a}ndez}, Carlos and Andrew Drainville, Robert and Sin, Vivian and Curiel, Laura and Hynynen, Kullervo}, + year = {2017}, + month = aug, + journal = {Physics in Medicine \& Biology}, + volume = {62}, + number = {17}, + pages = {6938--6962}, + issn = {1361-6560}, + doi = {10.1088/1361-6560/aa7ccc}, + urldate = {2023-09-20}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Pichardo2017.pdf} +} + +@patent{Pichardo2023, + title = {Systems and Methods for Controlling Directional Properties of Ultrasound Transducers via Biphasic Actuation}, + author = {Pichardo, Samuel and Curiel, Laura and Amparano, Sagid Alberto Delgado}, + year = {2023}, + month = feb, + number = {US20230033799A1}, + urldate = {2023-09-28}, + assignee = {Novustx Devices Inc}, + nationality = {US}, + keywords = {driving waveform,electrodes,lateral,ultrasound,ultrasound transducer}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Pichardo2023.pdf} +} + +@article{Pick2017, + title = {{{{\textsc{mG}}}} {{luR}} Long-term Depression Regulates {{GluA2}} Association with {{{\textsc{COPII}}}} Vesicles and Exit from the Endoplasmic Reticulum}, + author = {Pick, Joseph E and Khatri, Latika and Sathler, Matheus F and Ziff, Edward B}, + year = {2017}, + month = jan, + journal = {The EMBO Journal}, + volume = {36}, + number = {2}, + pages = {232--244}, + issn = {0261-4189, 1460-2075}, + doi = {10.15252/embj.201694526}, + urldate = {2024-10-14}, + copyright = {http://onlinelibrary.wiley.com/termsAndConditions\#vor}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Pick2017.pdf} +} + +@article{Pieper, + title = {{{1Surgical Planning Laboratory}}, {{Brigham}} and {{Women}}'s {{Hospital}}; {{2Isomics}}, {{Inc}}.}, + author = {Pieper, Steve and Halle, Michael and Kikinis, Ron}, + abstract = {To be applied to practical clinical research problems, medical image computing software requires infrastructure including routines to read and write various file formats, manipulate 2D and 3D coordinate systems, and present a consistent user interface paradigm and visualization metaphor. At the same time, research software needs to be flexible to facilitate implementation of new ideas. 3D Slicer is a project that aims to provide a platform for a variety of applications through a community-development model. The resulting system has been used for research in both basic biomedical and clinically applied settings. 3D Slicer is built on a set of powerful and widely used software components (Tcl/Tk, VTK, ITK) to which is added an application layer that makes the system usable by non-programmer end-users. Using this approach, advanced applications including image guided surgery, robotics, brain mapping, and virtual colonoscopy have been implemented as 3D Slicer modules. In this paper we discuss some of the goals of the 3D Slicer project and how the architecture helps support those goals. We also point out some of the practical issues which arise from this approach.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Pieper.pdf} +} + +@article{Plaksin2014, + title = {Intramembrane {{Cavitation}} as a {{Predictive Bio-Piezoelectric Mechanism}} for {{Ultrasonic Brain Stimulation}}}, + author = {Plaksin, Michael and Shoham, Shy and Kimmel, Eitan}, + year = {2014}, + month = jan, + journal = {Physical Review X}, + volume = {4}, + number = {1}, + pages = {011004}, + issn = {2160-3308}, + doi = {10.1103/PhysRevX.4.011004}, + urldate = {2023-03-13}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Plaksin2014.pdf} +} + +@article{Plaksin2018, + title = {Thermal {{Transients Excite Neurons}} through {{Universal Intramembrane Mechanoelectrical Effects}}}, + author = {Plaksin, Michael and Shapira, Einat and Kimmel, Eitan and Shoham, Shy}, + year = {2018}, + month = mar, + journal = {Physical Review X}, + volume = {8}, + number = {1}, + pages = {011043}, + issn = {2160-3308}, + doi = {10.1103/PhysRevX.8.011043}, + urldate = {2023-03-13}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Plaksin2018.pdf} +} + +@book{Ploem1987, + title = {Introduction to Fluorescence Microscopy}, + author = {Ploem, J. S. and Tanke, H. J.}, + year = {1987}, + series = {Oxford Science Publications}, + number = {10}, + publisher = {Oxford University Press ; Royal Microscopical Society}, + address = {Oxford ; New York : Oxford}, + isbn = {978-0-19-856408-9}, + langid = {english}, + lccn = {QH212.F55 P57 1987}, + keywords = {Fluorescence microscopy}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Ploem1987.pdf} +} + +@inproceedings{Pohl2013, + title = {{{3D}} Printers May Reduce Animal Numbers to Train Neuroengineering Procedures}, + booktitle = {2013 6th {{International IEEE}}/{{EMBS Conference}} on {{Neural Engineering}} ({{NER}})}, + author = {Pohl, Bernd M. and Gasca, Fernando and Christ, Olaf and Hofmann, Ulrich G.}, + year = {2013}, + month = nov, + pages = {887--890}, + publisher = {IEEE}, + address = {San Diego, CA, USA}, + doi = {10.1109/NER.2013.6696077}, + urldate = {2024-10-16}, + abstract = {Neuroengineering related interventions to small animals always carry the high risk of missled procedures, frequently causing premature death of the animal. In this paper the manufacturing process to build a physical rat skull and brain model for educational use is presented. Out of MRI images a rat brain was segmented to build a negative mould. This form was used to cast an agarose rat brain. For an accompanying rat neurocranium model, CT images were rendered to a surface mesh and printed in 3D out of PLA. The presented workflow results in a high detailed rat skull and rat brain.}, + isbn = {978-1-4673-1969-0}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Pohl2013.pdf} +} + +@article{Poissonnier2007, + title = {Control of {{Prostate Cancer}} by {{Transrectal HIFU}} in 227 {{Patients}}}, + author = {Poissonnier, Laura and Chapelon, Jean-Yves and Rouvi{\`e}re, Olivier and Curiel, Laura and Bouvier, Raymonde and Martin, Xavier and Dubernard, Jean Michel and Gelet, Albert}, + year = {2007}, + month = feb, + journal = {European Urology}, + volume = {51}, + number = {2}, + pages = {381--387}, + publisher = {Elsevier BV}, + doi = {10.1016/j.eururo.2006.04.012} +} + +@article{Pollet2019, + title = {Does Power Ultrasound Affect Heterogeneous Electron Transfer Kinetics?}, + author = {Pollet, Bruno G.}, + year = {2019}, + month = apr, + journal = {Ultrasonics Sonochemistry}, + volume = {52}, + pages = {6--12}, + issn = {13504177}, + doi = {10.1016/j.ultsonch.2018.12.017}, + urldate = {2022-12-20}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Pollet22.pdf} +} + +@article{Ponce2021, + title = {A {{Brief History}} of {{Cerebellar Neurostimulation}}}, + author = {Ponce, Gustavo V. and Klaus, Jana and Schutter, Dennis J. L. G.}, + year = {2021}, + month = aug, + journal = {The Cerebellum}, + volume = {21}, + number = {4}, + pages = {715--730}, + issn = {1473-4230}, + doi = {10.1007/s12311-021-01310-2}, + urldate = {2025-02-02}, + abstract = {The first attempts at using electric stimulation to study human brain functions followed the experiments of Luigi Galvani and Giovanni Aldini on animal electricity during the eighteenth century. Since then, the cerebellum has been among the areas that have been studied by invasive and non-invasive forms of electrical and magnetic stimulation. During the nineteenth century, animal experiments were conducted to map the motor-related regions of cerebellar cortex by means of direct electric stimulation. As electric stimulation research on the cerebellum moved into the twentieth century, systematic research of electric cerebellar stimulation led to a better understanding of its effects and mechanism of action. In addition, the clinical potential of cerebellar stimulation in the treatment of motor diseases started to be explored. With the introduction of transcranial electric and magnetic stimulation, cerebellar research moved to non-invasive techniques. During the twenty-first century, following on groundbreaking research that linked the cerebellum to non-motor functions, non-invasive techniques have facilitated research into different aspects of cerebellar functioning. The present review provides a brief historical account of cerebellar neurostimulation and discusses current challenges and future direction in this field of research.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Ponce2021.pdf} +} + +@article{Pouget2020, + title = {Neuronavigated {{Repetitive Transcranial Ultrasound Stimulation Induces Long-Lasting}} and {{Reversible Effects}} on {{Oculomotor Performance}} in {{Non-human Primates}}}, + author = {Pouget, Pierre and Frey, Stephen and Ahnine, Harry and Attali, David and Claron, Julien and Constans, Charlotte and Aubry, Jean-Francois and Arcizet, Fabrice}, + year = {2020}, + month = aug, + journal = {Frontiers in Physiology}, + volume = {11}, + publisher = {Frontiers Media SA}, + doi = {10.3389/fphys.2020.01042}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Pouget2020.pdf} +} + +@article{Prajzler2018, + title = {Flexible Multimode Polydimethyl-Diphenylsiloxane Optical Planar Waveguides}, + author = {Prajzler, V{\'a}clav and Neruda, Milo{\v s} and Nekvindov{\'a}, Pavla}, + year = {2018}, + month = jan, + journal = {Journal of Materials Science: Materials in Electronics}, + volume = {29}, + number = {7}, + pages = {5878--5884}, + publisher = {{Springer Science and Business Media LLC}}, + doi = {10.1007/s10854-018-8560-z} +} + +@book{Preston1991, + title = {Output {{Measurements}} for {{Medical Ultrasound}}}, + author = {Preston, Roy C. and Shaw, A. and Bacon, D. R. and Davidson, F. and Robinson, S. P. and Zeqiri, B. and Chivers, R. C.}, + editor = {Preston, Roy C.}, + year = {1991}, + publisher = {Springer London}, + address = {London}, + doi = {10.1007/978-1-4471-1883-1}, + urldate = {2023-03-14}, + isbn = {978-1-4471-1885-5 978-1-4471-1883-1}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Preston1991.pdf} +} + +@article{Prieto2013, + title = {Dynamic {{Response}} of {{Model Lipid Membranes}} to {{Ultrasonic Radiation Force}}}, + author = {Prieto, Martin Loynaz and Oralkan, {\"O}mer and {Khuri-Yakub}, Butrus T. and Maduke, Merritt C.}, + editor = {Phillips, William}, + year = {2013}, + month = oct, + journal = {PLoS ONE}, + volume = {8}, + number = {10}, + pages = {e77115}, + issn = {1932-6203}, + doi = {10.1371/journal.pone.0077115}, + urldate = {2022-09-27}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Prieto2013.pdf} +} + +@article{Prieto2020, + title = {Spike Frequency--Dependent Inhibition and Excitation of Neural Activity by High-Frequency Ultrasound}, + author = {Prieto, Martin Loynaz and Firouzi, Kamyar and {Khuri-Yakub}, Butrus T. and Madison, Daniel V. and Maduke, Merritt}, + year = {2020}, + month = nov, + journal = {Journal of General Physiology}, + volume = {152}, + number = {11}, + pages = {e202012672}, + issn = {0022-1295, 1540-7748}, + doi = {10.1085/jgp.202012672}, + urldate = {2023-03-10}, + abstract = {Ultrasound can modulate action potential firing in vivo and in vitro, but the mechanistic basis of this phenomenon is not well understood. To address this problem, we used patch-clamp recording to quantify the effects of focused, high-frequency (43 MHz) ultrasound on evoked action potential firing in CA1 pyramidal neurons in acute rodent hippocampal brain slices. We find that ultrasound can either inhibit or potentiate firing in a spike frequency--dependent manner: at low (near-threshold) input currents and low firing frequencies, ultrasound inhibits firing, while at higher input currents and higher firing frequencies, ultrasound potentiates firing. The net result of these two competing effects is that ultrasound increases the threshold current for action potential firing, the slope of frequency-input curves, and the maximum firing frequency. In addition, ultrasound slightly hyperpolarizes the resting membrane potential, decreases action potential width, and increases the depth of the after-hyperpolarization. All of these results can be explained by the hypothesis that ultrasound activates a sustained potassium conductance. According to this hypothesis, increased outward potassium currents hyperpolarize the resting membrane potential and inhibit firing at near-threshold input currents but potentiate firing in response to higher-input currents by limiting inactivation of voltage-dependent sodium channels during the action potential. This latter effect is a consequence of faster action potential repolarization, which limits inactivation of voltage-dependent sodium channels, and deeper (more negative) after-hyperpolarization, which increases the rate of recovery from inactivation. Based on these results, we propose that ultrasound activates thermosensitive and mechanosensitive two-pore-domain potassium (K2P) channels through heating or mechanical effects of acoustic radiation force. Finite-element modeling of the effects of ultrasound on brain tissue suggests that the effects of ultrasound on firing frequency are caused by a small (\<2{$^\circ$}C) increase in temperature, with possible additional contributions from mechanical effects.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Prieto2020.pdf} +} + +@article{Prieto2024, + title = {Toward an Ion-channel-centric Approach to Ultrasound Neuromodulation}, + author = {Prieto, Martin L and Maduke, Merritt}, + year = {2024}, + month = apr, + journal = {Current Opinion in Behavioral Sciences}, + volume = {56}, + pages = {101355}, + issn = {23521546}, + doi = {10.1016/j.cobeha.2024.101355}, + urldate = {2024-02-20}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Prieto2024.pdf} +} + +@article{Prieur2017, + title = {Modeling of the Acoustic Radiation Force in Elastography}, + author = {Prieur, Fabrice and Sapozhnikov, Oleg A.}, + year = {2017}, + month = aug, + journal = {The Journal of the Acoustical Society of America}, + volume = {142}, + number = {2}, + pages = {947--961}, + issn = {0001-4966}, + doi = {10.1121/1.4998585}, + urldate = {2022-10-19}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Prieur2017.pdf} +} + +@article{Qiu2019, + title = {The {{Mechanosensitive Ion Channel Piezo1 Significantly Mediates In~Vitro Ultrasonic Stimulation}} of {{Neurons}}}, + author = {Qiu, Zhihai and Guo, Jinghui and Kala, Shashwati and Zhu, Jiejun and Xian, Quanxiang and Qiu, Weibao and Li, Guofeng and Zhu, Ting and Meng, Long and Zhang, Rui and Chan, Hsiao Chang and Zheng, Hairong and Sun, Lei}, + year = {2019}, + month = nov, + journal = {iScience}, + volume = {21}, + pages = {448--457}, + issn = {2589-0042}, + doi = {10.1016/j.isci.2019.10.037}, + urldate = {2023-04-20}, + abstract = {Ultrasound brain stimulation is a promising modality for probing brain function and treating brain disease non-invasively and with high spatiotemporal resolution. However, the mechanism underlying its effects remains unclear. Here, we examine the role that the mouse piezo-type mechanosensitive ion channel component 1 (Piezo1) plays in mediating the in~vitro effects of ultrasound in mouse primary cortical neurons and a neuronal cell line. We show that ultrasound alone could activate heterologous and endogenous Piezo1, initiating calcium influx and increased nuclear c-Fos expression in primary neurons but not when pre-treated with a Piezo1 inhibitor. We also found that ultrasound significantly increased the expression of the important proteins phospho-CaMKII, phospho-CREB, and c-Fos in a neuronal cell line, but Piezo1 knockdown significantly reduced this effect. Our findings demonstrate that the activity of mechanosensitive ion channels such as Piezo1 stimulated by ultrasound is an important contributor to its ability to stimulate cells in~vitro.}, + langid = {english}, + keywords = {Cellular Neuroscience,Molecular Neuroscience,Neuroscience,Sensory Neuroscience}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Qiu2019a.pdf} +} + +@article{Rabut2020, + title = {Ultrasound {{Technologies}} for {{Imaging}} and {{Modulating Neural Activity}}}, + author = {Rabut, Claire and Yoo, Sangjin and Hurt, Robert C. and Jin, Zhiyang and Li, Hongyi and Guo, Hongsun and Ling, Bill and Shapiro, Mikhail G.}, + year = {2020}, + month = oct, + journal = {Neuron}, + volume = {108}, + number = {1}, + pages = {93--110}, + issn = {08966273}, + doi = {10.1016/j.neuron.2020.09.003}, + urldate = {2022-04-11}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Rabut2020.pdf} +} + +@article{Ravez1979, + title = {Les Materiaux Ferroelectriques et Leurs Applications}, + author = {Ravez, J and F, Micheron}, + year = {1979}, + journal = {Les materiaux ferroelectriques et leurs applications}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Ravez1979.pdf;/Users/tomaubier/Zotero/storage/9CE6VBG6/index.html} +} + +@article{Rawji2020, + title = {On the {{Use}} of {{TMS}} to {{Investigate}} the {{Pathophysiology}} of {{Neurodegenerative Diseases}}}, + author = {Rawji, Vishal and Latorre, Anna and Sharma, Nikhil and Rothwell, John C. and Rocchi, Lorenzo}, + year = {2020}, + month = nov, + journal = {Frontiers in Neurology}, + volume = {11}, + publisher = {Frontiers Media SA}, + doi = {10.3389/fneur.2020.584664}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Rawji2020.pdf} +} + +@book{Richoux2018, + title = {Integral {{Formalism}} in {{Acoustics}}}, + author = {Richoux, Olivier}, + year = {2018}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Richoux2018.pdf} +} + +@incollection{Robel1981, + title = {Estradiol and {{Progesterone Receptors}} in {{Human Endometrium}}}, + booktitle = {Biochemical {{Actions}} of {{Hormones}}}, + author = {Robel, Paul and Mortel, Rodrigue and Baulieu, Etienne-Emile}, + year = {1981}, + pages = {493--514}, + publisher = {Elsevier}, + doi = {10.1016/b978-0-12-452808-6.50013-x} +} + +@misc{RobertHaase2024, + title = {Haesleinhuepf/{{BioImageAnalysisNotebooks}}: Gpt-2024.1.6}, + shorttitle = {Haesleinhuepf/{{BioImageAnalysisNotebooks}}}, + author = {Robert Haase and Mara Lampert and Guillaume Witz and Till Korten and Markus J. Ankenbrand and Elisabeth Kugler and Marcelo Zoccoler and {amgfernandes} and Shannon Taylor and Anirban Ray}, + year = {2024}, + month = jan, + doi = {10.5281/ZENODO.10465773}, + urldate = {2024-03-14}, + abstract = {First release of the Bio-image Analysis GPT, with selected topics}, + copyright = {Creative Commons Attribution 4.0 International}, + howpublished = {[object Object]} +} + +@article{Robinson1996, + title = {Stimulation of Secretion from Bovine Adrenal Chromaffin Cells by Microsecond Bursts of Therapeutic Levels of Ultrasound.}, + author = {Robinson, I M and Kinnick, R R and Greenleaf, J F and Fernandez, J M}, + year = {1996}, + month = apr, + journal = {The Journal of Physiology}, + volume = {492}, + number = {1}, + pages = {257--263}, + issn = {0022-3751, 1469-7793}, + doi = {10.1113/jphysiol.1996.sp021306}, + urldate = {2024-03-11}, + abstract = {1. In this study the secretory response of individual bovine adrenal chromaffin cells was monitored using amperometric carbon-fibre microelectrodes. Cells were stimulated to secrete by exposure to 20-100 microseconds long tonebursts of ultrasound (2-4 x 10(5) Pa; peak pressure at 1 MHz). 2. Three types of secretory responses were observed: an almost instantaneous response, a delayed release of catecholamines, or a series of `burst-like' secretory bouts. 3. Fura-2 measurements of intracellular Ca2+ concentrations showed that the release of catecholamines was accompanied by an increase in the intracellular Ca2+ concentration. In the absence of extracellular Ca2+, secretory responses were not evoked showing that Ca2+ entry was necessary to elicit catecholamine release.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Robinson1996.pdf} +} + +@inproceedings{Rocklin2015, + title = {Dask: {{Parallel Computation}} with {{Blocked}} Algorithms and {{Task Scheduling}}}, + shorttitle = {Dask}, + booktitle = {Python in {{Science Conference}}}, + author = {Rocklin, Matthew}, + year = {2015}, + pages = {126--132}, + address = {Austin, Texas}, + doi = {10.25080/Majora-7b98e3ed-013}, + urldate = {2023-10-31}, + abstract = {Dask enables parallel and out-of-core computation. We couple blocked algorithms with dynamic and memory aware task scheduling to achieve a parallel and out-of-core NumPy clone. We show how this extends the effective scale of modern hardware to larger datasets and discuss how these ideas can be more broadly applied to other parallel collections.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Rocklin2015.pdf} +} + +@article{Roderick, + title = {Calcium-Induced Calcium Release}, + author = {Roderick, H Llewelyn and Bootman, Martin D}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Roderick.pdf} +} + +@article{Ross2012, + title = {Understanding Calcium Waves and Sparks in Central Neurons}, + author = {Ross, William N.}, + year = {2012}, + month = mar, + journal = {Nature Reviews Neuroscience}, + volume = {13}, + number = {3}, + pages = {157--168}, + issn = {1471-003X, 1471-0048}, + doi = {10.1038/nrn3168}, + urldate = {2023-01-18}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Ross2012.pdf} +} + +@article{Ross2014, + title = {Mechanical Stimulation Evokes Rapid Increases in Extracellular Adenosine Concentration in the Prefrontal Cortex}, + author = {Ross, Ashley E. and Nguyen, Michael D. and Privman, Eve and Venton, B. Jill}, + year = {2014}, + month = jul, + journal = {Journal of Neurochemistry}, + volume = {130}, + number = {1}, + pages = {50--60}, + issn = {0022-3042, 1471-4159}, + doi = {10.1111/jnc.12711}, + urldate = {2024-04-04}, + abstract = {Mechanical perturbations can release ATP, which is broken down to adenosine. In this work, we used carbon-fiber microelectrodes and fast-scan cyclic voltammetry to measure mechanically stimulated adenosine in the brain by lowering the electrode 50 lm. Mechanical stimulation evoked adenosine in vivo (average: 3.3 {\AE} 0.6 lM) and in brain slices (average: 0.8 {\AE} 0.1 lM) in the prefrontal cortex. The release was transient, lasting 18 {\AE} 2 s. Lowering a 15-lm-diameter glass pipette near the carbon-fiber microelectrode produced similar results as lowering the actual microelectrode. However, applying a small puff of artificial cerebral spinal fluid was not sufficient to evoke adenosine. Multiple stimulations within a 50-lm region of a slice did not significantly change over time or damage cells. Chelating calcium with EDTA or blocking sodium channels with tetrodotoxin significantly decreased mechanically evoked adenosine, signifying that the release is activity dependent. An alpha-amino-3-hydroxy5-methylisoxazole-4-propionate receptor antagonist, 6-cyano7-nitroquinoxaline-2,3-dione, did not affect mechanically stimulated adenosine; however, the nucleoside triphosphate diphosphohydrolase 1,2 and 3 (NTDPase) inhibitor POM-1 significantly reduced adenosine so a portion of adenosine is dependent on extracellular ATP metabolism. Thus, mechanical perturbations from inserting a probe in the brain cause rapid, transient adenosine signaling which might be neuroprotective.}, + copyright = {http://onlinelibrary.wiley.com/termsAndConditions\#vor}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Ross2014.pdf} +} + +@article{Rossini2015, + title = {Non-Invasive Electrical and Magnetic Stimulation of the Brain, Spinal Cord, Roots and Peripheral Nerves: {{Basic}} Principles and Procedures for Routine Clinical and Research Application. {{An}} Updated Report from an {{I}}.{{F}}.{{C}}.{{N}}. {{Committee}}}, + shorttitle = {Non-Invasive Electrical and Magnetic Stimulation of the Brain, Spinal Cord, Roots and Peripheral Nerves}, + author = {Rossini, P.M. and Burke, D. and Chen, R. and Cohen, L.G. and Daskalakis, Z. and Di Iorio, R. and Di Lazzaro, V. and Ferreri, F. and Fitzgerald, P.B. and George, M.S. and Hallett, M. and Lefaucheur, J.P. and Langguth, B. and Matsumoto, H. and Miniussi, C. and Nitsche, M.A. and {Pascual-Leone}, A. and Paulus, W. and Rossi, S. and Rothwell, J.C. and Siebner, H.R. and Ugawa, Y. and Walsh, V. and Ziemann, U.}, + year = {2015}, + month = jun, + journal = {Clinical Neurophysiology}, + volume = {126}, + number = {6}, + pages = {1071--1107}, + issn = {13882457}, + doi = {10.1016/j.clinph.2015.02.001}, + urldate = {2023-09-04}, + abstract = {These guidelines provide an up-date of previous IFCN report on ``Non-invasive electrical and magnetic stimulation of the brain, spinal cord and roots: basic principles and procedures for routine clinical application'' (Rossini et al., 1994). A new Committee, composed of international experts, some of whom were in the panel of the 1994 ``Report'', was selected to produce a current state-of-the-art review of noninvasive stimulation both for clinical application and research in neuroscience.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Rossini2015.pdf} +} + +@article{Rougier2014, + title = {Ten {{Simple Rules}} for {{Better Figures}}}, + author = {Rougier, Nicolas P. and Droettboom, Michael and Bourne, Philip E.}, + year = {2014}, + month = sep, + journal = {PLoS Computational Biology}, + volume = {10}, + number = {9}, + pages = {e1003833}, + issn = {1553-7358}, + doi = {10.1371/journal.pcbi.1003833}, + urldate = {2024-08-06}, + langid = {english}, + file = {/Users/tomaubier/Zotero/storage/6QX7I84P/Rougier et al. - 2014 - Ten Simple Rules for Better Figures.pdf} +} + +@article{Roy2018, + title = {State of the {{Art}}: {{Novel Applications}} for {{Deep Brain Stimulation}}}, + shorttitle = {State of the {{Art}}}, + author = {Roy, Holly A. and Green, Alexander L. and Aziz, Tipu Z.}, + year = {2018}, + month = feb, + journal = {Neuromodulation: Technology at the Neural Interface}, + volume = {21}, + number = {2}, + pages = {126--134}, + issn = {10947159}, + doi = {10.1111/ner.12604}, + urldate = {2023-08-30}, + abstract = {Objectives: Deep brain stimulation (DBS) is a rapidly developing field of neurosurgery with potential therapeutic applications that are relevant to conditions traditionally viewed as beyond the limits of neurosurgery. Our objective, in this review, is to highlight some of the emerging applications of DBS within three distinct but overlapping spheres, namely trauma, neuropsychiatry, and autonomic physiology. Review Methods: An extensive literature review was carried out in MEDLINE, to identify relevant studies and review articles describing applications of DBS in the areas of trauma, neuropsychiatry and autonomic neuroscience. Results: A wide range of applications of DBS in these spheres was identified, some having only been tested in one or two cases, others much better studied. Conclusions: We have identified various avenues for DBS to be applied for patient benefit in cases relevant to trauma, neuropsychiatry and autonomic neuroscience. Further developments in DBS technology and clinical trial design will enable these novel applications to be effectively and rigorously assessed and utilized most effectively.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Roy2018.pdf} +} + +@book{Russ2006, + title = {The {{Image Processing Handbook}}}, + author = {Russ, John C.}, + year = {2006}, + month = dec, + edition = {0}, + publisher = {CRC Press}, + doi = {10.1201/9780203881095}, + urldate = {2022-04-15}, + isbn = {978-0-203-88109-5}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Russ2006.pdf} +} + +@misc{Russel, + title = {{{ALongitudinal}} and {{Transverse Wave Motion}} - {{Acoustics}} and {{Vibration Animations}}}, + author = {Russel, Daniel A.} +} + +@article{Sabraoui2011, + title = {Feedback Loop Process to Control Acoustic Cavitation}, + author = {Sabraoui, Abbas and Inserra, Claude and Gilles, Bruno and B{\'e}ra, Jean-Christophe and Mestas, Jean-Louis}, + year = {2011}, + month = mar, + journal = {Ultrasonics Sonochemistry}, + volume = {18}, + number = {2}, + pages = {589--594}, + issn = {13504177}, + doi = {10.1016/j.ultsonch.2010.07.011}, + urldate = {2024-03-16}, + abstract = {Applications involving acoustic cavitation mechanisms, such as sonoporation, are often poorly reproducible because of the unstationary behavior of cavitation. For this purpose, this study proposes to work at a fixed cavitation level instead of a fixed acoustic intensity. A regulated cavitation generator has been developed in an in vitro configuration of standing wave field. This system implements the regulation of the cavitation level during sonication by modulating the applied acoustic intensity with a feedback loop based on acoustic measurements. The experimental setup consists of a plane piezoelectric transducer for sonication (continuous wave, frequency 445 kHz) and a hydrophone pointing to the sonicated medium. The cavitation level is quantified every 5 ms from a spectral analysis of the acoustic signal. The results show that the regulation device generates reproducible mean cavitation levels with a standard deviation lower than 1.6\% in the applied intensity range (from 0.12 to 3.44 W/cm2), while this standard deviation can reach 76\% without regulation. The feedback loop process imposes precise cavitation level even in low applied acoustic intensity.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Sabraoui2011.pdf} +} + +@article{Salahshoor2021, + title = {Mechanics {{Of Ultrasonic Neuromodulation In A Mouse Subject}}}, + author = {Salahshoor, Hossein and Guo, Hongsun and Shapiro, Mikhail G. and Ortiz, Michael}, + year = {2021}, + journal = {bioRxiv}, + doi = {10.1101/2021.09.23.461613}, + abstract = {Ultrasound neuromodulation (UNM), where a region in the brain is targeted by focused ultrasound (FUS), which, in turn, causes excitation or inhibition of neural activity, has recently received considerable attention as a promising tool for neuroscience. Despite its great potential, several aspects of UNM are still unknown. An important question pertains to the off-target sensory effects of UNM and their dependence on stimulation frequency. To understand these effects, we have developed a finite-element model of a mouse, including elasticity and viscoelasticity, and used it to interrogate the response of mouse models to focused ultrasound (FUS). We find that, while some degree of focusing and magnification of the signal is achieved within the brain, the induced pressure-wave pattern is complex and delocalized. In addition, we find that the brain is largely insulated, or 9cloaked9, from shear waves by the cranium and that the shear waves are largely carried away from the skull by the vertebral column, which acts as a waveguide. We find that, as expected, this waveguide mechanism is strongly frequency dependent, which may contribute to the frequency dependence of UNM effects. Our calculations further suggest that off-target skin locations experience displacements and stresses at levels that, while greatly attenuated from the source, could nevertheless induce sensory responses in the subject.}, + annotation = {MAG ID: 3201754743}, + file = {/Users/tomaubier/Zotero/storage/VCP7DSSV/FUS evoked motor response.mp4} +} + +@article{Salahshoor2022, + title = {Mechanics of Ultrasonic Neuromodulation in a Mouse Subject}, + author = {Salahshoor, Hossein and Guo, Hongsun and Shapiro, Mikhail G. and Ortiz, Michael}, + year = {2022}, + month = jan, + journal = {Extreme Mechanics Letters}, + volume = {50}, + pages = {101539}, + issn = {23524316}, + doi = {10.1016/j.eml.2021.101539}, + urldate = {2022-06-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Salahshoor2022.pdf} +} + +@article{Salatino2017, + title = {Glial Responses to Implanted Electrodes in the Brain}, + author = {Salatino, Joseph W. and Ludwig, Kip A. and Kozai, Takashi D. Y. and Purcell, Erin K.}, + year = {2017}, + month = nov, + journal = {Nature Biomedical Engineering}, + volume = {1}, + number = {11}, + pages = {862--877}, + issn = {2157-846X}, + doi = {10.1038/s41551-017-0154-1}, + urldate = {2023-08-07}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Salatino2017.pdf} +} + +@article{Saleem2014, + title = {Interactions of Antagonists with Subtypes of Inositol 1,4,5-trisphosphate ( {{{\textsc{IP}}}} {\textsubscript{3}} ) Receptor}, + shorttitle = {Interactions of Antagonists with Subtypes of Inositol 1,4,5-trisphosphate (}, + author = {Saleem, Huma and Tovey, Stephen C and Molinski, Tadeusz F and Taylor, Colin W}, + year = {2014}, + month = jul, + journal = {British Journal of Pharmacology}, + volume = {171}, + number = {13}, + pages = {3298--3312}, + issn = {0007-1188, 1476-5381}, + doi = {10.1111/bph.12685}, + urldate = {2024-10-10}, + abstract = {Background and Purpose Inositol 1,4,5-trisphosphate receptors ( IP 3 Rs ) are intracellular Ca 2+ channels. Interactions of the commonly used antagonists of IP 3 Rs with IP 3 R subtypes are poorly understood. Experimental Approach IP 3 -evoked Ca 2+ release from permeabilized DT 40 cells stably expressing single subtypes of mammalian I P 3 R was measured using a luminal Ca 2+ indicator. The effects of commonly used antagonists on IP 3 -evoked Ca 2+ release and 3 H-IP 3 binding were characterized. Key Results Functional analyses showed that heparin was a competitive antagonist of all IP 3 R subtypes with different affinities for each ( IP 3 R 3 {$>$} IP 3 R 1 {$\geq$} IP 3 R 2). This sequence did not match the affinities for heparin binding to the isolated N -terminal from each IP 3 R subtype. 2-aminoethoxydiphenyl borate (2- APB ) and high concentrations of caffeine selectively inhibited IP 3 R 1 without affecting IP 3 binding. Neither X estospongin C nor X estospongin D effectively inhibited IP 3 -evoked Ca 2+ release via any IP 3 R subtype. Conclusions and Implications Heparin competes with IP 3 , but its access to the IP 3 -binding core is substantially hindered by additional IP 3 R residues. These interactions may contribute to its modest selectivity for IP 3 R 3. Practicable concentrations of caffeine and 2- APB inhibit only IP 3 R 1. X estospongins do not appear to be effective antagonists of IP 3 R s.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Saleem2014.pdf} +} + +@article{Sassaroli2016, + title = {Acoustic Neuromodulation from a Basic Science Prospective}, + author = {Sassaroli, Elisabetta and Vykhodtseva, Natalia}, + year = {2016}, + month = may, + journal = {Journal of Therapeutic Ultrasound}, + volume = {4}, + number = {1}, + publisher = {{Springer Science and Business Media LLC}}, + doi = {10.1186/s40349-016-0061-z}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Sassaroli2016.pdf} +} + +@article{Sato2018, + title = {Ultrasonic {{Neuromodulation Causes Widespread Cortical Activation}} via an {{Indirect Auditory Mechanism}}}, + author = {Sato, Tomokazu and Shapiro, Mikhail G. and Tsao, Doris Y.}, + year = {2018}, + month = jun, + journal = {Neuron}, + volume = {98}, + number = {5}, + pages = {1031-1041.e5}, + issn = {08966273}, + doi = {10.1016/j.neuron.2018.05.009}, + urldate = {2023-06-01}, + abstract = {Ultrasound has received widespread attention as an emerging technology for targeted, non-invasive neuromodulation based on its ability to evoke electrophysiological and motor responses in animals. However, little is known about the spatiotemporal pattern of ultrasound-induced brain activity that could drive these responses. Here, we address this question by combining focused ultrasound with wide-field optical imaging of calcium signals in transgenic mice. Surprisingly, we find cortical activity patterns consistent with indirect activation of auditory pathways rather than direct neuromodulation at the ultrasound focus. Ultrasound-induced activity is similar to that evoked by audible sound. Furthermore, both ultrasound and audible sound elicit motor responses consistent with a startle reflex, with both responses reduced by chemical deafening. These findings reveal an indirect auditory mechanism for ultrasound-induced cortical activity and movement requiring careful consideration in future development of ultrasonic neuromodulation as a tool in neuroscience research.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Sato2018.pdf} +} + +@article{Scemes2006, + title = {Astrocyte Calcium Waves: {{What}} They Are and What They Do}, + shorttitle = {Astrocyte Calcium Waves}, + author = {Scemes, Eliana and Giaume, Christian}, + year = {2006}, + month = nov, + journal = {Glia}, + volume = {54}, + number = {7}, + pages = {716--725}, + issn = {0894-1491, 1098-1136}, + doi = {10.1002/glia.20374}, + urldate = {2024-04-25}, + abstract = {Several lines of evidence indicate that the elaborated calcium signals and the occurrence of calcium waves in astrocytes provide these cells with a specific form of excitability. The identification of the cellular and molecular steps involved in the triggering and transmission of Ca21 waves between astrocytes resulted in the identification of two pathways mediating this form of intercellular communication. One of them involves the direct communication between the cytosols of two adjoining cells through gap junction channels, while the other depends upon the release of ``gliotransmitters'' that activates membrane receptors on neighboring cells. In this review we summarize evidence in favor of these two mechanisms of Ca21 wave transmission and we discuss that they may not be mutually exclusive, but are likely to work in conjunction to coordinate the activity of a group of cells. To address a key question regarding the functional consequences following the passage of a Ca21 wave, we list, in this review, some of the potential intracellular targets of these Ca21 transients in astrocytes, and discuss the functional consequences of the activation of these targets for the interactions that astrocytes maintain with themselves and with other cellular partners, including those at the glial/vasculature interface and at perisynaptic sites where astrocytic processes tightly interact with neurons. VC 2006 Wiley-Liss, Inc.}, + copyright = {http://onlinelibrary.wiley.com/termsAndConditions\#vor}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Scemes2006.pdf} +} + +@article{Schipke2008, + title = {Temperature and Nitric Oxide Control Spontaneous Calcium Transients in Astrocytes}, + author = {Schipke, Carola G. and Heidemann, Antje and Skupin, Alexander and Peters, Oliver and Falcke, Martin and Kettenmann, Helmut}, + year = {2008}, + month = mar, + journal = {Cell Calcium}, + volume = {43}, + number = {3}, + pages = {285--295}, + issn = {01434160}, + doi = {10.1016/j.ceca.2007.06.002}, + urldate = {2024-06-30}, + abstract = {Transient spontaneous increases in the intracellular Ca2+ concentration have been frequently observed in astrocytes in cell culture and in acutely isolated slices from several brain regions. Recent in vivo experiments, however, reported only a low frequency of spontaneous Ca2+ events in astrocytes. Since the ex vivo experiments were usually performed at temperatures lower than physiological body temperature, we addressed the question whether temperature could influence the spontaneous Ca2+ activity in astrocytes. Indeed, comparing the frequency and spike width of spontaneous Ca2+ transients in astrocytes at temperatures between 20 and 37 {\textopenbullet}C in culture as well as in acute cortical slices from mouse brain, revealed that spontaneous Ca2+ responses occurred frequently at low temperature and became less frequent at higher temperature. Moreover, the single Ca2+ events had a longer duration at low temperature. We found that nitric oxide (NO) mimicked the increase in spontaneous Ca2+ activity and that an NO-synthase inhibitor attenuated the effect of lowering the temperature. Thus, temperature and NO are major determinants of spontaneous astrocytic Ca2+ signalling.}, + copyright = {https://www.elsevier.com/tdm/userlicense/1.0/}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Schipke2008.pdf} +} + +@article{Schwalm2017, + title = {Cortex-Wide {{BOLD fMRI}} Activity Reflects Locally-Recorded Slow Oscillation-Associated Calcium Waves}, + author = {Schwalm, Miriam and Schmid, Florian and Wachsmuth, Lydia and Backhaus, Hendrik and Kronfeld, Andrea and Aedo Jury, Felipe and Prouvot, Pierre-Hugues and Fois, Consuelo and Albers, Franziska and {van Alst}, Timo and Faber, Cornelius and Stroh, Albrecht}, + year = {2017}, + month = sep, + journal = {eLife}, + volume = {6}, + pages = {e27602}, + issn = {2050-084X}, + doi = {10.7554/eLife.27602}, + urldate = {2023-01-18}, + abstract = {Spontaneous slow oscillation-associated slow wave activity represents an internally generated state which is characterized by alternations of network quiescence and stereotypical episodes of neuronal activity - slow wave events. However, it remains unclear which macroscopic signal is related to these active periods of the slow wave rhythm. We used optic fiber-based calcium recordings of local neural populations in cortex and thalamus to detect neurophysiologically defined slow calcium waves in isoflurane anesthetized rats. The individual slow wave events were used for an event-related analysis of simultaneously acquired whole-brain BOLD fMRI. We identified BOLD responses directly related to onsets of slow calcium waves, revealing a cortex-wide BOLD correlate: the entire cortex was engaged in this specific type of slow wave activity. These findings demonstrate a direct relation of defined neurophysiological events to a specific BOLD activity pattern and were confirmed for ongoing slow wave activity by independent component and seed-based analyses. , When a person is in a deep non-dreaming sleep, neurons in their brain alternate slowly between periods of silence and periods of activity. This gives rise to low-frequency brain rhythms called slow waves, which are thought to help stabilize memories. Slow wave activity can be detected on multiple scales, from the pattern of electrical impulses sent by an individual neuron to the collective activity of the brain's entire outer layer, the cortex. But does slow wave activity in an individual group of neurons in the cortex affect the activity of the rest of the brain? To find out, Schwalm, Schmid, Wachsmuth et al. took advantage of the fact that slow waves also occur under general anesthesia, and placed anesthetized rats inside miniature whole-brain scanners. A small region of cortex in each rat had been injected with a dye that fluoresces whenever the neurons in that region are active. An optical fiber was lowered into the rat's brain to transmit the fluorescence signals to a computer. Monitoring these signals while the animals lay inside the scanner revealed that slow-wave activity in any one group of cortical neurons was accompanied by slow-wave activity across the cortex as a whole. This relationship was seen only for slow waves, and not for other brain rhythms. Slow waves seem to occur in all species of animal with a backbone, and in both healthy and diseased brains. While it is not possible to inject fluorescent dyes into the human brain, it is possible to monitor neuronal activity using electrodes. Comparing local electrode recordings with measures of whole-brain activity from scanners could thus allow similar experiments to be performed in people. There is growing evidence -- from animal models and from studies of patients -- that slow waves may be altered in Alzheimer's disease. Further work is required to determine whether detecting these changes could help diagnose disease at earlier stages, and whether reversing them may have therapeutic potential.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Schwalm2017.pdf} +} + +@book{Seifter2005, + title = {Concepts in Medical Physiology}, + author = {Seifter, Julian and Sloane, David and Ratner, Austin}, + year = {2005}, + publisher = {Lippincott Williams \& Wilkins}, + address = {Philadelphia, PA}, + isbn = {978-0-7817-4489-8}, + keywords = {Human physiology,Physiological Processes} +} + +@article{Sepehrirahnama2022, + title = {Acoustofluidics 24: Theory and Experimental Measurements of Acoustic Interaction Force}, + shorttitle = {Acoustofluidics 24}, + author = {Sepehrirahnama, Shahrokh and Ray Mohapatra, Abhishek and Oberst, Sebastian and Chiang, Yan Kei and Powell, David A. and Lim, Kian-Meng}, + year = {2022}, + journal = {Lab on a Chip}, + volume = {22}, + number = {18}, + pages = {3290--3313}, + issn = {1473-0197, 1473-0189}, + doi = {10.1039/D2LC00447J}, + urldate = {2023-10-02}, + abstract = {This tutorial review covers theoretical and experimental aspects of acoustic interaction force, as one of the driving forces of acoustophoresis. The non-reciprocity, rotational coupling, viscosity effects, and particle agglomeration are discussed. , The motion of small objects in acoustophoresis depends on the acoustic radiation force and torque. These are nonlinear phenomena originating from wave scattering, and consist of primary and secondary components. The primary radiation force is the force acting on an object due to the incident field, in the absence of other objects. The secondary component, known as acoustic interaction force, accounts for the interaction among objects, and contributes to the clustering patterns of objects, as commonly observed in experiments. In this tutorial, the theory of acoustic interaction forces is presented using the force potential and partial-wave expansion approaches, and the distinguishing features of these forces such as rotational coupling and non-reciprocity are described. Theoretical results are compared to experimental measurements of interaction forces using a glass micro-capillary setup to explain the practical challenges. Finally, the phenomenon of clustering patterns induced by the close-range interaction of objects is demonstrated to point out the considerations about multiple collision and the predicted clustering patterns entirely due to the interaction force. Understanding the principles of acoustic interaction enables us to develop novel acoustofluidic applications beyond the typical processing of large populations of particles and with focus on the controlled manipulation of small clusters.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Sepehrirahnama2022.pdf} +} + +@article{Shah2024, + title = {When Millimeters Matter}, + author = {Shah, Bhavya R.}, + year = {2024}, + month = jun, + journal = {European Radiology}, + pages = {s00330-024-10757-w}, + issn = {1432-1084}, + doi = {10.1007/s00330-024-10757-w}, + urldate = {2024-07-12}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Shah2024.pdf} +} + +@article{Shapiro2012, + title = {Infrared Light Excites Cells by Changing Their Electrical Capacitance}, + author = {Shapiro, Mikhail G. and Homma, Kazuaki and Villarreal, Sebastian and Richter, Claus-Peter and Bezanilla, Francisco}, + year = {2012}, + month = mar, + journal = {Nature Communications}, + volume = {3}, + number = {1}, + pages = {736}, + issn = {2041-1723}, + doi = {10.1038/ncomms1742}, + urldate = {2023-07-12}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Shapiro2012.pdf} +} + +@article{Shealy1967, + title = {Electrical {{Inhibition}} of {{Pain}} by {{Stimulation}} of the {{Dorsal Columns}}}, + author = {Shealy, C. Norman and Mortimer, J. Thomas and Reswick, James B.}, + year = {1967}, + month = jul, + journal = {Anesthesia \& Analgesia}, + volume = {46}, + number = {4}, + pages = {489--491}, + publisher = {Ovid Technologies (Wolters Kluwer Health)}, + doi = {10.1213/00000539-196707000-00025} +} + +@misc{Sherman2024, + title = {Ultrasound Pulse Repetition Frequency Preferentially Activates Different Neuron Populations Independent of Cell Type}, + author = {Sherman, Jack and Bortz, Emma and Antonio, Erynne San and Tseng, Hua-an and Raiff, Laura and Han, Xue}, + year = {2024}, + month = mar, + doi = {10.1101/2024.03.25.586645}, + urldate = {2024-04-08}, + abstract = {Transcranial ultrasound activates mechanosensitive cellular signaling and modulates neural dynamics. Given that intrinsic neuronal activity is limited to a couple hundred hertz and often exhibits frequency preference, we examined whether pulsing ultrasound at physiologic pulse repetition frequencies (PRFs) could selectively influence neuronal activity in the mammalian brain. We performed calcium imaging of individual motor cortex neurons, while delivering 0.35 MHz ultrasound at PRFs of 10, 40, and 140 Hz in awake mice. We found that most neurons were preferentially activated by only one of the three PRFs, highlighting unique cellular effects of physiologic PRFs. Further, ultrasound evoked responses were similar between excitatory neurons and parvalbumin positive interneurons regardless of PRFs, indicating that individual cell sensitivity dominates ultrasound-evoked effects, consistent with the heterogeneous mechanosensitive channel expression we found across single neurons in mice and humans. These results highlight the feasibility of tuning ultrasound neuromodulation effects through varying PRFs.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Sherman2024.pdf} +} + +@article{Shin2023, + title = {Improving the Quality of Ultrasound Images Acquired Using a Therapeutic Transducer}, + author = {Shin, Eui-Ji and Park, Sunghun and Kang, Sungwoo and Kim, Jinwoo and Chang, Jin Ho}, + year = {2023}, + month = sep, + journal = {Ultrasonics}, + volume = {134}, + pages = {107063}, + issn = {0041624X}, + doi = {10.1016/j.ultras.2023.107063}, + urldate = {2024-02-02}, + abstract = {To enhance the effectiveness and safety of focused ultrasound (FUS) therapy, ultrasound image-based guidance and treatment monitoring are crucial. However, the use of FUS transducers for both therapy and imaging is impractical due to their low spatial resolution, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR). To address this issue, we propose a new method that significantly improve the quality of images obtained by a FUS transducer. The proposed method employs coded excitation to enhance SNR and Wiener deconvolution to solve the problem of low axial resolution resulting from the narrow spectral bandwidth of FUS transducers. Specif\- ically, the method eliminates the impulse response of a FUS transducer from received ultrasound signals using Wiener deconvolution, and pulse compression is performed using a mismatched filter. Simulation and com\- mercial phantom experiments confirmed that the proposed method significantly improves the quality of images acquired by the FUS transducer. The - 6 dB axial resolution was improved 1.27 mm to 0.37 mm that was similar to the resolution achieved by the imaging transducer, i.e., 0.33 mm. SNR and CNR also increased from 16.5 dB and 0.69 to 29.1 dB and 3.03, respectively, that were also similar to those by the imaging transducer (27.8 dB and 3.16). Based on the results, we believe that the proposed method has great potential to enhance the clinical utility of FUS transducers in ultrasound image-guided therapy.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Shin2023.pdf} +} + +@article{Shirakawa2008, + title = {{{TRPV1}} Stimulation Triggers Apoptotic Cell Death of Rat Cortical Neurons}, + author = {Shirakawa, Hisashi and Yamaoka, Tomoko and Sanpei, Kazuaki and Sasaoka, Hirotoshi and Nakagawa, Takayuki and Kaneko, Shuji}, + year = {2008}, + month = dec, + journal = {Biochemical and Biophysical Research Communications}, + volume = {377}, + number = {4}, + pages = {1211--1215}, + issn = {0006-291X}, + doi = {10.1016/j.bbrc.2008.10.152}, + urldate = {2023-05-09}, + abstract = {Transient receptor potential vanilloid 1 (TRPV1) functions as a polymodal nociceptor and is activated by several vanilloids, including capsaicin, protons and heat. Although TRPV1 channels are widely distributed in the brain, their roles remain unclear. Here, we investigated the roles of TRPV1 in cytotoxic processes using TRPV1-expressing cultured rat cortical neurons. Capsaicin induced severe neuronal death with apoptotic features, which was completely inhibited by the TRPV1 antagonist capsazepine and was dependent on extracellular Ca2+ influx. Interestingly, nifedipine, a specific L-type Ca2+ channel blocker, attenuated capsaicin cytotoxicity, even when applied 2--4h after the capsaicin. ERK inhibitor PD98059 and several antioxidants, but not the JNK and p38 inhibitors, attenuated capsaicin cytotoxicity. Together, these data indicate that TRPV1 activation triggers apoptotic cell death of rat cortical cultures via L-type Ca2+ channel opening, Ca2+ influx, ERK phosphorylation, and reactive oxygen species production.}, + langid = {english}, + keywords = {Apoptosis,Ca entry,Capsaicin,Capsazepine,Caspase-3,ERK,L-type Ca channel,Neuronal death,Reactive oxygen species,TRPV1}, + file = {/Users/tomaubier/Zotero/storage/YMDDTKW9/S0006291X08021256.html} +} + +@article{Shou2006, + title = {Acoustic Power Measurement of High Intensity Focused Ultrasound in Medicine Based on Radiation Force}, + author = {Shou, Wende and Huang, Xiaowei and Duan, Shimei and Xia, Rongmin and Shi, Zhonglong and Geng, Xiaoming and Li, Faqi}, + year = {2006}, + month = dec, + journal = {Ultrasonics}, + volume = {44}, + pages = {e17-e20}, + issn = {0041624X}, + doi = {10.1016/j.ultras.2006.06.034}, + urldate = {2022-10-01}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Shou2006.pdf} +} + +@article{Smetters1999, + title = {Detecting {{Action Potentials}} in {{Neuronal Populations}} with {{Calcium Imaging}}}, + author = {Smetters, Diana and Majewska, Ania and Yuste, Rafael}, + year = {1999}, + month = jun, + journal = {Methods}, + volume = {18}, + number = {2}, + pages = {215--221}, + issn = {10462023}, + doi = {10.1006/meth.1999.0774}, + urldate = {2022-06-27}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Smetters1999.pdf} +} + +@article{Smith2004, + title = {Overview of {{fMRI}} Analysis}, + author = {Smith, Stephen M.}, + year = {2004}, + month = jan, + journal = {British Journal of Radiology}, + volume = {77}, + doi = {10.1259/bjr/33553595}, + abstract = {fMRI (functional magnetic resonance imaging) is a powerful non-invasive tool in the study of the function of the brain, used, for example, by psychologists, psychiatrists and neurologists. fMRI can give high quality visualization of the location of activity in the brain resulting from sensory stimulation or cognitive function. It therefore allows the study of how the healthy brain functions, how it is affected by different diseases, how it attempts to recover after damage and how drugs can modulate activity or post-damage recovery. After an fMRI experiment has been designed and carried out, the resulting data must be passed through various analysis steps before the experimenter can get answers to questions about experimentally related activations at the individual or multi-subject level. This paper gives a brief overview of the most commonly used analysis pipeline: data pre-processing, temporal linear modelling and activation thresholding. For more details, see Jezzard et al [1]. fMRI Data In a typical fMRI session a low-resolution functional volume is acquired every few seconds. (MR volumes are often also referred to as ``images'' or ``scans''). Over the course of the experiment, 100 volumes or more are typically recorded. In the simplest possible experiment, some images will be taken whilst stimulation (for the remainder of this chapter, reference to ``stimulation'' should be taken to include also the carrying out of physical or cognitive activity) is applied, and some will be taken with the subject at rest. Because the images are taken using an MR sequence which is sensitive to changes in local blood oxygenation level (BOLD imaging; see Chapters 2 and 3 in Jezzard et al [1]), parts of the images taken during stimulation should show increased intensity, compared with those taken whilst at rest. The parts of these images that show increased intensity should correspond to the brain areas which are activated by the stimulation. The goal of fMRI analysis is to detect, in a robust, sensitive and valid way, those parts of the brain that show increased intensity at the points in time that stimulation was applied. A single volume is made up of individual cuboid elements called voxels (Figure 1). An fMRI data set from a single session can either be thought of as t volumes, one taken every few seconds, or as v voxels, each with an associated time series of t time points. It is important to be able to conceptualize both of these representations, as some analysis steps make more sense when thinking of the data in one way, and others make more sense the other way. An example time-series from a single voxel is shown in Figure 2. Image intensity is shown on the y axis, and time (in scans) on the x axis. As described above, for some of the time points, stimulation was applied, (the higher intensity periods), and at some time points the subject was at rest. As well as the effect of the stimulation being clear, the high frequency noise is also apparent. The aim of fMRI analysis is to identify in which voxels' time-series the signal of interest is significantly greater than the noise level.}, + pmid = {15677358}, + annotation = {MAG ID: 2033777218} +} + +@article{Soe2012, + title = {Neuroscience Goes on a Chip}, + author = {Soe, Aung K. and Nahavandi, Saeid and Khoshmanesh, Khashayar}, + year = {2012}, + month = may, + journal = {Biosensors and Bioelectronics}, + volume = {35}, + number = {1}, + pages = {1--13}, + issn = {0956-5663}, + doi = {10.1016/j.bios.2012.02.012}, + urldate = {2023-05-22}, + abstract = {Advances in microelectronics, microfluidics, polymers and microfabrication have enabled the creation of disposable lab-on-a-chips (LOCs) as the new tools for neuroscience research. The LOCs have been applied for a wide range of neurobiology studies, including cellular and molecular biochemical experimentations, morphological observations and electrophysiological investigations. The integration of miniaturised components leads to analytical instrumentations with unprecedented automation, speed of analysis, and flexibility. These features make LOCs capable enough to replace their bulky and expensive bench-top counterparts. LOCs can be useful for genomic, proteomic, epigenomic, peptidomic, connectomic and electrophysiological studies and also as effective tools for reductionist neuroscientists. Moreover, they can be applied at higher level studies such as developmental neurobiology and behavioural investigations. This work provides an in-depth review of LOC platforms for neuroscience research. First, we review the essential bench-top neuroscience instrumentation as per their functions and features. Next, we present LOC counterparts for those bench-top instrumentations. Finally, we offer perspectives on persistent challenges and our perception of opportunities based on LOC instrumentations in neuroscience research.}, + langid = {english}, + keywords = {Lab-on-a-chip,Microfluidics,Molecular biochemistry,Neurobiology}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Soe2012.pdf} +} + +@article{Song2019, + title = {A Dynamic View of the Proteomic Landscape during Differentiation of {{ReNcell VM}} Cells, an Immortalized Human Neural Progenitor Line}, + author = {Song, Yuyu and Subramanian, Kartik and Berberich, Matthew J. and Rodriguez, Steven and Latorre, Isabel J. and Luria, Catherine M. and Everley, Robert and Albers, Mark W. and Mitchison, Timothy J. and Sorger, Peter K.}, + year = {2019}, + month = mar, + journal = {Scientific Data}, + volume = {6}, + number = {1}, + pages = {190016}, + issn = {2052-4463}, + doi = {10.1038/sdata.2019.16}, + urldate = {2022-04-01}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Song2019.pdf} +} + +@article{Song2023, + title = {Ultrasonic Neuromodulation Mediated by Mechanosensitive Ion Channels: Current and Future}, + shorttitle = {Ultrasonic Neuromodulation Mediated by Mechanosensitive Ion Channels}, + author = {Song, Mengyao and Zhang, Mingxia and He, Sixuan and Li, Le and Hu, Huijing}, + year = {2023}, + month = jul, + journal = {Frontiers in Neuroscience}, + volume = {17}, + pages = {1232308}, + issn = {1662-453X}, + doi = {10.3389/fnins.2023.1232308}, + urldate = {2024-02-20}, + abstract = {Ultrasound neuromodulation technology is a promising neuromodulation approach, with the advantages of noninvasiveness, high-resolution, deep penetration and good targeting, which aid in circumventing the side effects of drugs and invasive therapeutic interventions. Ultrasound can cause mechanical effects, activate mechanosensitive ion channels and alter neuronal excitability, producing biological effects. The structural determination of mechanosensitive ion channels will greatly contribute to our understanding of the molecular mechanisms underlying mechanosensory transduction. However, the underlying biological mechanism of ultrasonic neuromodulation remains poorly understood. Hence, this review aims to provide an outline of the properties of ultrasound, the structures of specific mechanosensitive ion channels, and their role in ultrasound neuromodulation.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Song2023.pdf} +} + +@article{Sorum2021, + title = {Ultrasound Activates Mechanosensitive {{TRAAK K}} {\textsuperscript{+}} Channels through the Lipid Membrane}, + author = {Sorum, Ben and Rietmeijer, Robert A. and Gopakumar, Karthika and Adesnik, Hillel and Brohawn, Stephen G.}, + year = {2021}, + month = feb, + journal = {Proceedings of the National Academy of Sciences}, + volume = {118}, + number = {6}, + pages = {e2006980118}, + issn = {0027-8424, 1091-6490}, + doi = {10.1073/pnas.2006980118}, + urldate = {2023-01-18}, + abstract = {Significance Ultrasound stimulation modulates the electrical activity of excitable cells, including in neurons of the brain and central nervous system. Compared to other neuromodulatory techniques, ultrasound offers several advantages; for example, it can be noninvasively transmitted through the skull and focused to deep brain regions. However, the molecular basis underlying the effects of ultrasound on neural activity is not known. Here, we show that ultrasound activates the mechanosensitive ion channel TRAAK through the membrane in a manner analogous to canonical mechanical activation, likely by increasing membrane tension to promote channel opening. These results suggest mechanosensitive channels underlie physiological responses to ultrasound and could serve as tools for acoustic neuromodulation of genetically targeted cells. , Ultrasound modulates the electrical activity of excitable cells and offers advantages over other neuromodulatory techniques; for example, it can be noninvasively transmitted through the skull and focused to deep brain regions. However, the fundamental cellular, molecular, and mechanistic bases of ultrasonic neuromodulation are largely unknown. Here, we demonstrate ultrasound activation of the mechanosensitive K + channel TRAAK with submillisecond kinetics to an extent comparable to canonical mechanical activation. Single-channel recordings reveal a common basis for ultrasonic and mechanical activation with stimulus-graded destabilization of long-duration closures and promotion of full conductance openings. Ultrasonic energy is transduced to TRAAK through the membrane in the absence of other cellular components, likely increasing membrane tension to promote channel opening. We further demonstrate ultrasonic modulation of neuronally expressed TRAAK. These results suggest mechanosensitive channels underlie physiological responses to ultrasound and could serve as sonogenetic actuators for acoustic neuromodulation of genetically targeted cells.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Sorum2021.pdf} +} + +@article{Sotelo2003, + title = {Viewing the Brain through the Master Hand of {{Ramon}} y {{Cajal}}}, + author = {Sotelo, Constantino}, + year = {2003}, + month = jan, + journal = {Nature Reviews Neuroscience}, + volume = {4}, + number = {1}, + pages = {71--77}, + issn = {1471-003X, 1471-0048}, + doi = {10.1038/nrn1010}, + urldate = {2024-11-09}, + copyright = {http://www.springer.com/tdm}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Sotelo2003.pdf} +} + +@article{Stagg2018, + title = {Physiology of {{Transcranial Direct Current Stimulation}}}, + author = {Stagg, Charlotte J. and Antal, Andrea and Nitsche, Michael A.}, + year = {2018}, + month = sep, + volume = {34}, + number = {3}, + pages = {144--152}, + publisher = {Ovid Technologies (Wolters Kluwer Health)}, + doi = {10.1097/yct.0000000000000510} +} + +@article{Steigerwald2018, + title = {Directional {{Deep Brain Stimulation}}}, + author = {Steigerwald, Frank and Matthies, Cordula and Volkmann, Jens}, + year = {2018}, + month = sep, + journal = {Neurotherapeutics}, + volume = {16}, + number = {1}, + pages = {100--104}, + publisher = {{Springer Science and Business Media LLC}}, + doi = {10.1007/s13311-018-0667-7} +} + +@article{Stern2017, + title = {External {{Excitation}} of {{Neurons Using Electric}} and {{Magnetic Fields}} in {{One-}} and {{Two-dimensional Cultures}}}, + author = {Stern, Shani and Rotem, Assaf and Burnishev, Yuri and Weinreb, Eyal and Moses, Elisha}, + year = {2017}, + month = may, + journal = {Journal of Visualized Experiments}, + number = {123}, + pages = {54357}, + issn = {1940-087X}, + doi = {10.3791/54357}, + urldate = {2023-01-10}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Stern2017.pdf} +} + +@article{Stilling2019, + title = {Transcranial {{Magnetic}} and {{Direct Current Stimulation}} ({{TMS}}/{{tDCS}}) for the {{Treatment}} of {{Headache}}: {{A Systematic Review}}}, + author = {Stilling, Joan M. and Monchi, Oury and Amoozegar, Farnaz and Debert, Chantel T.}, + year = {2019}, + month = jan, + journal = {Headache: The Journal of Head and Face Pain}, + volume = {59}, + number = {3}, + pages = {339--357}, + publisher = {Wiley}, + doi = {10.1111/head.13479}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Stilling2019.pdf} +} + +@article{Stone2007, + title = {Kynurenic Acid Blocks Nicotinic Synaptic Transmission to Hippocampal Interneurons in Young Rats}, + author = {Stone, Trevor W.}, + year = {2007}, + month = may, + journal = {The European Journal of Neuroscience}, + volume = {25}, + number = {9}, + pages = {2656--2665}, + issn = {0953-816X}, + doi = {10.1111/j.1460-9568.2007.05540.x}, + abstract = {The tryptophan metabolite kynurenic acid can block glutamate at ionotropic receptors, but recent evidence suggests a more potent antagonistic action at alpha7 nicotinic receptors for acetylcholine on cultured neurons. The present study examines activity of kynurenic acid at those nicotinic receptors, which mediate cholinergic neurotransmission onto interneurons in the rat hippocampus. Intracellular recordings were made from pyramidal cells and interneurons in the presence of atropine, bicuculline methobromide, (3-aminopropyl)(diethoxymethyl)-phosphinic acid [CGP35348, to block gamma-aminobutyric acid (GABA)(B) receptors] and 3-tropanyl-3,5-dichlorobenzoate (MDL 72222, to block 5-HT3 receptors). In the added presence of glutamate antagonists 2-amino-5-phosphono-pentanoic acid and 6-cyano-7-nitroquinoxaline-2,3-dione, interneurons exhibited a residual excitatory postsynaptic potential (EPSP) that could be blocked by the nicotinic alpha7 receptor blocker methyl-lycaconitine, but not by dihydro-beta-erythroidine which blocks alpha4beta2 receptors. Kynurenic acid reduced the amplitude of these EPSPs with an EC50 of 136 microM. The amplitudes of nicotinic spontaneous miniature EPSPs were also reduced by methyl-lycaconitine and kynurenic acid. The results show that kynurenic acid is more potent in blocking nicotinic EPSPs compared with the full, glutamate-mediated EPSPs, but it was substantially less potent than has been reported in cultures, possibly because of differences in the accessibility of synaptic and extrasynaptic receptors. It is suggested that blockade of nicotinic synaptic transmission may be relevant to the actions of kynurenic acid in the hippocampus, but that in the intact brain this activity is likely to be comparable in importance to the blockade of glutamate-mediated transmission.}, + langid = {english}, + pmid = {17459105}, + keywords = {Acetylcholine,Action Potentials,Aging,Animals,Cell Differentiation,Dose-Response Relationship Drug,Excitatory Amino Acid Antagonists,Excitatory Postsynaptic Potentials,GABA Antagonists,Hippocampus,Interneurons,Kynurenic Acid,Male,Neural Pathways,Nicotinic Antagonists,Organ Culture Techniques,Pyramidal Cells,Rats,Rats Wistar,Receptors Nicotinic,Serotonin Antagonists,Synaptic Transmission} +} + +@article{Stosiek2003, + title = {In Vivo Two-Photon Calcium Imaging of Neuronal Networks}, + author = {Stosiek, C. and Garaschuk, O. and Holthoff, K. and Konnerth, A.}, + year = {2003}, + month = jun, + journal = {Proceedings of the National Academy of Sciences}, + volume = {100}, + number = {12}, + pages = {7319--7324}, + issn = {0027-8424, 1091-6490}, + doi = {10.1073/pnas.1232232100}, + urldate = {2021-09-04}, + langid = {english} +} + +@article{Stringer2020, + title = {Cellpose: A Generalist Algorithm for Cellular Segmentation}, + author = {Stringer, Carsen and Wang, Tim and Michaelos, Michalis and Pachitariu, Marius}, + year = {2020}, + month = feb, + publisher = {Cold Spring Harbor Laboratory}, + doi = {10.1101/2020.02.02.931238} +} + +@article{Suarez-Castellanos2021, + title = {Spatio-Temporal Characterization of Causal Electrophysiological Activity Stimulated by Single Pulse Focused Ultrasound: An Ex Vivo Study on Hippocampal Brain Slices}, + author = {{Suarez-Castellanos}, Ivan M. and Dossi, Elena and {Vion-Bailly}, J{\'e}r{\'e}my and Salette, L{\'e}a and Chapelon, Jean-Yves and Carpentier, Alexandre and Huberfeld, Gilles and N'Djin, William Apoutou}, + year = {2021}, + month = mar, + journal = {Journal of Neural Engineering}, + volume = {18}, + number = {2}, + pages = {026022}, + publisher = {IOP Publishing}, + doi = {10.1088/1741-2552/abdfb1}, + abstract = {MEA (Micro Electrode Array)}, + keywords = {MEA}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Suarez-Castellanos2021.pdf} +} + +@article{Sydnor2022, + title = {Cortical-Subcortical Structural Connections Support Transcranial Magnetic Stimulation Engagement of the Amygdala}, + author = {Sydnor, Valerie J. and Cieslak, Matthew and Duprat, Romain and Deluisi, Joseph and Flounders, Matthew W. and Long, Hannah and Scully, Morgan and Balderston, Nicholas L. and Sheline, Yvette I. and Bassett, Dani S. and Satterthwaite, Theodore D. and Oathes, Desmond J.}, + year = {2022}, + month = jun, + journal = {Science Advances}, + volume = {8}, + number = {25}, + pages = {eabn5803}, + issn = {2375-2548}, + doi = {10.1126/sciadv.abn5803}, + urldate = {2022-12-20}, + abstract = {The amygdala processes valenced stimuli, influences emotion, and exhibits aberrant activity across anxiety disorders, depression, and PTSD. Interventions modulating amygdala activity hold promise as transdiagnostic psychiatric treatments. In 45 healthy participants, we investigated whether transcranial magnetic stimulation (TMS) elicits indirect changes in amygdala activity when applied to ventrolateral prefrontal cortex (vlPFC), a region important for emotion regulation. Harnessing in-scanner interleaved TMS/functional MRI (fMRI), we reveal that vlPFC neurostimulation evoked acute and focal modulations of amygdala fMRI BOLD signal. Larger TMS-evoked changes in the amygdala were associated with higher fiber density in a vlPFC--amygdala white matter pathway when stimulating vlPFC but not an anatomical control, suggesting this pathway facilitated stimulation-induced communication between cortex and subcortex. This work provides evidence of amygdala engagement by TMS, highlighting stimulation of vlPFC--amygdala circuits as a candidate treatment for transdiagnostic psychopathology. More broadly, it indicates that targeting cortical-subcortical structural connections may enhance the impact of TMS on subcortical neural activity and, by extension, subcortex-subserved behaviors. , Individualized, connectivity-guided transcranial magnetic stimulation modulates the amygdala, demonstrating therapeutic potential.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Sydnor2022.pdf} +} + +@book{Szabo2014, + title = {Diagnostic Ultrasound Imaging: Inside Out}, + shorttitle = {Diagnostic Ultrasound Imaging}, + author = {Szabo, Thomas L.}, + year = {2014}, + series = {{{MATLAB}} Examples}, + edition = {Second edition}, + publisher = {Elsevier/AP, Academic Press is an imprint of Elsevier}, + address = {Amsterdam ; Boston}, + isbn = {978-0-12-396487-8}, + langid = {english}, + lccn = {RC78.7.U4 S98 2014}, + keywords = {Bilderzeugung,Diagnostic ultrasonic imaging,Echografie,Ultraschalldiagnostik,Ultrasonic imaging,Ultrasonic Therapy,Ultrasonography}, + annotation = {OCLC: ocn858004544}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Szabo2014.pdf} +} + +@article{Taherinejad2012, + title = {Bloch-Type Domain Walls in Rhombohedral {{BaTiO}} 3}, + author = {Taherinejad, Maryam and Vanderbilt, David and Marton, Pavel and Stepkova, Vilgelmina and Hlinka, Jiri}, + year = {2012}, + month = oct, + journal = {Physical Review B}, + volume = {86}, + number = {15}, + pages = {155138}, + issn = {1098-0121, 1550-235X}, + doi = {10.1103/PhysRevB.86.155138}, + urldate = {2023-04-02}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Taherinejad2012.pdf} +} + +@article{Teplov2021, + title = {Involvement of {{NMDA}} and {{GABA}}({{A}}) Receptors in Modulation of Spontaneous Activity in Hippocampal Culture: {{Interrelations}} between Burst Firing and Intracellular Calcium Signal}, + shorttitle = {Involvement of {{NMDA}} and {{GABA}}({{A}}) Receptors in Modulation of Spontaneous Activity in Hippocampal Culture}, + author = {Teplov, I. Yu and Zinchenko, V.P. and Kosenkov, A.M. and Gaidin, S.G. and Nenov, M.N. and Sergeev, A.I.}, + year = {2021}, + month = may, + journal = {Biochemical and Biophysical Research Communications}, + volume = {553}, + pages = {99--106}, + issn = {0006291X}, + doi = {10.1016/j.bbrc.2021.02.149}, + urldate = {2024-09-26}, + abstract = {Spontaneous burst firing is a hallmark attributed to the neuronal network activity. It is known to be accompanied by intracellular calcium [{\cyrchar\CYRS}{\cyrchar\cyra}2{\th}]i oscillations within the bursting neurons. Studying mechanisms underlying regulation of burst firing is highly relevant, since impairment in neuronal bursting accompanies different neurological disorders. In the present study, the contribution of NMDA and GABA(A) receptors to the shape formation of spontaneous burst -was studied in cultured hippocampal neurons. A combination of inhibitory analysis with simultaneous registration of neuronal bursting by whole-cell patch clamp and calcium imaging was used to assess spontaneous burst firing and [{\cyrchar\CYRS}{\cyrchar\cyra}2{\th}]i level.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Teplov2021.pdf} +} + +@incollection{Thomas1994, + title = {Pharmacological {{Tools}} for {{Perturbing Intracellular Calcium Storage}}}, + booktitle = {Methods in {{Cell Biology}}}, + author = {Thomas, David and Hanley, Michael R.}, + year = {1994}, + volume = {40}, + pages = {65--89}, + publisher = {Elsevier}, + doi = {10.1016/S0091-679X(08)61110-3}, + urldate = {2024-10-07}, + copyright = {https://www.elsevier.com/tdm/userlicense/1.0/}, + isbn = {978-0-12-564141-8}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Thomas1994.pdf} +} + +@article{Thompson1985, + title = {Temperature Dependence of Intrinsic Membrane Properties and Synaptic Potentials in Hippocampal {{CA1}} Neurons in Vitro}, + author = {Thompson, Sm and Masukawa, Lm and Prince, Da}, + year = {1985}, + month = mar, + journal = {The Journal of Neuroscience}, + volume = {5}, + number = {3}, + pages = {817--824}, + issn = {0270-6474, 1529-2401}, + doi = {10.1523/JNEUROSCI.05-03-00817.1985}, + urldate = {2023-07-03}, + abstract = {The temperature dependence of intrinsic membrane conductances and synaptic potentials in guinea pig hippocampal CA1 pyramidal neurons were examined in vitro as they were cooled from 37 degrees C to between 33 and 27 degrees C. Cooling reversibly increased resting input resistance in a voltage-independent manner (Q10 = 0.58 to 0.75). The amplitude and duration of orthodromically evoked action potentials were increased by cooling (Q10 = 0.87 and 0.52 to 0.53, respectively), whereas the maximum rates of rise and fall were reduced (Q10 = 1.27 to 1.49 and 2.19 to 2.44, respectively). The amplitude and duration of the afterhyperpolarization which follows a directly evoked train of action potentials were substantially increased at low temperatures. It is possible to attribute this increase to an augmentation of Ca2+ influx during the train and also to a slowing of Ca2+ removal from the cytoplasm. Spike frequency adaptation during prolonged depolarizing pulses was enhanced at low temperatures. In addition, there was a decrement in spike amplitude during the train of action potentials. These observations all suggest an increase in Ca2+-activated K+ conductance at low temperature. A late, slow, hyperpolarizing synaptic potential in response to orthodromic stimulation became apparent at low temperature. This potential had an apparent reversal potential more negative than the early inhibitory postsynaptic potential, suggesting that it was mediated by a K+ conductance, possibly activated by Ca2+ influx. We conclude that reductions in temperature of as little as 5 to 10 degrees C from normal can significantly alter the intrinsic and synaptic physiology of hippocampal neurons and should, therefore, be considered an important variable in in vitro brain slice experiments.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Thompson1985.pdf} +} + +@article{Thompson2022, + title = {Laser-Induced Ultrasound Transmitters for Large-Volume Ultrasound Tomography}, + author = {Thompson, D. and Nagel, J.R. and Gasteau, D.B. and Manohar, S.}, + year = {2022}, + month = mar, + journal = {Photoacoustics}, + volume = {25}, + pages = {100312}, + issn = {22135979}, + doi = {10.1016/j.pacs.2021.100312}, + urldate = {2024-05-31}, + abstract = {We present a protocol for the design, fabrication and characterisation of laser-induced ultrasound transmitters with a specific, user-defined frequency response for the purpose of ultrasound tomography of large-volume biomedical samples. Using an analytic solution to the photoacoustic equation and measurements of the optical and acoustic properties of the materials used in the transmitters, we arrive at a required mixture of carbon black and polydimethylsiloxane to achieve the desired frequency response. After an in-depth explanation of the fabrication and characterisation approaches we show the performance of the fabricated transmitter, which has a centre frequency of 0.9 MHz, 200\% bandwidth and 45.8{\textopenbullet} opening angle, multi-kPa pressures over a large depth range in water.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Thompson2022.pdf} +} + +@article{Tokuno2009, + title = {Stereo {{Navi}} 2.0: {{Software}} for Stereotaxic Surgery of the Common Marmoset ({{Callithrix}} Jacchus)}, + shorttitle = {Stereo {{Navi}} 2.0}, + author = {Tokuno, Hironobu and Tanaka, Ikuko and Umitsu, Yoshitomo and Nakamura, Yasuhisa}, + year = {2009}, + month = nov, + journal = {Neuroscience Research}, + volume = {65}, + number = {3}, + pages = {312--315}, + issn = {01680102}, + doi = {10.1016/j.neures.2009.08.004}, + urldate = {2025-01-08}, + abstract = {Recently, we reported our web-accessible digital brain atlas of the common marmoset (Callithrix jacchus) at http://marmoset-brain.org:2008. Using digital images obtained during construction of this website, we developed stand-alone software for navigation of electrodes or injection needles for stereotaxic electrophysiological or anatomical experiments in vivo. This software enables us to draw lines on exchangeable section images, measure the length and angle of lines, superimpose a stereotaxic reference grid on the image, and send the image to the system clipboard. The software, Stereo Navi 2.0, is freely available at our brain atlas website.}, + copyright = {https://www.elsevier.com/tdm/userlicense/1.0/}, + langid = {english}, + file = {/Users/tomaubier/Zotero/storage/AIEWNYFY/Tokuno et al. - 2009 - Stereo Navi 2.0 Software for stereotaxic surgery .pdf} +} + +@article{Treeby, + title = {A {{MATLAB}} Toolbox for the Time Domain Simulation of Acoustic Wave Fields {{User Manual}}}, + author = {Treeby, Authored Bradley and Cox, Ben and Jaros, Jiri}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Treeby.pdf} +} + +@article{Treeby2010, + title = {K-{{Wave}}: {{MATLAB}} Toolbox for the Simulation and Reconstruction of Photoacoustic Wave Fields}, + shorttitle = {K-{{Wave}}}, + author = {Treeby, Bradley E. and Cox, B. T.}, + year = {2010}, + journal = {Journal of Biomedical Optics}, + volume = {15}, + number = {2}, + pages = {021314}, + issn = {10833668}, + doi = {10.1117/1.3360308}, + urldate = {2023-09-28}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Treeby2010.pdf} +} + +@article{Turovsky2020, + title = {Mechanosensory {{Signaling}} in {{Astrocytes}}}, + author = {Turovsky, Egor A. and Braga, Alice and Yu, Yichao and Esteras, Noemi and Korsak, Alla and Theparambil, Shefeeq M. and Hadjihambi, Anna and Hosford, Patrick S. and Teschemacher, Anja G. and Marina, Nephtali and Lythgoe, Mark F. and Haydon, Philip G. and Gourine, Alexander V.}, + year = {2020}, + month = dec, + journal = {The Journal of Neuroscience}, + volume = {40}, + number = {49}, + pages = {9364--9371}, + issn = {0270-6474, 1529-2401}, + doi = {10.1523/JNEUROSCI.1249-20.2020}, + urldate = {2024-02-20}, + abstract = {Mechanosensitivity is a well-known feature of astrocytes, however, its underlying mechanisms and functional significance remain unclear. There is evidence that astrocytes are acutely sensitive to decreases in cerebral perfusion pressure and may function as intracranial baroreceptors, tuned to monitor brain blood flow. This study investigated the mechanosensory signaling in brainstem astrocytes, as these cells reside alongside the cardiovascular control circuits and mediate increases in blood pressure and heart rate induced by falls in brain perfusion. It was found that mechanical stimulation-evoked Ca 2+ responses in astrocytes of the rat brainstem were blocked by (1) antagonists of connexin channels, connexin 43 (Cx43) blocking peptide Gap26, or Cx43 gene knock-down; (2) antagonists of TRPV4 channels; (3) antagonist of P2Y 1 receptors for ATP; and (4) inhibitors of phospholipase C or IP3 receptors. Proximity ligation assay demonstrated interaction between TRPV4 and Cx43 channels in astrocytes. Dye loading experiments showed that mechanical stimulation increased open probability of carboxyfluorescein-permeable membrane channels. These data suggest that mechanosensory Ca 2+ responses in astrocytes are mediated by interaction between TRPV4 and Cx43 channels, leading to Cx43-mediated release of ATP which propagates/amplifies Ca 2+ signals via P2Y 1 receptors and Ca 2+ recruitment from the intracellular stores. In astrocyte-specific Cx43 knock-out mice the magnitude of heart rate responses to acute increases in intracranial pressure was not affected by Cx43 deficiency. However, these animals displayed lower heart rates at different levels of cerebral perfusion, supporting the hypothesis of connexin hemichannel-mediated release of signaling molecules by astrocytes having an excitatory action on the CNS sympathetic control circuits. SIGNIFICANCE STATEMENT There is evidence suggesting that astrocytes may function as intracranial baroreceptors that play an important role in the control of systemic and cerebral circulation. To function as intracranial baroreceptors, astrocytes must possess a specialized membrane mechanism that makes them exquisitely sensitive to mechanical stimuli. This study shows that opening of connexin 43 (Cx43) hemichannels leading to the release of ATP is the key central event underlying mechanosensory Ca 2+ responses in astrocytes. This astroglial mechanism plays an important role in the autonomic control of heart rate. These data add to the growing body of evidence suggesting that astrocytes function as versatile surveyors of the CNS metabolic milieu, tuned to detect conditions of potential metabolic threat, such as hypoxia, hypercapnia, and reduced perfusion.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Turovsky2020.pdf} +} + +@article{Tyler2008, + title = {Remote {{Excitation}} of {{Neuronal Circuits Using Low-Intensity}}, {{Low-Frequency Ultrasound}}}, + author = {Tyler, William J. and Tufail, Yusuf and Finsterwald, Michael and Tauchmann, Monica L. and Olson, Emily J. and Majestic, Cassondra}, + editor = {Tanimoto, Hiromu}, + year = {2008}, + month = oct, + journal = {PLoS ONE}, + volume = {3}, + number = {10}, + pages = {e3511}, + publisher = {Public Library of Science (PLoS)}, + doi = {10.1371/journal.pone.0003511}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Tyler2008.pdf} +} + +@article{Tyler2012, + title = {The Mechanobiology of Brain Function}, + author = {Tyler, William J.}, + year = {2012}, + month = dec, + journal = {Nature Reviews Neuroscience}, + volume = {13}, + number = {12}, + pages = {867--878}, + issn = {1471-003X, 1471-0048}, + doi = {10.1038/nrn3383}, + urldate = {2024-03-25}, + abstract = {All cells are influenced by mechanical forces. In the brain, force-generating and load-bearing proteins twist, turn, ratchet, flex, compress, expand and bend to mediate neuronal signalling and plasticity. Although the functions of mechanosensitive proteins have been thoroughly described in classical sensory systems, the effects of endogenous mechanical energy on cellular function in the brain have received less attention, and many working models in neuroscience do not currently integrate principles of cellular mechanics. An understanding of cellular-mechanical concepts is essential to allow the integration of mechanobiology into ongoing studies of brain structure and function.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Tyler2012.pdf} +} + +@article{Tyler2018, + title = {Ultrasonic Modulation of Neural Circuit Activity}, + author = {Tyler, William J and Lani, Shane W and Hwang, Grace M}, + year = {2018}, + month = jun, + journal = {Current Opinion in Neurobiology}, + volume = {50}, + pages = {222--231}, + issn = {09594388}, + doi = {10.1016/j.conb.2018.04.011}, + urldate = {2022-07-18}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Tyler2018.pdf} +} + +@article{Ullah2006, + title = {Modeling the {{Statistics}} of {{Elementary Calcium Release Events}}}, + author = {Ullah, Ghanim and Jung, Peter}, + year = {2006}, + month = may, + volume = {90}, + number = {10}, + pages = {3485--3495}, + publisher = {Elsevier BV}, + doi = {10.1529/biophysj.105.073460}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Ullah2006.pdf} +} + +@article{Ullo2014, + title = {Functional Connectivity Estimation over Large Networks at Cellular Resolution Based on Electrophysiological Recordings and Structural Prior}, + author = {Ullo, Simona and Nieus, Thierry R. and Sona, Diego and Maccione, Alessandro and Berdondini, Luca and Murino, Vittorio}, + year = {2014}, + journal = {Frontiers in Neuroanatomy}, + volume = {8}, + issn = {1662-5129}, + urldate = {2023-05-22}, + abstract = {Despite many structural and functional aspects of the brain organization have been extensively studied in neuroscience, we are still far from a clear understanding of the intricate structure-function interactions occurring in the multi-layered brain architecture, where billions of different neurons are involved. Although structure and function can individually convey a large amount of information, only a combined study of these two aspects can probably shade light on how brain circuits develop and operate at the cellular scale. Here, we propose a novel approach for refining functional connectivity estimates within neuronal networks using the structural connectivity as prior. This is done at the mesoscale, dealing with thousands of neurons while reaching, at the microscale, an unprecedented cellular resolution. The High-Density Micro Electrode Array (HD-MEA) technology, combined with fluorescence microscopy, offers the unique opportunity to acquire structural and functional data from large neuronal cultures approaching the granularity of the single cell. In this work, an advanced method based on probabilistic directional features and heat propagation is introduced to estimate the structural connectivity from the fluorescence image while functional connectivity graphs are obtained from the cross-correlation analysis of the spiking activity. Structural and functional information are then integrated by reweighting the functional connectivity graph based on the structural prior. Results show that the resulting functional connectivity estimates are more coherent with the network topology, as compared to standard measures purely based on cross-correlations and spatio-temporal filters. We finally use the obtained results to gain some insights on which features of the functional activity are more relevant to characterize actual neuronal interactions.}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Ullo2014.pdf} +} + +@article{Urbano1998, + title = {{{BAPTA-AM}} Blocks Both Voltage-Gated and {{Ca2}}+-Activated {{K}}+ Currents in Cultured Bovine Chromaffin Cells:}, + shorttitle = {{{BAPTA-AM}} Blocks Both Voltage-Gated and {{Ca2}}+-Activated {{K}}+ Currents in Cultured Bovine Chromaffin Cells}, + author = {Urbano, Francisco J. and Bu{\~n}o, Washington}, + year = {1998}, + month = oct, + journal = {NeuroReport}, + volume = {9}, + number = {15}, + pages = {3403--3407}, + issn = {0959-4965}, + doi = {10.1097/00001756-199810260-00013}, + urldate = {2023-03-27}, + langid = {english} +} + +@article{VanTWout2022, + title = {Frequency-Robust Preconditioning of Boundary Integral Equations for Acoustic Transmission}, + author = {Van 'T Wout, Elwin and Haqshenas, Seyyed R. and G{\'e}lat, Pierre and Betcke, Timo and Saffari, Nader}, + year = {2022}, + month = aug, + journal = {Journal of Computational Physics}, + volume = {462}, + pages = {111229}, + issn = {00219991}, + doi = {10.1016/j.jcp.2022.111229}, + urldate = {2024-09-20}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/VanTWout2022.pdf} +} + +@article{Vasan2022, + title = {Ultrasound {{Mediated Cellular Deflection Results}} in {{Cellular Depolarization}}}, + author = {Vasan, Aditya and Orosco, Jeremy and Magaram, Uri and Duque, Marc and Weiss, Connor and Tufail, Yusuf and Chalasani, Sreekanth H and Friend, James}, + year = {2022}, + month = jan, + journal = {Advanced Science}, + volume = {9}, + number = {2}, + pages = {2101950}, + issn = {2198-3844, 2198-3844}, + doi = {10.1002/advs.202101950}, + urldate = {2023-08-07}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Vasan2022.pdf} +} + +@article{Vedam-Mai2021, + title = {Proceedings of the {{Eighth Annual Deep Brain Stimulation Think Tank}}: {{Advances}} in {{Optogenetics}}, {{Ethical Issues Affecting DBS Research}}, {{Neuromodulatory Approaches}} for {{Depression}}, {{Adaptive Neurostimulation}}, and {{Emerging DBS Technologies}}}, + shorttitle = {Proceedings of the {{Eighth Annual Deep Brain Stimulation Think Tank}}}, + author = {{Vedam-Mai}, Vinata and Deisseroth, Karl and Giordano, James and {Lazaro-Munoz}, Gabriel and Chiong, Winston and Suthana, Nanthia and Langevin, Jean-Philippe and Gill, Jay and Goodman, Wayne and Provenza, Nicole R. and Halpern, Casey H. and Shivacharan, Rajat S. and Cunningham, Tricia N. and Sheth, Sameer A. and Pouratian, Nader and Scangos, Katherine W. and Mayberg, Helen S. and Horn, Andreas and Johnson, Kara A. and Butson, Christopher R. and Gilron, Ro'ee and De Hemptinne, Coralie and Wilt, Robert and Yaroshinsky, Maria and Little, Simon and Starr, Philip and Worrell, Greg and Shirvalkar, Prasad and Chang, Edward and Volkmann, Jens and Muthuraman, Muthuraman and Groppa, Sergiu and K{\"u}hn, Andrea A. and Li, Luming and Johnson, Matthew and Otto, Kevin J. and Raike, Robert and Goetz, Steve and Wu, Chengyuan and Silburn, Peter and Cheeran, Binith and Pathak, Yagna J. and Malekmohammadi, Mahsa and Gunduz, Aysegul and Wong, Joshua K. and Cernera, Stephanie and Hu, Wei and Wagle Shukla, Aparna and {Ramirez-Zamora}, Adolfo and Deeb, Wissam and Patterson, Addie and Foote, Kelly D. and Okun, Michael S.}, + year = {2021}, + month = apr, + journal = {Frontiers in Human Neuroscience}, + volume = {15}, + pages = {644593}, + issn = {1662-5161}, + doi = {10.3389/fnhum.2021.644593}, + urldate = {2023-08-30}, + abstract = {We estimate that 208,000 deep brain stimulation (DBS) devices have been implanted to address neurological and neuropsychiatric disorders worldwide. DBS Think Tank presenters pooled data and determined that DBS expanded in its scope and has been applied to multiple brain disorders in an effort to modulate neural circuitry. The DBS Think Tank was founded in 2012 providing a space where clinicians, engineers, researchers from industry and academia discuss current and emerging DBS technologies and logistical and ethical issues facing the field. The emphasis is on cutting edge research and collaboration aimed to advance the DBS field. The Eighth Annual DBS Think Tank was held virtually on September 1 and 2, 2020 (Zoom Video Communications) due to restrictions related to the COVID-19 pandemic. The meeting focused on advances in: (1) optogenetics as a tool for comprehending neurobiology of diseases and on optogenetically-inspired DBS, (2) cutting edge of emerging DBS technologies, (3) ethical issues affecting DBS research and access to care, (4) neuromodulatory approaches for depression, (5) advancing novel hardware, software and imaging methodologies, (6) use of neurophysiological signals in adaptive neurostimulation, and (7) use of more advanced technologies to improve DBS clinical outcomes. There were 178 attendees who participated in a DBS Think Tank survey, which revealed the expansion of DBS into several indications such as obesity, post-traumatic stress disorder, addiction and Alzheimer's disease. This proceedings summarizes the advances discussed at the Eighth Annual DBS Think Tank.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Vedam-Mai22.pdf} +} + +@article{Verhagen2019, + title = {Offline Impact of Transcranial Focused Ultrasound on Cortical Activation in Primates}, + author = {Verhagen, Lennart and Gallea, C{\'e}cile and Folloni, Davide and Constans, Charlotte and Jensen, Daria EA and Ahnine, Harry and Roumazeilles, L{\'e}a and Santin, Mathieu and Ahmed, Bashir and Lehericy, St{\'e}phane and {Klein-Fl{\"u}gge}, Miriam C and Krug, Kristine and Mars, Rogier B and Rushworth, Matthew FS and Pouget, Pierre and Aubry, Jean-Fran{\c c}ois and Sallet, Jerome}, + year = {2019}, + month = feb, + journal = {eLife}, + volume = {8}, + pages = {e40541}, + issn = {2050-084X}, + doi = {10.7554/eLife.40541}, + urldate = {2023-03-06}, + abstract = {To understand brain circuits it is necessary both to record and manipulate their activity. Transcranial ultrasound stimulation (TUS) is a promising non-invasive brain stimulation technique. To date, investigations report short-lived neuromodulatory effects, but to deliver on its full potential for research and therapy, ultrasound protocols are required that induce longer-lasting `offline' changes. Here, we present a TUS protocol that modulates brain activation in macaques for more than one hour after 40 s of stimulation, while circumventing auditory confounds. Normally activity in brain areas reflects activity in interconnected regions but TUS caused stimulated areas to interact more selectively with the rest of the brain. In a within-subject design, we observe regionally specific TUS effects for two medial frontal brain regions -- supplementary motor area and frontal polar cortex. Independently of these site-specific effects, TUS also induced signal changes in the meningeal compartment. TUS effects were temporary and not associated with microstructural changes. , Ultrasound is well known for making visible what is hidden, for example, when giving parents a glimpse of their child before birth. But researchers are now using these high-frequency sound waves -- beyond the range of human hearing -- for a wholly different purpose: to manipulate the activity of the brain. Conventional brain stimulation techniques use electric currents or magnetic fields to alter brain activity. These techniques, however, have limitations. They can only reach the surface of the brain and are not particularly precise. By contrast, beams of ultrasound can be focused at a millimetre scale, even deep within the brain. Ultrasound thus has the potential to provide new insights into how the brain works. Most studies of ultrasound stimulation have looked at what happens to the brain during the stimulation itself. But could ultrasound also induce longer-lasting changes in brain activity? Changes that persist after the stimulation has ended would be valuable for research. They would also make it more likely that we could use ultrasound to treat brain disorders by changing brain activity. Verhagen, Gallea et al. used a brain scanner to measure brain activity in macaque monkeys after ultrasound stimulation. The results showed that 40 seconds of repetitive ultrasound changed brain activity for up to two hours. Ultrasound caused the stimulated brain area to interact more selectively with the rest of the brain. Notably, only the stimulated area changed its activity in this way. This helps rule out the possibility that the changes reflect non-specific effects. If the monkeys had been able to hear the ultrasound, for example, it would have changed the activity of the parts of the brain related to hearing. Most important of all, the changes were reversible and did not harm the brain. The results of Verhagen, Gallea et al. show that repetitive ultrasound can induce long-lasting alterations in brain activity. It can target areas deep within the brain, including those that are out of reach with other techniques. If this procedure also shows longer-lasting effects in people, it could yield valuable insights into the links between brain and behaviour. It could also help us develop new treatments for neurological and psychiatric disorders.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Verhagen2019.pdf} +} + +@article{Verisokin2021, + title = {Modeling of {{Astrocyte Networks}}: {{Toward Realistic Topology}} and {{Dynamics}}}, + author = {Verisokin, Andrey Yu and Verveyko, Darya V. and Postnov, Dmitry E. and Brazhe, Alexey R.}, + year = {2021}, + month = mar, + volume = {15}, + publisher = {Frontiers Media SA}, + doi = {10.3389/fncel.2021.645068}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Verisokin2021.pdf} +} + +@article{Verma2018, + title = {A Review of an Innovative Concept to Increase the Toughness of the Ceramics by Piezoelectric Secondary Phases}, + author = {Verma, Alok and Kumar, Devendra and Dubey, Ashutosh}, + year = {2018}, + month = jun, + journal = {Ceramics International}, + volume = {44}, + doi = {10.1016/j.ceramint.2018.06.063}, + abstract = {Despite of wide range scope of ceramics for various applications, such as healthcare, space, and energy storage etc., poor fracture toughness restricts their multifunctional performance. The development of various techniques/approaches to improve the fracture toughness of ceramics is in continuum thrust. The present work reviews one of the novel techniques to enhance the toughness of ceramics with the incorporation of piezoelectric secondary phase in the matrix. In addition to the piezoelectricity induced toughening mechanisms such as, energy dissipation due to electro-mechanical phenomenon as well as stress-induced domain switching toughening, other toughening mechanisms such as, transformation toughening, crack bridging, crack deflection and microcrack toughening also contributes to the total observed toughening of piezo-composites. As far as the piezoelectricity induced toughening is concerned, the poling direction and electrical field parameters also affect the toughness of the ceramics.}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Verma2018.pdf} +} + +@article{Verma2018a, + title = {Causality {{Analysis}} and {{Cell Network Modeling}} of {{Spatial Calcium Signaling Patterns}} in {{Liver Lobules}}}, + author = {Verma, Aalap and Antony, Anil Noronha and Ogunnaike, Babatunde A. and Hoek, Jan B. and Vadigepalli, Rajanikanth}, + year = {2018}, + month = oct, + journal = {Frontiers in Physiology}, + volume = {9}, + pages = {1377}, + issn = {1664-042X}, + doi = {10.3389/fphys.2018.01377}, + urldate = {2024-03-12}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Verma2018a2.pdf} +} + +@phdthesis{Vion-Bailly, + title = {{Study of the Mechanisms Underlying Neurostimulation Induced by Low- Energy Pulsed Ultrasound: Towards Approaches for the Management of Cancer-Related Chronic Pain - Etude des M{\'e}canismes de Neurostimulation par Ultrasons Puls{\'e}s de Faible Energie : Vers des applications {\`a} la Gestion des Douleurs Chroniques d'Origine Tumorale}}, + author = {{Vion-Bailly}, J{\'e}r{\'e}my}, + langid = {french}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Vion-Bailly.pdf} +} + +@article{Vion-Bailly2019, + title = {A Causal Study of the Phenomenon of Ultrasound Neurostimulation Applied to an in Vivo Invertebrate Nervous Model}, + author = {{Vion-Bailly}, J{\'e}r{\'e}my and N'Djin, W. Apoutou and Castellanos, Ivan Mauricio Suarez and Mestas, Jean-Louis and Carpentier, Alexandre and Chapelon, Jean-Yves}, + year = {2019}, + month = sep, + journal = {Scientific Reports}, + volume = {9}, + number = {1}, + publisher = {{Springer Science and Business Media LLC}}, + doi = {10.1038/s41598-019-50147-7}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Vion-Bailly2019.pdf} +} + +@article{Vion-Bailly2022, + title = {Neurostimulation Success Rate of Repetitive-pulse Focused Ultrasound in an in Vivo Giant Axon Model: {{An}} Acoustic Parametric Study}, + shorttitle = {Neurostimulation Success Rate of Repetitive-pulse Focused Ultrasound in an in Vivo Giant Axon Model}, + author = {Vion-Bailly, J{\'e}r{\'e}my and Suarez-Castellanos, Ivan M. and Chapelon, Jean-Yves and Carpentier, Alexandre and N'Djin, W. Apoutou}, + year = {2022}, + month = jan, + journal = {Medical Physics}, + volume = {49}, + number = {1}, + pages = {682--701}, + issn = {0094-2405, 2473-4209}, + doi = {10.1002/mp.15358}, + urldate = {2022-04-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Vion-Bailly2022.pdf} +} + +@article{Wagner2009, + title = {Biophysical Foundations Underlying {{TMS}}: {{Setting}} the Stage for an Effective Use of Neurostimulation in the Cognitive Neurosciences}, + author = {Wagner, Tim and Rushmore, Jarrett and Eden, Uri and {Valero-Cabre}, Antoni}, + year = {2009}, + month = oct, + volume = {45}, + number = {9}, + pages = {1025--1034}, + publisher = {Elsevier BV}, + doi = {10.1016/j.cortex.2008.10.002} +} + +@article{Wallach2014, + title = {Glutamate {{Mediated Astrocytic Filtering}} of {{Neuronal Activity}}}, + author = {Wallach, Gilad and Lallouette, Jules and Herzog, Nitzan and De Pitt{\`a}, Maurizio and Jacob, Eshel Ben and Berry, Hugues and Hanein, Yael}, + editor = {Graham, Lyle J.}, + year = {2014}, + month = dec, + journal = {PLoS Computational Biology}, + volume = {10}, + number = {12}, + pages = {e1003964}, + issn = {1553-7358}, + doi = {10.1371/journal.pcbi.1003964}, + urldate = {2023-08-11}, + abstract = {Neuron-astrocyte communication is an important regulatory mechanism in various brain functions but its complexity and role are yet to be fully understood. In particular, the temporal pattern of astrocyte response to neuronal firing has not been fully characterized. Here, we used neuron-astrocyte cultures on multi-electrode arrays coupled to Ca2+ imaging and explored the range of neuronal stimulation frequencies while keeping constant the amount of stimulation. Our results reveal that astrocytes specifically respond to the frequency of neuronal stimulation by intracellular Ca2+ transients, with a clear onset of astrocytic activation at neuron firing rates around 3-5 Hz. The cell-to-cell heterogeneity of the astrocyte Ca2+ response was however large and increasing with stimulation frequency. Astrocytic activation by neurons was abolished with antagonists of type I metabotropic glutamate receptor, validating the glutamate-dependence of this neuron-to-astrocyte pathway. Using a realistic biophysical model of glutamate-based intracellular calcium signaling in astrocytes, we suggest that the stepwise response is due to the supralinear dynamics of intracellular IP3 and that the heterogeneity of the responses may be due to the heterogeneity of the astrocyte-to-astrocyte couplings via gap junction channels. Therefore our results present astrocyte intracellular Ca2+ activity as a nonlinear integrator of glutamate-dependent neuronal activity.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Wallach2014.pdf} +} + +@article{Wang2020, + title = {The {{Allen Mouse Brain Common Coordinate Framework}}: {{A 3D Reference Atlas}}}, + shorttitle = {The {{Allen Mouse Brain Common Coordinate Framework}}}, + author = {Wang, Quanxin and Ding, Song-Lin and Li, Yang and Royall, Josh and Feng, David and Lesnar, Phil and Graddis, Nile and Naeemi, Maitham and Facer, Benjamin and Ho, Anh and Dolbeare, Tim and Blanchard, Brandon and Dee, Nick and Wakeman, Wayne and Hirokawa, Karla E. and Szafer, Aaron and Sunkin, Susan M. and Oh, Seung Wook and Bernard, Amy and Phillips, John W. and Hawrylycz, Michael and Koch, Christof and Zeng, Hongkui and Harris, Julie A. and Ng, Lydia}, + year = {2020}, + month = may, + journal = {Cell}, + volume = {181}, + number = {4}, + pages = {936-953.e20}, + publisher = {Elsevier}, + issn = {0092-8674, 1097-4172}, + doi = {10.1016/j.cell.2020.04.007}, + urldate = {2025-01-30}, + abstract = {{$<$}h2{$>$}Summary{$<$}/h2{$><$}p{$>$}Recent large-scale collaborations are generating major surveys of cell types and connections in the mouse brain, collecting large amounts of data across modalities, spatial scales, and brain areas. Successful integration of these data requires a standard 3D reference atlas. Here, we present the Allen Mouse Brain Common Coordinate Framework (CCFv3) as such a resource. We constructed an average template brain at 10 {$\mu$}m voxel resolution by interpolating high resolution in-plane serial two-photon tomography images with 100 {$\mu$}m z-sampling from 1,675 young adult C57BL/6J mice. Then, using multimodal reference data, we parcellated the entire brain directly in 3D, labeling every voxel with a brain structure spanning 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures. CCFv3 can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D and is openly accessible (https://atlas.brain-map.org/).{$<$}/p{$>$}}, + langid = {english}, + pmid = {32386544}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Wang2020.pdf} +} + +@article{Wang2021, + title = {Automatic Velocity Picking from Semblances with a New Deep-Learning Regression Strategy: {{Comparison}} with a Classification Approach}, + shorttitle = {Automatic Velocity Picking from Semblances with a New Deep-Learning Regression Strategy}, + author = {Wang, Wenlong and McMechan, George A. and Ma, Jianwei and Xie, Fei}, + year = {2021}, + month = mar, + journal = {GEOPHYSICS}, + volume = {86}, + number = {2}, + pages = {U1-U13}, + issn = {0016-8033, 1942-2156}, + doi = {10.1190/geo2020-0423.1}, + urldate = {2022-04-15}, + abstract = {The physical basis, parameterization, and assumptions involved in root-mean-square (rms) velocity estimation have not significantly changed since they were first developed. However, these three aspects are all good targets for novel application of the recent emergence of machine learning (ML). Therefore, it is useful at this time to provide a tutorial overview of two state-of-the-art ML implementations; we have designed and evaluated classification and regression neural networks for the extraction of apparent rms velocity trajectories from semblance data. Both networks share a similar end-to-end trainable structure, except for the final layer. In the classification network, the velocity picking is performed by finding the largest amplitude trajectory through all velocity bins. The regression network, on the other hand, applies a differentiable soft-argmax function that converts the feature maps directly to apparent rms velocity values as functions of traveltime. Relative confidence maps can also be estimated from both neural networks. A large number of synthetic models with horizontal layers are created, and common-midpoint gathers are simulated from those models as training samples. Transfer learning is applied to fine-tune the networks with a small number of samples for testing with synthetic and field data from more complicated (2D) models. Tests using synthetic data show that the regression and classification networks can give reasonable velocity predictions from semblances, but the regression network gives higher accuracy.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Wang2021.pdf} +} + +@article{Wang2023, + title = {Genetically Encoded Mediators for Sonogenetics and Their Applications in Neuromodulation}, + author = {Wang, Hsien-Chu and Phan, Thi-Nhan and Kao, Chi-Ling and Yeh, Chih-Kuang and Lin, Yu-Chun}, + year = {2023}, + month = dec, + journal = {Frontiers in Cellular Neuroscience}, + volume = {17}, + pages = {1326279}, + issn = {1662-5102}, + doi = {10.3389/fncel.2023.1326279}, + urldate = {2024-03-26}, + abstract = {Sonogenetics is an emerging approach that harnesses ultrasound for the manipulation of genetically modified cells. The great penetrability of ultrasound waves enables the non-invasive application of external stimuli to deep tissues, particularly advantageous for brain stimulation. Genetically encoded ultrasound mediators, a set of proteins that respond to ultrasound-induced bio-effects, play a critical role in determining the effectiveness and applications of sonogenetics. In this context, we will provide an overview of these ultrasound-responsive mediators, delve into the molecular mechanisms governing their response to ultrasound stimulation, and summarize their applications in neuromodulation.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Wang2023.pdf} +} + +@article{Wattiez2017, + title = {Transcranial Ultrasonic Stimulation Modulates Single-Neuron Discharge in Macaques Performing an Antisaccade Task}, + author = {Wattiez, Nicolas and Constans, Charlotte and Deffieux, Thomas and Daye, Pierre M. and Tanter, Mickael and Aubry, Jean-Fran{\c c}ois and Pouget, Pierre}, + year = {2017}, + month = nov, + journal = {Brain Stimulation}, + volume = {10}, + number = {6}, + pages = {1024--1031}, + issn = {1935861X}, + doi = {10.1016/j.brs.2017.07.007}, + urldate = {2024-02-19}, + abstract = {Background: Low intensity transcranial ultrasonic stimulation (TUS) has been demonstrated to noninvasively and transiently stimulate the nervous system. Although US neuromodulation has appeared robust in rodent studies, the effects of US in large mammals and humans have been modest at best. In addition, there is a lack of direct recordings from the stimulated neurons in response to US. Our study investigates the magnitude of the US effects on neuronal discharge in awake behaving monkeys and thus fills the void on both fronts. Objective/Hypothesis: In this study, we demonstrate the feasibility of recording action potentials in the supplementary eye field (SEF) as TUS is applied simultaneously to the frontal eye field (FEF) in macaques performing an antisaccade task. Results: We show that compared to a control stimulation in the visual cortex, SEF activity is significantly modulated shortly after TUS onset. Among all cell types 40\% of neurons significantly changed their activity after TUS. Half of the neurons showed a transient increase of activity induced by TUS. Conclusion: Our study demonstrates that the neuromodulatory effects of non-invasive focused ultrasound can be assessed in real time in awake behaving monkeys by recording discharge activity from a brain region reciprocally connected with the stimulated region. The study opens the door for further parametric studies for fine-tuning the ultrasonic parameters. The ultrasonic effect could indeed be quantified based on the direct measurement of the intensity of the modulation induced on a single neuron in a freely performing animal. The technique should be readily reproducible in other primate laboratories studying brain function, both for exploratory and therapeutic purposes and to facilitate the development of future clinical TUS devices.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Wattiez2017.pdf} +} + +@article{Wear2022, + title = {Spatiotemporal {{Deconvolution}} of {{Hydrophone Response}} for {{Linear}} and {{Nonlinear Beams}}---{{Part I}}: {{Theory}}, {{Spatial-Averaging Correction Formulas}}, and {{Criteria}} for {{Sensitive Element Size}}}, + shorttitle = {Spatiotemporal {{Deconvolution}} of {{Hydrophone Response}} for {{Linear}} and {{Nonlinear Beams}}---{{Part I}}}, + author = {Wear, Keith A.}, + year = {2022}, + month = apr, + journal = {IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control}, + volume = {69}, + number = {4}, + pages = {1243--1256}, + issn = {0885-3010, 1525-8955}, + doi = {10.1109/TUFFC.2022.3150186}, + urldate = {2022-10-14}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Wear2022.pdf} +} + +@article{Weinreb2022, + title = {Mechanistic Insights into Ultrasonic Neurostimulation of Disconnected Neurons Using Single Short Pulses}, + author = {Weinreb, Eyal and Moses, Elisha}, + year = {2022}, + month = may, + journal = {Brain Stimulation}, + pages = {S1935861X22000833}, + issn = {1935861X}, + doi = {10.1016/j.brs.2022.05.004}, + urldate = {2022-05-13}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Weinreb2022.pdf} +} + +@article{Wise2019, + title = {Representing Arbitrary Acoustic Source and Sensor Distributions in {{Fourier}} Collocation Methods}, + author = {Wise, Elliott S. and Cox, B. T. and Jaros, Jiri and Treeby, Bradley E.}, + year = {2019}, + month = jul, + journal = {The Journal of the Acoustical Society of America}, + volume = {146}, + number = {1}, + pages = {278--288}, + issn = {0001-4966, 1520-8524}, + doi = {10.1121/1.5116132}, + urldate = {2025-01-28}, + abstract = {Accurately representing acoustic source distributions is an important part of ultrasound simulation. This is challenging for grid-based collocation methods when such distributions do not coincide with the grid points, for instance when the source is a curved, two-dimensional surface embedded in a three-dimensional domain. Typically, grid points close to the source surface are defined as source points, but this can result in ``staircasing'' and substantial errors in the resulting acoustic fields. This paper describes a technique for accurately representing arbitrary source distributions within Fourier collocation methods. The method works by applying a discrete, band-limiting convolution operator to the continuous source distribution, after which source grid weights can be generated. This allows arbitrarily shaped sources, for example, focused bowls and circular pistons, to be defined on the grid without staircasing errors. The technique is examined through simulations of a range of ultrasound sources, and comparisons with analytical solutions show excellent accuracy and convergence rates. Extensions of the technique are also discussed, including application to initial value problems, distributed sensors, and moving sources.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Wise2019.pdf} +} + +@article{Wong2022, + title = {Proceedings of the {{Ninth Annual Deep Brain Stimulation Think Tank}}: {{Advances}} in {{Cutting Edge Technologies}}, {{Artificial Intelligence}}, {{Neuromodulation}}, {{Neuroethics}}, {{Pain}}, {{Interventional Psychiatry}}, {{Epilepsy}}, and {{Traumatic Brain Injury}}}, + shorttitle = {Proceedings of the {{Ninth Annual Deep Brain Stimulation Think Tank}}}, + author = {Wong, Joshua K. and Deuschl, G{\"u}nther and Wolke, Robin and Bergman, Hagai and Muthuraman, Muthuraman and Groppa, Sergiu and Sheth, Sameer A. and {Bronte-Stewart}, Helen M. and Wilkins, Kevin B. and Petrucci, Matthew N. and Lambert, Emilia and Kehnemouyi, Yasmine and Starr, Philip A. and Little, Simon and Anso, Juan and Gilron, Ro'ee and Poree, Lawrence and Kalamangalam, Giridhar P. and Worrell, Gregory A. and Miller, Kai J. and Schiff, Nicholas D. and Butson, Christopher R. and Henderson, Jaimie M. and Judy, Jack W. and {Ramirez-Zamora}, Adolfo and Foote, Kelly D. and Silburn, Peter A. and Li, Luming and Oyama, Genko and Kamo, Hikaru and Sekimoto, Satoko and Hattori, Nobutaka and Giordano, James J. and DiEuliis, Diane and Shook, John R. and Doughtery, Darin D. and Widge, Alik S. and Mayberg, Helen S. and Cha, Jungho and Choi, Kisueng and Heisig, Stephen and Obatusin, Mosadolu and Opri, Enrico and Kaufman, Scott B. and Shirvalkar, Prasad and Rozell, Christopher J. and Alagapan, Sankaraleengam and Raike, Robert S. and Bokil, Hemant and Green, David and Okun, Michael S.}, + year = {2022}, + month = mar, + journal = {Frontiers in Human Neuroscience}, + volume = {16}, + pages = {813387}, + issn = {1662-5161}, + doi = {10.3389/fnhum.2022.813387}, + urldate = {2024-10-29}, + abstract = {DBS Think Tank IX was held on August 25--27, 2021 in Orlando FL with US based participants largely in person and overseas participants joining by video conferencing technology. The DBS Think Tank was founded in 2012 and provides an open platform where clinicians, engineers and researchers (from industry and academia) can freely discuss current and emerging deep brain stimulation (DBS) technologies as well as the logistical and ethical issues facing the field. The consensus among the DBS Think Tank IX speakers was that DBS expanded in its scope and has been applied to multiple brain disorders in an effort to modulate neural circuitry. After collectively sharing our experiences, it was estimated that globally more than 230,000 DBS devices have been implanted for neurological and neuropsychiatric disorders. As such, this year's meeting was focused on advances in the following areas: neuromodulation in Europe, Asia and Australia; cutting-edge technologies, neuroethics, interventional psychiatry, adaptive DBS, neuromodulation for pain, network neuromodulation for epilepsy and neuromodulation for traumatic brain injury.}, + file = {/Users/tomaubier/Zotero/storage/8PDX5JXU/Wong et al. - 2022 - Proceedings of the Ninth Annual Deep Brain Stimula.pdf} +} + +@article{Wong2023, + title = {Proceedings of the 10th Annual Deep Brain Stimulation Think Tank: {{Advances}} in Cutting Edge Technologies, Artificial Intelligence, Neuromodulation, Neuroethics, Interventional Psychiatry, and Women in Neuromodulation}, + shorttitle = {Proceedings of the 10th Annual Deep Brain Stimulation Think Tank}, + author = {Wong, Joshua K. and Mayberg, Helen S. and Wang, Doris D. and Richardson, R. Mark and Halpern, Casey H. and Krinke, Lothar and Arlotti, Mattia and Rossi, Lorenzo and Priori, Alberto and Marceglia, Sara and Gilron, Ro'ee and Cavanagh, James F. and Judy, Jack W. and Miocinovic, Svjetlana and Devergnas, Annaelle D. and Sillitoe, Roy V. and Cernera, Stephanie and Oehrn, Carina R. and Gunduz, Aysegul and Goodman, Wayne K. and Petersen, Erika A. and {Bronte-Stewart}, Helen and Raike, Robert S. and Malekmohammadi, Mahsa and Greene, David and Heiden, Petra and Tan, Huiling and Volkmann, Jens and Voon, Valerie and Li, Luming and Sah, Pankaj and Coyne, Terry and Silburn, Peter A. and Kubu, Cynthia S. and Wexler, Anna and Chandler, Jennifer and Provenza, Nicole R. and Heilbronner, Sarah R. and Luciano, Marta San and Rozell, Christopher J. and Fox, Michael D. and De Hemptinne, Coralie and Henderson, Jaimie M. and Sheth, Sameer A. and Okun, Michael S.}, + year = {2023}, + month = jan, + journal = {Frontiers in Human Neuroscience}, + volume = {16}, + pages = {1084782}, + issn = {1662-5161}, + doi = {10.3389/fnhum.2022.1084782}, + urldate = {2023-08-29}, + abstract = {The deep brain stimulation (DBS) Think Tank X was held on August 17--19, 2022 in Orlando FL. The session organizers and moderators were all women with the theme women in neuromodulation . Dr. Helen Mayberg from Mt. Sinai, NY was the keynote speaker. She discussed milestones and her experiences in developing depression DBS. The DBS Think Tank was founded in 2012 and provides an open platform where clinicians, engineers and researchers (from industry and academia) can freely discuss current and emerging DBS technologies as well as the logistical and ethical issues facing the field. The consensus among the DBS Think Tank X speakers was that DBS has continued to expand in scope however several indications have reached the ``trough of disillusionment.'' DBS for depression was considered as ``re-emerging'' and approaching a slope of enlightenment. DBS for depression will soon re-enter clinical trials. The group estimated that globally more than 244,000 DBS devices have been implanted for neurological and neuropsychiatric disorders. This year's meeting was focused on advances in the following areas: neuromodulation in Europe, Asia, and Australia; cutting-edge technologies, closed loop DBS, DBS tele-health, neuroethics, lesion therapy, interventional psychiatry, and adaptive DBS.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Wong2023.pdf} +} + +@article{Woo2012, + title = {{{TREK-1}} and {{Best1 Channels Mediate Fast}} and {{Slow Glutamate Release}} in {{Astrocytes}} upon {{GPCR Activation}}}, + author = {Woo, Dong~Ho and Han, Kyung-Seok and Shim, Jae~Wan and Yoon, Bo-Eun and Kim, Eunju and Bae, Jin~Young and Oh, Soo-Jin and Hwang, Eun~Mi and Marmorstein, Alan~D. and Bae, Yong~Chul and Park, Jae-Yong and Lee, C.~Justin}, + year = {2012}, + month = sep, + journal = {Cell}, + volume = {151}, + number = {1}, + pages = {25--40}, + issn = {00928674}, + doi = {10.1016/j.cell.2012.09.005}, + urldate = {2024-10-10}, + abstract = {Astrocytes release glutamate upon activation of various GPCRs to exert important roles in synaptic functions. However, the molecular mechanism of release has been controversial. Here, we report two kinetically distinct modes of nonvesicular, channelmediated glutamate release. The fast mode requires activation of Gai, dissociation of Gbg, and subsequent opening of glutamate-permeable, two-pore domain potassium channel TREK-1 through direct interaction between Gbg and N terminus of TREK-1. The slow mode is Ca2+ dependent and requires Gaq activation and opening of glutamate-permeable, Ca2+-activated anion channel Best1. Ultrastructural analyses demonstrate that TREK-1 is preferentially localized at cell body and processes, whereas Best1 is mostly found in microdomains of astrocytes near synapses. Diffusion modeling predicts that the fast mode can target neuronal mGluR with peak glutamate concentration of 100 mM, whereas slow mode targets neuronal NMDA receptors at around 1 mM. Our results reveal two distinct sources of astrocytic glutamate that can differentially influence neighboring neurons.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Woo2012.pdf} +} + +@article{WorldHealthOrganization2006, + title = {Neurological Disorders : Public Health Challenges}, + shorttitle = {Neurological Disorders}, + author = {{World Health Organization}}, + year = {2006}, + pages = {218}, + publisher = {World Health Organization}, + address = {Geneva}, + issn = {9241563362}, + urldate = {2023-08-29}, + langid = {english}, + keywords = {Cost of Illness,Nervous System Diseases,Public Health}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/WorldHealthOrganization2006.pdf} +} + +@article{XiaodongLiu2022, + title = {Review of {{Noninvasive}} or {{Minimally Invasive Deep Brain Stimulation}}}, + author = {{Xiaodong Liu} and {Fang Qiu} and {Lijuan Hou} and {Xiaohui Wang}}, + year = {2022}, + month = jan, + journal = {Frontiers in Behavioral Neuroscience}, + volume = {15}, + doi = {10.3389/fnbeh.2021.820017}, + abstract = {Brain stimulation is a critical technique in neuroscience research and clinical application. Traditional transcranial brain stimulation techniques, such as transcranial magnetic stimulation (TMS), transcranial direct current stimulation (tDCS), and deep brain stimulation (DBS) have been widely investigated in neuroscience for decades. However, TMS and tDCS have poor spatial resolution and penetration depth, and DBS requires electrode implantation in deep brain structures. These disadvantages have limited the clinical applications of these techniques. Owing to developments in science and technology, substantial advances in noninvasive and precise deep stimulation have been achieved by neuromodulation studies. Second-generation brain stimulation techniques that mainly rely on acoustic, electronic, optical, and magnetic signals, such as focused ultrasound, temporal interference, near-infrared optogenetic, and nanomaterial-enabled magnetic stimulation, offer great prospects for neuromodulation. This review summarized the mechanisms, development, applications, and strengths of these techniques and the prospects and challenges in their development. We believe that these second-generation brain stimulation techniques pave the way for brain disorder therapy.}, + pmid = {35145384}, + annotation = {MAG ID: 4207081848}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/XiaodongLiu2022.pdf} +} + +@article{Xiong2022, + title = {Non-Invasive {{Brain Stimulation}} for {{Chronic Pain}}: {{State}} of the {{Art}} and {{Future Directions}}}, + shorttitle = {Non-Invasive {{Brain Stimulation}} for {{Chronic Pain}}}, + author = {Xiong, Huan-Yu and Zheng, Jie-Jiao and Wang, Xue-Qiang}, + year = {2022}, + month = may, + journal = {Frontiers in Molecular Neuroscience}, + volume = {15}, + pages = {888716}, + issn = {1662-5099}, + doi = {10.3389/fnmol.2022.888716}, + urldate = {2023-08-29}, + abstract = {As a technique that can guide brain plasticity, non-invasive brain stimulation (NIBS) has the potential to improve the treatment of chronic pain (CP) because it can interfere with ongoing brain neural activity to regulate specific neural networks related to pain management. Treatments of CP with various forms of NIBS, such as repetitive transcranial magnetic stimulation (rTMS) and transcranial direct current stimulation (tDCS), using new parameters of stimulation have achieved encouraging results. Evidence of moderate quality indicates that high-frequency rTMS of the primary motor cortex has a clear effect on neuropathic pain (NP) and fibromyalgia. However, evidence on its effectiveness regarding pain relief in other CP conditions is conflicting. Concerning tDCS, evidence of low quality supports its benefit for CP treatment. However, evidence suggesting that it exerts a small treatment effect on NP and headaches is also conflicting. In this paper, we describe the underlying principles behind these commonly used stimulation techniques; and summarize the results of randomized controlled trials, systematic reviews, and meta-analyses. Future research should focus on a better evaluation of the short-term and long-term effectiveness of all NIBS techniques and whether they decrease healthcare use, as well as on the refinement of selection criteria.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Xiong2022.pdf} +} + +@article{Xu2020, + title = {Acoustic {{Characterization}} of {{Polydimethylsiloxane}} for {{Microscale Acoustofluidics}}}, + author = {Xu, Guangyao and Ni, Zhengyang and Chen, Xizhou and Tu, Juan and Guo, Xiasheng and Bruus, Henrik and Zhang, Dong}, + year = {2020}, + month = may, + journal = {Physical Review Applied}, + volume = {13}, + number = {5}, + pages = {054069}, + issn = {2331-7019}, + doi = {10.1103/PhysRevApplied.13.054069}, + urldate = {2024-05-31}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Xu2020.pdf} +} + +@article{Yaakub2023, + title = {Transcranial Focused Ultrasound-Mediated Neurochemical and Functional Connectivity Changes in Deep Cortical Regions in Humans}, + author = {Yaakub, Siti N. and White, Tristan A. and Roberts, Jamie and Martin, Eleanor and Verhagen, Lennart and Stagg, Charlotte J. and Hall, Stephen and Fouragnan, Elsa F.}, + year = {2023}, + month = sep, + journal = {Nature Communications}, + volume = {14}, + number = {1}, + pages = {5318}, + issn = {2041-1723}, + doi = {10.1038/s41467-023-40998-0}, + urldate = {2023-10-18}, + abstract = {Abstract Low-intensity transcranial ultrasound stimulation (TUS) is an emerging non-invasive technique for focally modulating human brain function. The mechanisms and neurochemical substrates underlying TUS neuromodulation in humans and how these relate to excitation and inhibition are still poorly understood. In 24 healthy controls, we separately stimulated two deep cortical regions and investigated the effects of theta-burst TUS, a protocol shown to increase corticospinal excitability, on the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) and functional connectivity. We show that theta-burst TUS in humans selectively reduces GABA levels in the posterior cingulate, but not the dorsal anterior cingulate cortex. Functional connectivity increased following TUS in both regions. Our findings suggest that TUS changes overall excitability by reducing GABAergic inhibition and that changes in TUS-mediated neuroplasticity last at least 50\,mins after stimulation. The difference in TUS effects on the posterior and anterior cingulate could suggest state- or location-dependency of the TUS effect---both mechanisms increasingly recognized to influence the brain's response to neuromodulation.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Yaakub2023.pdf} +} + +@misc{Yagubbbayli2024, + title = {K-{{Wave-Python}}}, + author = {Yagubbbayli and {Farid {and} Sinden} and {David {and} Simson} and Walter}, + year = {2024} +} + +@article{Yang2012, + title = {Transcranial {{Focused Ultrasound}} to the {{Thalamus Is Associated}} with {{Reduced Extracellular GABA Levels}} in {{Rats}}}, + author = {Yang, Po Song and Kim, Hyungmin and Lee, Wonhye and Bohlke, Mark and Park, Shinsuk and Maher, Timothy J. and Yoo, Seung-Schik}, + year = {2012}, + journal = {Neuropsychobiology}, + volume = {65}, + number = {3}, + pages = {153--160}, + issn = {0302-282X, 1423-0224}, + doi = {10.1159/000336001}, + urldate = {2023-12-08}, + abstract = {\emph{Objective:} Transcranial focused ultrasound (FUS), with its ability to non-invasively modulate the excitability of region-specific brain areas, is gaining attention as a potential neurotherapeutic modality. The aim of this study was to examine whether or not FUS administered to the brain could alter the extracellular levels of glutamate and {$\gamma$}-aminobutyric acid (GABA), which are representative excitatory and inhibitory amino acid neurotransmitters, respectively. \emph{Methods:} FUS, delivered in the form of a train of pulses, was applied to the thalamus of Sprague-Dawley rats transcranially. Glutamate and GABA were directly sampled from the frontal lobe of the rat brain via a direct microdialysis technique before, during, and after the sonication. The dialysate concentrations were determined by high-performance liquid chromatography. \emph{Results:} The individual levels of the neurotransmitters sampled were normalized to the baseline level for each rat. In terms of the changes in extracellular glutamate levels, there was no difference between the FUS-treated group and the unsonicated control group. However, extracellular GABA levels started to decrease upon sonication and remained reduced (approximately 20\% below baseline; repeated-measures ANOVA, p {$<$} 0.05, adjusted for multiple comparisons) compared to the control group. \emph{Conclusion:} The ability to modulate region-specific brain activity, along with the present evidence of the ability to modulate neurotransmission, demonstrates the potential utility of FUS as a completely new non-invasive therapeutic modality.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Yang2012.pdf} +} + +@article{Yang2017, + title = {High-Intensity Focused Ultrasound Ablation: {{An}} in Vitro Agarose Gel Model}, + author = {Yang, S. and Chen, Y.-J and Cui, R. and Zhao, H.-X and Zhao, Y. and Liu, Z.-Q and Yu, Y. and Shao, X.-Y and Xu, Q.}, + year = {2017}, + month = nov, + journal = {International Journal of Clinical and Experimental Medicine}, + volume = {10}, + pages = {15302--15308}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Yang2017.pdf} +} + +@inproceedings{Yen2020, + title = {Active {{Damping}} of {{Air-backed Ultrasonic Transducers Using Arbitrary Waveform Generators}}}, + booktitle = {2020 {{IEEE International Ultrasonics Symposium}} ({{IUS}})}, + author = {Yen, Jesse and Nussbaum, Zoe}, + year = {2020}, + month = sep, + pages = {1--4}, + publisher = {IEEE}, + address = {Las Vegas, NV, USA}, + doi = {10.1109/IUS46767.2020.9251816}, + urldate = {2024-02-02}, + abstract = {Ultrasound technologies such as high-intensity focused ultrasound and acoustic radiation force imaging require advanced or sophisticated transducer designs. Oftentimes, these designs have transducer requirements of wide power ranges, high sensitivity, and broad bandwidth. However, it would often times be desirable to use the same transducer for both. The objective of this proof-of-concept study is to demonstrate the feasibility of using active damping of air-backed, narrowband transducers to achieve broadband capability. Active damping is accomplished through the use of arbitrary waveform generators to cancel subsequent oscillations beyond the initial excitation. A modified 1-D KLM model written in Matlab is used to guide the design of the waveforms. Optimization of the waveforms is applied to the KLM model using minimization function that minimizes ripple. In the model, - 3 dB transmitted bandwidth increased from 10\% to 44\% for 1.5-cycle excitation and 11.4\% to 63.8\% for 1-cycle excitation. Comparable increases in bandwidth were also observed experimentally.}, + isbn = {978-1-72815-448-0}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Yen2020.pdf} +} + +@article{Yong2024, + title = {Advancement in Modulation of Brain Extracellular Space and Unlocking Its Potential for Intervention of Neurological Diseases}, + author = {Yong, Yu and Cai, Yicong and Lin, Jiawei and Ma, Lin and Han, HongBin and Li, Fenfang}, + year = {2024}, + month = may, + journal = {Med-X}, + volume = {2}, + number = {1}, + pages = {6}, + issn = {2731-8710}, + doi = {10.1007/s44258-024-00021-7}, + urldate = {2024-07-02}, + abstract = {Cells in the brain are surrounded by extracellular space (ECS), which forms porous nets and interconnected routes for molecule transportation. Our view of brain ECS has changed from a largely static compartment to dynamic and diverse structures that actively regulate neural activity and brain states. Emerging evidence supports that dysregulation of brain ECS contributes to the pathogenesis and development of many neurological disorders, highlighting the importance of therapeutic modulation of brain ECS function. Here, we aim to provide an overview of the regulation and dysfunction of ECS in healthy and pathological brains, as well as advanced tools to investigate properties of brain ECS. This review emphasizes modulation methods to manipulate ECS with implications to restore their function in brain diseases.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Yong2024.pdf} +} + +@article{Yoo2011, + title = {Focused Ultrasound Modulates Region-Specific Brain Activity}, + author = {Yoo, Seung-Schik and Bystritsky, Alexander and Lee, Jong-Hwan and Zhang, Yongzhi and Fischer, Krisztina and Min, Byoung-Kyong and McDannold, Nathan J. and {Pascual-Leone}, Alvaro and Jolesz, Ferenc A.}, + year = {2011}, + month = jun, + journal = {NeuroImage}, + volume = {56}, + number = {3}, + pages = {1267--1275}, + issn = {1053-8119}, + doi = {10.1016/j.neuroimage.2011.02.058}, + urldate = {2023-08-31}, + abstract = {We demonstrated the in vivo feasibility of using focused ultrasound (FUS) to transiently modulate (through either stimulation or suppression) the function of regional brain tissue in rabbits. FUS was delivered in a train of pulses at low acoustic energy, far below the cavitation threshold, to the animal's somatomotor and visual areas, as guided by anatomical and functional information from magnetic resonance imaging (MRI). The temporary alterations in the brain function affected by the sonication were characterized by both electrophysiological recordings and functional brain mapping achieved through the use of functional MRI (fMRI). The modulatory effects were bimodal, whereby the brain activity could either be stimulated or selectively suppressed. Histological analysis of the excised brain tissue after the sonication demonstrated that the FUS did not elicit any tissue damages. Unlike transcranial magnetic stimulation, FUS can be applied to deep structures in the brain with greater spatial precision. Transient modulation of brain function using image-guided and anatomically-targeted FUS would enable the investigation of functional connectivity between brain regions and will eventually lead to a better understanding of localized brain functions. It is anticipated that the use of this technology will have an impact on brain research and may offer novel therapeutic interventions in various neurological conditions and psychiatric disorders.}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Yoo2011.pdf} +} + +@article{Yoo2022, + title = {Focused Ultrasound Excites Cortical Neurons via Mechanosensitive Calcium Accumulation and Ion Channel Amplification}, + author = {Yoo, Sangjin and Mittelstein, David R. and Hurt, Robert C. and Lacroix, Jerome and Shapiro, Mikhail G.}, + year = {2022}, + month = jan, + journal = {Nature Communications}, + volume = {13}, + number = {1}, + pages = {493}, + issn = {2041-1723}, + doi = {10.1038/s41467-022-28040-1}, + urldate = {2023-02-17}, + abstract = {Abstract Ultrasonic neuromodulation has the unique potential to provide non-invasive control of neural activity in deep brain regions with high spatial precision and without chemical or genetic modification. However, the biomolecular and cellular mechanisms by which focused ultrasound excites mammalian neurons have remained unclear, posing significant challenges for the use of this technology in research and potential clinical applications. Here, we show that focused ultrasound excites primary murine cortical neurons in culture through a primarily mechanical mechanism mediated by specific calcium-selective mechanosensitive ion channels. The activation of these channels results in a gradual build-up of calcium, which is amplified by calcium- and voltage-gated channels, generating a burst firing response. Cavitation, temperature changes, large-scale deformation, and synaptic transmission are not required for this excitation to occur. Pharmacological and genetic inhibition of specific ion channels leads to reduced responses to ultrasound, while over-expressing these channels results in stronger ultrasonic stimulation. These findings provide a mechanistic explanation for the effect of ultrasound on neurons to facilitate the further development of ultrasonic neuromodulation and sonogenetics as tools for neuroscience research.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Yoo2022.pdf} +} + +@article{Younan2013, + title = {Influence of the Pressure Field Distribution in Transcranial Ultrasonic Neurostimulation: {{Influence}} of Pressure Distribution in Transcranial Ultrasonic Neurostimulation}, + shorttitle = {Influence of the Pressure Field Distribution in Transcranial Ultrasonic Neurostimulation}, + author = {Younan, Youliana and Deffieux, Thomas and Larrat, Benoit and Fink, Mathias and Tanter, Mickael and Aubry, Jean-Francois}, + year = {2013}, + month = jul, + journal = {Medical Physics}, + volume = {40}, + number = {8}, + pages = {082902}, + issn = {00942405}, + doi = {10.1118/1.4812423}, + urldate = {2022-04-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Younan2013.pdf} +} + +@article{Younan2014, + title = {Non-Invasive Therapy of Brain Disorders with Focused Ultrasound: {{From}} Animal Experiments to Clinical Transfer}, + author = {Younan, Youliana and Aubry, Jean-Francois and Tanter, Micka{\"e}l}, + year = {2014}, + month = mar, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Younan2014.pdf} +} + +@article{Young2023, + title = {The Energetics of Rapid Cellular Mechanotransduction}, + author = {Young, Michael N. and Sindoni, Michael J. and Lewis, Amanda H. and Zauscher, Stefan and Grandl, J{\"o}rg}, + year = {2023}, + month = feb, + journal = {Proceedings of the National Academy of Sciences}, + volume = {120}, + number = {8}, + pages = {e2215747120}, + issn = {0027-8424, 1091-6490}, + doi = {10.1073/pnas.2215747120}, + urldate = {2023-06-12}, + abstract = {Cells throughout the human body detect mechanical forces. While it is known that the rapid (millisecond) detection of mechanical forces is mediated by force-gated ion channels, a detailed quantitative understanding of cells as sensors of mechanical energy is still lacking. Here, we combine atomic force microscopy with patch-clamp electrophysiology to determine the physical limits of cells expressing the force-gated ion channels (FGICs) Piezo1, Piezo2, TREK1, and TRAAK. We find that, depending on the ion channel expressed, cells can function either as proportional or nonlinear transducers of mechanical energy and detect mechanical energies as little as {\textasciitilde}100 fJ, with a resolution of up to {\textasciitilde}1 fJ. These specific energetic values depend on cell size, channel density, and cytoskeletal architecture. We also make the surprising discovery that cells can transduce forces either nearly instantaneously ({$<$}1 ms) or with a substantial time delay ({\textasciitilde}10 ms). Using a chimeric experimental approach and simulations, we show how such delays can emerge from channel-intrinsic properties and the slow diffusion of tension in the membrane. Overall, our experiments reveal the capabilities and limits of cellular mechanosensing and provide insights into molecular mechanisms that different cell types may employ to specialize for their distinct physiological roles.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Young2023.pdf} +} + +@article{Yu2020, + title = {A Review of Computational Modeling and Deep Brain Stimulation: Applications to {{Parkinson}}'s Disease}, + shorttitle = {A Review of Computational Modeling and Deep Brain Stimulation}, + author = {Yu, Ying and Wang, Xiaomin and Wang, Qishao and Wang, Qingyun}, + year = {2020}, + month = dec, + journal = {Applied Mathematics and Mechanics}, + volume = {41}, + number = {12}, + pages = {1747--1768}, + issn = {0253-4827, 1573-2754}, + doi = {10.1007/s10483-020-2689-9}, + urldate = {2023-05-17}, + abstract = {Biophysical computational models are complementary to experiments and theories, providing powerful tools for the study of neurological diseases. The focus of this review is the dynamic modeling and control strategies of Parkinson's disease (PD). In previous studies, the development of parkinsonian network dynamics modeling has made great progress. Modeling mainly focuses on the cortex-thalamus-basal ganglia (CTBG) circuit and its sub-circuits, which helps to explore the dynamic behavior of the parkinsonian network, such as synchronization. Deep brain stimulation (DBS) is an effective strategy for the treatment of PD. At present, many studies are based on the side effects of the DBS. However, the translation from modeling results to clinical disease mitigation therapy still faces huge challenges. Here, we introduce the progress of DBS improvement. Its specific purpose is to develop novel DBS treatment methods, optimize the treatment effect of DBS for each patient, and focus on the study in closed-loop DBS. Our goal is to review the inspiration and insights gained by combining the system theory with these computational models to analyze neurodynamics and optimize DBS treatment.}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Yu2020.pdf} +} + +@article{Zarahn1997, + title = {Empirical {{Analyses}} of {{BOLD fMRI Statistics}}}, + author = {Zarahn, E. and Aguirre, G.K. and D'Esposito, M.}, + year = {1997}, + month = apr, + journal = {NeuroImage}, + volume = {5}, + number = {3}, + pages = {179--197}, + issn = {10538119}, + doi = {10.1006/nimg.1997.0263}, + urldate = {2022-03-23}, + langid = {english} +} + +@article{Zhai2020, + title = {Calcium {{Entry}} through {{TRPV1}}: {{A Potential Target}} for the {{Regulation}} of {{Proliferation}} and {{Apoptosis}} in {{Cancerous}} and {{Healthy Cells}}}, + shorttitle = {Calcium {{Entry}} through {{TRPV1}}}, + author = {Zhai, Kevin and Liskova, Alena and Kubatka, Peter and B{\"u}sselberg, Dietrich}, + year = {2020}, + month = jun, + journal = {International Journal of Molecular Sciences}, + volume = {21}, + number = {11}, + pages = {4177}, + issn = {1422-0067}, + doi = {10.3390/ijms21114177}, + urldate = {2023-05-09}, + abstract = {Intracellular calcium (Ca2+) concentration ([Ca2+]i) is a key determinant of cell fate and is implicated in carcinogenesis. Membrane ion channels are structures through which ions enter or exit the cell, depending on the driving forces. The opening of transient receptor potential vanilloid 1 (TRPV1) ligand-gated ion channels facilitates transmembrane Ca2+ and Na+ entry, which modifies the delicate balance between apoptotic and proliferative signaling pathways. Proliferation is upregulated through two mechanisms: (1) ATP binding to the G-protein-coupled receptor P2Y2, commencing a kinase signaling cascade that activates the serine-threonine kinase Akt, and (2) the transactivation of the epidermal growth factor receptor (EGFR), leading to a series of protein signals that activate the extracellular signal-regulated kinases (ERK) 1/2. The TRPV1-apoptosis pathway involves Ca2+ influx and efflux between the cytosol, mitochondria, and endoplasmic reticulum (ER), the release of apoptosis-inducing factor (AIF) and cytochrome c from the mitochondria, caspase activation, and DNA fragmentation and condensation. While proliferative mechanisms are typically upregulated in cancerous tissues, shifting the balance to favor apoptosis could support anti-cancer therapies. TRPV1, through [Ca2+]i signaling, influences cancer cell fate; therefore, the modulation of the TRPV1-enforced proliferation--apoptosis balance is a promising avenue in developing anti-cancer therapies and overcoming cancer drug resistance. As such, this review characterizes and evaluates the role of TRPV1 in cell death and survival, in the interest of identifying mechanistic targets for drug discovery.}, + langid = {english}, + file = {/Users/tomaubier/Zotero/storage/FP2DEF7B/Zhai et al. - 2020 - Calcium Entry through TRPV1 A Potential Target fo.pdf} +} + +@article{Zwier2004, + title = {Image Calibration in Fluorescence Microscopy}, + author = {Zwier, J. M. and Van Rooij, G. J. and Hofstraat, J. W. and Brakenhoff, G. J.}, + year = {2004}, + month = oct, + journal = {Journal of Microscopy}, + volume = {216}, + number = {1}, + pages = {15--24}, + issn = {0022-2720, 1365-2818}, + doi = {10.1111/j.0022-2720.2004.01390.x}, + urldate = {2022-04-15}, + langid = {english}, + file = {/Users/tomaubier/Library/Mobile Documents/iCloud~md~obsidian/Documents/UsNeuStim/Files/Zwier2004.pdf} +} diff --git a/joss_paper/paper.md b/joss_paper/paper.md index 64214b6..e1a0f39 100644 --- a/joss_paper/paper.md +++ b/joss_paper/paper.md @@ -1,105 +1,58 @@ --- -title: 'Gala: A Python package for galactic dynamics' +title: 'CoperniFUS: A flexible Python-based GUI for stereotaxic experiment planning' tags: - Python - Experimental Neuroscience - Ultrasound neurostimulation authors: - - name: Adrian M. Price-Whelan - orcid: 0000-0000-0000-0000 - equal-contrib: true - affiliation: "1, 2" # (Multiple affiliations must be quoted) - - name: Author Without ORCID - equal-contrib: true # (This is how you can denote equal contributions between multiple authors) - affiliation: 2 - - name: Author with no affiliation + - name: Tom Aubier + orcid: 0009-0004-5558-8435 + affiliation: 1 # (Multiple affiliations must be quoted) + - name: Ivan M. Suarez-Castellanos corresponding: true # (This is how to denote the corresponding author) - affiliation: 3 - - given-names: Ludwig - dropping-particle: van - surname: Beethoven - affiliation: 3 + affiliation: 1 + - name: Sandrine Parrot + affiliation: 2 + - name: W. Apoutou N'Djin + affiliation: 1 affiliations: - - name: Lyman Spitzer, Jr. Fellow, Princeton University, United States + - name: LabTAU, INSERM, Centre Léon Bérard, Université Claude Bernard Lyon 1, F-69003, Lyon, France index: 1 - ror: 00hx57361 - - name: Institution Name, Country + - name: Université Claude Bernard Lyon 1, INSERM, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292, F-69500 Bron, France index: 2 - - name: Independent Researcher, Country - index: 3 -date: 13 August 2017 -bibliography: paper.bib +date: 00 February 2025 +bibliography: neustim.bib # Optional fields if submitting to a AAS journal too, see this blog post: # https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing -aas-doi: 10.3847/xxxxx <- update this with the DOI from AAS once you know it. -aas-journal: Astrophysical Journal <- The name of the AAS journal. +# aas-doi: 10.3847/xxxxx <- update this with the DOI from AAS once you know it. +# aas-journal: Astrophysical Journal <- The name of the AAS journal. --- # Summary -The forces on stars, galaxies, and dark matter under external gravitational -fields lead to the dynamical evolution of structures in the universe. The orbits -of these bodies are therefore key to understanding the formation, history, and -future state of galaxies. The field of "galactic dynamics," which aims to model -the gravitating components of galaxies to study their structure and evolution, -is now well-established, commonly taught, and frequently used in astronomy. -Aside from toy problems and demonstrations, the majority of problems require -efficient numerical tools, many of which require the same base code (e.g., for -performing numerical orbit integration). +Focused UltraSound (FUS) is gaining increasing interest for its potential as a minimally-invasive yet targeted alternative to existing neurostimulation modalities. +% relying on highly diffuse electrical or magnetic fields to affect the activity of neural structures. +Although reversible changes in the neural activity of structures have been reported as far back as 1928 [@Harvey1928], comprehensive descriptions of the short- and long-term effects of ultrasound on neural structures are still laking to achieved neurostimulation with satisfactory levels of control and safety. Delivering well characterized FUS pulses with a high degree of spatial selectivity along with local assessment of the state and activity of specific brain regions is crucial in pursuing this research. +Unlike most electrophysiology procedures involving compact needle-like probes that can be achieved using stereotaxic frame limited to three degrees of freedom, FUS experiments on small *in vivo* models often require the implementation of complex probe layouts to assess the activity of the stimulated neural structures. +Treatment planning, evaluation of acoustic parameters through simulations, and post-precessing of results often rely on distinct softwares with their own coordinate systems which greatly complicates the detailed characterization of the spatial and temporal effects of FUS stimulations. +`CoperniFUS` aims to overcome this obstacle by providing a flexible software platform to plan procedures on stereotaxic frames thanks to a unified coordinate system architecture, which additionally allows for the management of anatomical variability based on the registration of anatomical landmark. # Statement of need -`Gala` is an Astropy-affiliated Python package for galactic dynamics. Python -enables wrapping low-level languages (e.g., C) for speed without losing -flexibility or ease-of-use in the user-interface. The API for `Gala` was -designed to provide a class-based and user-friendly interface to fast (C or -Cython-optimized) implementations of common operations such as gravitational -potential and force evaluation, orbit integration, dynamical transformations, -and chaos indicators for nonlinear dynamics. `Gala` also relies heavily on and -interfaces well with the implementations of physical units and astronomical -coordinate systems in the `Astropy` package [@astropy] (`astropy.units` and -`astropy.coordinates`). - -`Gala` was designed to be used by both astronomical researchers and by -students in courses on gravitational dynamics or astronomy. It has already been -used in a number of scientific publications [@Pearson:2017] and has also been -used in graduate courses on Galactic dynamics to, e.g., provide interactive -visualizations of textbook material [@Binney:2008]. The combination of speed, -design, and support for Astropy functionality in `Gala` will enable exciting -scientific explorations of forthcoming data releases from the *Gaia* mission -[@gaia] by students and experts alike. - -# Mathematics - -Single dollars ($) are required for inline mathematics e.g. $f(x) = e^{\pi/x}$ - -Double dollars make self-standing equations: - -$$\Theta(x) = \left\{\begin{array}{l} -0\textrm{ if } x < 0\cr -1\textrm{ else} -\end{array}\right.$$ - -You can also use plain \LaTeX for equations -\begin{equation}\label{eq:fourier} -\hat f(\omega) = \int_{-\infty}^{\infty} f(x) e^{i\omega x} dx -\end{equation} -and refer to \autoref{eq:fourier} from text. + +In an effort to assess the therapeutic potential of ultrasound neurostimulation, studies have been attempted to characterize the effect of ultrasound on the biochemical micro-environment of brain structures after stimulations. While tools like Magnetic Resonance Spectroscopy (MRS) offer a non-invasive way of assessing the concentrations of metabolites *in vivo*, they come with significant limitations. Concentration evaluation are non-specific, only representative of the total amount metabolic, extra- and intra-cellular quantity of a compound [@Dyke2017]. The spatial selectivity of the method is also limited to minimum voxel volumes of several $cm^3$. Finally, the difficulties arising from the integration of FUS transducers in MRIs are holding back the investigation of *online* effects [@Yaakub2023]. -# Citations + +Studies on rodent models have been pursued using invasive methods such as microdialysis [@Min2011; @Yang2012]. Although these studies report effects of FUS stimulations on Dopamine, Serotonin or GABA levels, their observations are restricted to low ultrasound central frequencies resulting in poorly spatially-selective stimulation, which complicates the assessment of region-specific responses. The choice of low frequencies is typically done to maximize energy transfer through the skull and minimize pressure field distortions. Transducer placement and targeting of the structure is empirical, based on trigonometric evaluation of the focus relative to reference atlases. -Citations to entries in paper.bib should be in -[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html) -format. + +With the growing interest in transcranial ultrasound therapeutic approaches, extensive research has been conducted to develop and validate computational models of acoustic wave propagation through the skull. Although a number of tools and formalisms exist [@Aubry2022a], k-Wave [@Treeby2010] has been widely adopted in the field of ultrasound neurostimulation specifically [@Constans2018; @Verhagen2019; @Yaakub2023]. Acoustic simulations in this context are performed using standalone Matlab scripts for the definition of acoustic sources and domains. Acoustic domains are defined either directly based on CT or pseudo-CT scans [@Aubry2003], or by constructing maps from rasterized brain and skull meshes. Registration of the transducer location relative to targeted brain structures is achieved using optical tracking systems on human or non-human primate subjects, however empirical methods are usually chosen in small rodents experiments due to the space constraints associated with these models. -If you want to cite a software repository URL (e.g. something on GitHub without a preferred -citation) then you can do it with the example BibTeX entry below for @fidgit. + +Targeting of brain structures is achieved using reference atlases registered to MRI scans of subjects when available. However for small animals, these are typically not performed in a systematic way. Targeted structures coordinates are thus directly evaluated on reference atlases, based on anatomical landmarks such as the Bregma skull suture on rats and mice [@Kleven2023; @Wang2020]. Morphological variability between subjects can compromise experiments if it is not taken into account however registration of reference atlases to anatomical measurements can be tedious and is rarely reported in rodent studies. -For a quick reference, the following citation commands can be used: -- `@author:2001` -> "Author et al. (2001)" -- `[@author:2001]` -> "(Author et al., 2001)" -- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)" +# Features # Figures @@ -112,7 +65,6 @@ Figure sizes can be customized by adding an optional second parameter: # Acknowledgements -We acknowledge contributions from Brigitta Sipocz, Syrtis Major, and Semyeong -Oh, and support from Kathryn Johnston during the genesis of this project. +This project was supported by the French National Research Agency (ANR-16-TERC0017, ANR-21-CE19-0007 \& ANR-21-CE19-0030), the American Focused Ultrasound Foundation (LabTAU, FUSF Center of Excellence). Additionally, this work was performed within the framework of the LABEX DEV WECAN (ANR-10-LABX-0061) and CORTEX (ANR-11-LABX-0042) of Université de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR). The work of the communities behind k-Wave and the Python packages used throughout this work was integral to its completion. # References \ No newline at end of file