[ { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/t04f7-qt783", "eprint_id": 120143, "eprint_status": "archive", "datestamp": "2023-08-20 09:06:24", "lastmod": "2023-12-22 23:32:58", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Trautmann-Eric-M", "name": { "family": "Trautmann", "given": "Eric M." }, "orcid": "0000-0001-5552-2023" }, { "id": "Hesse-Janis-K", "name": { "family": "Hesse", "given": "Janis K." }, "orcid": "0000-0003-0405-8632" }, { "id": "Stine-Gabriel-M", "name": { "family": "Stine", "given": "Gabriel M." }, "orcid": "0000-0003-4906-0461" }, { "id": "Xia-Ruobing", "name": { "family": "Xia", "given": "Ruobing" }, "orcid": "0000-0002-1460-5882" }, { "id": "Zhu-Shude", "name": { "family": "Zhu", "given": "Shude" }, "orcid": "0000-0002-8674-9607" }, { "id": "O'Shea-Daniel-J", "name": { "family": "O'Shea", "given": "Daniel J." }, "orcid": "0000-0002-1366-1743" }, { "id": "Karsh-Bill", "name": { "family": "Karsh", "given": "Bill" } }, { "id": "Colonell-Jennifer", "name": { "family": "Colonell", "given": "Jennifer" } }, { "id": "Lanfranchi-Frank-F", "name": { "family": "Lanfranchi", "given": "Frank F." }, "orcid": "0000-0001-8176-320X" }, { "id": "Vyas-Saurabh", "name": { "family": "Vyas", "given": "Saurabh" }, "orcid": "0000-0002-5406-3272" }, { "id": "Zimnik-Andrew", "name": { "family": "Zimnik", "given": "Andrew" }, "orcid": "0000-0002-8313-2476" }, { "id": "Steinmann-Natalie-A", "name": { "family": "Steinmann", "given": "Natalie A." }, "orcid": "0000-0002-6350-2038" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Andrei-Alexandru", "name": { "family": "Andrei", "given": "Alexandru" } }, { "id": "Mora-Lopez-Carolina", "name": { "family": "Mora Lopez", "given": "Carolina" }, "orcid": "0000-0003-4200-0001" }, { "id": "O'Callaghan-John", "name": { "family": "O'Callaghan", "given": "John" }, "orcid": "0000-0003-2313-8697" }, { "id": "Putzeys-Jan", "name": { "family": "Putzeys", "given": "Jan" }, "orcid": "0000-0001-8834-5852" }, { "id": "Raducanu-Bogdan-C", "name": { "family": "Raducanu", "given": "Bogdan C." }, "orcid": "0000-0003-2207-6260" }, { "id": "Welkenhuysen-Marleen", "name": { "family": "Welkenhuysen", "given": "Marleen" }, "orcid": "0000-0001-6729-9391" }, { "id": "Churchland-Mark", "name": { "family": "Churchland", "given": "Mark" }, "orcid": "0000-0001-9123-6526" }, { "id": "Moore-Trin", "name": { "family": "Moore", "given": "Tirin" }, "orcid": "0000-0002-3345-2930" }, { "id": "Shadlen-Michael", "name": { "family": "Shadlen", "given": "Michael" }, "orcid": "0000-0002-2002-2210" }, { "id": "Shenoy-Krishna", "name": { "family": "Shenoy", "given": "Krishna" }, "orcid": "0000-0003-1534-9240" }, { "id": "Tsao-D-Y", "name": { "family": "Tsao", "given": "Doris" }, "orcid": "0000-0003-1083-1919" }, { "id": "Dutta-Barundeb", "name": { "family": "Dutta", "given": "Barundeb" }, "orcid": "0000-0003-4781-9630" }, { "id": "Harris-Timothy-D", "name": { "family": "Harris", "given": "Timothy" }, "orcid": "0000-0002-6289-4439" } ] }, "title": "Large-scale brain-wide neural recording in nonhuman primates", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. \n\nWe dedicate this manuscript to Krishna Shenoy (1968-2023), whose visionary leadership set this work in motion. His passion and dedication inspired a generation of neuroscientists and engineers, and his presence will continue to resonate within our field and community. \n\nWe thank the support of the Howard Hughes Medical Institute, who funded the development of the probe. We thank Yanina Pavlova, Danielle Abreu Lopes, Stephen Cital, Cornel Duhaney, Brian Madeira, Mackenzie Risch, and Michelle Wechsler for surgical assistance and expert veterinary care. for their assistance in the planning and execution of surgeries, animal training and general support, and Stephen Ryu for surgical expertise. We thank Bob Schneeveis and Tanya Tabachnik for engineering assistance. In addition, we thank Columbia University's ICM for the quality of care they provide for our animals, especially during the pandemic and lockdown. We thank Wei-lung Sun, for probe testing and software development (HHMI Janelia). E.M.T. is supported by the Grossman center and the Brain and Behavior Research Foundation. S.V is supported by NIH NRSA NINDS F32, N.A.S is supported by NIH Brain Initiative (MR01NS113113). T.M. is supported by EY014924, NS116623. A.Z. is supported by the American Parkinson Disease Post-Doctoral Fellowship. D.J.O is supported by SCGB (543045). \n\nThe authors have declared no competing interest.\n\n
Submitted - 2023.02.01.526664v2.full.pdf
", "abstract": "High-density, integrated silicon electrodes have begun to transform systems neuroscience, by enabling large-scale neural population recordings with single cell resolution. Existing technologies, however, have provided limited functionality in nonhuman primate species such as macaques, which offer close models of human cognition and behavior. Here, we report the design, fabrication, and performance of Neuropixels 1.0-NHP, a high channel count linear electrode array designed to enable large-scale simultaneous recording in superficial and deep structures within the macaque or other large animal brain. These devices were fabricated in two versions: 4416 electrodes along a 45 mm shank, and 2496 along a 25 mm shank. For both versions, users can programmably select 384 channels, enabling simultaneous multi-area recording with a single probe. We demonstrate recording from over 3000 single neurons within a session, and simultaneous recordings from over 1000 neurons using multiple probes. This technology represents a significant increase in recording access and scalability relative to existing technologies, and enables new classes of experiments involving fine-grained electrophysiological characterization of brain areas, functional connectivity between cells, and simultaneous brain-wide recording at scale.", "date": "2023-02-04", "date_type": "published", "id_number": "CaltechAUTHORS:20230316-182335000.26", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230316-182335000.26", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Howard Hughes Medical Institute (HHMI)" }, { "agency": "Columbia University" }, { "agency": "Brain and Behavior Research Foundation" }, { "agency": "NIH Postdoctoral Fellowship" }, { "agency": "NIH", "grant_number": "MR01NS113113" }, { "agency": "NIH", "grant_number": "EY014924" }, { "agency": "NIH", "grant_number": "NS116623" }, { "agency": "American Parkinson Disease Association" }, { "agency": "Simons Foundation", "grant_number": "543045" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2023.02.01.526664", "primary_object": { "basename": "2023.02.01.526664v2.full.pdf", "url": "https://authors.library.caltech.edu/records/t04f7-qt783/files/2023.02.01.526664v2.full.pdf" }, "resource_type": "monograph", "pub_year": "2023", "author_list": "Trautmann, Eric M.; Hesse, Janis K.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/6ftpg-4wj22", "eprint_id": 111337, "eprint_status": "archive", "datestamp": "2023-08-22 11:18:17", "lastmod": "2023-12-22 23:08:14", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kahan-Anat", "name": { "family": "Kahan", "given": "Anat" }, "orcid": "0000-0002-4799-3017" }, { "id": "Greenbaum-Alon", "name": { "family": "Greenbaum", "given": "Alon" }, "orcid": "0000-0002-2897-876X" }, { "id": "Jang-Min-Jee", "name": { "family": "Jang", "given": "Min J." }, "orcid": "0000-0002-1536-7177" }, { "id": "Robinson-J-Elliott", "name": { "family": "Robinson", "given": "J. Elliott" }, "orcid": "0000-0001-9417-3938" }, { "id": "Cho-Jounhong-Ryan", "name": { "family": "Cho", "given": "Jounhong Ryan" }, "orcid": "0000-0001-9542-716X" }, { "id": "Chen-Xinhong", "name": { "family": "Chen", "given": "Xinhong" }, "orcid": "0000-0003-0408-0813" }, { "id": "Kassraian-Fard-Pegah", "name": { "family": "Kassraian", "given": "Pegah" }, "orcid": "0000-0002-6562-7918" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Gradinaru-V", "name": { "family": "Gradinaru", "given": "Viviana" }, "orcid": "0000-0001-5868-348X" } ] }, "title": "Light-guided sectioning for precise in situ localization and tissue interface analysis for brain-implanted optical fibers and GRIN lenses", "ispublished": "pub", "full_text_status": "public", "keywords": "two-photon imaging; fiber photometry; optogenetics; histology; clearing; GRIN lens; chronic implants", "note": "\u00a9 2021 The Author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). \n\nReceived 25 November 2020, Revised 22 June 2021, Accepted 31 August 2021, Available online 29 September 2021. Published: September 28, 2021. \n\nWe would like to thank the Gradinaru laboratory and Prof. Justin Bois for helpful discussions, the Caltech Neurotechnology Laboratory for the two-photon microscope support, the Caltech Biological Imaging Center for the training and use of the Airyscan confocal microscope, and Dr. Ariane Helou for editorial comments. Professor Gradinaru is a Heritage Principal Investigator supported by the Heritage Medical Research Institute; this work was also funded by the NIH Director's New Innovator IDP20D017782-01, the NSF NeuroNex Technology Hub 1707316, Presidential Early Career Awards for Scientists and Engineers (V.G.), NIH Brain Research through Advancing Innovative Neurotechnologies RF1MH117069, and the Beckman Institute's Resource Center on CLARITY, Optogenetics, and Vector Engineering (CLOVER). We would also like to thank CLOVER for technology development and broad dissemination (https://beckmaninstitute.caltech.edu/clover.shtml). A.K. is supported by a Caltech Biology and Biological Engineering department postdoctoral fellowship and the Hebrew University Postdoctoral Fellowship for Women, Israel. A.G. is a Good Ventures Fellow of the Life Sciences Research Foundation. P.K. is supported by the Swiss National Science Foundation (P2EZP3-181896). \n\nAuthor contributions. Conceptualization, A.K., A.G., and V.G.; methodology, A.K. and A.G.; software, A.K., A.G., J.R.C., P.K., and D.A.W; investigation, A.K.; resources, A.K., A.G., M.J.J., J.E.R, J.R.C., X.C., D.A.W., and V.G.; writing \u2013 original draft, A.K., and A.G.; writing \u2013 review & editing, A.K., A.G., M.J.J., J.E.R, J.R.C., X.C., P.K., D.A.W, and V.G.; visualization, A.K. and A.G.; supervision, V.G. \n\nThe authors declare no competing interests. \n\nData and code availability\nThe datasets supporting the current study have not been deposited in a public repository but are available from the corresponding author upon reasonable request.\n\nAll original code has been deposited at github.com and is publicly available as of the date of publication. DOIs are listed in the key resources table. \n\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.\n\nPublished - 1-s2.0-S2211124721011979-main.pdf
Supplemental Material - 1-s2.0-S2211124721011979-mmc1.pdf
Supplemental Material - 1-s2.0-S2211124721011979-mmc2.mp4
Supplemental Material - 1-s2.0-S2211124721011979-mmc3.mp4
Supplemental Material - 1-s2.0-S2211124721011979-mmc4.mp4
Supplemental Material - 1-s2.0-S2211124721011979-mmc5.mp4
Supplemental Material - 1-s2.0-S2211124721011979-mmc6.mp4
Supplemental Material - 1-s2.0-S2211124721011979-mmc7.mp4
Supplemental Material - 1-s2.0-S2211124721011979-mmc8.mp4
Supplemental Material - 1-s2.0-S2211124721011979-mmc9.mp4
", "abstract": "Optical implants to control and monitor neuronal activity in vivo have become foundational tools of neuroscience. Standard two-dimensional histology of the implant location, however, often suffers from distortion and loss during tissue processing. To address that, we developed a three-dimensional post hoc histology method called \"light-guided sectioning\" (LiGS), which preserves the tissue with its optical implant in place and allows staining and clearing of a volume up to 500 \u03bcm in depth. We demonstrate the use of LiGS to determine the precise location of an optical fiber relative to a deep brain target and to investigate the implant-tissue interface. We show accurate cell registration of ex vivo histology with single-cell, two-photon calcium imaging, obtained through gradient refractive index (GRIN) lenses, and identify subpopulations based on immunohistochemistry. LiGS provides spatial information in experimental paradigms that use optical fibers and GRIN lenses and could help increase reproducibility through identification of fiber-to-target localization and molecular profiling.", "date": "2021-09-28", "date_type": "published", "publication": "Cell Reports", "volume": "36", "number": "13", "publisher": "Cell Press", "pagerange": "Art. No. 109744", "id_number": "CaltechAUTHORS:20211008-224633454", "issn": "2211-1247", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20211008-224633454", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Heritage Medical Research Institute" }, { "agency": "NIH", "grant_number": "IDP20D017782-01" }, { "agency": "NSF", "grant_number": "DBI-1707316" }, { "agency": "NIH", "grant_number": "RF1MH117069" }, { "agency": "Caltech Beckman Institute Resource Center on CLARITY, Optogenetics, and Vector Engineering (CLOVER)" }, { "agency": "Caltech Division of Biology and Biological Engineering" }, { "agency": "Hebrew University Postdoctoral Fellowship for Women" }, { "agency": "Life Sciences Research Foundation" }, { "agency": "Swiss National Science Foundation (SNSF)", "grant_number": "P2EZP3-181896" } ] }, "local_group": { "items": [ { "id": "Heritage-Medical-Research-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1016/j.celrep.2021.109744", "pmcid": "PMC8552649", "primary_object": { "basename": "1-s2.0-S2211124721011979-mmc8.mp4", "url": "https://authors.library.caltech.edu/records/6ftpg-4wj22/files/1-s2.0-S2211124721011979-mmc8.mp4" }, "related_objects": [ { "basename": "1-s2.0-S2211124721011979-mmc9.mp4", "url": "https://authors.library.caltech.edu/records/6ftpg-4wj22/files/1-s2.0-S2211124721011979-mmc9.mp4" }, { "basename": "1-s2.0-S2211124721011979-main.pdf", "url": "https://authors.library.caltech.edu/records/6ftpg-4wj22/files/1-s2.0-S2211124721011979-main.pdf" }, { "basename": "1-s2.0-S2211124721011979-mmc1.pdf", "url": "https://authors.library.caltech.edu/records/6ftpg-4wj22/files/1-s2.0-S2211124721011979-mmc1.pdf" }, { "basename": "1-s2.0-S2211124721011979-mmc4.mp4", "url": "https://authors.library.caltech.edu/records/6ftpg-4wj22/files/1-s2.0-S2211124721011979-mmc4.mp4" }, { "basename": "1-s2.0-S2211124721011979-mmc5.mp4", "url": "https://authors.library.caltech.edu/records/6ftpg-4wj22/files/1-s2.0-S2211124721011979-mmc5.mp4" }, { "basename": "1-s2.0-S2211124721011979-mmc6.mp4", "url": "https://authors.library.caltech.edu/records/6ftpg-4wj22/files/1-s2.0-S2211124721011979-mmc6.mp4" }, { "basename": "1-s2.0-S2211124721011979-mmc7.mp4", "url": "https://authors.library.caltech.edu/records/6ftpg-4wj22/files/1-s2.0-S2211124721011979-mmc7.mp4" }, { "basename": "1-s2.0-S2211124721011979-mmc2.mp4", "url": "https://authors.library.caltech.edu/records/6ftpg-4wj22/files/1-s2.0-S2211124721011979-mmc2.mp4" }, { "basename": "1-s2.0-S2211124721011979-mmc3.mp4", "url": "https://authors.library.caltech.edu/records/6ftpg-4wj22/files/1-s2.0-S2211124721011979-mmc3.mp4" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Kahan, Anat; Greenbaum, Alon; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rp04a-ngr87", "eprint_id": 109247, "eprint_status": "archive", "datestamp": "2023-08-20 03:18:29", "lastmod": "2023-12-13 17:21:50", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Andreev-Andrey", "name": { "family": "Andreev", "given": "Andrey" }, "orcid": "0000-0002-7833-1390" }, { "id": "Vasnarungruengkul-Pavee", "name": { "family": "Vasnarungruengkul", "given": "Pavee" } }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Prober-D-A", "name": { "family": "Prober", "given": "David A." }, "orcid": "0000-0002-7371-4675" } ] }, "title": "Open-Source Thermometer, Temperature Controller, and Light Meter for Use in Animal Facilities and During Experiments", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license. \n\nThis version posted May 20, 2021. \n\nWe thank Prober lab members for providing animals for the experiments, and especially Dr. Amina Kinkhabwala for testing the design and instructions. The first version of the code used to extract heart rate from images was developed by A.A. during work in Truong/Fraser lab at University of Southern California. This work was supported by grants from the NIH to D.A.P. (R35 NS122172 and R01 MH121601). \n\nThe authors have declared no competing interest.\n\nSubmitted - 2021.05.18.444705v1.full.pdf
", "abstract": "Experiments with biological samples require precise control of environmental conditions. In our work we use zebrafish (Danio rerio) to understand the neurobiology of sleep, which requires precise control of temperature and lighting. Like many labs, lighting and temperature in the animal facility are centrally controlled in the building. During behavioral experiments and microscopy sessions, we use custom-built heating systems and perform occasional manual checks of conditions. However, without a system to precisely record conditions, gradual changes in temperature can go unnoticed for a long time, and temporary failures may be missed entirely. Here we present the design and characterization of affordable open-source tools to record temperature and light conditions during animal experiments using an Arduino microcontroller or a Raspberry Pi compact computer. The waterproof temperature sensor has high stability over 50 days of recording and is precise to 0.1\u00b0C. The Arduino device can be used through a common serial port interface for which we present code in Python and MATLAB. The Raspberry Pi version can be accessed through a web interface, for which we provide an installation guide. We use the device to record and review temperature and lighting conditions in two zebrafish animal facilities. We use our platform to add a water heating system to maintain temperature at 28\u00b0C during in vivo light-sheet imaging of larval zebrafish. We show that a change in temperature from 28\u00b0C to 32\u00b0C affects resting heart rate of the animal, highlighting the importance of maintaining and recording conditions. The protocols presented here do not require advanced engineering, fabrication, or software skills, and provide an approach to accurately record and report experimental conditions.", "date": "2021-05-26", "date_type": "published", "id_number": "CaltechAUTHORS:20210525-083740510", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210525-083740510", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R35 NS122172" }, { "agency": "NIH", "grant_number": "R01 MH121601" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2021.05.18.444705", "primary_object": { "basename": "2021.05.18.444705v1.full.pdf", "url": "https://authors.library.caltech.edu/records/rp04a-ngr87/files/2021.05.18.444705v1.full.pdf" }, "resource_type": "monograph", "pub_year": "2021", "author_list": "Andreev, Andrey; Vasnarungruengkul, Pavee; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hk6b4-y9189", "eprint_id": 104602, "eprint_status": "archive", "datestamp": "2023-08-22 09:19:37", "lastmod": "2023-12-22 23:07:45", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cho-Jounhong-Ryan", "name": { "family": "Cho", "given": "Jounhong Ryan" }, "orcid": "0000-0001-9542-716X" }, { "id": "Chen-Xinhong", "name": { "family": "Chen", "given": "Xinhong" }, "orcid": "0000-0003-0408-0813" }, { "id": "Kahan-Anat", "name": { "family": "Kahan", "given": "Anat" }, "orcid": "0000-0002-4799-3017" }, { "id": "Robinson-J-Elliott", "name": { "family": "Robinson", "given": "J. Elliott" }, "orcid": "0000-0001-9417-3938" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Gradinaru-V", "name": { "family": "Gradinaru", "given": "Viviana" }, "orcid": "0000-0001-5868-348X" } ] }, "title": "Dorsal Raphe Dopamine Neurons Signal Motivational Salience Dependent on Internal State, Expectation, and Behavioral Context", "ispublished": "pub", "full_text_status": "public", "keywords": "dopamine; dorsal raphe nucleus; fiber photometry; head fixation; motivational salience; two-photon imaging", "note": "\u00a9 2021 the authors. \n\nReceived Oct. 19, 2020; revised Jan. 19, 2021; accepted Jan. 26, 2021. \n\nThis work was supported by the National Institutes of Health (NIH) Director's New Innovator Grant IDP20D091182-01, Presidential Early Career Award for Scientists and Engineers, the NIH/National Institute on Aging Grant 1R01AG047664-01, the NIH Grant BRAIN 1U01NS090577, Heritage Medical Research Institute, Chen Institute (V.G.), Beckman Institute (V.G. and D.A.W.), Tianqiao & Chrissy Chen Institute Chen Graduate Fellowship (X.C.), Colvin Divisional Fellowship at Caltech (A.K.), and the Children's Tumor Foundation Young Investigator Award 2016-01-00 (to J.E.R.). We thank the entire Gradinaru lab for critical feedback. \n\nAuthor contributions: J.R.C. and V.G. designed research; J.R.C., X.C., A.K., and J.E.R. performed research; A. K. and D.A.W. contributed unpublished reagents/analytic tools; J.R.C. and X.C. analyzed data; J.R.C. and V.G. wrote the paper. \n\nThe authors declare no competing financial interests.\n\nPublished - 2645.full.pdf
Submitted - 2020.07.27.222729v1.full.pdf
", "abstract": "The ability to recognize motivationally salient events and respond to them adaptively is critical for survival. Here we tested whether dopamine (DA) neurons in the dorsal raphe nucleus (DRN) contribute to this process. Population recordings of DRN^(DA) neurons during associative learning tasks showed that their activity dynamically tracks salience, developing excitation to both reward- and punishment-paired cues. The DRNDA response to reward-predicting cues was diminished after satiety, suggesting modulation by internal states. DRN^(DA) activity was also greater for unexpected outcomes than for expected outcomes. Two-photon imaging of DRN^(DA) neurons demonstrated that the majority of individual neurons developed activation to reward predicting cues but not to punishment-predicting cues, which was surprising and qualitatively distinct from the population results. Head-fixation during fear learning abolished the neural response to aversive cues, indicating modulation by behavioral context. Overall, these results suggest that DRN^(DA) neurons encode motivational salience, dependent on internal and external factors.", "date": "2021-03-24", "date_type": "published", "publication": "Journal of Neuroscience", "volume": "41", "number": "12", "publisher": "Society for Neuroscience", "pagerange": "2645-2655", "id_number": "CaltechAUTHORS:20200728-094010838", "issn": "0270-6474", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200728-094010838", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "IDP20D091182-01" }, { "agency": "NIH", "grant_number": "1R01AG047664-01" }, { "agency": "NIH", "grant_number": "1U01NS090577" }, { "agency": "Heritage Medical Research Institute" }, { "agency": "Tianqiao and Chrissy Chen Institute for Neuroscience" }, { "agency": "Caltech Beckman Institute" }, { "agency": "Caltech Division of Biology and Biological Engineering" }, { "agency": "Children's Tumor Foundation", "grant_number": "2016-01-00" } ] }, "local_group": { "items": [ { "id": "Heritage-Medical-Research-Institute" }, { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1523/JNEUROSCI.2690-20.2021", "pmcid": "PMC8018733", "primary_object": { "basename": "2020.07.27.222729v1.full.pdf", "url": "https://authors.library.caltech.edu/records/hk6b4-y9189/files/2020.07.27.222729v1.full.pdf" }, "related_objects": [ { "basename": "2645.full.pdf", "url": "https://authors.library.caltech.edu/records/hk6b4-y9189/files/2645.full.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Cho, Jounhong Ryan; Chen, Xinhong; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/zgzy5-9p539", "eprint_id": 101894, "eprint_status": "archive", "datestamp": "2023-08-20 01:51:47", "lastmod": "2023-12-22 23:29:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Ashaber-M\u00e1ria", "name": { "family": "Ashaber", "given": "M\u00e1ria" }, "orcid": "0000-0002-5586-9585" }, { "id": "Tomina-Yusuke", "name": { "family": "Tomina", "given": "Yusuke" }, "orcid": "0000-0001-9406-1493" }, { "id": "Kassraian-Fard-Pegah", "name": { "family": "Kassraian", "given": "Pegah" }, "orcid": "0000-0002-6562-7918" }, { "id": "Bushong-Eric-A", "name": { "family": "Bushong", "given": "Eric A." }, "orcid": "0000-0001-6195-2433" }, { "id": "Kristan-William-B-Jr.", "name": { "family": "Kristan", "given": "William B." } }, { "id": "Ellisman-Mark-H", "name": { "family": "Ellisman", "given": "Mark H." }, "orcid": "0000-0001-8893-8455" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" } ] }, "title": "Anatomy and activity patterns in a multifunctional motor neuron and its surrounding circuits", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2021 Ashaber et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. \n\nReceived: 07 August 2020; Accepted: 12 February 2021; Published: 15 February 2021. \n\nWe thank Evan Miller (Berkeley) for sharing of the VF2.1(OMe).H dye, Art Wetzel (Pittsburgh Supercomputer Center) and Tom Bartol (The Salk Institute) for many useful discussions about image alignment, Tunde Magyar and Renata Pop (University of Veterinary Medicine, Department of Anatomy and Histology, Budapest, Hungary) for help with TEM, and Jason Pipkin (Brandeis University) for advice about tracing. \n\nFunding: National Institute of Neurological Disorders and Stroke (R01-NS094403), William B Kristan Jnr, Mark H Ellisman, Daniel A Wagenaar. \n\nNational Institute of General Medical Sciences (P41-GM103412), Mark H Ellisman. \n\nJapan Society for the Promotion of Science (201800526), Yusuke Tomina. \n\nJapan Society for the Promotion of Science (19K16191), Yusuke Tomina. \n\nSwiss National Science Foundation (P2EZP3-181896), Pegah Kassraian. \n\nNational Institute of Neurological Disorders and Stroke (1U24NS120055), Mark H Ellisman. \n\nThe funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. \n\nData availability: The easiest way to access the raw electrophysiology and voltage-dye data as well as the tracing results used in this paper is through a series of Python modules that we made available at https://github.com/wagenadl/leechem-public (copy archived at https://archive.softwareheritage.org/swh:1:rev:73eee24e387e11c259a3f3fe0bd4e469048b25e6/). Included in the package is a file called \"demo.py\" that demonstrates the use of the modules. Table 4 lists the available VSD trials. The aligned EM volume may be accessed through the Neuroglancer instance at https://leechem.caltech.edu or by pointing SBEMViewer to https://leechem.caltech.edu/emdata. The API is documented at https://leechem.caltech.edu/emdata/help. \n\nAuthor contributions: Maria Ashaber, Formal analysis, Investigation, Visualization, Methodology, Writing - original draft, Writing - review and editing; Yusuke Tomina, Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Visualization, Methodology, Writing - original draft, Writing - review and editing; Pegah Kassraian, Conceptualization, Software, Formal analysis, Funding acquisition, Investigation, Visualization, Methodology, Writing - original draft, Writing - review and editing; Eric A Bushong, Investigation, Methodology; William B Kristan, Conceptualization, Funding acquisition, Methodology; Mark H Ellisman, Conceptualization, Supervision, Funding acquisition, Methodology, Project administration; Daniel A Wagenaar, Conceptualization, Data curation, Software, Formal analysis, Supervision, Funding acquisition, Visualization, Methodology, Writing - original draft, Project administration, Writing - review and editing.\n\nPublished - elife-61881-v2.pdf
Submitted - 2020.03.09.984013v3.full.pdf
Supplemental Material - elife-61881-supp-v1.zip
Supplemental Material - elife-61881-transrepform-v2.pdf
Supplemental Material - elife-61881-video1.mp4
", "abstract": "Dorsal Excitor motor neuron DE-3 in the medicinal leech plays three very different dynamical roles in three different behaviors. Without rewiring its anatomical connectivity, how can a motor neuron dynamically switch roles to play appropriate roles in various behaviors? We previously used voltage-sensitive dye imaging to record from DE-3 and most other neurons in the leech segmental ganglion during (fictive) swimming, crawling, and local-bend escape (Tomina and Wagenaar, 2017). Here, we repeated that experiment, then re-imaged the same ganglion using serial blockface electron microscopy and traced DE-3's processes. Further, we traced back the processes of DE-3's presynaptic partners to their respective somata. This allowed us to analyze the relationship between circuit anatomy and the activity patterns it sustains. We found that input synapses important for all the behaviors were widely distributed over DE-3's branches, yet that functional clusters were different during (fictive) swimming vs. crawling.", "date": "2021-02-15", "date_type": "published", "publication": "eLife", "volume": "10", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e61881", "id_number": "CaltechAUTHORS:20200312-124530478", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200312-124530478", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01-NS094403" }, { "agency": "NIH", "grant_number": "P41GM103412" }, { "agency": "Japan Society for Promotion of Science (JSPS)", "grant_number": "201800526" }, { "agency": "Japan Society for Promotion of Science (JSPS)", "grant_number": "19K16191" }, { "agency": "Swiss National Science Foundation (SNSF)", "grant_number": "P2EZP3_181896" }, { "agency": "NIH", "grant_number": "1U24NS120055" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.7554/eLife.61881", "primary_object": { "basename": "2020.03.09.984013v3.full.pdf", "url": "https://authors.library.caltech.edu/records/zgzy5-9p539/files/2020.03.09.984013v3.full.pdf" }, "related_objects": [ { "basename": "elife-61881-supp-v1.zip", "url": "https://authors.library.caltech.edu/records/zgzy5-9p539/files/elife-61881-supp-v1.zip" }, { "basename": "elife-61881-transrepform-v2.pdf", "url": "https://authors.library.caltech.edu/records/zgzy5-9p539/files/elife-61881-transrepform-v2.pdf" }, { "basename": "elife-61881-v2.pdf", "url": "https://authors.library.caltech.edu/records/zgzy5-9p539/files/elife-61881-v2.pdf" }, { "basename": "elife-61881-video1.mp4", "url": "https://authors.library.caltech.edu/records/zgzy5-9p539/files/elife-61881-video1.mp4" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Ashaber, M\u00e1ria; Tomina, Yusuke; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/70esk-xma64", "eprint_id": 99316, "eprint_status": "archive", "datestamp": "2023-08-22 07:02:19", "lastmod": "2023-12-22 23:32:56", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Kennedy-Ann", "name": { "family": "Kennedy", "given": "Ann" }, "orcid": "0000-0002-3782-0518" }, { "id": "Kunwar-Prabhat-S", "name": { "family": "Kunwar", "given": "Prabhat S." } }, { "id": "Li-Ling-yun", "name": { "family": "Li", "given": "Ling-yun" } }, { "id": "Stagkourakis-Stefanos", "name": { "family": "Stagkourakis", "given": "Stefanos" }, "orcid": "0000-0003-1218-791X" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Anderson-D-J", "name": { "family": "Anderson", "given": "David J." }, "orcid": "0000-0001-6175-3872" } ] }, "title": "Stimulus-specific hypothalamic encoding of a persistent defensive state", "ispublished": "pub", "full_text_status": "public", "keywords": "Dynamical systems; Emotion", "note": "\u00a9 2020 Nature Publishing Group. \n\nReceived 02 October 2019; Accepted 22 June 2020; Published 16 September 2020. \n\nWe thank R. Palmiter for providing TetTox\u2013GFP in advance of publication; H. Inagaki, M. Meister, L. F. Abbott, U. Rutishauser, and members of the Anderson lab for helpful comments on the manuscript; R. Remedios for help with miniscope imaging; L. Liu for teaching silicon probe recording; A. Vinograd for preliminary imaging experiments; T. Davidson and K. Deisseroth for teaching fibre photometry; B. Yang for helping with the TetTox fibre photometry experiment; X. Da, J. S. Chang and C. Kim for technical assistance, X. Da and C. Chiu for laboratory management and G. Mancuso for administrative support. This work was supported by NIH Grant R01 MH112593. K99 MH117264 to A.K., a Helen Hay Whitney Foundation Postdoctoral Fellowship to L.L., and the EMBO ALTF 736-2018 to S.S. D.J.A. is an Investigator of the Howard Hughes Medical Institute. \n\nData availability: The data that support the findings of this study are available from the corresponding author upon reasonable request. \n\nCode availability: Code for data analysis and modelling portions of this paper has been made publicly available at https://github.com/DJALab/VMHdm_persistence. \n\nThese authors contributed equally: Ann Kennedy, Prabhat S. Kunwar, Ling-yun Li. \n\nAuthor Contributions: A.K., P.S.K., and D.J.A. conceptualized and designed the fibre photometry and microendoscopic imaging experiments. A.K., L.L., P.S.K., and D.J.A. conceptualized and designed the optogenetic loss-of-function experiments. D.A.W. and P.S.K. designed and built the imaging acquisition setup. P.S.K. performed imaging experiments. L.L. performed loss-of-function, rat exposure assay and imaging, tetanus toxin, and extracellular recording experiments. S.S. performed brain slice electrophysiology and Ca2+ imaging experiments and analysis. A.K. performed imaging data analysis and modeling. A.K., P.S.K., L.L., and D.J.A. wrote the manuscript. \n\nThe authors declare no competing interests. \n\nPeer review information: Nature thanks Jaideep Bains, Larry Zweifel and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.\n\nAccepted Version - nihms-1606924.pdf
Submitted - 805317.full.pdf
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Supplemental Material - 41586_2020_2728_Fig11_ESM.webp
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Supplemental Material - 41586_2020_2728_Fig14_ESM.webp
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Supplemental Material - 41586_2020_2728_Fig7_ESM.webp
Supplemental Material - 41586_2020_2728_Fig8_ESM.webp
Supplemental Material - 41586_2020_2728_Fig9_ESM.webp
Supplemental Material - 41586_2020_2728_MOESM1_ESM.pdf
Supplemental Material - 41586_2020_2728_MOESM2_ESM.pdf
", "abstract": "Persistent neural activity in cortical, hippocampal, and motor networks has been described as mediating working memory for transiently encountered stimuli. Internal emotional states, such as fear, also persist following exposure to an inciting stimulus, but it is unclear whether slow neural dynamics are involved in this process. Neurons in the dorsomedial and central subdivisions of the ventromedial hypothalamus (VMHdm/c) that express the nuclear receptor protein NR5A1 (also known as SF1) are necessary for defensive responses to predators in mice. Optogenetic activation of these neurons, referred to here as VMHdm^(SF1) neurons, elicits defensive behaviours that outlast stimulation, which suggests the induction of a persistent internal state of fear or anxiety. Here we show that in response to naturalistic threatening stimuli, VMHdm^(SF1) neurons in mice exhibit activity that lasts for many tens of seconds. This persistent activity was correlated with, and required for, persistent defensive behaviour in an open-field assay, and depended on neurotransmitter release from VMHdm^(SF1) neurons. Stimulation and calcium imaging in acute slices showed that there is local excitatory connectivity between VMHdm^(SF1) neurons. Microendoscopic calcium imaging of VMHdm^(SF1) neurons revealed that persistent activity at the population level reflects heterogeneous dynamics among individual cells. Unexpectedly, distinct but overlapping VMHdm^(SF1) subpopulations were persistently activated by different modalities of threatening stimulus. Computational modelling suggests that neither recurrent excitation nor slow-acting neuromodulators alone can account for persistent activity that maintains stimulus identity. Our results show that stimulus-specific slow neural dynamics in the hypothalamus, on a time scale orders of magnitude longer than that of working memory in the cortex, contribute to a persistent emotional state.", "date": "2020-10-29", "date_type": "published", "publication": "Nature", "volume": "586", "number": "7831", "publisher": "Nature Publishing Group", "pagerange": "730-734", "id_number": "CaltechAUTHORS:20191017-074022753", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191017-074022753", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 MH112593" }, { "agency": "NIH", "grant_number": "K99 MH117264" }, { "agency": "Helen Hay Whitney Foundation" }, { "agency": "European Molecular Biology Organization (EMBO)", "grant_number": "ALTF 736-2018" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1038/s41586-020-2728-4", "pmcid": "PMC7606611", "primary_object": { "basename": "41586_2020_2728_Fig10_ESM.webp", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/41586_2020_2728_Fig10_ESM.webp" }, "related_objects": [ { "basename": "41586_2020_2728_Fig14_ESM.webp", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/41586_2020_2728_Fig14_ESM.webp" }, { "basename": "41586_2020_2728_Fig6_ESM.webp", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/41586_2020_2728_Fig6_ESM.webp" }, { "basename": "41586_2020_2728_Fig9_ESM.webp", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/41586_2020_2728_Fig9_ESM.webp" }, { "basename": "41586_2020_2728_MOESM2_ESM.pdf", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/41586_2020_2728_MOESM2_ESM.pdf" }, { "basename": "41586_2020_2728_Fig7_ESM.webp", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/41586_2020_2728_Fig7_ESM.webp" }, { "basename": "nihms-1606924.pdf", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/nihms-1606924.pdf" }, { "basename": "41586_2020_2728_Fig5_ESM.webp", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/41586_2020_2728_Fig5_ESM.webp" }, { "basename": "41586_2020_2728_Fig8_ESM.webp", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/41586_2020_2728_Fig8_ESM.webp" }, { "basename": "41586_2020_2728_Fig11_ESM.webp", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/41586_2020_2728_Fig11_ESM.webp" }, { "basename": "41586_2020_2728_Fig12_ESM.webp", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/41586_2020_2728_Fig12_ESM.webp" }, { "basename": "41586_2020_2728_Fig13_ESM.webp", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/41586_2020_2728_Fig13_ESM.webp" }, { "basename": "41586_2020_2728_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/41586_2020_2728_MOESM1_ESM.pdf" }, { "basename": "805317.full.pdf", "url": "https://authors.library.caltech.edu/records/70esk-xma64/files/805317.full.pdf" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Kennedy, Ann; Kunwar, Prabhat S.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qxsmb-0bw43", "eprint_id": 106367, "eprint_status": "archive", "datestamp": "2023-08-19 23:58:55", "lastmod": "2023-12-22 23:29:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "He-Yun", "name": { "family": "He", "given": "Yun" }, "orcid": "0000-0001-8430-6370" }, { "id": "Shi-Junhui", "name": { "family": "Shi", "given": "Junhui" }, "orcid": "0000-0002-5741-2781" }, { "id": "Pleitez-M-A", "name": { "family": "Pleitez", "given": "Miguel A." } }, { "id": "Maslov-K-I", "name": { "family": "Maslov", "given": "Konstantin" }, "orcid": "0000-0003-3408-8840" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Wang-Lihong-V", "name": { "family": "Wang", "given": "Lihong V." }, "orcid": "0000-0001-9783-4383" } ] }, "title": "Label-free imaging of lipid-rich biological tissues by mid-infrared photoacoustic microscopy", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2020 The Authors. Published by SPIE under a Creative Commons Attribution 4.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI. \n\nReceived: 16 May 2020; Accepted: 14 October 2020; Published: 28 October 2020. \n\nThe authors appreciate Prof. James Ballard's editing of this article. This work was supported by the National Institutes of Health under Grant Nos. R01 CA186567 (NIH Director's Transformative Research Award), R01 NS102213, U01 NS090579 (BRAIN Initiative), and U01 NS099717 (BRAIN Initiative), as well as the National Institute of Neurological Disorders and Stroke (Grant R01 NS094403). \n\nDisclosures: L.V.W. and K.M. have financial interests in Microphotoacoustics, Inc., CalPACT, LLC, and Union Photoacoustic Technologies, Ltd., which, however, did not support this work. \n\nCode, Data, and Materials Availability: The data that support the plots within this paper and other findings of this study are available from the corresponding author upon reasonable request.\n\nPublished - 106506_1.pdf
", "abstract": "Significance: Mid-infrared (IR) imaging based on the vibrational transition of biomolecules provides good chemical-specific contrast in label-free imaging of biology tissues, making it a popular tool in both biomedical studies and clinical applications. However, the current technology typically requires thin and dried or extremely flat samples, whose complicated processing limits this technology's broader translation. \n\nAim: To address this issue, we report mid-IR photoacoustic microscopy (PAM), which can readily work with fresh and thick tissue samples, even when they have rough surfaces.\nApproach: We developed a transmission-mode mid-IR PAM system employing an optical parametric oscillation laser operating in the wavelength range from 2.5 to 12\u2009\u03bcm. Due to its high sensitivity to optical absorption and the low ultrasonic attenuation of tissue, our PAM achieved greater probing depth than Fourier transform IR spectroscopy, thus enabling imaging fresh and thick tissue samples with rough surfaces.\nResults: In our spectroscopy study, the CH\u2082 symmetric stretching at 2850\u2009\u2009cm\u207b\u00b9 (3508 nm) was found to be an excellent source of endogenous contrast for lipids. At this wavenumber, we demonstrated label-free imaging of the lipid composition in fresh, manually cut, and unprocessed tissue sections of up to 3-mm thickness. \n\nConclusions: Our technology requires no time-consuming sample preparation procedure and has great potential in both fast clinical histological analysis and fundamental biological studies.", "date": "2020-10-28", "date_type": "published", "publication": "Journal of Biomedical Optics", "volume": "25", "number": "10", "publisher": "Society of Photo-Optical Instrumentation Engineers", "pagerange": "Art. No. 106506", "id_number": "CaltechAUTHORS:20201030-151256559", "issn": "1083-3668", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20201030-151256559", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "R01 CA186567" }, { "agency": "NIH", "grant_number": "R01 NS102213" }, { "agency": "NIH", "grant_number": "U01 NS090579" }, { "agency": "NIH", "grant_number": "U01 NS099717" }, { "agency": "NIH", "grant_number": "R01 NS094403" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1117/1.jbo.25.10.106506", "primary_object": { "basename": "106506_1.pdf", "url": "https://authors.library.caltech.edu/records/qxsmb-0bw43/files/106506_1.pdf" }, "resource_type": "article", "pub_year": "2020", "author_list": "He, Yun; Shi, Junhui; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/16ywz-0cj69", "eprint_id": 92975, "eprint_status": "archive", "datestamp": "2023-08-19 16:55:11", "lastmod": "2023-10-20 22:03:52", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Stowasser-A", "name": { "family": "Stowasser", "given": "Annette" } }, { "id": "Stahl-A", "name": { "family": "Stahl", "given": "Aaron" } }, { "id": "Benoit-J-B", "name": { "family": "Benoit", "given": "Joshua B." } }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" } ] }, "title": "Electrophysiology and transcriptomics reveal two photoreceptor classes and complex visual integration in Hirudo verbana", "ispublished": "pub", "full_text_status": "public", "keywords": "Invertebrate vision, Opsins, Visual processing, S-cell interneuron, Medicinal leech", "note": "\u00a9 2019 Published by The Company of Biologists Ltd. \n\nReceived 15 February 2019; Accepted 22 June 2019. Published 7 August 2019. \n\nWe wish to thank Elke Buschbeck and John Layne for the use of equipment and lab space. \n\nThe authors declare no competing or financial interests. \n\nAuthor contributions: Conceptualization: A. Stowasser, D.A.W.; Methodology: A. Stowasser, J.B.B., D.A.W.; Software: D.A.W.; Formal analysis: A. Stowasser, A. Stahl, J.B.B., D.A.W.; Investigation: A. Stowasser, A. Stahl, J.B.B.; Resources: J.B.B.; Data curation: J.B.B., D.A.W.; Writing - original draft: A. Stowasser, J.B.B., D.A.W.; Writing - review & editing: A. Stowasser, J.B.B., D.A.W.; Visualization: A. Stowasser, J.B.B., D.A.W.; Supervision: D.A.W.; Project administration: D.A.W.; Funding acquisition: D.A.W. \n\nFunding was provided by the National Institute of Neurological Disorders and Stroke (NS094403, to D.A.W.) and by the Burroughs Wellcome Fund in the form of a Career Award at the Scientific Interface (to D.A.W.). Deposited in PMC for release after 12 months. \n\nData availability: Illumina sequencing files have been deposited in the NCBI SRA: Bioproject PRJNA504032. \n\nSupplementary information: Supplementary information available online at http://jeb.biologists.org/lookup/doi/10.1242/jeb.201764.supplemental\n\nPublished - jeb201764.full.pdf
Submitted - 552018.full.pdf
Supplemental Material - JEB201764supp.pdf
", "abstract": "Among animals with visual processing mechanisms, the leech Hirudo verbana is a rare example in which all neurons can be identified. However, little is known about its visual system, which is composed of several pigmented head eyes and photosensitive non-pigmented sensilla that are distributed across its entire body. Although several interneurons are known to respond to visual stimuli, their response properties are poorly understood. Among these, the S-cell system is especially intriguing: it is multimodal, spans the entire body of the leech and is thought to be involved in sensory integration. To improve our understanding of the role of this system, we tested its spectral sensitivity, spatial integration and adaptation properties. The response of the S-cell system to visual stimuli was found to be strongly dependent on the size of the area stimulated, and adaptation was local. Furthermore, an adaptation experiment demonstrated that at least two color channels contributed to the response, and that their contribution was dependent on the adaptation to the background. The existence of at least two color channels was further supported by transcriptomic evidence, which indicated the existence of at least two distinct groups of putative opsins for leeches. Taken together, our results show that the S-cell system has response properties that could be involved in the processing of spatial and color information of visual stimuli. We propose the leech as a novel system to understand visual processing mechanisms with many practical advantages.", "date": "2019-08", "date_type": "published", "publication": "Journal of Experimental Biology", "volume": "222", "number": "15", "publisher": "Company of Biologists", "pagerange": "Art. No. jeb201764", "id_number": "CaltechAUTHORS:20190219-112051503", "issn": "0022-0949", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190219-112051503", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "NS094403" }, { "agency": "Burroughs Wellcome Fund" }, { "agency": "National Institute of Neurological Disorders and Stroke (NINDS)" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" } ] }, "doi": "10.1242/jeb.201764", "pmcid": "PMC6703701", "primary_object": { "basename": "552018.full.pdf", "url": "https://authors.library.caltech.edu/records/16ywz-0cj69/files/552018.full.pdf" }, "related_objects": [ { "basename": "JEB201764supp.pdf", "url": "https://authors.library.caltech.edu/records/16ywz-0cj69/files/JEB201764supp.pdf" }, { "basename": "jeb201764.full.pdf", "url": "https://authors.library.caltech.edu/records/16ywz-0cj69/files/jeb201764.full.pdf" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Stowasser, Annette; Stahl, Aaron; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/c5an0-87j84", "eprint_id": 98126, "eprint_status": "archive", "datestamp": "2023-08-19 14:47:47", "lastmod": "2024-01-14 21:53:23", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Arbabi-E", "name": { "family": "Arbabi", "given": "Ehsan" }, "orcid": "0000-0002-5328-3863" }, { "id": "Li-Jiaqi", "name": { "family": "Li", "given": "Jiaqi" }, "orcid": "0000-0003-2021-2310" }, { "id": "Hutchins-R-J", "name": { "family": "Hutchins", "given": "Romanus J." } }, { "id": "Kamali-S-M", "name": { "family": "Kamali", "given": "Seyedeh Mahsa" }, "orcid": "0000-0002-6968-811X" }, { "id": "Arbabi-A", "name": { "family": "Arbabi", "given": "Amir" }, "orcid": "0000-0001-8831-7552" }, { "id": "Horie-Yu", "name": { "family": "Horie", "given": "Yu" }, "orcid": "0000-0001-7083-1270" }, { "id": "Van-Dorpe-P", "name": { "family": "Van Dorpe", "given": "Pol" } }, { "id": "Gradinaru-V", "name": { "family": "Gradinaru", "given": "Viviana" }, "orcid": "0000-0001-5868-348X" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Faraon-A", "name": { "family": "Faraon", "given": "Andrei" }, "orcid": "0000-0002-8141-391X" } ] }, "title": "Double-wavelength metasurface objective lens for two-photon microscopy (Conference Presentation)", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2019 Society of Photo-Optical Instrumentation Engineers (SPIE).", "abstract": "Two-photon microscopy is a key imaging technique in biological sciences because of its superior deep tissue imaging capabilities in addition to high transverse and axial resolution. In recent years, development of low-weight miniature two-photon microscopes has been of great interest for in vivo imaging of brain activity. Limited by these mechanical constraints, most of the developed miniature two-photon microscopes utilize graded index objective lenses that usually have inferior optical characteristics compared to conventional refractive objective lenses. Dielectric metasurfaces, a recent category of diffractive optical elements with enhanced capabilities, have proven versatile in various applications ranging from lensing to holography and polarization control. Their ultrathin form factor and potentially extremely low-weight make them very attractive for applications with stringent size and weight constraints. However, despite their success in various types of microscopy and imaging applications, they have not been previously utilized for multi-photon fluorescence microscopy. The main barrier for using metasurface lenses in multi-photon microscopy arises from their large chromatic dispersion that effectively makes them single-wavelength. Here we will present a double-wavelength metasurface lens especially designed to have the same focal length at 820 and 605 nm, corresponding to the excitation and emission wavelengths of a certain fluorophore. After characterizing the poly-silicon metasurface lens at both wavelengths, we used it in a two-photon microscopy setup and demonstrated its capability to capture two-photon images qualitatively similar to images taken with a conventional objective lens. We will also discuss the effects of chromatic dispersion of the metasurface lens on its two-photon imaging performance.", "date": "2019-03-08", "date_type": "published", "publisher": "Society of Photo-optical Instrumentation Engineers (SPIE)", "place_of_pub": "Bellingham, WA", "pagerange": "Art. No. 109280K", "id_number": "CaltechAUTHORS:20190822-134054530", "isbn": "9781510624986", "book_title": "High Contrast Metastructures VIII", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190822-134054530", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Chang-Hasnain-C-J", "name": { "family": "Chang-Hasnain", "given": "Connie J." } }, { "id": "Faraon-A", "name": { "family": "Faraon", "given": "Andrei" } }, { "id": "Zhou-Weimin", "name": { "family": "Zhou", "given": "Weimin" } } ] }, "doi": "10.1117/12.2510596", "resource_type": "book_section", "pub_year": "2019", "author_list": "Arbabi, Ehsan; Li, Jiaqi; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/ypdcy-0an48", "eprint_id": 90477, "eprint_status": "archive", "datestamp": "2023-08-19 03:34:58", "lastmod": "2023-10-18 23:28:48", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tomina-Yusuke", "name": { "family": "Tomina", "given": "Yusuke" }, "orcid": "0000-0001-9406-1493" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" } ] }, "title": "Whole-ganglion imaging of voltage in the medicinal leech using a double-sided microscope", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. \n\nbioRxiv preprint first posted online Jun. 2, 2017. \n\nWe thank Evan Miller for sharing of the VF2.1(OMe).H dye; Annette Stowasser for her role in developing a prototype of the double-sided microscope and many helpful conversations; and Angela Bruno for useful discussions regarding data analysis. This work was supported by the Burroughs Welcome Fund through a Career Award at the Scientific Interface and by the National Institute of Neurological Disorders and Stroke through grant R01 NS094403 (both to DAW). YT was supported by JSPS Overseas Research Fellowships. \n\nThe authors declare no competing interests.\n\nSubmitted - 145144.full.pdf
Supplemental Material - 145144-1.pdf
Supplemental Material - 145144-2.mov
Supplemental Material - 145144-3.mov
Supplemental Material - 145144-4.mov
Supplemental Material - 145144-5.mov
", "abstract": "Studies of neuronal network emergence during sensory processing and motor control are greatly promoted by technologies that allow us to simultaneously record the membrane potential dynamics of a large population of neurons in single cell resolution. To achieve whole-brain recording with the ability to detect both small synaptic potentials and action potentials, we developed a voltage-sensitive dye (VSD) imaging technique based on a double-sided microscope that can image two sides of a nervous system simultaneously. We applied this system to the segmental ganglia of the medicinal leech Hirudo verbana. Double-sided VSD imaging enabled simultaneous recording of membrane potential events from almost all of the identifiable neurons. Using data obtained from double-sided VSD imaging we analyzed neuronal dynamics in both sensory processing and generation of behavior and constructed functional maps for identification of neurons contributing to these processes.", "date": "2018-10-30", "date_type": "published", "id_number": "CaltechAUTHORS:20181029-145904673", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181029-145904673", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Burroughs Wellcome Fund" }, { "agency": "NIH", "grant_number": "R01 NS094403" }, { "agency": "Japan Society for the Promotion of Science (JSPS)" } ] }, "doi": "10.1101/145144", "primary_object": { "basename": "145144-3.mov", "url": "https://authors.library.caltech.edu/records/ypdcy-0an48/files/145144-3.mov" }, "related_objects": [ { "basename": "145144-4.mov", "url": "https://authors.library.caltech.edu/records/ypdcy-0an48/files/145144-4.mov" }, { "basename": "145144-5.mov", "url": "https://authors.library.caltech.edu/records/ypdcy-0an48/files/145144-5.mov" }, { "basename": "145144.full.pdf", "url": "https://authors.library.caltech.edu/records/ypdcy-0an48/files/145144.full.pdf" }, { "basename": "145144-1.pdf", "url": "https://authors.library.caltech.edu/records/ypdcy-0an48/files/145144-1.pdf" }, { "basename": "145144-2.mov", "url": "https://authors.library.caltech.edu/records/ypdcy-0an48/files/145144-2.mov" } ], "resource_type": "monograph", "pub_year": "2018", "author_list": "Tomina, Yusuke and Wagenaar, Daniel A." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3ngwx-46089", "eprint_id": 87937, "eprint_status": "archive", "datestamp": "2023-08-19 11:00:46", "lastmod": "2023-10-18 21:32:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Arbabi-E", "name": { "family": "Arbabi", "given": "Ehsan" }, "orcid": "0000-0002-5328-3863" }, { "id": "Li-Jiaqi", "name": { "family": "Li", "given": "Jiaqi" }, "orcid": "0000-0003-2021-2310" }, { "id": "Hutchins-R-J", "name": { "family": "Hutchins", "given": "Romanus J." } }, { "id": "Kamali-S-M", "name": { "family": "Kamali", "given": "Seyedeh Mahsa" }, "orcid": "0000-0002-6968-811X" }, { "id": "Arbabi-A", "name": { "family": "Arbabi", "given": "Amir" }, "orcid": "0000-0001-8831-7552" }, { "id": "Horie-Yu", "name": { "family": "Horie", "given": "Yu" }, "orcid": "0000-0001-7083-1270" }, { "id": "Van-Dorpe-P", "name": { "family": "Van Dorpe", "given": "Pol" } }, { "id": "Gradinaru-V", "name": { "family": "Gradinaru", "given": "Viviana" }, "orcid": "0000-0001-5868-348X" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Faraon-A", "name": { "family": "Faraon", "given": "Andrei" }, "orcid": "0000-0002-8141-391X" } ] }, "title": "Two-photon microscopy with a double-wavelength metasurface objective lens", "ispublished": "pub", "full_text_status": "public", "keywords": "Optical metasurface, flat optics, multiwavelength lens, two-photon microscopy", "note": "\u00a9 2018 American Chemical Society. \n\nReceived: April 28, 2018; Revised: July 12, 2018; Published: July 17, 2018. \n\nThis work was supported by National Science Foundation Award 1512266. J.L. gratefully acknowledges the financial support from FWO (Flanders). We gratefully acknowledge critical support and infrastructure provided for this work by the Kavli Nanoscience Institute at Caltech. The two-photon microscope was designed and built at the Caltech Neurotechnology Center with support from the Beckman Institute. The authors would like to express thanks for the helpful discussions with Dr. Alon Greenbaum, Dr. Min Jee Jang, and Sripriya Kumar. \n\nThe authors declare no competing financial interest.\n\nSupplemental Material - nl8b01737_si_001.pdf
", "abstract": "Two-photon microscopy is a key imaging technique in life sciences due to its superior deep-tissue imaging capabilities. Light-weight and compact two-photon microscopes are of great interest because of their applications for in vivo deep brain imaging. Recently, dielectric metasurfaces have enabled a new category of small and lightweight optical elements, including objective lenses. Here we experimentally demonstrate two-photon microscopy using a double-wavelength metasurface lens. It is specifically designed to focus 820 and 605 nm light, corresponding to the excitation and emission wavelengths of the measured fluorophors, to the same focal distance. The captured two-photon images are qualitatively comparable to the ones taken by a conventional objective lens. Our metasurface lens can enable ultracompact two-photon microscopes with similar performance compared to current systems that are usually based on graded-index-lenses. In addition, further development of tunable metasurface lenses will enable fast axial scanning for volumetric imaging.", "date": "2018-08-08", "date_type": "published", "publication": "Nano Letters", "volume": "18", "number": "8", "publisher": "American Chemical Society", "pagerange": "4943-4948", "id_number": "CaltechAUTHORS:20180717-145659939", "issn": "1530-6984", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180717-145659939", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CBET-1512266" }, { "agency": "Fonds Wetenschappelijk Onderzoek (FWO)" }, { "agency": "Kavli Nanoscience Institute" }, { "agency": "Caltech Beckman Institute" } ] }, "local_group": { "items": [ { "id": "Kavli-Nanoscience-Institute" } ] }, "doi": "10.1021/acs.nanolett.8b01737", "primary_object": { "basename": "nl8b01737_si_001.pdf", "url": "https://authors.library.caltech.edu/records/3ngwx-46089/files/nl8b01737_si_001.pdf" }, "resource_type": "article", "pub_year": "2018", "author_list": "Arbabi, Ehsan; Li, Jiaqi; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/p8s3m-bv811", "eprint_id": 85551, "eprint_status": "archive", "datestamp": "2023-08-19 08:13:54", "lastmod": "2023-10-18 18:19:16", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tomina-Yusuke", "name": { "family": "Tomina", "given": "Yusuke" }, "orcid": "0000-0001-9406-1493" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel" }, "orcid": "0000-0002-6222-761X" } ] }, "title": "Dual-sided Voltage-sensitive Dye Imaging of Leech Ganglia", "ispublished": "pub", "full_text_status": "public", "keywords": "Voltage-sensitive dye imaging, Whole-brain recording, VoltageFluor, Microdissection, Dye-loading process", "note": "\u00a9 2018 Tomina and Wagenaar. This article is distributed under the terms of the Creative Commons Attribution License (CC BY 4.0). \n\nWe thank Evan Miller for supplying the VF2.1(OMe).H dye; Annette Stowasser for her role in developing a prototype of the double-sided microscope and many helpful conversations; Angela Bruno for useful discussions regarding data analysis; Ng Cai Tong for reading and checking the manuscript. This work was supported by the Burroughs Welcome Fund through a Career Award at the Scientific Interface and by the National Institute of Neurological Disorders and Stroke through grant R01 NS094403 (both to DAW). YT was supported by JSPS Overseas Research Fellowships. This protocol was adapted from procedures published in Tomina and Wagenaar (2017). The authors of this work declare no conflicts of interest.\n\nPublished - Bio-protocol2751.pdf
Accepted Version - nihms948707.pdf
", "abstract": "In this protocol, we introduce an effective method for voltage-sensitive dye (VSD) loading and imaging of leech ganglia as used in Tomina and Wagenaar (2017). Dissection and dye loading procedures are the most critical steps toward successful whole-ganglion VSD imaging. The former entails the removal of the sheath that covers neurons in the segmental ganglion of the leech, which is required for successful dye loading. The latter entails gently flowing a new generation VSD, VF2.1(OMe).H, onto both sides of the ganglion simultaneously using a pair of peristaltic pumps. We expect the described techniques to translate broadly to wide-field VSD imaging in other thin and relatively transparent nervous systems.", "date": "2018-03-05", "date_type": "published", "publication": "Bio-protocol", "volume": "8", "number": "5", "publisher": "Bio-Protocol", "pagerange": "Art. No. e2751", "id_number": "CaltechAUTHORS:20180402-075326031", "issn": "2331-8325", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180402-075326031", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Burroughs Welcome Fund" }, { "agency": "NIH", "grant_number": "R01 NS094403" }, { "agency": "Japan Society for the Promotion of Science (JSPS)" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" } ] }, "doi": "10.21769/BioProtoc.2751", "pmcid": "PMC5867905", "primary_object": { "basename": "nihms948707.pdf", "url": "https://authors.library.caltech.edu/records/p8s3m-bv811/files/nihms948707.pdf" }, "related_objects": [ { "basename": "Bio-protocol2751.pdf", "url": "https://authors.library.caltech.edu/records/p8s3m-bv811/files/Bio-protocol2751.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Tomina, Yusuke and Wagenaar, Daniel" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/rh132-fa824", "eprint_id": 84971, "eprint_status": "archive", "datestamp": "2023-08-19 07:55:30", "lastmod": "2023-10-20 21:50:17", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Lehmkuhl-Andrew-M", "name": { "family": "Lehmkuhl", "given": "Andrew M." }, "orcid": "0000-0002-5712-2012" }, { "id": "Muthusamy-Arunkumar", "name": { "family": "Muthusamy", "given": "Arunkumar" }, "orcid": "0000-0002-1804-586X" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" } ] }, "title": "Responses to mechanically and visually cued water waves in the nervous system of the medicinal leech", "ispublished": "pub", "full_text_status": "public", "keywords": "Hirudo verbana, Electrophysiology, S cell, Sensory systems, Aquatic predators", "note": "\u00a9 2018. Published by The Company of Biologists Ltd. \n\nReceived October 6, 2017. Accepted December 5, 2017. \n\nWe gratefully acknowledge help from Annette Stowasser in teaching dissection skills and useful discussions on optics and visual systems. \n\nThe authors declare no competing or financial interests.\n\nAuthor contributions: Conceptualization: A.M., D.A.W.; Methodology: D.A.W.; Software: D.A.W.; Validation: D.A.W.; Formal analysis: A.M.L., A.M., D.A.W.; Investigation: A.M.L., A.M., D.A.W.; Data curation: D.A.W.; Writing - original draft: A.M.L., A.M., D.A.W.; Writing - review & editing: A.M.L., A.M., D.A.W.; Visualization: D.A.W.; Supervision: D.A.W.; Project administration: D.A.W.; Funding acquisition: D.A.W. \n\nThis work was supported by the Burroughs Wellcome Fund through a Career Award at the Scientific Interface and by the National Institute of Neurological Disorders and Stroke through R01 NS094403 (both to D.A.W.). Deposited in PMC for release after 12 months.\n\nPublished - jeb171728.full.pdf
Submitted - 137588.full.pdf
Supplemental Material - JEB171728supp.pdf
", "abstract": "Sensitivity to water waves is a key modality by which aquatic predators can detect and localize their prey. For one such predator \u2013 the medicinal leech, Hirudo verbana \u2013 behavioral responses to visual and mechanical cues from water waves are well documented. Here, we quantitatively characterized the response patterns of a multisensory interneuron, the S cell, to mechanically and visually cued water waves. As a function of frequency, the response profile of the S cell replicated key features of the behavioral prey localization profile in both visual and mechanical modalities. In terms of overall firing rate, the S cell response was not direction selective, and although the direction of spike propagation within the S cell system did follow the direction of wave propagation under certain circumstances, it is unlikely that downstream neuronal targets can use this information. Accordingly, we propose a role for the S cell in the detection of waves but not in the localization of their source. We demonstrated that neither the head brain nor the tail brain are required for the S cell to respond to visually cued water waves.", "date": "2018-02-22", "date_type": "published", "publication": "Journal of Experimental Biology", "volume": "221", "number": "4", "publisher": "Company of Biologists", "pagerange": "Art. No. jeb171728", "id_number": "CaltechAUTHORS:20180227-093930741", "issn": "0022-0949", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180227-093930741", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Burroughs Wellcome Fund" }, { "agency": "NIH", "grant_number": "R01 NS094403" }, { "agency": "National Institute of Neurological Disorders and Stroke (NINDS)" } ] }, "local_group": { "items": [ { "id": "Tianqiao-and-Chrissy-Chen-Institute-for-Neuroscience" } ] }, "doi": "10.1242/jeb.171728", "pmcid": "PMC5868928", "primary_object": { "basename": "137588.full.pdf", "url": "https://authors.library.caltech.edu/records/rh132-fa824/files/137588.full.pdf" }, "related_objects": [ { "basename": "JEB171728supp.pdf", "url": "https://authors.library.caltech.edu/records/rh132-fa824/files/JEB171728supp.pdf" }, { "basename": "jeb171728.full.pdf", "url": "https://authors.library.caltech.edu/records/rh132-fa824/files/jeb171728.full.pdf" } ], "resource_type": "article", "pub_year": "2018", "author_list": "Lehmkuhl, Andrew M.; Muthusamy, Arunkumar; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/j63et-aw064", "eprint_id": 82216, "eprint_status": "archive", "datestamp": "2023-08-19 05:12:50", "lastmod": "2023-10-23 15:06:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Tomina-Yusuke", "name": { "family": "Tomina", "given": "Yusuke" }, "orcid": "0000-0001-9406-1493" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" } ] }, "title": "A double-sided microscope to realize whole-ganglion imaging of membrane potential in the medicinal leech", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2017 Tomina and Wagenaar. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited. Received: 22 June 2017; Accepted: 25 September 2017; Published: 25 September. We thank Evan Miller for sharing of the VF2.1(OMe).H dye; Annette Stowasser for her role in developing a prototype of the double-sided microscope and many helpful conversations; and Angela Bruno for useful discussions regarding data analysis. This work was supported by the Burroughs Welcome Fund through a Career Award at the Scientific Interface and by the National Institute of Neurological Disorders and Stroke through grant R01 NS094403 (both to DAW). YT was supported by JSPS Overseas Research Fellowships. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. Author Contributions: Yusuke Tomina, Conceptualization, Data curation, Software, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing\u2014original draft, Project administration; Daniel A Wagenaar, Conceptualization, Resources, Data curation, Software, Formal analysis, Supervision, Funding acquisition, Validation, Visualization, Methodology, Project administration, Writing\u2014review and editing.\n\nPublished - elife-29839.pdf
Submitted - 145144.full.pdf
Supplemental Material - elife-29839-transrepform-v3.docx
", "abstract": "Studies of neuronal network emergence during sensory processing and motor control are greatly facilitated by technologies that allow us to simultaneously record the membrane potential dynamics of a large population of neurons in single cell resolution. To achieve whole-brain recording with the ability to detect both small synaptic potentials and action potentials, we developed a voltage-sensitive dye (VSD) imaging technique based on a double-sided microscope that can image two sides of a nervous system simultaneously. We applied this system to the segmental ganglia of the medicinal leech. Double-sided VSD imaging enabled simultaneous recording of membrane potential events from almost all of the identifiable neurons. Using data obtained from double-sided VSD imaging, we analyzed neuronal dynamics in both sensory processing and generation of behavior and constructed functional maps for identification of neurons contributing to these processes.", "date": "2017-09-25", "date_type": "published", "publication": "eLife", "volume": "6", "publisher": "eLife Sciences Publications", "pagerange": "Art. No. e29839", "id_number": "CaltechAUTHORS:20171009-132459678", "issn": "2050-084X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20171009-132459678", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Burroughs Welcome Fund" }, { "agency": "NIH", "grant_number": "R01 NS094403" }, { "agency": "Japan Society for the Promotion of Science (JSPS)" } ] }, "doi": "10.7554/eLife.29839", "pmcid": "PMC5656430", "primary_object": { "basename": "145144.full.pdf", "url": "https://authors.library.caltech.edu/records/j63et-aw064/files/145144.full.pdf" }, "related_objects": [ { "basename": "elife-29839-transrepform-v3.docx", "url": "https://authors.library.caltech.edu/records/j63et-aw064/files/elife-29839-transrepform-v3.docx" }, { "basename": "elife-29839.pdf", "url": "https://authors.library.caltech.edu/records/j63et-aw064/files/elife-29839.pdf" } ], "resource_type": "article", "pub_year": "2017", "author_list": "Tomina, Yusuke and Wagenaar, Daniel A." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/cqwf8-5ca47", "eprint_id": 61993, "eprint_status": "archive", "datestamp": "2023-08-20 08:41:39", "lastmod": "2023-10-25 16:07:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nagarah-J-M", "name": { "family": "Nagarah", "given": "John M." } }, { "id": "Stowasser-A", "name": { "family": "Stowasser", "given": "Annette" } }, { "id": "Parker-R-L", "name": { "family": "Parker", "given": "Rell L." } }, { "id": "Asari-H", "name": { "family": "Asari", "given": "Hiroki" } }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" } ] }, "title": "Optically transparent multi-suction electrode arrays", "ispublished": "pub", "full_text_status": "public", "keywords": "electrophysiology, multielectrode array, voltage-sensitive dye, neural interface, brain slice, retina, leech", "note": "\u00a9 2015 Nagarah, Stowasser, Parker, Asari and Wagenaar. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. \n\nReceived: 07 September 2015; Accepted: 02 October 2015; Published: 20 October 2015. \n\nWe are grateful to the following people: James Heath for use of his cleanroom facility; Jen-Kan Yu, Slobodan Mitrovic, and the UCLA Nanoelectronics Research Facility staff, especially Joe Zendejas and Tom Lee, for their support with device fabrication; Markus Meister for aid in the retina experiments; Henry Lester and Bruce Cohen for the use of lab space and equipment for slice recordings; Bill Eggers for discussions on electrochemical impedance analysis; Karl-Heinz Boven and Frank Hofmann for discussions on slice recordings and perforated MEAs; Eugene Lubenov and Julie Miwa for further discussions on slice recordings; Habib Ahmad for help with 3D renderings. \n\nFunding for this work was provided by the Broad Foundations, by a Career Award at the Scientific Interface (#1007977) from the Burroughs Wellcome Fund to DW, and by funds provided by the Regents of the University of California, Tobacco-Related Diseases Research Program (grant no 22DT-0008) to RP. \n\nThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.\n\nPublished - fnins-09-00384.pdf
Supplemental Material - presentation_1.pdf
", "abstract": "Multielectrode arrays (MEAs) allow for acquisition of multisite electrophysiological activity with submillisecond temporal resolution from neural preparations. The signal to noise ratio from such arrays has recently been improved by substrate perforations that allow negative pressure to be applied to the tissue; however, such arrays are not optically transparent, limiting their potential to be combined with optical-based technologies. We present here multi-suction electrode arrays (MSEAs) in quartz that yield a substantial increase in the detected number of units and in signal to noise ratio from mouse cortico-hippocampal slices and mouse retina explants. This enables the visualization of stronger cross correlations between the firing rates of the various sources. Additionally, the MSEA's transparency allows us to record voltage sensitive dye activity from a leech ganglion with single neuron resolution using widefield microscopy simultaneously with the electrode array recordings. The combination of enhanced electrical signals and compatibility with optical-based technologies should make the MSEA a valuable tool for investigating neuronal circuits.", "date": "2015-10-20", "date_type": "published", "publication": "Frontiers in Neuroscience", "volume": "9", "publisher": "Frontiers", "pagerange": "Art. No. 384", "id_number": "CaltechAUTHORS:20151109-105331416", "issn": "1662-453X", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20151109-105331416", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Eli and Edythe Broad Foundation" }, { "agency": "Burroughs Wellcome Fund", "grant_number": "1007977" }, { "agency": "Regents of the University of California" }, { "agency": "California Tobacco-Related Disease Research Program", "grant_number": "22DT-0008" } ] }, "doi": "10.3389/fnins.2015.00384", "pmcid": "PMC4611137", "primary_object": { "basename": "fnins-09-00384.pdf", "url": "https://authors.library.caltech.edu/records/cqwf8-5ca47/files/fnins-09-00384.pdf" }, "related_objects": [ { "basename": "presentation_1.pdf", "url": "https://authors.library.caltech.edu/records/cqwf8-5ca47/files/presentation_1.pdf" } ], "resource_type": "article", "pub_year": "2015", "author_list": "Nagarah, John M.; Stowasser, Annette; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/pa3k2-5p382", "eprint_id": 55742, "eprint_status": "archive", "datestamp": "2023-08-20 04:56:29", "lastmod": "2023-10-20 23:05:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Baljon-P-L", "name": { "family": "Baljon", "given": "Pieter Laurens" } }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" } ] }, "title": "Responses to Conflicting Stimuli in a Simple Stimulus\u2013Response Pathway", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2015 Baljon and Wagenaar.\nThis article is freely available online through the J Neurosci Author Open Choice option.\n\nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution and reproduction in any\nmedium provided that the original work is properly attributed.\n\nReceived Sept. 12, 2014; revised Dec. 2, 2014; accepted Dec. 12, 2014.\n\nThis work was supported by the Broad Foundations. D.A.W. is the recipient of a Career Award at the Scientific Interface from the Burroughs Wellcome Fund. We thank an anonymous reviewer for many valuable comments and in particular for the suggestion to consider bilateral pressure in the context of being pinched by a predator.\n\nThe authors declare no competing financial interests.\n\nAuthor contributions: P.L.B. and D.A.W. designed research; P.L.B. performed research; P.L.B. and D.A.W. analyzed data; D.A.W. wrote the paper.\n\nPublished - 2398.full.pdf
", "abstract": "The \"local bend response\" of the medicinal leech (Hirudo verbana) is a stimulus\u2013response pathway that enables the animal to bend away from a pressure stimulus applied anywhere along its body. The neuronal circuitry that supports this behavior has been well described, and its responses to individual stimuli are understood in quantitative detail. We probed the local bend system with pairs of electrical stimuli to sensory neurons that could not logically be interpreted as a single touch to the body wall and used multiple suction electrodes to record simultaneously the responses in large numbers of motor neurons. In all cases, responses lasted much longer than the stimuli that triggered them, implying the presence of some form of positive feedback loop to sustain the response. When stimuli were delivered simultaneously, the resulting motor neuron output could be described as an evenly weighted linear combination of the responses to the constituent stimuli. However, when stimuli were delivered sequentially, the second stimulus had greater impact on the motor neuron output, implying that the positive feedback in the system is not strong enough to render it immune to further input.", "date": "2015-02-11", "date_type": "published", "publication": "Journal of Neuroscience", "volume": "35", "number": "6", "publisher": "Society for Neuroscience", "pagerange": "2398-2406", "id_number": "CaltechAUTHORS:20150313-092545773", "issn": "0270-6474", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150313-092545773", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Eli and Edythe Broad Foundation" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1523/JNEUROSCI.3823-14.2015", "pmcid": "PMC4323524", "primary_object": { "basename": "2398.full.pdf", "url": "https://authors.library.caltech.edu/records/pa3k2-5p382/files/2398.full.pdf" }, "resource_type": "article", "pub_year": "2015", "author_list": "Baljon, Pieter Laurens and Wagenaar, Daniel A." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/hn7fp-qp783", "eprint_id": 48742, "eprint_status": "archive", "datestamp": "2023-08-20 03:41:52", "lastmod": "2023-10-17 20:23:39", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Romanenko-S", "name": { "family": "Romanenko", "given": "Sergii" } }, { "id": "Siegel-P-H", "name": { "family": "Siegel", "given": "Peter H." }, "orcid": "0000-0002-2539-4646" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Pikov-V", "name": { "family": "Pikov", "given": "Victor" } } ] }, "title": "Effects of millimeter wave irradiation and equivalent thermal heating on the activity of individual neurons in the leech ganglion", "ispublished": "pub", "full_text_status": "public", "keywords": "millimeter wave, action potential, thermal, heating, leech ganglion", "note": "\u00a9 2014, Journal of Neurophysiology. Licensed under Creative Commons Attribution CC-BY 3.0.\n\nPublished 13 August 2014. \n\nSergii Romanenko was funded through a Boswell Postdoctoral Fellowship from Caltech/HMRI and is presently a postdoctoral fellow at LABEX Sigma-Lim \u2013 XLIM, Facult\u00e9 des Sciences et Techniques, Limoges, Cedex, France. Daniel A. Wagenaar was funded through a Career Award at the Scientific Interface from the Burroughs Wellcome Fund and is presently an Assistant Professor at the Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA. Disclosures. The authors declare no competing financial interests.\n\nPublished - 2423.full.pdf
", "abstract": "Many of today's radiofrequency-emitting devices in telecommunication, telemedicine, transportation safety, and security/military applications use the millimeter-wave (MMW) band (30-300 GHz). To evaluate the biological safety and possible applications of this radiofrequency band for neuroscience and neurology, we have investigated the physiological effects of low-intensity 60 GHz electromagnetic irradiation on individual neurons in the leech midbody ganglia. We applied incident power densities of 1, 2, and 4 mW/cm^2 to the whole ganglion for a period of 1 minute, while recording the action potential with a standard sharp-electrode electrophysiology setup. For comparison, the recognized U.S. safe exposure limit is 1 mW/cm^2 for 6 minutes. During the exposure to MMWs and gradual bath heating at a rate of 0.04 \u00baC/sec (2.4 \u00baC/min), the ganglionic neurons exhibited similar dose-dependent hyperpolarization of the plasma membrane and decrease in the action potential amplitude. However, narrowing of the action potential half-width during MMW irradiation at 4 mW/cm^2 was 5 times more pronounced, as compared to equivalent bath heating of 0.6 \u00baC. Even more dramatic difference in the effects of MMW irradiation and bath heating was on the firing rate, which was suppressed at all applied MMW power densities and was increased in a dose-dependent manner during gradual bath heating. The mechanism of enhanced narrowing of action potentials and suppressed firing by MMW irradiation, as compared to gradual bath heating, is hypothesized to involve specific coupling of MMW energy with the neuronal plasma membrane.", "date": "2014-11-15", "date_type": "published", "publication": "Journal of Neurophysiology", "volume": "112", "number": "10", "publisher": "American Physiological Society", "pagerange": "2423-2431", "id_number": "CaltechAUTHORS:20140820-140703376", "issn": "0022-3077", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140820-140703376", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Caltech/HMRI Boswell Postdoctoral Fellowship" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1152/jn.00357.2014", "pmcid": "PMC4233276", "primary_object": { "basename": "2423.full.pdf", "url": "https://authors.library.caltech.edu/records/hn7fp-qp783/files/2423.full.pdf" }, "resource_type": "article", "pub_year": "2014", "author_list": "Romanenko, Sergii; Siegel, Peter H.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1h1ew-94k46", "eprint_id": 47114, "eprint_status": "archive", "datestamp": "2023-08-19 23:14:28", "lastmod": "2023-10-26 20:19:27", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nagarah-J-M", "name": { "family": "Nagarah", "given": "John M." } }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" } ] }, "title": "Transparent Multi-Suction Electrode Arrays for in vitro Neural Network Investigations", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2014 Biophysical Society. Published by Elsevier Inc.", "abstract": "Large-scale multisite electrophysiology recordings with high temporal resolution\nare essential to discover neural circuitry and elucidate their structurefunction\nrelationship. We contribute to this effort by combining multielectrode\narrays (MEAs) with through pore arrays in quartz substrates to create multisuction\nelectrode arrays. The MEA allows for multisite extracellular recordings\nfrom neural tissue while the through pore array permits suction to be applied to\nthe tissue to form more intimate contact with the electrodes. We successfully\nrecorded from mouse hippocampi, mouse retina, and leech segmental ganglia.\nHippocampus and retina tissue show at least a 50% increase in S/N and twofold\nincrease in detectable spikes following suction. (Interestingly, spiking activity\nand S/N of spikes in leech ganglia mostly do not increase after applied suction,\nsuggesting sources deeper in the tissue.) Finally, we demonstrate optical imaging\nthrough the transparent substrate to visualize the neurons at the electrode\ninterface simultaneously with electrophysiology recordings. This technology\nwill facilitate the combination of optical-based measurements such as\nvoltage-sensitive dye imaging with multisite electrophysiological recordings\nwith high temporal resolution of neuronal networks in a wide range of vertebrate\nand invertebrate preparations, at the single spike level.", "date": "2014-01-28", "date_type": "published", "publication": "Biophysical Journal", "volume": "106", "number": "2", "publisher": "Biophysical Society", "pagerange": "417A", "id_number": "CaltechAUTHORS:20140710-080237054", "issn": "0006-3495", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140710-080237054", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1016/j.bpj.2013.11.2346", "resource_type": "article", "pub_year": "2014", "author_list": "Nagarah, John M. and Wagenaar, Daniel A." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/kejhn-02471", "eprint_id": 38830, "eprint_status": "archive", "datestamp": "2023-08-19 19:56:09", "lastmod": "2023-10-23 23:31:18", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Harley-Cynthia-M", "name": { "family": "Harley", "given": "Cynthia M." } }, { "id": "Rossi-Matthew", "name": { "family": "Rossi", "given": "Matthew" } }, { "id": "Cienfuegos-Javier", "name": { "family": "Cienfuegos", "given": "Javier" } }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel" }, "orcid": "0000-0002-6222-761X" } ] }, "title": "Discontinuous locomotion and prey sensing in the leech", "ispublished": "pub", "full_text_status": "public", "keywords": "behavioral choice, crawl, leech, locomotion, sensory, swim", "note": "\u00a9 2013 Published by The Company of Biologists Ltd.\n\nReceived 12 June 2012; Accepted 23 January 2013.\n\nThe authors thank Karen Mesce for her valuable input on the discussion of this\nmanuscript, as well as two anonymous reviewers, whose comments aided in\nimproving the manuscript.\nAuthor Contributions:\nC.M.H and D.A.W. designed the experiments. C.M.H, J.C. and M.R. performed\ndata analysis and experiment execution. C.M.H. wrote the manuscript. D.A.W.\nand C.M.H. edited the manuscript.\nFunding:\nFunding for this study was provided by the Burroughs Wellcome Fund and the\nBroad Foundations (to D.A.W).\n\nPublished - 1890.full.pdf
", "abstract": "The medicinal leech, Hirudo verbana, is an aquatic predator that utilizes water waves to locate its prey. However, to reach their prey, the leeches must move within the same water that they are using to sense prey. This requires that they either move ballistically towards a pre-determined prey location or that they account for their self-movement and continually track prey. We found that leeches do not localize prey ballistically. Instead, they require continual sensory information to track their prey. Indeed, in the event that the prey moves, leeches will approach the prey's new location. While leeches need to continually sense water disturbances to update their percept of prey location, their own behavior is discontinuous \u2013 approaching prey involves switching between swimming, crawling and non-locomoting. Each of these behaviors may allow for different sensory capabilities and may require different sensory filters. Here, we examined the sensory capabilities of leeches during each of these behaviors. We found that while one could expect the non-locomoting phases to direct subsequent behaviors, crawling phases were more effective than non-locomotor phases for providing direction. During crawling bouts, leeches adjusted their heading so as to become more directed towards the stimulus. This was not observed during swimming. Furthermore, in the presence of prey-like stimuli, leeches crawled more often and for longer periods of time.", "date": "2013-05-15", "date_type": "published", "publication": "Journal of Experimental Biology", "volume": "216", "number": "10", "publisher": "Company of Biologists", "pagerange": "1890-1897", "id_number": "CaltechAUTHORS:20130606-100422173", "issn": "0022-0949", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130606-100422173", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Burroughs Wellcome Fund" }, { "agency": "Eli and Edythe Broad Foundation" } ] }, "doi": "10.1242/jeb.075911", "primary_object": { "basename": "1890.full.pdf", "url": "https://authors.library.caltech.edu/records/kejhn-02471/files/1890.full.pdf" }, "resource_type": "article", "pub_year": "2013", "author_list": "Harley, Cynthia M.; Rossi, Matthew; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/gak3p-xp670", "eprint_id": 42356, "eprint_status": "archive", "datestamp": "2023-08-22 08:43:51", "lastmod": "2024-01-13 06:04:51", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Romanenko-S", "name": { "family": "Romanenko", "given": "Sergii" } }, { "id": "Siegel-P-H", "name": { "family": "Siegel", "given": "Peter H." }, "orcid": "0000-0002-2539-4646" }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Pikov-V", "name": { "family": "Pikov", "given": "Victor" } } ] }, "title": "Comparison of the effects of millimeter wave irradiation, general bath heating, and localized heating on neuronal activity in the leech ganglion", "ispublished": "unpub", "full_text_status": "public", "keywords": "Neuron; action potential; leech; millimeter waves; non-invasive; brain; GHz; terahertz", "note": "\u00a9 2013 SPIE.\n\nPublished - Romanenko_2013p85850N.pdf
", "abstract": "The use of electrically-induced neuromodulation has grown in importance in the treatment of multiple neurological disorders such as Parkinson's disease, dystonia, epilepsy, chronic pain, cluster headaches and others. While electrical current can be applied locally, it requires placing stimulation electrodes in direct contact with the neural tissue. Our goal is to develop a method for localized application of electromagnetic energy to the brain without direct tissue contact. Toward this goal, we are experimenting with the wireless transmission of millimeter wave (MMW) energy in the 10-100 GHz frequency range, where penetration and focusing can be traded off to provide non-contact irradiation of the cerebral cortex. Initial experiments have been conducted on freshly-isolated leech ganglia to evaluate the real-time changes in the activity of individual neurons upon exposure to the MMW radiation. The initial results indicate that low-intensity MMWs can partially suppress the neuronal activity. This is in contrast to general bath heating, which had an excitatory effect on the neuronal activity. Further studies are underway to determine the changes in the state of the membrane channels that might be responsible for the observed neuromodulatory effects. \u00a9 (2013) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.", "date": "2013-02-23", "date_type": "published", "publisher": "Society of Photo-Optical Engineers", "place_of_pub": "Bellingham, WA", "pagerange": "Art. No. 85850N", "id_number": "CaltechAUTHORS:20131111-140845262", "isbn": "978-0-8194-9354-5", "book_title": "Terahertz and Ultrashort Electromagnetic Pulses for Biomedical Applications", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20131111-140845262", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Wilmink-G-J", "name": { "family": "Wilmink", "given": "Gerald J." } }, { "id": "Ibey-B-L", "name": { "family": "Ibey", "given": "Bennett L." } } ] }, "doi": "10.1117/12.2006504", "primary_object": { "basename": "Romanenko_2013p85850N.pdf", "url": "https://authors.library.caltech.edu/records/gak3p-xp670/files/Romanenko_2013p85850N.pdf" }, "resource_type": "book_section", "pub_year": "2013", "author_list": "Romanenko, Sergii; Siegel, Peter H.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/0hk4a-42582", "eprint_id": 30110, "eprint_status": "archive", "datestamp": "2023-08-19 10:06:04", "lastmod": "2023-10-17 15:23:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Nagarah-J-M", "name": { "family": "Nagarah", "given": "John M." } }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" } ] }, "title": "Ultradeep fused silica glass etching with an HF-resistant photosensitive resist for optical imaging applications", "ispublished": "pub", "full_text_status": "restricted", "note": "\u00a9 2012 IOP Publishing Ltd.\n\nReceived 8 October 2011, in final form 7 January 2012. Published 14 February 2012.\n\nFunding for this work was provided by The Broad\nFoundations. DAW is the recipient of a Career Award at the\nScientific Interface from the Burroughs Wellcome Fund. We\nthank James R. Heath for granting us use of his clean room\nfacility and Habib Ahmad for contributions in creating figures\nin this manuscript. We also thank Jen-Kan Yu, Slobodan\nMitrovic and the UCLA Nanoelectronics Research Facility\nstaff, especially Joe Zendejas and Tom Lee, for their support\nin device fabrication.", "abstract": "Microfluidic and optical sensing platforms are commonly fabricated in glass and fused silica (quartz) because of their optical transparency and chemical inertness. Hydrofluoric acid (HF) solutions are the etching media of choice for deep etching into silicon dioxide substrates, but processing schemes become complicated and expensive for etching times greater than 1 h due to the aggressiveness of HF migration through most masking materials. We present here etching into fused silica more than 600 \u00b5m deep while keeping the substrate free of pits and maintaining a polished etched surface suitable for biological imaging. We utilize an HF-resistant photosensitive resist (HFPR) which is not attacked in 49% HF solution. Etching characteristics are compared for substrates masked with the HFPR alone and the HFPR patterned on top of Cr/Au and polysilicon masks. We used this etching process to fabricate suspended fused silica membranes, 8\u201316 \u00b5m thick, and show that imaging through the membranes does not negatively affect image quality of fluorescence microscopy of biological tissue. Finally, we realize small through-pore arrays in the suspended membranes. Such devices will have applications in planar electrophysiology platforms, especially where optical imaging is required.", "date": "2012-03", "date_type": "published", "publication": "Journal of Micromechanics and Microengineering", "volume": "22", "number": "3", "publisher": "IOP", "pagerange": "Art. No. 035011", "id_number": "CaltechAUTHORS:20120416-142037502", "issn": "0960-1317", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120416-142037502", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Eli and Edythe Broad Foundation" }, { "agency": "Burroughs Wellcome Fund" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1088/0960-1317/22/3/035011", "resource_type": "article", "pub_year": "2012", "author_list": "Nagarah, John M. and Wagenaar, Daniel A." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/k56hx-vqt07", "eprint_id": 30051, "eprint_status": "archive", "datestamp": "2023-08-19 09:31:13", "lastmod": "2023-10-17 15:15:48", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" } ] }, "title": "An Optically Stabilized Fast-Switching Light Emitting Diode as a Light Source for Functional Neuroimaging", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2012 Daniel A. Wagenaar. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits\nunrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.\nReceived September 5, 2011; Accepted December 6, 2011; Published January 6, 2012.\nEditor: Bj\u00f6rn Brembs, Freie Universitaet Berlin, Germany.\nFunding: This work was supported by a Senior Research Fellowship from the Broad Foundations. The author holds a Career Award at the Scientic Interface from\nthe Burroughs Wellcome Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\nJohn Nagarah, Sotiris Masmanidis, William B. Kristan, and Andrew Steele\nprovided valuable comments.\nAuthor Contributions:\nConceived and designed the experiments: DAW. Performed the experiments:\nDAW. Analyzed the data: DAW. Contributed reagents/materials/\nanalysis tools: DAW. Wrote the paper: DAW.\n\nPublished - Wagenaar2012p17704PLoS_ONE.pdf
", "abstract": "Neuroscience research increasingly relies on optical methods for evoking neuronal activity as well as for measuring it, making bright and stable light sources critical building blocks of modern experimental setups. This paper presents a method to control the brightness of a high-power light emitting diode (LED) light source to an unprecedented level of stability. By continuously monitoring the actual light output of the LED with a photodiode and feeding the result back to the LED's driver by way of a proportional-integral controller, drift was reduced to as little as 0.007% per hour over a 12-h period, and short-term fluctuations to 0.005% root-mean-square over 10 seconds. The LED can be switched on and off completely within 100 \u00b5s, a feature that is crucial when visual stimuli and light for optical recording need to be interleaved to obtain artifact-free recordings. The utility of the system is demonstrated by recording visual responses in the central nervous system of the medicinal leech Hirudo verbana using voltage-sensitive dyes.", "date": "2012-01-06", "date_type": "published", "publication": "PLoS ONE", "volume": "7", "number": "1", "publisher": "Public Library of Science", "pagerange": "Art. No. e29822", "id_number": "CaltechAUTHORS:20120410-144819396", "issn": "1932-6203", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120410-144819396", "rights": "This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits\nunrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.", "funders": { "items": [ { "agency": "Eli and Edythe Broad Foundation" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1371/journal.pone.0029822", "pmcid": "PMC3253093", "primary_object": { "basename": "Wagenaar2012p17704PLoS_ONE.pdf", "url": "https://authors.library.caltech.edu/records/k56hx-vqt07/files/Wagenaar2012p17704PLoS_ONE.pdf" }, "resource_type": "article", "pub_year": "2012", "author_list": "Wagenaar, Daniel A." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1bhp1-ztn48", "eprint_id": 27992, "eprint_status": "archive", "datestamp": "2023-08-19 08:29:53", "lastmod": "2023-10-24 17:33:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Harley-C-M", "name": { "family": "Harley", "given": "Cynthia M." } }, { "id": "Cienfuegos-J", "name": { "family": "Cienfuegos", "given": "Javier" } }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" } ] }, "title": "Developmentally regulated multisensory integration for prey localization in the medicinal leech", "ispublished": "pub", "full_text_status": "public", "keywords": "development, leech, mechanosensory, multisensory, vision.", "note": "\u00a9 2011. Published by The Company of Biologists Ltd. Accepted 17 August 2011. We would like to thank two anonymous reviewers in addition to Andrew Steele for their comments, which greatly improved the manuscript. In addition, we thank the Kristan lab for their gift of juvenile leeches. All funding for this work and its authors was supplied by the Burroughs Wellcome Fund and The Broad Foundations. Presentation of this work at the Society for\nNeuroscience meeting was funded by a travel award from The Journal of Experimental Biology.\n\nPublished - Harley2011p16328J_Exp_Biol.pdf
Supplemental Material - JEB059618FigS1.pdf
", "abstract": "Medicinal leeches, like many aquatic animals, use water disturbances to localize their prey, so they need to be able to determine if a wave disturbance is created by prey or by another source. Many aquatic predators perform this separation by responding only to those wave frequencies representing their prey. As leeches' prey preference changes over the course of their development, we examined their responses at three different life stages. We found that juveniles more readily localize wave sources of lower frequencies (2 Hz) than their adult counterparts (8\u201312 Hz), and that adolescents exhibited elements of both juvenile and adult behavior, readily localizing sources of both frequencies. Leeches are known to be able to localize the source of waves through the use of either mechanical or visual information. We separately characterized their ability to localize various frequencies of stimuli using unimodal cues. Within a single modality, the frequency\u2013response curves of adults and juveniles were virtually indistinguishable. However, the differences between the responses for each modality (visual and mechanosensory) were striking. The optimal visual stimulus had a much lower frequency (2 Hz) than the optimal mechanical stimulus (12 Hz). These frequencies matched, respectively, the juvenile and the adult preferred frequency for multimodally sensed waves. This suggests that, in the multimodal condition, adult behavior is driven more by mechanosensory information and juvenile behavior more by visual. Indeed, when stimuli of the two modalities were placed in conflict with one another, adult leeches, unlike juveniles, were attracted to the mechanical stimulus much more strongly than to the visual stimulus.", "date": "2011-11", "date_type": "published", "publication": "Journal of Experimental Biology", "volume": "214", "number": "22", "publisher": "Company of Biologists", "pagerange": "3801-3807", "id_number": "CaltechAUTHORS:20111129-104156137", "issn": "0022-0949", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111129-104156137", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Burroughs Wellcome Fund" }, { "agency": "Eli and Edythe Broad Foundation" }, { "agency": "Journal of Experimental Biology travel award" } ] }, "doi": "10.1242/jeb.059618", "primary_object": { "basename": "Harley2011p16328J_Exp_Biol.pdf", "url": "https://authors.library.caltech.edu/records/1bhp1-ztn48/files/Harley2011p16328J_Exp_Biol.pdf" }, "related_objects": [ { "basename": "JEB059618FigS1.pdf", "url": "https://authors.library.caltech.edu/records/1bhp1-ztn48/files/JEB059618FigS1.pdf" } ], "resource_type": "article", "pub_year": "2011", "author_list": "Harley, Cynthia M.; Cienfuegos, Javier; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/fzfr2-21071", "eprint_id": 20580, "eprint_status": "archive", "datestamp": "2023-08-22 01:25:15", "lastmod": "2023-10-20 23:13:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Gonzalez-R", "name": { "family": "Gonzalez", "given": "Ruben" } }, { "id": "Ries-D-C", "name": { "family": "Ries", "given": "David C." } }, { "id": "Kristan-W-B", "name": { "family": "Kristan", "given": "Wiliam B., Jr." } }, { "id": "French-K-A", "name": { "family": "French", "given": "Kathleen A." } } ] }, "title": "Alpha-conotoxin ImI disrupts central control of swimming in the medicinal leech", "ispublished": "pub", "full_text_status": "public", "keywords": "Swimming; Central pattern generator; Intersegmental coordination; Medicinal leech; Hirudo verbana", "note": "\u00a9 2010 Elsevier Ireland Ltd.\n\nReceived 26 May 2010; revised 5 August 2010; accepted 26 August 2010. Available online 15 September 2010.\n\nWe thank Dr. Baldomero Olivera and his laboratory for supplying Conus venoms and ImI in the early phases of this work. This work was supported by NIH Research Grants MH43396 and NS35336 (to WBK), by a Senior Research Fellowship from the Broad Foundations (to DAW) and by Microsoft Research Labs. DAW holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund.\n\nAccepted Version - nihms236374.pdf
Supplemental Material - f.pdf
", "abstract": "Medicinal leeches (Hirudo spp.) swim using a metachronal, front-to-back undulation. The behavior is generated by central pattern generators (CPGs) distributed along the animal's midbody ganglia and is coordinated by both central and peripheral mechanisms. Here we report that a component of the venom of Conus imperialis, \u03b1-conotoxin ImI, known to block nicotinic acetyl-choline receptors in other species,\ndisrupts swimming. Leeches injected with the toxin swam in circles with exaggerated dorsoventral bends and reduced forward velocity. Fictive swimming in isolated nerve cords was even more strongly disrupted, indicating that the toxin targets the CPGs and central coordination, while peripheral coordination partially rescues the behavior in intact animals.", "date": "2010-11-26", "date_type": "published", "publication": "Neuroscience Letters", "volume": "485", "number": "3", "publisher": "Elsevier", "pagerange": "151-156", "id_number": "CaltechAUTHORS:20101028-094759611", "issn": "0304-3940", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20101028-094759611", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "MH43396" }, { "agency": "NIH", "grant_number": "NS35336" }, { "agency": "Eli and Edythe Broad Foundation" }, { "agency": "Microsoft Research Labs" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1016/j.neulet.2010.08.078", "pmcid": "PMC2956871", "primary_object": { "basename": "f.pdf", "url": "https://authors.library.caltech.edu/records/fzfr2-21071/files/f.pdf" }, "related_objects": [ { "basename": "nihms236374.pdf", "url": "https://authors.library.caltech.edu/records/fzfr2-21071/files/nihms236374.pdf" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Wagenaar, Daniel A.; Gonzalez, Ruben; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/x15dn-8kd85", "eprint_id": 17921, "eprint_status": "archive", "datestamp": "2023-08-19 02:01:02", "lastmod": "2023-10-20 15:25:19", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Hamilton-M-S", "name": { "family": "Hamilton", "given": "M. Sarhas" } }, { "id": "Huang-Tracy", "name": { "family": "Huang", "given": "Tracy" } }, { "id": "Kristan-W-B", "name": { "family": "Kristan", "given": "William B." } }, { "id": "French-K-A", "name": { "family": "French", "given": "Kathleen A." } } ] }, "title": "A Hormone-Activated Central Pattern Generator for Courtship", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2010 Elsevier Ltd.\nReceived 22 December 2009; \nrevised 1 February 2010; \naccepted 5 February 2010. \nPublished online: March 11, 2010. \nAvailable online 11 March 2010.\nWe thank B. Olivera for his role in earlier stages of this work, K. Murphy and\nJ. Chang Han for preliminary work (while they were undergraduates) on\ncharacterizing how conopressin affects behavior, C.R. Lee for her careful\nstudies on latency measurement, J. Ram for sharing his specimens and\nknowledge of Nereis with us, and J. Murphy for maintaining our breeding\ncolony and observing reproduction. This work was supported by grants\nMH43396 from the National Institutes of Health and IOS0825741 from the\nNational Science Foundation (both to W.B.K.), by a fellowship from the\nBroad Foundations (to D.A.W.), by Microsoft Research, and by a private\ngift from R. Geckler. D.A.W. holds a Career Award at the Scientific Interface\nfrom the Burroughs Wellcome Fund.\n\nAccepted Version - nihms182518.pdf
Supplemental Material - mmc1.pdf
Supplemental Material - mmc2.mpg
Supplemental Material - mmc3.mpg
", "abstract": "Background:\nMedicinal leeches (Hirudo spp.) are simultaneous hermaphrodites. Mating occurs after a stereotyped twisting and oral exploration that result in the alignment of the male and/or female gonopores of one leech with the complementary gonopores of a partner. The neural basis of this behavior is presently unknown and currently impossible to study directly because electrophysiological recording techniques disrupt the behavior.\nResults:\nHere we report that (Arg^8)-conopressin G and two other members of the oxytocin/vasopressin family of peptide hormones induce in Hirudo verbana a sequence of behaviors that closely mimic elements of spontaneous reproductive behavior. Through a series of progressively more reduced preparations, we show that one of these behaviors, a stereotyped twisting that is instrumental in aligning gonopores in preparation for copulation, is the product of a central pattern generator that consists of oscillators in ganglia M5 and M6 (the ganglia in the reproductive segments of the leech), and also in ganglion M4, which was not previously known to play a role in reproductive behavior. We find that the behavior is periodic, with a remarkably long cycle period of around five minutes, placing it among the slowest behavioral rhythms (other than diurnal and annual rhythms) yet described.\nConclusion: \nThese results establish the leech as a new model system for studying aspects of the neuronal basis of reproductive behavior.\nHighlights: \n\nOxytocin/vasopressin homologs induce precopulatory movements in a leech. These movements are generated by a central pattern generator. Segmental ganglia M4, M5, and M6 can each generate fictive behavior in isolation", "date": "2010-03-23", "date_type": "published", "publication": "Current Biology", "volume": "20", "number": "6", "publisher": "Cell Press", "pagerange": "487-495", "id_number": "CaltechAUTHORS:20100412-080058326", "issn": "0960-9822", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100412-080058326", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "MH43396" }, { "agency": "NSF", "grant_number": "IOS0825741" }, { "agency": "Broad Foundations" }, { "agency": "Microsoft Research" }, { "agency": "Burroughs Wellcome Fund" } ] }, "collection": "CaltechAUTHORS", "doi": "10.1016/j.cub.2010.02.027", "pmcid": "PMC2858972", "primary_object": { "basename": "nihms182518.pdf", "url": "https://authors.library.caltech.edu/records/x15dn-8kd85/files/nihms182518.pdf" }, "related_objects": [ { "basename": "mmc1.pdf", "url": "https://authors.library.caltech.edu/records/x15dn-8kd85/files/mmc1.pdf" }, { "basename": "mmc2.mpg", "url": "https://authors.library.caltech.edu/records/x15dn-8kd85/files/mmc2.mpg" }, { "basename": "mmc3.mpg", "url": "https://authors.library.caltech.edu/records/x15dn-8kd85/files/mmc3.mpg" } ], "resource_type": "article", "pub_year": "2010", "author_list": "Wagenaar, Daniel A.; Hamilton, M. Sarhas; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/y3g4g-42354", "eprint_id": 18307, "eprint_status": "archive", "datestamp": "2023-08-21 23:28:58", "lastmod": "2023-10-20 15:57:51", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Kristan-W-B-Jr", "name": { "family": "Kristan", "given": "Wiliam B., Jr." } } ] }, "title": "Automated Video Analysis of Animal Movements Using Gabor Orientation Filters", "ispublished": "pub", "full_text_status": "public", "keywords": "Image analysis; Animal detection; Natural scenes; Gabor filter; Shape extraction; Matlab", "note": "\u00a9 The Author(s) 2010. This article is published with open access at Springerlink.com.\n\nPublished online: 2 February 2010.\nThis work was supported by a fellowship\nfrom the Broad Foundations (to DAW), by grant IOS-0825741\nfrom the NSF (to WBK), and by grant RO1 MH043396 from\nNIH/NIMH (to WBK). DAW holds a Career Award at the\nScientific Interface from the Burroughs Wellcome Fund.\nOpen Access This article is distributed under the terms of the\nCreative Commons Attribution Noncommercial License which\npermits any noncommercial use, distribution, and reproduction\nin any medium, provided the original author(s) and source are\ncredited.\n\nPublished - Wagenaar2010p9853Neuroinformatics.pdf
", "abstract": "To quantify locomotory behavior, tools for determining the location and shape of an animal's body are a first requirement. Video recording is a convenient technology to store raw movement data, but extracting body coordinates from video recordings is a nontrivial task. The algorithm described in this paper solves this task for videos of leeches or other quasi-linear animals in a manner inspired by the mammalian visual processing system: the video frames are fed through a bank of Gabor filters, which locally detect segments of the animal at a particular orientation. The algorithm assumes that the image location with maximal filter output lies on the animal's body and traces its shape out in both directions from there. The algorithm successfully extracted location and shape information from video clips of swimming leeches, as well as from still photographs of swimming and crawling snakes. A Matlab implementation with a graphical user interface is available online, and should make this algorithm conveniently usable in many other contexts.", "date": "2010-03", "date_type": "published", "publication": "Neuroinformatics", "volume": "8", "number": "1", "publisher": "Humana Press Inc.", "pagerange": "33-42", "id_number": "CaltechAUTHORS:20100514-100202108", "issn": "1539-2791", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100514-100202108", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Eli and Edythe Broad Foundation" }, { "agency": "NSF", "grant_number": "IOS-0825741" }, { "agency": "NIH", "grant_number": "RO1 MH043396" }, { "agency": "Burroughs Wellcome Fund" } ] }, "doi": "10.1007/s12021-010-9062-1", "pmcid": "PMC2841272", "primary_object": { "basename": "Wagenaar2010p9853Neuroinformatics.pdf", "url": "https://authors.library.caltech.edu/records/y3g4g-42354/files/Wagenaar2010p9853Neuroinformatics.pdf" }, "resource_type": "article", "pub_year": "2010", "author_list": "Wagenaar, Daniel A. and Kristan, Wiliam B., Jr." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/dscam-eeg20", "eprint_id": 5782, "eprint_status": "archive", "datestamp": "2023-08-22 07:02:30", "lastmod": "2023-10-23 17:37:07", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Pine-J", "name": { "family": "Pine", "given": "Jerome" } }, { "id": "Potter-S-M", "name": { "family": "Potter", "given": "Steve M." } } ] }, "title": "Searching for plasticity in dissociated cortical cultures on multi-electrode arrays", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 Wagenaar et al., licensee BioMed Central Ltd. \nThis is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nSubmission date 2 June 2006. Acceptance date 26 October 2006. Publication date 26 October 2006 \n\nWe thank our lab technician, Sheri McKinney. This work was partially supported by NINDS grants NS38628 (to SMP) and NS44134 (to JP), by NIBIB grant EB00786 (to SMP), by the Whitaker Foundation, and the Center for Behavioral Neuroscience. \n\nAuthors' contributions: DAW collected all data, performed the analysis, and prepared text and figures for the manuscript. JP and SMP contributed to the design of the study and to the preparation of the manuscript. \n\nThe authors declare that they have no competing interests.\n\nCorrection: searching for plasticity in dissociated cortical cultures on multi-electrode arrays\nDaniel A Wagenaar, Jerome Pine, and Steve M Potter\nJ Negat Results Biomed. 2007; 6: 3.doi: 10.1186/1477-5751-6-3\n\nPublished - WAGjnrb06.pdf
Erratum - art_3A10.1186_2F1477-5751-6-3.pdf
", "abstract": "We attempted to induce functional plasticity in dense cultures of cortical cells using stimulation through extracellular electrodes embedded in the culture dish substrate (multi-electrode arrays, or MEAs). We looked for plasticity expressed in changes in spontaneous burst patterns, and in array-wide response patterns to electrical stimuli, following several induction protocols related to those used in the literature, as well as some novel ones. Experiments were performed with spontaneous culture-wide bursting suppressed by either distributed electrical stimulation or by elevated extracellular magnesium concentrations as well as with spontaneous bursting untreated. Changes concomitant with induction were no larger in magnitude than changes that occurred spontaneously, except in one novel protocol in which spontaneous bursts were quieted using distributed electrical stimulation.", "date": "2006-10-26", "date_type": "published", "publication": "Journal of Negative Results in BioMedicine", "volume": "5", "publisher": "BioMed Central", "pagerange": "Art. No. 16", "id_number": "CaltechAUTHORS:WAGjnrb06", "issn": "1477-5751", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:WAGjnrb06", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "NS38628" }, { "agency": "NIH", "grant_number": "NS44134" }, { "agency": "NIH", "grant_number": "EB00786" }, { "agency": "Whitaker Foundation" }, { "agency": "Center for Behavioral Neuroscience" } ] }, "doi": "10.1186/1477-5751-5-16", "pmcid": "PMC1800351", "primary_object": { "basename": "WAGjnrb06.pdf", "url": "https://authors.library.caltech.edu/records/dscam-eeg20/files/WAGjnrb06.pdf" }, "related_objects": [ { "basename": "art_3A10.1186_2F1477-5751-6-3.pdf", "url": "https://authors.library.caltech.edu/records/dscam-eeg20/files/art_3A10.1186_2F1477-5751-6-3.pdf" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Wagenaar, Daniel A.; Pine, Jerome; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/1dtz8-e5h52", "eprint_id": 3670, "eprint_status": "archive", "datestamp": "2023-08-22 05:34:31", "lastmod": "2023-10-16 16:05:37", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "N\u00e1dasdy-Z", "name": { "family": "N\u00e1dasdy", "given": "Zoltan" } }, { "id": "Potter-S-M", "name": { "family": "Potter", "given": "Steve M." } } ] }, "title": "Persistent dynamic attractors in activity patterns of cultured neuronal networks", "ispublished": "pub", "full_text_status": "public", "keywords": "neurophysiology; bioelectric phenomena; neural nets; spatiotemporal phenomena; oscillations", "note": "\u00a92006 The American Physical Society \n\n(Received 31 January 2006; published 11 May 2006) \n\nWe thank Jerry Pine for useful discussions, and Sheri McKinney for technical assistance with cell culture. This work was partially supported by Grants Nos. NS38628 and NS44134 from NINDS, and EB00786 from NIBIB, and by the Whitaker Foundation and the NSF Center for Behavioral Neuroscience.\n\nPublished - WAGpre06.pdf
Supplemental Material - WAGpre06Movie1.mov
Supplemental Material - WAGpre06README.txt
", "abstract": "Three remarkable features of the nervous system\u2014complex spatiotemporal patterns, oscillations, and persistent activity\u2014are fundamental to such diverse functions as stereotypical motor behavior, working memory, and awareness. Here we report that cultured cortical networks spontaneously generate a hierarchical structure of periodic activity with a strongly stereotyped population-wide spatiotemporal structure demonstrating all three fundamental properties in a recurring pattern. During these \"superbursts,\" the firing sequence of the culture periodically converges to a dynamic attractor orbit. Precursors of oscillations and persistent activity have previously been reported as intrinsic properties of the neurons. However, complex spatiotemporal patterns that are coordinated in a large population of neurons and persist over several hours\u2014and thus are capable of representing and preserving information\u2014cannot be explained by known oscillatory properties of isolated neurons. Instead, the complexity of the observed spatiotemporal patterns implies large-scale self-organization of neurons interacting in a precise temporal order even in vitro, in cultures usually considered to have random connectivity.", "date": "2006-05", "date_type": "published", "publication": "Physical Review E", "volume": "73", "number": "5", "publisher": "American Physical Society", "pagerange": "Art. No. 051907", "id_number": "CaltechAUTHORS:WAGpre06", "issn": "1539-3755", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:WAGpre06", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH-NINDS", "grant_number": "NS38628" }, { "agency": "NIH-NINDS", "grant_number": "NS44134" }, { "agency": "NIBIB", "grant_number": "EB00786" }, { "agency": "Whitaker Foundation" }, { "agency": "NSF" } ] }, "doi": "10.1103/PhysRevE.73.051907", "pmcid": "PMC2570189", "primary_object": { "basename": "WAGpre06.pdf", "url": "https://authors.library.caltech.edu/records/1dtz8-e5h52/files/WAGpre06.pdf" }, "related_objects": [ { "basename": "WAGpre06Movie1.mov", "url": "https://authors.library.caltech.edu/records/1dtz8-e5h52/files/WAGpre06Movie1.mov" }, { "basename": "WAGpre06README.txt", "url": "https://authors.library.caltech.edu/records/1dtz8-e5h52/files/WAGpre06README.txt" } ], "resource_type": "article", "pub_year": "2006", "author_list": "Wagenaar, Daniel A.; N\u00e1dasdy, Zoltan; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/s7m4b-tf846", "eprint_id": 1628, "eprint_status": "archive", "datestamp": "2023-08-22 05:08:15", "lastmod": "2023-10-13 22:54:40", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Pine-J", "name": { "family": "Pine", "given": "Jerome" } }, { "id": "Potter-S-M", "name": { "family": "Potter", "given": "Steve M." } } ] }, "title": "An extremely rich repertoire of bursting patterns during the development of cortical cultures", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2006 Wagenaar et al., licensee BioMed Central Ltd. \nThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. \n\nSubmission date 1 Sep 2005; Acceptance date 7 Feb 2006; Publication date 7 Feb 2006 \n\nAuthors' contributions: DAW collected all data, performed the analysis, and prepared text and figures for the manuscript. JP contributed to the design of the study and to the preparation of the manuscript. SMP was instrumental to the conception of this study, helped interpret the results, and contributed to the preparation of the manuscript. \n\nAcknowledgments: We thank our lab technician, Sheri McKinney. This work was partially supported by NINDS grants NS38628 (to SMP) and NS44134 (to JP), by NIBIB grant EB00786 (to SMP), by the NSF Center for Behavioral Neuroscience, and by the Whitaker Foundation. \n\nAll raw data used for this report may be obtained from the web, at http://potterlab.bme.gatech.edu/development-data. Analogues of Figure 1 for each of the 58 cultures studied are available at the same location. Requests for access may be sent to Steve Potter (steve.potter@bme.gatech.edu)\n\nPublished - WAGbmcn06.pdf
", "abstract": "Background: We have collected a comprehensive set of multi-unit data on dissociated cortical cultures. Previous studies of the development of the electrical activity of dissociated cultures of cortical neurons each focused on limited aspects of its dynamics, and were often based on small numbers of observed cultures. We followed 58 cultures of different densities---3000 to 50,000 neurons on areas of 30 to 75 mm^2---growing on multi-electrode arrays (MEAs) during the first five weeks of their development. \n\nResults: Plating density had a profound effect on development. While the aggregate spike detection rate scaled linearly with density, as expected from the number of cells in proximity to electrodes, dense cultures started to exhibit bursting behavior earlier in development than sparser cultures. Analysis of responses to electrical stimulation suggests that axonal outgrowth likewise occurred faster in dense cultures. After two weeks, the network activity was dominated by population bursts in most cultures. In contrast to previous reports, development continued with changing burst patterns throughout the observation period. Burst patterns were extremely varied, with inter-burst intervals between 1 and 300 s, different amounts of temporal clustering of bursts, and different firing rate profiles during bursts. During certain stages of development bursts were organized into tight clusters with highly conserved internal structure. \n\nConclusions: Dissociated cultures of cortical cells exhibited a much richer repertoire of activity patterns than previously reported. Except for the very sparsest cultures, all cultures exhibited globally synchronized bursts, but bursting patterns changed over the course of development, and varied considerably between preparations. This emphasizes the importance of using multiple preparations---not just multiple cultures from one preparation---in any study involving neuronal cultures. These results are based on 963 half-hour-long recordings. To encourage further investigation of the rich range of behaviors exhibited by cortical cells in vitro, we are making the data available to other researchers, together with Matlab code to facilitate access.", "date": "2006-02-07", "date_type": "published", "publication": "BMC Neuroscience", "volume": "7", "publisher": "BioMed Central", "pagerange": "Art. No. 11", "id_number": "CaltechAUTHORS:WAGbmcn06", "issn": "1471-2202", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:WAGbmcn06", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1186/1471-2202-7-11", "pmcid": "PMC1420316", "primary_object": { "basename": "WAGbmcn06.pdf", "url": "https://authors.library.caltech.edu/records/s7m4b-tf846/files/WAGbmcn06.pdf" }, "resource_type": "article", "pub_year": "2006", "author_list": "Wagenaar, Daniel A.; Pine, Jerome; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/b0mw2-cwe70", "eprint_id": 102816, "eprint_status": "archive", "datestamp": "2023-08-22 04:35:37", "lastmod": "2023-10-20 00:31:31", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fonck-Carlos", "name": { "family": "Fonck", "given": "Carlos" } }, { "id": "Cohen-Bruce-N", "name": { "family": "Cohen", "given": "Bruce N." } }, { "id": "Nashmi-Raad", "name": { "family": "Nashmi", "given": "Raad" } }, { "id": "Whiteaker-Paul", "name": { "family": "Whiteaker", "given": "Paul" } }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Rodrigues-Pinguet-Nivalda-O", "name": { "family": "Rodrigues-Pinguet", "given": "Nivalda" } }, { "id": "Deshpande-Purnima", "name": { "family": "Deshpande", "given": "Purnima" } }, { "id": "McKinney-Sheri", "name": { "family": "McKinney", "given": "Sheri" } }, { "id": "Kwoh-Steven", "name": { "family": "Kwoh", "given": "Steven" } }, { "id": "Munoz-Jose", "name": { "family": "Munoz", "given": "Jose" } }, { "id": "Labarca-C-G", "name": { "family": "Labarca", "given": "Cesar" } }, { "id": "Collins-Allan-C", "name": { "family": "Collins", "given": "Allan C." } }, { "id": "Marks-Michael-J", "name": { "family": "Marks", "given": "Michael J." } }, { "id": "Lester-H-A", "name": { "family": "Lester", "given": "Henry A." }, "orcid": "0000-0002-5470-5255" } ] }, "title": "Novel Seizure Phenotype and Sleep Disruptions in Knock-In Mice with Hypersensitive \u03b14* Nicotinic Receptors", "ispublished": "pub", "full_text_status": "public", "keywords": "epilepsy; ADNFLE; nicotinic receptors; sleep disorders; \u03b14\u03b22; nicotine", "note": "\u00a9 2005 Society for Neuroscience. \n\nReceived Feb. 9, 2005; revised Oct. 18, 2005; accepted Oct. 21, 2005. \n\nThis work was supported by National Institute of Health Grants NS46464, NS43800, NS11756, DA10156, DA03194, and DA17279 and a National Institutes of Health\u2013National Research Service Award (C.F.). The California Tobacco-Related Disease Research Program and Philip Morris USA/International are gratefully acknowledged. We thank J. Stitzel for the mouse \u03b14 cDNA, Chana Simon for oocyte data analysis, Robert Paz for help with photography, and Sharon Grady, Andrew Tapper, and Johannes Schwarz for insightful discussion.\n\nPublished - 11396.full.pdf
", "abstract": "A leucine to alanine substitution (L9\u2032A) was introduced in the M2 region of the mouse \u03b14 neuronal nicotinic acetylcholine receptor (nAChR) subunit. Expressed in Xenopus oocytes, \u03b14(L9\u2032A)\u03b22 nAChRs were \u226530-fold more sensitive than wild type (WT) to both ACh and nicotine. We generated knock-in mice with the L9\u2032A mutation and studied their cellular responses, seizure phenotype, and sleep-wake cycle. Seizure studies on \u03b14-mutated animals are relevant to epilepsy research because all known mutations linked to autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE) occur in the M2 region of \u03b14or \u03b22 subunits. Thalamic cultures and synaptosomes from L9\u2032A mice were hypersensitive to nicotine-induced ion flux. L9\u2032A mice were \u223c15-fold more sensitive to seizures elicited by nicotine injection than their WT littermates. Seizures in L9\u2032A mice differed qualitatively from those in WT: L9\u2032A seizures started earlier, were prevented by nicotine pretreatment, lacked EEG spike-wave discharges, and consisted of fast repetitive movements. Nicotine-induced seizures in L9\u2032A mice were partial, whereas WT seizures were generalized. When L9\u2032A homozygous mice received a 10 mg/kg nicotine injection, there was temporal and phenomenological separation of mutant and WT-like seizures: an initial seizure \u223c20 s after injection was clonic and showed no EEG changes. A second seizure began 3-4 min after injection, was tonic-clonic, and had EEG spike-wave activity. No spontaneous seizures were detected in L9\u2032A mice during chronic video/EEG recordings, but their sleep-wake cycle was altered. Our findings show that hypersensitive \u03b14* nicotinic receptors in mice mediate changes in the sleep-wake cycle and nicotine-induced seizures resembling ADNFLE.", "date": "2005-12-07", "date_type": "published", "publication": "Journal of Neuroscience", "volume": "25", "number": "49", "publisher": "Society for Neuroscience", "pagerange": "11396-11411", "id_number": "CaltechAUTHORS:20200427-144703784", "issn": "0270-6474", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200427-144703784", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "NS46464" }, { "agency": "NIH", "grant_number": "NS43800" }, { "agency": "NIH", "grant_number": "NS11756" }, { "agency": "NIH", "grant_number": "DA10156" }, { "agency": "NIH", "grant_number": "DA03194" }, { "agency": "NIH", "grant_number": "DA17279" }, { "agency": "NIH Predoctoral Fellowship" }, { "agency": "California Tobacco-Related Disease Research Program" }, { "agency": "Philip Morris USA/International" } ] }, "doi": "10.1523/jneurosci.3597-05.2005", "pmcid": "PMC6725918", "primary_object": { "basename": "11396.full.pdf", "url": "https://authors.library.caltech.edu/records/b0mw2-cwe70/files/11396.full.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Fonck, Carlos; Cohen, Bruce N.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/3zb2s-2mk87", "eprint_id": 102015, "eprint_status": "archive", "datestamp": "2023-08-22 04:08:05", "lastmod": "2023-10-19 23:44:47", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chao-Zenas-C", "name": { "family": "Chao", "given": "Zenas C." } }, { "id": "Bakkum-D-J", "name": { "family": "Bakkum", "given": "Douglas J." } }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Potter-S-M", "name": { "family": "Potter", "given": "Steve M." } } ] }, "title": "Effects of Random External Background Stimulation on Network Synaptic Stability After Tetanization: A Modeling Study", "ispublished": "pub", "full_text_status": "public", "keywords": "Cultured neural network; spike-timing-dependent plasticity (STDP); frequency-dependent depression; multi-electrode array (MEA); spatio-temporal dynamics; tetanization; model; plasticity; cortex; bursting; population coding", "note": "\u00a9 2005 Humana Press Inc. \n\nIssue Date: September 2005. \n\nThis work was partially supported by grants NS38628 from NIH/NINDS, and EB000786 from NIH/NIBIB, and by the Whitaker Foundation and the NSF Center for Behavioral Neuroscience. We thank Radhika Madhavan, Sheri McKinney and Eno Ekong for technical assistance.\n\nAccepted Version - nihms50042.pdf
", "abstract": "We constructed a simulated spiking neural network model to investigate the effects of random background stimulation on the dynamics of network activity patterns and tetanus induced network plasticity. The simulated model was a \"leaky integrate-and-fire\" (LIF) neural model with spike-timing-dependent plasticity (STDP) and frequency-dependent synaptic depression. Spontaneous and evoked activity patterns were compared with those of living neuronal networks cultured on multielectrode arrays. To help visualize activity patterns and plasticity in our simulated model, we introduced new population measures called Center of Activity (CA) and Center of Weights (CW) to describe the spatio-temporal dynamics of network-wide firing activity and network-wide synaptic strength, respectively. Without random background stimulation, the network synaptic weights were unstable and often drifted after tetanization. In contrast, with random background stimulation, the network synaptic weights remained close to their values immediately after tetanization. The simulation suggests that the effects of tetanization on network synaptic weights were difficult to control because of ongoing synchronized spontaneous bursts of action potentials, or \"barrages.\" Random background stimulation helped maintain network synaptic stability after tetanization by reducing the number and thus the influence of spontaneous barrages. We used our simulated network to model the interaction between ongoing neural activity, external stimulation and plasticity, and to guide our choice of sensory-motor mappings for adaptive behavior in hybrid neural-robotic systems or \"hybrots.\"", "date": "2005-09", "date_type": "published", "publication": "Neuroinformatics", "volume": "3", "number": "3", "publisher": "Springer", "pagerange": "263-280", "id_number": "CaltechAUTHORS:20200320-082655455", "issn": "1539-2791", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200320-082655455", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "NS38628" }, { "agency": "NIH", "grant_number": "EB000786" }, { "agency": "Whitaker Foundation" }, { "agency": "NSF" } ] }, "doi": "10.1385/ni:3:3:263", "pmcid": "PMC2584804", "primary_object": { "basename": "nihms50042.pdf", "url": "https://authors.library.caltech.edu/records/3zb2s-2mk87/files/nihms50042.pdf" }, "resource_type": "article", "pub_year": "2005", "author_list": "Chao, Zenas C.; Bakkum, Douglas J.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/qs8ft-f1r70", "eprint_id": 25142, "eprint_status": "archive", "datestamp": "2023-08-19 15:24:29", "lastmod": "2024-01-13 05:23:10", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel" }, "orcid": "0000-0002-6222-761X" }, { "id": "DeMarse-T-B", "name": { "family": "DeMarse", "given": "Thomas B." } }, { "id": "Potter-S-M", "name": { "family": "Potter", "given": "Steve M." } } ] }, "title": "MeaBench: A toolset for multi-electrode data acquisition and on-line analysis", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2005 IEEE. Issue Date: 16-19 March 2005. Date of Current Version: 18 April 2005. This work was partially supported by grants NS044134 and NS38628 from NIH-NINDS, and EB000786 from NIH-NIBIB, and by the Burroughs-Wellcome Fund and the Whitaker Foundation. We thank Jerry Pine for many useful discussions, and Sheri McKinney for assistance with animal handling and culture preparation.\n\nPublished - 01419673.pdf
Published - WAGembsne05.pdf
", "abstract": "We present a software suite, MeaBench, for data acquisition and online analysis of multi-electrode recordings, especially from micro-electrode arrays. Besides controlling data acquisition hardware, MeaBench includes algorithms for real-time stimulation artifact suppression and spike detection, as well as programs for online display of voltage traces from 60 electrodes and continuously updated spike raster plots. MeaBench features real-time output streaming, allowing easy integration with stimulator systems. We have been able to generate stimulation sequences in response to live neuronal activity with less than 20 ms lag time. MeaBench is open-source software, and is available for free public download at http://www.its.caltech.edu/~pinelab/wagenaar/meabench.html.", "date": "2005-03", "date_type": "published", "publisher": "IEEE", "place_of_pub": "Piscataway, NJ", "pagerange": "518-521", "id_number": "CaltechAUTHORS:20110829-103001358", "isbn": "0-7803-8709-0", "book_title": "Proceedings of the 2nd International IEEE EBMS Conference on Neural Engineering", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110829-103001358", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH-NINDS", "grant_number": "NS044134" }, { "agency": "NIH-NINDS", "grant_number": "NS38628" }, { "agency": "NIH-NIBIB", "grant_number": "EB000786" }, { "agency": "Burroughs-Wellcome Fund" }, { "agency": "Whitaker Foundation" } ] }, "other_numbering_system": { "items": [ { "id": "8521339", "name": "INSPEC Accession Number" } ] }, "doi": "10.1109/CNE.2005.1419673", "primary_object": { "basename": "01419673.pdf", "url": "https://authors.library.caltech.edu/records/qs8ft-f1r70/files/01419673.pdf" }, "related_objects": [ { "basename": "WAGembsne05.pdf", "url": "https://authors.library.caltech.edu/records/qs8ft-f1r70/files/WAGembsne05.pdf" } ], "resource_type": "book_section", "pub_year": "2005", "author_list": "Wagenaar, Daniel; DeMarse, Thomas B.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/mpy4y-t6g31", "eprint_id": 25243, "eprint_status": "archive", "datestamp": "2023-08-19 13:09:38", "lastmod": "2023-10-24 15:43:54", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Potter-S-M", "name": { "family": "Potter", "given": "Steve M." } } ] }, "title": "A versatile all-channel stimulator for electrode arrays, with real-time control", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2004 IOP Publishing Ltd. Received 19 January 2004;\nAccepted for publication 19 February 2004; Published 15 March 2004.\n\nThis work was partially supported by grants NS044134\nand NS38628 from NIH/NINDS, and EB000786 from\nNIH/NIBIB, and by the Whitaker Foundation and the NSF\nCenter for Behavioral Neuroscience. We thank Jerry Pine and\nThomas DeMarse for useful conversations about many design\nissues.\n\nPublished - WAGjne04.pdf
Accepted Version - nihms-50046.pdf
", "abstract": "Over the last few decades, technology to record through ever increasing numbers of electrodes has become available to electrophysiologists. For the study of distributed neural processing, however, the ability to stimulate through equal numbers of electrodes, and thus to attain bidirectional communication, is of paramount importance. Here, we present a stimulation system for multi-electrode arrays which interfaces with existing commercial recording hardware, and allows stimulation through any electrode in the array, with rapid switching between channels. The system is controlled through real-time Linux, making it extremely flexible: stimulation sequences can be constructed on-the-fly, and arbitrary stimulus waveforms can be used if desired. A key feature of this design is that it can be readily and inexpensively reproduced in other labs, since it interfaces to standard PC parallel ports and uses only off-the-shelf components. Moreover, adaptation for use with in vivo multi-electrode probes would be straightforward. In combination with our freely available data-acquisition software, MeaBench, this system can provide feedback stimulation in response to recorded action potentials within 15 ms.", "date": "2004-03", "date_type": "published", "publication": "Journal of Neural Engineering", "volume": "1", "number": "1", "publisher": "IOP", "pagerange": "39-45", "id_number": "CaltechAUTHORS:20110907-093554097", "issn": "1741-2560", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110907-093554097", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH-NINDS", "grant_number": "NS044134" }, { "agency": "NIH-NINDS", "grant_number": "NS38628" }, { "agency": "NIH-NIBIB", "grant_number": "EB000786" }, { "agency": "Whitaker Foundation" }, { "agency": "NSF" } ] }, "doi": "10.1088/1741-2560/1/1/006", "pmcid": "PMC2570177", "primary_object": { "basename": "WAGjne04.pdf", "url": "https://authors.library.caltech.edu/records/mpy4y-t6g31/files/WAGjne04.pdf" }, "related_objects": [ { "basename": "nihms-50046.pdf", "url": "https://authors.library.caltech.edu/records/mpy4y-t6g31/files/nihms-50046.pdf" } ], "resource_type": "article", "pub_year": "2004", "author_list": "Wagenaar, Daniel A. and Potter, Steve M." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/7hqm2-g3890", "eprint_id": 13485, "eprint_status": "archive", "datestamp": "2023-08-19 13:09:09", "lastmod": "2023-10-17 23:56:00", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Adami-Christoph-C", "name": { "family": "Adami", "given": "Christoph" }, "orcid": "0000-0002-2915-9504" } ] }, "title": "Influence of chance, history, and adaptation on digital evolution", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2004 Massachusetts Institute of Technology.\nPosted Online March 11, 2006.\nD.A.W. wishes to thank Justin Smith for useful discussions. This material is based upon\nwork supported by the NSF under Award No. DEB-9981397.\n\nPublished - WAGal04.pdf
", "abstract": "We evolved multiple clones of populations of digital organisms to study the effects of chance, history, and adaptation in evolution. We show that clones adapted to a specific environment can adapt to new environments quickly and efficiently, although their history remains a significant factor in their fitness. Adaptation is most significant (and the effects of history less so) if the old and new environments are dissimilar. For more similar environments, adaptation is slower while history is more prominent. For both similar and dissimilar transfer environments, populations quickly lose the ability to perform computations (the analogue of beneficial chemical reactions) that are no longer rewarded in the new environment. Populations that developed few computational \"genes\" in their original environment were unable to acquire them in the new environment.", "date": "2004-03", "date_type": "published", "publication": "Artificial Life", "volume": "10", "number": "2", "publisher": "MIT Press", "pagerange": "181-190", "id_number": "CaltechAUTHORS:WAGal04", "issn": "1064-5462", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:WAGal04", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "DEB-9981397" } ] }, "doi": "10.1162/106454604773563603", "primary_object": { "basename": "WAGal04.pdf", "url": "https://authors.library.caltech.edu/records/7hqm2-g3890/files/WAGal04.pdf" }, "resource_type": "article", "pub_year": "2004", "author_list": "Wagenaar, Daniel A. and Adami, Christoph" }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/5wsh0-69f13", "eprint_id": 27336, "eprint_status": "archive", "datestamp": "2023-08-22 00:50:58", "lastmod": "2024-01-13 05:43:55", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Potter-S-M", "name": { "family": "Potter", "given": "Steven M." } }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Madhavan-R", "name": { "family": "Madhavan", "given": "Radhika" } }, { "id": "DeMarse-T-B", "name": { "family": "DeMarse", "given": "Thomas B." } } ] }, "title": "Long-Term Bidirectional Neuron Interfaces for Robotic Control, and In Vitro Learning Studies", "ispublished": "unpub", "full_text_status": "public", "keywords": "MEA; rat; mouse; cortex; multi-electrode array; hybrot; animat; voltage-sensitive dye; 2-photon microscopy; culture networks", "note": "\u00a9 2003 IEEE.\n\nIssue Date: 17-21 Sept. 2003; Date of Current Version: 05 April 2004.\n\nMuch of the work was carried out with help and support from Prof. Jerome Pine and Prof. Scott E. Fraser at Caltech.\n\nPublished - POTembs03.pdf
", "abstract": "There are two fundamentally different goals for neural interfacing. On the biology side, to interface living neurons to external electronics allows the observation and manipulation of neural circuits to elucidate their fundamental mechanisms. On the engineering side, neural interfaces in animals, people, or in cell culture have the potential to restore missing functionality, or someday, to enhance existing functionality. At the Laboratory for NeuroEngineering at Georgia Tech, we are developing new technologies to help make both goals attainable. We culture dissociated mammalian neurons on multi-electrode arrays, and use them as the brain of a 'Hybrot', or hybrid neural-robotic system. Distributed neural activity patterns are used to control mobile robots. We have created the hardware and software necessary to feed the robots' sensory inputs back to the cultures in real time, as electrical stimuli. By embodying cultured networks, we study learning and memory at the cellular and network level, using 2-photon laser-scanning microscopy to image plasticity while it happens. We have observed a very rich dynamical landscape of activity patterns in networks of only a few thousand cells. We can alter this landscape via electrical stimuli, and use the hybrot system to study the emergent properties of networks in vitro.", "date": "2003-09", "date_type": "published", "publisher": "IEEE", "place_of_pub": "Piscataway, NJ", "pagerange": "3690-3693", "id_number": "CaltechAUTHORS:20111020-154335843", "isbn": "0-7803-7789-3", "book_title": "Proceedings of the 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111020-154335843", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "other_numbering_system": { "items": [ { "id": "7954464", "name": "INSPEC Accession Number" } ] }, "doi": "10.1109/IEMBS.2003.1280959", "primary_object": { "basename": "POTembs03.pdf", "url": "https://authors.library.caltech.edu/records/5wsh0-69f13/files/POTembs03.pdf" }, "resource_type": "book_section", "pub_year": "2003", "author_list": "Potter, Steven M.; Wagenaar, Daniel A.; et el." }, { "id": "https://authors.library.caltech.eduhttps://authors.library.caltech.edu/records/jjvm8-6ek69", "eprint_id": 72364, "eprint_status": "archive", "datestamp": "2023-08-21 22:40:49", "lastmod": "2023-10-23 22:30:02", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "DeMarse-T-B", "name": { "family": "DeMarse", "given": "Thomas B." } }, { "id": "Wagenaar-D-A", "name": { "family": "Wagenaar", "given": "Daniel A." }, "orcid": "0000-0002-6222-761X" }, { "id": "Blau-A-W", "name": { "family": "Blau", "given": "Axel W." } }, { "id": "Potter-S-M", "name": { "family": "Potter", "given": "Steve M." } } ] }, "title": "The Neurally Controlled Animat: Biological Brains Acting with Simulated Bodies", "ispublished": "pub", "full_text_status": "public", "keywords": "MEA; multi-electrode arrays; rat cortex; prosthetics; hybrid system cybernetics", "note": "\u00a9 2001 Kluwer Academic Publishers. \n\nWe thank C. Michael Atkin, Gray Rybka, and Samuel Thompson for early programming on the Animat and neural interface and MultiChannel Systems (http://www.multichannelsystems.com) for their gracious technical support; Sami Barghshoon and Sheri McKinney for help with cell culture; Jerome Pine and Scott E. Fraser for support, advice, and infrastructure; and Mary Flowers, Shannan Boss, and Vanna Santoro for ordering and lab management. This research was supported by a grant from the National Institute of Neurological Disorders and Stroke, RO1 NS38628 (SMP) and by the Burroughs-Wellcome/Caltech Computational Molecular Biology fund (DAW).\n\nAccepted Version - nihms48715.pdf
", "abstract": "The brain is perhaps the most advanced and robust computation system known. We are creating a method to study how information is processed and encoded in living cultured neuronal networks by interfacing them to a computer-generated animal, the Neurally-Controlled Animat, within a virtual world. Cortical neurons from rats are dissociated and cultured on a surface containing a grid of electrodes (multi-electrode arrays, or MEAs) capable of both recording and stimulating neural activity. Distributed patterns of neural activity are used to control the behavior of the Animat in a simulated environment. The computer acts as its sensory system providing electrical feedback to the network about the Animat's movement within its environment. Changes in the Animat's behavior due to interaction with its surroundings are studied in concert with the biological processes (e.g., neural plasticity) that produced those changes, to understand how information is processed and encoded within a living neural network. Thus, we have created a hybrid real-time processing engine and control system that consists of living, electronic, and simulated components. Eventually this approach may be applied to controlling robotic devices, or lead to better real-time silicon-based information processing and control algorithms that are fault tolerant and can repair themselves.", "date": "2001-11", "date_type": "published", "publication": "Autonomous Robots", "volume": "11", "number": "3", "publisher": "Kluwer Academic Publishers", "pagerange": "305-310", "id_number": "CaltechAUTHORS:20161129-085404424", "issn": "0929-5593", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161129-085404424", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "RO1 NS38628" }, { "agency": "Caltech Burroughs-Wellcome Center for Computational Molecular Biology" }, { "agency": "National Institute of Neurological Disorders and Stroke (NINDS)" } ] }, "doi": "10.1023/A:1012407611130", "pmcid": "PMC2440704", "primary_object": { "basename": "nihms48715.pdf", "url": "https://authors.library.caltech.edu/records/jjvm8-6ek69/files/nihms48715.pdf" }, "resource_type": "article", "pub_year": "2001", "author_list": "DeMarse, Thomas B.; Wagenaar, Daniel A.; et el." } ]