Machine learning of dissection photographs and surface scanning for quantitative 3D neuropathology

Autor: Harshvardhan Gazula, Henry FJ Tregidgo, Benjamin Billot, Yael Balbastre, Jonathan Williams-Ramirez, Rogeny Herisse, Lucas J Deden-Binder, Adria Casamitjana, Erica J Melief, Caitlin S Latimer, Mitchell D Kilgore, Mark Montine, Eleanor Robinson, Emily Blackburn, Michael S Marshall, Theresa R Connors, Derek H Oakley, Matthew P Frosch, Sean I Young, Koen Van Leemput, Adrian V Dalca, Bruce Fischl, Christine L MacDonald, C Dirk Keene, Bradley T Hyman, Juan E Iglesias

Publikováno v: eLife, Vol 12 (2024)

We present open-source tools for three-dimensional (3D) analysis of photographs of dissected slices of human brains, which are routinely acquired in brain banks but seldom used for quantitative analysis. Our tools can: (1) 3D reconstruct a volume fro

Externí odkaz: https://doaj.org/article/bee5031ed3ac4569bd31db0c5630fc96

The Delayed Neuropathological Consequences of Traumatic Brain Injury in a Community-Based Sample

Autor: Nadia Postupna, Shannon E. Rose, Laura E. Gibbons, Natalie M. Coleman, Leanne L. Hellstern, Kayla Ritchie, Angela M. Wilson, Eiron Cudaback, Xianwu Li, Erica J. Melief, Allison E. Beller, Jeremy A. Miller, Amber L. Nolan, Desiree A. Marshall, Rod Walker, Thomas J. Montine, Eric B. Larson, Paul K. Crane, Richard G. Ellenbogen, Edward S. Lein, Kristen Dams-O'Connor, C. Dirk Keene

Publikováno v: Frontiers in Neurology, Vol 12 (2021)

The late neuropathological effects of traumatic brain injury have yet to be fully elucidated, particularly with respect to community-based cohorts. To contribute to this critical gap in knowledge, we designed a multimodal neuropathological study, int

Externí odkaz: https://doaj.org/article/9d4ce0378ae94ea494bf39044a1146f3

Human neocortical expansion involves glutamatergic neuron diversification

Autor: Tim S. Heistek, Thomas Braun, Natalia A. Goriounova, Michael Tieu, Lindsay Ng, Michael Hawrylycz, Kris Bickley, Anton Arkhipov, Colin Farrell, Trangthanh Pham, Alexandra Glandon, Daniel Park, Gábor Molnár, Herman Tung, Allan R. Jones, Lisa Keene, Gáspár Oláh, Thomas Chartrand, Amy Torkelson, Jae Geun Yoon, Rachel A. Dalley, Aaron Szafer, Nick Dee, Brian E. Kalmbach, Eliza Barkan, Allison Beller, Krissy Brouner, Andrew L. Ko, Alex M. Henry, Viktor Szemenyei, Julie Nyhus, Staci A. Sorensen, Samuel Dingman Lee, Norbert Mihut, Amy Bernard, Lisa Kim, Anatoly Buchin, Melissa Gorham, Lucas T. Graybuck, Lydia Potekhina, Katelyn Ward, Caitlin S. Latimer, Aaron Oldre, Gabe J. Murphy, Boaz P. Levi, Trygve E. Bakken, René Wilbers, Jonathan T. Ting, Kimberly A. Smith, Amanda Gary, Songlin Ding, Alice Mukora, Matthew Kroll, Anoop P. Patel, Wayne Wakeman, Hongkui Zeng, Nadezhda Dotson, Rusty Mann, Victoria Omstead, Leona Mezei, Desiree A. Marshall, Shea Ransford, Lydia Ng, Sara Kebede, Gábor Tamás, Jeffrey G. Ojemann, Stephanie Mok, Nathan Hansen, Christina A. Pom, Brian Lee, Jim Berg, Ramkumar Rajanbabu, John W. Phillips, Philip R. Nicovich, Matthew Mallory, Richard G. Ellenbogen, Rachel Enstrom, Luke Esposito, Tim Jarsky, Di Jon Hill, Idan Segev, Darren Bertagnolli, Agata Budzillo, Sander Idema, Daniel L. Silbergeld, Costas A. Anastassiou, Chris Hill, Michelle Maxwell, Mean Hwan Kim, Charles Cobbs, Delissa McMillen, Bosiljka Tasic, Olivia Fong, Medea McGraw, Hong Gu, Kirsten Crichton, David Reid, Kristen Hadley, Lauren Alfiler, Manuel Ferreira, Elliot R. Thomsen, Kiet Ngo, Josef Sulc, Augustin Ruiz, Katherine Baker, Zizhen Yao, Erica J. Melief, Femke Waleboer, Hanchuan Peng, Grace Williams, Rebecca D. Hodge, Kyla Berry, Katherine E. Link, David Sandman, Tsega Desta, Christine Rimorin, Jeff Goldy, Ryder P. Gwinn, Djai B. Heyer, Changkyu Lee, Jeremy A. Miller, Nathan W. Gouwens, Pál Barzó, Attila Ozsvár, Huibert D. Mansvelder, Sergey L. Gratiy, Rafael Yuste, David Feng, Jessica Trinh, Clare Gamlin, Tamara Casper, C. Dirk Keene, Susan M. Sunkin, Tom Egdorf, Philip C. De Witt Hamer, Rebecca de Frates, Peter Chong, Szabina Furdan, Patrick R. Hof, Jasmine Bomben, Christiaan P. J. de Kock, Eline J. Mertens, Ed S. Lein, Anna A. Galakhova, Florence D’Orazi, Christof Koch, Madie Hupp

Publikováno v: Berg, J, Sorensen, S A, Ting, J T, Miller, J A, Chartrand, T, Buchin, A, Bakken, T E, Budzillo, A, Dee, N, Ding, S L, Gouwens, N W, Hodge, R D, Kalmbach, B, Lee, C, Lee, B R, Alfiler, L, Baker, K, Barkan, E, Beller, A, Berry, K, Bertagnolli, D, Bickley, K, Bomben, J, Braun, T, Brouner, K, Casper, T, Chong, P, Crichton, K, Dalley, R, de Frates, R, Desta, T, Lee, S D, D’Orazi, F, Dotson, N, Egdorf, T, Enstrom, R, Farrell, C, Feng, D, Fong, O, Furdan, S, Galakhova, A A, Gamlin, C, Gary, A, Glandon, A, Goldy, J, Gorham, M, Goriounova, N A, Gratiy, S, Graybuck, L, Gu, H, Hadley, K, Hansen, N, Heistek, T S, Henry, A M, Heyer, D B, Hill, D J, Hill, C, Hupp, M, Jarsky, T, Kebede, S, Keene, L, Kim, L, Kim, M H, Kroll, M, Latimer, C, Levi, B P, Link, K E, Mallory, M, Mann, R, Marshall, D, Maxwell, M, McGraw, M, McMillen, D, Melief, E, Mertens, E J, Mezei, L, Mihut, N, Mok, S, Molnar, G, Mukora, A, Ng, L, Ngo, K, Nicovich, P R, Nyhus, J, Olah, G, Oldre, A, Omstead, V, Ozsvar, A, Park, D, Peng, H, Pham, T, Pom, C A, Potekhina, L, Rajanbabu, R, Ransford, S, Reid, D, Rimorin, C, Ruiz, A, Sandman, D, Sulc, J, Sunkin, S M, Szafer, A, Szemenyei, V, Thomsen, E R, Tieu, M, Torkelson, A, Trinh, J, Tung, H, Wakeman, W, Waleboer, F, Ward, K, Wilbers, R, Williams, G, Yao, Z, Yoon, J G, Anastassiou, C, Arkhipov, A, Barzo, P, Bernard, A, Cobbs, C, de Witt Hamer, P C, Ellenbogen, R G, Esposito, L, Ferreira, M, Gwinn, R P, Hawrylycz, M J, Hof, P R, Idema, S, Jones, A R, Keene, C D, Ko, A L, Murphy, G J, Ng, L, Ojemann, J G, Patel, A P, Phillips, J W, Silbergeld, D L, Smith, K, Tasic, B, Yuste, R, Segev, I, de Kock, C P J, Mansvelder, H D, Tamas, G, Zeng, H, Koch, C & Lein, E S 2021, ' Human neocortical expansion involves glutamatergic neuron diversification ', Nature, vol. 598, no. 7879, pp. 151-158 . https://doi.org/10.1038/s41586-021-03813-8
Nature, 598(7879), 151-158. Nature Publishing Group
Nature
Nature, Vol. 598, No. 7879
Berg, J, Sorensen, S A, Ting, J T, Miller, J A, Chartrand, T, Buchin, A, Bakken, T E, Budzillo, A, Dee, N, Ding, S-L, Gouwens, N W, Hodge, R D, Kalmbach, B, Lee, C, Lee, B R, Alfiler, L, Baker, K, Barkan, E, Beller, A, Berry, K, Bertagnolli, D, Bickley, K, Bomben, J, Braun, T, Brouner, K, Casper, T, Chong, P, Crichton, K, Dalley, R, de Frates, R, Desta, T, Lee, S D, D’Orazi, F, Dotson, N, Egdorf, T, Enstrom, R, Farrell, C, Feng, D, Fong, O, Furdan, S, Galakhova, A A, Gamlin, C, Gary, A, Glandon, A, Goldy, J, Gorham, M, Goriounova, N A, Gratiy, S, Graybuck, L, Gu, H, Hadley, K, Hansen, N, Heistek, T S, Henry, A M, Heyer, D B, Hill, D, Hill, C, Hupp, M, Jarsky, T, Kebede, S, Keene, L, Kim, L, Kim, M-H, Kroll, M, Latimer, C, Levi, B P, Link, K E, Mallory, M, Mann, R, Marshall, D, Maxwell, M, McGraw, M, McMillen, D, Melief, E, Mertens, E J, Mezei, L, Mihut, N, Mok, S, Molnar, G, Mukora, A, Ng, L, Ngo, K, Nicovich, P R, Nyhus, J, Olah, G, Oldre, A, Omstead, V, Ozsvar, A, Park, D, Peng, H, Pham, T, Pom, C A, Potekhina, L, Rajanbabu, R, Ransford, S, Reid, D, Rimorin, C, Ruiz, A, Sandman, D, Sulc, J, Sunkin, S M, Szafer, A, Szemenyei, V, Thomsen, E R, Tieu, M, Torkelson, A, Trinh, J, Tung, H, Wakeman, W, Waleboer, F, Ward, K, Wilbers, R, Williams, G, Yao, Z, Yoon, J-G, Anastassiou, C, Arkhipov, A, Barzo, P, Bernard, A, Cobbs, C, de Witt Hamer, P C, Ellenbogen, R G, Esposito, L, Ferreira, M, Gwinn, R P, Hawrylycz, M J, Hof, P R, Idema, S, Jones, A R, Keene, C D, Ko, A L, Murphy, G J, Ng, L, Ojemann, J G, Patel, A P, Phillips, J W, Silbergeld, D L, Smith, K, Tasic, B, Yuste, R, Segev, I, de Kock, C P J, Mansvelder, H D, Tamas, G, Zeng, H, Koch, C & Lein, E S 2021, ' Human neocortical expansion involves glutamatergic neuron diversification ', Nature, vol. 598, no. 7879, pp. 151-158 . https://doi.org/10.1038/s41586-021-03813-8

The neocortex is disproportionately expanded in human compared with mouse1,2, both in its total volume relative to subcortical structures and in the proportion occupied by supragranular layers composed of neurons that selectively make connections wit

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8c41f5015a297892f279cb761e2d9f21
https://hdl.handle.net/1871.1/df908a46-b182-41b3-b732-326dddbab23b

Protocol for the Systematic Fixation, Circuit-Based Sampling, and Qualitative and Quantitative Neuropathological Analysis of Human Brain Tissue

Autor: Caitlin S. Latimer, Erica J. Melief, Jeanelle Ariza-Torres, Kim Howard, Amanda R. Keen, Lisa M. Keene, Aimee M. Schantz, Trevor M. Sytsma, Angela M. Wilson, Thomas J. Grabowski, Martin Darvas, Kristen Dams O’Connor, Amber L. Nolan, Brian L. Edlow, Christine L. Mac Donald, C. Dirk Keene

Publikováno v: Methods in Molecular Biology ISBN: 9781071626542

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::2fce82b12fa41a730d1f89b7e3bba607
https://doi.org/10.1007/978-1-0716-2655-9_1

Signature morpho-electric properties of diverse GABAergic interneurons in the human neocortex

Autor: Brian Lee, Rachel Dalley, Jeremy A Miller, Thomas Chartrand, Jennie Close, Rusty Mann, Alice Mukora, Lindsay Ng, Lauren Alfiler, Katherine Baker, Darren Bertagnolli, Krissy Brouner, Tamara Casper, Eva Csajbok, Nick Dee, Nicholas Donadio, Stan L.W. Driessens, Tom Egdorf, Rachel Enstrom, Anna A Galakhova, Amanda Gary, Emily Gelfand, Jeff Goldy, Kristen Hadley, Tim S. Heistek, Dijon Hill, Nelson Johansen, Nik Jorstad, Lisa Kim, Agnes Katalin Kocsis, Lauren Kruse, Michael Kunst, Gabriela Leon, Brian Long, Matthew Mallory, Michelle Maxwell, Medea McGraw, Delissa McMillen, Erica J Melief, Gabor Molnar, Marty T Mortrud, Dakota Newman, Julie Nyhus, Ximena Opitz-Araya, Trangthanh Pham, Alice Pom, Lydia Potekhina, Ram Rajanbabu, Augustin Ruiz, Susan M Sunkin, Ildiko Szots, Naz Taskin, Bargavi Thyagarajan, Michael Tieu, Jessica Trinh, Sara Vargas, David Vumbaco, Femke Waleboer, Natalie Weed, Grace Williams, Julia Wilson, Shenqin Yao, Thomas Zhou, Pal Barzo, Trygve Bakken, Charles Cobbs, Richard G. Ellenbogen, Luke Esposito, Manuel Ferreira, Nathan W Gouwens, Benjamin Grannan, Ryder P. Gwinn, Jason S. Hauptman, Rebecca Hodge, Tim Jarsky, C.Dirk Keene, Andrew L. Ko, Boaz Levi, Jeffrey G. Ojemann, Anoop Patel, Jacob Ruzevick, Daniel L. Silbergeld, Kim Smith, Jack Waters, Hongkui Zeng, Jim Berg, Natalia A. Goriounova, Brian Kalmbach, Christiaan P.J. de Kock, Huib D Mansvelder, Staci A Sorensen, Gabor Tamas, Ed S. Lein, Jonathan T Ting

Human cortical interneurons have been challenging to study due to high diversity and lack of mature brain tissue platforms and genetic targeting tools. We employed rapid GABAergic neuron viral labeling plus unbiased Patch-seq sampling in brain slices

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::8e3b2ea84d0322f928f32322290e8a03
https://doi.org/10.1101/2022.11.08.515739