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51. Author Correction: A consensus protocol for functional connectivity analysis in the rat brain (Nature Neuroscience, (2023), 26, 4, (673-681), 10.1038/s41593-023-01286-8)

Author

In Vivo NMR ISI, Trialbureau Beeld, Brain, Circulatory Health, Stroke, Hubrecht Institute with UMC, Projectafdeling KIND, Grandjean, Joanes, Desrosiers-Gregoire, Gabriel, Anckaerts, Cynthia, Angeles-Valdez, Diego, Ayad, Fadi, Barrière, David A., Blockx, Ines, Bortel, Aleksandra, Broadwater, Margaret, Cardoso, Beatriz M., Célestine, Marina, Chavez-Negrete, Jorge E., Choi, Sangcheon, Christiaen, Emma, Clavijo, Perrin, Colon-Perez, Luis, Cramer, Samuel, Daniele, Tolomeo, Dempsey, Elaine, Diao, Yujian, Doelemeyer, Arno, Dopfel, David, Dvořáková, Lenka, Falfán-Melgoza, Claudia, Fernandes, Francisca F., Fowler, Caitlin F., Fuentes-Ibañez, Antonio, Garin, Clément M., Gelderman, Eveline, Golden, Carla E.M., Guo, Chao C.G., Henckens, Marloes J.A.G., Hennessy, Lauren A., Herman, Peter, Hofwijks, Nita, Horien, Corey, Ionescu, Tudor M., Jones, Jolyon, Kaesser, Johannes, Kim, Eugene, Lambers, Henriette, Lazari, Alberto, Lee, Sung Ho, Lillywhite, Amanda, Liu, Yikang, Liu, Yanyan Y., López -Castro, Alejandra, López-Gil, Xavier, Ma, Zilu, MacNicol, Eilidh, Madularu, Dan, Mandino, Francesca, Marciano, Sabina, McAuslan, Matthew J., McCunn, Patrick, McIntosh, Alison, Meng, Xianzong, Meyer-Baese, Lisa, Missault, Stephan, Moro, Federico, Naessens, Daphne M.P., Nava-Gomez, Laura J., Nonaka, Hiroi, Ortiz, Juan J., Paasonen, Jaakko, Peeters, Lore M., Pereira, Mickaël, Perez, Pablo D., Pompilus, Marjory, Prior, Malcolm, Rakhmatullin, Rustam, Reimann, Henning M., Reinwald, Jonathan, Del Rio, Rodrigo Triana, Rivera-Olvera, Alejandro, Ruiz-Pérez, Daniel, Russo, Gabriele, Rutten, Tobias J., Ryoke, Rie, Sack, Markus, Salvan, Piergiorgio, Sanganahalli, Basavaraju G., Schroeter, Aileen, Seewoo, Bhedita J., Selingue, Erwan, Seuwen, Aline, Shi, Bowen, Sirmpilatze, Nikoloz, Smith, Joanna A.B., Smith, Corrie, Sobczak, Filip, Stenroos, Petteri J., Straathof, Milou, Strobelt, Sandra, Sumiyoshi, Akira, Takahashi, Kengo, Torres-García, Maria E., Tudela, Raul, van den Berg, Monica, van der Marel, Kajo, van Hout, Aran T.B., Vertullo, Roberta, Vidal, Benjamin, Vrooman, Roël M., Wang, Victora X., Wank, Isabel, Watson, David J.G., Yin, Ting, Zhang, Yongzhi, Zurbruegg, Stefan, Achard, Sophie, Alcauter, Sarael, Auer, Dorothee P., Barbier, Emmanuel L., Baudewig, Jürgen, Beckmann, Christian F., Beckmann, Nicolau, Becq, Guillaume J.P.C., Blezer, Erwin L.A., Bolbos, Radu, Boretius, Susann, Bouvard, Sandrine, Budinger, Eike, Buxbaum, Joseph D., Cash, Diana, Chapman, Victoria, Chuang, Kai Hsiang, Ciobanu, Luisa, Coolen, Bram F., Dalley, Jeffrey W., Dhenain, Marc, Dijkhuizen, Rick M., Esteban, Oscar, Faber, Cornelius, Febo, Marcelo, Feindel, Kirk W., Forloni, Gianluigi, Fouquet, Jérémie, Garza-Villarreal, Eduardo A., Gass, Natalia, Glennon, Jeffrey C., Gozzi, Alessandro, Gröhn, Olli, Harkin, Andrew, Heerschap, Arend, Helluy, Xavier, Herfert, Kristina, Heuser, Arnd, Homberg, Judith R., Houwing, Danielle J., Hyder, Fahmeed, Ielacqua, Giovanna Diletta, Jelescu, Ileana O., Johansen-Berg, Heidi, Kaneko, Gen, Kawashima, Ryuta, Keilholz, Shella D., Keliris, Georgios A., Kelly, Clare, Kerskens, Christian, Khokhar, Jibran Y., Kind, Peter C., Langlois, Jean Baptiste, Lerch, Jason P., López-Hidalgo, Monica A., Manahan-Vaughan, Denise, Marchand, Fabien, Mars, Rogier B., Marsella, Gerardo, Micotti, Edoardo, Muñoz-Moreno, Emma, Near, Jamie, Niendorf, Thoralf, Otte, Willem M., Pais-Roldán, Patricia, Pan, Wen Ju, Prado-Alcalá, Roberto A., Quirarte, Gina L., Rodger, Jennifer, Rosenow, Tim, Sampaio-Baptista, Cassandra, Sartorius, Alexander, Sawiak, Stephen J., Scheenen, Tom W.J., Shemesh, Noam, Shih, Yen Yu Ian, Shmuel, Amir, Soria, Guadalupe, Stoop, Ron, Thompson, Garth J., Till, Sally M., Todd, Nick, Van Der Linden, Annemie, van der Toorn, Annette, van Tilborg, Geralda A.F., Vanhove, Christian, Veltien, Andor, Verhoye, Marleen, Wachsmuth, Lydia, Weber-Fahr, Wolfgang, Wenk, Patricia, Yu, Xin, Zerbi, Valerio, Zhang, Nanyin, Zhang, Baogui B., Zimmer, Luc, Devenyi, Gabriel A., Chakravarty, M. Mallar, Hess, Andreas, In Vivo NMR ISI, Trialbureau Beeld, Brain, Circulatory Health, Stroke, Hubrecht Institute with UMC, Projectafdeling KIND, Grandjean, Joanes, Desrosiers-Gregoire, Gabriel, Anckaerts, Cynthia, Angeles-Valdez, Diego, Ayad, Fadi, Barrière, David A., Blockx, Ines, Bortel, Aleksandra, Broadwater, Margaret, Cardoso, Beatriz M., Célestine, Marina, Chavez-Negrete, Jorge E., Choi, Sangcheon, Christiaen, Emma, Clavijo, Perrin, Colon-Perez, Luis, Cramer, Samuel, Daniele, Tolomeo, Dempsey, Elaine, Diao, Yujian, Doelemeyer, Arno, Dopfel, David, Dvořáková, Lenka, Falfán-Melgoza, Claudia, Fernandes, Francisca F., Fowler, Caitlin F., Fuentes-Ibañez, Antonio, Garin, Clément M., Gelderman, Eveline, Golden, Carla E.M., Guo, Chao C.G., Henckens, Marloes J.A.G., Hennessy, Lauren A., Herman, Peter, Hofwijks, Nita, Horien, Corey, Ionescu, Tudor M., Jones, Jolyon, Kaesser, Johannes, Kim, Eugene, Lambers, Henriette, Lazari, Alberto, Lee, Sung Ho, Lillywhite, Amanda, Liu, Yikang, Liu, Yanyan Y., López -Castro, Alejandra, López-Gil, Xavier, Ma, Zilu, MacNicol, Eilidh, Madularu, Dan, Mandino, Francesca, Marciano, Sabina, McAuslan, Matthew J., McCunn, Patrick, McIntosh, Alison, Meng, Xianzong, Meyer-Baese, Lisa, Missault, Stephan, Moro, Federico, Naessens, Daphne M.P., Nava-Gomez, Laura J., Nonaka, Hiroi, Ortiz, Juan J., Paasonen, Jaakko, Peeters, Lore M., Pereira, Mickaël, Perez, Pablo D., Pompilus, Marjory, Prior, Malcolm, Rakhmatullin, Rustam, Reimann, Henning M., Reinwald, Jonathan, Del Rio, Rodrigo Triana, Rivera-Olvera, Alejandro, Ruiz-Pérez, Daniel, Russo, Gabriele, Rutten, Tobias J., Ryoke, Rie, Sack, Markus, Salvan, Piergiorgio, Sanganahalli, Basavaraju G., Schroeter, Aileen, Seewoo, Bhedita J., Selingue, Erwan, Seuwen, Aline, Shi, Bowen, Sirmpilatze, Nikoloz, Smith, Joanna A.B., Smith, Corrie, Sobczak, Filip, Stenroos, Petteri J., Straathof, Milou, Strobelt, Sandra, Sumiyoshi, Akira, Takahashi, Kengo, Torres-García, Maria E., Tudela, Raul, van den Berg, Monica, van der Marel, Kajo, van Hout, Aran T.B., Vertullo, Roberta, Vidal, Benjamin, Vrooman, Roël M., Wang, Victora X., Wank, Isabel, Watson, David J.G., Yin, Ting, Zhang, Yongzhi, Zurbruegg, Stefan, Achard, Sophie, Alcauter, Sarael, Auer, Dorothee P., Barbier, Emmanuel L., Baudewig, Jürgen, Beckmann, Christian F., Beckmann, Nicolau, Becq, Guillaume J.P.C., Blezer, Erwin L.A., Bolbos, Radu, Boretius, Susann, Bouvard, Sandrine, Budinger, Eike, Buxbaum, Joseph D., Cash, Diana, Chapman, Victoria, Chuang, Kai Hsiang, Ciobanu, Luisa, Coolen, Bram F., Dalley, Jeffrey W., Dhenain, Marc, Dijkhuizen, Rick M., Esteban, Oscar, Faber, Cornelius, Febo, Marcelo, Feindel, Kirk W., Forloni, Gianluigi, Fouquet, Jérémie, Garza-Villarreal, Eduardo A., Gass, Natalia, Glennon, Jeffrey C., Gozzi, Alessandro, Gröhn, Olli, Harkin, Andrew, Heerschap, Arend, Helluy, Xavier, Herfert, Kristina, Heuser, Arnd, Homberg, Judith R., Houwing, Danielle J., Hyder, Fahmeed, Ielacqua, Giovanna Diletta, Jelescu, Ileana O., Johansen-Berg, Heidi, Kaneko, Gen, Kawashima, Ryuta, Keilholz, Shella D., Keliris, Georgios A., Kelly, Clare, Kerskens, Christian, Khokhar, Jibran Y., Kind, Peter C., Langlois, Jean Baptiste, Lerch, Jason P., López-Hidalgo, Monica A., Manahan-Vaughan, Denise, Marchand, Fabien, Mars, Rogier B., Marsella, Gerardo, Micotti, Edoardo, Muñoz-Moreno, Emma, Near, Jamie, Niendorf, Thoralf, Otte, Willem M., Pais-Roldán, Patricia, Pan, Wen Ju, Prado-Alcalá, Roberto A., Quirarte, Gina L., Rodger, Jennifer, Rosenow, Tim, Sampaio-Baptista, Cassandra, Sartorius, Alexander, Sawiak, Stephen J., Scheenen, Tom W.J., Shemesh, Noam, Shih, Yen Yu Ian, Shmuel, Amir, Soria, Guadalupe, Stoop, Ron, Thompson, Garth J., Till, Sally M., Todd, Nick, Van Der Linden, Annemie, van der Toorn, Annette, van Tilborg, Geralda A.F., Vanhove, Christian, Veltien, Andor, Verhoye, Marleen, Wachsmuth, Lydia, Weber-Fahr, Wolfgang, Wenk, Patricia, Yu, Xin, Zerbi, Valerio, Zhang, Nanyin, Zhang, Baogui B., Zimmer, Luc, Devenyi, Gabriel A., Chakravarty, M. Mallar, and Hess, Andreas

Published
2023

54. Application of pseudocontinuous arterial spin labeling perfusion imaging in children with autism spectrum disorders

Author

Ye, Fang, primary, Du, Lei, additional, Liu, Bing, additional, Gao, Xinying, additional, Yang, Aocai, additional, Liu, Die, additional, Chen, Yue, additional, Lv, Kuan, additional, Xu, Pengfei, additional, Chen, Yuanmei, additional, Liu, Jing, additional, Zhang, Lipeng, additional, Li, Shijun, additional, Shmuel, Amir, additional, Zhang, Qi, additional, and Ma, Guolin, additional

Published
2022
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58. versaFlow: a versatile pipeline for resolution adapted diffusion MRI processing and its application to studying the variability of the PRIME-DE database.

Author

Caron, Alex Valcourt, Shmuel, Amir, Hao, Ziqi, and Descoteaux, Maxime

Subjects
DIFFUSION magnetic resonance imaging, MAGNETIC resonance imaging, DATABASES, DIFFUSION tensor imaging, FUNCTIONAL magnetic resonance imaging, GAMMA distributions, OPTICAL scanners
Abstract

The lack of “gold standards” in Diffusion Weighted Imaging (DWI) makes validation cumbersome. To tackle this task, studies use translational analysis where results in humans are benchmarked against findings in other species. Non-Human Primates (NHP) are particularly interesting for this, as their cytoarchitecture is closely related to humans. However, tools used for processing and analysis must be adapted and finely tuned to work well on NHP images. Here, we propose versaFlow, a modular pipeline implemented in Nextflow, designed for robustness and scalability. The pipeline is tailored to in vivo NHP DWI at any spatial resolution; it allows for maintainability and customization. Processes and workflows are implemented using cutting-edge and state-of-the-art Magnetic Resonance Imaging (MRI) processing technologies and diffusion modeling algorithms, namely Diffusion Tensor Imaging (DTI), Constrained Spherical Deconvolution (CSD), and DIstribution of Anisotropic MicrOstructural eNvironments in Diffusion- compartment imaging (DIAMOND). Using versaFlow, we provide an in-depth study of the variability of diffusion metrics computed on 32 subjects from 3 sites of the Primate Data Exchange (PRIME-DE), which contains anatomical T1-weighted (T1w) and T2-weighted (T2w) images, functional MRI (fMRI), and DWI of NHP brains. This dataset includes images acquired over a range of resolutions, using single and multi-shell gradient samplings, on multiple scanner vendors. We perform a reproducibility study of the processing of versaFlow using the Aix-Marseilles site’s data, to ensure that our implementation has minimal impact on the variability observed in subsequent analyses. We report very high reproducibility for the majority of metrics; only gamma distribution parameters of DIAMOND display less reproducible behaviors, due to the absence of a mechanism to enforce a random number seed in the software we used. This should be taken into consideration when future applications are performed. We show that the PRIME- DE diffusion data exhibits a great level of variability, similar or greater than results obtained in human studies. Its usage should be done carefully to prevent instilling uncertainty in statistical analyses. This hints at a need for sufficient harmonization in acquisition protocols and for the development of robust algorithms capable of managing the variability induced in imaging due to differences in scanner models and/or vendors. [ABSTRACT FROM AUTHOR]

Published
2023
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59. Cap-independent translation and a precisely located RNA sequence enable SARS-CoV-2 to control host translation and escape anti-viral response

Author

Slobodin, Boris, primary, Sehrawat, Urmila, additional, Lev, Anastasia, additional, Hayat, Daniel, additional, Zuckerman, Binyamin, additional, Fraticelli, Davide, additional, Ogran, Ariel, additional, Ben-Shmuel, Amir, additional, Bar-David, Elad, additional, Levy, Haim, additional, Ulitsky, Igor, additional, and Dikstein, Rivka, additional

Published
2022
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62. SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

Author

Jansen, Jitske, Reimer, Katharina C., Nagai, James S., Varghese, Finny S., Overheul, Gijs J., de Beer, Marit, Roverts, Rona, Daviran, Deniz, Fermin, Liline A.S., Willemsen, Brigith, Beukenboom, Marcel, Djudjaj, Sonja, von Stillfried, Saskia, van Eijk, Larissa E., Mastik, Mirjam, Bulthuis, Marian, Dunnen, Wilfred den, van Goor, Harry, Hillebrands, Jan Luuk, Triana, Sergio H., Alexandrov, Theodore, Timm, Marie Cherelle, van den Berge, Bartholomeus T., van den Broek, Martijn, Nlandu, Quincy, Heijnert, Joelle, Bindels, Eric M.J., Hoogenboezem, Remco M., Mooren, Fieke, Kuppe, Christoph, Miesen, Pascal, Grünberg, Katrien, Ijzermans, Ties, Steenbergen, Eric J., Czogalla, Jan, Schreuder, Michiel F., Sommerdijk, Nico, Akiva, Anat, Boor, Peter, Puelles, Victor G., Floege, Jürgen, Huber, Tobias B., Achdout, Hagit, Aimon, Anthony, Bar-David, Elad, Barr, Haim, Ben-Shmuel, Amir, Bennett, James, Schneider, Rebekka K., Kramann, Rafael, Jansen, Jitske, Reimer, Katharina C., Nagai, James S., Varghese, Finny S., Overheul, Gijs J., de Beer, Marit, Roverts, Rona, Daviran, Deniz, Fermin, Liline A.S., Willemsen, Brigith, Beukenboom, Marcel, Djudjaj, Sonja, von Stillfried, Saskia, van Eijk, Larissa E., Mastik, Mirjam, Bulthuis, Marian, Dunnen, Wilfred den, van Goor, Harry, Hillebrands, Jan Luuk, Triana, Sergio H., Alexandrov, Theodore, Timm, Marie Cherelle, van den Berge, Bartholomeus T., van den Broek, Martijn, Nlandu, Quincy, Heijnert, Joelle, Bindels, Eric M.J., Hoogenboezem, Remco M., Mooren, Fieke, Kuppe, Christoph, Miesen, Pascal, Grünberg, Katrien, Ijzermans, Ties, Steenbergen, Eric J., Czogalla, Jan, Schreuder, Michiel F., Sommerdijk, Nico, Akiva, Anat, Boor, Peter, Puelles, Victor G., Floege, Jürgen, Huber, Tobias B., Achdout, Hagit, Aimon, Anthony, Bar-David, Elad, Barr, Haim, Ben-Shmuel, Amir, Bennett, James, Schneider, Rebekka K., and Kramann, Rafael

Abstract

Kidney failure is frequently observed during and after COVID-19, but it remains elusive whether this is a direct effect of the virus. Here, we report that SARS-CoV-2 directly infects kidney cells and is associated with increased tubule-interstitial kidney fibrosis in patient autopsy samples. To study direct effects of the virus on the kidney independent of systemic effects of COVID-19, we infected human-induced pluripotent stem-cell-derived kidney organoids with SARS-CoV-2. Single-cell RNA sequencing indicated injury and dedifferentiation of infected cells with activation of profibrotic signaling pathways. Importantly, SARS-CoV-2 infection also led to increased collagen 1 protein expression in organoids. A SARS-CoV-2 protease inhibitor was able to ameliorate the infection of kidney cells by SARS-CoV-2. Our results suggest that SARS-CoV-2 can directly infect kidney cells and induce cell injury with subsequent fibrosis. These data could explain both acute kidney injury in COVID-19 patients and the development of chronic kidney disease in long COVID.

Published
2022

63. Turning high-throughput structural biology into predictive inhibitor design.

Author

Saar, Kadi L., McCorkindale, William, Fearon, Daren, Boby, Melissa, Barr, Haim, Ben-Shmuel, Amir, London, Nir, von Delft, Frank, Chodera, John D., and Lee, Alpha A.

Subjects
COSMOCHEMISTRY, DRUG design, BIOLOGY, SIMPLE machines, MACHINE learning, EXCHANGE
Abstract

A common challenge in drug design pertains to finding chemical modifications to a ligand that increases its affinity to the target protein. An underutilized advance is the increase in structural biology throughput, which has progressed from an artisanal endeavor to a monthly throughput of hundreds of different ligands against a protein in modern synchrotrons. However, the missing piece is a framework that turns high-throughput crystallography data into predictive models for ligand design. Here, we designed a simple machine learning approach that predicts protein-ligand affinity from experimental structures of diverse ligands against a single protein paired with biochemical measurements. Our key insight is using physics-based energy descriptors to represent protein-ligand complexes and a learning-to-rank approach that infers the relevant differences between binding modes. We ran a high-throughput crystallography campaign against the SARS-CoV-2 main protease (MPro), obtaining parallel measurements of over 200 protein-ligand complexes and their binding activities. This allows us to design one-step library syntheses which improved the potency of two distinct micromolar hits by over 10-fold, arriving at a noncovalent and nonpeptidomimetic inhibitor with 120 nM antiviral efficacy. Crucially, our approach successfully extends ligands to unexplored regions of the binding pocket, executing large and fruitful moves in chemical space with simple chemistry. [ABSTRACT FROM AUTHOR]

Published
2023
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65. StandardRat: A multi-center consensus protocol to enhance functional connectivity specificity in the rat brain

Author

Grandjean, Joanes, primary, Desrosiers-Gregoire, Gabriel, additional, Anckaerts, Cynthia, additional, Angeles-Valdez, Diego, additional, Ayad, Fadi, additional, Barrière, David A, additional, Blockx, Ines, additional, Bortel, Aleksandra B, additional, Broadwater, Margaret, additional, Cardoso, Beatriz M, additional, Célestine, Marina, additional, Chavez-Negrete, Jorge E, additional, Choi, Sangcheon, additional, Christiaen, Emma, additional, Clavijo, Perrin, additional, Colon-Perez, Luis, additional, Cramer, Samuel, additional, Daniele, Tolomeo, additional, Dempsey, Elaine, additional, Diao, Yujian, additional, Doelemeyer, Arno, additional, Dopfel, David, additional, Dvořáková, Lenka, additional, Falfán-Melgoza, Claudia, additional, Fernandes, Francisca F, additional, Fowler, Caitlin F, additional, Fuentes-Ibañez, Antonio, additional, Garin, Clément, additional, Gelderman, Eveline, additional, Golden, Carla EM, additional, Guo, Chao CG, additional, Henckens, Marloes JAG, additional, Hennessy, Lauren A, additional, Herman, Peter, additional, Hofwijks, Nita, additional, Horien, Corey, additional, Ionescu, Tudor M, additional, Jones, Jolyon, additional, Kaesser, Johannes, additional, Kim, Eugene, additional, Lambers, Henriette, additional, Lazari, Alberto, additional, Lee, Sung-Ho, additional, Lillywhite, Amanda, additional, Liu, Yikang, additional, Liu, Yanyan Y, additional, López-Castro, Alejandra, additional, López-Gil, Xavier, additional, Ma, Zilu, additional, MacNicol, Eilidh, additional, Madularu, Dan, additional, Mandino, Francesca, additional, Marciano, Sabina, additional, McAuslan, Matthew J, additional, McCunn, Patrick, additional, McIntosh, Alison, additional, Meng, Xianzong, additional, Meyer-Baese, Lisa, additional, Missault, Stephan, additional, Moro, Federico, additional, Naessens, Daphne, additional, Nava-Gomez, Laura J, additional, Nonaka, Hiroi, additional, Ortiz, Juan J, additional, Paasonen, Jaakko, additional, Peeters, Lore M, additional, Pereira, Mickaël, additional, Perez, Pablo D, additional, Pompilus, Marjory, additional, Prior, Malcolm, additional, Rakhmatullin, Rustam, additional, Reimann, Henning M, additional, Reinwald, Jonathan, additional, de Rio, Rodrigo Triana, additional, Rivera-Olvera, Alejandro, additional, Ruiz-Pérez, Daniel, additional, Russo, Gabriele, additional, Rutten, Tobias J, additional, Ryoke, Rie, additional, Sack, Markus, additional, Salvan, Piergiorgio, additional, Sanganahalli, Basavaraju G, additional, Schroeter, Aileen, additional, Seewoo, Bhedita J, additional, Selingue, Erwan, additional, Seuwen, Aline, additional, Shi, Bowen, additional, Sirmpilatze, Nikoloz, additional, Smith, Joanna AB, additional, Smith, Corrie, additional, Sobczak, Filip, additional, Stenroos, Petteri J, additional, Straathof, Milou, additional, Strobelt, Sandra, additional, Sumiyoshi, Akira, additional, Takahashi, Kengo, additional, Torres-García, Maria E, additional, Tudela, Raul, additional, van den Berg, Monica, additional, van der Marel, Kajo, additional, van Hout, Aran TB, additional, Vertullo, Roberta, additional, Vidal, Benjamin, additional, Vrooman, Roel M, additional, Wang, Victora X, additional, Wank, Isabel, additional, Watson, David JG, additional, Yin, Ting, additional, Zhang, Yongzhi, additional, Zurbruegg, Stefan, additional, Achard, Sophie, additional, Alcauter, Sarael, additional, Auer, Dorothee P, additional, Barbier, Emmanuel L, additional, Baudewig, Jürgen, additional, Beckmann, Christian F, additional, Beckmann, Nicolau, additional, Becq, Guillaume JPC, additional, Blezer, Erwin LA, additional, Bolbos, Radu, additional, Boretius, Susann, additional, Bouvard, Sandrine, additional, Budinger, Eike, additional, Buxbaum, Joseph D, additional, Cash, Diana, additional, Chapman, Victoria, additional, Chuang, Kai-Hsiang, additional, Ciobanu, Luisa, additional, Coolen, Bram, additional, Dalley, Jeffrey W, additional, Dhenain, Marc, additional, Dijkhuizen, Rick M, additional, Esteban, Oscar, additional, Faber, Cornelius, additional, Febo, Marcelo, additional, Feindel, Kirk W, additional, Forloni, Gianluigi, additional, Fouquet, Jérémie, additional, Garza-Villarreal, Eduardo A, additional, Gass, Natalia, additional, Glennon, Jeffrey C, additional, Gozzi, Alessandro, additional, Gröhn, Olli, additional, Harkin, Andrew, additional, Heerschap, Arend, additional, Helluy, Xavier, additional, Herfert, Kristina, additional, Heuser, Arnd, additional, Homberg, Judith R, additional, Houwing, Danielle J, additional, Hyder, Fahmeed, additional, Ielacqua, Giovanna Diletta, additional, Jelescu, Ileana O, additional, Johansen-Berg, Heidi, additional, Kaneko, Gen, additional, Kawashima, Ryuta, additional, Keilholz, Shella D, additional, Keliris, Georgios A, additional, Kelly, Clare, additional, Kerskens, Christian, additional, Khokhar, Jibran Y, additional, Kind, Peter C, additional, Langlois, Jean-Baptiste, additional, Lerch, Jason P, additional, López-Hidalgo, Monica A, additional, Manahan-Vaughan, Denise, additional, Marchand, Fabien, additional, Mars, Rogier B, additional, Marsella, Gerardo, additional, Micotti, Edoardo, additional, Muñoz-Moreno, Emma, additional, Near, Jamie, additional, Niendorf, Thoralf, additional, Otte, Willem M, additional, Pais, Patricia, additional, Pan, Wen-Ju, additional, Prado-Alcalá, Roberto A, additional, Quirarte, Gina L, additional, Rodger, Jennifer, additional, Rosenow, Tim, additional, Baptista, Cassandra Sampaio, additional, Sartorius, Alexander, additional, Sawiak, Stephen J, additional, Scheenen, Tom WJ, additional, Shemesh, Noam, additional, Shih, Yen-Yu Ian, additional, Shmuel, Amir, additional, Soria, Guadalupe, additional, Stoop, Ron, additional, Thompson, Garth J, additional, Till, Sally M, additional, Todd, Nick, additional, Van Der Linden, Annemie, additional, van der Toorn, Annette, additional, van Tilborg, Geralda AF, additional, Vanhove, Christian, additional, Veltien, Andor, additional, Verhoye, Marleen, additional, Wachsmuth, Lydia, additional, Weber-Fahr, Wolfgang, additional, Wenk, Patricia, additional, Yu, Xin, additional, Zerbi, Valerio, additional, Zhang, Nanyin, additional, Zhang, Baogui B, additional, Zimmer, Luc, additional, Devenyi, Gabriel A, additional, Chakravarty, M Mallar, additional, and Hess, Andreas, additional

Published
2022
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69. Toward next-generation primate neuroscience: A collaboration-based strategic plan for integrative neuroimaging

Author

Milham, Michael, primary, Petkov, Chris, additional, Belin, Pascal, additional, Ben Hamed, Suliann, additional, Evrard, Henry, additional, Fair, Damien, additional, Fox, Andrew, additional, Froudist-Walsh, Sean, additional, Hayashi, Takuya, additional, Kastner, Sabine, additional, Klink, Chris, additional, Majka, Piotr, additional, Mars, Rogier, additional, Messinger, Adam, additional, Poirier, Colline, additional, Schroeder, Charles, additional, Shmuel, Amir, additional, Silva, Afonso C., additional, Vanduffel, Wim, additional, Van Essen, David C., additional, Wang, Zheng, additional, Roe, Anna Wang, additional, Wilke, Melanie, additional, Xu, Ting, additional, Aarabi, Mohammad Hadi, additional, Adolphs, Ralph, additional, Ahuja, Aarit, additional, Alvand, Ashkan, additional, Amiez, Celine, additional, Autio, Joonas, additional, Azadi, Reza, additional, Baeg, Eunha, additional, Bai, Ruiliang, additional, Bao, Pinglei, additional, Basso, Michele, additional, Behel, Austin K., additional, Bennett, Yvonne, additional, Bernhardt, Boris, additional, Biswal, Bharat, additional, Boopathy, Sethu, additional, Boretius, Susann, additional, Borra, Elena, additional, Boshra, Rober, additional, Buffalo, Elizabeth, additional, Cao, Long, additional, Cavanaugh, James, additional, Celine, Amiez, additional, Chavez, Gianfranco, additional, Chen, Li Min, additional, Chen, Xiaodong, additional, Cheng, Luqi, additional, Chouinard-Decorte, Francois, additional, Clavagnier, Simon, additional, Cléry, Justine, additional, Colcombe, Stan J., additional, Conway, Bevil, additional, Cordeau, Melina, additional, Coulon, Olivier, additional, Cui, Yue, additional, Dadarwal, Rakshit, additional, Dahnke, Robert, additional, Desrochers, Theresa, additional, Deying, Li, additional, Dougherty, Kacie, additional, Doyle, Hannah, additional, Drzewiecki, Carly M., additional, Duyck, Marianne, additional, Arachchi, Wasana Ediri, additional, Elorette, Catherine, additional, Essamlali, Abdelhadi, additional, Evans, Alan, additional, Fajardo, Alfonso, additional, Figueroa, Hector, additional, Franco, Alexandre, additional, Freches, Guilherme, additional, Frey, Steve, additional, Friedrich, Patrick, additional, Fujimoto, Atsushi, additional, Fukunaga, Masaki, additional, Gacoin, Maeva, additional, Gallardo, Guillermo, additional, Gao, Lixia, additional, Gao, Yang, additional, Garside, Danny, additional, Garza-Villarreal, Eduardo A., additional, Gaudet-Trafit, Maxime, additional, Gerbella, Marzio, additional, Giavasis, Steven, additional, Glen, Daniel, additional, Ribeiro Gomes, Ana Rita, additional, Torrecilla, Sandra Gonzalez, additional, Gozzi, Alessandro, additional, Gulli, Roberto, additional, Haber, Suzanne, additional, Hadj-Bouziane, Fadila, additional, Fujimoto, Satoka Hashimoto, additional, Hawrylycz, Michael, additional, He, Quansheng, additional, He, Ye, additional, Heuer, Katja, additional, Hiba, Bassem, additional, Hoffstaedter, Felix, additional, Hong, Seok-Jun, additional, Hori, Yuki, additional, Hou, Yujie, additional, Howard, Amy, additional, de la Iglesia-Vaya, Maria, additional, Ikeda, Takuro, additional, Jankovic-Rapan, Lucija, additional, Jaramillo, Jorge, additional, Jedema, Hank P., additional, Jin, Hecheng, additional, Jiang, Minqing, additional, Jung, Benjamin, additional, Kagan, Igor, additional, Kahn, Itamar, additional, Kiar, Gregory, additional, Kikuchi, Yuki, additional, Kilavik, Bjørg, additional, Kimura, Nobuyuki, additional, Klatzmann, Ulysse, additional, Kwok, Sze Chai, additional, Lai, Hsin-Yi, additional, Lamberton, Franck, additional, Lehman, Julia, additional, Li, Pengcheng, additional, Li, Xinhui, additional, Li, Xinjian, additional, Liang, Zhifeng, additional, Liston, Conor, additional, Little, Roger, additional, Liu, Cirong, additional, Liu, Ning, additional, Liu, Xiaojin, additional, Liu, Xinyu, additional, Lu, Haidong, additional, Loh, Kep Kee, additional, Madan, Christopher, additional, Magrou, Loïc, additional, Margulies, Daniel, additional, Mathilda, Froesel, additional, Mejia, Sheyla, additional, Meng, Yao, additional, Menon, Ravi, additional, Meunier, David, additional, Mitchell, A.J., additional, Mitchell, Anna, additional, Murphy, Aidan, additional, Mvula, Towela, additional, Ortiz-Rios, Michael, additional, Ortuzar Martinez, Diego Emanuel, additional, Pagani, Marco, additional, Palomero-Gallagher, Nicola, additional, Pareek, Vikas, additional, Perkins, Pierce, additional, Ponce, Fernanda, additional, Postans, Mark, additional, Pouget, Pierre, additional, Qian, Meizhen, additional, Ramirez, Julian “Bene”, additional, Raven, Erika, additional, Restrepo, Isabel, additional, Rima, Samy, additional, Rockland, Kathleen, additional, Rodriguez, Nadira Yusif, additional, Roger, Elise, additional, Hortelano, Eduardo Rojas, additional, Rosa, Marcello, additional, Rossi, Andrew, additional, Rudebeck, Peter, additional, Russ, Brian, additional, Sakai, Tomoko, additional, Saleem, Kadharbatcha S., additional, Sallet, Jerome, additional, Sawiak, Stephen, additional, Schaeffer, David, additional, Schwiedrzik, Caspar M., additional, Seidlitz, Jakob, additional, Sein, Julien, additional, Sharma, Jitendra, additional, Shen, Kelly, additional, Sheng, Wei-an, additional, Shi, Neo Sunhang, additional, Shim, Won Mok, additional, Simone, Luciano, additional, Sirmpilatze, Nikoloz, additional, Sivan, Virginie, additional, Song, Xiaowei, additional, Tanenbaum, Aaron, additional, Tasserie, Jordy, additional, Taylor, Paul, additional, Tian, Xiaoguang, additional, Toro, Roberto, additional, Trambaiolli, Lucas, additional, Upright, Nick, additional, Vezoli, Julien, additional, Vickery, Sam, additional, Villalon, Julio, additional, Wang, Xiaojie, additional, Wang, Yufan, additional, Weiss, Alison R., additional, Wilson, Charlie, additional, Wong, Ting-Yat, additional, Woo, Choong-Wan, additional, Wu, Bichan, additional, Xiao, Du, additional, Xu, Augix Guohua, additional, Xu, Dongrong, additional, Xufeng, Zhou, additional, Yacoub, Essa, additional, Ye, Ningrong, additional, Ying, Zhang, additional, Yokoyama, Chihiro, additional, Yu, Xiongjie, additional, Yue, Shasha, additional, Yuheng, Lu, additional, Yumeng, Xin, additional, Zaldivar, Daniel, additional, Zhang, Shaomin, additional, Zhao, Yuguang, additional, and Zuo, Zhanguang, additional

Published
2022
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71. Alternate atxA and acpA dependent response of Bacillus anthracis to serum, HCO3- and CO2.

Author

Glinert, Itai, Bar-David, Elad, Ben-Shmuel, Amir, Sittner, Assa, Puni, Reut, Laredo, Shira, Kobiler, David, Weiss, Shay, and Levy, Haim

Subjects
BACILLUS anthracis, DENDRITIC cells, FACTORS of production, CELL migration, QUORUM sensing, TOXINS
Abstract

Bacillus anthracis overcomes host immune responses by producing capsule and secreting toxins. Production of these virulence factors in response to entering the host environment was shown to be regulated by atxA, the major virulence regulator, known to be activated by HCO3- and CO2. While toxin production is regulated directly by atxA, capsule production is independently mediated by two regulators; acpA and acpB. In addition, it was demonstrated that acpA has at least two promotors, one of them shared with atxA. We used a genetic approach to study capsule and toxin production under different conditions. Unlike previous works utilizing NBY, CA or R-HCO3- medium under CO2 enriched conditions, we used a sDMEM-based medium. Thus, toxin and capsule production can be induced in ambient or CO2 enriched atmosphere. Using this system, we could differentiate between induction by 10% NRS, 10% CO2 or 0.75% HCO3-. In response to high CO2, capsule production is induced by acpA based response in an atxA-independent manner, with little to no toxin (protective antigen PA) production. atxA based response is activated in response to serum independently of CO2, inducing toxin and capsule production in an acpA or acpB dependent manner. HCO3- was also found to activate atxA based response, but in non-physiological concentrations. Our findings may help explain the first stages of inhalational infection, in which spores germinating in dendritic cells require protection (by encapsulation) without affecting cell migration to the draining lymph-node by toxin secretion. [ABSTRACT FROM AUTHOR]

Published
2023
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76. LAMP-Seq: Sensitive, Scalable, and Multiplexable COVID-19 Diagnostics Using Molecular Barcoding

Author

Ludwig, Kerstin U., Schmithausen, Ricarda M., Li, David, Jacobs, Max L., Hollstein, Ronja, Blumenstock, Katja, Liebing, Jana, Słabicki, Mikołaj, Ben-Shmuel, Amir, Israeli, Ofir, Weiss, Shay, Ebert, Thomas S., Paran, Nir, Rüdiger, Wibke, Wilbring, Gero, Feldman, David, Lippke, Bärbel, Ishorst, Nina, Hochfeld, Lara M., Beins, Eva C., Kaltheuner, Ines H., Schmitz, Maximilian, Wöhler, Aliona, Döhla, Manuel, Sib, Esther, Jentzsch, Marius, Borrajo, Jacob D., Strecker, Jonathan, Reinhardt, Julia, Cleary, Brian, Geyer, Matthias, Hölzel, Michael, Macrae, Rhiannon, Nöthen, Markus M., Hoffmann, Per, Exner, Martin, Regev, Aviv, Zhang, Feng, and Schmid-Burgk, Jonathan L.

Subjects
Article
Abstract

Frequent testing of large population groups combined with contact tracing and isolation measures will be crucial for containing COVID-19 outbreaks. Here, we present LAMP-Seq, a modified, highly scalable reverse-transcription loop-mediated isothermal amplification (RT-LAMP) method. Unpurified biosamples are barcoded and amplified in a single heat step, and pooled products are analyzed en masse by sequencing. Using commercial reagents, LAMP-Seq has a limit of detection of ~2.2 molecules/µl at 95% confidence, and near-perfect specificity for SARS-CoV-2 given its sequence readout. Clinical validation of an open-source protocol with 676 swab samples, 98 of which were deemed positive by standard RT-qPCR, demonstrated 100% sensitivity in individuals with Ct values up to 33, and a specificity of 99.7%, at material cost of 2.73 USD per sample. With a time-to-result less than 24 hours, low cost, and little new infrastructure requirement, LAMP-Seq can be readily deployed for frequent testing as part of an integrated public health surveillance program.

Published
2021

78. A Serological Snapshot of COVID-19 Initial Stages in Israel by a 6-Plex Antigen Array

Author

Fisher, Morly, primary, Levy, Haim, additional, Fatelevich, Ella, additional, Afrimov, Yafa, additional, Ben-Shmuel, Amir, additional, Rosenfeld, Ronit, additional, Noy-Porat, Tal, additional, Glinert, Itai, additional, Sittner, Assa, additional, Biber, Asaf, additional, Belkin, Ana, additional, Bar-David, Elad, additional, Puni, Reut, additional, Levy, Itzchak, additional, Mazor, Ohad, additional, Weiss, Shay, additional, and Mechaly, Adva, additional

Published
2021
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80. Application of pseudocontinuous arterial spin labeling perfusion imaging in children with autism spectrum disorders.

Author

Fang Ye, Lei Du, Bing Liu, Xinying Gao, Aocai Yang, Die Liu, Yue Chen, Kuan Lv, Pengfei Xu, Yuanmei Chen, Jing Liu, Lipeng Zhang, Shijun Li, Shmuel, Amir, Qi Zhang, and Guolin Ma

Subjects
CHILDREN with autism spectrum disorders, PERFUSION imaging, SPIN labels, PARIETAL lobe, CEREBRAL circulation
Abstract

Introduction: Pseudocontinuous Arterial Spin Labeling (pCASL) perfusion imaging allows non-invasive quantification of regional cerebral blood flow (CBF) as part of a multimodal magnetic resonance imaging (MRI) protocol. This study aimed to compare regional CBF in autism spectrum disorders (ASD) individuals with their age-matched typically developing (TD) children using pCASL perfusion imaging. Materials and methods: This cross-sectional study enrolled 17 individuals with ASD and 13 TD children. All participants underwent pCASL examination on a 3.0 T MRI scanner. Children in two groups were assessed for clinical characteristics and developmental profiles using Autism Behavior Checklist (ABC) and Gesell development diagnosis scale (GDDS), respectively. We compared CBF in different cerebral regions of ASD and TD children. We also assessed the association between CBF and clinical characteristics/developmental profile. Results: Compared with TD children, individuals with ASD demonstrated a reduction in CBF in the left frontal lobe, the bilateral parietal lobes, and the bilateral temporal lobes. Within the ASD group, CBF was significantly higher in the right parietal lobe than in the left side. Correlation analysis of behavior characteristics and CBF in different regions showed a positive correlation between body and object domain scores on the ABC and CBF of the bilateral occipital lobes, and separately, between language domain scores and CBF of the left frontal lobe. The score of the social and self-help domain was negatively correlated with the CBF of the left frontal lobe, the left parietal lobe, and the left temporal lobe. Conclusion: Cerebral blood flow was found to be negatively correlated with scores in the social and self-help domain, and positively correlated with those in the body and object domain, indicating that CBF values are a potential MRIbased biomarker of disease severity in ASD patients. The findings may provide novel insight into the pathophysiological mechanisms of ASD. [ABSTRACT FROM AUTHOR]

Published
2022
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81. Cap-independent translation and a precisely localized RNA sequence enable SARS-CoV-2 to control host translation and escape anti-viral response

Author

Slobodin, Boris, primary, Sehrawat, Urmila, additional, Lev, Anastasia, additional, Ogran, Ariel, additional, Fraticelli, Davide, additional, Hayat, Daniel, additional, Zuckerman, Binyamin, additional, Ulitsky, Igor, additional, Ben-Shmuel, Amir, additional, Bar-David, Elad, additional, Levy, Haim, additional, and Dikstein, Rivka, additional

Published
2021
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82. Nonclinical Safety and Immunogenicity of an rVSV-ΔG-SARS-CoV-2-S vaccine in mice, hamsters, rabbits and pigs

Author

Madar-Balakirski, Noa, primary, Rosner, Amir, additional, Melamed, Sharon, additional, Politi, Boaz, additional, Steiner, Michal, additional, Tamir, Hadas, additional, Yahalom-Ronen, Yfat, additional, David, Elad Bar, additional, Ben-Shmuel, Amir, additional, Sittner, Assa, additional, Glinert, Itai, additional, Weiss, Shay, additional, Bar-Haim, Erez, additional, Cohen, Hila, additional, Elia, Uri, additional, Achdout, Hagit, additional, Erez, Noam, additional, Rotem, Shahar, additional, Lazar, Shlomi, additional, Nyska, Abraham, additional, Yitzhaki, Shmuel, additional, Beth-Din, Adi, additional, Levy, Haim, additional, Paran, Nir, additional, Israely, Tomer, additional, and Marcus, Hadar, additional

Published
2021
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83. Mice with induced pulmonary morbidities display severe lung inflammation and mortality following exposure to SARS-CoV-2

Author

Falach, Reut, primary, Bar-On, Liat, additional, Lazar, Shlomi, additional, Kadar, Tamar, additional, Mazor, Ohad, additional, Aftalion, Moshe, additional, Gur, David, additional, Evgy, Yentl, additional, Shifman, Ohad, additional, Aminov, Tamar, additional, Israeli, Ofir, additional, Cohen-Gihon, Inbar, additional, Zaide, Galia, additional, Gutman, Hila, additional, Vagima, Yaron, additional, Makdasi, Efi, additional, Stein, Dana, additional, Rosenfeld, Ronit, additional, Alcalay, Ron, additional, Zahavy, Eran, additional, Levy, Haim, additional, Glinert, Itai, additional, Ben-Shmuel, Amir, additional, Israely, Tomer, additional, Melamed, Sharon, additional, Politi, Boaz, additional, Achdout, Hagit, additional, Yitzhaki, Shmuel, additional, Kronman, Chanoch, additional, and Sabo, Tamar, additional

Published
2021
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85. Population growth and the environment: Can we eat the cake and have it?

Author

Shmuel Amir

Subjects
Environmental costs, Period of production, Population growth, Sustainability, Technological progress, Thermodynamics-based theory of value., Mathematics, QA1-939
Abstract

Continuous population growth and the concomitant maintenance of a growth sustaining environment are not in conflict only if the rates of both economic and biological processes are slowed down steadily. For this to happen, individual and social impatience-lowering adaptations should be adopted, and the capital of the system, both economic and natural, has to be redistributed among the system interacting components to result in an ever more complex organizational web. In addition, these factors have to corroborate with a third element, the incorporation of an arsenal of varied technological innovations that improves the use of existing stocks.

Published
1999
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88. Spike vs nucleocapsid SARS-CoV-2 antigen detection: application in nasopharyngeal swab specimens

Author

Barlev-Gross, Moria, primary, Weiss, Shay, additional, Ben-Shmuel, Amir, additional, Sittner, Assa, additional, Eden, Keren, additional, Mazuz, Noam, additional, Glinert, Itai, additional, Bar-David, Elad, additional, Puni, Reut, additional, Amit, Sharon, additional, Kriger, Or, additional, Schuster, Ofir, additional, Alcalay, Ron, additional, Makdasi, Efi, additional, Epstein, Eyal, additional, Noy-Porat, Tal, additional, Rosenfeld, Ronit, additional, Achdout, Hagit, additional, Mazor, Ohad, additional, Israely, Tomer, additional, Levy, Haim, additional, and Mechaly, Adva, additional

Published
2021
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89. Accelerating the Evolution of Nonhuman Primate Neuroimaging

Author

Milham, Michael, Petkov, Christopher I., Margulies, Daniel S., Schroeder, Charles E., Basso, Michele A., Belin, Pascal, Fair, Damien A., Fox, Andrew, Kastner, Sabine, Mars, Rogier B., Messinger, Adam, Poirier, Colline, Vanduffel, Wim, Van Essen, David C., Alvand, Ashkan, Becker, Yannick, Ben Hamed, Suliann, Benn, Austin, Bodin, Clementine, Boretius, Susann, Cagna, Bastien, Coulon, Olivier, El-Gohary, Sherif Hamdy, Evrard, Henry, Forkel, Stephanie J., Friedrich, Patrick, Froudist-Walsh, Sean, Garza-Villarreal, Eduardo A., Gao, Yang, Gozzi, Alessandro, Grigis, Antoine, Hartig, Renee, Hayashi, Takuya, Heuer, Katja, Howells, Henrietta, Ardesch, Dirk Jan, Jarrett, Wendy, Jedema, Hank P., Kagan, Igor, Kelly, Clare, Kennedy, Henry, Klink, P. Christiaan, Kwok, Sze Chai, Leech, Robert, Liu, Xiaojin, Madan, Christopher, Madushanka, Wasana, Majka, Piotr, Mallon, Ann-Marie, Marche, Kevin, Meguerditchian, Adrien, Menon, Ravi S., Merchant, Hugo, Mitchell, Anna, Nenning, Karl-Heinz, Nikolaidis, Aki, Ortiz-Rios, Michael, Pagani, Marco, Pareek, Vikas, Prescott, Mark, Procyk, Emmanuel, Rajimehr, Reza, Rautu, Ioana-Sabina, Raz, Amir, Roe, Anna Wang, Roumazeilles, Lea, Sakai, Tomoko, Sallet, Jerome, Sato, Chika, Sawiak, Stephen, Schiffer, Marike, Schwiedrzik, Caspar M., Seidlitz, Jakob, Sein, Julien, Shen, Zhi-ming, Shmuel, Amir, Silva, Afonso C., Simone, Luciano, Sirmpilatze, Nikoloz, Sliwa, Julia, Smallwood, Jonathan, Tasserie, Jordy, Thiebaut de Schotten, Michel, Toro, Roberto, Trapeau, Regis, Uhrig, Lynn, Vezoli, Julien, Wang, Zheng, Wells, Sara, Williams, Bella, Xu, Ting, Xu, Augix Guohua, Yacoub, Essa, Zhan, Ming, Ai, Lei, Balezeau, Fabien, Baxter, Mark G., Blezer, Erwin L.A., Brochier, Thomas, Chen, Aihua, Croxson, Paula L., Damatac, Christienne G., Dehaene, Stanislas, Everling, Stefan, Fleysher, Lazar, Freiwald, Winrich, Griffiths, Timothy D., Guedj, Carole, Hadj-Bouziane, Fadila, Harel, Noam, Hiba, Bassem, Jung, Benjamin, Koo, Bonhwang, Laland, Kevin N., Leopold, David A., Lindenfors, Patrik, Meunier, Martine, Mok, Kelvin, Morrison, John H., Nacef, Jennifer, Nagy, Jamie, Pinsk, Mark, Reader, Simon M., Roelfsema, Pieter R., Rudko, David A., Rushworth, Matthew F.S., Russ, Brian E., Schmid, Michael Christoph, Sullivan, Elinor L., Thiele, Alexander, Todorov, Orlin S., Tsao, Doris, Ungerleider, Leslie, Wilson, Charles R.E., Ye, Frank Q., Zarco, Wilbert, and Zhou, Yong-di

Subjects
General Neuroscience
Abstract

Nonhuman primate neuroimaging is on the cusp of a transformation, much in the same way its human counterpart was in 2010, when the Human Connectome Project was launched to accelerate progress. Inspired by an open data-sharing initiative, the global community recently met and, in this article, breaks through obstacles to define its ambitions.

Published
2020

90. Dexmedetomidine — commonly used in resting-state and neurovascular coupling studies — is prone to inducing seizures in rats but not in wild type mice

Author

Bortel, Aleksandra, Yao, Ze Shan, and Shmuel, Amir

Abstract

Functional MRI (fMRI) of the resting-state utilizes spontaneous fluctuations in metabolic and hemodynamic signals to indirectly infer the underlying local changes in neuronal activity. For correct interpretation of spontaneous fluctuations and functional connectivity in the resting-state, it is important to characterize the neuronal mechanisms of fMRI in animal models. Animal studies of the evoked response and resting-state commonly use dexmedetomidine sedation. It has been demonstrated that dexmedetomidine combined with potent sensory stimuli is prone to inducing seizures in Sprague-Dawley (SD) rats. To characterize these seizures, here we combined optical imaging of intrinsic signals and cerebral blood flow with neurophysiological recordings. We characterize the susceptibility to seizures as a function of time from the beginning of dexmedetomidine administration. We show that these seizures are associated with spatially extensive high-amplitude cerebral blood flow and blood oxygenation responses, prone to be misinterpreted as normal responses in functional imaging studies that do not use neurophysiological recordings. We demonstrate that such seizures are generated not only in SD rats but also in Long-Evans rats. In contrast, we did not observe any seizures in C57BL6 mice that were similarly sedated with dexmedetomidine and stimulated with similar potent stimuli. We conclude that caution should be practiced in experiments that combine the administration of potent stimuli with dexmedetomidine sedation because high-amplitude hemodynamic responses evoked by peripheral stimulations are possibly due to the induction of epileptic activity in the cortical brain area. We further conclude that the susceptibility to dexmedetomidine-induced seizures is species dependent.

Published
2019
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98. Mice with Induced Pulmonary Comorbidities Display Severe Lung Inflammation and Mortality following Exposure to SARS-CoV-2

Author

Falach, Reut, primary, Bar-On, Liat, additional, Lazar, Shlomi, additional, Kadar, Tamar, additional, Mazor, Ohad, additional, Aftalion, Moshe, additional, Gur, David, additional, Shifman, Ohad, additional, Israeli, Ofir, additional, Cohen-Gihon, Inbar, additional, Zaide, Galia, additional, Gutman, Hila, additional, Evgy, Yentl, additional, Vagima, Yaron, additional, Makdasi, Efi, additional, Stein, Dana, additional, Rosenfeld, Ronit, additional, Alcalay, Ron, additional, Zahavy, Eran, additional, Levy, Haim, additional, Glinert, Itai, additional, Ben-Shmuel, Amir, additional, Israely, Tomer, additional, Melamed, Sharon, additional, Politi, Boaz, additional, Achdout, Hagit, additional, Yitzhaki, Shmuel, additional, Kronman, Chanoch, additional, and Sabo, Tamar, additional

Published
2020
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100. Paranode stability requires UNC5B expression by oligodendrocytes

Author

de Faria, Omar, primary, Nakamura, Diane S., additional, Clemot, Samuel, additional, Kim, Doyeun, additional, Mocanu, Mihai Victor, additional, Pilgram, Roland, additional, Bin, Jenea M., additional, Wong, Edwin W., additional, Shmuel, Amir, additional, Sadikot, Abbas, additional, Ackerman, Susan L., additional, and Kennedy, Timothy E., additional

Published
2020
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