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2. Neuroscience needs Network Science

Author

Barabási, Dániel L, Bianconi, Ginestra, Bullmore, Ed, Burgess, Mark, Chung, SueYeon, Eliassi-Rad, Tina, George, Dileep, Kovács, István A., Makse, Hernán, Papadimitriou, Christos, Nichols, Thomas E., Sporns, Olaf, Stachenfeld, Kim, Toroczkai, Zoltán, Towlson, Emma K., Zador, Anthony M, Zeng, Hongkui, Barabási, Albert-László, Bernard, Amy, and Buzsáki, György

Subjects
Quantitative Biology - Neurons and Cognition
Abstract

The brain is a complex system comprising a myriad of interacting elements, posing significant challenges in understanding its structure, function, and dynamics. Network science has emerged as a powerful tool for studying such intricate systems, offering a framework for integrating multiscale data and complexity. Here, we discuss the application of network science in the study of the brain, addressing topics such as network models and metrics, the connectome, and the role of dynamics in neural networks. We explore the challenges and opportunities in integrating multiple data streams for understanding the neural transitions from development to healthy function to disease, and discuss the potential for collaboration between network science and neuroscience communities. We underscore the importance of fostering interdisciplinary opportunities through funding initiatives, workshops, and conferences, as well as supporting students and postdoctoral fellows with interests in both disciplines. By uniting the network science and neuroscience communities, we can develop novel network-based methods tailored to neural circuits, paving the way towards a deeper understanding of the brain and its functions., Comment: 19 pages, 1 figure, 1 box

Published
2023

3. Neurobiology and Changing Ecosystems: toward understanding the impact of anthropogenic influences on neurons and circuits

Author

Michaiel, Angie and Bernard, Amy

Subjects
Quantitative Biology - Neurons and Cognition
Abstract

Rapid anthropogenic environmental changes, including those due to habitat contamination, degradation, and climate change, have far-reaching effects on biological systems that may outpace animals' adaptive responses (Radchuk et al., 2019). Neurobiological systems mediate interactions between animals and their environments and evolved over millions of years to detect and respond to change. To gain an understanding of the adaptive capacity of nervous systems given and unprecedented pace of environmental change, mechanisms of physiology and behavior at the cellular and biophysical level must be examined. While behavioral changes resulting from anthropogenic activity are becoming increasingly described, identification and examination of the cellular, molecular, and circuit-level processes underlying those changes are profoundly under-explored. Hence, the field of neuroscience lacks predictive frameworks to describe which neurobiology systems may be resilient or vulnerable to rapidly changing ecosystems, or what modes of adaptation are represented in our natural world. In this review, we highlight examples of animal behavior modification and corresponding nervous system adaptation in response to rapid environmental change. The underlying cellular, molecular, and circuit-level component processes underlying these behaviors are not known and emphasize the unmet need for rigorous scientific enquiry into the neurobiology of changing ecosystems., Comment: In review at Frontiers in Neural Circuits

Published
2022

4. Opportunities and challenges for innovative and equitable healthcare

Author

Ecker, David J., Aiello, Clarice D., Arron, Joseph R., Bennett, C. Frank, Bernard, Amy, Breakefield, Xandra O., Broderick, Timothy J., Callier, Shawneequa L., Canton, Barry, Chen, Janice S., Fishburn, C. Simone, Garrett, Banning, Hecht, Sidney M., Janowitz, Tobias, Kliegman, Melinda, Krainer, Adrian, Louis, Chrystal U., Lowe, Christopher, Sehgal, Alfica, Tozan, Yesim, Tracey, Kevin J., Urnov, Fyodor, Wattendorf, Daniel, Williams, Thomas W., Zhao, Xuanhe, and Hayden, Michael R.

Published
2024
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5. International data governance for neuroscience

Author

Eke, Damian O, Bernard, Amy, Bjaalie, Jan G, Chavarriaga, Ricardo, Hanakawa, Takashi, Hannan, Anthony J, Hill, Sean L, Martone, Maryann E, McMahon, Agnes, Ruebel, Oliver, Crook, Sharon, Thiels, Edda, and Pestilli, Franco

Subjects
Neurosciences, 8.3 Policy, ethics, and research governance, Health and social care services research, Peace, Justice and Strong Institutions, Computer Security, Ecosystem, Information Dissemination, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

As neuroscience projects increase in scale and cross international borders, different ethical principles, national and international laws, regulations, and policies for data sharing must be considered. These concerns are part of what is collectively called data governance. Whereas neuroscience data transcend borders, data governance is typically constrained within geopolitical boundaries. An international data governance framework and accompanying infrastructure can assist investigators, institutions, data repositories, and funders with navigating disparate policies. Here, we propose principles and operational considerations for how data governance in neuroscience can be navigated at an international scale and highlight gaps, challenges, and opportunities in a global brain data ecosystem. We consider how to approach data governance in a way that balances data protection requirements and the need for open science, so as to promote international collaboration through federated constructs such as the International Brain Initiative (IBI).

Published
2022

6. Common Cell type Nomenclature for the mammalian brain: A systematic, extensible convention

Author

Miller, Jeremy A., Gouwens, Nathan W., Tasic, Bosiljka, Collman, Forrest, van Velthoven, Cindy T. J., Bakken, Trygve E., Hawrylycz, Michael J., Zeng, Hongkui, Lein, Ed S., and Bernard, Amy

Subjects
Quantitative Biology - Neurons and Cognition
Abstract

The advancement of single cell RNA-sequencing technologies has led to an explosion of cell type definitions across multiple organs and organisms. While standards for data and metadata intake are arising, organization of cell types has largely been left to individual investigators, resulting in widely varying nomenclature and limited alignment between taxonomies. To facilitate cross-dataset comparison, the Allen Institute created the Common Cell type Nomenclature (CCN) for matching and tracking cell types across studies that is qualitatively similar to gene transcript management across different genome builds. The CCN can be readily applied to new or established taxonomies and was applied herein to diverse cell type datasets derived from multiple quantifiable modalities. The CCN facilitates assigning accurate yet flexible cell type names in the mammalian cortex as a step towards community-wide efforts to organize multi-source, data-driven information related to cell type taxonomies from any organism., Comment: 29 pages, 5 figures, 4 tables, 1 supplementary table

Published
2020

7. Transcriptomic evidence that von Economo neurons are regionally specialized extratelencephalic-projecting excitatory neurons

Author

Hodge, Rebecca D, Miller, Jeremy A, Novotny, Mark, Kalmbach, Brian E, Ting, Jonathan T, Bakken, Trygve E, Aevermann, Brian D, Barkan, Eliza R, Berkowitz-Cerasano, Madeline L, Cobbs, Charles, Diez-Fuertes, Francisco, Ding, Song-Lin, McCorrison, Jamison, Schork, Nicholas J, Shehata, Soraya I, Smith, Kimberly A, Sunkin, Susan M, Tran, Danny N, Venepally, Pratap, Yanny, Anna Marie, Steemers, Frank J, Phillips, John W, Bernard, Amy, Koch, Christof, Lasken, Roger S, Scheuermann, Richard H, and Lein, Ed S

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Neurosciences, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Animals, Brain, Electrophysiology, Gene Expression Profiling, Humans, In Situ Hybridization, Fluorescence, Mice, Neurons, Pyramidal Cells, Telencephalon, Temporal Lobe, Transcriptome
Abstract

von Economo neurons (VENs) are bipolar, spindle-shaped neurons restricted to layer 5 of human frontoinsula and anterior cingulate cortex that appear to be selectively vulnerable to neuropsychiatric and neurodegenerative diseases, although little is known about other VEN cellular phenotypes. Single nucleus RNA-sequencing of frontoinsula layer 5 identifies a transcriptomically-defined cell cluster that contained VENs, but also fork cells and a subset of pyramidal neurons. Cross-species alignment of this cell cluster with a well-annotated mouse classification shows strong homology to extratelencephalic (ET) excitatory neurons that project to subcerebral targets. This cluster also shows strong homology to a putative ET cluster in human temporal cortex, but with a strikingly specific regional signature. Together these results suggest that VENs are a regionally distinctive type of ET neuron. Additionally, we describe the first patch clamp recordings of VENs from neurosurgically-resected tissue that show distinctive intrinsic membrane properties relative to neighboring pyramidal neurons.

Published
2020

8. Conserved cell types with divergent features in human versus mouse cortex.

Author

Hodge, Rebecca D, Bakken, Trygve E, Miller, Jeremy A, Smith, Kimberly A, Barkan, Eliza R, Graybuck, Lucas T, Close, Jennie L, Long, Brian, Johansen, Nelson, Penn, Osnat, Yao, Zizhen, Eggermont, Jeroen, Höllt, Thomas, Levi, Boaz P, Shehata, Soraya I, Aevermann, Brian, Beller, Allison, Bertagnolli, Darren, Brouner, Krissy, Casper, Tamara, Cobbs, Charles, Dalley, Rachel, Dee, Nick, Ding, Song-Lin, Ellenbogen, Richard G, Fong, Olivia, Garren, Emma, Goldy, Jeff, Gwinn, Ryder P, Hirschstein, Daniel, Keene, C Dirk, Keshk, Mohamed, Ko, Andrew L, Lathia, Kanan, Mahfouz, Ahmed, Maltzer, Zoe, McGraw, Medea, Nguyen, Thuc Nghi, Nyhus, Julie, Ojemann, Jeffrey G, Oldre, Aaron, Parry, Sheana, Reynolds, Shannon, Rimorin, Christine, Shapovalova, Nadiya V, Somasundaram, Saroja, Szafer, Aaron, Thomsen, Elliot R, Tieu, Michael, Quon, Gerald, Scheuermann, Richard H, Yuste, Rafael, Sunkin, Susan M, Lelieveldt, Boudewijn, Feng, David, Ng, Lydia, Bernard, Amy, Hawrylycz, Michael, Phillips, John W, Tasic, Bosiljka, Zeng, Hongkui, Jones, Allan R, Koch, Christof, and Lein, Ed S

Subjects
Cerebral Cortex, Astrocytes, Neurons, Animals, Humans, Mice, Species Specificity, Neural Inhibition, Principal Component Analysis, Adolescent, Adult, Aged, Middle Aged, Female, Male, Young Adult, Biological Evolution, Single-Cell Analysis, Transcriptome, RNA-Seq, Genetics, Neurosciences, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Aetiology, Underpinning research, Neurological, General Science & Technology
Abstract

Elucidating the cellular architecture of the human cerebral cortex is central to understanding our cognitive abilities and susceptibility to disease. Here we used single-nucleus RNA-sequencing analysis to perform a comprehensive study of cell types in the middle temporal gyrus of human cortex. We identified a highly diverse set of excitatory and inhibitory neuron types that are mostly sparse, with excitatory types being less layer-restricted than expected. Comparison to similar mouse cortex single-cell RNA-sequencing datasets revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of properties of human cell types. Despite this general conservation, we also found extensive differences between homologous human and mouse cell types, including marked alterations in proportions, laminar distributions, gene expression and morphology. These species-specific features emphasize the importance of directly studying human brain.

Published
2019

9. Integrative functional genomic analysis of human brain development and neuropsychiatric risks

Author

Li, Mingfeng, Santpere, Gabriel, Imamura Kawasawa, Yuka, Evgrafov, Oleg V, Gulden, Forrest O, Pochareddy, Sirisha, Sunkin, Susan M, Li, Zhen, Shin, Yurae, Zhu, Ying, Sousa, André MM, Werling, Donna M, Kitchen, Robert R, Kang, Hyo Jung, Pletikos, Mihovil, Choi, Jinmyung, Muchnik, Sydney, Xu, Xuming, Wang, Daifeng, Lorente-Galdos, Belen, Liu, Shuang, Giusti-Rodríguez, Paola, Won, Hyejung, de Leeuw, Christiaan A, Pardiñas, Antonio F, Hu, Ming, Jin, Fulai, Li, Yun, Owen, Michael J, O’Donovan, Michael C, Walters, James TR, Posthuma, Danielle, Reimers, Mark A, Levitt, Pat, Weinberger, Daniel R, Hyde, Thomas M, Kleinman, Joel E, Geschwind, Daniel H, Hawrylycz, Michael J, State, Matthew W, Sanders, Stephan J, Sullivan, Patrick F, Gerstein, Mark B, Lein, Ed S, Knowles, James A, Sestan, Nenad, Willsey, A Jeremy, Oldre, Aaron, Szafer, Aaron, Camarena, Adrian, Cherskov, Adriana, Charney, Alexander W, Abyzov, Alexej, Kozlenkov, Alexey, Safi, Alexias, Jones, Allan R, Ashley-Koch, Allison E, Ebbert, Amanda, Price, Amanda J, Sekijima, Amanda, Kefi, Amira, Bernard, Amy, Amiri, Anahita, Sboner, Andrea, Clark, Andrew, Jaffe, Andrew E, Tebbenkamp, Andrew TN, Sodt, Andy J, Guillozet-Bongaarts, Angie L, Nairn, Angus C, Carey, Anita, Huttner, Anita, Chervenak, Ann, Szekely, Anna, Shieh, Annie W, Harmanci, Arif, Lipska, Barbara K, Carlyle, Becky C, Gregor, Ben W, Kassim, Bibi S, Sheppard, Brooke, Bichsel, Candace, Hahn, Chang-Gyu, Lee, Chang-Kyu, Chen, Chao, Kuan, Chihchau L, Dang, Chinh, Lau, Chris, Cuhaciyan, Christine, Armoskus, Christoper, Mason, Christopher E, Liu, Chunyu, Slaughterbeck, Cliff R, Bennet, Crissa, Pinto, Dalila, Polioudakis, Damon, Franjic, Daniel, Miller, Daniel J, Bertagnolli, Darren, and Lewis, David A

Subjects
Human Genome, Genetics, Neurosciences, Biotechnology, Pediatric, Mental Health, Brain, Epigenesis, Genetic, Epigenomics, Gene Expression Regulation, Developmental, Gene Regulatory Networks, Humans, Mental Disorders, Nervous System Diseases, Neurogenesis, Single-Cell Analysis, Transcriptome, BrainSpan Consortium, PsychENCODE Consortium, PsychENCODE Developmental Subgroup, General Science & Technology
Abstract

To broaden our understanding of human neurodevelopment, we profiled transcriptomic and epigenomic landscapes across brain regions and/or cell types for the entire span of prenatal and postnatal development. Integrative analysis revealed temporal, regional, sex, and cell type-specific dynamics. We observed a global transcriptomic cup-shaped pattern, characterized by a late fetal transition associated with sharply decreased regional differences and changes in cellular composition and maturation, followed by a reversal in childhood-adolescence, and accompanied by epigenomic reorganizations. Analysis of gene coexpression modules revealed relationships with epigenomic regulation and neurodevelopmental processes. Genes with genetic associations to brain-based traits and neuropsychiatric disorders (including MEF2C, SATB2, SOX5, TCF4, and TSHZ3) converged in a small number of modules and distinct cell types, revealing insights into neurodevelopment and the genomic basis of neuropsychiatric risks.

Published
2018

10. Anatomical structures, cell types and biomarkers of the Human Reference Atlas

Author

Börner, Katy, Teichmann, Sarah A., Quardokus, Ellen M., Gee, James C., Browne, Kristen, Osumi-Sutherland, David, Herr, II, Bruce W., Bueckle, Andreas, Paul, Hrishikesh, Haniffa, Muzlifah, Jardine, Laura, Bernard, Amy, Ding, Song-Lin, Miller, Jeremy A., Lin, Shin, Halushka, Marc K., Boppana, Avinash, Longacre, Teri A., Hickey, John, Lin, Yiing, Valerius, M. Todd, He, Yongqun, Pryhuber, Gloria, Sun, Xin, Jorgensen, Marda, Radtke, Andrea J., Wasserfall, Clive, Ginty, Fiona, Ho, Jonhan, Sunshine, Joel, Beuschel, Rebecca T., Brusko, Maigan, Lee, Sujin, Malhotra, Rajeev, Jain, Sanjay, and Weber, Griffin

Published
2021
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11. Human neocortical expansion involves glutamatergic neuron diversification

Author

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

Published
2021
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12. Factors Predictive of Knowledge and Self-Management Behaviors among Male Military Veterans with Diabetes Residing in a Homeless Shelter for People Recovering from Addiction

Author

Rojas-Guyler, Liliana, Inniss-Richter, Zipporah M., Lee, Rebecca, Bernard, Amy, and King, Keith

Abstract

Diabetes disproportionately affects individuals with lower income in the U.S. (CDC, 2012). Specifically the control of diabetes through self-management has been found to be sub-par and an important contributor to complications (Seligman, Davis, Schillinger, & Wolf, 2010). People experiencing homelessness also experience barriers. One such group is homeless veterans who have diabetes. The purpose of this study was to investigate self-management behaviors and knowledge regarding diabetes among homeless military veterans in order to establish a baseline of knowledge, self-management behaviors, attitudes, and barriers. A cross-sectional convenience sample of 27 homeless military veterans at a local shelter completed face-to-face structured survey interviews. Blood glucose monitoring behaviors were adequate but foot and eye care behaviors need improvement. Gaps existed in knowledge and attitudes about diabetes. Barriers such as lack of access to healthy food and lack of knowledge of how to cook limited their ability to self-manage diabetes. Veterans who had higher knowledge scores, and had been diagnosed longer, had higher self-management scores. Findings from this study help to inform the existing need for health educators to engage with veterans diagnosed with diabetes to improve health outcomes.

Published
2014

13. Using a Modified Theory of Planned Behavior to Examine Teachers' Intention to Implement a Work Safety and Health Curriculum

Author

Guerin, Rebecca J., Toland, Michael D., Okun, Andrea H., Rojas-Guyler, Liliana, Baker, Devin S., and Bernard, Amy L.

Abstract

Background: Workplace safety and health is a major public health concern, but largely absent from the school health curriculum. Little is known about teachers' perceptions of teaching workplace safety and health topics. Methods: We administered a 41-item questionnaire reflecting the theory of planned behavior, modified to measure knowledge, to 242 middle and high school teachers in career and technical education and academic subjects. We conducted confirmatory factor analysis to assess the measures' psychometric properties and factorial ANOVAs to compare differences among participants' knowledge, attitude toward, self-efficacy, and intention (to teach) workplace safety and health by sex, prior work injury, and main subject taught. Results: Confirmatory factor analyses indicated the measures reflected the theory. Factorial ANOVAs suggested female teachers had statistically significantly lower mean self-efficacy scores than did male teachers to teach workplace safety and health. Male occupational career and technical education teachers demonstrated higher mean knowledge scores than male teachers in other subjects. Participants not injured at work had higher knowledge scores than those who had been injured. Conclusion: Self-efficacy (influenced by sex) and knowledge (influenced by subject taught and previous workplace injury) revealed factors that may affect teachers' provision of workplace safety and health education, a critical yet overlooked component of school health.

Published
2019
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14. Survey of spiking in the mouse visual system reveals functional hierarchy

Author

Siegle, Joshua H., Jia, Xiaoxuan, Durand, Séverine, Gale, Sam, Bennett, Corbett, Graddis, Nile, Heller, Greggory, Ramirez, Tamina K., Choi, Hannah, Luviano, Jennifer A., Groblewski, Peter A., Ahmed, Ruweida, Arkhipov, Anton, Bernard, Amy, Billeh, Yazan N., Brown, Dillan, Buice, Michael A., Cain, Nicolas, Caldejon, Shiella, Casal, Linzy, Cho, Andrew, Chvilicek, Maggie, Cox, Timothy C., Dai, Kael, Denman, Daniel J., de Vries, Saskia E. J., Dietzman, Roald, Esposito, Luke, Farrell, Colin, Feng, David, Galbraith, John, Garrett, Marina, Gelfand, Emily C., Hancock, Nicole, Harris, Julie A., Howard, Robert, Hu, Brian, Hytnen, Ross, Iyer, Ramakrishnan, Jessett, Erika, Johnson, Katelyn, Kato, India, Kiggins, Justin, Lambert, Sophie, Lecoq, Jerome, Ledochowitsch, Peter, Lee, Jung Hoon, Leon, Arielle, Li, Yang, Liang, Elizabeth, Long, Fuhui, Mace, Kyla, Melchior, Jose, Millman, Daniel, Mollenkopf, Tyler, Nayan, Chelsea, Ng, Lydia, Ngo, Kiet, Nguyen, Thuyahn, Nicovich, Philip R., North, Kat, Ocker, Gabriel Koch, Ollerenshaw, Doug, Oliver, Michael, Pachitariu, Marius, Perkins, Jed, Reding, Melissa, Reid, David, Robertson, Miranda, Ronellenfitch, Kara, Seid, Sam, Slaughterbeck, Cliff, Stoecklin, Michelle, Sullivan, David, Sutton, Ben, Swapp, Jackie, Thompson, Carol, Turner, Kristen, Wakeman, Wayne, Whitesell, Jennifer D., Williams, Derric, Williford, Ali, Young, Rob, Zeng, Hongkui, Naylor, Sarah, Phillips, John W., Reid, R. Clay, Mihalas, Stefan, Olsen, Shawn R., and Koch, Christof

Published
2021
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15. A comprehensive transcriptional map of primate brain development.

Author

Bakken, Trygve E, Miller, Jeremy A, Ding, Song-Lin, Sunkin, Susan M, Smith, Kimberly A, Ng, Lydia, Szafer, Aaron, Dalley, Rachel A, Royall, Joshua J, Lemon, Tracy, Shapouri, Sheila, Aiona, Kaylynn, Arnold, James, Bennett, Jeffrey L, Bertagnolli, Darren, Bickley, Kristopher, Boe, Andrew, Brouner, Krissy, Butler, Stephanie, Byrnes, Emi, Caldejon, Shiella, Carey, Anita, Cate, Shelby, Chapin, Mike, Chen, Jefferey, Dee, Nick, Desta, Tsega, Dolbeare, Tim A, Dotson, Nadia, Ebbert, Amanda, Fulfs, Erich, Gee, Garrett, Gilbert, Terri L, Goldy, Jeff, Gourley, Lindsey, Gregor, Ben, Gu, Guangyu, Hall, Jon, Haradon, Zeb, Haynor, David R, Hejazinia, Nika, Hoerder-Suabedissen, Anna, Howard, Robert, Jochim, Jay, Kinnunen, Marty, Kriedberg, Ali, Kuan, Chihchau L, Lau, Christopher, Lee, Chang-Kyu, Lee, Felix, Luong, Lon, Mastan, Naveed, May, Ryan, Melchor, Jose, Mosqueda, Nerick, Mott, Erika, Ngo, Kiet, Nyhus, Julie, Oldre, Aaron, Olson, Eric, Parente, Jody, Parker, Patrick D, Parry, Sheana, Pendergraft, Julie, Potekhina, Lydia, Reding, Melissa, Riley, Zackery L, Roberts, Tyson, Rogers, Brandon, Roll, Kate, Rosen, David, Sandman, David, Sarreal, Melaine, Shapovalova, Nadiya, Shi, Shu, Sjoquist, Nathan, Sodt, Andy J, Townsend, Robbie, Velasquez, Lissette, Wagley, Udi, Wakeman, Wayne B, White, Cassandra, Bennett, Crissa, Wu, Jennifer, Young, Rob, Youngstrom, Brian L, Wohnoutka, Paul, Gibbs, Richard A, Rogers, Jeffrey, Hohmann, John G, Hawrylycz, Michael J, Hevner, Robert F, Molnár, Zoltán, Phillips, John W, Dang, Chinh, Jones, Allan R, Amaral, David G, Bernard, Amy, and Lein, Ed S

Subjects
Brain, Neocortex, Animals, Macaca mulatta, Humans, Microcephaly, Risk Factors, Schizophrenia, Cell Adhesion, Species Specificity, Transcription, Genetic, Conserved Sequence, Aging, Female, Male, Neurogenesis, Intellectual Disability, Transcriptome, Spatio-Temporal Analysis, Autism Spectrum Disorder, Neurodevelopmental Disorders, Transcription, Genetic, General Science & Technology
Abstract

The transcriptional underpinnings of brain development remain poorly understood, particularly in humans and closely related non-human primates. We describe a high-resolution transcriptional atlas of rhesus monkey (Macaca mulatta) brain development that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical division of cortical and subcortical regions associated with human neuropsychiatric disease. Gene expression changes more rapidly before birth, both in progenitor cells and maturing neurons. Cortical layers and areas acquire adult-like molecular profiles surprisingly late in postnatal development. Disparate cell populations exhibit distinct developmental timing of gene expression, but also unexpected synchrony of processes underlying neural circuit construction including cell projection and adhesion. Candidate risk genes for neurodevelopmental disorders including primary microcephaly, autism spectrum disorder, intellectual disability, and schizophrenia show disease-specific spatiotemporal enrichment within developing neocortex. Human developmental expression trajectories are more similar to monkey than rodent, although approximately 9% of genes show human-specific regulation with evidence for prolonged maturation or neoteny compared to monkey.

Published
2016

16. Teachers' Strategies to Positively Connect Students to School

Author

Vidourek, Rebecca A., King, Keith A., and Bernard, Amy L.

Abstract

Background: School connectedness is a leading school-based protective factor against youth engagement in risky behaviors. Research on teachers' individual practices in fostering school connections with their students is currently lacking. Purpose: The purpose of the present study was to address gaps in the research by examining elementary and middle school teachers' use of specific strategies to positively connect students to school. Methods: An electronic survey was completed by 419 (60% response rate) elementary and middle school teachers. Results: On average, teachers reported using connection-building strategies at least once a week. The most frequently used strategies were acting like a positive role model for students and calling students by their first names. MANOVAs were conducted and found teachers who most frequently reported using connection-building strategies were elementary school teachers, those who had received training on school connectedness outside of/after college, and those working at a school with connection-building as a leading priority. Discussion: Training teachers on positively connecting students to school was associated with increased use of connection-building techniques in the classroom. Translation to Health Education Practice: Findings have implications for health education professionals interested in increasing school connectedness among students through teacher practices and school priorities. (Contains 5 tables.)

Published
2011

17. A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex

Author

de Vries, Saskia E. J., Lecoq, Jerome A., Buice, Michael A., Groblewski, Peter A., Ocker, Gabriel K., Oliver, Michael, Feng, David, Cain, Nicholas, Ledochowitsch, Peter, Millman, Daniel, Roll, Kate, Garrett, Marina, Keenan, Tom, Kuan, Leonard, Mihalas, Stefan, Olsen, Shawn, Thompson, Carol, Wakeman, Wayne, Waters, Jack, Williams, Derric, Barber, Chris, Berbesque, Nathan, Blanchard, Brandon, Bowles, Nicholas, Caldejon, Shiella D., Casal, Linzy, Cho, Andrew, Cross, Sissy, Dang, Chinh, Dolbeare, Tim, Edwards, Melise, Galbraith, John, Gaudreault, Nathalie, Gilbert, Terri L., Griffin, Fiona, Hargrave, Perry, Howard, Robert, Huang, Lawrence, Jewell, Sean, Keller, Nika, Knoblich, Ulf, Larkin, Josh D., Larsen, Rachael, Lau, Chris, Lee, Eric, Lee, Felix, Leon, Arielle, Li, Lu, Long, Fuhui, Luviano, Jennifer, Mace, Kyla, Nguyen, Thuyanh, Perkins, Jed, Robertson, Miranda, Seid, Sam, Shea-Brown, Eric, Shi, Jianghong, Sjoquist, Nathan, Slaughterbeck, Cliff, Sullivan, David, Valenza, Ryan, White, Casey, Williford, Ali, Witten, Daniela M., Zhuang, Jun, Zeng, Hongkui, Farrell, Colin, Ng, Lydia, Bernard, Amy, Phillips, John W., Reid, R. Clay, and Koch, Christof

Published
2020
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18. Spatiotemporal dynamics of the postnatal developing primate brain transcriptome.

Author

Bakken, Trygve E, Miller, Jeremy A, Luo, Rui, Bernard, Amy, Bennett, Jeffrey L, Lee, Chang-Kyu, Bertagnolli, Darren, Parikshak, Neelroop N, Smith, Kimberly A, Sunkin, Susan M, Amaral, David G, Geschwind, Daniel H, and Lein, Ed S

Subjects
Cerebral Cortex, Animals, Macaca mulatta, Humans, Gene Expression Profiling, Age Factors, Gene Expression Regulation, Developmental, Gene Regulatory Networks, Neurogenesis, Transcriptome, Autism Spectrum Disorder, Gene Expression Regulation, Developmental, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Developmental changes in the temporal and spatial regulation of gene expression drive the emergence of normal mature brain function, while disruptions in these processes underlie many neurodevelopmental abnormalities. To solidify our foundational knowledge of such changes in a primate brain with an extended period of postnatal maturation like in human, we investigated the whole-genome transcriptional profiles of rhesus monkey brains from birth to adulthood. We found that gene expression dynamics are largest from birth through infancy, after which gene expression profiles transition to a relatively stable state by young adulthood. Biological pathway enrichment analysis revealed that genes more highly expressed at birth are associated with cell adhesion and neuron differentiation, while genes more highly expressed in juveniles and adults are associated with cell death. Neocortex showed significantly greater differential expression over time than subcortical structures, and this trend likely reflects the protracted postnatal development of the cortex. Using network analysis, we identified 27 co-expression modules containing genes with highly correlated expression patterns that are associated with specific brain regions, ages or both. In particular, one module with high expression in neonatal cortex and striatum that decreases during infancy and juvenile development was significantly enriched for autism spectrum disorder (ASD)-related genes. This network was enriched for genes associated with axon guidance and interneuron differentiation, consistent with a disruption in the formation of functional cortical circuitry in ASD.

Published
2015

19. Do the Depictions of Sexual Attire and Sexual Behavior in Music Videos Differ Based on Video Network and Character Gender?

Author

King, Keith, Laake, Rebecca A., and Bernard, Amy

Abstract

This study examined the sexual messages depicted in music videos aired on MTV, MTV2, BET, and GAC from August 2, 2004 to August 15, 2004. One-hour segments of music videos were taped daily for two weeks. Depictions of sexual attire and sexual behavior were analyzed via a four-page coding sheet (interrater-reliability = 0.93). Results indicated that there were 39,559 depictions of female sexual attire (M = 278.58 per video, SD = 626.93) and 3,032 depictions of male sexual attire (M = 21.35 per video, SD = 55.14). There were 7,291 depictions of sexual behavior for females (M = 51.35 per video, SD = 135.07) compared to 2,511 sexual behaviors for males (M = 17.68 per video, SD = 40.35). Female sexual attire and sexual behavior were displayed more frequently than male sexual attire and sexual behavior. Sexual attire and sexual behavior were displayed significantly more frequently on BET than on MTV, MTV2, or GAC. Music videos on BET scored an average of 758.88 sexual depictions per video, followed by MTV with an average of 206.75 sexual depictions per video. Potential implications of these results and recommendations for future research are offered. (Contains 5 tables.)

Published
2006

20. Melanoma Knowledge and Sun Protection Attitudes and Behaviors among College Students by Gender and Skin Type

Author

Cottrell, Randall, McClamroch, Leslie, and Bernard, Amy L.

Abstract

The purpose of this study was to evaluate the melanoma and sun protection knowledge, attitudes and behaviors of college students attending a large Midwestern university. Further, gender and skin type (fair, medium, or dark) were examined as potential intervening variables. Results indicate that the college students studied had low knowledge levels related to melanoma and sun prevention behaviors. Their attitudes toward sun protection were in the medium range, being neither strongly positive nor negative. Their general sun protection behaviors and specific sunscreen use behaviors were fairly poor. Both gender and skin type were found to have a significant impact on melanoma knowledge and sun protection attitudes and behaviors. Females and those with fair skin were more knowledgeable and had better attitudes and behaviors. Implications of these findings for health educators are thoroughly discussed.

Published
2005

21. A High-Resolution Spatiotemporal Atlas of Gene Expression of the Developing Mouse Brain

Author

Thompson, Carol L, Ng, Lydia, Menon, Vilas, Martinez, Salvador, Lee, Chang-Kyu, Glattfelder, Katie, Sunkin, Susan M, Henry, Alex, Lau, Christopher, Dang, Chinh, Garcia-Lopez, Raquel, Martinez-Ferre, Almudena, Pombero, Ana, Rubenstein, John LR, Wakeman, Wayne B, Hohmann, John, Dee, Nick, Sodt, Andrew J, Young, Rob, Smith, Kimberly, Nguyen, Thuc-Nghi, Kidney, Jolene, Kuan, Leonard, Jeromin, Andreas, Kaykas, Ajamete, Miller, Jeremy, Page, Damon, Orta, Geri, Bernard, Amy, Riley, Zackery, Smith, Simon, Wohnoutka, Paul, Hawrylycz, Michael J, Puelles, Luis, and Jones, Allan R

Subjects
Neurosciences, Biotechnology, Genetics, Pediatric, 1.1 Normal biological development and functioning, Underpinning research, Neurological, Animals, Brain, Brain Mapping, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Developmental, Mice, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for ∼2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).

Published
2014

22. Transcriptional landscape of the prenatal human brain.

Author

Miller, Jeremy A, Ding, Song-Lin, Sunkin, Susan M, Smith, Kimberly A, Ng, Lydia, Szafer, Aaron, Ebbert, Amanda, Riley, Zackery L, Royall, Joshua J, Aiona, Kaylynn, Arnold, James M, Bennet, Crissa, Bertagnolli, Darren, Brouner, Krissy, Butler, Stephanie, Caldejon, Shiella, Carey, Anita, Cuhaciyan, Christine, Dalley, Rachel A, Dee, Nick, Dolbeare, Tim A, Facer, Benjamin AC, Feng, David, Fliss, Tim P, Gee, Garrett, Goldy, Jeff, Gourley, Lindsey, Gregor, Benjamin W, Gu, Guangyu, Howard, Robert E, Jochim, Jayson M, Kuan, Chihchau L, Lau, Christopher, Lee, Chang-Kyu, Lee, Felix, Lemon, Tracy A, Lesnar, Phil, McMurray, Bergen, Mastan, Naveed, Mosqueda, Nerick, Naluai-Cecchini, Theresa, Ngo, Nhan-Kiet, Nyhus, Julie, Oldre, Aaron, Olson, Eric, Parente, Jody, Parker, Patrick D, Parry, Sheana E, Stevens, Allison, Pletikos, Mihovil, Reding, Melissa, Roll, Kate, Sandman, David, Sarreal, Melaine, Shapouri, Sheila, Shapovalova, Nadiya V, Shen, Elaine H, Sjoquist, Nathan, Slaughterbeck, Clifford R, Smith, Michael, Sodt, Andy J, Williams, Derric, Zöllei, Lilla, Fischl, Bruce, Gerstein, Mark B, Geschwind, Daniel H, Glass, Ian A, Hawrylycz, Michael J, Hevner, Robert F, Huang, Hao, Jones, Allan R, Knowles, James A, Levitt, Pat, Phillips, John W, Sestan, Nenad, Wohnoutka, Paul, Dang, Chinh, Bernard, Amy, Hohmann, John G, and Lein, Ed S

Subjects
Brain, Neocortex, Fetus, Animals, Humans, Mice, Anatomy, Artistic, Species Specificity, Gene Expression Regulation, Developmental, Conserved Sequence, Gene Regulatory Networks, Atlases as Topic, Transcriptome, Anatomy, Artistic, Gene Expression Regulation, Developmental, General Science & Technology
Abstract

The anatomical and functional architecture of the human brain is mainly determined by prenatal transcriptional processes. We describe an anatomically comprehensive atlas of the mid-gestational human brain, including de novo reference atlases, in situ hybridization, ultra-high-resolution magnetic resonance imaging (MRI) and microarray analysis on highly discrete laser-microdissected brain regions. In developing cerebral cortex, transcriptional differences are found between different proliferative and post-mitotic layers, wherein laminar signatures reflect cellular composition and developmental processes. Cytoarchitectural differences between human and mouse have molecular correlates, including species differences in gene expression in subplate, although surprisingly we find minimal differences between the inner and outer subventricular zones even though the outer zone is expanded in humans. Both germinal and post-mitotic cortical layers exhibit fronto-temporal gradients, with particular enrichment in the frontal lobe. Finally, many neurodevelopmental disorder and human-evolution-related genes show patterned expression, potentially underlying unique features of human cortical formation. These data provide a rich, freely-accessible resource for understanding human brain development.

Published
2014

23. An anatomic transcriptional atlas of human glioblastoma

Author

Puchalski, Ralph B., Shah, Nameeta, Miller, Jeremy, Dalley, Rachel, Nomura, Steve R., Yoon, Jae-Guen, Smith, Kimberly A., Lankerovich, Michael, Bertagnolli, Darren, Bickley, Kris, Boe, Andrew F., Brouner, Krissy, Butler, Stephanie, Caldejon, Shiella, Chapin, Mike, Datta, Suvro, Dee, Nick, Desta, Tsega, Dolbeare, Tim, Dotson, Nadezhda, Ebbert, Amanda, Feng, David, Feng, Xu, Fisher, Michael, Gee, Garrett, Goldy, Jeff, Gourley, Lindsey, Gregor, Benjamin W., Gu, Guangyu, Hejazinia, Nika, Hohmann, John, Hothi, Parvinder, Howard, Robert, Joines, Kevin, Kriedberg, Ali, Kuan, Leonard, Lau, Chris, Lee, Felix, Lee, Hwahyung, Lemon, Tracy, Long, Fuhui, Mastan, Naveed, Mott, Erika, Murthy, Chantal, Ngo, Kiet, Olson, Eric, Reding, Melissa, Riley, Zack, Rosen, David, Sandman, David, Shapovalova, Nadiya, Slaughterbeck, Clifford R., Sodt, Andrew, Stockdale, Graham, Szafer, Aaron, Wakeman, Wayne, Wohnoutka, Paul E., White, Steven J., Marsh, Don, Rostomily, Robert C., Ng, Lydia, Dang, Chinh, Jones, Allan, Keogh, Bart, Gittleman, Haley R., Barnholtz-Sloan, Jill S., Cimino, Patrick J., Uppin, Megha S., Keene, C. Dirk, Farrokhi, Farrokh R., Lathia, Justin D., Berens, Michael E., Iavarone, Antonio, Bernard, Amy, Lein, Ed, Phillips, John W., Rostad, Steven W., Cobbs, Charles, Hawrylycz, Michael J., and Foltz, Greg D.

Published
2018

24. Hierarchical organization of cortical and thalamic connectivity

Author

Harris, Julie A., Mihalas, Stefan, Hirokawa, Karla E., Whitesell, Jennifer D., Choi, Hannah, Bernard, Amy, and Bohn, Phillip

Subjects
Neural circuitry -- Structure, Thalamus -- Comparative analysis, Cerebral cortex -- Comparative analysis, Memory -- Analysis, Connectionism -- Analysis, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The mammalian cortex is a laminar structure containing many areas and cell types that are densely interconnected in complex ways, and for which generalizable principles of organization remain mostly unknown. Here we describe a major expansion of the Allen Mouse Brain Connectivity Atlas resource.sup.1, involving around a thousand new tracer experiments in the cortex and its main satellite structure, the thalamus. We used Cre driver lines (mice expressing Cre recombinase) to comprehensively and selectively label brain-wide connections by layer and class of projection neuron. Through observations of axon termination patterns, we have derived a set of generalized anatomical rules to describe corticocortical, thalamocortical and corticothalamic projections. We have built a model to assign connection patterns between areas as either feedforward or feedback, and generated testable predictions of hierarchical positions for individual cortical and thalamic areas and for cortical network modules. Our results show that cell-class-specific connections are organized in a shallow hierarchy within the mouse corticothalamic network. Using mouse lines in which subsets of neurons are genetically labelled, the authors provide generalized anatomical rules for connections within and between the cortex and thalamus., Author(s): Julie A. Harris [sup.1] , Stefan Mihalas [sup.1] , Karla E. Hirokawa [sup.1] , Jennifer D. Whitesell [sup.1] , Hannah Choi [sup.1] [sup.2] , Amy Bernard [sup.1] , Phillip [...]

Published
2019
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25. Classification of electrophysiological and morphological neuron types in the mouse visual cortex

Author

Gouwens, Nathan W., Sorensen, Staci A., Berg, Jim, Lee, Changkyu, Jarsky, Tim, Ting, Jonathan, Sunkin, Susan M., Feng, David, Anastassiou, Costas A., Barkan, Eliza, Bickley, Kris, Blesie, Nicole, Braun, Thomas, Brouner, Krissy, Budzillo, Agata, Caldejon, Shiella, Casper, Tamara, Castelli, Dan, Chong, Peter, Crichton, Kirsten, Cuhaciyan, Christine, Daigle, Tanya L., Dalley, Rachel, Dee, Nick, Desta, Tsega, Ding, Song-Lin, Dingman, Samuel, Doperalski, Alyse, Dotson, Nadezhda, Egdorf, Tom, Fisher, Michael, de Frates, Rebecca A., Garren, Emma, Garwood, Marissa, Gary, Amanda, Gaudreault, Nathalie, Godfrey, Keith, Gorham, Melissa, Gu, Hong, Habel, Caroline, Hadley, Kristen, Harrington, James, Harris, Julie A., Henry, Alex, Hill, DiJon, Josephsen, Sam, Kebede, Sara, Kim, Lisa, Kroll, Matthew, Lee, Brian, Lemon, Tracy, Link, Katherine E., Liu, Xiaoxiao, Long, Brian, Mann, Rusty, McGraw, Medea, Mihalas, Stefan, Mukora, Alice, Murphy, Gabe J., Ng, Lindsay, Ngo, Kiet, Nguyen, Thuc Nghi, Nicovich, Philip R., Oldre, Aaron, Park, Daniel, Parry, Sheana, Perkins, Jed, Potekhina, Lydia, Reid, David, Robertson, Miranda, Sandman, David, Schroedter, Martin, Slaughterbeck, Cliff, Soler-Llavina, Gilberto, Sulc, Josef, Szafer, Aaron, Tasic, Bosiljka, Taskin, Naz, Teeter, Corinne, Thatra, Nivretta, Tung, Herman, Wakeman, Wayne, Williams, Grace, Young, Rob, Zhou, Zhi, Farrell, Colin, Peng, Hanchuan, Hawrylycz, Michael J., Lein, Ed, Ng, Lydia, Arkhipov, Anton, Bernard, Amy, Phillips, John W., Zeng, Hongkui, and Koch, Christof

Published
2019
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26. Author Correction: Human neocortical expansion involves glutamatergic neuron diversification

Author

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

Published
2022
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27. Neuroscience Needs Network Science

Author

Barabási, Dániel L., primary, Bianconi, Ginestra, additional, Bullmore, Ed, additional, Burgess, Mark, additional, Chung, SueYeon, additional, Eliassi-Rad, Tina, additional, George, Dileep, additional, Kovács, István A., additional, Makse, Hernán, additional, Nichols, Thomas E., additional, Papadimitriou, Christos, additional, Sporns, Olaf, additional, Stachenfeld, Kim, additional, Toroczkai, Zoltán, additional, Towlson, Emma K., additional, Zador, Anthony M., additional, Zeng, Hongkui, additional, Barabási, Albert-László, additional, Bernard, Amy, additional, and Buzsáki, György, additional

Published
2023
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29. Shared and distinct transcriptomic cell types across neocortical areas

Author

Tasic, Bosiljka, Yao, Zizhen, Graybuck, Lucas T., Smith, Kimberly A., Nguyen, Thuc Nghi, Bertagnolli, Darren, Goldy, Jeff, Garren, Emma, Economo, Michael N., Viswanathan, Sarada, Penn, Osnat, Bakken, Trygve, Menon, Vilas, Miller, Jeremy, Fong, Olivia, Hirokawa, Karla E., Lathia, Kanan, Rimorin, Christine, Tieu, Michael, Larsen, Rachael, Casper, Tamara, Barkan, Eliza, Kroll, Matthew, Parry, Sheana, Shapovalova, Nadiya V., Hirschstein, Daniel, Pendergraft, Julie, Sullivan, Heather A., Kim, Tae Kyung, Szafer, Aaron, Dee, Nick, Groblewski, Peter, Wickersham, Ian, Cetin, Ali, Harris, Julie A., Levi, Boaz P., Sunkin, Susan M., Madisen, Linda, Daigle, Tanya L., Looger, Loren, Bernard, Amy, Phillips, John, Lein, Ed, Hawrylycz, Michael, Svoboda, Karel, Jones, Allan R., Koch, Christof, and Zeng, Hongkui

Published
2018
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32. Next-generation brain observatories

Author

Koch, Christof, primary, Svoboda, Karel, additional, Bernard, Amy, additional, Basso, Michele A., additional, Churchland, Anne K., additional, Fairhall, Adrienne L., additional, Groblewski, Peter A., additional, Lecoq, Jérôme A., additional, Mainen, Zachary F., additional, Mathis, Mackenzie W., additional, Olsen, Shawn R., additional, Phillips, John w., additional, Pouget, Alexandre, additional, Saxena, Shreya, additional, Siegle, Josh H., additional, and Zador, Anthony M., additional

Published
2022
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33. Convergent transcriptional specializations in the brains of humans and song-learning birds

Author

Pfenning, Andreas R., Hara, Erina, Whitney, Osceola, Rivas, Miriam V., Wang, Rui, Roulhac, Petra L., Howard, Jason T., Wirthlin, Morgan, Lovell, Peter V., Ganapathy, Ganeshkumar, Mouncastle, Jacquelyn, Moseley, M. Arthur, Thompson, J. Will, Soderblom, Erik J., Iriki, Atsushi, Kato, Masaki, Gilbert, M. Thomas P., Zhang, Guojie, Bakken, Trygve, Bongaarts, Angie, Bernard, Amy, Lein, Ed, Mello, Claudio V., Hartemink, Alexander J., and Jarvis, Erich D.

Published
2014

34. Highly Multiplexed Subcellular RNA Sequencing in Situ

Author

Lee, Je Hyuk, Daugharthy, Evan R., Scheiman, Jonathan, Kalhor, Reza, Yang, Joyce L., Ferrante, Thomas C., Terry, Richard, Jeanty, Sauveur S. F., Li, Chao, Amamoto, Ryoji, Peters, Derek T., Turczyk, Brian M., Marblestone, Adam H., Inverso, Samuel A., Bernard, Amy, Mali, Prashant, Rios, Xavier, Aach, John, and Church, George M.

Published
2014

35. A Theory of Planned Behavior Research Model for Predicting the Sleep Intentions and Behaviors of Undergraduate College Students

Author

Knowlden, Adam P., Sharma, Manoj, and Bernard, Amy L.

Abstract

The purpose of this study was to operationalize the constructs of the Theory of Planned Behavior (TPB) to predict the sleep intentions and behaviors of undergraduate college students attending a Midwestern University. Data collection spanned three phases. The first phase included a semi-structured qualitative interview (n = 11), readability by Flesch-Kincaid, face and content validity by a panel of six experts. The second phase included stability reliability by test-retest (n = 37). The final phase included construct validation applying confirmatory factor analysis, internal consistency by Cronbach's alpha, and predictive validity (n = 197) employing multiple regression analysis. The majority of the participants reported receiving insufficient sleep (M = 407.3 min, SD = 100.75). Multiple regression modeled perceived behavioral control, subjective norm, and attitude toward adequate sleep behavior on behavioral intention. Collectively, the significant predictors produced an R adjusted[superscript 2] value of 0.362. Further specification of the model identified behavioral intention as a significant predictor of sleep behavior (R adjusted[superscript 2] = 0.185). As a population, undergraduate college students are not achieving adequate sleep. The TPB was found to be a useful framework for predicting the sleep intentions and behaviors of undergraduate students. Practical implications and recommendations for future research are discussed.

Published
2012
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37. Effective Parent Connectedness Components in Sexuality Education Interventions for African American Youth: A Review of the Literature

Author

Vidourek, Rebecca A., Bernard, Amy L., and King, Keith A.

Abstract

African American youth are at risk for negative sexual behaviors such as early initiation and unplanned pregnancy. The purpose of the article is to identify the effective parent connectedness components in sexuality education interventions solely targeting African American youth. A total of 12 articles were found describing six intervention programs that met inclusion criteria. A summary of each was developed, and commonly used parent connectedness components were identified. In this manner, effective strategies and lessons learned from the research regarding parental connectedness and African American sexual risk reduction could be more clearly discussed. Recommendations for future programming are offered. (Contains 1 table.)

Published
2009
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38. Foster Parents' Involvement in Authoritative Parenting and Interest in Future Parenting Training

Author

King, Keith A., Kraemer, Linda K., Bernard, Amy L., and Vidourek, Rebecca A.

Abstract

We surveyed 191 Southwest Ohio foster parents regarding their involvement in authoritative parenting and interest for additional parenting education. Our results showed that most respondents reported using an authoritative parenting style and were interested in receiving future training. Involvement in authoritative parenting differed significantly based on level of education and number of years as a foster parent. Foster parents with a college degree or higher were significantly more involved in authoritative parenting than foster parents with a high school diploma or less. Those who had been a foster parent for greater than five years were significantly more likely than those who been a foster parent for five years or less to use authoritative parenting and desire future training in authoritative parenting.

Published
2007
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40. Comprehensive cellular‐resolution atlas of the adult human brain

Author

Ding, Song‐Lin, Royall, Joshua J., Sunkin, Susan M., Ng, Lydia, Facer, Benjamin A.C., Lesnar, Phil, Guillozet‐Bongaarts, Angie, McMurray, Bergen, Szafer, Aaron, Dolbeare, Tim A., Stevens, Allison, Tirrell, Lee, Benner, Thomas, Caldejon, Shiella, Dalley, Rachel A., Dee, Nick, Lau, Christopher, Nyhus, Julie, Reding, Melissa, Riley, Zackery L., Sandman, David, Shen, Elaine, van der Kouwe, Andre, Varjabedian, Ani, Write, Michelle, Zollei, Lilla, Dang, Chinh, Knowles, James A., Koch, Christof, Phillips, John W., Sestan, Nenad, Wohnoutka, Paul, Zielke, H. Ronald, Hohmann, John G., Jones, Allan R., Bernard, Amy, Hawrylycz, Michael J., Hof, Patrick R., Fischl, Bruce, and LeinReference, Ed S.

Published
2017
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41. Canonical genetic signatures of the adult human brain

Author

Hawrylycz, Michael, Miller, Jeremy A, Menon, Vilas, Feng, David, Dolbeare, Tim, Guillozet-Bongaarts, Angela L, Jegga, Anil G, Aronow, Bruce J, Lee, Chang-Kyu, Bernard, Amy, Glasser, Matthew F, Dierker, Donna L, Menche, Jörg, Szafer, Aaron, Collman, Forrest, Grange, Pascal, Berman, Kenneth A, Mihalas, Stefan, Yao, Zizhen, Stewart, Lance, Barabási, Albert-László, Schulkin, Jay, Phillips, John, Ng, Lydia, Dang, Chinh, Haynor, David R, Jones, Allan, Van Essen, David C, Koch, Christof, and Lein, Ed

Published
2015
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43. Author Correction:Human neocortical expansion involves glutamatergic neuron diversification (Nature, (2021), 598, 7879, (151-158), 10.1038/s41586-021-03813-8)

Author

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

Abstract

In the version of this Article initially published, the Acknowledgements statement contained an error. Originally appearing with thanks for support given in part as follows, “R01EY023173 from The National Eye Institute, U01MH105982 from the National Institute of Mental Health and Eunice Kennedy Shriver National Institute of Child Health and Human Development, and R011EY023173 from The National Institute of Allergy and Infectious Disease,” the last number (R011EY023173) was mistakenly added and is not in fact a grant or one provided by the NIAID. The mention has been removed. The changes have been made to the online version of the Article.

Published
2022
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44. Increasing Response Rates to Mail Questionnaires: A Review of Inducement Strategies.

Author

King, Keith A., Pealer, Lisa N., and Bernard, Amy L.

Abstract

To help with the problem of nonresponse bias in mail survey research, this paper provides health education researchers with effective inducement strategies based on a comprehensive review of the professional literature, examining five areas of consideration regarding mail survey research: return envelopes and postage, cover letter, incentives, questionnaire characteristics, and participant contact. (SM)

Published
2001

45. Fibromyalgia Syndrome Symptoms and Effects: A Cross-Sectional Study.

Author

Prince, Alice, Bernard, Amy L., and Edsall, Patricia A.

Abstract

Surveyed fibromyalgia syndrome support group members about characteristics of the disease and how it affected their lives. Respondents had symptoms for many years before being diagnosed. Symptoms varied tremendously on a daily and yearly basis, so disease management was in a constant state of flux. Most symptoms significantly impacted quality of life. (SM)

Published
2000

46. Local connectivity and synaptic dynamics in mouse and human neocortex

Author

Campagnola, Luke, primary, Seeman, Stephanie C., additional, Chartrand, Thomas, additional, Kim, Lisa, additional, Hoggarth, Alex, additional, Gamlin, Clare, additional, Ito, Shinya, additional, Trinh, Jessica, additional, Davoudian, Pasha, additional, Radaelli, Cristina, additional, Kim, Mean-Hwan, additional, Hage, Travis, additional, Braun, Thomas, additional, Alfiler, Lauren, additional, Andrade, Julia, additional, Bohn, Phillip, additional, Dalley, Rachel, additional, Henry, Alex, additional, Kebede, Sara, additional, Alice, Mukora, additional, Sandman, David, additional, Williams, Grace, additional, Larsen, Rachael, additional, Teeter, Corinne, additional, Daigle, Tanya L., additional, Berry, Kyla, additional, Dotson, Nadia, additional, Enstrom, Rachel, additional, Gorham, Melissa, additional, Hupp, Madie, additional, Dingman Lee, Samuel, additional, Ngo, Kiet, additional, Nicovich, Philip R., additional, Potekhina, Lydia, additional, Ransford, Shea, additional, Gary, Amanda, additional, Goldy, Jeff, additional, McMillen, Delissa, additional, Pham, Trangthanh, additional, Tieu, Michael, additional, Siverts, La’Akea, additional, Walker, Miranda, additional, Farrell, Colin, additional, Schroedter, Martin, additional, Slaughterbeck, Cliff, additional, Cobb, Charles, additional, Ellenbogen, Richard, additional, Gwinn, Ryder P., additional, Keene, C. Dirk, additional, Ko, Andrew L., additional, Ojemann, Jeffrey G., additional, Silbergeld, Daniel L., additional, Carey, Daniel, additional, Casper, Tamara, additional, Crichton, Kirsten, additional, Clark, Michael, additional, Dee, Nick, additional, Ellingwood, Lauren, additional, Gloe, Jessica, additional, Kroll, Matthew, additional, Sulc, Josef, additional, Tung, Herman, additional, Wadhwani, Katherine, additional, Brouner, Krissy, additional, Egdorf, Tom, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, Pom, Christina Alice, additional, Ruiz, Augustin, additional, Bomben, Jasmine, additional, Feng, David, additional, Hejazinia, Nika, additional, Shi, Shu, additional, Szafer, Aaron, additional, Wakeman, Wayne, additional, Phillips, John, additional, Bernard, Amy, additional, Esposito, Luke, additional, D’Orazi, Florence D., additional, Sunkin, Susan, additional, Smith, Kimberly, additional, Tasic, Bosiljka, additional, Arkhipov, Anton, additional, Sorensen, Staci, additional, Lein, Ed, additional, Koch, Christof, additional, Murphy, Gabe, additional, Zeng, Hongkui, additional, and Jarsky, Tim, additional

Published
2022
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49. Alcohol Use and Safer Sex Behaviors of Students at a Commuter University.

Author

Prince, Alice and Bernard, Amy L.

Abstract

Students (N=1919) at a commuter university responded to a questionnaire that assessed alcohol consumption issues and safer sex behaviors. Alcohol consumption prior to sexual activity was associated with number of sexual partners and frequency of sexual activity. No significant association between condom use and alcohol consumption prior to sexual intercourse was found. (MKA)

Published
1998

50. HIV/AIDS Knowledge in College Students: The Implications for Individuals and Society.

Author

Bernard, Amy L. and Prince, Alice

Abstract

Surveys of college students investigated their HIV/AIDS knowledge. Results indicated that significant sex differences existed on most subscales. Important gaps in students' knowledge include lack of awareness of HIV transmission through oral sex or from mother to infant, belief that donating blood can cause one to contract HIV, and lack of awareness that HIV infection is a lifelong disease. (SM)

Published
1998

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