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301. American Gut: an Open Platform for Citizen Science Microbiome Research

Author

McDonald, Daniel, Hyde, Embriette, Debelius, Justine W, Morton, James T, Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A, Behsaz, Bahar, Brennan, Caitriona, Chen, Yingfeng, Goldasich, Lindsay DeRight, Dorrestein, Pieter C, Dunn, Robert R, Fahimipour, Ashkaan K, Gaffney, James, Gilbert, Jack A, Gogul, Grant, Green, Jessica L, Hugenholtz, Philip, Humphrey, Greg, Huttenhower, Curtis, Jackson, Matthew A, Janssen, Stefan, Jeste, Dilip V, Jiang, Lingjing, Kelley, Scott T, Knights, Dan, Kosciolek, Tomasz, Ladau, Joshua, Leach, Jeff, Marotz, Clarisse, Meleshko, Dmitry, Melnik, Alexey V, Metcalf, Jessica L, Mohimani, Hosein, Montassier, Emmanuel, Navas-Molina, Jose, Nguyen, Tanya T, Peddada, Shyamal, Pevzner, Pavel, Pollard, Katherine S, Rahnavard, Gholamali, Robbins-Pianka, Adam, Sangwan, Naseer, Shorenstein, Joshua, Smarr, Larry, Song, Jin, Spector, Timothy, Swafford, Austin D, Thackray, Varykina G, Thompson, Luke R, Tripathi, Anupriya, Vázquez-Baeza, Yoshiki, Vrbanac, Alison, Wischmeyer, Paul, Wolfe, Elaine, Zhu, Qiyun, Mann, Allison E, Amir, Amnon, Frazier, Angel, Martino, Cameron, Lebrilla, Carlito, Lozupone, Catherine, Lewis, Cecil M, Raison, Charles, Zhang, Chi, Lauber, Christian L, Warinner, Christina, Lowry, Christopher A, Callewaert, Chris, Bloss, Cinnamon, Willner, Dana, Galzerani, Daniela Domingos, Gonzalez, David J, Mills, David A, Chopra, Deepak, Gevers, Dirk, Berg-Lyons, Donna, Sears, Dorothy D, Wendel, Doug, Lovelace, Elijah, Pierce, Emily, TerAvest, Emily, Bolyen, Evan, Bushman, Frederic D, Wu, Gary D, Church, George M, Saxe, Gordon, Holscher, Hanna D, Ugrina, Ivo, German, J Bruce, Caporaso, J Gregory, Wozniak, Jacob M, Kerr, Jacqueline, Ravel, Jacques, Lewis, James D, Suchodolski, Jan S, Jansson, Janet K, Hampton-Marcell, Jarrad T, and Bobe, Jason

Subjects
Microbiology, Biological Sciences, Biomedical and Clinical Sciences, Medical Biochemistry and Metabolomics, Human Genome, Microbiome, Genetics, Clinical Research, 4.1 Discovery and preclinical testing of markers and technologies, citizen science, microbiome, American Gut Consortium
Abstract

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.

Published
2018

303. Genomic Approaches to Posttraumatic Stress Disorder: The Psychiatric Genomic Consortium Initiative

Author

Nievergelt, Caroline M, Ashley-Koch, Allison E, Dalvie, Shareefa, Hauser, Michael A, Morey, Rajendra A, Smith, Alicia K, and Uddin, Monica

Subjects
Biological Psychology, Biological Sciences, Genetics, Psychology, Mental Health, Human Genome, Anxiety Disorders, Biotechnology, Clinical Research, Prevention, Post-Traumatic Stress Disorder (PTSD), Brain Disorders, 2.1 Biological and endogenous factors, Aetiology, Mental health, Good Health and Well Being, Epigenomics, Genetic Predisposition to Disease, Genome-Wide Association Study, Genomics, Humans, Stress Disorders, Post-Traumatic, Epigenetics, Gene expression, Imaging, Psychiatric Genomics Consortium, Systems biology, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry, Biological sciences, Biomedical and clinical sciences
Abstract

Posttraumatic stress disorder (PTSD) after exposure to a traumatic event is a highly prevalent psychiatric disorder. Heritability estimates from twin studies as well as from recent molecular data (single nucleotide polymorphism-based heritability) indicate moderate to high heritability, yet robust genetic variants for PTSD have not yet been identified and the genetic architecture of this polygenic disorder remains largely unknown. To date, fewer than 10 large-scale genome-wide association studies of PTSD have been published, with findings that highlight the unique challenges for PTSD genomics, including a complex diagnostic entity with contingency of PTSD diagnosis on trauma exposure and the large genetic diversity of the study populations. The Psychiatric Genomics Consortium PTSD group has brought together more than 200 scientists with the goal to increase sample size for genome-wide association studies and other genomic analyses to sufficient numbers where robust discoveries of molecular signatures can be achieved. The sample currently includes more than 32,000 PTSD cases and 100,000 trauma-exposed control subjects, and collection is ongoing. The first results found a significant shared genetic risk of PTSD with other psychiatric disorders and sex-biased heritability estimates with higher heritability in female individuals compared with male individuals. This review describes the scope and current focus of the Psychiatric Genomics Consortium PTSD group and its expansion from the initial genome-wide association study group to nine working groups, including epigenetics, gene expression, imaging, and integrative systems biology. We further briefly outline recent findings and future directions of "omics"-based studies of PTSD, with the ultimate goal of elucidating the molecular architecture of this complex disorder to improve prevention and intervention strategies.

Published
2018

305. Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors

Author

Wray, Naomi R., Ripke, Stephan, Mattheisen, Manuel, Trzaskowski, Maciej, Byrne, Enda M., Abdellaoui, Abdel, Adams, Mark J., Agerbo, Esben, Air, Tracy M., Andlauer, Till F.M., Bacanu, Silviu-Alin, Bækvad-Hansen, Marie, Beekman, Aartjan T.F., Bigdeli, Tim B., Binder, Elisabeth B., Bryois, Julien, Buttenschøn, Henriette N., Bybjerg-Grauholm, Jonas, Cai, Na, Castelao, Enrique, Christensen, Jane Hvarregaard, Clarke, Toni-Kim, Coleman, Jonathan R.I., Colodro-Conde, Lucía, Couvy-Duchesne, Baptiste, Craddock, Nick, Crawford, Gregory E., Davies, Gail, Degenhardt, Franziska, Derks, Eske M., Direk, Nese, Dolan, Conor V., Dunn, Erin C., Eley, Thalia C., Escott-Price, Valentina, Hassan Kiadeh, Farnush Farhadi, Finucane, Hilary K., Foo, Jerome C., Forstner, Andreas J., Frank, Josef, Gaspar, Héléna A., Gill, Michael, Goes, Fernando S., Gordon, Scott D., Weinsheimer, Shantel Marie, Wellmann, Jürgen, Willemsen, Gonneke, Witt, Stephanie H., Wu, Yang, Xi, Hualin S., Yang, Jian, Zhang, Futao, Arolt, Volker, Baune, Bernhard T., Berger, Klaus, Boomsma, Dorret I., Cichon, Sven, Dannlowski, Udo, de Geus, E.J.C., Depaulo, J. Raymond, Domenici, Enrico, Domschke, Katharina, Esko, Tõnu, Grabe, Hans J., Hamilton, Steven P., Grove, Jakob, Hall, Lynsey S., Hansen, Christine Søholm, Hansen, Thomas F., Herms, Stefan, Hickie, Ian B., Hoffmann, Per, Homuth, Georg, Horn, Carsten, Hottenga, Jouke-Jan, Hougaard, David M., Howard, David M., Ising, Marcus, Jansen, Rick, Jones, Ian, Jones, Lisa A., Jorgenson, Eric, Knowles, James A., Kohane, Isaac S., Kraft, Julia, Kretzschmar, Warren W., Kutalik, Zoltán, Li, Yihan, Lind, Penelope A., MacIntyre, Donald J., MacKinnon, Dean F., Maier, Robert M., Maier, Wolfgang, Marchini, Jonathan, Mbarek, Hamdi, McGrath, Patrick, McGuffin, Peter, Medland, Sarah E., Mehta, Divya, Middeldorp, Christel M., Mihailov, Evelin, Milaneschi, Yuri, Milani, Lili, Mondimore, Francis M., Montgomery, Grant W., Mostafavi, Sara, Mullins, Niamh, Nauck, Matthias, Ng, Bernard, Nivard, Michel G., Nyholt, Dale R., O’Reilly, Paul F., Oskarsson, Hogni, Hayward, Caroline, Heath, Andrew C., Kendler, Kenneth S., Kloiber, Stefan, Lewis, Glyn, Li, Qingqin S., Lucae, Susanne, Madden, Pamela A.F., Magnusson, Patrik K., Martin, Nicholas G., McIntosh, Andrew M., Metspalu, Andres, Mors, Ole, Mortensen, Preben Bo, Müller-Myhsok, Bertram, Nordentoft, Merete, Nöthen, Markus M., O’Donovan, Michael C., Paciga, Sara A., Pedersen, Nancy L., Owen, Michael J., Painter, Jodie N., Pedersen, Carsten Bøcker, Pedersen, Marianne Giørtz, Peterson, Roseann E., Peyrot, Wouter J., Pistis, Giorgio, Posthuma, Danielle, Quiroz, Jorge A., Qvist, Per, Rice, John P., Riley, Brien P., Rivera, Margarita, Mirza, Saira Saeed, Schoevers, Robert, Schulte, Eva C., Shen, Ling, Shi, Jianxin, Shyn, Stanley I., Sigurdsson, Engilbert, Sinnamon, Grant C.B., Smit, Johannes H., Smith, Daniel J., Stefansson, Hreinn, Steinberg, Stacy, Streit, Fabian, Strohmaier, Jana, Tansey, Katherine E., Teismann, Henning, Teumer, Alexander, Thompson, Wesley, Thomson, Pippa A., Thorgeirsson, Thorgeir E., Traylor, Matthew, Treutlein, Jens, Trubetskoy, Vassily, Uitterlinden, André G., Umbricht, Daniel, der Auwera, Sandra Van, van Hemert, Albert M., Viktorin, Alexander, Visscher, Peter M., Wang, Yunpeng, Webb, Bradley T., Penninx, Brenda W.J.H., Perlis, Roy H., Porteous, David J., Potash, James B., Preisig, Martin, Rietschel, Marcella, Schaefer, Catherine, Schulze, Thomas G., Smoller, Jordan W., Stefansson, Kari, Tiemeier, Henning, Uher, Rudolf, Völzke, Henry, Weissman, Myrna M., Werge, Thomas, Lewis, Cathryn M., Levinson, Douglas F., Breen, Gerome, Børglum, Anders D., Sullivan, Patrick F., O’Connell, Kevin S., Coombes, Brandon, Qiao, Zhen, Als, Thomas D., Børte, Sigrid, Charney, Alexander W., Drange, Ole Kristian, Gandal, Michael J., Hagenaars, Saskia P., Ikeda, Masashi, Kamitaki, Nolan, Kim, Minsoo, Krebs, Kristi, Panagiotaropoulou, Georgia, Schilder, Brian M., Sloofman, Laura G., Winsvold, Bendik S., Won, Hong-Hee, Abramova, Liliya, Adorjan, Kristina, Al Eissa, Mariam, Albani, Diego, Alliey-Rodriguez, Ney, Anjorin, Adebayo, Antilla, Verneri, Antoniou, Anastasia, Awasthi, Swapnil, Baek, Ji Hyun, Bass, Nicholas, Bauer, Michael, Beins, Eva C., Bergen, Sarah E., Birner, Armin, Bøen, Erlend, Boks, Marco P., Bosch, Rosa, Brum, Murielle, Brumpton, Ben M., Brunkhorst-Kanaan, Nathalie, Budde, Monika, Byerley, William, Cairns, Murray, Casas, Miquel, Cervantes, Pablo, Cruceanu, Cristiana, Cuellar-Barboza, Alfredo, Cunningham, Julie, Curtis, David, Czerski, Piotr M., Dale, Anders M., Dalkner, Nina, David, Friederike S., Djurovic, Srdjan, Dobbyn, Amanda L., Douzenis, Athanassios, Elvsåshagen, Torbjørn, Ferrier, I. Nicol, Fiorentino, Alessia, Foroud, Tatiana M., Forty, Liz, Frei, Oleksandr, Freimer, Nelson B., Frisén, Louise, Gade, Katrin, Garnham, Julie, Gelernter, Joel, Gizer, Ian R., Gordon-Smith, Katherine, Greenwood, Tiffany A., Guzman-Parra, José, Ha, Kyooseob, Haraldsson, Magnus, Hautzinger, Martin, Heilbronner, Urs, Hellgren, Dennis, Holmans, Peter A., Huckins, Laura, Jamain, Stéphane, Johnson, Jessica S., Kalman, Janos L., Kamatani, Yoichiro, Kennedy, James L., Kittel-Schneider, Sarah, Kogevinas, Manolis, Koromina, Maria, Kranz, Thorsten M., Kranzler, Henry R., Kubo, Michiaki, Kupka, Ralph, Kushner, Steven A., Lavebratt, Catharina, Lawrence, Jacob, Leber, Markus, Lee, Heon-Jeong, Lee, Phil H., Levy, Shawn E., Lewis, Catrin, Liao, Calwing, Lundberg, Martin, Magnusson, Sigurdur H., Maihofer, Adam, Malaspina, Dolores, Maratou, Eirini, Martinsson, Lina, McGregor, Nathaniel W., McKay, James D., Medeiros, Helena, Millischer, Vincent, Moran, Jennifer L., Morris, Derek W., Mühleisen, Thomas W., O’Brien, Niamh, O’Donovan, Claire, Olde Loohuis, Loes M., Oruc, Lilijana, Papiol, Sergi, Pardiñas, Antonio F., Perry, Amy, Pfennig, Andrea, Porichi, Evgenia, Quested, Digby, Raj, Towfique, Rapaport, Mark H., DePaulo, J. Raymond, Regeer, Eline J., Rivas, Fabio, Roth, Julian, Roussos, Panos, Ruderfer, Douglas M., Sánchez-Mora, Cristina, Senner, Fanny, Sharp, Sally, Shilling, Paul D., Sirignano, Lea, Slaney, Claire, Smeland, Olav B., Sobell, Janet L., Artigas, Maria Soler, Spijker, Anne T., Stein, Dan J., Strauss, John S., Świątkowska, Beata, Terao, Chikashi, Toma, Claudio, Tooney, Paul, Tsermpini, Evangelia-Eirini, Vawter, Marquis P., Vedder, Helmut, Walters, James T.R., Xi, Simon, Xu, Wei, Kay Yang, Jessica Mei, Young, Allan H., Young, Hannah, Zandi, Peter P., Zhou, Hang, Zillich, Lea, HUNT All-In Psychiatry, Adolfsson, Rolf, Agartz, Ingrid, Alda, Martin, Alfredsson, Lars, Babadjanova, Gulja, Backlund, Lena, Bellivier, Frank, Bengesser, Susanne, Berrettini, Wade H., Blackwood, Douglas H.R., Boehnke, Michael, Carr, Vaughan J., Catts, Stanley, Corvin, Aiden, Craddock, Nicholas, Dikeos, Dimitris, Etain, Bruno, Ferentinos, Panagiotis, Frye, Mark, Fullerton, Janice M., Gawlik, Micha, Gershon, Elliot S., Green, Melissa J., Grigoroiu-Serbanescu, Maria, Hauser, Joanna, Henskens, Frans, Hillert, Jan, Hong, Kyung Sue, Hultman, Christina M., Hveem, Kristian, Iwata, Nakao, Jablensky, Assen V., Kahn, René S., Kelsoe, John R., Kirov, George, Landén, Mikael, Leboyer, Marion, Lissowska, Jolanta, Lochner, Christine, Loughland, Carmel, Mathews, Carol A., Mayoral, Fermin, McElroy, Susan L., McMahon, Francis J., Melle, Ingrid, Michie, Patricia, Mitchell, Philip B., Morken, Gunnar, Mowry, Bryan, Myers, Richard M., Neale, Benjamin M., Nievergelt, Caroline M., Oedegaard, Ketil J., Olsson, Tomas, Pantelis, Chris, Pato, Carlos, Pato, Michele T., Patrinos, George P., Ramos-Quiroga, Josep Antoni, Reif, Andreas, Reininghaus, Eva Z., Ribasés, Marta, Rouleau, Guy A., Saito, Takeo, Schall, Ulrich, Schalling, Martin, Schofield, Peter R., Scott, Laura J., Scott, Rodney J., Serretti, Alessandro, Weickert, Cynthia Shannon, Stordal, Eystein, Turecki, Gustavo, Vaaler, Arne E., Vieta, Eduard, Vincent, John B., Waldman, Irwin D., Weickert, Thomas W., Zwart, John-Anker, Biernacka, Joanna M., Nurnberger, John I., Edenberg, Howard J., Stahl, Eli A., McQuillin, Andrew, Di Florio, Arianna, Ophoff, Roel A., Andreassen, Ole A., Adan, Roger A.H., Ando, Tetsuya, Aschauer, Harald, Baker, Jessica H., Bencko, Vladimir, Bergen, Andrew W., Birgegård, Andreas, Boden, Joseph M., Boehm, Ilka, Boni, Claudette, Perica, Vesna Boraska, Brandt, Harry, Buehren, Katharina, Bulik, Cynthia M., Burghardt, Roland, Carlberg, Laura, Cassina, Matteo, Clementi, Maurizio, Cone, Roger D., Courtet, Philippe, Crawford, Steven, Crow, Scott, Crowley, James J., Danner, Unna N., Davis, Oliver S.P., de Zwaan, Martina, Dedoussis, George, Degortes, Daniela, DeSocio, Janiece E., Dick, Danielle M., Dina, Christian, Dmitrzak-Weglarz, Monika, Martinez, Elisa Docampo, Duncan, Laramie E., Egberts, Karin, Marshall, Christian R., Mattingsdal, Morten, McDevitt, Sara, Meulenbelt, Ingrid, Micali, Nadia, Mitchell, James, Mitchell, Karen, Monteleone, Palmiero, Monteleone, Alessio Maria, Munn-Chernoff, Melissa A., Nacmias, Benedetta, Navratilova, Marie, Ntalla, Ioanna, Olsen, Catherine M., O’Toole, Julie K., Padyukov, Leonid, Palotie, Aarno, Pantel, Jacques, Papezova, Hana, Parker, Richard, Pearson, John F., Ehrlich, Stefan, Escaramís, Geòrgia, Espeseth, Thomas, Estivill, Xavier, Farmer, Anne, Favaro, Angela, Fernández-Aranda, Fernando, Fichter, Manfred M., Fischer, Krista, Floyd, James A.B., Föcker, Manuel, Foretova, Lenka, Forzan, Monica, Franklin, Christopher S., Gallinger, Steven, Gambaro, Giovanni, Giegling, Ina, Giuranna, Johanna, Giusti-Rodríquez, Paola, Gonidakis, Fragiskos, Gordon, Scott, Gorwood, Philip, Mayora, Monica Gratacos, Guillaume, Sébastien, Guo, Yiran, Hakonarson, Hakon, Halmi, Katherine A., Hanscombe, Ken B., Hatzikotoulas, Konstantinos, Hebebrand, Johannes, Helder, Sietske G., Henders, Anjali K., Herpertz-Dahlmann, Beate, Herzog, Wolfgang, Hinney, Anke, Horwood, L. John, Hübel, Christopher, Petersen, Liselotte V., Pinto, Dalila, Purves, Kirstin L., Raevuori, Anu, Ramoz, Nicolas, Reichborn-Kjennerud, Ted, Ricca, Valdo, Ripatti, Samuli, Ritschel, Franziska, Roberts, Marion, Rujescu, Dan, Rybakowski, Filip, Santonastaso, Paolo, Scherag, André, Scherer, Stephen W., Schmidt, Ulrike, Schork, Nicholas J., Schosser, Alexandra, Seitz, Jochen, Slachtova, Lenka, Slagboom, P. Eline, Slof-Op ‘t Landt, Margarita C.T., Slopien, Agnieszka, Soranzo, Nicole, Sorbi, Sandro, Southam, Lorraine, Steen, Vidar W., Strober, Michael, Huckins, Laura M., Hudson, James I., Imgart, Hartmut, Inoko, Hidetoshi, Janout, Vladimir, Jiménez-Murcia, Susana, Johnson, Craig, Jordan, Jennifer, Julià, Antonio, Kalsi, Gursharan, Kaminská, Deborah, Kaplan, Allan S., Kaprio, Jaakko, Karhunen, Leila, Karwautz, Andreas, Kas, Martien J.H., Kaye, Walter H., Kennedy, Martin A., Keski-Rahkonen, Anna, Kiezebrink, Kirsty, Kim, Youl-Ri, Kirk, Katherine M., Klareskog, Lars, Klump, Kelly L., Knudsen, Gun Peggy S., Larsen, Janne T., Le Hellard, Stephanie, Leppä, Virpi M., Li, Dong, Lichtenstein, Paul, Lilenfeld, Lisa, Lin, Bochao Danae, Lundervold, Astri, Luykx, Jurjen, Magistretti, Pierre J., Maj, Mario, Mannik, Katrin, Marsal, Sara, Stuber, Garret D., Szatkiewicz, Jin P., Tachmazidou, Ioanna, Tenconi, Elena, Thornton, Laura M., Tortorella, Alfonso, Tozzi, Federica, Treasure, Janet, Tsitsika, Artemis, Tyszkiewicz-Nwafor, Marta, Tziouvas, Konstantinos, van Elburg, Annemarie A., van Furth, Eric F., Wade, Tracey D., Wagner, Gudrun, Walton, Esther, Watson, Hunna J., Whiteman, David C., Wichmann, H. Erich, Widen, Elisabeth, Woodside, D. Blake, Yao, Shuyang, Yilmaz, Zeynep, Zeggini, Eleftheria, Zerwas, Stephanie, Zipfel, Stephan, Jungkunz, Martin, Dietl, Lydie, Schwarze, Cornelia E., Dahmen, Norbert, Schott, Björn H., Mobascher, Arian, Lieb, Klaus, Roepke, Stefan, Schmahl, Christian, Bohus, Martin, Crivelli, Silvia, Dennis, Michelle F., Harvey, Phillip D., Carter, Bruce W., Huffman, Jennifer E., Jacobson, Daniel, Madduri, Ravi, Olsen, Maren K., Pestian, John, Gaziano, J. Michael, Muralidhar, Sumitra, Ramoni, Rachel, Beckham, Jean, Chang, Kyong-Mi, O’Donnell, Christopher J., Tsao, Philip S., Breeling, James, Huang, Grant, Romero, J.P. Casas, Moser, Jennifer, Whitbourne, Stacey B., Brewer, Jessica V., Aslan, Mihaela, Connor, Todd, Argyres, Dean P., Stephens, Brady, Brophy, Mary T., Humphries, Donald E., Selva, Luis E., Do, Nhan, Shayan, Shahpoor, Cho, Kelly, Pyarajan, Saiju, Hauser, Elizabeth, Sun, Yan, Zhao, Hongyu, Wilson, Peter, McArdle, Rachel, Dellitalia, Louis, Mattocks, Kristin, Harley, John, Zablocki, Clement J., Whittle, Jeffrey, Jacono, Frank, Gutierrez, Salvador, Gibson, Gretchen, Hammer, Kimberly, Kaminsky, Laurence, Villareal, Gerardo, Kinlay, Scott, Xu, Junzhe, Hamner, Mark, Mathew, Roy, Bhushan, Sujata, Iruvanti, Pran, Godschalk, Michael, Ballas, Zuhair, Ivins, Douglas, Mastorides, Stephen, Moorman, Jonathan, Gappy, Saib, Klein, Jon, Ratcliffe, Nora, Florez, Hermes, Okusaga, Olaoluwa, Murdoch, Maureen, Sriram, Peruvemba, Yeh, Shing Shing, Tandon, Neeraj, Jhala, Darshana, Aguayo, Samuel, Cohen, David, Sharma, Satish, Liangpunsakul, Suthat, Oursler, Kris Ann, Whooley, Mary, Ahuja, Sunil, Constans, Joseph, Meyer, Paul, Greco, Jennifer, Rauchman, Michael, Servatius, Richard, Gaddy, Melinda, Wallbom, Agnes, Morgan, Timothy, Stapley, Todd, Sherman, Scott, Ross, George, Tsao, Philip, Strollo, Patrick, Jr., Boyko, Edward, Meyer, Laurence, Gupta, Samir, Huq, Mostaqul, Fayad, Joseph, Hung, Adriana, Lichy, Jack, Hurley, Robin, Robey, Brooks, Striker, Robert, Kang, JooEun, Campos, Adrian I., Edwards, Alexis C., Galfalvy, Hanga, Levey, Daniel F., Lori, Adriana, Shabalin, Andrey, Starnawska, Anna, Su, Mei-Hsin, Adams, Mark, Gandal, Michael, Hafferty, Jonathan D., Hishimoto, Akitoyo, Okazaki, Satoshi, Otsuka, Ikuo, Ware, Erin B., Chang, Xiao, Chen, Wei J., Chen, Hsi-Chung, DiBlasi, Emily, Duriez, Philibert, Glatt, Stephen J., Hwu, Hai-Gwo, Jain, Sonia, Keel, Pamela K., Liao, Shih-Cheng, Liu, Chih-Min, Mitchell, James E., Monson, Eric T., Powers, Abigail, Rozanov, Vsevolod, Sokolowski, Marcus, Tsuang, Ming T., Appadurai, Vivek, Soler Artigas, María, Van der Auwera, Sandra, Azevedo, M. Helena, Bau, Claiton H.D., Braff, David L., Bryant, Richard, Cahn, Wiepke, Casas, Miguel, Cervilla, Jorge A., Chaumette, Boris, Craig, David, Fanous, Ayman H., Gatt, Justine M., Gejman, Pablo V., Grevet, Eugenio H., Gutierrez, Blanca, Guzman-Parra, Jose, Hamshere, Marian L., Hartmann, Annette, Heilmann-Heimbach, Stefanie, Jonsson, Lina, Koenen, Karestan C., Konte, Bettina, Krebs, Marie-Odile, Molina, Esther, Nievergelt, Caroline, Nimgaonkar, Vishwajit, Pimm, Jonathan, Power, Robert A., Richarte, Vanesa, Roberts, Andrea, Roberts, Gloria, Rovaris, Diego L., Sanders, Alan R., Sklar, Pamela, Sonuga-Barke, Edmund J.S., Spalletta, Gianfranco, Vilar-Ribó, Laura, Shannon Weickert, Cynthia, Williams, Leanne M., Zai, Clement C., Ashley-Koch, Allison E., Beckham, Jean C., Hauser, Elizabeth R., Hauser, Michael A., Kimbrel, Nathan A., Lindquist, Jennifer H., McMahon, Benjamin, Oslin, David W., Qin, Xuejun, Erlangsen, Annette, Kessler, Ronald C., Porteous, David, Ursano, Robert J., Wasserman, Danuta, Coon, Hilary, Demontis, Ditte, Docherty, Anna R., Kuo, Po-Hsiu, Mann, J. John, Rentería, Miguel E., Stein, Murray B., and Willour, Virginia

Published
2022
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309. MTHFD2 is a metabolic checkpoint controlling effector and regulatory T cell fate and function

Author

Sugiura, Ayaka, Andrejeva, Gabriela, Voss, Kelsey, Heintzman, Darren R., Xu, Xincheng, Madden, Matthew Z., Ye, Xiang, Beier, Katherine L., Chowdhury, Nowrin U., Wolf, Melissa M., Young, Arissa C., Greenwood, Dalton L., Sewell, Allison E., Shahi, Shailesh K., Freedman, Samantha N., Cameron, Alanna M., Foerch, Patrik, Bourne, Tim, Garcia-Canaveras, Juan C., Karijolich, John, Newcomb, Dawn C., Mangalam, Ashutosh K., Rabinowitz, Joshua D., and Rathmell, Jeffrey C.

Published
2022
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310. Predictors of Mortality, Withdrawal of Life-Sustaining Measures, and Discharge Disposition in Octogenarians with Subdural Hematomas

Author

Ghneim, Mira, Albrecht, Jennifer S., Brasel, Karen, Livaris, Anna, Watras, Jill B., Michetti, Christopher P., Haan, James M., Lightwine, Kelly, Winfield, Robert D., Adams, Sasha D., Podbielski, Jeanette M., Armen, Scott B., Zacko, J. Christopher, Nasrallah, Fady S., Schaffer, Kathryn B., Dunn, Julie, Widdel, Lars, Schroeppel, Thomas J., Stillman, Zachery, Cooper, Zara, Stein, Deborah, Adams, Charles, Lueckel, Stephanie, Murry, Jason, Patel, Nikita, Hsu, Cindy, Bhatti, Umer F., Lissauer, Matthew E., LaFonte, Marc, Najafi, Kaveh, Lewandowski, Karen, Mukherjee, Kaushik, Imperio-Lagabon, Kristelle J., Martin, Niels D., Hirsch, Kathleen, Berry, Cherisse, Freitas, Derek, Cullinane, Daniel, Ramawi, Roshini, Truitt, Michael, Pearcy, Chris, Hashimi, Habiba, Kaups, Krista, Claridge, Jeffrey, Hartwell, Jennifer L., Ballou, Jessica, Croce, Martin, Markle, Stephanie, Osserwaarde, Sally, Posluszny, Joseph, Stocker, Benjamin, Hranjec, Tjasa, Solomon, Rachele, Martinek, Lucy, Gupta, Alok, Grabo, Daniel J., Khan, Uzer, Tatum, Danielle, Jacome, Tomas, Gates, Jonathan, Jawani, Alisha, Berndtson, Allison E., Curry, Terry G., Bala, Miklosh, Dultz, Linda A., Houshmand, Natasha N., Pieri, Paola, Zielinski, Martin D., Hughes, Joy D., Hartwell, Jennifer, Malhotra, Ajai K., Lee, Tim, Petrone, Patrizio, Joseph, D'andrea, Marshall, Gary T., Carrick, Matthew M., Pathak, Abhijit, Van Zandt, Andrea, Glass, Nina, Livingston, David, Gregg, Shea, Webb, Travis, Drumheller, Byron, Kozar, Rosemary, Barraco, Robert, Joseph, Bellal, Kashkoush, Ahmed, Petitt, Jordan C., Ladhani, Husayn, Ho, Vanessa P., and Kelly, Michael L.

Published
2022
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315. Potential Association of Legionnaires' Disease with Hot Spring Water, Hot Springs National Park and Hot Springs, Arkansas, USA, 2018-2019

Author

James, Allison E., Kesteloot, Kurt, Paul, J. Terry, McMullen, Richard L., Louie, Shirley, Waters, Catherine, Dillaha, Jennifer, Tumlison, Joel, Haselow, Dirk T., Smith, Jessica C., Lee, Sooji, Ritter, Troy, Lucas, Claressa, Kunz, Jasen, Miller, Laura A., and Said, Maria A.

Subjects
Hot Springs National Park, Arkansas -- Health aspects, Risk factors, Health aspects, Environmental aspects, Legionnaires' disease -- Risk factors -- Environmental aspects, Hot springs -- Health aspects, Legionellosis -- Risk factors -- Environmental aspects
Abstract

Legionnaires' disease is caused by inhalation of water containing Legionella bacteria and can lead to life-threatening pneumonia. Legionella pneumophila bacteria thrive in water temperatures of 77[degrees]F-113[degrees]F, and exposure commonly occurs [...]

Published
2022
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319. Inside the flux footprint: The role of organized land cover heterogeneity on the dynamics of observed land-atmosphere exchange fluxes

Author

Leila C. Hernandez Rodriguez, Allison E. Goodwell, and Praveen Kumar

Subjects
land cover heterogeneity, eddy covariance, flux footprint, fetch rose, flux partitioning, ecohydrological modeling, Environmental technology. Sanitary engineering, TD1-1066
Abstract

Eddy covariance measurements quantify the magnitude and temporal variability of land-atmosphere exchanges of water, heat, and carbon dioxide (CO2) among others. However, they also carry information regarding the influence of spatial heterogeneity within the flux footprint, the temporally dynamic source/sink area that contributes to the measured fluxes. A 25 m tall eddy covariance flux tower in Central Illinois, USA, a region where drastic seasonal land cover changes from intensive agriculture of maize and soybean occur, provides a unique setting to explore how the organized heterogeneity of row crop agriculture contributes to observations of land-atmosphere exchange. We characterize the effects of this heterogeneity on latent heat (LE), sensible heat (H), and CO2 fluxes (Fc) using a combined flux footprint and eco-hydrological modeling approach. We estimate the relative contribution of each crop type resulting from the structured spatial organization of the land cover to the observed fluxes from April 2016 to April 2019. We present the concept of a fetch rose, which represents the frequency of the location and length of the prevalent upwind distance contributing to the observations. The combined action of hydroclimatological drivers and land cover heterogeneity within the dynamic flux footprint explain interannual flux variations. We find that smaller flux footprints associated with unstable conditions are more likely to be dominated by a single crop type, but both crops typically influence any given flux measurement. Meanwhile, our ecohydrological modeling suggests that land cover heterogeneity leads to a greater than 10% difference in flux magnitudes for most time windows relative to an assumption of equally distributed crop types. This study shows how the observed flux magnitudes and variability depend on the organized land cover heterogeneity and is extensible to other intensively managed or otherwise heterogeneous landscapes.

Published
2023
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320. Genome-wide association study identifies four pan-ancestry loci for suicidal ideation in the Million Veteran Program.

Author

Allison E Ashley-Koch, Nathan A Kimbrel, Xue J Qin, Jennifer H Lindquist, Melanie E Garrett, Michelle F Dennis, Lauren P Hair, Jennifer E Huffman, Daniel A Jacobson, Ravi K Madduri, Hilary Coon, Anna R Docherty, Jooeun Kang, Niamh Mullins, Douglas M Ruderfer, VA Million Veteran Program (MVP), MVP Suicide Exemplar Workgroup, International Suicide Genetics Consortium, Philip D Harvey, Benjamin H McMahon, David W Oslin, Elizabeth R Hauser, Michael A Hauser, and Jean C Beckham

Subjects
Genetics, QH426-470
Abstract

Suicidal ideation (SI) often precedes and predicts suicide attempt and death, is the most common suicidal phenotype and is over-represented in veterans. The genetic architecture of SI in the absence of suicide attempt (SA) is unknown, yet believed to have distinct and overlapping risk with other suicidal behaviors. We performed the first GWAS of SI without SA in the Million Veteran Program (MVP), identifying 99,814 SI cases from electronic health records without a history of SA or suicide death (SD) and 512,567 controls without SI, SA or SD. GWAS was performed separately in the four largest ancestry groups, controlling for sex, age and genetic substructure. Ancestry-specific results were combined via meta-analysis to identify pan-ancestry loci. Four genome-wide significant (GWS) loci were identified in the pan-ancestry meta-analysis with loci on chromosomes 6 and 9 associated with suicide attempt in an independent sample. Pan-ancestry gene-based analysis identified GWS associations with DRD2, DCC, FBXL19, BCL7C, CTF1, ANNK1, and EXD3. Gene-set analysis implicated synaptic and startle response pathways (q's

Published
2023
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321. Multidisciplinary Community-Based Investigation of a COVID-19 Outbreak Among Marshallese and Hispanic/Latino Communities — Benton and Washington Counties, Arkansas, March–June 2020

Author

Center, Katherine E., Silva, Juliana Da, Hernandez, Angela L., Vang, Kristyn, Martin, Daniel W., Mazurek, Jerry, Lilo, Emily A., Zimmerman, Nichole K., Krow-Lucal, Elisabeth, Campbell, Ellsworth M., Cowins, Janet V., Walker, Chastity, Dominguez, Kenneth L., Gallo, Bill, Gunn, Jayleen K.L., McCormick, Donald, Cochran, Cassie, Smith, Michelle R., Dillaha, Jennifer A., and James, Allison E.

Published
2020

324. Estimating the effect of anticipated depression treatment-related stigma on depression remission among people with noncommunicable diseases and depressive symptoms in Malawi.

Author

Josée M Dussault, Chifundo Zimba, Harriet Akello, Melissa Stockton, Sherika Hill, Allison E Aiello, Alexander Keil, Bradley N Gaynes, Michael Udedi, and Brian W Pence

Subjects
Medicine, Science
Abstract

PurposeWhile mental health stigma research is sparse in Malawi, research in other settings suggests that stigma represents a barrier to mental health treatment and recovery. Accordingly, we conducted an analysis to understand the role of treatment-related stigma in depression care in Malawi by estimating the effect of patients' baseline anticipated treatment-related stigma on their 3-month probability of depression remission when newly identified with depression.MethodsWe conducted depression screening and treatment at 10 noncommunicable disease (NCD) clinics across Malawi from April 2019 through December 2021. Eligible cohort participants were 18-65 years with depressive symptoms indicated by a PHQ-9 score ≥5. Questionnaires at the baseline and 3-month interviews included a vignette-based quantitative stigma instrument that measured treatment-related stigma, i.e., concerns about external stigma because of receiving depression treatment. Using inverse probability weighting to adjust for confounding and multiple imputation to account for missing data, this analysis relates participants' baseline levels of anticipated treatment stigma to the 3-month probability of achieving depression remission (i.e., PHQ-9 score < 5).ResultsOf 743 included participants, 273 (37%) achieved depression remission by their 3-month interview. The probability of achieving depression remission at the 3-month interview among participants with high anticipated treatment stigma (0.31; 95% Confidence Interval [CI]: 0.23, 0.39)) was 10 percentage points lower than among the low/neutral stigma group (risk: 0.41; 95% CI: 0.36, 0.45; RD: -0.10; 95% CI: -0.19, -0.003).ConclusionIn Malawi, a reduction in anticipated depression treatment-related stigma among NCD patients initiating depression treatment could improve depression outcomes. Further investigation is necessary to understand the modes by which stigma can be successfully reduced to improve mental health outcomes and quality of life among people living with depression.

Published
2023
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325. Biological expressions of early life trauma in the immune system of older adults

Author

Grace A. Noppert, Kate A. Duchowny, Rebecca Stebbins, Allison E. Aiello, Jennifer B. Dowd, and Philippa Clarke

Subjects
Medicine, Science
Abstract

Background Poor immune function is associated with increased risk for a number of age-related diseases, however, little is known about the impact of early life trauma on immune function in late-life. Methods Using nationally representative data from the Health and Retirement Study (n = 5,823), we examined the association between experiencing parental/caregiver death or separation before age 16 and four indicators of immune function in late-life: C-reactive Protein (CRP), Interleukin-6 (IL-6), soluble Tumor Necrosis Factor (sTNFR), and Immunoglobulin G (IgG) response to cytomegalovirus (CMV). We also examined racial/ethnic differences. Findings Individuals that identified as racial/ethnic minorities were more likely to experience parental/caregiver loss and parental separation in early life compared to Non-Hispanic Whites, and had poorer immune function in late-life. We found consistent associations between experiencing parental/caregiver loss and separation and poor immune function measured by CMV IgG levels and IL-6 across all racial/ethnic subgroups. For example, among Non-Hispanic Blacks, those that experienced parental/caregiver death before age 16 had a 26% increase in CMV IgG antibodies in late-life (β = 1.26; 95% CI: 1.17, 1.34) compared to a 3% increase in CMV antibodies among Non-Hispanic Whites (β = 1.03; 95% CI: 0.99, 1.07) controlling for age, gender, and parental education. Interpretation Our results suggest a durable association between experiencing early life trauma and immune health in late-life, and that structural forces may shape the ways in which these relationships unfold over the life course.

Published
2023

327. Serial Laboratory Testing for SARS-CoV-2 Infection Among Incarcerated and Detained Persons in a Correctional and Detention Facility — Louisiana, April–May 2020

Author

Njuguna, Henry, Wallace, Megan, Simonson, Sean, Tobolowsky, Farrell A., James, Allison E., Bordelon, Keith, Fukunaga, Rena, Gold, Jeremy A. W., Wortham, Jonathan, Sokol, Theresa, Haydel, Danielle, Tran, Ha, Kim, Kaylee, Fisher, Kiva A., Marlow, Mariel, Tate, Jacqueline E., Doshi, Reena H., and Curran, Kathryn G.

Published
2020

328. COVID-19 in Correctional and Detention Facilities — United States, February–April 2020

Author

Wallace, Megan, Hagan, Liesl, Curran, Kathryn G., Williams, Samantha P., Handanagic, Senad, Bjork, Adam, Davidson, Sherri L., Lawrence, Robert T., McLaughlin, Joseph, Butterfield, Marilee, James, Allison E., Patil, Naveen, Lucas, Kimberley, Hutchinson, Justine, Sosa, Lynn, Jara, Amanda, Griffin, Phillip, Simonson, Sean, Brown, Catherine M., Smoyer, Stephanie, Weinberg, Meghan, Pattee, Brittany, Howell, Molly, Donahue, Matthew, Hesham, Soliman, Shelley, Ellen, Philips, Grace, Selvage, David, Staley, E. Michele, Lee, Anthony, Mannell, Mike, McCotter, Orion, Villalobos, Raul, Bell, Linda, Diedhiou, Abdoulaye, Ortbahn, Dustin, Clayton, Joshua L., Sanders, Kelsey, Cranford, Hannah, Barbeau, Bree, McCombs, Katherine G., Holsinger, Caroline, Kwit, Natalie A., Pringle, Julia C., Kariko, Sara, Strick, Lara, Allord, Matt, Tillman, Courtney, Morrison, Andrea, Rowe, Devin, and Marlow, Mariel

Published
2020

329. Observations of the Formation, Development, and Structure of a Current Sheet in an Eruptive Solar Flare

Author

Seaton, Daniel B., Bartz, Allison E., and Darnel, Jonathan M.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

We present AIA observations of a structure we interpret as a current sheet associated with an X4.9 flare and coronal mass ejection that occurred on 2014~February~25 in NOAA Active Region 11990. We characterize the properties of the current sheet, finding that the sheet remains on the order of a few thousand km thick for much of the duration of the event and that its temperature generally ranged between $8-10\,\mathrm{MK}$. We also note the presence of other phenomena believed to be associated with magnetic reconnection in current sheets, including supra-arcade downflows and shrinking loops. We estimate that the rate of reconnection during the event was $M_{A} \approx 0.004-0.007$, a value consistent with model predictions. We conclude with a discussion of the implications of this event for reconnection-based eruption models., Comment: Animation accompanying Figure 2 available at https://figshare.com/articles/SDO_AIA_131_2014-Feb-25_Current_Sheet/4052061

Published
2016
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331. City Of Greater Sudbury Exercised Due Diligence In Construction Site Fatality As Appeal Dismissed By Ontario Superior Court Of Justice

Author

MacIsaac, Allison E.

Subjects
Work-related injuries -- Cases -- Laws, regulations and rules, Company legal issue, Government regulation, Business, international
Abstract

A long-awaited decision from the Ontario Superior Court of Justice (SCJ) was released on August 23, 2024, dismissing an appeal by the Crown who challenged the trial judge's finding that [...]

Published
2024

342. Brilliant bird brains: object recognition in Herring Gulls ( Larus argentatus smithsonianus )

Author

Kristen M. Covino, F. Dylan Titmuss, Joseph E. Brosseau, Dora C Donacik, Maddie E Ellms, Allison E Fisante, Olivia K Maday, Alyssa R. Nowicki, Daphne Okuyama, Jessica M Robinson, Katherine A Schickfus, Eliza L Stanley, and Mary Elizabeth Everett

Subjects
animal behavior, memory, object recognition, seabirds, visual stimuli, Zoology, QL1-991, Animal culture, SF1-1100
Abstract

The ability to recognize and associate objects with prior experiences has been demonstrated in several avian taxa. Corvids, for example, recognize visual stimuli associated with negative previous experiences and will modify their behavioral responses according to the level of perceived threat. However, the extent to which similar memory-based behaviors exist in seabirds is poorly understood. Our study investigated object recognition by Herring Gulls ( Larus argentatus smithsonianus ) on their breeding grounds, the site of a long-term monitoring project. When handling gulls and conducting field research, researchers wear standard bicycle helmets as a protective measure against physical aggression by nesting gulls. We tested whether previously banded gulls vary their behavioral responses based on the headgear worn by human researchers. Herring Gulls were significantly more aggressive when approached by helmeted observers compared to those wearing neutral headwear or even holding a helmet, thus indicating a potential association between wearing bike helmets and the negative experience with researchers. Our study demonstrates that Herring Gulls are capable of object memory and object recognition within context, and display different behaviors toward different objects according to their levels of perceived threat. This information is key when designing studies with nesting gulls to ensure that behavioral biases are not unintentionally created due to gull prior experiences or researcher safety gear.

Published
2023
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343. A Synthetic Formula Amino Acid Diet Leads to Microbiome Dysbiosis, Reduced Colon Length, Inflammation, and Altered Locomotor Activity in C57BL/6J Mice

Author

Viviana J. Mancilla, Paige N. Braden-Kuhle, Kelly N. Brice, Allison E. Mann, Megan T. Williams, Yan Zhang, Michael J. Chumley, Robert C. Barber, Sabrina N. White, Gary W. Boehm, and Michael S. Allen

Subjects
SCFA, inflammation, mouse model, fiber, synthetic diet, gut-brain axis, Biology (General), QH301-705.5
Abstract

The effects of synthetic, free-amino acid diets, similar to those prescribed as supplements for (phenylketonuria) PKU patients, on gut microbiota and overall health are not well understood. In the current, multidisciplinary study, we examined the effects of a synthetically-derived, low-fiber, amino acid diet on behavior, cognition, gut microbiome composition, and inflammatory markers. A cohort of 20 male C57BL/6J mice were randomly assigned to either a standard or synthetic diet (n = 10) at post-natal day 21 and maintained for 13 weeks. Sequencing of the 16S rRNA gene from fecal samples revealed decreased bacterial diversity, increased abundance of bacteria associated with disease, such as Prevotella, and a downward shift in gut microbiota associated with fermentation pathways in the synthetic diet group. Furthermore, there were decreased levels of short chain fatty acids and shortening of the colon in mice consuming the synthetic diet. Finally, we measured TNF-α, IL-6, and IL-10 in serum, the hippocampus, and colon, and found that the synthetic diet significantly increased IL-6 production in the hippocampus. These results demonstrate the importance of a multidisciplinary approach to future diet and microbiome studies, as diet not only impacts the gut microbiome composition but potentially systemic health as well.

Published
2023
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344. Epigenome-wide meta-analysis of PTSD across 10 military and civilian cohorts identifies methylation changes in AHRR

Author

Alicia K. Smith, Andrew Ratanatharathorn, Adam X. Maihofer, Robert K. Naviaux, Allison E. Aiello, Ananda B. Amstadter, Allison E. Ashley-Koch, Dewleen G. Baker, Jean C. Beckham, Marco P. Boks, Evelyn Bromet, Michelle Dennis, Sandro Galea, Melanie E. Garrett, Elbert Geuze, Guia Guffanti, Michael A. Hauser, Seyma Katrinli, Varun Kilaru, Ronald C. Kessler, Nathan A. Kimbrel, Karestan C. Koenen, Pei-Fen Kuan, Kefeng Li, Mark W. Logue, Adriana Lori, Benjamin J. Luft, Mark W. Miller, Jane C. Naviaux, Nicole R. Nugent, Xuejun Qin, Kerry J. Ressler, Victoria B. Risbrough, Bart P. F. Rutten, Murray B. Stein, Robert J. Ursano, Eric Vermetten, Christiaan H. Vinkers, Lin Wang, Nagy A. Youssef, INTRuST Clinical Consortium, VA Mid-Atlantic MIRECC Workgroup, PGC PTSD Epigenetics Workgroup, Monica Uddin, and Caroline M. Nievergelt

Subjects
Science
Abstract

PTSD has been associated with DNA methylation of specific loci in the genome, but studies have been limited by small sample sizes. Here, the authors perform a meta-analysis of DNA methylation data from 10 different cohorts and identify CpGs in AHRR that are associated with PTSD.

Published
2020
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345. Designing Customization Technologies That Support Teachers to Integrate Social Justice into Science Teaching

Author

Bradford, Allison E

Subjects
Education, Educational technology
Abstract

Over the last decade, the demands on secondary science teachers have shifted to encompass a new range of objectives. Science teachers need support in their efforts to be responsive as they navigate shifting demands in the teaching profession: new state standards, an ever-diversifying student body, and a drive to integrate social justice into science learning. In the US, for example, the K-12 population has immensely diversified, necessitating curriculum adaptations to support the diverse lived experiences and range of prior knowledge represented in their classrooms. Moreover, new curriculum standards such as the Next Generation Science Standards in the US, have required teachers to adapt curriculum materials to meet new performance expectations. Further, technology has become ubiquitous in classrooms, requiring teachers to learn how to meaningfully integrate new tools into their practice. My dissertation project explores how to support teachers as they navigate these emerging trends within the context of a Research Practice Partnership devoted to promoting coherent science learning in technology-enhanced learning environments. The studies presented in this dissertation are guided by the overarching research questions: How can we leverage technology to support teachers in their efforts to be more responsive to the needs and ideas of their students? Taken together, the three studies presented in this dissertation shed light on teachers’ trajectories for customizing curriculum to be more responsive, their trajectories for teaching science for social justice, and their trajectories for leveraging technology as a support for their teaching practice. Specifically, the first study leverages the Knowledge Integration Framework to design and study a professional development workshop to empower teachers to customize their curriculum to better support their students develop understanding of NGSS performance expectations. The workshop activities and supporting technologies foreground pedagogy and emphasize using student work as evidence to inform customization decisions. The second study applies the professional development model from the first study to support teachers to customize the curriculum to feature social justice issues. The study follows the development and implementation of the units with three teachers across two school years. The third study focuses on the design and implementation of automatic scoring models that increase teachers’ access to the social justice and science ideas students use to explain the focal phenomena in the units designed in the second study. Across the studies, the findings have implications for expanding our understanding of Knowledge Integration pedagogy by integrating social justice principles and for the design of technologies that support teachers in principled customization.

Published
2023

346. A Subpopulation of Striatal Neurons Mediates Levodopa-Induced Dyskinesia

Author

Girasole, Allison E, Lum, Matthew Y, Nathaniel, Diane, Bair-Marshall, Chloe J, Guenthner, Casey J, Luo, Liqun, Kreitzer, Anatol C, and Nelson, Alexandra B

Subjects
Biological Psychology, Biomedical and Clinical Sciences, Psychology, Neurodegenerative, Neurosciences, Parkinson's Disease, Brain Disorders, Neurological, Animals, Antiparkinson Agents, Corpus Striatum, Disease Models, Animal, Dyskinesia, Drug-Induced, Female, Levodopa, Male, Mice, Inbred C57BL, Mice, Transgenic, Motor Cortex, Neural Pathways, Neurons, Optogenetics, Parkinson Disease, Basal ganglia, Parkinson’s disease, direct pathway, dopamine, levodopa-induced dyskinesia, optogenetics, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

Parkinson's disease is characterized by the progressive loss of midbrain dopamine neurons. Dopamine replacement therapy with levodopa alleviates parkinsonian motor symptoms but is complicated by the development of involuntary movements, termed levodopa-induced dyskinesia (LID). Aberrant activity in the striatum has been hypothesized to cause LID. Here, to establish a direct link between striatal activity and dyskinesia, we combine optogenetics and a method to manipulate dyskinesia-associated neurons, targeted recombination in active populations (TRAP). We find that TRAPed cells are a stable subset of sensorimotor striatal neurons, predominantly from the direct pathway, and that reactivation of TRAPed striatal neurons causes dyskinesia in the absence of levodopa. Inhibition of TRAPed cells, but not a nonspecific subset of direct pathway neurons, ameliorates LID. These results establish that a distinct subset of striatal neurons is causally involved in LID and indicate that successful therapeutic strategies for treating LID may require targeting functionally selective neuronal subtypes.

Published
2018

347. Association Between Immigration History and Inflammatory Marker Profiles Among Older Adult Mexican Americans

Author

Martin, Chantel L, Haan, Mary N, Fernandez-Rhodes, Lindsay, Lee, Anne, and Aiello, Allison E

Subjects
Human Society, Demography, Clinical Research, 2.1 Biological and endogenous factors, Aetiology, Age Factors, Aged, Biomarkers, C-Reactive Protein, Emigrants and Immigrants, Female, Humans, Inflammation, Interleukin-6, Male, Mexican Americans, Middle Aged, Prospective Studies, Risk Factors, Tumor Necrosis Factor-alpha, United States
Abstract

Foreign-born Hispanics have better cardiometabolic health upon arrival in the US than their US-born counterparts, yet this advantage diminishes as duration of residence in the US increases. Underlying mechanisms explaining this paradox have been understudied. Using data from the Sacramento Area Latino Study on Aging (SALSA), this study examined immigration history (immigrant generation and duration of US residence) in relation to biomarkers of inflammation (interleukin-6 (IL-6), soluble forms of type 1 and 2 receptors of tumor necrosis factor-alpha (sTNF-R1 and sTNF-R2), C-reactive protein (CRP), leptin, adiponectin) in a sample of 1,290 predominantly Mexican-origin immigrants. Second and ≥3rd generation immigrants had higher IL-6 and leptin levels than 1st generation immigrants living in the US for less than 15 years (2nd generation percent difference = 45.9; 95% CI: 24.7, 70.7 and 3rd generation percent difference = 41.8; 95% CI: 17.7, 70.4). CRP and sTNF-R1 levels were higher among ≥3rd generation immigrants than 1st generation immigrants with less than 15 years of US residency. Worse inflammatory profiles were observed among Mexican-origin immigrants with longer US immigration histories, independent of health, and behavioral factors. Additional research is warranted to understand the factors that shape trajectories of biological risk across generations of Hispanics.

Published
2018

348. Can Barn Owls Help Control Rodents in Winegrape Vineyard Landscapes? A Review of Key Questions and Suggested Next Steps

Author

Johnson, Matthew D., Wendt, Carrie, St. George, Dane, Huysman, Allison E., Estes, Brooks R., and Castañeda, Xerónimo A.

Subjects
barn owl, biological control, ecosystem service, gopher, pocket, Napa, CA, nest box, raptor, Tyto alba, vineyard, vole, wine
Abstract

Many winegrape farmers have installed nest boxes to attract barn owls to manage rodent pests, but this prospect has not been rigorously examined. We provide a brief history and context of the use of, and research on, barn owl nest boxes in California vineyards, and we suggest six key research questions necessary to better evaluate the capacity for barn owls to help control rodent pests: 1) How and where should boxes be placed to enhance barn owl occupancy? 2) How much are owls hunting in vineyards versus surrounding habitat? 3) How many rodents do they remove from vineyards? 4) Do they remove enough to meaningfully reduce rodent numbers and decrease crop damage? 5) What can farmers do to maximize hunting on their vineyards? and 6) What factors influence farmers’ decisions to use or not use nest boxes? Some work has recently been aimed at questions 1-3, but additional work is needed to confirm and generalize those results, and questions 4-6 remain, to date, unanswered. We suggest a research agenda to help address those unmet needs and advance our understanding of the potential for and application of barn owl nest boxes for pest management in winegrape vineyards.

Published
2018

349. Compatibility of High-Moisture Storage for Biochemical Conversion of Corn Stover: Storage Performance at Laboratory and Field Scales

Author

Wendt, Lynn M, Murphy, J Austin, Smith, William A, Robb, Thomas, Reed, David W, Ray, Allison E, Liang, Ling, He, Qian, Sun, Ning, Hoover, Amber N, and Nguyen, Quang A

Subjects
Chemical Engineering, Engineering, Affordable and Clean Energy, Corn stover, Ritter pile, biomass storage, ensiling, feedstock reactivity, field storage, Other Biological Sciences, Biomedical Engineering, Medical Biotechnology, Industrial biotechnology, Medical biotechnology, Biomedical engineering
Abstract

Wet anaerobic storage of corn stover can provide a year-round supply of feedstock to biorefineries meanwhile serving an active management approach to reduce the risks associated with fire loss and microbial degradation. Wet logistics systems employ particle size reduction early in the supply chain through field-chopping which removes the dependency on drying corn stover prior to baling, expands the harvest window, and diminishes the biorefinery size reduction requirements. Over two harvest years, in-field forage chopping was capable of reducing over 60% of the corn stover to a particle size of 6 mm or less. Aerobic and anaerobic storage methods were evaluated for wet corn stover in 100 L laboratory reactors. Of the methods evaluated, traditional ensiling resulted in

Published
2018

350. Trauma and posttraumatic stress disorder modulate polygenic predictors of hippocampal and amygdala volume

Author

Yuanchao Zheng, Melanie E. Garrett, Delin Sun, Emily K. Clarke-Rubright, Courtney C. Haswell, Adam X. Maihofer, Jeremy A. Elman, Carol E. Franz, Michael J. Lyons, William S. Kremen, Matthew Peverill, Kelly Sambrook, Katie A. McLaughlin, Nicholas D. Davenport, Seth Disner, Scott R. Sponheim, Elpiniki Andrew, Mayuresh Korgaonkar, Richard Bryant, Tim Varkevisser, Elbert Geuze, Jonathan Coleman, Jean C. Beckham, Nathan A. Kimbrel, Danielle Sullivan, Mark Miller, Jasmeet Hayes, Mieke Verfaellie, Erika Wolf, David Salat, Jeffrey M. Spielberg, William Milberg, Regina McGlinchey, Emily L. Dennis, Paul M. Thompson, Sarah Medland, Neda Jahanshad, Caroline M. Nievergelt, Allison E. Ashley-Koch, Mark W. Logue, and Rajendra A. Morey

Subjects
Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract

Abstract The volume of subcortical structures represents a reliable, quantitative, and objective phenotype that captures genetic effects, environmental effects such as trauma, and disease effects such as posttraumatic stress disorder (PTSD). Trauma and PTSD represent potent exposures that may interact with genetic markers to influence brain structure and function. Genetic variants, associated with subcortical volumes in two large normative discovery samples, were used to compute polygenic scores (PGS) for the volume of seven subcortical structures. These were applied to a target sample enriched for childhood trauma and PTSD. Subcortical volume PGS from the discovery sample were strongly associated in our trauma/PTSD enriched sample (n = 7580) with respective subcortical volumes of the hippocampus (p = 1.10 × 10−20), thalamus (p = 7.46 × 10−10), caudate (p = 1.97 × 10−18), putamen (p = 1.7 × 10−12), and nucleus accumbens (p = 1.99 × 10−7). We found a significant association between the hippocampal volume PGS and hippocampal volume in control subjects from our sample, but was absent in individuals with PTSD (GxE; (beta = −0.10, p = 0.027)). This significant GxE (PGS × PTSD) relationship persisted (p

Published
2021
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