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7,917 results on '"Kelly, G."'

1. A compendium of multi-omics data illuminating host responses to lethal human virus infections

Author

Eisfeld, Amie J., Anderson, Lindsey N., Fan, Shufang, Walters, Kevin B., Halfmann, Peter J., Westhoff Smith, Danielle, Thackray, Larissa B., Tan, Qing, Sims, Amy C., Menachery, Vineet D., Schäfer, Alexandra, Sheahan, Timothy P., Cockrell, Adam S., Stratton, Kelly G., Webb-Robertson, Bobbie-Jo M., Kyle, Jennifer E., Burnum-Johnson, Kristin E., Kim, Young-Mo, Nicora, Carrie D., Peralta, Zuleyma, N’jai, Alhaji U., Sahr, Foday, van Bakel, Harm, Diamond, Michael S., Baric, Ralph S., Metz, Thomas O., Smith, Richard D., Kawaoka, Yoshihiro, and Waters, Katrina M.

Published
2024
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2. Morrey Award 2023: radial head donor plug for capitellum osteochondral autograft transfer: a cadaveric biomechanical analysis

Author

MAJMD Bryan G. Adams, LTMD Jeremy Tran, Steven Voinier, PhD, MAJMD Donald F. Colantonio, PhD, LTCMD Michael A. Donohue, PhD, LTCMD Kelly G. Kilcoyne, PhD, and LTCDO Joseph W. Galvin, PhD

Subjects
Radial heada, Capitellum, Osteochondral autograft transfer, Osteochondral defect, Osteochondritis dissecans, Elbow cartilage, Orthopedic surgery, RD701-811, Diseases of the musculoskeletal system, RC925-935
Abstract

Background: Limitations to using the knee as donor cartilage include cartilage thickness mismatch and donor site morbidity. Using the radial head as donor autograft for capitellar lesions may allow for local graft harvest without distant donor site morbidity. The purpose of this study is to demonstrate the feasibility of performing local osteochondral autograft transfer from the nonarticular cartilaginous rim of the radial head to the capitellum. Additionally, we sought to determine the load to failure of the radial head after harvest. Methods: Sixteen matched cadaveric elbows were used. A Kaplan approach was performed in half of the specimens and an extensor digitorum communis split in the other half. 6-mm and 8-mm capitellar cartilage defects were created. A donor plug was harvested from the rim of the radial head and transferred to the capitellum. In half of the specimens, the donor site was backfilled with autograft from the recipient plug. The other half was backfilled with calcium phosphate cement. The radial head was removed from the specimen and biomechanical analysis performed. Results: Both surgical approaches had adequate exposure to access the lateral two-third capitellar lesions in all specimens. The medial third of the capitellum was less accessible in extensor digitorum communis split approaches (1/8) compared to the Kaplan approach (6/8; P = .01). The average cartilage thickness of the peripheral rim of the radial head and capitellum was 2.5 mm (range 1.8-3.2, standard deviation 0.4) and 2.2 mm (range 1.8-3, standard deviation 0.3), respectively. During the procedure, 2 of 8 radial heads fractured in the 8-mm plug group. No radial heads fractured in the 6-mm group (P = .47). Biomechanical testing demonstrated a mean load to failure of 1993N with no difference between groups when stratified by donor plug size or type of backfill. Conclusion: This study demonstrates that the nonarticulating peripheral cartilaginous rim of the radial head could be a local harvest site for osteochondral autograft transfer for capitellar lesions up to 8 mm in diameter. The cartilage thickness of the radial head closely approximates the capitellum. Biomechanical analysis did not demonstrate a significant difference in load to fracture when backfilling the radial head harvest site with autograft bone or calcium phosphate cement. After harvest, the radial head could withstand forces much greater than those seen across the elbow when nonweight-bearing. Further investigation is needed to determine how to mitigate the risk of iatrogenic fracture with this operation.

Published
2024
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3. Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging

Author

Renton, Angela I., Dao, Thuy T., Johnstone, Tom, Civier, Oren, Sullivan, Ryan P., White, David J., Lyons, Paris, Slade, Benjamin M., Abbott, David F., Amos, Toluwani J., Bollmann, Saskia, Botting, Andy, Campbell, Megan E. J., Chang, Jeryn, Close, Thomas G., Dörig, Monika, Eckstein, Korbinian, Egan, Gary F., Evas, Stefanie, Flandin, Guillaume, Garner, Kelly G., Garrido, Marta I., Ghosh, Satrajit S., Grignard, Martin, Halchenko, Yaroslav O., Hannan, Anthony J., Heinsfeld, Anibal S., Huber, Laurentius, Hughes, Matthew E., Kaczmarzyk, Jakub R., Kasper, Lars, Kuhlmann, Levin, Lou, Kexin, Mantilla-Ramos, Yorguin-Jose, Mattingley, Jason B., Meier, Michael L., Morris, Jo, Narayanan, Akshaiy, Pestilli, Franco, Puce, Aina, Ribeiro, Fernanda L., Rogasch, Nigel C., Rorden, Chris, Schira, Mark M., Shaw, Thomas B., Sowman, Paul F., Spitz, Gershon, Stewart, Ashley W., Ye, Xincheng, Zhu, Judy D., Narayanan, Aswin, and Bollmann, Steffen

Published
2024
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7. A compendium of multi-omics data illuminating host responses to lethal human virus infections

Author

Amie J. Eisfeld, Lindsey N. Anderson, Shufang Fan, Kevin B. Walters, Peter J. Halfmann, Danielle Westhoff Smith, Larissa B. Thackray, Qing Tan, Amy C. Sims, Vineet D. Menachery, Alexandra Schäfer, Timothy P. Sheahan, Adam S. Cockrell, Kelly G. Stratton, Bobbie-Jo M. Webb-Robertson, Jennifer E. Kyle, Kristin E. Burnum-Johnson, Young-Mo Kim, Carrie D. Nicora, Zuleyma Peralta, Alhaji U. N’jai, Foday Sahr, Harm van Bakel, Michael S. Diamond, Ralph S. Baric, Thomas O. Metz, Richard D. Smith, Yoshihiro Kawaoka, and Katrina M. Waters

Subjects
Science
Abstract

Abstract Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology.

Published
2024
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15. An integrated multi-omics approach allowed ultra-rapid diagnosis of a deep intronic pathogenic variant in PDHX and precision treatment in a neonate critically ill with lactic acidosis

Author

Starosta, Rodrigo T., Larson, Austin A., Meeks, Naomi J.L., Gracie, Sara, Friederich, Marisa W., Gaughan, Sommer M., Baker, Peter R., II, Knupp, Kelly G., Michel, Cole R., Reisdorph, Richard, Hock, Daniella H., Stroud, David A., Wood, Tim, and Van Hove, Johan L.K.

Published
2024
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18. Safety, tolerability, and efficacy of subcutaneous efgartigimod in patients with chronic inflammatory demyelinating polyradiculoneuropathy (ADHERE): a multicentre, randomised-withdrawal, double-blind, placebo-controlled, phase 2 trial

Author

Grinzinger, Susanne, Wanschitz, Julia, Seifert-Held, Thomas, Claeys, Kristl G., Baets, Jonathan, Remiche, Gauthier, Bissay, Véronique, Dubuisson, Nicolas, Delstanche, Stephanie, Tarnev, Ivaylo, Genov, Krasimir, Tsvetanov, Plamen, Milanov, Ivan, Zhao, Chongbo, Bu, Bitao, Yu, Xuefan, Li, Wei, Jiang, Haishan, Da, Yuwei, Lu, Zuneng, Liang, Hui, Guo, Fuqiang, Li, Zunbo, Zou, Zhangyu, Hong, Daojun, Yang, Huan, Guo, Junhong, Shi, Jianquan, Tu, Jianglong, He, Dian, Wang, Yiqi, Ding, Jing, Zhang, Yali, Zhao, Yuanqi, Xu, Renxi, Yue, Yunhua, Guo, Aihong, Wang, Yuzhong, Talab, Radomir, Harbo, Thomas, Sindrup, Soeren, De Seze, Jérôme, Sacconi, Sabrina, Péréon, Yann, Echaniz-Laguna, Andoni, Magy, Laurent, Nicolas, Guillaume, Taithe, Frédéric, Cassereau, Julien, Debs, Rabab, Shakarishvili, Roman, Tsiskaridze, Alexander, Mania, Maka, Janelidze, Marina, Janelidze, Tamar, Schroeter, Michael, Skripuletz, Thomas, Lee, De-Hyung, Klehmet, Juliane, Hotter, Benjamin, Hoffmann, Olaf, Baum, Petra, Zschuentzsch, Jana, Pitarokoili, Kalliopi, Stettner, Mark, Bereczki, Dániel, Pánczél, Gyula, Abraham, Alon, Dori, Amir, Lampl, Yair, Manganelli, Fiore, Morino, Stefania, Padovani, Alessandro, Siciliano, Gabriele, Schenone, Angelo, Magri, Francesca, Mazzeo, Anna, Giannini, Fabio, Sorbi, Sandro, Chiò, Adriano, Kuwahara, Motoi, Okuno, Tatsusada, Okamoto, Tomoko, Kokubun, Norito, Nishiyama, Kazutoshi, Kaida, Kenichi, Bokuda, Kota, Katsuno, Masahisa, Yabe, Ichiro, Saji, Etsuji, Yokota, Takanori, Hatanaka, Yuki, Nakahara, Jin, Sugimoto, Takamichi, Tanaka, Fumiaki, Tomita, Satoshi, Yamano, Yoshihisa, Hayashi, Tomohiro, Yamazaki, Hiroki, Tokashiki, Takashi, Horiuchi, Kazuhiro, Karelis, Guntis, Eftimov, Filip, Banach, Marta, Chyrchel-Paszkiewicz, Urszula, Kochanowicz, Jan, Selmaj, Krzysztof, Zielinski, Tomasz, Banaszkiewicz, Krzysztof, Mitrea, Dan, Scutaru-Kadar, Ana-Maria, Axelerad, Any, Stuchevskaya, Fatima, Boyko, Alexey, Khabirov, Farit, Trushnikova, Tatiana, Goncharova, Zoya, Suponeva, Natalia, Dorogov, Nikolay, Yakupov, Eduard, Raicevic, Ranko, Miletic Drakulic, Svetlana, Cabrera Serrano, Macarena, Muñoz Blanco, Jose Luis, Guerrero Sola, Antonio, Aguera Morales, Eduardo, Diaz Marin, Carmen, Juntas Morales, Raúl, Yeh, Jiann-Horng, Sung, Jia-Ying, Huang, Han-Wei, Tsai, Nai-Wen, Guo, Yuh-Cherng, Chao, Chi-Chao, Ro, Long-Sun, Sengun, Ihsan, Terzi, Murat, Alpaydin Baslo, Sezin, Koç, Filiz, Necdet Karli, Hamdi, Shulga, Olga, Smolko, Dmytro, Doroshenko, Oleksandr, Tomakh, Nataliya, Kyrychenko, Alla, Seliuk, Olga, Kalbus, Oleksandr, Skrypchenko, Iryna, Novakovska, Olha, Carod-Artal, Francisco Javier, Rinaldi, Simon, Brennan, Kathryn, Ellis, Simon, Carr, Aisling, Matthews, Emma, Traub, Rebecca, Mozaffar, Tahseen, Elliott, Matthew, Bhavaraju-Sanka, Ratna, Nance, Christopher, Levine, Todd, Lisak, Robert, Pasnoor, Mamatha, Pulley, Michael, Roy, Bhaskar, Govindarajan, Raghav, Sahagian, Gregory, Khella, Sami, Jacob, Daniel, Kushlaf, Hani, Sivakumar, Kumaraswamy, Melamed, Isaac, Sharma, Khema, Quick, Adam, Ubogu, Eroboghene, Lacomis, David, Isa, Arnaldo, Brannagan, Thomas, Chen, Shan, Katz, Jonathan, Feinberg, Marc, Pavlakis, Pantelis, Lange, Dale, Gudesblatt, Mark, Tandan, Rup, Gable, Karissa, Rivner, Michael, Barnes, Benjamin, Luke, Donna, Mahuwala, Zabeen, Macwan, Samir, Kwon, Patrick, Scott, James, Altamimi, Sadiq, Sabharwal, Priyanka, Allen, Jeffrey A, Lin, Jie, Basta, Ivana, Dysgaard, Tina, Eggers, Christian, Guptill, Jeffrey T, Gwathmey, Kelly G, Hewamadduma, Channa, Hofman, Erik, Hussain, Yessar M, Kuwabara, Satoshi, Le Masson, Gwendal, Leypoldt, Frank, Chang, Ting, Lipowska, Marta, Lowe, Murray, Lauria, Giuseppe, Querol, Luis, Simu, Mihaela-Adriana, Suresh, Niraja, Tse, Anissa, Ulrichts, Peter, Van Hoorick, Benjamin, Yamasaki, Ryo, Lewis, Richard A, and van Doorn, Pieter A

Published
2024
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21. Multi-scale signaling and tumor evolution in high-grade gliomas

Author

Liu, Jingxian, Cao, Song, Imbach, Kathleen J., Gritsenko, Marina A., Lih, Tung-Shing M., Kyle, Jennifer E., Yaron-Barir, Tomer M., Binder, Zev A., Li, Yize, Strunilin, Ilya, Wang, Yi-Ting, Tsai, Chia-Feng, Ma, Weiping, Chen, Lijun, Clark, Natalie M., Shinkle, Andrew, Naser Al Deen, Nataly, Caravan, Wagma, Houston, Andrew, Simin, Faria Anjum, Wyczalkowski, Matthew A., Wang, Liang-Bo, Storrs, Erik, Chen, Siqi, Illindala, Ritvik, Li, Yuping D., Jayasinghe, Reyka G., Rykunov, Dmitry, Cottingham, Sandra L., Chu, Rosalie K., Weitz, Karl K., Moore, Ronald J., Sagendorf, Tyler, Petyuk, Vladislav A., Nestor, Michael, Bramer, Lisa M., Stratton, Kelly G., Schepmoes, Athena A., Couvillion, Sneha P., Eder, Josie, Kim, Young-Mo, Gao, Yuqian, Fillmore, Thomas L., Zhao, Rui, Monroe, Matthew E., Southard-Smith, Austin N., Li, Yang E., Jui-Hsien Lu, Rita, Johnson, Jared L., Wiznerowicz, Maciej, Hostetter, Galen, Newton, Chelsea J., Ketchum, Karen A., Thangudu, Ratna R., Barnholtz-Sloan, Jill S., Wang, Pei, Fenyö, David, An, Eunkyung, Thiagarajan, Mathangi, Robles, Ana I., Mani, D.R., Smith, Richard D., Porta-Pardo, Eduard, Cantley, Lewis C., Iavarone, Antonio, Chen, Feng, Mesri, Mehdi, Nasrallah, MacLean P., Zhang, Hui, Resnick, Adam C., Chheda, Milan G., Rodland, Karin D., Liu, Tao, and Ding, Li

Published
2024
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23. Elucidating regulatory processes of intense physical activity by multi-omics analysis

Author

Ernesto S. Nakayasu, Marina A. Gritsenko, Young-Mo Kim, Jennifer E. Kyle, Kelly G. Stratton, Carrie D. Nicora, Nathalie Munoz, Kathleen M. Navarro, Daniel Claborne, Yuqian Gao, Karl K. Weitz, Vanessa L. Paurus, Kent J. Bloodsworth, Kelsey A. Allen, Lisa M. Bramer, Fernando Montes, Kathleen A. Clark, Grant Tietje, Justin Teeguarden, and Kristin E. Burnum-Johnson

Subjects
Multi-omics analysis, Intense exercise, Human performance, Biofluids, Metabolism, Immunity, Medicine (General), R5-920, Military Science
Abstract

Abstract Background Physiological and biochemical processes across tissues of the body are regulated in response to the high demands of intense physical activity in several occupations, such as firefighting, law enforcement, military, and sports. A better understanding of such processes can ultimately help improve human performance and prevent illnesses in the work environment. Methods To study regulatory processes in intense physical activity simulating real-life conditions, we performed a multi-omics analysis of three biofluids (blood plasma, urine, and saliva) collected from 11 wildland firefighters before and after a 45 min, intense exercise regimen. Omics profiles post- versus pre-exercise were compared by Student’s t-test followed by pathway analysis and comparison between the different omics modalities. Results Our multi-omics analysis identified and quantified 3835 proteins, 730 lipids and 182 metabolites combining the 3 different types of samples. The blood plasma analysis revealed signatures of tissue damage and acute repair response accompanied by enhanced carbon metabolism to meet energy demands. The urine analysis showed a strong, concomitant regulation of 6 out of 8 identified proteins from the renin-angiotensin system supporting increased excretion of catabolites, reabsorption of nutrients and maintenance of fluid balance. In saliva, we observed a decrease in 3 pro-inflammatory cytokines and an increase in 8 antimicrobial peptides. A systematic literature review identified 6 papers that support an altered susceptibility to respiratory infection. Conclusion This study shows simultaneous regulatory signatures in biofluids indicative of homeostatic maintenance during intense physical activity with possible effects on increased infection susceptibility, suggesting that caution against respiratory diseases could benefit workers on highly physical demanding jobs.

Published
2023
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33. Posterior Shoulder Instability, Part II—Glenoid Bone Grafting, Glenoid Osteotomy, and Rehabilitation/Return to Play—An International Expert Delphi Consensus Statement

Author

Athwal, George S., Bishop, Julie Y., Boache-Adjei, Yaw, Bradley, Kendall E., Brophy, Robert H., Calvo, Emilio, Camp, Christopher L., Cassidy, Tristan, Cordasco, Frank A., Danilkowicz, Richard M., Dekker, Travis A., Delaney, Ruth A., Denard, Patrick J., Duralde, Xavier A., Ernstbrunner, Lukas, Frangiamore, Salvatore J., Freehill, Michael T., Garrigues, Grant E., Goltz, Daniel E., Griffith, Timothy B., Heuberer, Philipp R., Hoy, Greg, Hoyt, Benjamin W., Hsu, Jason E., Imhoff, Andreas B., Itoi, Eiji, Jazrawi, Laith M., Kilcoyne, Kelly G., Laedermann, Alexandre, Lau, Brian C., Leclere, Lance E., Levine, William N., Martinez-Catalan, Natalia, McCarty, Eric C., Menendez, Mariano E., Millett, Peter J., Mirzayan, Raffy, Moroder, Philipp, Mullett, Hannan, Namdari, Surena, Neyton, Lionel, Nicholson, Gregory P., O'Brien, Michael J., Owens, Brett D., Parada, Stephen A., Parnes, Nata, Pasqualini, Ignacio, Pauzenberger, Leo, Provencher, Matthew T., Frank, Rachel M., Ranalletta, Maximiliano, Rodeo, Scott A., Rossi, Luciano A., Sanchez-Sotelo, Joaquin, Scanaliato, John P., Lassiter, Tally, Taylor, Dean C., Toth, Alison P., Trasolini, Nicholas A., Wagner, Eric R., Whelan, Daniel B., Wickman, John R., Wittstein, Jocelyn R., Wong, Ivan, Hurley, Eoghan T., Aman, Zachary S., Doyle, Tom R., Levin, Jay M., Matache, Bogdan A., Chalmers, Peter N., Waterman, Brian R., Erickson, Brandon J., Klifto, Christopher S., Anakwenze, Oke A., and Dickens, Jonathan F.

Published
2024
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34. Posterior Shoulder Instability, Part I—Diagnosis, Nonoperative Management, and Labral Repair for Posterior Shoulder Instability—An International Expert Delphi Consensus Statement

Author

Athwal, George S., Bishop, Julie Y., Boache-Adjei, Yaw, Bradley, Kendall E., Brophy, Robert H., Calvo, Emilio, Camp, Christopher L., Cassidy, Tristan, Chalmers, Peter N., Cordasco, Frank A., Danilkowicz, Richard M., Dekker, Travis A., Delaney, Ruth A., Denard, Patrick J., Duralde, Xavier A., Erickson, Brandon J., Ernstbrunner, Lukas, Frangiamore, Salvatore J., Freehill, Michael T., Goltz, Daniel E., Griffith, Timothy B., Heuberer, Philipp R., Hoy, Greg, Hoyt, Benjamin W., Imhoff, Andreas B., Itoi, Eiji, Kilcoyne, Kelly G., Laedermann, Alexandre, Lau, Brian C., Leclere, Lance E., Levine, William N., Martinez-Catalan, Natalia, Matache, Bogdan A., McCarty, Eric C., Menendez, Mariano E., Millett, Peter J., Mirzayan, Raffy, Moroder, Philipp, Mullett, Hannan, Neyton, Lionel, Nicholson, Gregory P., O'Brien, Michael J., Owens, Brett D., Parada, Stephen A., Parnes, Nata, Pasqualini, Ignacio, Pauzenberger, Leo, Provencher, Matthew T., Frank, Rachel M., Ranalletta, Maximiliano, Rodeo, Scott A., Rossi, Luciano A., Sanchez-Sotelo, Joaquin, Scanaliato, John P., Lassiter, Tally, Taylor, Dean C., Toth, Alison P., Trasolini, Nicholas A., Wagner, Eric R., Waterman, Brian R., Whelan, Daniel B., Wickman, John R., Wittstein, Jocelyn R., Wong, Ivan, Hurley, Eoghan T., Aman, Zachary S., Doyle, Tom R., Levin, Jay M., Jazrawi, Laith M., Garrigues, Grant E., Namdari, Surena, Hsu, Jason E., Klifto, Christopher S., Anakwenze, Oke, and Dickens, Jonathan F.

Published
2024
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35. Incidence, demographics, and survival of malignant hemangioendothelioma in the United States

Author

Kelly G. Paulson, Vinod Ravi, Brian P. Rubin, Min Park, Elizabeth T. Loggers, Lee D. Cranmer, and Michael J. Wagner

Subjects
EHE, epithelioid hemangioendothelioma, hemangioendothelioma, rare cancer, sarcoma, SEER, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Malignant hemangioendothelioma is an endothelial cancer with heterogeneous clinical behavior that can range from indolent to aggressive, of which the majority are epithelioid (EHE). Its incidence and demographics have not been previously well defined in a large cohort. Methods This retrospective analysis used the US Cancer Statistics National Program of Cancer Registries – Surveillance Epidemiology End Results (SEER) combined database to identify patients in the US newly diagnosed with hemangioendothelioma between the years of 2001 and 2017 (n = 1986). Survival analyses were performed on a subset of patients within the SEER‐18 database with survival information available (n = 417). Outcomes included incidence, demographics of patients newly diagnosed with hemangioendothelioma, extent of disease at presentation, and overall survival. Results The incidence of hemangioendothelioma in the US is 0.4 cases per million person‐years. Although cases rose to 122 newly diagnosed in the year 2017 (90 EHE, 32 other hemangioendothelioma), incidence rates were stable. Skin and connective tissues were the most common presenting sites (33.4%), followed by liver (24.5%), lung (17.6%), and bone (12.5%). Median age at diagnosis was 55 years; 27.2% of patients were pediatric, adolescent, or young adult (

Published
2023
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36. Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response

Author

Feng, Song, Heath, Emily, Jefferson, Brett, Joslyn, Cliff, Kvinge, Henry, Mitchell, Hugh D., Praggastis, Brenda, Eisfeld, Amie J., Sims, Amy C., Thackray, Larissa B., Fan, Shufang, Walters, Kevin B., Halfmann, Peter J., Westhoff-Smith, Danielle, Tan, Qing, Menachery, Vineet D., Sheahan, Timothy P., Cockrell, Adam S., Kocher, Jacob F., Stratton, Kelly G., Heller, Natalie C., Bramer, Lisa M., Diamond, Michael S., Baric, Ralph S., Waters, Katrina M., Kawaoka, Yoshihiro, McDermott, Jason E., and Purvine, Emilie

Subjects
Quantitative Biology - Quantitative Methods, Mathematics - Combinatorics, 92C42, 92-08, 05C65
Abstract

Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way relationships present among genes and proteins in biological systems. Hypergraphs are generalizations of graphs that naturally model multi-way relationships and have shown promise in modeling systems such as protein complexes and metabolic reactions. In this paper we seek to understand how hypergraphs can more faithfully identify, and potentially predict, important genes based on complex relationships inferred from genomic expression data sets. Results: We compiled a novel data set of transcriptional host response to pathogenic viral infections and formulated relationships between genes as a hypergraph where hyperedges represent significantly perturbed genes, and vertices represent individual biological samples with specific experimental conditions. We find that hypergraph betweenness centrality is a superior method for identification of genes important to viral response when compared with graph centrality. Conclusions: Our results demonstrate the utility of using hypergraphs to represent complex biological systems and highlight central important responses in common to a variety of highly pathogenic viruses.

Published
2020

37. Epidemic modelling of bovine tuberculosis in cattle herds and badgers in Ireland

Author

White, L. M. and Kelly, G. E.

Subjects
Quantitative Biology - Populations and Evolution, Statistics - Applications
Abstract

Bovine tuberculosis, a disease that affects cattle and badgers in Ireland, was studied via stochastic epidemic modeling using incidence data from the Four Area Project (Griffin et al., 2005). The Four Area Project was a large scale field trial conducted in four diverse farming regions of Ireland over a five-year period (1997-2002) to evaluate the impact of badger culling on bovine tuberculosis incidence in cattle herds. Based on the comparison of several models, the model with no between-herd transmission and badger-to-herd transmission proportional to the total number of infected badgers culled was best supported by the data. Detailed model validation was conducted via model prediction, identifiability checks and sensitivity analysis. The results suggest that badger-to-cattle transmission is of more importance than between-herd transmission and that if there was no badger-to-herd transmission, levels of bovine tuberculosis in cattle herds in Ireland could decrease considerably., Comment: 32 pages, 2 figures

Published
2020

38. Elucidating regulatory processes of intense physical activity by multi-omics analysis

Author

Nakayasu, Ernesto S., Gritsenko, Marina A., Kim, Young-Mo, Kyle, Jennifer E., Stratton, Kelly G., Nicora, Carrie D., Munoz, Nathalie, Navarro, Kathleen M., Claborne, Daniel, Gao, Yuqian, Weitz, Karl K., Paurus, Vanessa L., Bloodsworth, Kent J., Allen, Kelsey A., Bramer, Lisa M., Montes, Fernando, Clark, Kathleen A., Tietje, Grant, Teeguarden, Justin, and Burnum-Johnson, Kristin E.

Published
2023
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39. Rapid remodeling of the soil lipidome in response to a drying-rewetting event

Author

Couvillion, Sneha P., Danczak, Robert E., Naylor, Dan, Smith, Montana L., Stratton, Kelly G., Paurus, Vanessa L., Bloodsworth, Kent J., Farris, Yuliya, Schmidt, Darren J., Richardson, Rachel E., Bramer, Lisa M., Fansler, Sarah J., Nakayasu, Ernesto S., McDermott, Jason E., Metz, Thomas O., Lipton, Mary S., Jansson, Janet K., and Hofmockel, Kirsten S.

Published
2023
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41. Comparative Effectiveness of Initial Treatment for Infantile Spasms in a Contemporary US Cohort

Author

Grinspan, Zachary M, Knupp, Kelly G, Patel, Anup D, Yozawitz, Elissa G, Wusthoff, Courtney J, Wirrell, Elaine C, Valencia, Ignacio, Singhal, Nilika S, Nordli, Douglas R, Mytinger, John R, Mitchell, Wendy G, Keator, Cynthia G, Loddenkemper, Tobias, Hussain, Shaun A, Harini, Chellamani, Gaillard, William D, Fernandez, Ivan S, Coryell, Jason, Chu, Catherine J, Berg, Anne T, and Shellhaas, Renee A

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Pediatric, Comparative Effectiveness Research, Brain Disorders, Neurosciences, Cognitive Sciences, Neurology & Neurosurgery, Clinical sciences
Abstract

ObjectiveTo compare the effectiveness of initial treatment for infantile spasms.MethodsThe National Infantile Spasms Consortium prospectively followed up children with new-onset infantile spasms that began at age 2 to 24 months at 23 US centers (2012-2018). Freedom from treatment failure at 60 days required no second treatment for infantile spasms and no clinical spasms after 30 days of treatment initiation. We managed treatment selection bias with propensity score weighting and within-center correlation with generalized estimating equations.ResultsFreedom from treatment failure rates were as follows: adrenocorticotropic hormone (ACTH) 88 of 190 (46%), oral steroids 42 of 95 (44%), vigabatrin 32 of 87 (37%), and nonstandard therapy 4 of 51 (8%). Changing from oral steroids to ACTH was not estimated to affect response (observed 44% estimated to change to 44% [95% confidence interval 34%-54%]). Changing from nonstandard therapy to ACTH would improve response from 8% to 39% (17%-67%), and changing to oral steroids would improve response from 8% to 38% (15%-68%). There were large but not statistically significant estimated effects of changing from vigabatrin to ACTH (29% to 42% [15%-75%]), from vigabatrin to oral steroids (29% to 42% [28%-57%]), and from nonstandard therapy to vigabatrin (8% to 20% [6%-50%]). Among children treated with vigabatrin, those with tuberous sclerosis complex (TSC) responded more often than others (62% vs 29%; p < 0.05).DiscussionCompared to nonstandard therapy, ACTH and oral steroids are superior for initial treatment of infantile spasms. The estimated effectiveness of vigabatrin is between that of ACTH/oral steroids and nonstandard therapy, although the sample was underpowered for statistical confidence. When used, vigabatrin worked best for TSC.Classification of evidenceThis study provides Class III evidence that for children with new-onset infantile spasms, ACTH or oral steroids were superior to nonstandard therapies.

Published
2021

42. Alterations in the gut microbiota contribute to cognitive impairment induced by the ketogenic diet and hypoxia

Author

Olson, Christine A, Iñiguez, Alonso J, Yang, Grace E, Fang, Ping, Pronovost, Geoffrey N, Jameson, Kelly G, Rendon, Tomiko K, Paramo, Jorge, Barlow, Jacob T, Ismagilov, Rustem F, and Hsiao, Elaine Y

Subjects
Microbiology, Biological Sciences, Biomedical and Clinical Sciences, Genetics, Nutrition, Complementary and Integrative Health, Prevention, Aetiology, 2.1 Biological and endogenous factors, Oral and gastrointestinal, Animals, Bilophila, Cognitive Dysfunction, Diet, Ketogenic, Gastrointestinal Microbiome, Hippocampus, Hypoxia, Brain, Interferon-gamma, Mice, Mice, Inbred C57BL, Mice, Knockout, Th1 Cells, brain, cognition, hippocampus, microbiota, neuroimmune, Medical Microbiology, Immunology, Biochemistry and cell biology, Medical microbiology
Abstract

Many genetic and environmental factors increase susceptibility to cognitive impairment (CI), and the gut microbiome is increasingly implicated. However, the identity of gut microbes associated with CI risk, their effects on CI, and their mechanisms remain unclear. Here, we show that a carbohydrate-restricted (ketogenic) diet potentiates CI induced by intermittent hypoxia in mice and alters the gut microbiota. Depleting the microbiome reduces CI, whereas transplantation of the risk-associated microbiome or monocolonization with Bilophila wadsworthia confers CI in mice fed a standard diet. B. wadsworthia and the risk-associated microbiome disrupt hippocampal synaptic plasticity, neurogenesis, and gene expression. The CI is associated with microbiome-dependent increases in intestinal interferon-gamma (IFNg)-producing Th1 cells. Inhibiting Th1 cell development abrogates the adverse effects of both B. wadsworthia and environmental risk factors on CI. Together, these findings identify select gut bacteria that contribute to environmental risk for CI in mice by promoting inflammation and hippocampal dysfunction.

Published
2021

43. Centering inclusivity in the design of online conferences—An OHBM–Open Science perspective

Author

Levitis, Elizabeth, van Praag, Cassandra D Gould, Gau, Rémi, Heunis, Stephan, DuPre, Elizabeth, Kiar, Gregory, Bottenhorn, Katherine L, Glatard, Tristan, Nikolaidis, Aki, Whitaker, Kirstie Jane, Mancini, Matteo, Niso, Guiomar, Afyouni, Soroosh, Alonso-Ortiz, Eva, Appelhoff, Stefan, Arnatkeviciute, Aurina, Atay, Selim Melvin, Auer, Tibor, Baracchini, Giulia, Bayer, Johanna MM, Beauvais, Michael JS, Bijsterbosch, Janine D, Bilgin, Isil P, Bollmann, Saskia, Bollmann, Steffen, Botvinik-Nezer, Rotem, Bright, Molly G, Calhoun, Vince D, Chen, Xiao, Chopra, Sidhant, Chuan-Peng, Hu, Close, Thomas G, Cookson, Savannah L, Craddock, R Cameron, De La Vega, Alejandro, De Leener, Benjamin, Demeter, Damion V, Di Maio, Paola, Dickie, Erin W, Eickhoff, Simon B, Esteban, Oscar, Finc, Karolina, Frigo, Matteo, Ganesan, Saampras, Ganz, Melanie, Garner, Kelly G, Garza-Villarreal, Eduardo A, Gonzalez-Escamilla, Gabriel, Goswami, Rohit, Griffiths, John D, Grootswagers, Tijl, Guay, Samuel, Guest, Olivia, Handwerker, Daniel A, Herholz, Peer, Heuer, Katja, Huijser, Dorien C, Iacovella, Vittorio, Joseph, Michael JE, Karakuzu, Agah, Keator, David B, Kobeleva, Xenia, Kumar, Manoj, Laird, Angela R, Larson-Prior, Linda J, Lautarescu, Alexandra, Lazari, Alberto, Legarreta, Jon Haitz, Li, Xue-Ying, Lv, Jinglei, L., Sina Mansour, Meunier, David, Moraczewski, Dustin, Nandi, Tulika, Nastase, Samuel A, Nau, Matthias, Noble, Stephanie, Norgaard, Martin, Obungoloch, Johnes, Oostenveld, Robert, Orchard, Edwina R, Pinho, Ana Luísa, Poldrack, Russell A, Qiu, Anqi, Raamana, Pradeep Reddy, Rokem, Ariel, Rutherford, Saige, Sharan, Malvika, Shaw, Thomas B, Syeda, Warda T, Testerman, Meghan M, Toro, Roberto, Valk, Sofie L, Van Den Bossche, Sofie, Varoquaux, Gaël, Váša, František, Veldsman, Michele, Vohryzek, Jakub, Wagner, Adina S, and Walsh, Reubs J

Subjects
online conferences, diversity, inclusivity, open science, collaborative events
Abstract

As the global health crisis unfolded, many academic conferences moved online in 2020. This move has been hailed as a positive step towards inclusivity in its attenuation of economic, physical, and legal barriers and effectively enabled many individuals from groups that have traditionally been underrepresented to join and participate. A number of studies have outlined how moving online made it possible to gather a more global community and has increased opportunities for individuals with various constraints, e.g., caregiving responsibilities. Yet, the mere existence of online conferences is no guarantee that everyone can attend and participate meaningfully. In fact, many elements of an online conference are still significant barriers to truly diverse participation: the tools used can be inaccessible for some individuals; the scheduling choices can favour some geographical locations; the set-up of the conference can provide more visibility to well-established researchers and reduce opportunities for early-career researchers. While acknowledging the benefits of an online setting, especially for individuals who have traditionally been underrepresented or excluded, we recognize that fostering social justice requires inclusivity to actively be centered in every aspect of online conference design. Here, we draw from the literature and from our own experiences to identify practices that purposefully encourage a diverse community to attend, participate in, and lead online conferences. Reflecting on how to design more inclusive online events is especially important as multiple scientific organizations have announced that they will continue offering an online version of their event when in-person conferences can resume.

Published
2021

44. Brainhack: Developing a culture of open, inclusive, community-driven neuroscience

Author

Gau, Rémi, Noble, Stephanie, Heuer, Katja, Bottenhorn, Katherine L, Bilgin, Isil P, Yang, Yu-Fang, Huntenburg, Julia M, Bayer, Johanna MM, Bethlehem, Richard AI, Rhoads, Shawn A, Vogelbacher, Christoph, Borghesani, Valentina, Levitis, Elizabeth, Wang, Hao-Ting, Van Den Bossche, Sofie, Kobeleva, Xenia, Legarreta, Jon Haitz, Guay, Samuel, Atay, Selim Melvin, Varoquaux, Gael P, Huijser, Dorien C, Sandström, Malin S, Herholz, Peer, Nastase, Samuel A, Badhwar, AmanPreet, Dumas, Guillaume, Schwab, Simon, Moia, Stefano, Dayan, Michael, Bassil, Yasmine, Brooks, Paula P, Mancini, Matteo, Shine, James M, O’Connor, David, Xie, Xihe, Poggiali, Davide, Friedrich, Patrick, Heinsfeld, Anibal S, Riedl, Lydia, Toro, Roberto, Caballero-Gaudes, César, Eklund, Anders, Garner, Kelly G, Nolan, Christopher R, Demeter, Damion V, Barrios, Fernando A, Merchant, Junaid S, McDevitt, Elizabeth A, Oostenveld, Robert, Craddock, R Cameron, Rokem, Ariel, Doyle, Andrew, Ghosh, Satrajit S, Nikolaidis, Aki, Stanley, Olivia W, Uruñuela, Eneko, Community, The Brainhack, Anousheh, Nasim, Arnatkeviciute, Aurina, Auzias, Guillaume, Bachar, Dipankar, Bannier, Elise, Basanisi, Ruggero, Basavaraj, Arshitha, Bedini, Marco, Bellec, Pierre, Benn, R Austin, Berluti, Kathryn, Bollmann, Steffen, Bollmann, Saskia, Bradley, Claire, Brown, Jesse, Buchweitz, Augusto, Callahan, Patrick, Chan, Micaela Y, Chandio, Bramsh Q, Cheng, Theresa, Chopra, Sidhant, Chung, Ai Wern, Close, Thomas G, Combrisson, Etienne, Cona, Giorgia, Constable, R Todd, Cury, Claire, Dadi, Kamalaker, Damasceno, Pablo F, Das, Samir, De Vico Fallani, Fabrizio, DeStasio, Krista, Dickie, Erin W, Dorfschmidt, Lena, Duff, Eugene P, DuPre, Elizabeth, Dziura, Sarah, Esper, Nathalia B, Esteban, Oscar, Fadnavis, Shreyas, Flandin, Guillaume, Flannery, Jessica E, and Flournoy, John

Subjects
Biological Psychology, Biomedical and Clinical Sciences, Neurosciences, Psychology, Communication, Congresses as Topic, Internet, Practice Guidelines as Topic, Brainhack Community, Brainhack, best practices, collaboration, community building, hackathon, inclusivity, neuroscience, open science, reproducibility, training, Cognitive Sciences, Neurology & Neurosurgery, Biological psychology
Abstract

Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress.

Published
2021

45. A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases.

Author

Kyle, Jennifer E, Stratton, Kelly G, Zink, Erika M, Kim, Young-Mo, Bloodsworth, Kent J, Monroe, Matthew E, Undiagnosed Diseases Network, Waters, Katrina M, Webb-Robertson, Bobbie-Jo M, Koeller, David M, and Metz, Thomas O

Subjects
Undiagnosed Diseases Network, Humans, Metabolic Diseases, Adolescent, Adult, Middle Aged, Child, Child, Preschool, Infant, Infant, Newborn, Female, Male, Mass Spectrometry, Metabolomics, Young Adult, Datasets as Topic, Undiagnosed Diseases, Lipidomics, Clinical Research, Metabolic and endocrine
Abstract

Every year individuals experience symptoms that remain undiagnosed by healthcare providers. In the United States, these rare diseases are defined as a condition that affects fewer than 200,000 individuals. However, there are an estimated 7000 rare diseases, and there are an estimated 25-30 million Americans in total (7.6-9.2% of the population as of 2018) affected by such disorders. The NIH Common Fund Undiagnosed Diseases Network (UDN) seeks to provide diagnoses for individuals with undiagnosed disease. Mass spectrometry-based metabolomics and lipidomics analyses could advance the collective understanding of individual symptoms and advance diagnoses for individuals with heretofore undiagnosed disease. Here, we report the mass spectrometry-based metabolomics and lipidomics analyses of blood plasma, urine, and cerebrospinal fluid from 148 patients within the UDN and their families, as well as from a reference population of over 100 individuals with no known metabolic diseases. The raw and processed data are available to the research community so that they might be useful in the diagnoses of current or future patients suffering from undiagnosed disorders.

Published
2021

47. Identifying and sharing per-and polyfluoroalkyl substances hot-spot areas and exposures in drinking water

Author

Sweta Ojha, P. Travis Thompson, Christian D. Powell, Hunter N. B. Moseley, and Kelly G. Pennell

Subjects
Science
Abstract

Abstract Exposure to per- and polyfluoroalkyl substances (PFAS) in drinking water is widely recognized as a public health concern. Decision-makers who are responsible for managing PFAS drinking water risks lack the tools to acquire the information they need. In response to this need, we provide a detailed description of a Kentucky dataset that allows decision-makers to visualize potential hot-spot areas and evaluate drinking water systems that may be susceptible to PFAS contamination. The dataset includes information extracted from publicly available sources to create five different maps in ArcGIS Online and highlights potential sources of PFAS contamination in the environment in relation to drinking water systems. As datasets of PFAS drinking water sampling continue to grow as part of evolving regulatory requirements, we used this Kentucky dataset as an example to promote the reuse of this dataset and others like it. We incorporated the FAIR (Findable, Accessible, Interoperable, and Reusable) principles by creating a Figshare item that includes all data and associated metadata with these five ArcGIS maps.

Published
2023
Full Text
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48. A proposed FAIR approach for disseminating geospatial information system maps

Author

P. Travis Thompson, Sweta Ojha, Christian D. Powell, Kelly G. Pennell, and Hunter N. B. Moseley

Subjects
Science
Abstract

Abstract We present a draft Minimum Information About Geospatial Information System (MIAGIS) standard for facilitating public deposition of geospatial information system (GIS) datasets that follows the FAIR (Findable, Accessible, Interoperable and Reusable) principles. The draft MIAGIS standard includes a deposition directory structure and a minimum javascript object notation (JSON) metadata formatted file that is designed to capture critical metadata describing GIS layers and maps as well as their sources of data and methods of generation. The associated miagis Python package facilitates the creation of this MIAGIS metadata file and directly supports metadata extraction from both Esri JSON and GEOJSON GIS data formats plus options for extraction from user-specified JSON formats. We also demonstrate their use in crafting two example depositions of ArcGIS generated maps. We hope this draft MIAGIS standard along with the supporting miagis Python package will assist in establishing a GIS standards group that will develop the draft into a full standard for the wider GIS community as well as a future public repository for GIS datasets.

Published
2023
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49. Short sleep duration and interest in sleep improvement in a multi-ethnic cohort of diverse women participating in a community-based wellness intervention: an unmet need for improvement

Author

Sara E. Simonsen, Grant R. Sunada, Kathleen Digre, Louisa A. Stark, Valentine Mukundente, Ed Napia, Fahina Tavake-Pasi, Jeannette Villalta, Doriena Lee, France Davis, Ana Sanchez-Birkhead, B. Heather Brown, and Kelly G. Baron

Subjects
Short sleep, Disparities, Health behavior change, Community-engaged research, Obesity, Gynecology and obstetrics, RG1-991, Public aspects of medicine, RA1-1270
Abstract

Abstract Background Disparities in sleep duration are a modifiable contributor to increased risk for cardiometabolic disorders in communities of color. We examined the prevalence of short sleep duration and interest in improving sleep among a multi-ethnic sample of women participating in a culturally tailored wellness coaching program and discussed steps to engage communities in sleep health interventions. Methods Secondary analysis of data from a randomized trial were used. The wellness coaching trial utilized a Community-Based Participatory Research (CBPR) approach. Data were from the baseline survey and baseline wellness coaching notes. Short sleep duration was defined as

Published
2023
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50. Progression of ACT

Author

Zettle, Robert D., Wilson, Kelly G., Twohig, Michael P., book editor, Levin, Michael E., book editor, and Petersen, Julie M., book editor

Published
2023
Full Text
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