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9. GA4GH Phenopackets: A Practical Introduction

Author

Ladewig, Markus S, Jacobsen, Julius OB, Wagner, Alex H, Danis, Daniel, Kassaby, Baha El, Gargano, Michael, Groza, Tudor, Baudis, Michael, Steinhaus, Robin, Seelow, Dominik, Bechrakis, Nikolaos E, Mungall, Christopher J, Schofield, Paul N, Elemento, Olivier, Smith, Lindsay, McMurry, Julie A, Munoz‐Torres, Monica, Haendel, Melissa A, and Robinson, Peter N

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Health Services and Systems, Health Sciences, Biotechnology, Networking and Information Technology R&D (NITRD), Rare Diseases, Human Genome, Cancer, Generic health relevance, Good Health and Well Being, FAIR data, Global Alliance for Genomics and Health, Human Phenotype Ontology, Phenopacket Schema, deep phenotyping
Abstract

The Global Alliance for Genomics and Health (GA4GH) is developing a suite of coordinated standards for genomics for healthcare. The Phenopacket is a new GA4GH standard for sharing disease and phenotype information that characterizes an individual person, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. A detailed example is presented that illustrates how to use the schema to represent the clinical course of a patient with retinoblastoma, including demographic information, the clinical diagnosis, phenotypic features and clinical measurements, an examination of the extirpated tumor, therapies, and the results of genomic analysis. The Phenopacket Schema, together with other GA4GH data and technical standards, will enable data exchange and provide a foundation for the computational analysis of disease and phenotype information to improve our ability to diagnose and conduct research on all types of disorders, including cancer and rare diseases.

Published
2023

11. Learning Continuous Chaotic Attractors with a Reservoir Computer

Author

Smith, Lindsay M., Kim, Jason Z., Lu, Zhixin, and Bassett, Dani S.

Subjects
Computer Science - Neural and Evolutionary Computing, Nonlinear Sciences - Chaotic Dynamics
Abstract

Neural systems are well known for their ability to learn and store information as memories. Even more impressive is their ability to abstract these memories to create complex internal representations, enabling advanced functions such as the spatial manipulation of mental representations. While recurrent neural networks (RNNs) are capable of representing complex information, the exact mechanisms of how dynamical neural systems perform abstraction are still not well-understood, thereby hindering the development of more advanced functions. Here, we train a 1000-neuron RNN -- a reservoir computer (RC) -- to abstract a continuous dynamical attractor memory from isolated examples of dynamical attractor memories. Further, we explain the abstraction mechanism with new theory. By training the RC on isolated and shifted examples of either stable limit cycles or chaotic Lorenz attractors, the RC learns a continuum of attractors, as quantified by an extra Lyapunov exponent equal to zero. We propose a theoretical mechanism of this abstraction by combining ideas from differentiable generalized synchronization and feedback dynamics. Our results quantify abstraction in simple neural systems, enabling us to design artificial RNNs for abstraction, and leading us towards a neural basis of abstraction., Comment: 9 pages

Published
2021
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12. The GA4GH Phenopacket schema defines a computable representation of clinical data

Author

Jacobsen, Julius OB, Baudis, Michael, Baynam, Gareth S, Beckmann, Jacques S, Beltran, Sergi, Buske, Orion J, Callahan, Tiffany J, Chute, Christopher G, Courtot, Mélanie, Danis, Daniel, Elemento, Olivier, Essenwanger, Andrea, Freimuth, Robert R, Gargano, Michael A, Groza, Tudor, Hamosh, Ada, Harris, Nomi L, Kaliyaperumal, Rajaram, Lloyd, Kevin C Kent, Khalifa, Aly, Krawitz, Peter M, Köhler, Sebastian, Laraway, Brian J, Lehväslaiho, Heikki, Matalonga, Leslie, McMurry, Julie A, Metke-Jimenez, Alejandro, Mungall, Christopher J, Munoz-Torres, Monica C, Ogishima, Soichi, Papakonstantinou, Anastasios, Piscia, Davide, Pontikos, Nikolas, Queralt-Rosinach, Núria, Roos, Marco, Sass, Julian, Schofield, Paul N, Seelow, Dominik, Siapos, Anastasios, Smedley, Damian, Smith, Lindsay D, Steinhaus, Robin, Sundaramurthi, Jagadish Chandrabose, Swietlik, Emilia M, Thun, Sylvia, Vasilevsky, Nicole A, Wagner, Alex H, Warner, Jeremy L, Weiland, Claus, Haendel, Melissa A, and Robinson, Peter N

Subjects
GAGH Phenopacket Modeling Consortium
Published
2022

15. Recognizing and Remedying

Author

Rudes, Danielle S., primary, Magnuson, Shannon, additional, Shaw, Cameron, additional, Smith, Lindsay, additional, Kushmerick-McCune, Bryce, additional, Hartwell, Taylor N., additional, and Appleton, CJ, additional

Published
2023
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17. Using Nail Salons, Beauty Spas, and Hair Salons for Health Education with Black Women

Author

Dixon, Ashlee, Earls, Eldria, Handberry, Maya, Moon, Brianna, Smith, Lindsay, and Mincey, Krista

Subjects
Beauty shops -- Usage -- Educational aspects -- Health aspects, Women, Black -- Education -- Health aspects, Health education -- Demographic aspects -- Methods, Health resorts -- Usage -- Educational aspects, Ethnic, cultural, racial issues/studies, Social sciences
Abstract

A historical lack of access to healthcare and the mistreatment of Black women among those in the medical field have contributed to the health disparities against this group today. Based on existing health disparities affecting Black women, this study examined the feasibility of using nail salons, beauty salons, and hair salons as an avenue for health education efforts for Black women. An online survey was used to reach Black-owned salon workers. A total of 20 female participants completed the survey. Most participants preferred sharing health information with their clients through one-on-one conversations. Eighty percent of participants were willing to receive training on health topics so they could educate their clients. Findings suggest that it is feasible to utilize beauty stylists as lay health workers to promote positive health education among Black women. Further studies are needed to address health topics that clients would be willing to discuss with their stylists., Author(s): Ashlee Dixon [sup.1] , Eldria Earls [sup.2] , Maya Handberry [sup.1] , Brianna Moon [sup.1] , Lindsay Smith [sup.1] , Krista Mincey [sup.1] Author Affiliations: (1) grid.259906.1, 0000 0001 [...]

Published
2023
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19. GA4GH: International policies and standards for data sharing across genomic research and healthcare

Author

Rehm, Heidi L, Page, Angela JH, Smith, Lindsay, Adams, Jeremy B, Alterovitz, Gil, Babb, Lawrence J, Barkley, Maxmillian P, Baudis, Michael, Beauvais, Michael JS, Beck, Tim, Beckmann, Jacques S, Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K, Boughtwood, Tiffany F, Bourque, Guillaume, Bowers, Sarion R, Brookes, Anthony J, Brudno, Michael, Brush, Matthew H, Bujold, David, Burdett, Tony, Buske, Orion J, Cabili, Moran N, Cameron, Daniel L, Carroll, Robert J, Casas-Silva, Esmeralda, Chakravarty, Debyani, Chaudhari, Bimal P, Chen, Shu Hui, Cherry, J Michael, Chung, Justina, Cline, Melissa, Clissold, Hayley L, Cook-Deegan, Robert M, Courtot, Mélanie, Cunningham, Fiona, Cupak, Miro, Davies, Robert M, Denisko, Danielle, Doerr, Megan J, Dolman, Lena I, Dove, Edward S, Dursi, L Jonathan, Dyke, Stephanie OM, Eddy, James A, Eilbeck, Karen, Ellrott, Kyle P, Fairley, Susan, Fakhro, Khalid A, Firth, Helen V, Fitzsimons, Michael S, Fiume, Marc, Flicek, Paul, Fore, Ian M, Freeberg, Mallory A, Freimuth, Robert R, Fromont, Lauren A, Fuerth, Jonathan, Gaff, Clara L, Gan, Weiniu, Ghanaim, Elena M, Glazer, David, Green, Robert C, Griffith, Malachi, Griffith, Obi L, Grossman, Robert L, Groza, Tudor, Auvil, Jaime M Guidry, Guigó, Roderic, Gupta, Dipayan, Haendel, Melissa A, Hamosh, Ada, Hansen, David P, Hart, Reece K, Hartley, Dean Mitchell, Haussler, David, Hendricks-Sturrup, Rachele M, Ho, Calvin WL, Hobb, Ashley E, Hoffman, Michael M, Hofmann, Oliver M, Holub, Petr, Hsu, Jacob Shujui, Hubaux, Jean-Pierre, Hunt, Sarah E, Husami, Ammar, Jacobsen, Julius O, Jamuar, Saumya S, Janes, Elizabeth L, Jeanson, Francis, Jené, Aina, Johns, Amber L, Joly, Yann, Jones, Steven JM, Kanitz, Alexander, Kato, Kazuto, Keane, Thomas M, and Kekesi-Lafrance, Kristina

Subjects
Biological Sciences, Genetics, Human Genome, Clinical Research, Health Services, Generic health relevance, Good Health and Well Being
Abstract

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.

Published
2021

22. Equity, diversity, and inclusion at the Global Alliance for Genomics and Health

Author

Skantharajah, Neerjah, Baichoo, Shakuntala, Boughtwood, Tiffany F., Casas-Silva, Esmeralda, Chandrasekharan, Subhashini, Dave, Sanjay M., Fakhro, Khalid A., Falcon de Vargas, Aida B., Gayle, Sylvia S., Gupta, Vivek K., Hendricks-Sturrup, Rachele, Hobb, Ashley E., Li, Stephanie, Llamas, Bastien, Lopez-Correa, Catalina, Machirori, Mavis, Melendez-Zajgla, Jorge, Millner, Mareike A., Page, Angela J.H., Paglione, Laura D., Raven-Adams, Maili C., Smith, Lindsay, Thomas, Ericka M., Kumuthini, Judit, and Corpas, Manuel

Published
2023
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27. Closing the Revolving Door: PIVOTAL PARTNERSHIPS AND COLLABORATIVE SERVICES FOR MEN'S REENTRY SUCCESS

Author

Smith, Lindsay, Lerch, Jennifer, West, Allen, and Taxman, Faye S.

Subjects
Prison administration -- Methods, Offender reintegration -- Methods, Rehabilitation of criminals -- Methods, Law
Abstract

On average, about 10 million individuals are admitted to jails per year (Minton & Zeng, 2021). These individuals, especially those with repeated jail incarcerations, are disproportionately of lower socioeconomic status, [...]

Published
2023

30. Value in Digital Technologies and Services

Author

Riss, Uwe V., Ziegler, Michael, Smith, Lindsay J., Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Uden, Lorna, editor, Ting, I-Hsien, editor, and Feldmann, Birgit, editor

Published
2022
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32. Group A Streptococcus Bacteremia in Persons Who Inject Drugs--Northern Vermont, January 2020-October 2023

Author

Raymond, Monica J., Wolfe, Tonda R., and Smith, Lindsay M.

Subjects
Medical centers -- Health aspects, Medical records -- Health aspects, Drugs -- Health aspects, Infection -- Health aspects, Bacteremia -- Health aspects, Health
Abstract

CDC has recently reported increases in invasive group A Streptococcus (GAS) infections.* * Injection of illicit drugs and homelessness are two documented risk factors for invasive GAS infections (1). In [...]

Published
2024

44. Early Neolithic forest farming at Seven Springs, Martlesham, Suffolk inferred from sedaDNA and pollen

Author

Hudson, Samuel M, primary, Allen, Steven J, additional, Alsos, Inger Greve, additional, Curl, Julie, additional, Heintzman, Peter D, additional, Hughes, Paul, additional, Gardiner, Lynne, additional, Lloyd-Smith, Lindsay, additional, Pears, Ben R, additional, Scaife, Rob, additional, Stoof-Leichsenring, Kathleen R, additional, and Brown, Antony, additional

Published
2023
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46. Disaster preparedness of health professionals at mass gatherings: a scoping review

Author

Althagafi, Ibrahim, Edwards, Dale G, and Smith, Lindsay

Abstract

Mass gathering disasters involving large numbers of casualties can adversely affect the performance of healthcare systems. This scoping review aims to explore the current literature on the preparedness of health professionals for disasters during mass gathering events. Four databases were searched to identify papers examining health professionals' disaster preparedness during mass gatherings between 2011 and 2022. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis for Scoping Reviews was applied to undertake this review. A total of 2024 articles were identified, of which 18 qualified for inclusion in the scoping review. Some studies reported the level of professionals' preparedness for disaster management, while others reported strategies to enhance preparedness and challenges associated with disaster preparedness during mass gatherings. More studies are needed in this field to better understand the level of disaster preparedness of health professionals to improve response and management of potential disasters during mass gathering events.

Published
2024
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50. BCR signaling contributes to autophagy regulation in chronic lymphocytic leukemia

Author

Smith, Lindsay D., Minton, Annabel R., Blunt, Matthew D., Karydis, Laura I., Dutton, David A., Rogers-Broadway, Karly-Rai, Dobson, Rachel, Liu, Rena, Norster, Faith, Hogg, Elizabeth, Ashton-Key, Margaret, Strefford, Jonathan C., Jia, Li, Efremov, Dimitar G., Helgason, G. Vignir, Johnson, Peter W. M., Stevenson, Freda K., Forconi, Francesco, Cragg, Mark S., Tumbarello, David A., Packham, Graham, and Steele, Andrew J.

Published
2020
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