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5. Moving towards FAIR practices in epidemiological research

Author

Garcia-Closas, Montserrat, Ahearn, Thomas U., Gaudet, Mia M., Hurson, Amber N., Balasubramanian, Jeya Balaji, Choudhury, Parichoy Pal, Gerlanc, Nicole M., Patel, Bhaumik, Russ, Daniel, Abubakar, Mustapha, Freedman, Neal D., Wong, Wendy S. W., Chanock, Stephen J., de Gonzalez, Amy Berrington, and Almeida, Jonas S

Subjects
Quantitative Biology - Populations and Evolution
Abstract

Reproducibility and replicability of research findings are central to the scientific integrity of epidemiology. In addition, many research questions require combiningdata from multiple sources to achieve adequate statistical power. However, barriers related to confidentiality, costs, and incentives often limit the extent and speed of sharing resources, both data and code. Epidemiological practices that follow FAIR principles can address these barriers by making resources (F)indable with the necessary metadata , (A)ccessible to authorized users and (I)nteroperable with other data, to optimize the (R)e-use of resources with appropriate credit to its creators. We provide an overview of these principles and describe approaches for implementation in epidemiology. Increasing degrees of FAIRness can be achieved by moving data and code from on-site locations to the Cloud, using machine-readable and non-proprietary files, and developing open-source code. Adoption of these practices will improve daily work and collaborative analyses, and facilitate compliance with data sharing policies from funders and scientific journals. Achieving a high degree of FAIRness will require funding, training, organizational support, recognition, and incentives for sharing resources. But these costs are amply outweighed by the benefits of making research more reproducible, impactful, and equitable by facilitating the re-use of precious research resources by the scientific community.

Published
2022

14. Identification of large offspring syndrome during pregnancy through ultrasonography and maternal blood transcriptome analyses

Author

Rivera, Rocío Melissa, Goldkamp, Anna Katherine, Patel, Bhaumik Narendrabhai, Hagen, Darren Erich, Soto-Moreno, Edgar Joel, Li, Yahan, Kim, Chris Nayoon, Miller, Cliff, Williams, III, Fred, Jannaman, Elizabeth, Xiao, Yao, Tribulo, Paula, Estrada-Cortés, Eliab, Brau-Rodríguez, Astrid Roshealy, Hansen, Peter James, Wu, Zhoulin, Spinka, Christine Marie, Martin, Neal, and Elsik, Christine G.

Published
2022
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16. Postlaryngectomy pharyngoplasty with melolabial flap.

Author

Gupta, Devendra Kumar, Patel, Bhaumik, and Tanwar, Deepika

Abstract

To the best of our knowledge, this is the largest case series describing the use of a melolabial flap for postlaryngectomy pharyngoplasty. It is an excellent alternative for pharyngoplasty, especially in cases post chemoradiotherapy. It accomplishes the goal while removing the restrictions of local and distant flaps. Although donor site morbidity is acceptable, specific consent is required due to the possibility of functional and cosmetic impairment. Additional cases with a larger sample size and a longer follow-up period can assist corroborate our first findings. In addition, because we tend to protect facial vessels for this flap, a follow-up about the compromise of oncological safety at level IB is required. In our case series, however, there was no recurrence until the final follow-up. As a result, it is a better option to pharyngoplasty post laryngectomy [ABSTRACT FROM AUTHOR]

Published
2024
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17. Precision Medicine for CRC Patients in the Veteran Population: State-of-the-Art, Challenges and Research Directions.

Author

Mohapatra, Shyam S, Batra, Surinder K, Bharadwaj, Srinivas, Bouvet, Michael, Cosman, Bard, Goel, Ajay, Jogunoori, Wilma, Kelley, Michael J, Mishra, Lopa, Mishra, Bibhuti, Mohapatra, Subhra, Patel, Bhaumik, Pisegna, Joseph R, Raufman, Jean-Pierre, Rao, Shuyun, Roy, Hemant, Scheuner, Maren, Singh, Satish, Vidyarthi, Gitanjali, and White, Jon

Subjects
Humans, Colorectal Neoplasms, Prognosis, Combined Modality Therapy, Early Detection of Cancer, Veterans Health, Biomarkers, Tumor, Precision Medicine, Biomarkers, Cancer stem cells, Clinical drug response, Colorectal cancer, FiSS, Genomic testing, Next generation sequencing, Precision Oncology Program, Tumoroids, Genetics, Human Genome, Prevention, Cancer, Digestive Diseases, Colo-Rectal Cancer, Gastroenterology & Hepatology, Clinical Sciences
Abstract

Colorectal cancer (CRC) accounts for ~9% of all cancers in the Veteran population, a fact which has focused a great deal of the attention of the VA's research and development efforts. A field-based meeting of CRC experts was convened to discuss both challenges and opportunities in precision medicine for CRC. This group, designated as the VA Colorectal Cancer Cell-genomics Consortium (VA4C), discussed advances in CRC biology, biomarkers, and imaging for early detection and prevention. There was also a discussion of precision treatment involving fluorescence-guided surgery, targeted chemotherapies and immunotherapies, and personalized cancer treatment approaches. The overarching goal was to identify modalities that might ultimately lead to personalized cancer diagnosis and treatment. This review summarizes the findings of this VA field-based meeting, in which much of the current knowledge on CRC prescreening and treatment was discussed. It was concluded that there is a need and an opportunity to identify new targets for both the prevention of CRC and the development of effective therapies for advanced disease. Also, developing methods integrating genomic testing with tumoroid-based clinical drug response might lead to more accurate diagnosis and prognostication and more effective personalized treatment of CRC.

Published
2018

26. Optimized Vitamin D Repletion in Refractory Patients Undergoing Stem Cell Transplant with Oral Thin Film Cholecalciferol

Author

Bartlett, Allison L, primary, Zhang, Grace, additional, Wallace, Gregory, additional, McLean, Stacie, additional, Myers, Kasiani C, additional, Teusink-Cross, Ashley, additional, Taggart, Cynthia, additional, Patel, Bhaumik, additional, Davidson, Robert, additional, Davies, Stella M, additional, and Jodele, Sonata, additional

Published
2023
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29. epiDonate – distributed serverless data infrastructure for epidemiological studies

Author

Almeida, Jonas S, Patel, Bhaumik, Russ, Daniel E, Bhawsar, Praphulla, Maurice, Pedro F Saint, Matthews, Charles, Anand, Adit, Ferguson, Martin, Johnson, Davin, Brotzman, Michelle, Gerlanc, Nicole, Chanock, Stephen, de Gonzalez, Amy Berrington, Gaudet, Mia, and Garcia-Closas, Montserrat

Subjects
Articles
Abstract

Motivation: Epidemiological studies face two important challenges: the need to ingest ever more complex data types, and mounting concerns about participant privacy and data governance. These two challenges are compounded by the expectation that data infrastructure will eventually need to facilitate cross-registration of participants by multiple epidemiological studies. Implementation: The portable web-service epiDonate was developed using the serverless model known as FaaS (Function-as-a-Service). The reference implementation uses nodejs. The implementation relies on a simple tokenization scheme, mediated by a public API, that a) distinguishes admin from participant roles, with b) extensible permission configuration operating a read/write structure. General Features: The critical design feature of epiDonate is the absence of business logic on the server-side (the web service). The simplicity removes the need to customize virtual machines and enables ecosystems of multiple web Applications backed by one or more data donation deployments. Availability: https://episphere.github.io/donate

Published
2023

35. Data from The Codon 72 TP53 Polymorphism Contributes to TSC Tumorigenesis through the Notch–Nodal Axis

Author

Cho, Jun-Hung, primary, Patel, Bhaumik, primary, Bonala, Santosh, primary, Mansouri, Hossein, primary, Manne, Sasikanth, primary, Vadrevu, Surya Kumari, primary, Ghouse, Shanawaz, primary, Kung, Che-Pei, primary, Murphy, Maureen E., primary, Astrinidis, Aristotelis, primary, Henske, Elizabeth P., primary, Kwiatkowski, David J., primary, Markiewski, Maciej M., primary, and Karbowniczek, Magdalena, primary

Published
2023
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36. Supplementary Figure, Figure Legends, Tables and Material and Methods from The Codon 72 TP53 Polymorphism Contributes to TSC Tumorigenesis through the Notch–Nodal Axis

Author

Cho, Jun-Hung, primary, Patel, Bhaumik, primary, Bonala, Santosh, primary, Mansouri, Hossein, primary, Manne, Sasikanth, primary, Vadrevu, Surya Kumari, primary, Ghouse, Shanawaz, primary, Kung, Che-Pei, primary, Murphy, Maureen E., primary, Astrinidis, Aristotelis, primary, Henske, Elizabeth P., primary, Kwiatkowski, David J., primary, Markiewski, Maciej M., primary, and Karbowniczek, Magdalena, primary

Published
2023
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37. Supplementary Data from ErbB-Inhibitory Protein: A Modified Ectodomain of Epidermal Growth Factor Receptor Synergizes with Dasatinib to Inhibit Growth of Breast Cancer Cells

Author

Nautiyal, Jyoti, primary, Yu, Yingjie, primary, Aboukameel, Amro, primary, Kanwar, Shailender S., primary, Das, Jayanta K., primary, Du, Jianhua, primary, Patel, Bhaumik B., primary, Sarkar, Fazlul H., primary, Rishi, Arun K., primary, Mohammad, Ramzi M., primary, and Majumdar, Adhip P.N., primary

Published
2023
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38. Moving towards FAIR practices in epidemiological research

Author

García-Closas, Montserrat, primary, Ahearn, Thomas U, additional, Gaudet, Mia M, additional, Hurson, Amber N, additional, Balasubramanian, Jeya Balaji, additional, Choudhury, Parichoy Pal, additional, Gerlanc, Nicole M, additional, Patel, Bhaumik, additional, Russ, Daniel, additional, Abubakar, Mustapha, additional, Freedman, Neal D, additional, Wong, Wendy S W, additional, Chanock, Stephen J, additional, de Gonzalez, Amy Berrington, additional, and Almeida, Jonas S, additional

Published
2023
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42. Designing Synthetic, Sulfated Glycosaminoglycan Mimetics That Are Orally Bioavailable and Exhibiting In Vivo Anticancer Activity

Author

Morla, Shravan, primary, Ravikumar, Ongolu, additional, O’Hara, Connor, additional, Boothello, Rio, additional, Vera, Alberto, additional, Abdelfadiel, Elsamani I., additional, Fayyad, Rawan, additional, Afosah, Daniel K., additional, Sharon, Chetna, additional, Fernandez, Leopoldo, additional, Shah, Syed Ammer, additional, Patel, Bhaumik B., additional, and Desai, Umesh R., additional

Published
2023
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46. Glycan Modulation of Insulin‐like Growth Factor‐1 Receptor

Author

Boothello, Rio S., primary, Sankaranarayanan, Nehru Viji, additional, Sistla, Jyothi C., additional, Nagarajan, Balaji, additional, Sharon, Chetna, additional, Chittum, John E., additional, Niyaz, Rabiya Y., additional, Roy, Swarnali, additional, Nandi, Aditi, additional, O'Hara, Connor P., additional, Gangji, Rahaman Navaz, additional, Afosah, Daniel K., additional, Ongolu, Ravikumar, additional, Patel, Bhaumik B., additional, and Desai, Umesh R., additional

Published
2022
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48. Moving Toward Findable, Accessible, Interoperable, Reusable Practices in Epidemiologic Research.

Author

García-Closas, Montserrat, Ahearn, Thomas U, Gaudet, Mia M, Hurson, Amber N, Balasubramanian, Jeya Balaji, Choudhury, Parichoy Pal, Gerlanc, Nicole M, Patel, Bhaumik, Russ, Daniel, Abubakar, Mustapha, Freedman, Neal D, Wong, Wendy S W, Chanock, Stephen J, Gonzalez, Amy Berrington de, and Almeida, Jonas S

Subjects
PRIVACY, RESEARCH evaluation, METADATA, DATABASE management, COST benefit analysis, SEARCH engines, ACCESS to information, MEDICAL ethics, APPLICATION service providers, INTERPROFESSIONAL relations, ELECTRONIC health records, CONSORTIA, EPIDEMIOLOGICAL research
Abstract

Data sharing is essential for reproducibility of epidemiologic research, replication of findings, pooled analyses in consortia efforts, and maximizing study value to address multiple research questions. However, barriers related to confidentiality, costs, and incentives often limit the extent and speed of data sharing. Epidemiological practices that follow Findable, Accessible, Interoperable, Reusable (FAIR) principles can address these barriers by making data resources findable with the necessary metadata, accessible to authorized users, and interoperable with other data, to optimize the reuse of resources with appropriate credit to its creators. We provide an overview of these principles and describe approaches for implementation in epidemiology. Increasing degrees of FAIRness can be achieved by moving data and code from on-site locations to remote, accessible ("Cloud") data servers, using machine-readable and nonproprietary files, and developing open-source code. Adoption of these practices will improve daily work and collaborative analyses and facilitate compliance with data sharing policies from funders and scientific journals. Achieving a high degree of FAIRness will require funding, training, organizational support, recognition, and incentives for sharing research resources, both data and code. However, these costs are outweighed by the benefits of making research more reproducible, impactful, and equitable by facilitating the reuse of precious research resources by the scientific community. [ABSTRACT FROM AUTHOR]

Published
2023
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