Article
Computer Science, Information Systems
Thomas R. Campion, Evan T. Sholle, Jyotishman Pathak, Stephen B. Johnson, John P. Leonard, Curtis L. Cole
Summary: Obtaining electronic patient data, especially from EHR systems, for clinical and translational research can be challenging. The Architecture for Research Computing in Health (ARCH) at Weill Cornell Medicine provides tools and services to match investigators with electronic patient data, supporting a wide range of scientific functions. ARCH has supported over 1200 unique investigators through more than 4177 consultations since 2016, enabling critical response activities for research and patient care, and may serve as a model for other institutions.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2022)
Article
Computer Science, Information Systems
Craig Barnes, Binam Bajracharya, Matthew Cannalte, Zakir Gowani, Will Haley, Taha Kass-Hout, Kyle Hernandez, Michael Ingram, Hara Prasad Juvvala, Gina Kuffel, Plamen Martinov, J. Montgomery Maxwell, John McCann, Ankit Malhotra, Noah Metoki-Shlubsky, Chris Meyer, Andre Paredes, Jawad Qureshi, Xenia Ritter, Philip Schumm, Mingfei Shao, Urvi Sheth, Trevar Simmons, Alexander VanTol, Zhenyu Zhang, Robert L. Grossman
Summary: The objective of this study was to develop and operate a cloud-based federated system called the Biomedical Research Hub (BRH) for managing, analyzing, and sharing patient data for research purposes. The BRH contains multiple data resources and workspaces, providing access to over 6 PB of research data for analysis and research purposes.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2022)
Article
Computer Science, Information Systems
William R. Hogan, Elizabeth A. Shenkman, Temple Robinson, Olveen Carasquillo, Patricia S. Robinson, Rebecca Z. Essner, Jiang Bian, Gigi Lipori, Christopher Harle, Tanja Magoc, Lizabeth Manini, Tona Mendoza, Sonya White, Alex Loiacono, Jackie Hall, Dave Nelson
Summary: The OneFlorida Data Trust is a centralized research patient data repository managed by the OneFlorida Clinical Research Consortium, collecting structured electronic health record and other data on 17.2 million individuals in Florida. The Data Trust uses privacy-preserving entity resolution for patient deduplication and establishes mother-baby relationships, serving as a valuable and relatively unique research resource.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2022)
Article
Computer Science, Information Systems
Boyd M. Knosp, Catherine K. Craven, David A. Dorr, Elmer Bernstam, Thomas R. Campion
Summary: The study examines the operations of CTSA EDW4R within academic medical centers and technology contexts. Key findings include the importance of executive leadership support and strong relationships between EDW4R teams and enterprise IT for success. Challenges in data governance and cloud migration were also highlighted.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2022)
Article
Computer Science, Information Systems
Wenjun He, Katie G. Kirchoff, Royce R. Sampson, Kimberly K. McGhee, Andrew M. Cates, Jihad S. Obeid, Leslie A. Lenert
Summary: The South Carolina Clinical & Translational Research Institute at the Medical University of South Carolina successfully reduced data fragmentation and promoted research systems integration by implementing RMIDs and RINS. Within four years, a total of 5513 RMIDs were created, with 13% linked to systems needed to evaluate research study performance and 18% linked to electronic health records.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2021)
Correction
Computer Science, Information Systems
Boyd M. Knosp, Catherine K. Craven, David A. Dorr, Elmer Bernstam, Thomas R. Campion
Summary: This qualitative study aimed to understand the operations of CTSA EDW4R within the context of academic medical centers and technology. The findings provide insights into the use of enterprise information technology, management of EDW4R teams, data governance, and cloud computing.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2023)
Article
Chemistry, Multidisciplinary
Xiaoxiao Cao, Makoto Watanabe, Kenta Ono
Summary: This study evaluates the perceptual quality of six categories of games with character elements in their icons using a two-stage perceptual matching procedure. Highly visual matching icons were selected and their affective matching quality was measured through the semantic differential method and correlation analysis. The research provides methods for improving the perceptual quality of game icons.
APPLIED SCIENCES-BASEL
(2021)
Review
Construction & Building Technology
Amir Tabadkani, Astrid Roetzel, Hong Xian Li, Aris Tsangrassoulis
Summary: The importance of occupant-centric control strategies in controlling shading systems is emphasized in this research, as it can enhance user satisfaction and comfort. Automatic control strategies may lead to users being unable to intervene in the operation of shading systems.
AUTOMATION IN CONSTRUCTION
(2021)
Article
Materials Science, Multidisciplinary
Johanne Medina, Abdul Wahab Ziaullah, Heesoo Park, Ivano E. Castelli, Arif Shaon, Halima Bensmail, Fedwa El-Mellouhi
Summary: The need for good research data management (RDM) practices is increasingly recognized in the materials science community as it embraces data-driven science. Efforts are being made to standardize, curate, preserve, and disseminate massive datasets in a FAIR manner. User stories from researchers provide valuable insights into the challenges faced in RDM and help in developing effective RDM systems following FAIR principles.
Article
Clinical Neurology
Mahdi Habibi-koolaee, Leila Shahmoradi, Sharareh R. Niakan Kalhori, Hossein Ghannadan, Erfan Younesi
Summary: The stroke ontology (STO) covers a wide range of major biomedical and risk factor concepts, enriched with synonyms, definitions, and references. It attempts to incorporate different users' views on the stroke domain such as neuroscientists, molecular biologists, and clinicians. Evaluation shows that STO has acceptable coverage of the stroke knowledge domain and can be used to answer expert questions in light of published evidence.
NEUROLOGY AND THERAPY
(2021)
Article
Computer Science, Artificial Intelligence
Amar Tauqeer, Ismaheel Hammid, Sareh Aghaei, Parvaneh Parvin, Elbrich M. Postma, Anna Fensel
Summary: Due to their association with Covid-19, smell and taste disorders have become a prominent issue with a significant impact on quality of life and health outcomes. However, the relevant information regarding these disorders is often inaccessible and poorly organized. To address this problem, the use of a knowledge graph, capable of digitizing and integrating health data, presents a viable solution.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Multidisciplinary Sciences
Nikolay T. Garabedian, Paul J. Schreiber, Nico Brandt, Philipp Zschumme, Ines L. Blatter, Antje Dollmann, Christian Haug, Daniel Kuemmel, Yulong Li, Franziska Meyer, Carina E. Morstein, Julia S. Rau, Manfred Weber, Johannes Schneider, Peter Gumbsch, Michael Selzer, Christian Greiner
Summary: This paper discusses the lack of FAIR (Findable, Accessible, Interoperable, and Reusable) data and metadata in experimental tribology and proposes a scalable framework for generating FAIR data. Through collaboration with developers, crowdsourcing controlled vocabulary, ontology building, and the use of digital tools, this paper demonstrates a collection of scalable non-intrusive techniques to improve the lifespan, reliability, and reusability of experimental tribological data.
Article
Oncology
Steven D. Forsythe, Hemamylammal Sivakumar, Richard A. Erali, Nadeem Wajih, Wencheng Li, Perry Shen, Edward A. Levine, Katherine E. Miller, Aleksander Skardal, Konstantinos Votanopoulos
Summary: Engineering hydrogel-based sarcoma organoids directly from the patient without xenogeneic extracellular matrices (ECMs) or growth factors is feasible. A large subset of organoids does not respond to chemotherapy or immunotherapy. This provides a feasible platform for personalized translational research.
ANNALS OF SURGICAL ONCOLOGY
(2022)
Article
Computer Science, Cybernetics
Yeqing Pei, Zhenghe Song, Xiaoping Jin
Summary: With the development of technology, future tractors will become more intelligent. However, the complex interfaces and control components may overload drivers' cognitive load. Therefore, a method to evaluate the control interface from the perspective of cognitive load is proposed. The research investigates the influence of design elements on behaviour time and establishes a behaviour time model, which effectively predicts the behaviour time of operating interfaces. An evaluation index based on behaviour time is proposed to assess the design level of the interface. The validity of the evaluation method is verified, providing theoretical guidance for tractor's human-machine interfaces from the perspective of drivers' cognitive load.
INTERNATIONAL JOURNAL OF HUMAN-COMPUTER INTERACTION
(2023)
Review
Oncology
Peng Jiang, Sanju Sinha, Kenneth Aldape, Sridhar Hannenhalli, Cenk Sahinalp, Eytan Ruppin
Summary: Historically, cancer research has focused on a few essential pathways and genes, but recent advances in high-throughput technologies have led to the rapid accumulation of large-scale cancer omics data. The analysis of this "big data" requires significant computational resources and has the potential to bring new insights to cancer research. The combination of big data, bioinformatics, and artificial intelligence has already made notable advances in our understanding of cancer biology and translational research. Future progress will require collaboration among data scientists, clinicians, biologists, and policymakers.
NATURE REVIEWS CANCER
(2022)
Review
Pharmacology & Pharmacy
Elizabeth J. Baker, Nancy A. Beck, Ellen L. Berg, Helene D. Clayton-Jeter, P. Charukeshi Chandrasekera, J. Lowry Curley, Bruce A. Donzanti, Lorna C. Ewart, Jane M. Gunther, J. Gerry Kenna, Edward L. LeCluysell, Michael N. Liebman, Catherine L. Pugh, Paul B. Watkins, Kristie M. Sullivan
DRUG DISCOVERY TODAY
(2019)
Article
Oncology
Cody Plasterer, Shirng-Wern Tsaih, Amy R. Peck, Inna Chervoneva, Caitlin O'Meara, Yunguang Sun, Angela Lemke, Dana Murphy, Jennifer Smith, Sophia Ran, Albert J. Kovatich, Jeffrey A. Hooke, Craig D. Shriver, Hai Hu, Edith P. Mitchell, Carmen Bergom, Amit Joshi, Paul Auer, Jeremy Prokop, Hallgeir Rui, Michael J. Flister
BREAST CANCER RESEARCH AND TREATMENT
(2019)
Correction
Immunology
Vesteinn Thorsson, David L. Gibbs, Scott D. Brown, Denise Wolf, Dante S. Bortone, Tai-Hsien Ou Yang, Eduard Porta-Pardo, Galen F. Gao, Christopher L. Plaisier, James A. Eddy, Elad Ziv, Aedin C. Culhane, Evan O. Paull, I. K. Ashok Sivakumar, Andrew J. Gentles, Raunaq Malhotra, Farshad Farshidfar, Antonio Colaprico, Joel S. Parker, Lisle E. Mose, Nam Sy Vo, Jianfang Liu, Yuexin Liu, Janet Rader, Varsha Dhankani, Sheila M. Reynolds, Reanne Bowlby, Andrea Califano, Andrew D. Cherniack, Dimitris Anastassiou, Davide Bedognetti, Younes Mokrab, Aaron M. Newman, Arvind Rao, Ken Chen, Alexander Krasnitz, Hai Hu, Tathiane M. Malta, Houtan Noushmehr, Chandra Sekhar Pedamallu, Susan Bullman, Akinyemi I. Ojesina, Andrew Lamb, Wanding Zhou, Hui Shen, Toni K. Choueiri, John N. Weinstein, Justin Guinney, Joel Saltz, Robert A. Holt, Charles S. Rabkin, Alexander J. Lazar, Jonathan S. Serody, Elizabeth G. Demicco, Mary L. Disis, Benjamin G. Vincent, Ilya Shmulevich
Editorial Material
Pharmacology & Pharmacy
Caitrin W. McDonough, Matthew K. Breitenstein, Mohamed Shahin, Philip E. Empey, Robert R. Freimuth, Lang Li, Michael Liebman, Sony Tuteja
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2020)
Article
Oncology
Olena Odnokoz, Pengfei Yu, Amy R. Peck, Yunguang Sun, Albert J. Kovatich, Jeffrey A. Hooke, Hai Hu, Edith P. Mitchell, Hallgeir Rui, Serge Y. Fuchs
CANCER BIOLOGY & THERAPY
(2020)
Article
Oncology
Yi Zhang, Jianfang Liu, Praveen-Kumar Raj-Kumar, Lori A. Sturtz, Anupama Praveen-Kumar, Howard H. Yang, Maxwell P. Lee, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, Hai Hu
BREAST CANCER RESEARCH AND TREATMENT
(2020)
Article
Environmental Sciences
Michela Franchini, Stefania Pieroni, Nicola Martini, Andrea Ripoli, Dante Chiappino, Francesca Denoth, Michael Norman Liebman, Sabrina Molinaro, Daniele Della Latta
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2020)
Article
Oncology
Brenton A. Maisel, Misung Yi, Amy R. Peck, Yunguang Sun, Jeffrey A. Hooke, Albert J. Kovatich, Craig D. Shriver, Hai Hu, Marja T. Nevalainen, Takemi Tanaka, Nicole Simone, Li Lily Wang, Hallgeir Rui, Inna Chervoneva
Summary: The density and spatial relationship of CD163(+) TAMs in tumor tissue are associated with unfavorable prognosis in breast cancer.
Article
Oncology
Andrew Zhang, Hai Hu
Summary: Development of noninvasive diagnostic tests for early detection of multiple cancer types is crucial. A serum-based 4-microRNA diagnostic model showed superior performance in detecting 12 cancer types compared to existing sequencing-based tests. The simplicity of the model enables decentralized testing and wide adoption in the at-risk general population.
Meeting Abstract
Oncology
Praveen-Kumar Raj-Kumar, Tao Liu, Lori A. Sturtz, Albert J. Kovatich, Marina A. Gritsenko, Vladislav A. Petyuk, Brenda Deyarmin, Jianfang Liu, Anupama Praveen-Kumar, Jason E. McDermott, Anil K. Shukla, Ronald J. Moore, Matthew E. Monroe, Bobbie-Jo M. Webb-Robertson, Jeffrey A. Hooke, Leigh Fantacone-Campbell, Leonid Kvecher, Jennifer Kane, Jennifer Melley, Stella Somiari, Stephen C. Benz, Justin Golovato, Shahrooz Rabizadeh, Patrick Soon-Shiong, Richard D. Smith, Richard J. Mural, Karin D. Rodland, Craig D. Shriver, Zhaoyu Li, Hai Hu
Meeting Abstract
Oncology
Valerie Bussberg, Vladimir Tolstikov, Guisong Wang, Punit Shah, Rick Searfoss, Leigh Fantacone-Campbell, Jeffrey A. Hooke, Brenda Deyarmin, Rebecca N. Zingmark, Stella Somiari, Jianfang Liu, Leonid Kvecher, Bradley Mostoller, Lori Sturtz, Praveen-Kumar Raj-Kumar, Elder Granger, Linda Vahdat, Mary L. Cutler, Chas Bountra, Rangaprasad Sarangarajan, Hai Hu, Albert J. Kovatich, Michael A. Kiebish, Niven R. Narain, Craig D. Shriver
Article
Biochemical Research Methods
Lori A. Sturtz, Guisong Wang, Punit Shah, Richard Searfoss, Praveen-Kumar Raj-Kumar, Jeffrey A. Hooke, J. Leigh Fantacone-Campbell, Brenda Deyarmin, Mary Lou Cutler, Rangaprasad Sarangarajan, Niven R. Narain, Hai Hu, Michael A. Kiebish, Albert J. Kovatich, Craig D. Shriver
CLINICAL PROTEOMICS
(2020)
Meeting Abstract
Oncology
Jianfang Liu, J. Leigh Fantacone-Campbell, Albert J. Kovatich, Brenda Deyarmin, Bradley J. Mostoller, Jeffrey A. Hooke, Hallgeir Rui, Craig D. Shriver, Hai Hu
Meeting Abstract
Oncology
Praveen-Kumar Raj-Kumar, Lori A. Sturtz, Albert J. Kovatich, Brenda Deyarmin, Jeffrey A. Hooke, Leigh Fantacone-Campbell, Anupama Praveen-Kumar, Jianfang Liu, James Craig, Leonid Kvecher, Jennifer Kane, Jennifer Melley, Stella Somiari, Stephen C. Benz, Justin Golovato, Shahrooz Rabizadeh, Patrick Soon-Shiong, Richard Mural, Craig D. Shriver, Hai Hu