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Measuring associations between the microbiota and repeated measures of continuous clinical variables using a lasso-penalized generalized linear mixed model

Laura Tipton, Karen T. Cuenco, Laurence Huang, Ruth M. Greenblatt, Eric Kleerup, Frank Sciurba, Steven R. Duncan, Michael P. Donahoe, Alison Morris, Elodie Ghedin
2018 BioData Mining  
While the temporal data from clinical and microbiome samples may be informative, analysis of this type of data can be problematic for standard statistical methods.  ...  We assessed the use of this adapted two-stage LassoGLMM for its ability to determine which microbes are associated with continuous repeated clinical measures.  ...  A complementary analytic method, penalized regression, has been used in genomics and metagenomics for several years [8] .  ... 
doi:10.1186/s13040-018-0173-9 pmid:29983746 pmcid:PMC6003033 fatcat:owqpka5qpjebxm2qcf3oyb4me4

Perspectives on Precision Nutrition Research in Heart, Lung, and Blood Diseases and Sleep Disorders

Charlotte A Pratt, Alison G M Brown, Shilpy Dixit, Nicole Farmer, Aruna Natarajan, Josephine Boyington, Scarlet Shi, Qing Lu, Paul Cotton
2022 Advances in Nutrition  
These strategic goals and objectives serve as blueprints for research and training.  ...  The release of the 2020-2030 Strategic Plan for NIH Nutrition Research (SPNR) and its emphasis on precision nutrition has provided an opportunity to identify future nutrition research that addresses individual  ...  Michael Wolz and the NHLBI Nutrition Research Working Group for their help with this manuscript.  ... 
doi:10.1093/advances/nmac053 pmid:35561742 fatcat:4knj2r7xgzerxpnvulcvnvjaye

Collaborative Cohort of Cohorts for COVID-19 Research (C4R) Study: Study Design

Elizabeth C Oelsner, Akshaya Krishnaswamy, Pallavi P Balte, Norrina Bai Allen, Tauqeer Ali, Pramod Anugu, Howard Andrews, Komal Arora, Alyssa Asaro, R Graham Barr, Alain G Bertoni, Jessica Bon (+74 others)
2022 American Journal of Epidemiology  
Master protocols leverage existing robust retention rates for telephone and in-person examinations, and high-quality events surveillance.  ...  The Collaborative Cohort of Cohorts for COVID-19 Research (C4R) is a national prospective study of adults comprising 14 established United States (US) prospective cohort studies.  ...  O R I G I N A L U N E D I T E D M A N U S C R I P T elements will be transferred as a limited dataset for public access on BioData Catalyst in accord with cohort-specific consents and commitments.  ... 
doi:10.1093/aje/kwac032 pmid:35279711 pmcid:PMC8992336 fatcat:5run3hfunze3jnmmjm5k2mmspe

Medical Informatics Education & Research in Greece

I. Chouvarda, N. Maglaveras
2015 IMIA Yearbook of Medical Informatics  
While ePrescription deployment has been an important step, ICT for integrated care and telehealth have a lot of room for further deployment.  ...  for Alzheimer's, FP7: CHRONIOUS for COPD).  ...  analytics and the Telemedicine and Personal Health Systems.  ... 
doi:10.15265/iy-2015-022 pmid:26123910 pmcid:PMC4587067 fatcat:n6wbz2sosbearl2a4w4aex24qa

Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module [article]

Amitabh Sharma, Maksim Kitsak, Michael C Cho, Asher Ameli, Xiaobo Zhou, Zhiqiang Jiang, James D Crapo, Terri H Beaty, Joerg Menche, Per S Bakke, Marc Santolini, Edwin K Silverman
2018 bioRxiv   pre-print
to COPD, to find a more comprehensive disease network module.  ...  complex diseases like chronic obstructive pulmonary disease (COPD).  ...  DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization. BioData Min 4, 19, doi:10.1186/1756-0381-4-19 (2011). 21 Liu, J. Z. et al.  ... 
doi:10.1101/408229 fatcat:l2v4sgolwnah7dwhhfpaxsiu6q

Representing and querying disease networks using graph databases

Artem Lysenko, Irina A. Roznovăţ, Mansoor Saqi, Alexander Mazein, Christopher J Rawlings, Charles Auffray
2016 BioData Mining  
Here, we describe how graph databases provide a powerful framework for storage, querying and envisioning of biological data.  ...  We outline an application case that uses the Neo4j graph database for building and querying a prototype network to provide biological context to asthma related genes.  ...  Marshall (BioSciConsulting, Belgium) for his valuable advice on the licenses of the interrogated databases. Authors are also grateful to reviewers for their valuable comments on the manuscript.  ... 
doi:10.1186/s13040-016-0102-8 pmid:27462371 pmcid:PMC4960687 fatcat:k2i6pyrtqnaafdcyxmi6xkz7pu

Data analytics and clinical feature ranking of medical records of patients with sepsis

Davide Chicco, Luca Oneto
2021 BioData Mining  
analysis for the SOFA score).  ...  The medical record of each patient has 29 clinical features, and includes a binary value for survival, a binary value for septic shock, and a numerical value for the sequential organ failure assessment  ...  Acknowledgments The authors thankn Julia Lin (University of Toronto) for her help in the English proof-reading of this manuscript.  ... 
doi:10.1186/s13040-021-00235-0 pmid:33536030 fatcat:34tppwwnbvhadg3pkavuxe2uqa

Translational genomics and precision medicine: Moving from the lab to the clinic

Eleftheria Zeggini, Anna L. Gloyn, Anne C. Barton, Louise V. Wain
2019 Science  
This progress has been made possible by technological advances in genomics and analytics and by the digital revolution.  ...  We are at the cusp of predicting disease risk for some disorders by means of polygenic risk scores integrated with classical epidemiological risk factors.  ...  estimates for COPD amongst smokers, an absolute risk of COPD of 82.4% for smokers in the highest risk score decile (compared to 17.4% for those in the lowest decile) (27) .  ... 
doi:10.1126/science.aax4588 pmid:31604268 fatcat:66pmvbcdl5eprfiwbw5jsgrcmm

A System for Phenotype Harmonization in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program

Adrienne M Stilp, Leslie S Emery, Jai G Broome, Erin J Buth, Alyna T Khan, Cecelia A Laurie, Fei Fei Wang, Quenna Wong, Dongquan Chen, Catherine M D'Augustine, Nancy L Heard-Costa, Chancellor R Hohensee (+60 others)
2021 American Journal of Epidemiology  
This system was developed for the National Heart, Lung and Blood Institute's Trans-Omics for Precision Medicine program, which is generating genomic and other omics data for >80 studies with extensive  ...  The harmonized phenotype data and associated documentation have been submitted to National Institutes of Health data repositories for controlled-access by the scientific community.  ...  , Coronary Artery Risk Development in Young Adults; COPD, chronic obstructive pulmonary disease; COPDGene, Genetic Epidemiology of COPD; CRA, Genetic Epidemiology of Asthma in Costa Rica; GENOA, Genetic  ... 
doi:10.1093/aje/kwab115 pmid:33861317 pmcid:PMC8485147 fatcat:dojylsyogngrbfxfr7f7xfoupq

LungMAP Portal Ecosystem: Systems-Level Exploration of the Lung [article]

Nathan Gaddis, Joshua Fortriede, Minzhe Guo, Eric E Bardes, Michal Kouril, Scott Tabar, Kevin Burns, Maryanne E Ardini-Poleske, Stephanie Loos, Daniel Schnell, Kang Jin, Balaji Iyer (+21 others)
2021 bioRxiv   pre-print
To cultivate future discoveries, we have aggregated a diverse collection of single-cell atlases for multiple species (human, rhesus, mouse), to enable consistent queries across technologies, cohorts, age  ...  at CCHMC for the contributions.  ...  We would like to thank the Cincinnati Children's Research Foundation for their additional support and the Data and Technology Services and Research IT Services in the Division of Biomedical Informatics  ... 
doi:10.1101/2021.12.05.471312 fatcat:ufvimh2dsvfqjors2lxj55sciy

A system for phenotype harmonization in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program [article]

Adrienne M Stilp, Leslie S Emery, Jai G Broome, Erin J Buth, Alyna T Khan, Cecelia A Laurie, Fei Fei Wang, Quenna Wong, Dongquan Chen, Catherine M D'Augustine, Nancy L Heard-Costa, Chancellor R Hohensee (+60 others)
2020 bioRxiv   pre-print
This system was developed for the National Heart, Lung and Blood Institute's Trans-Omics for Precision Medicine (TOPMed) program, which is generating genomic and other omics data for >80 studies with extensive  ...  The harmonized phenotype data and associated documentation have been submitted to National Institutes of Health data repositories for controlled-access by the scientific community.  ...  Individual data points with impossible values (such as a negative analyte concentration) were excluded from the harmonized phenotype variable.  ... 
doi:10.1101/2020.06.18.146423 fatcat:4yloxtpd4fcedirt3mewlt2v5m

Analyzing the heterogeneity of rule-based EHR phenotyping algorithms in CALIBER and the UK Biobank [article]

Spiros Denaxas, Helen Parkinson, Natalie Fitzpatrick, Cathie Sudlow, Harry Hemingway
2019 biorxiv/medrxiv   pre-print
While considerable effort goes into the phenotyping process, no consistent methodology for representing algorithms exists in the UK.  ...  Phenotyping however is challenging since EHR are collected for different purposes, have variable data quality and often require significant harmonization.  ...  Where possible analytical scripts should be attached using markdown or a similar approach.  ... 
doi:10.1101/685156 fatcat:ahuktxzyirexde36isgoaunfiq

Towards AI-Enabled Multimodal Diagnostics and Management of COVID-19 and Comorbidities in Resource-Limited Settings

Olawande Daramola, Peter Nyasulu, Tivani Mashamba-Thompson, Thomas Moser, Sean Broomhead, Ameera Hamid, Jaishree Naidoo, Lindiwe Whati, Maritha J. Kotze, Karl Stroetmann, Victor Chukwudi Osamor
2021 Informatics  
The objective of the AI-enabled framework is to leverage multimodal diagnostics of COVID-19 and associated comorbidities in RLS for the diagnosis and management of COVID-19 cases and general support for  ...  A conceptual artificial intelligence (AI)-enabled framework is presented in this study involving triangulation of various diagnostic methods for management of coronavirus disease 2019 (COVID-19) and its  ...  Moremi at the Division of Chemical Pathology, Stellenbosch University, for her contribution to the incorporation of COVID-19 risk assessment into the PSGT case study.  ... 
doi:10.3390/informatics8040063 fatcat:iq6fjziqenhmhlju3ytijbn3ci

Personalised physical exercise regime for chronic patients through a wearable ICT platform

Pantelis A. Angelidis
2010 International Journal of Electronic Healthcare  
Reference to this paper should be made as follows: Angelidis, P.A. (2010) 'Personalised physical exercise regime for chronic patients through a wearable ICT platform', Int.  ...  it will look into wearable electronics embedded in textile capable of performing regular or exceptional measurements of vital physiological parameters and communicating them to an application server for  ...  Acknowledgements The author wishes to thank John Moore, MD, from MIT Media Lab for insightful discussions on the health record and data sharing, Markela Psymarnou from VIDAVO for her inspiring comments  ... 
doi:10.1504/ijeh.2010.036207 pmid:21041175 fatcat:7hxn2jisxrck7nkxu5swicc5oi

Study of Two Dose Regimens of Ticagrelor Compared with Clopidogrel in Patients Undergoing Percutaneous Coronary Intervention for Stable Coronary Artery Disease (STEEL-PCI)

Rachel C. Orme, William A. E. Parker, Mark R. Thomas, Heather M. Judge, Kathleen Baster, Wael Sumaya, Kenneth P. Morgan, Hannah C. McMellon, James D. Richardson, Ever D. Grech, Nigel M. Wheeldon, Ian R. Hall (+4 others)
2018 Circulation  
Median (IQR) hsTnT increase was 16.9 (6.5-46.9) ng/l for clopidogrel, 22.4 (5.5-53.8) ng/L for T60 and 17.7 (8.1-43.5) ng/L for T90 (P = 0.95).  ...  et al. (13 more authors) (2018) Study of two dose regimens of ticagrelor compared with clopidogrel in patients undergoing percutaneous coronary intervention for stable coronary artery disease (STEEL-PCI  ...  Sven Nylander for their support. Downloaded from http://ahajournals.org by on August 22, 2018  ... 
doi:10.1161/circulationaha.118.034790 pmid:29930021 pmcid:PMC6159686 fatcat:mxhzfskt4ven3m6txhog6u6hs4
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