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Chirag J Patel

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https://www.readbyqxmd.com/read/27896967/methods-to-ensure-the-reproducibility-of-biomedical-research
#1
Konrad J Karczewski, Nicholas P Tatonetti, Arjun K Manrai, Chirag J Patel, C Titus Brown, John P A Ioannidis
Science is not done in a vacuum - across fields of biomedicine, scientists have built on previous research and used data published in previous papers. A mainstay of scientific inquiry is the publication of one's research and recognition for this work is given in the form of citations and notoriety - ideally given in proportion to the quality of the work. Academic incentives, however, may encourage individual researchers to prioritize career ambitions over scientific truth. Recently, the New England Journal of Medicine published a commentary calling scientists who repurpose data "research parasites" who misuse data generated by others to demonstrate alternative hypotheses...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27881429/a-review-of-validation-strategies-for-computational-drug-repositioning
#2
Adam S Brown, Chirag J Patel
Repositioning of previously approved drugs is a promising methodology because it reduces the cost and duration of the drug development pipeline and reduces the likelihood of unforeseen adverse events. Computational repositioning is especially appealing because of the ability to rapidly screen candidates in silico and to reduce the number of possible repositioning candidates. What is unclear, however, is how useful such methods are in producing clinically efficacious repositioning hypotheses. Furthermore, there is no agreement in the field over the proper way to perform validation of in silico predictions, and in fact no systematic review of repositioning validation methodologies...
November 22, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27867238/comment-addressing-the-need-for-portability-in-big-data-model-building-and-calibration
#3
Chirag J Patel, Francesca Dominici
No abstract text is available yet for this article.
2016: Journal of the American Statistical Association
https://www.readbyqxmd.com/read/27842954/a-three-dimensional-approach-for-quantifying-resultant-loading-at-the-knee
#4
Ryan T Lewinson, Chad P Maag, Victor M Y Lun, J Preston Wiley, Chirag Patel, Darren J Stefanyshyn
BACKGROUND: Clinical effectiveness of lateral wedges for knee osteoarthritis is inconsistent across studies. One explanation is that knee loading is not fully described by the peak frontal-plane knee moment. The purpose of this study was to propose a 3D resultant approach to describing moments at the knee and evaluate how this moment changes in response to lateral wedges. METHODS: Walking gait analysis was performed on 20 individuals with knee osteoarthritis, in their own shoes, with and without a six millimeter lateral wedge insole...
November 11, 2016: Knee
https://www.readbyqxmd.com/read/27837427/microwave-assisted-zrsio2-catalysed-synthesis-characterization-and-computational-study-of-novel-spiro-indole-thiazolidines-derivatives-as-anti-tubercular-agents
#5
Mayuri A Borad, Manoj N Bhoi, Sanjay K Rathwa, Mahesh S Vasava, Hitesh D Patel, Chirag N Patel, Himanshu A Pandya, Edwin A Pithawala, John J Georrge
In the current investigation, we prepared a series of novel spiro[indole-thiazolidines] derivatives (5a-5h) from 5-substituted isatin derivatives and thioglycolic acid (TGA) with ZrSiO2 as an efficient catalyst under microwave irradiation. The significant merits of this protocol have some significant merits such as simplicity in operation, simple, efficient workup, good practical yields of product and the employment of recyclable catalyst. All the new synthesized scaffold has been well characterized by various spectroscopic methods and elemental analysis...
November 11, 2016: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/27779619/a-database-of-human-exposomes-and-phenomes-from-the-us-national-health-and-nutrition-examination-survey
#6
Chirag J Patel, Nam Pho, Michael McDuffie, Jeremy Easton-Marks, Cartik Kothari, Isaac S Kohane, Paul Avillach
The National Health and Nutrition Examination Survey (NHANES) is a population survey implemented by the Centers for Disease Control and Prevention (CDC) to monitor the health of the United States whose data is publicly available in hundreds of files. This Data Descriptor describes a single unified and universally accessible data file, merging across 255 separate files and stitching data across 4 surveys, encompassing 41,474 individuals and 1,191 variables. The variables consist of phenotype and environmental exposure information on each individual, specifically (1) demographic information, physical exam results (e...
October 25, 2016: Scientific Data
https://www.readbyqxmd.com/read/27678460/meshdd-literature-based-drug-drug-similarity-for-drug-repositioning
#7
Adam S Brown, Chirag J Patel
OBJECTIVE: Drug repositioning is a promising methodology for reducing the cost and duration of the drug discovery pipeline. We sought to develop a computational repositioning method leveraging annotations in the literature, such as Medical Subject Heading (MeSH) terms. METHODS: We developed software to determine significantly co-occurring drug-MeSH term pairs and a method to estimate pair-wise literature-derived distances between drugs. RESULTS: We found that literature-based drug-drug similarities predicted the number of shared indications across drug-drug pairs...
September 27, 2016: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/27580080/reduced-knee-adduction-moments-for-management-of-knee-osteoarthritis-a-three-month-phase-i-ii-randomized-controlled-trial
#8
Ryan T Lewinson, Isabelle A Vallerand, Kelsey H Collins, J Preston Wiley, Victor M Y Lun, Chirag Patel, Linda J Woodhouse, Raylene A Reimer, Jay T Worobets, Walter Herzog, Darren J Stefanyshyn
Wedged insoles are believed to be of clinical benefit to individuals with knee osteoarthritis by reducing the knee adduction moment (KAM) during gait. However, previous clinical trials have not specifically controlled for KAM reduction at baseline, thus it is unknown if reduced KAMs actually confer a clinical benefit. Forty-eight participants with medial knee osteoarthritis were randomly assigned to either a control group where no footwear intervention was given, or a wedged insole group where KAM reduction was confirmed at baseline...
October 2016: Gait & Posture
https://www.readbyqxmd.com/read/27572827/influence-of-same-day-admission-on-outcomes-following-transcatheter-aortic-valve-replacement
#9
Samir V Patel, Sunny Jhamnani, Palak Patel, Rajesh Sonani, Chirag Savani, Nilay Patel, Nileshkumar J Patel, Sidakpal S Panaich, Mihir Patel, Schreiber Theodore, Cindy Grines, Apurva O Badheka
BACKGROUND: Since elective transcatheter aortic valve replacements (TAVRs) can be performed on the day of admission, i.e., Day 0, or on the next day of admission, i.e., Day 1, we sought to investigate if there is an advantage to either approach. METHODS: We performed a retrospective cohort study, using the Healthcare Cost and Utilization Project's Nationwide Inpatient Sample database of 2012 and identified subjects undergoing endovascular (Transfemoral/Transaortic) TAVRs using the ICD-9-CM procedure code of 35...
October 2016: Journal of Cardiac Surgery
https://www.readbyqxmd.com/read/27507038/systematic-assessment-of-pharmaceutical-prescriptions-in-association-with-cancer-risk-a-method-to-conduct-a-population-wide-medication-wide-longitudinal-study
#10
Chirag J Patel, Jianguang Ji, Jan Sundquist, John P A Ioannidis, Kristina Sundquist
It is a public health priority to identify the adverse and non-adverse associations between pharmaceutical medications and cancer. We search for and evaluate associations between all prescribed medications and longitudinal cancer risk in participants of the Swedish Cancer Register (N = 9,014,975). We associated 552 different medications with incident cancer risk (any, breast, colon, and prostate) during 5.5 years of follow-up (7/1/2005-12/31/2010) in two types of statistical models, time-to-event and case-crossover...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27457472/environment-wide-association-study-of-blood-pressure-in-the-national-health-and-nutrition-examination-survey-1999-2012
#11
Denise P McGinnis, John S Brownstein, Chirag J Patel
Identifying environmental exposures associated with blood pressure is a priority. Recently, we proposed the environment-wide association study to search for and replicate environmental factors associated with phenotypes. We conducted the environment-wide association study (EWAS) using the National Health and Nutrition Examination Surveys (1999-2012) which evaluated a total of 71,916 participants to prioritize environmental factors associated with systolic and diastolic blood pressure. We searched for factors on participants from survey years 1999-2006 and tentatively replicated findings in participants from years 2007-2012...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27427428/mendelian-randomization-study-of-adiposity-related-traits-and-risk-of-breast-ovarian-prostate-lung-and-colorectal-cancer
#12
Chi Gao, Chirag J Patel, Kyriaki Michailidou, Ulrike Peters, Jian Gong, Joellen Schildkraut, Fredrick R Schumacher, Wei Zheng, Paolo Boffetta, Isabelle Stucker, Walter Willett, Stephen Gruber, Douglas F Easton, David J Hunter, Thomas A Sellers, Christopher Haiman, Brian E Henderson, Rayjean J Hung, Christopher Amos, Brandon L Pierce, Sara Lindström, Peter Kraft
BACKGROUND: Adiposity traits have been associated with risk of many cancers in observational studies, but whether these associations are causal is unclear. Mendelian randomization (MR) uses genetic predictors of risk factors as instrumental variables to eliminate reverse causation and reduce confounding bias. We performed MR analyses to assess the possible causal relationship of birthweight, childhood and adult body mass index (BMI), and waist-hip ratio (WHR) on the risks of breast, ovarian, prostate, colorectal and lung cancers...
June 2016: International Journal of Epidemiology
https://www.readbyqxmd.com/read/27307606/comparative-analyses-of-population-scale-phenomic-data-in-electronic-medical-records-reveal-race-specific-disease-networks
#13
Benjamin S Glicksberg, Li Li, Marcus A Badgeley, Khader Shameer, Roman Kosoy, Noam D Beckmann, Nam Pho, Jörg Hakenberg, Meng Ma, Kristin L Ayers, Gabriel E Hoffman, Shuyu Dan Li, Eric E Schadt, Chirag J Patel, Rong Chen, Joel T Dudley
MOTIVATION: Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability...
June 15, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27226061/traumatic-atlanto-occipital-dislocation-do-children-and-adolescents-have-better-or-worse-outcomes-than-adults-a-narrative-review
#14
REVIEW
R Shane Tubbs, Chirag Patel, Marios Loukas, Rod J Oskouian, Jens R Chapman
BACKGROUND: Traumatic atlanto-occipital dislocation is an uncommon, severely unstable pathology, which can lead to detrimental or even fatal neurological impairment. Specifically, children have consistently been reported to be more susceptible to this type of injury because of their disproportionately larger head, ligament laxity, and injury mechanisms. However, to date, rates of missed injury and outcomes including neurologic recovery of pediatric and adult populations following this insult have not been comparatively evaluated...
August 2016: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://www.readbyqxmd.com/read/27152142/influence-of-hospital-volume-and-outcomes-of-adult-structural-heart-procedures
#15
REVIEW
Sidakpal S Panaich, Nilay Patel, Shilpkumar Arora, Nileshkumar J Patel, Samir V Patel, Chirag Savani, Vikas Singh, Rajesh Sonani, Abhishek Deshmukh, Michael Cleman, Abeel Mangi, John K Forrest, Apurva O Badheka
Hospital volume is regarded amongst many in the medical community as an important quality metric. This is especially true in more complicated and less commonly performed procedures such as structural heart disease interventions. Seminal work on hospital volume relationships was done by Luft et al more than 4 decades ago, when they demonstrated that hospitals performing > 200 surgical procedures a year had 25%-41% lower mortality than those performing fewer procedures. Numerous volume-outcome studies have since been done for varied surgical procedures...
April 26, 2016: World Journal of Cardiology
https://www.readbyqxmd.com/read/27091369/the-next-generation-of-risk-assessment-multiyear-study-highlights-of-findings-applications-to-risk-assessment-and-future-directions
#16
Ila Cote, Melvin E Andersen, Gerald T Ankley, Stanley Barone, Linda S Birnbaum, Kim Boekelheide, Frederic Y Bois, Lyle D Burgoon, Weihsueh A Chiu, Douglas Crawford-Brown, Kevin M Crofton, Michael DeVito, Robert B Devlin, Stephen W Edwards, Kathryn Z Guyton, Dale Hattis, Richard S Judson, Derek Knight, Daniel Krewski, Jason Lambert, Elizabeth Anne Maull, Donna Mendrick, Gregory M Paoli, Chirag Jagdish Patel, Edward J Perkins, Gerald Poje, Christopher J Portier, Ivan Rusyn, Paul A Schulte, Anton Simeonov, Martyn T Smith, Kristina A Thayer, Russell S Thomas, Reuben Thomas, Raymond R Tice, John J Vandenberg, Daniel L Villeneuve, Scott Wesselkamper, Maurice Whelan, Christine Whittaker, Ronald White, Menghang Xia, Carole Yauk, Lauren Zeise, Jay Zhao, Robert S DeWoskin
BACKGROUND: The Next Generation (NexGen) of Risk Assessment effort is a multiyear collaboration among several organizations evaluating new, potentially more efficient molecular, computational and systems biology approaches to risk assessment. This paper summarizes our findings, suggests applications to risk assessment, and identifies strategic research directions. OBJECTIVE: Our specific objectives were to test whether advanced biological data and methods could better inform our understanding of public health risks posed by environmental exposures...
April 19, 2016: Environmental Health Perspectives
https://www.readbyqxmd.com/read/27081073/developing-a-pro-regenerative-biomaterial-scaffold-microenvironment-requires-t-helper-2-cells
#17
Kaitlyn Sadtler, Kenneth Estrellas, Brian W Allen, Matthew T Wolf, Hongni Fan, Ada J Tam, Chirag H Patel, Brandon S Luber, Hao Wang, Kathryn R Wagner, Jonathan D Powell, Franck Housseau, Drew M Pardoll, Jennifer H Elisseeff
Immune-mediated tissue regeneration driven by a biomaterial scaffold is emerging as an innovative regenerative strategy to repair damaged tissues. We investigated how biomaterial scaffolds shape the immune microenvironment in traumatic muscle wounds to improve tissue regeneration. The scaffolds induced a pro-regenerative response, characterized by an mTOR/Rictor-dependent T helper 2 pathway that guides interleukin-4-dependent macrophage polarization, which is critical for functional muscle recovery. Manipulating the adaptive immune system using biomaterials engineering may support the development of therapies that promote both systemic and local pro-regenerative immune responses, ultimately stimulating tissue repair...
April 15, 2016: Science
https://www.readbyqxmd.com/read/27064374/asymmetric-inheritance-of-mtorc1-kinase-activity-during-division-dictates-cd8-t-cell-differentiation
#18
Kristen N Pollizzi, Im-Hong Sun, Chirag H Patel, Ying-Chun Lo, Min-Hee Oh, Adam T Waickman, Ada J Tam, Richard L Blosser, Jiayu Wen, Greg M Delgoffe, Jonathan D Powell
The asymmetric partitioning of fate-determining proteins has been shown to contribute to the generation of CD8(+) effector and memory T cell precursors. Here we demonstrate the asymmetric partitioning of mTORC1 activity after the activation of naive CD8(+) T cells. This results in the generation of two daughter T cells, one of which shows increased mTORC1 activity, increased glycolytic activity and increased expression of effector molecules. The other daughter T cell has relatively low mTORC1 activity and increased lipid metabolism, expresses increased amounts of anti-apoptotic molecules and subsequently displays enhanced long-term survival...
June 2016: Nature Immunology
https://www.readbyqxmd.com/read/27059547/systematic-correlation-of-environmental-exposure-and-physiological-and-self-reported-behaviour-factors-with-leukocyte-telomere-length
#19
Chirag J Patel, Arjun K Manrai, Erik Corona, Isaac S Kohane
BACKGROUND: It is hypothesized that environmental exposures and behaviour influence telomere length, an indicator of cellular ageing. We systematically associated 461 indicators of environmental exposures, physiology and self-reported behaviour with telomere length in data from the US National Health and Nutrition Examination Survey (NHANES) in 1999-2002. Further, we tested whether factors identified in the NHANES participants are also correlated with gene expression of telomere length modifying genes...
April 8, 2016: International Journal of Epidemiology
https://www.readbyqxmd.com/read/26960424/percutaneous-coronary-intervention-relationship-between-procedural-volume-and-outcomes
#20
Apurva O Badheka, Sidakpal S Panaich, Shilpkumar Arora, Nilay Patel, Nileshkumar J Patel, Chirag Savani, Abhishek Deshmukh, Mauricio G Cohen
Percutaneous coronary intervention (PCI) is an integral treatment modality for acute coronary syndromes (ACS) as well as chronic stable coronary artery disease (CAD) not responsive to optimal medical therapy. This coupled with studies on the feasibility and safety of performing PCI in centers without on-site surgical backup led to widespread growth of PCI centers. However, this has been accompanied by a recent steep decline in the volume of PCIs at both the operator and hospital level, which raises concerns regarding minimal procedural volumes required to maintain necessary skills and favorable clinical outcomes...
April 2016: Current Cardiology Reports
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