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Chirag J Patel

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https://www.readbyqxmd.com/read/28291243/a-standard-database-for-drug-repositioning
#1
Adam S Brown, Chirag J Patel
Drug repositioning, the process of discovering, validating, and marketing previously approved drugs for new indications, is of growing interest to academia and industry due to reduced time and costs associated with repositioned drugs. Computational methods for repositioning are appealing because they putatively nominate the most promising candidate drugs for a given indication. Comparing the wide array of computational repositioning methods, however, is a challenge due to inconsistencies in method validation in the field...
March 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/28251040/analytic-complexity-and-challenges-in-identifying-mixtures-of-exposures-associated-with-phenotypes-in-the-exposome-era
#2
REVIEW
Chirag J Patel
PURPOSE OF REVIEW: Mixtures, or combinations and interactions between multiple environmental exposures, are hypothesized to be causally linked with disease and health-related phenotypes. Established and emerging molecular measurement technologies to assay the exposome, the comprehensive battery of exposures encountered from birth to death, promise a new way of identifying mixtures in disease in the epidemiological setting. In this opinion, we describe the analytic complexity and challenges in identifying mixtures associated with phenotype and disease...
2017: Current Epidemiology Reports
https://www.readbyqxmd.com/read/28194614/the-exposome-research-paradigm-an-opportunity-to-understand-the-environmental-basis-for-human-health-and-disease
#3
REVIEW
Germaine M Buck Louis, Melissa M Smarr, Chirag J Patel
PURPOSE OF REVIEW: This paper presents an overview of the exposome research paradigm with particular application to understanding human reproduction and development and its implications for health across a lifespan. RECENT FINDINGS: The exposome research paradigm has generated considerable discussion about its feasibility and utility for delineating the impact of environmental exposures on human health. Early initiatives are underway, including smaller proof-of-principle studies and larger concerted efforts...
March 2017: Current Environmental Health Reports
https://www.readbyqxmd.com/read/28176476/recurrent-atypical-haemolytic-uraemic-syndrome-post-kidney-transplant-due-to-a-cd46-mutation-in-the-setting-of-smarcal1-mediated-inherited-kidney-disease
#4
REVIEW
Samuel Chan, Andrew J Mallett, Chirag Patel, Ross S Francis, David W Johnson, David W Mudge, Nicole M Isbel
Disorders in the regulation of the alternate complement pathway often result in complement-mediated damage to the microvascular endothelium and can be associated with both glomerulonephritis and atypical haemolytic uraemic syndrome. Inherited defects in complement regulatory genes or autoantibodies against complement regulatory proteins are predictive of the severity of the disease and the risk of recurrence post kidney transplantation. Heterozygous mutations in CD46, which codes for a transmembrane cofactor glycoprotein membrane cofactor protein, usually have a lower incidence of end-stage kidney disease and decreased risk of recurrent disease post transplant, as wild-type membrane cofactor protein is present in the transplanted kidney...
February 2017: Nephrology
https://www.readbyqxmd.com/read/28068484/informatics-and-data-analytics-to-support-exposome-based-discovery-for-public-health
#5
Arjun K Manrai, Yuxia Cui, Pierre R Bushel, Molly Hall, Spyros Karakitsios, Carolyn J Mattingly, Marylyn Ritchie, Charles Schmitt, Denis A Sarigiannis, Duncan C Thomas, David Wishart, David M Balshaw, Chirag J Patel
The complexity of the human exposome-the totality of environmental exposures encountered from birth to death-motivates systematic, high-throughput approaches to discover new environmental determinants of disease. In this review, we describe the state of science in analyzing the human exposome and provide recommendations for the public health community to consider in dealing with analytic challenges of exposome-based biomedical research. We describe extant and novel analytic methods needed to associate the exposome with critical health outcomes and contextualize the data-centered challenges by drawing parallels to other research endeavors such as human genomics research...
March 20, 2017: Annual Review of Public Health
https://www.readbyqxmd.com/read/28004011/methods-to-enhance-the-reproducibility-of-precision-medicine
#6
Arjun K Manrai, Chirag J Patel, Nils Gehlenborg, Nicholas P Tatonetti, John P A Ioannidis, Isaac S Kohane
No abstract text is available yet for this article.
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896967/methods-to-ensure-the-reproducibility-of-biomedical-research
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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...
May 1, 2017: 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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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