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Jason H Moore

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https://www.readbyqxmd.com/read/28628665/a-chromosome-5q31-1-locus-associates-with-tuberculin-skin-test-reactivity-in-hiv-positive-individuals-from-tuberculosis-hyper-endemic-regions-in-east-africa
#1
Rafal S Sobota, Catherine M Stein, Nuri Kodaman, Isaac Maro, Wendy Wieland-Alter, Robert P Igo, Albert Magohe, LaShaunda L Malone, Keith Chervenak, Noemi B Hall, Mecky Matee, Harriet Mayanja-Kizza, Moses Joloba, Jason H Moore, William K Scott, Timothy Lahey, W Henry Boom, C Fordham von Reyn, Scott M Williams, Giorgio Sirugo
One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an "experiment of nature" design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts of tuberculosis from Tanzania and Uganda to identify genetic loci associated with MTB infection in the context of HIV-infection...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28617599/effects-of-the-adulteration-technique-on-the-near-infrared-detection-of-melamine-in-milk-powder
#2
Peter F Scholl, Marti Mamula Bergana, Betsy Jean Yakes, Zhuohong Xie, Steven Zbylut, Gerard Downey, Magdi Mossoba, Joseph Jablonski, Robert Magaletta, Stephen E Holroyd, Martin Buehler, Jianwei Qin, William Hurst, Joseph H LaPointe, Dean Roberts, Carol Zrybko, Andrew Mackey, Jason D Holton, Greg A Israelson, Anitra Payne, Moon S Kim, Kuanglin Chao, Jeffrey C Moore
The United States Pharmacopeial Convention has led an international collaborative project to develop a toolbox of screening methods and reference standards for the detection of milk powder adulteration. During the development of adulterated milk powder reference standards, blending methods used to combine melamine and milk had unanticipated strong effects on the near-infrared (NIR) spectrum of melamine. The prominent absorbance band at 1468 nm of melamine was retained when it was dry-blended with skim milk powder but disappeared in wet-blended mixtures, where spray-dried milk powder samples were prepared from solution...
July 6, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28612213/influence-of-substance-use-disorders-on-2-year-hiv-care-retention-in-the-united-states
#3
Bryan Hartzler, Julia C Dombrowski, Jason R Williams, Heidi M Crane, Joseph J Eron, Elvin H Geng, Christopher Mathews, Kenneth H Mayer, Richard D Moore, Michael J Mugavero, Sonia Napravnik, Benigno Rodriguez, Dennis M Donovan
Substance use disorders (SUDs) are thought to predict care discontinuity, though magnitude and substance-specific variance of effects are unclear. This report of analytic work undertaken with a multi-regional American cohort of 9153 care enrollees addresses these gaps. Care retention was computed from 24-month post-linkage clinic visit documentation, with SUD cases identified from patient-report screening instruments. Two generalized estimating equations tested binary and hierarchial SUD predictors of retention, and potential effect modification by patient age-group, sex, and care site...
June 13, 2017: AIDS and Behavior
https://www.readbyqxmd.com/read/28575147/tissue-specific-network-based-genome-wide-study-of-amygdala-imaging-phenotypes-to-identify-functional-interaction-modules
#4
Xiaohui Yao, Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L Risacher, Casey S Greene, Jason H Moore, Andrew J Saykin, Li Shen
Motivation: Network-based genome-wide association studies (GWAS) aim to identify functional modules from biological networks that are enriched by top GWAS findings. Although gene functions are relevant to tissue context, most existing methods analyze tissue-free networks without reflecting phenotypic specificity. Results: We propose a novel module identification framework for imaging genetic studies using the tissue-specific functional interaction network. Our method includes three steps: 1) re-prioritize imaging GWAS findings by applying machine learning methods to incorporate network topological information and enhance the connectivity among top genes; 2) detect densely connected modules based on interactions among top re-prioritized genes; and 3) identify phenotype-relevant modules enriched by top GWAS findings...
May 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28572842/grid-based-stochastic-search-for-hierarchical-gene-gene-interactions-in-population-based-genetic-studies-of-common-human-diseases
#5
Jason H Moore, Peter C Andrews, Randal S Olson, Sarah E Carlson, Curt R Larock, Mario J Bulhoes, James P O'Connor, Ellen M Greytak, Steven L Armentrout
BACKGROUND: Large-scale genetic studies of common human diseases have focused almost exclusively on the independent main effects of single-nucleotide polymorphisms (SNPs) on disease susceptibility. These studies have had some success, but much of the genetic architecture of common disease remains unexplained. Attention is now turning to detecting SNPs that impact disease susceptibility in the context of other genetic factors and environmental exposures. These context-dependent genetic effects can manifest themselves as non-additive interactions, which are more challenging to model using parametric statistical approaches...
2017: BioData Mining
https://www.readbyqxmd.com/read/28559929/gene-set-enrichment-analyses-lessons-learned-from-the-heart-failure-phenotype
#6
Vinicius Tragante, Johannes M I H Gho, Janine F Felix, Ramachandran S Vasan, Nicholas L Smith, Benjamin F Voight, Colin Palmer, Pim van der Harst, Jason H Moore, Folkert W Asselbergs
BACKGROUND: Genetic studies for complex diseases have predominantly discovered main effects at individual loci, but have not focused on genomic and environmental contexts important for a phenotype. Gene Set Enrichment Analysis (GSEA) aims to address this by identifying sets of genes or biological pathways contributing to a phenotype, through gene-gene interactions or other mechanisms, which are not the focus of conventional association methods. RESULTS: Approaches that utilize GSEA can now take input from array chips, either gene-centric or genome-wide, but are highly sensitive to study design, SNP selection and pruning strategies, SNP-to-gene mapping, and pathway definitions...
2017: BioData Mining
https://www.readbyqxmd.com/read/28538102/effects-of-wet-blending-on-detection-of-melamine-in-spray-dried-lactose
#7
Betsy Jean Yakes, Marti M Bergana, Peter F Scholl, Magdi M Mossoba, Sanjeewa R Karunathilaka, Luke K Ackerman, Jason D Holton, Boyan Gao, Jeffrey C Moore
During the development of rapid screening methods to detect economic adulteration, spray-dried milk powders prepared by dissolving melamine in liquid milk exhibited an unexpected loss of characteristic melamine features in the near-infrared (NIR) and Raman spectra. To further characterize this "wet-blending" phenomenon, spray-dried melamine and lactose samples were produced as a simplified model and investigated by NIR spectroscopy, Raman spectroscopy, proton nuclear magnetic resonance ((1)H NMR), and direct analysis in real time Fourier transform mass spectrometry (DART-FTMS)...
July 6, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28520685/pelvic-fracture-pattern-predicts-the-need-for-hemorrhage-control-intervention-results-of-an-aast-multi-institutional-study
#8
Todd W Costantini, Raul Coimbra, John B Holcomb, Jeanette M Podbielski, Richard D Catalano, Allie Blackburn, Thomas M Scalea, Deborah M Stein, Lashonda Williams, Joseph Conflitti, Scott Keeney, Christy Hoey, Tianhua Zhou, Jason Sperry, Dimitra Skiada, Kenji Inaba, Brian H Williams, Joseph P Minei, Alicia Privette, Robert C Mackersie, Brenton R Robinson, Forrest O Moore
BACKGROUND: Early identification of patients with pelvic fractures at risk of severe bleeding requiring intervention is critical. We performed a multi-institutional study to test our hypothesis that pelvic fracture patterns predict the need for a pelvic hemorrhage control intervention. METHODS: This prospective, observational, multicenter study enrolled patients with pelvic fracture due to blunt trauma. Inclusion criteria included shock on admission (systolic blood pressure <90 mm Hg or heart rate >120 beats/min and base deficit >5, and the ability to review pelvic imaging)...
June 2017: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/28450890/multi-class-computational-evolution-development-benchmark-evaluation-and-application-to-rna-seq-biomarker-discovery
#9
Nathaniel M Crabtree, Jason H Moore, John F Bowyer, Nysia I George
BACKGROUND: A computational evolution system (CES) is a knowledge discovery engine that can identify subtle, synergistic relationships in large datasets. Pareto optimization allows CESs to balance accuracy with model complexity when evolving classifiers. Using Pareto optimization, a CES is able to identify a very small number of features while maintaining high classification accuracy. A CES can be designed for various types of data, and the user can exploit expert knowledge about the classification problem in order to improve discrimination between classes...
2017: BioData Mining
https://www.readbyqxmd.com/read/28445112/tracking-the-evolution-of-non-small-cell-lung-cancer
#10
Mariam Jamal-Hanjani, Gareth A Wilson, Nicholas McGranahan, Nicolai J Birkbak, Thomas B K Watkins, Selvaraju Veeriah, Seema Shafi, Diana H Johnson, Richard Mitter, Rachel Rosenthal, Max Salm, Stuart Horswell, Mickael Escudero, Nik Matthews, Andrew Rowan, Tim Chambers, David A Moore, Samra Turajlic, Hang Xu, Siow-Ming Lee, Martin D Forster, Tanya Ahmad, Crispin T Hiley, Christopher Abbosh, Mary Falzon, Elaine Borg, Teresa Marafioti, David Lawrence, Martin Hayward, Shyam Kolvekar, Nikolaos Panagiotopoulos, Sam M Janes, Ricky Thakrar, Asia Ahmed, Fiona Blackhall, Yvonne Summers, Rajesh Shah, Leena Joseph, Anne M Quinn, Phil A Crosbie, Babu Naidu, Gary Middleton, Gerald Langman, Simon Trotter, Marianne Nicolson, Hardy Remmen, Keith Kerr, Mahendran Chetty, Lesley Gomersall, Dean A Fennell, Apostolos Nakas, Sridhar Rathinam, Girija Anand, Sajid Khan, Peter Russell, Veni Ezhil, Babikir Ismail, Melanie Irvin-Sellers, Vineet Prakash, Jason F Lester, Malgorzata Kornaszewska, Richard Attanoos, Haydn Adams, Helen Davies, Stefan Dentro, Philippe Taniere, Brendan O'Sullivan, Helen L Lowe, John A Hartley, Natasha Iles, Harriet Bell, Yenting Ngai, Jacqui A Shaw, Javier Herrero, Zoltan Szallasi, Roland F Schwarz, Aengus Stewart, Sergio A Quezada, John Le Quesne, Peter Van Loo, Caroline Dive, Allan Hackshaw, Charles Swanton
BACKGROUND: Among patients with non-small-cell lung cancer (NSCLC), data on intratumor heterogeneity and cancer genome evolution have been limited to small retrospective cohorts. We wanted to prospectively investigate intratumor heterogeneity in relation to clinical outcome and to determine the clonal nature of driver events and evolutionary processes in early-stage NSCLC. METHODS: In this prospective cohort study, we performed multiregion whole-exome sequencing on 100 early-stage NSCLC tumors that had been resected before systemic therapy...
June 1, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28414475/cognitive-functioning-of-adolescent-and-young-adult-cannabis-users-in-the-philadelphia-neurodevelopmental-cohort
#11
J Cobb Scott, Daniel H Wolf, Monica E Calkins, Emily C Bach, Jennifer Weidner, Kosha Ruparel, Tyler M Moore, Jason D Jones, Chad T Jackson, Raquel E Gur, Ruben C Gur
Cannabis use in youth is rising and has been linked to deficits in cognitive functioning. However, cognitive findings have primarily been based on small samples of users seeking treatment, and few studies have evaluated cognition in occasional cannabis users. Here, we examined 4,568 adolescents and young adults (ages 14-21 years) drawn from the Philadelphia Neurodevelopmental Cohort, a prospective, population-based study. Participants were classified as cannabis Non-Users (n = 3,401), Occasional Users (twice per week or less; n = 940), or Frequent Users (>3 times per week; n = 227)...
June 2017: Psychology of Addictive Behaviors: Journal of the Society of Psychologists in Addictive Behaviors
https://www.readbyqxmd.com/read/28408189/genetic-effects-on-the-correlation-structure-of%C3%A2-cvd-risk-factors-exome-wide-data-from-a-ghanaian-population
#12
REVIEW
Nuri Kodaman, Rafal S Sobota, Folkert W Asselbergs, Matthew T Oetjens, Jason H Moore, Nancy J Brown, Melinda C Aldrich, Scott M Williams
Plasma concentration of plasminogen activator inhibitor-1 (PAI-1) is highly correlated with several cardiovascular disease (CVD) risk factors. It also plays a direct role in CVD, including myocardial infarction and stroke, by impeding the dissolution of thrombi in the blood. Insofar as PAI-1 links CVD's risk factors to its endpoints, genetic variants modulating the relationship between PAI-1 and risk factors may be of particular clinical and biological interest. The high heritability of PAI-1, which has not been explained by genetic association studies, may also, in large part, be due to this relationship with CVD risk factors...
April 10, 2017: Global Heart
https://www.readbyqxmd.com/read/28338600/pelvic-fracture-pattern-predicts-the-need-for-hemorrhage-control-intervention-results-of-a-aast-multi-institutional-study
#13
Todd W Costantini, Raul Coimbra, John B Holcomb, Jeanette M Podbielski, Richard Catalano, Allie Blackburn, Thomas M Scalea, Deborah M Stein, Lashonda Williams, Joseph Conflitti, Scott Keeney, Christy Hoey, Tianhua Zhou, Jason Sperry, Dimitra Skiada, Kenji Inaba, Brian H Williams, Joseph P Minei, Alicia Privette, Robert C Mackersie, Brenton R Robinson, Forrest O Moore
BACKGROUND: Early identification of patients with pelvic fractures at risk for severe bleeding requiring intervention is critical. We performed a multi-institutional study to test our hypothesis that pelvic fracture patterns predict the need for a pelvic hemorrhage control intervention. METHODS: This prospective, observational multi-center study enrolled patients with pelvic fracture due to blunt trauma. Inclusion criteria included shock on admission (SBP<90 or HR>120 and base deficit > 5, and the ability to review pelvic imaging...
March 23, 2017: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/28271566/minimum-lymph-node-yield-in-elective-level-i-iii-neck-dissection
#14
Jason D Pou, Blair M Barton, Claire M Lawlor, Christopher H Frederick, Brian A Moore, Christian P Hasney
OBJECTIVES/HYPOTHESIS: Unlike lymphadenectomy at other sites, there is no discrete lymph node count defining an adequate neck dissection. The purpose of this study was to determine the minimum lymph node yield (LNY) of an elective level I-III neck dissection required to reliably capture any positive nodes present in these nodal basins. STUDY DESIGN: Retrospective single-institution analysis. METHODS: All patients with the diagnosis of head and neck squamous cell carcinoma who underwent elective level I-III neck dissection between 2004 and 2015 at our institution were analyzed...
March 8, 2017: Laryngoscope
https://www.readbyqxmd.com/read/28239419/variant-set-enrichment-an-r-package-to-identify-disease-associated-functional-genomic-regions
#15
Musaddeque Ahmed, Richard C Sallari, Haiyang Guo, Jason H Moore, Housheng Hansen He, Mathieu Lupien
BACKGROUND: Genetic predispositions to diseases populate the noncoding regions of the human genome. Delineating their functional basis can inform on the mechanisms contributing to disease development. However, this remains a challenge due to the poor characterization of the noncoding genome. Here, we propose an R package that can pinpoint which genomic features are etiologically important based on the genetic predispositions. RESULTS: Variant Set Enrichment (VSE) is an R package to calculate the enrichment of a set of disease-associated variants across functionally annotated genomic regions, consequently highlighting the mechanisms important in the etiology of the disease studied...
2017: BioData Mining
https://www.readbyqxmd.com/read/28155079/fluorescence-imaging-for-cancer-screening-and-surveillance
#16
K E Tipirneni, E L Rosenthal, L S Moore, A D Haskins, N Udayakumar, A H Jani, W R Carroll, A B Morlandt, M Bogyo, J Rao, Jason M Warram
The advent of fluorescence imaging (FI) for cancer cell detection in the field of oncology is promising for both cancer screening and surgical resection. Particularly, FI in cancer screening and surveillance is actively being evaluated in many new clinical trials with over 30 listed on Clinical Trials.gov . While surgical resection forms the foundation of many oncologic treatments, early detection is the cornerstone for improving outcomes and reducing cancer-related morbidity and mortality. The applications of FI are twofold as it can be applied to high-risk patients in addition to those undergoing active surveillance...
February 2, 2017: Molecular Imaging and Biology: MIB: the Official Publication of the Academy of Molecular Imaging
https://www.readbyqxmd.com/read/28092686/epigenomic-reprogramming-during-pancreatic-cancer-progression-links-anabolic-glucose-metabolism-to-distant-metastasis
#17
Oliver G McDonald, Xin Li, Tyler Saunders, Rakel Tryggvadottir, Samantha J Mentch, Marc O Warmoes, Anna E Word, Alessandro Carrer, Tal H Salz, Sonoko Natsume, Kimberly M Stauffer, Alvin Makohon-Moore, Yi Zhong, Hao Wu, Kathryn E Wellen, Jason W Locasale, Christine A Iacobuzio-Donahue, Andrew P Feinberg
During the progression of pancreatic ductal adenocarcinoma (PDAC), heterogeneous subclonal populations emerge that drive primary tumor growth, regional spread, distant metastasis, and patient death. However, the genetics of metastases largely reflects that of the primary tumor in untreated patients, and PDAC driver mutations are shared by all subclones. This raises the possibility that an epigenetic process might operate during metastasis. Here we report large-scale reprogramming of chromatin modifications during the natural evolution of distant metastasis...
March 2017: Nature Genetics
https://www.readbyqxmd.com/read/28089180/enteric-coating-and-aspirin%C3%A2-nonresponsiveness-in-patients%C3%A2-with-type%C3%A2-2%C3%A2-diabetes-mellitus
#18
RANDOMIZED CONTROLLED TRIAL
Deepak L Bhatt, Tilo Grosser, Jing-Fei Dong, Douglas Logan, Walter Jeske, Dominick J Angiolillo, Andrew L Frelinger, Lanyu Lei, Juan Liang, Jason E Moore, Byron Cryer, Upendra Marathi
BACKGROUND: A limitation of aspirin is that some patients, particularly those with diabetes, may not have an optimal antiplatelet effect. OBJECTIVES: The goal of this study was to determine if oral bioavailability mediates nonresponsiveness. METHODS: The rate and extent of serum thromboxane generation and aspirin pharmacokinetics were measured in 40 patients with diabetes in a randomized, single-blind, triple-crossover study. Patients were exposed to three 325-mg aspirin formulations: plain aspirin, PL2200 (a modified-release lipid-based aspirin), and a delayed-release enteric-coated (EC) aspirin...
February 14, 2017: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/28076415/structure-and-recognition-of-a-novel-hiv-1-gp120-gp41-interface-antibody-that-caused-mper-exposure-through-viral-escape
#19
Constantinos Kurt Wibmer, Jason Gorman, Gabriel Ozorowski, Jinal N Bhiman, Daniel J Sheward, Debra H Elliott, Julie Rouelle, Ashley Smira, M Gordon Joyce, Nonkululeko Ndabambi, Aliaksandr Druz, Mangai Asokan, Dennis R Burton, Mark Connors, Salim S Abdool Karim, John R Mascola, James E Robinson, Andrew B Ward, Carolyn Williamson, Peter D Kwong, Lynn Morris, Penny L Moore
A comprehensive understanding of the regions on HIV-1 envelope trimers targeted by broadly neutralizing antibodies may contribute to rational design of an HIV-1 vaccine. We previously identified a participant in the CAPRISA cohort, CAP248, who developed trimer-specific antibodies capable of neutralizing 60% of heterologous viruses at three years post-infection. Here, we report the isolation by B cell culture of monoclonal antibody CAP248-2B, which targets a novel membrane proximal epitope including elements of gp120 and gp41...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28045715/oncologic-procedures-amenable-to-fluorescence-guided-surgery
#20
Kiranya E Tipirneni, Jason M Warram, Lindsay S Moore, Andrew C Prince, Esther de Boer, Aditi H Jani, Irene L Wapnir, Joseph C Liao, Michael Bouvet, Nicole K Behnke, Mary T Hawn, George A Poultsides, Alexander L Vahrmeijer, William R Carroll, Kurt R Zinn, Eben Rosenthal
OBJECTIVE: Although fluorescence imaging is being applied to a wide range of cancers, it remains unclear which disease populations will benefit greatest. Therefore, we review the potential of this technology to improve outcomes in surgical oncology with attention to the various surgical procedures while exploring trial endpoints that may be optimal for each tumor type. BACKGROUND: For many tumors, primary treatment is surgical resection with negative margins, which corresponds to improved survival and a reduction in subsequent adjuvant therapies...
July 2017: Annals of Surgery
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