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Jason H Moore

Xiaohui Yao, Jingwen Yan, Sungeun Kim, Kwangsik Nho, Shannon L Risacher, Mark Inlow, Jason H Moore, Andrew J Saykin, Li Shen
Enrichment analysis has been widely applied in the genome-wide association studies, where gene sets corresponding to biological pathways are examined for significant associations with a phenotype to help increase statistical power and improve biological interpretation. In this work, we expand the scope of enrichment analysis into brain imaging genetics, an emerging field that studies how genetic variation influences brain structure and function measured by neuroimaging quantitative traits (QT). Given the high dimensionality of both imaging and genetic data, we propose to study Imaging Genetic Enrichment Analysis (IGEA), a new enrichment analysis paradigm that jointly considers meaningful gene sets (GS) and brain circuits (BC) and examines whether any given GS-BC pair is enriched in a list of gene-QT findings...
May 13, 2016: Brain Informatics
Nuri Kodaman, Melinda C Aldrich, Rafal Sobota, Folkert W Asselbergs, Kwabena A Poku, Nancy J Brown, Jason H Moore, Scott M Williams
Populations in sub-Saharan Africa are shifting from rural to increasingly urban. Although the burden of cardiovascular disease is expected to increase with this changing landscape, few large studies have assessed a wide range of risk factors in urban and rural populations, particularly in West Africa. We conducted a cross-sectional, population-based survey of 3317 participants from Ghana (≥18 years old), of whom 2265 (57% female) were from a mid-sized city (Sunyani, population ~250,000) and 1052 (55% female) were from surrounding villages (populations <5000)...
2016: PloS One
Sarah A Moore, Prashant Nighot, Cynthia Reyes, Manmeet Rawat, Jason McKee, David Lemon, Joshua Hanson, Thomas Y Ma
BACKGROUND: Intestinal barrier dysfunction has been implicated in necrotizing enterocolitis (NEC), but has not been directly measured in human NEC. METHODS: Small intestines removed during surgery were immediately mounted in an Ussing chamber. mRNA expression of tight junction (TJ) proteins was measured with RT-PCR. RESULTS: Fifteen infants were included, 5 with NEC and 10 with other diagnoses. Average transepithelial resistance (TER) was 11...
September 15, 2016: Journal of Pediatric Surgery
Michael G Stanford, Kyle Mahady, Brett B Lewis, Jason D Fowlkes, Shida Tan, Richard H Livengood, Gregory A Magel, Thomas M Moore, Philip D Rack
Focused helium ion (He+) milling has been demonstrated as a high-resolution nanopatterning technique, however it can be limited by its low sputter yield as well as the introduction of undesired sub-surface damage. Here, we introduce pulsed laser and gas assisted processes to enhance the material removal rate and patterning fidelity. A pulsed laser-assisted He+ milling process is shown to enable high resolution milling of titanium while reducing sub-surface damage in situ. Gas-assisted focused ion beam induced etching (FIBIE) of Ti is also demonstrated in which the XeF2 precursor provides a chemical assist for enhanced material removal rate...
October 4, 2016: ACS Applied Materials & Interfaces
Nuri Kodaman, Melinda C Aldrich, Rafal Sobota, Folkert W Asselbergs, Nancy J Brown, Jason H Moore, Scott M Williams
BACKGROUND: Metabolic syndrome (MetS) is diagnosed by the presence of at least 3 of the following: obesity, hypertension, hyperglycemia, hypertriglyceridemia, and low high-density lipoprotein. Individuals with MetS also typically have elevated plasma levels of the antifibrinolytic factor, plasminogen activator inhibitor-1 (PAI-1), but the relationships between PAI-1 and MetS diagnostic criteria are not clear. Understanding these relationships can elucidate the relevance of MetS to cardiovascular disease risk, because PAI-1 is associated with ischemic events and directly involved in thrombosis...
October 3, 2016: Journal of the American Heart Association
Spiros C Denaxas, Folkert W Asselbergs, Jason H Moore
Modern cohort studies include self-reported measures on disease, behavior and lifestyle, sensor-based observations from mobile phones and wearables, and rich -omics data. Follow-up is often achieved through electronic health record (EHR) linkages across primary and secondary healthcare providers. Historically however, researchers typically only get to see the tip of the iceberg: coded administrative data relating to healthcare claims which mainly record billable diagnoses and procedures. The rich data generated during the clinical pathway remain submerged and inaccessible...
2016: BioData Mining
Joseph Zenga, Ryan S Jackson, Evan M Graboyes, Parul Sinha, Miranda Lindberg, Eliot J Martin, Daniel Ma, Wade L Thorstad, Jason T Rich, Eric J Moore, Bruce H Haughey
OBJECTIVES: To examine outcomes of selective neck dissection (SND) in patients with human papillomavirus (HPV)-related oropharyngeal squamous cell carcinoma (OPSCC) who present with clinical neck disease. STUDY DESIGN: Multi-institutional retrospective review. METHODS: Two institutional databases of patients with HPV-related OPSCC were reviewed to identify patients with clinical (c) N1-N3 neck disease who underwent SND ± adjuvant therapy...
September 16, 2016: Laryngoscope
Lyndon D Bastatas, Kuo-Yao Lin, Matthew D Moore, Kristin J Suhr, Melanie H Bowler, Yulong Shen, Bradley J Holliday, Jason D Slinker
Light-emitting electrochemical cells (LEECs) from small molecules, such as iridium complexes, have great potential as low-cost emissive devices. In these devices, ions rearrange during operation to facilitate carrier injection, bringing about efficient operation from simple, single-layer devices. Prior work has shown that the luminance, efficiency, and responsiveness of iridium LEECs is greatly enhanced by the inclusion of small fractions of lithium salts, but much remains to be understood about the origin of this enhancement...
September 20, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
H Robert Frost, Li Shen, Andrew J Saykin, Scott M Williams, Jason H Moore
Although gene-environment (G× E) interactions play an important role in many biological systems, detecting these interactions within genome-wide data can be challenging due to the loss in statistical power incurred by multiple hypothesis correction. To address the challenge of poor power and the limitations of existing multistage methods, we recently developed a screening-testing approach for G× E interaction detection that combines elastic net penalized regression with joint estimation to support a single omnibus test for the presence of G× E interactions...
November 2016: Genetic Epidemiology
Haiquan Li, Ikbel Achour, Lisa Bastarache, Joanne Berghout, Vincent Gardeux, Jianrong Li, Younghee Lee, Lorenzo Pesce, Xinan Yang, Kenneth S Ramos, Ian Foster, Joshua C Denny, Jason H Moore, Yves A Lussier
Functionally altered biological mechanisms arising from disease-associated polymorphisms, remain difficult to characterize when those variants are intergenic, or, fall between genes. We sought to identify shared downstream mechanisms by which inter- and intragenic single nucleotide polymorphisms (SNPs) contribute to a specific physiopathology. Using computational modeling of 2 million pairs of disease-associated SNPs drawn from genome wide association studies (GWAS), integrated with expression Quantitative Trait Loci (eQTL) and Gene Ontology functional annotations, we predicted 3,870 inter-intra and inter-intra SNP pairs with convergent biological mechanisms (FDR<0...
2016: NPJ Genomic Medicine
Runmin Wei, Immaculata De Vivo, Sijia Huang, Xun Zhu, Harvey Risch, Jason H Moore, Herbert Yu, Lana X Garmire
Endometrial Cancer (EC) is one of the most common female cancers. Genome-wide association studies (GWAS) have been investigated to identify genetic polymorphisms that are predictive of EC risks. Here we utilized a meta-dimensional integrative approach to seek genetically susceptible pathways that may be associated with tumorigenesis and progression of EC. We analyzed GWAS data obtained from Connecticut Endometrial Cancer Study (CECS) and identified the top 20 EC susceptible pathways. To further verify the significance of top 20 EC susceptible pathways, we conducted pathway-level multi-omics analyses using EC exome-Seq, RNA-Seq and survival data, all based on The Cancer Genome Atlas (TCGA) samples...
July 9, 2016: Oncotarget
Molly A Hall, Jason H Moore, Marylyn D Ritchie
Genome-wide association studies (GWAS) have identified numerous loci associated with human phenotypes. This approach, however, does not consider the richly diverse and complex environment with which humans interact throughout the life course, nor does it allow for interrelationships between genetic loci and across traits. As we move toward making precision medicine a reality, whereby we make predictions about disease risk based on genomic profiles, we need to identify improved predictive models of the relationship between genome and phenome...
August 2016: Trends in Genetics: TIG
H Robert Frost, Christopher I Amos, Jason H Moore
Statistical interactions between markers of genetic variation, or gene-gene interactions, are believed to play an important role in the etiology of many multifactorial diseases and other complex phenotypes. Unfortunately, detecting gene-gene interactions is extremely challenging due to the large number of potential interactions and ambiguity regarding marker coding and interaction scale. For many data sets, there is insufficient statistical power to evaluate all candidate gene-gene interactions. In these cases, a global test for gene-gene interactions may be the best option...
July 7, 2016: Genetic Epidemiology
Hui Zhang, Tao Liu, Zhen Zhang, Samuel H Payne, Bai Zhang, Jason E McDermott, Jian-Ying Zhou, Vladislav A Petyuk, Li Chen, Debjit Ray, Shisheng Sun, Feng Yang, Lijun Chen, Jing Wang, Punit Shah, Seong Won Cha, Paul Aiyetan, Sunghee Woo, Yuan Tian, Marina A Gritsenko, Therese R Clauss, Caitlin Choi, Matthew E Monroe, Stefani Thomas, Song Nie, Chaochao Wu, Ronald J Moore, Kun-Hsing Yu, David L Tabb, David Fenyö, Vineet Bafna, Yue Wang, Henry Rodriguez, Emily S Boja, Tara Hiltke, Robert C Rivers, Lori Sokoll, Heng Zhu, Ie-Ming Shih, Leslie Cope, Akhilesh Pandey, Bing Zhang, Michael P Snyder, Douglas A Levine, Richard D Smith, Daniel W Chan, Karin D Rodland
To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive mass-spectrometry-based proteomic characterization of 174 ovarian tumors previously analyzed by The Cancer Genome Atlas (TCGA), of which 169 were high-grade serous carcinomas (HGSCs). Integrating our proteomic measurements with the genomic data yielded a number of insights into disease, such as how different copy-number alternations influence the proteome, the proteins associated with chromosomal instability, the sets of signaling pathways that diverse genome rearrangements converge on, and the ones most associated with short overall survival...
July 28, 2016: Cell
Stanley H Benedict, Karen Hoffman, Mary K Martel, Amy P Abernethy, Anthony L Asher, Jacek Capala, Ronald C Chen, Bhisham Chera, Jennifer Couch, James Deye, Jason A Efstathiou, Eric Ford, Benedick A Fraass, Peter E Gabriel, Vojtech Huser, Brian D Kavanagh, Deepak Khuntia, Lawrence B Marks, Charles Mayo, Todd McNutt, Robert S Miller, Kevin L Moore, Fred Prior, Erik Roelofs, Barry S Rosenstein, Jeff Sloan, Anna Theriault, Bhadrasain Vikram
No abstract text is available yet for this article.
July 1, 2016: International Journal of Radiation Oncology, Biology, Physics
Erin Nz Yu, Jason J Winnick, Dale S Edgerton, Melanie F Scott, Marta S Smith, Ben Farmer, Phillip E Williams, Alan D Cherrington, Mary Courtney Moore
Insulin resistance occurs during various stages of the estrus cycle in dogs. To quantify the effects of proestrus-estrus (PE) and determine whether PE affects liver insulin sensitivity, 11 female mongrel dogs were implanted with sampling and intraportal infusion catheters. Five of the dogs (PE group) entered proestrus after surgery; those remaining in anestrus were controls. The dogs were fasted overnight, [3-(3)H]glucose and somatostatin were infused through peripheral veins, and glucagon was infused intraportally...
2016: Comparative Medicine
Takashi Nakai, Nicholas R Perl, Timothy C Barden, Andrew Carvalho, Angelika Fretzen, Peter Germano, G-Yoon J Im, Hong Jin, Charles Kim, Thomas W-H Lee, Kimberly Long, Joel Moore, Jason M Rohde, Renee Sarno, Chrissie Segal, Erik O Solberg, Jenny Tobin, Daniel P Zimmer, Mark G Currie
In recent years, soluble guanylate cyclase (sGC, EC has emerged as an attractive therapeutic target for treating cardiovascular diseases and diseases associated with fibrosis and end-organ failure. Herein, we describe our design and synthesis of a series of 4-hydroxypyrimidine sGC stimulators starting with an internally discovered lead. Our efforts have led to the discovery of IWP-051, a molecule that achieves good alignment of potency, stability, selectivity, and pharmacodynamic effects while maintaining favorable pharmacokinetic properties with once-daily dosing potential in humans...
May 12, 2016: ACS Medicinal Chemistry Letters
V Bala Chaudhary, Megan A Rúa, Anita Antoninka, James D Bever, Jeffery Cannon, Ashley Craig, Jessica Duchicela, Alicia Frame, Monique Gardes, Catherine Gehring, Michelle Ha, Miranda Hart, Jacob Hopkins, Baoming Ji, Nancy Collins Johnson, Wittaya Kaonongbua, Justine Karst, Roger T Koide, Louis J Lamit, James Meadow, Brook G Milligan, John C Moore, Thomas H Pendergast Iv, Bridget Piculell, Blake Ramsby, Suzanne Simard, Shubha Shrestha, James Umbanhowar, Wolfgang Viechtbauer, Lawrence Walters, Gail W T Wilson, Peter C Zee, Jason D Hoeksema
Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity...
2016: Scientific Data
Michael G Currier, Sujin Lee, Christopher C Stobart, Anne L Hotard, Remi Villenave, Jia Meng, Carla D Pretto, Michael D Shields, Minh Trang Nguyen, Sean O Todd, Michael H Chi, Jason Hammonds, Stefanie A Krumm, Paul Spearman, Richard K Plemper, Kaori Sakamoto, R Stokes Peebles, Ultan F Power, Martin L Moore
Respiratory syncytial virus (RSV) is the major cause of viral lower respiratory tract illness in children. In contrast to the RSV prototypic strain A2, clinical isolate RSV 2-20 induces airway mucin expression in mice, a clinically relevant phenotype dependent on the fusion (F) protein of the RSV strain. Epidermal growth factor receptor (EGFR) plays a role in airway mucin expression in other systems; therefore, we hypothesized that the RSV 2-20 F protein stimulates EGFR signaling. Infection of cells with chimeric strains RSV A2-2-20F and A2-2-20GF or over-expression of 2-20 F protein resulted in greater phosphorylation of EGFR than infection with RSV A2 or over-expression of A2 F, respectively...
May 2016: PLoS Pathogens
Carolina Montano, Margaret A Taub, Andrew Jaffe, Eirikur Briem, Jason I Feinberg, Rakel Trygvadottir, Adrian Idrizi, Arni Runarsson, Birna Berndsen, Ruben C Gur, Tyler M Moore, Rodney T Perry, Doug Fugman, Sarven Sabunciyan, Robert H Yolken, Thomas M Hyde, Joel E Kleinman, Janet L Sobell, Carlos N Pato, Michele T Pato, Rodney C Go, Vishwajit Nimgaonkar, Daniel R Weinberger, David Braff, Raquel E Gur, Margaret Daniele Fallin, Andrew P Feinberg
IMPORTANCE: DNA methylation may play an important role in schizophrenia (SZ), either directly as a mechanism of pathogenesis or as a biomarker of risk. OBJECTIVE: To scan genome-wide DNA methylation data to identify differentially methylated CpGs between SZ cases and controls. DESIGN, SETTING, AND PARTICIPANTS: Epigenome-wide association study begun in 2008 using DNA methylation levels of 456 513 CpG loci measured on the Infinium HumanMethylation450 array (Illumina) in a consortium of case-control studies for initial discovery and in an independent replication set...
May 1, 2016: JAMA Psychiatry
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