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Jason H Moore

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https://www.readbyqxmd.com/read/29843621/summary-results-of-the-2014-2015-darpa-chikungunya-challenge
#1
Sara Y Del Valle, Benjamin H McMahon, Jason Asher, Richard Hatchett, Joceline C Lega, Heidi E Brown, Mark E Leany, Yannis Pantazis, David J Roberts, Sean Moore, A Townsend Peterson, Luis E Escobar, Huijie Qiao, Nicholas W Hengartner, Harshini Mukundan
BACKGROUND: Emerging pathogens such as Zika, chikungunya, Ebola, and dengue viruses are serious threats to national and global health security. Accurate forecasts of emerging epidemics and their severity are critical to minimizing subsequent mortality, morbidity, and economic loss. The recent introduction of chikungunya and Zika virus to the Americas underscores the need for better methods for disease surveillance and forecasting. METHODS: To explore the suitability of current approaches to forecasting emerging diseases, the Defense Advanced Research Projects Agency (DARPA) launched the 2014-2015 DARPA Chikungunya Challenge to forecast the number of cases and spread of chikungunya disease in the Americas...
May 30, 2018: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29797095/leveraging-epigenomics-and-contactomics-data-to-investigate-snp-pairs-in-gwas
#2
Elisabetta Manduchi, Scott M Williams, Alessandra Chesi, Matthew E Johnson, Andrew D Wells, Struan F A Grant, Jason H Moore
Although Genome Wide Association Studies (GWAS) have led to many valuable insights into the genetic bases of common diseases over the past decade, the issue of missing heritability has surfaced, as the discovered main effect genetic variants found to date do not account for much of a trait's predicted genetic component. We present a workflow, integrating epigenomics and topologically associating domain data, aimed at discovering trait-associated SNP pairs from GWAS where neither SNP achieved independent genome-wide significance...
May 2018: Human Genetics
https://www.readbyqxmd.com/read/29795209/the-premature-infant-gut-microbiome-during-the-first-6-weeks-of-life-differs-based-on-gestational-maturity-at-birth
#3
Diana A Chernikova, Juliette C Madan, Molly L Housman, Muhammad Zain-Ul-Abideen, Sara N Lundgren, Hilary G Morrison, Mitchell L Sogin, Scott M Williams, Jason H Moore, Margaret R Karagas, Anne G Hoen
BACKGROUND: The impact of degree of prematurity at birth on premature infant gut microbiota has not been extensively studied in comparison to term infants in large cohorts. METHODS: To determine the effect of gestational age at birth and postnatal exposures on gut bacterial colonization in infants, we analyzed 65 stool samples from 17 premature infants in the neonatal intensive care unit, as well as 13 samples from 13 mostly moderate-to-late premature infants and 189 samples from 176 term infants in the New Hampshire Birth Cohort Study...
May 23, 2018: Pediatric Research
https://www.readbyqxmd.com/read/29790909/ebic-an-evolutionary-based-parallel-biclustering-algorithm-for-pattern-discovery
#4
Patryk Orzechowski, Moshe Sipper, Xiuzhen Huang, Jason H Moore
Motivation: Biclustering algorithms are commonly used for gene expression data analysis. However, accurate identification of meaningful structures is very challenging and state-of-the-art methods are incapable of discovering with high accuracy different patterns of high biological relevance. Results: In this paper a novel biclustering algorithm based on evolutionary computation, a subfield of artificial intelligence (AI), is introduced. The method called EBIC aims to detect order-preserving patterns in complex data...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29746157/a-probabilistic-and-multi-objective-analysis-of-lexicase-selection-and-%C3%AE%C2%B5-lexicase-selection
#5
William La Cava, Thomas Helmuth, Lee Spector, Jason H Moore
Lexicase selection is a parent selection method that considers training cases individually, rather than in aggregate, when performing parent selection. Whereas previous work has demonstrated the ability of lexicase selection to solve difficult problems in program synthesis and symbolic regression, the central goal of this paper is to develop the theoretical underpinnings that explain its performance. To this end, we derive an analytical formula that gives the expected probabilities of selection under lexicase selection, given a population and its behavior...
May 10, 2018: Evolutionary Computation
https://www.readbyqxmd.com/read/29717215/dnap-a-pipeline-for-dna-seq-data-analysis
#6
Jason L Causey, Cody Ashby, Karl Walker, Zhiping Paul Wang, Mary Yang, Yuanfang Guan, Jason H Moore, Xiuzhen Huang
Next-generation sequencing is empowering genetic disease research. However, it also brings significant challenges for efficient and effective sequencing data analysis. We built a pipeline, called DNAp, for analyzing whole exome sequencing (WES) and whole genome sequencing (WGS) data, to detect mutations from disease samples. The pipeline is containerized, convenient to use and can run under any system, since it is a fully automatic process in Docker container form. It is also open, and can be easily customized with user intervention points, such as for updating reference files and different software or versions...
May 1, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29713384/improving-machine-learning-reproducibility-in-genetic-association-studies-with-proportional-instance-cross-validation-picv
#7
Elizabeth R Piette, Jason H Moore
Background: Machine learning methods and conventions are increasingly employed for the analysis of large, complex biomedical data sets, including genome-wide association studies (GWAS). Reproducibility of machine learning analyses of GWAS can be hampered by biological and statistical factors, particularly so for the investigation of non-additive genetic interactions. Application of traditional cross validation to a GWAS data set may result in poor consistency between the training and testing data set splits due to an imbalance of the interaction genotypes relative to the data as a whole...
2018: BioData Mining
https://www.readbyqxmd.com/read/29713383/collective-feature-selection-to-identify-crucial-epistatic-variants
#8
Shefali S Verma, Anastasia Lucas, Xinyuan Zhang, Yogasudha Veturi, Scott Dudek, Binglan Li, Ruowang Li, Ryan Urbanowicz, Jason H Moore, Dokyoon Kim, Marylyn D Ritchie
Background: Machine learning methods have gained popularity and practicality in identifying linear and non-linear effects of variants associated with complex disease/traits. Detection of epistatic interactions still remains a challenge due to the large number of features and relatively small sample size as input, thus leading to the so-called "short fat data" problem. The efficiency of machine learning methods can be increased by limiting the number of input features. Thus, it is very important to perform variable selection before searching for epistasis...
2018: BioData Mining
https://www.readbyqxmd.com/read/29708428/interpathologist-diagnostic-agreement-for-non-small-cell-lung-carcinomas-using-current-and-recent-classifications
#9
William K Funkhouser, D Neil Hayes, Dominic T Moore, W Keith Funkhouser, Jason P Fine, HeeJoon Jo, Nana Nikolaishvilli-Feinberg, Mervi Eeva, Juneko E Grilley-Olson, Peter M Banks, Paolo Graziano, Elizabeth L Boswell, Goran Elmberger, Kirtee Raparia, Craig F Hart, Lynette M Sholl, Norris J Nolan, Karen J Fritchie, Ersie Pouagare, Timothy C Allen, Keith E Volmar, Paul W Biddinger, Daniel T Kleven, Michael J Papez, Deborah V Spencer, Natasha Rekhtman, Mari Mino-Kenudson, Lida Hariri, Brandon Driver, Philip T Cagle
CONTEXT: - Measurement of interpathologist diagnostic agreement (IPDA) should allow pathologists to improve current diagnostic criteria and disease classifications. OBJECTIVES: - To determine how IPDA for pathologists' diagnoses of non-small cell lung carcinoma (NSCLC) is affected by the addition of a set of mucin and immunohistochemical (IHC) stains to hematoxylin-eosin (H&E) alone, by recent NSCLC reclassifications, by simplification of these classifications, and by pathologists' practice location, pulmonary pathology expertise, practice duration, and lung carcinoma case exposure...
April 30, 2018: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29691798/gpu-accelerated-browser-for-neuroimaging-genomics
#10
Bob Zigon, Huang Li, Xiaohui Yao, Shiaofen Fang, Mohammad Al Hasan, Jingwen Yan, Jason H Moore, Andrew J Saykin, Li Shen
Neuroimaging genomics is an emerging field that provides exciting opportunities to understand the genetic basis of brain structure and function. The unprecedented scale and complexity of the imaging and genomics data, however, have presented critical computational bottlenecks. In this work we present our initial efforts towards building an interactive visual exploratory system for mining big data in neuroimaging genomics. A GPU accelerated browsing tool for neuroimaging genomics is created that implements the ANOVA algorithm for single nucleotide polymorphism (SNP) based analysis and the VEGAS algorithm for gene-based analysis, and executes them at interactive rates...
April 25, 2018: Neuroinformatics
https://www.readbyqxmd.com/read/29655375/association-between-traumatic-stress-load-psychopathology-and-cognition-in-the-philadelphia-neurodevelopmental-cohort
#11
Ran Barzilay, Monica E Calkins, Tyler M Moore, Daniel H Wolf, Theodore D Satterthwaite, J Cobb Scott, Jason D Jones, Tami D Benton, Ruben C Gur, Raquel E Gur
BACKGROUND: Traumatic stressors during childhood and adolescence are associated with psychopathology, mostly studied in the context of post-traumatic stress disorder (PTSD) and depression. We investigated broader associations of traumatic stress exposure with psychopathology and cognition in a youth community sample. METHODS: The Philadelphia Neurodevelopmental Cohort (N = 9498) is an investigation of clinical and neurobehavioral phenotypes in a diverse (56% Caucasian, 33% African American, 11% other) US youth community population (aged 8-21)...
April 15, 2018: Psychological Medicine
https://www.readbyqxmd.com/read/29596416/eleven-quick-tips-for-architecting-biomedical-informatics-workflows-with-cloud-computing
#12
Brian S Cole, Jason H Moore
Cloud computing has revolutionized the development and operations of hardware and software across diverse technological arenas, yet academic biomedical research has lagged behind despite the numerous and weighty advantages that cloud computing offers. Biomedical researchers who embrace cloud computing can reap rewards in cost reduction, decreased development and maintenance workload, increased reproducibility, ease of sharing data and software, enhanced security, horizontal and vertical scalability, high availability, a thriving technology partner ecosystem, and much more...
March 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29538381/taxonomy-based-on-science-is-necessary-for-global-conservation
#13
Scott A Thomson, Richard L Pyle, Shane T Ahyong, Miguel Alonso-Zarazaga, Joe Ammirati, Juan Francisco Araya, John S Ascher, Tracy Lynn Audisio, Valter M Azevedo-Santos, Nicolas Bailly, William J Baker, Michael Balke, Maxwell V L Barclay, Russell L Barrett, Ricardo C Benine, James R M Bickerstaff, Patrice Bouchard, Roger Bour, Thierry Bourgoin, Christopher B Boyko, Abraham S H Breure, Denis J Brothers, James W Byng, David Campbell, Luis M P Ceríaco, István Cernák, Pierfilippo Cerretti, Chih-Han Chang, Soowon Cho, Joshua M Copus, Mark J Costello, Andras Cseh, Csaba Csuzdi, Alastair Culham, Guillermo D'Elía, Cédric d'Udekem d'Acoz, Mikhail E Daneliya, René Dekker, Edward C Dickinson, Timothy A Dickinson, Peter Paul van Dijk, Klaas-Douwe B Dijkstra, Bálint Dima, Dmitry A Dmitriev, Leni Duistermaat, John P Dumbacher, Wolf L Eiserhardt, Torbjørn Ekrem, Neal L Evenhuis, Arnaud Faille, José L Fernández-Triana, Emile Fiesler, Mark Fishbein, Barry G Fordham, André V L Freitas, Natália R Friol, Uwe Fritz, Tobias Frøslev, Vicki A Funk, Stephen D Gaimari, Guilherme S T Garbino, André R S Garraffoni, József Geml, Anthony C Gill, Alan Gray, Felipe G Grazziotin, Penelope Greenslade, Eliécer E Gutiérrez, Mark S Harvey, Cornelis J Hazevoet, Kai He, Xiaolan He, Stephan Helfer, Kristofer M Helgen, Anneke H van Heteren, Francisco Hita Garcia, Norbert Holstein, Margit K Horváth, Peter H Hovenkamp, Wei Song Hwang, Jaakko Hyvönen, Melissa B Islam, John B Iverson, Michael A Ivie, Zeehan Jaafar, Morgan D Jackson, J Pablo Jayat, Norman F Johnson, Hinrich Kaiser, Bente B Klitgård, Dániel G Knapp, Jun-Ichi Kojima, Urmas Kõljalg, Jenő Kontschán, Frank-Thorsten Krell, Irmgard Krisai-Greilhuber, Sven Kullander, Leonardo Latella, John E Lattke, Valeria Lencioni, Gwilym P Lewis, Marcos G Lhano, Nathan K Lujan, Jolanda A Luksenburg, Jean Mariaux, Jader Marinho-Filho, Christopher J Marshall, Jason F Mate, Molly M McDonough, Ellinor Michel, Vitor F O Miranda, Mircea-Dan Mitroiu, Jesús Molinari, Scott Monks, Abigail J Moore, Ricardo Moratelli, Dávid Murányi, Takafumi Nakano, Svetlana Nikolaeva, John Noyes, Michael Ohl, Nora H Oleas, Thomas Orrell, Barna Páll-Gergely, Thomas Pape, Viktor Papp, Lynne R Parenti, David Patterson, Igor Ya Pavlinov, Ronald H Pine, Péter Poczai, Jefferson Prado, Divakaran Prathapan, Richard K Rabeler, John E Randall, Frank E Rheindt, Anders G J Rhodin, Sara M Rodríguez, D Christopher Rogers, Fabio de O Roque, Kevin C Rowe, Luis A Ruedas, Jorge Salazar-Bravo, Rodrigo B Salvador, George Sangster, Carlos E Sarmiento, Dmitry S Schigel, Stefan Schmidt, Frederick W Schueler, Hendrik Segers, Neil Snow, Pedro G B Souza-Dias, Riaan Stals, Soili Stenroos, R Douglas Stone, Charles F Sturm, Pavel Štys, Pablo Teta, Daniel C Thomas, Robert M Timm, Brian J Tindall, Jonathan A Todd, Dagmar Triebel, Antonio G Valdecasas, Alfredo Vizzini, Maria S Vorontsova, Jurriaan M de Vos, Philipp Wagner, Les Watling, Alan Weakley, Francisco Welter-Schultes, Daniel Whitmore, Nicholas Wilding, Kipling Will, Jason Williams, Karen Wilson, Judith E Winston, Wolfgang Wüster, Douglas Yanega, David K Yeates, Hussam Zaher, Guanyang Zhang, Zhi-Qiang Zhang, Hong-Zhang Zhou
No abstract text is available yet for this article.
March 2018: PLoS Biology
https://www.readbyqxmd.com/read/29521452/genomes-of-ubiquitous-marine-and-hypersaline-hydrogenovibrio-thiomicrorhabdus-and-thiomicrospira-spp-encode-a-diversity-of-mechanisms-to-sustain-chemolithoautotrophy-in-heterogeneous-environments
#14
Kathleen M Scott, John Williams, Cody M B Porter, Sydney Russel, Tara L Harmer, John H Paul, Kirsten M Antonen, Megan K Bridges, Gary J Camper, Christie K Campla, Leila G Casella, Eva Chase, James W Conrad, Mercedez C Cruz, Darren S Dunlap, Laura Duran, Elizabeth M Fahsbender, Dawn B Goldsmith, Ryan F Keeley, Matthew R Kondoff, Breanna I Kussy, Marannda K Lane, Stephanie Lawler, Brittany A Leigh, Courtney Lewis, Lygia M Lostal, Devon Marking, Paola A Mancera, Evan C McClenthan, Emily A McIntyre, Jessica A Mine, Swapnil Modi, Brittney D Moore, William A Morgan, Kaleigh M Nelson, Kimmy N Nguyen, Nicholas Ogburn, David G Parrino, Anangamanjari D Pedapudi, Rebecca P Pelham, Amanda M Preece, Elizabeth A Rampersad, Jason C Richardson, Christina M Rodgers, Brent L Schaffer, Nancy E Sheridan, Michael R Solone, Zachery R Staley, Maki Tabuchi, Ramond J Waide, Pauline W Wanjugi, Suzanne Young, Alicia Clum, Chris Daum, Marcel Huntemann, Natalia Ivanova, Nikos Kyrpides, Natalia Mikhailova, Krishnaveni Palaniappan, Manoj Pillay, T B K Reddy, Nicole Shapiro, Dimitrios Stamatis, Neha Varghese, Tanja Woyke, Rich Boden, Sharyn K Freyermuth, Cheryl A Kerfeld
Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2...
March 9, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29480817/cancer-vaccine-formulation-dictates-synergy-with-ctla-4-and-pd-l1-checkpoint-blockade-therapy
#15
Yared Hailemichael, Amber Woods, Tihui Fu, Qiuming He, Michael C Nielsen, Farah Hasan, Jason Roszik, Zhilan Xiao, Christina Vianden, Hiep Khong, Manisha Singh, Meenu Sharma, Faisal Faak, Derek Moore, Zhimin Dai, Scott M Anthony, Kimberly S Schluns, Padmanee Sharma, Victor H Engelhard, Willem W Overwijk
Anticancer vaccination is a promising approach to increase the efficacy of cytotoxic T lymphocyte-associated protein 4 (CTLA-4) and programmed death ligand 1 (PD-L1) checkpoint blockade therapies. However, the landmark FDA registration trial for anti-CTLA-4 therapy (ipilimumab) revealed a complete lack of benefit of adding vaccination with gp100 peptide formulated in incomplete Freund's adjuvant (IFA). Here, using a mouse model of melanoma, we found that gp100 vaccination induced gp100-specific effector T cells (Teffs), which dominantly forced trafficking of anti-CTLA-4-induced, non-gp100-specific Teffs away from the tumor, reducing tumor control...
April 2, 2018: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29475824/characterizing-and-managing-missing-structured-data-in-electronic-health-records-data-analysis
#16
Brett K Beaulieu-Jones, Daniel R Lavage, John W Snyder, Jason H Moore, Sarah A Pendergrass, Christopher R Bauer
BACKGROUND: Missing data is a challenge for all studies; however, this is especially true for electronic health record (EHR)-based analyses. Failure to appropriately consider missing data can lead to biased results. While there has been extensive theoretical work on imputation, and many sophisticated methods are now available, it remains quite challenging for researchers to implement these methods appropriately. Here, we provide detailed procedures for when and how to conduct imputation of EHR laboratory results...
February 23, 2018: JMIR Medical Informatics
https://www.readbyqxmd.com/read/29467825/investigating-the-parameter-space-of-evolutionary-algorithms
#17
Moshe Sipper, Weixuan Fu, Karuna Ahuja, Jason H Moore
Evolutionary computation (EC) has been widely applied to biological and biomedical data. The practice of EC involves the tuning of many parameters, such as population size, generation count, selection size, and crossover and mutation rates. Through an extensive series of experiments over multiple evolutionary algorithm implementations and 25 problems we show that parameter space tends to be rife with viable parameters, at least for the problems studied herein. We discuss the implications of this finding in practice for the researcher employing EC...
2018: BioData Mining
https://www.readbyqxmd.com/read/29457381/a-multicenter-study-of-the-validity-and-reliability-of-responses-to-hand-cold-challenge-as-measured-by-laser-speckle-contrast-imaging-and-thermography-outcome-measures-for-systemic-sclerosis-related-raynaud-s-phenomenon
#18
Jack D Wilkinson, Sarah A Leggett, Elizabeth J Marjanovic, Tonia L Moore, John Allen, Marina E Anderson, Jason Britton, Maya H Buch, Francesco Del Galdo, Christopher P Denton, Graham Dinsdale, Bridgett Griffiths, Frances Hall, Kevin Howell, Audrey MacDonald, Neil J McHugh, Joanne B Manning, John D Pauling, Christopher Roberts, Jacqueline A Shipley, Ariane L Herrick, Andrea K Murray
OBJECTIVE: Reliable and objective outcome measures to facilitate clinical trials of novel treatments for systemic sclerosis (SSc)-related Raynaud's phenomenon (RP) are badly needed. Laser speckle contrast imaging (LSCI) and thermography are noninvasive measures of perfusion that have shown excellent potential. This multicenter study was undertaken to determine the reliability and validity of a hand cold challenge protocol using LSCI, standard thermography, and low-cost cell phone/mobile phone thermography (henceforth referred to as mobile thermography) in patients with SSc-related RP...
February 18, 2018: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/29378062/medication-class-enrichment-analysis-a-novel-algorithm-to-analyze-multiple-pharmacologic-exposures-simultaneously-using-electronic-health-record-data
#19
Ravy K Vajravelu, Frank I Scott, Ronac Mamtani, Hongzhe Li, Jason H Moore, James D Lewis
Objective: Observational studies analyzing multiple exposures simultaneously have been limited by difficulty distinguishing relevant results from chance associations due to poor specificity. Set-based methods have been successfully used in genomics to improve signal-to-noise ratio. We present and demonstrate medication class enrichment analysis (MCEA), a signal-to-noise enhancement algorithm for observational data inspired by set-based methods. Materials and Methods: We used The Health Improvement Network database to study medications associated with Clostridium difficile infection (CDI)...
January 25, 2018: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29377416/oncologic-outcomes-of-extended-neck-dissections-in-human-papillomavirus-related-oropharyngeal-squamous-cell-carcinoma
#20
Joseph Zenga, Patrik Pipkorn, Evan M Graboyes, Eliot J Martin, Jason T Rich, Eric J Moore, Bruce H Haughey, Ryan S Jackson
BACKGROUND: Oncologic outcomes of human papillomavirus (HPV)-related oropharyngeal squamous cell carcinoma (SCC) requiring resection of major muscular or neurovascular tissue during neck dissection for invasive nodal disease remain uncertain. METHODS: Patients with HPV-related oropharyngeal SCC requiring resection of major muscular or neurovascular tissue during their neck dissections were retrospectively identified. RESULTS: Seventy-two patients were included...
May 2018: Head & Neck
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