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Jason Moore

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https://www.readbyqxmd.com/read/29746157/a-probabilistic-and-multi-objective-analysis-of-lexicase-selection-and-%C3%AE%C2%B5-lexicase-selection
#1
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/29738429/body-weight-misperception-and-its-association-with-unhealthy-eating-behaviors-among-adolescents-in-china
#2
Hanyi Yan, Yingru Wu, Theresa Oniffrey, Jason Brinkley, Rui Zhang, Xinge Zhang, Yueqiao Wang, Guoxun Chen, Rui Li, Justin B Moore
This study aims to examine associations between body weight misperception and eating behaviors among Chinese adolescents. Students ( N = 2641) from a middle school and a high school in Wuhan, China participated in a cross-sectional study in May 2016. A questionnaire based on the World Health Organization’s Global School-Based Student Health Survey was employed to assess responses. Self-reported data, including weight, height, body weight perception, and eating habits, were collected. Body Mass Index (BMI) for age z-score was calculated from self-reported height and weight using WHO AnthroPlus...
May 8, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29717215/dnap-a-pipeline-for-dna-seq-data-analysis
#3
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
#4
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
#5
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/29710074/association-of-cannabis-with-cognitive-functioning-in-adolescents-and-young-adults-a-systematic-review-and-meta-analysis
#6
J Cobb Scott, Samantha T Slomiak, Jason D Jones, Adon F G Rosen, Tyler M Moore, Ruben C Gur
Importance: Substantial shifts in perception and policy regarding cannabis have recently occurred, with use of cannabis increasing while its perceived harm decreases. One possible risk of increased cannabis use is poorer cognitive functioning, especially in youth. Objective: To provide the first quantitative synthesis of the literature examining cannabis and cognitive functioning in adolescents and young adults (with a mean age of 26 years and younger). Data Sources: PubMed, PsycInfo, Academic Search Premier, Scopus, and bibliographies of relevant reviews were searched for peer-reviewed, English-language studies from the date the databases began through May 2017...
April 18, 2018: JAMA Psychiatry
https://www.readbyqxmd.com/read/29708428/interpathologist-diagnostic-agreement-for-non-small-cell-lung-carcinomas-using-current-and-recent-classifications
#7
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
#8
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/29686108/-rna-polymerase-ii-transcription-attenuation-at-the-yeast-dna-repair-gene-def1-involves-sen1-dependent-and-polyadenylation-site-dependent-termination
#9
Courtney Whalen, Christine Tuohy, Thomas Tallo, James W Kaufman, Claire Moore, Jason N Kuehner
Termination of RNA Polymerase II (Pol II) activity serves a vital cellular function by separating ubiquitous transcription units and influencing RNA fate and function. In the yeast Saccharomyces cerevisiae , Pol II termination is carried out by cleavage and polyadenylation factor (CPF-CF) and Nrd1-Nab3-Sen1 (NNS) complexes, which operate primarily at mRNA and non-coding RNA genes, respectively. Premature Pol II termination (attenuation) contributes to gene regulation, but there is limited knowledge of its prevalence and biological significance...
April 23, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29666181/accuracy-of-image-guided-percutaneous-injection-into-a-phantom-spinal-cord-utilizing-flat-panel-detector-ct-with-mr-fusion-and-integrated-navigational-software
#10
Jason F Talbott, Daniel L Cooke, Marc C Mabray, Paul S Larson, Matthew R Amans, Steven W Hetts, Mark W Wilson, Terilyn Moore, Ernesto A Salegio
PURPOSE: To evaluate the accuracy of percutaneous fluoroscopic injection into the spinal cord of a spine phantom utilizing integrated navigational guidance from fused flat panel detector CT (FDCT) and MR datasets. Conventional and convection-enhanced delivery (CED) techniques were evaluated. MATERIALS AND METHODS: FDCT and MR datasets of a swine thoracic spine phantom were co-registered using an integrated guidance system and surface to spinal cord target trajectory planning was performed on the fused images...
April 17, 2018: Journal of Neurointerventional Surgery
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/29620705/building-ultrasound-phantoms-with-modified-polyvinyl-chloride-a-comparison-of-needle-insertion-forces-and-sonographic-appearance-with-commercial-and-traditional-simulation-materials
#12
David Frederick Pepley, Cheyenne Cassel Sonntag, Rohan Sunil Prabhu, Mary Alice Yovanoff, David C Han, Scarlett Rae Miller, Jason Zachary Moore
INTRODUCTION: Training using ultrasound phantoms allows for safe introduction to clinical skills and is associated with improved in-hospital performance. Many materials have been used to simulate human tissue in phantoms including commercial manikins, agar, gelatin, and Ballistics Gel; however, phantom tissues could be improved to provide higher-fidelity ultrasound images or tactile sensation. This article describes a novel phantom tissue mixture of a modified polyvinyl chloride (PVC) polymer, mineral oil, and chalk powder and evaluates needle cutting and ultrasonic properties of the modified PVC polymer mixture compared with a variety of phantom tissues...
April 3, 2018: Simulation in Healthcare: Journal of the Society for Simulation in Healthcare
https://www.readbyqxmd.com/read/29600991/response-to-unexpected-mutations-after-crispr-cas9-editing-in-vivo
#13
Lauryl M J Nutter, Jason D Heaney, K C Kent Lloyd, Stephen A Murray, John R Seavitt, William C Skarnes, Lydia Teboul, Steve D M Brown, Mark Moore
No abstract text is available yet for this article.
March 30, 2018: Nature Methods
https://www.readbyqxmd.com/read/29596416/eleven-quick-tips-for-architecting-biomedical-informatics-workflows-with-cloud-computing
#14
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/29574019/investigating-the-effect-of-simulator-functional-fidelity-and-personalized-feedback-on-central-venous-catheterization-training
#15
Mary A Yovanoff, Hong-En Chen, David F Pepley, Katelin A Mirkin, David C Han, Jason Z Moore, Scarlett R Miller
OBJECTIVE: To compare the effect of simulator functional fidelity (manikin vs a Dynamic Haptic Robotic Trainer [DHRT]) and personalized feedback on surgical resident self-efficacy and self-ratings of performance during ultrasound-guided internal jugular central venous catheterization (IJ CVC) training. In addition, we seek to explore how self-ratings of performance compare to objective performance scores generated by the DHRT system. DESIGN: Participants were randomly assigned to either manikin or DHRT IJ CVC training over a 6-month period...
March 21, 2018: Journal of Surgical Education
https://www.readbyqxmd.com/read/29559880/acute-calcific-tendonitis-of-the-longus-colli
#16
Blake S Raggio, Samuel C Ficenec, Jason Pou, Brian Moore
Background: Acute calcific tendonitis of the longus colli (ACTLC) is an aseptic inflammatory response to deposition of calcium in the longus colli muscle tendons. Although reports in the literature are scarce, ACTLC likely represents an underreported disease process that routinely goes misdiagnosed. We report a case of ACTLC and provide a brief review of the literature. Case Report: A 45-year-old otherwise healthy female presented with a 3-day history of progressive neck pain, decreased neck mobility, and odynophagia...
2018: Ochsner Journal
https://www.readbyqxmd.com/read/29559870/the-submental-island-flap-is-a-viable-reconstructive-option-for-a-variety-of-head-and-neck-ablative-defects
#17
Blair M Barton, Charles A Riley, Jason D Pou, Christian P Hasney, Brian A Moore
Background: The submental island flap (SIF) is a pedicled flap based upon the submental artery and vein. Its utility in reconstruction following ablative head and neck procedures has been applied to various subsites including skin, lip, buccal mucosa, retromolar trigone, parotidectomy defects, and tongue. We review our experience using the SIF for reconstruction following tumor ablation. Methods: This prospective case series with medical record review includes consecutive patients undergoing SIF reconstruction following ablative surgery for malignancy at a single tertiary care facility between November 2014 and November 2016...
2018: Ochsner Journal
https://www.readbyqxmd.com/read/29559244/role-of-disc-area-and-trabecular-bone-density-on-lumbar-spinal-column-fracture-risk-curves-under-vertical-impact
#18
Narayan Yoganandan, Jason Moore, Frank A Pintar, Anjishnu Banerjee, Nicholas DeVogel, JiangYue Zhang
While studies have been conducted using human cadaver lumbar spines to understand injury biomechanics in terms of stability/energy to fracture, and physiological responses under pure-moment/follower loads, data are sparse for inferior-to-superior impacts. Injuries occur under this mode from underbody blasts. OBJECTIVES: determine role of age, disc area, and trabecular bone density on tolerances/risk curves under vertical loading from a controlled group of specimens. T12-S1 columns were obtained, pretest X-rays and CTs taken, load cells attached to both ends, impacts applied at S1-end using custom vertical accelerator device, and posttest X-ray, CT, and dissections done...
March 2, 2018: Journal of Biomechanics
https://www.readbyqxmd.com/read/29538381/taxonomy-based-on-science-is-necessary-for-global-conservation
#19
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
#20
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
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