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Jason Moore

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https://www.readbyqxmd.com/read/29333208/integrating-cadaver-needle-forces-into-a-haptic-robotic-simulator
#1
David F Pepley, Mary A Yovanoff, Katelin A Mirkin, Scarlett R Miller, David C Han, Jason Z Moore
Accurate force simulation is essential to haptic simulators for surgical training. Factors such as tissue inhomogeneity pose unique challenges for simulating needle forces. To aid in the development of haptic needle insertion simulators, a handheld force sensing syringe was created to measure the motion and forces of needle insertions. Five needle insertions were performed into the neck of a cadaver using the force sensing syringe. Based on these measurements a piecewise exponential needle force characterization, was implemented into a haptic central venous catheterization (CVC) simulator...
March 2018: Journal of Medical Devices
https://www.readbyqxmd.com/read/29316397/discovery-of-potent-and-orally-bioavailable-dihydropyrazole-gpr40-agonists
#2
Jun Shi, Zhengxiang Gu, Elizabeth Anne Jurica, Ximao Wu, Lauren E Haque, Kristin N Williams, Andres S Hernandez, Zhenqiu Hong, Qi Gao, Marta Dabros, Akin H Davulcu, Arvind Mathur, Richard A Rampulla, Arun Kumar Gupta, Ramya Jayaram, Atsu Apedo, Douglas B Moore, Heng Liu, Lori K Kunselman, Edward J Brady, Jason J Wilkes, Bradley A Zinker, Hong Cai, Yue-Zhong Shu, Qin Sun, Elizabeth A Dierks, Kimberly A Foster, Carrie Xu, Tao Wang, Reshma Panemangalore, Mary Ellen Cvijic, Chunshan Xie, Gary G Cao, Min Zhou, John Krupinski, Jean M Whaley, Jeffrey A Robl, William R Ewing, Bruce Alan Ellsworth
G protein-coupled receptor 40 (GPR40) has become an attractive target for the treatment of diabetes since it was shown clinically to promote glucose-stimulated insulin secretion. Herein, we report our efforts to develop highly selective and potent GPR40 agonists with a dual mechanism of action, promoting both glucose-dependent insulin and incretin secretion. Employing strategies to increase polarity and the ratio of sp3/sp2 character of the chemotype, we identified BMS-986118 (compound 4), which showed potent and selective GPR40 agonist activity in vitro...
January 9, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29258292/corrigendum-phylogenetic-ctdna-analysis-depicts-early-stage-lung-cancer-evolution
#3
Christopher Abbosh, Nicolai J Birkbak, Gareth A Wilson, Mariam Jamal-Hanjani, Tudor Constantin, Raheleh Salari, John Le Quesne, David A Moore, Selvaraju Veeriah, Rachel Rosenthal, Teresa Marafioti, Eser Kirkizlar, Thomas B K Watkins, Nicholas McGranahan, Sophia Ward, Luke Martinson, Joan Riley, Francesco Fraioli, Maise Al Bakir, Eva Grönroos, Francisco Zambrana, Raymondo Endozo, Wenya Linda Bi, Fiona M Fennessy, Nicole Sponer, Diana Johnson, Joanne Laycock, Seema Shafi, Justyna Czyzewska-Khan, Andrew Rowan, Tim Chambers, Nik Matthews, Samra Turajlic, Crispin Hiley, Siow Ming Lee, Martin D Forster, Tanya Ahmad, Mary Falzon, Elaine Borg, David Lawrence, Martin Hayward, Shyam Kolvekar, Nikolaos Panagiotopoulos, Sam M Janes, Ricky Thakrar, Asia Ahmed, Fiona Blackhall, Yvonne Summers, Dina Hafez, Ashwini Naik, Apratim Ganguly, Stephanie Kareht, Rajesh Shah, Leena Joseph, Anne Marie 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, Dahmane Oukrif, Ayse U Akarca, John A Hartley, Helen L Lowe, Sara Lock, Natasha Iles, Harriet Bell, Yenting Ngai, Greg Elgar, Zoltan Szallasi, Roland F Schwarz, Javier Herrero, Aengus Stewart, Sergio A Quezada, Karl S Peggs, Peter Van Loo, Caroline Dive, C Jimmy Lin, Matthew Rabinowitz, Hugo J W L Aerts, Allan Hackshaw, Jacqui A Shaw, Bernhard G Zimmermann, Charles Swanton
This corrects the article DOI: 10.1038/nature22364.
December 20, 2017: Nature
https://www.readbyqxmd.com/read/29238404/pmlb-a-large-benchmark-suite-for-machine-learning-evaluation-and-comparison
#4
Randal S Olson, William La Cava, Patryk Orzechowski, Ryan J Urbanowicz, Jason H Moore
Background: The selection, development, or comparison of machine learning methods in data mining can be a difficult task based on the target problem and goals of a particular study. Numerous publicly available real-world and simulated benchmark datasets have emerged from different sources, but their organization and adoption as standards have been inconsistent. As such, selecting and curating specific benchmarks remains an unnecessary burden on machine learning practitioners and data scientists...
2017: BioData Mining
https://www.readbyqxmd.com/read/29228144/randomized-controlled-trial-of-daily-text-messages-to-support-adherence-to-prep-in-at-risk-for-hiv-individuals-the-tapir-study
#5
David J Moore, Sonia Jain, Michael P Dubé, Eric S Daar, Xiaoying Sun, Jason Young, Katya Corado, Eric Ellorin, Joel Milam, Deborah Collins, Jill Blumenthal, Brookie M Best, Peter Anderson, Richard Haubrich, Sheldon R Morris
Background: Adherence is critical for efficacy of tenofovir disoproxil fumarate/emtricitabine as pre-exposure prophylaxis (PrEP). Methods: Between 02/2013 and 02/2016, 398 men who have sex with men and transgender women were randomized 1:1 to receive individualized Texting for Adherence Building (iTAB) or standard care (SoC) for 48 weeks. The primary endpoint was dried blood spot (DBS) tenofovir (TFV-DP) concentrations at both week 12 and week 48 (or the last on-drug visit) of >719 fmol/punch consistent with ≥4 doses per week (i...
November 24, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29227476/the-molecular-landscape-of-pediatric-acute-myeloid-leukemia-reveals-recurrent-structural-alterations-and-age-specific-mutational-interactions
#6
Hamid Bolouri, Jason E Farrar, Timothy Triche, Rhonda E Ries, Emilia L Lim, Todd A Alonzo, Yussanne Ma, Richard Moore, Andrew J Mungall, Marco A Marra, Jinghui Zhang, Xiaotu Ma, Yu Liu, Yanling Liu, Jaime M Guidry Auvil, Tanja M Davidsen, Patee Gesuwan, Leandro C Hermida, Bodour Salhia, Stephen Capone, Giridharan Ramsingh, Christian Michel Zwaan, Sanne Noort, Stephen R Piccolo, E Anders Kolb, Alan S Gamis, Malcolm A Smith, Daniela S Gerhard, Soheil Meshinchi
We present the molecular landscape of pediatric acute myeloid leukemia (AML) and characterize nearly 1,000 participants in Children's Oncology Group (COG) AML trials. The COG-National Cancer Institute (NCI) TARGET AML initiative assessed cases by whole-genome, targeted DNA, mRNA and microRNA sequencing and CpG methylation profiling. Validated DNA variants corresponded to diverse, infrequent mutations, with fewer than 40 genes mutated in >2% of cases. In contrast, somatic structural variants, including new gene fusions and focal deletions of MBNL1, ZEB2 and ELF1, were disproportionately prevalent in young individuals as compared to adults...
December 11, 2017: Nature Medicine
https://www.readbyqxmd.com/read/29218913/leveraging-putative-enhancer-promoter-interactions-to-investigate-two-way-epistasis-in-type-2-diabetes-gwas
#7
Elisabetta Manduchi, Alessandra Chesi, Molly A Hall, Struan F A Grant, Jason H Moore
We utilized evidence for enhancer-promoter interactions from functional genomics data in order to build biological filters to narrow down the search space for two-way Single Nucleotide Polymorphism (SNP) interactions in Type 2 Diabetes (T2D) Genome Wide Association Studies (GWAS). This has led us to the identification of a reproducible statistically significant SNP pair associated with T2D. As more functional genomics data are being generated that can help identify potentially interacting enhancer-promoter pairs in larger collection of tissues/cells, this approach has implications for investigation of epistasis from GWAS in general...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218909/reading-between-the-genes-computational-models-to-discover-function-from-noncoding-dna
#8
Yves A Lussier, Joanne Berghout, Francesca Vitali, Kenneth S Ramos, Maricel Kann, Jason H Moore
Noncoding DNA - once called "junk" has revealed itself to be full of function. Technology development has allowed researchers to gather genome-scale data pointing towards complex regulatory regions, expression and function of noncoding RNA genes, and conserved elements. Variation in these regions has been tied to variation in biological function and human disease. This PSB session tackles the problem of handling, analyzing and interpreting the data relating to variation in and interactions between noncoding regions through computational biology...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218905/considerations-for-automated-machine-learning-in-clinical-metabolic-profiling-altered-homocysteine-plasma-concentration-associated-with-metformin-exposure
#9
Alena Orlenko, Jason H Moore, Patryk Orzechowski, Randal S Olson, Junmei Cairns, Pedro J Caraballo, Richard M Weinshilboum, Liewei Wang, Matthew K Breitenstein
With the maturation of metabolomics science and proliferation of biobanks, clinical metabolic profiling is an increasingly opportunistic frontier for advancing translational clinical research. Automated Machine Learning (AutoML) approaches provide exciting opportunity to guide feature selection in agnostic metabolic profiling endeavors, where potentially thousands of independent data points must be evaluated. In previous research, AutoML using high-dimensional data of varying types has been demonstrably robust, outperforming traditional approaches...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218887/a-heuristic-method-for-simulating-open-data-of-arbitrary-complexity-that-can-be-used-to-compare-and-evaluate-machine-learning-methods
#10
Jason H Moore, Maksim Shestov, Peter Schmitt, Randal S Olson
A central challenge of developing and evaluating artificial intelligence and machine learning methods for regression and classification is access to data that illuminates the strengths and weaknesses of different methods. Open data plays an important role in this process by making it easy for computational researchers to easily access real data for this purpose. Genomics has in some examples taken a leading role in the open data effort starting with DNA microarrays. While real data from experimental and observational studies is necessary for developing computational methods it is not sufficient...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218881/data-driven-advice-for-applying-machine-learning-to-bioinformatics-problems
#11
Randal S Olson, William La Cava, Zairah Mustahsan, Akshay Varik, Jason H Moore
As the bioinformatics field grows, it must keep pace not only with new data but with new algorithms. Here we contribute a thorough analysis of 13 state-of-the-art, commonly used machine learning algorithms on a set of 165 publicly available classification problems in order to provide data-driven algorithm recommendations to current researchers. We present a number of statistical and visual comparisons of algorithm performance and quantify the effect of model selection and algorithm tuning for each algorithm and dataset...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218875/mapping-patient-trajectories-using-longitudinal-extraction-and-deep-learning-in-the-mimic-iii-critical-care-database
#12
Brett K Beaulieu-Jones, Patryk Orzechowski, Jason H Moore
Electronic Health Records (EHRs) contain a wealth of patient data useful to biomedical researchers. At present, both the extraction of data and methods for analyses are frequently designed to work with a single snapshot of a patient's record. Health care providers often perform and record actions in small batches over time. By extracting these care events, a sequence can be formed providing a trajectory for a patient's interactions with the health care system. These care events also offer a basic heuristic for the level of attention a patient receives from health care providers...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29215023/a-pilot-characterization-of-the-human-chronobiome
#13
Carsten Skarke, Nicholas F Lahens, Seth D Rhoades, Amy Campbell, Kyle Bittinger, Aubrey Bailey, Christian Hoffmann, Randal S Olson, Lihong Chen, Guangrui Yang, Thomas S Price, Jason H Moore, Frederic D Bushman, Casey S Greene, Gregory R Grant, Aalim M Weljie, Garret A FitzGerald
Physiological function, disease expression and drug effects vary by time-of-day. Clock disruption in mice results in cardio-metabolic, immunological and neurological dysfunction; circadian misalignment using forced desynchrony increases cardiovascular risk factors in humans. Here we integrated data from remote sensors, physiological and multi-omics analyses to assess the feasibility of detecting time dependent signals - the chronobiome - despite the "noise" attributable to the behavioral differences of free-living human volunteers...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29213332/artificial-intelligence-more-human-with-human
#14
Moshe Sipper, Jason H Moore
No abstract text is available yet for this article.
2017: BioData Mining
https://www.readbyqxmd.com/read/29208777/short-a%C3%AE-peptides-attenuate-a%C3%AE-42-toxicity-in-vivo
#15
Brenda D Moore, Jason Martin, Lorena de Mena, Jonatan Sanchez, Pedro E Cruz, Carolina Ceballos-Diaz, Thomas B Ladd, Yong Ran, Yona Levites, Thomas L Kukar, Justin J Kurian, Robert McKenna, Edward H Koo, David R Borchelt, Christopher Janus, Diego Rincon-Limas, Pedro Fernandez-Funez, Todd E Golde
Processing of amyloid-β (Aβ) precursor protein (APP) by γ-secretase produces multiple species of Aβ: Aβ40, short Aβ peptides (Aβ37-39), and longer Aβ peptides (Aβ42-43). γ-Secretase modulators, a class of Alzheimer's disease therapeutics, reduce production of the pathogenic Aβ42 but increase the relative abundance of short Aβ peptides. To evaluate the pathological relevance of these peptides, we expressed Aβ36-40 and Aβ42-43 in Drosophila melanogaster to evaluate inherent toxicity and potential modulatory effects on Aβ42 toxicity...
December 5, 2017: Journal of Experimental Medicine
https://www.readbyqxmd.com/read/29206922/pie-a-prior-knowledge-guided-integrated-likelihood-estimation-method-for-bias-reduction-in-association-studies-using-electronic-health-records-data
#16
Jing Huang, Rui Duan, Rebecca A Hubbard, Yonghui Wu, Jason H Moore, Hua Xu, Yong Chen
Objectives: This study proposes a novel Prior knowledge guided Integrated likelihood Estimation (PIE) method to correct bias in estimations of associations due to misclassification of electronic health record (EHR)-derived binary phenotypes, and evaluates the performance of the proposed method by comparing it to 2 methods in common practice. Methods: We conducted simulation studies and data analysis of real EHR-derived data on diabetes from Kaiser Permanente Washington to compare the estimation bias of associations using the proposed method, the method ignoring phenotyping errors, the maximum likelihood method with misspecified sensitivity and specificity, and the maximum likelihood method with correctly specified sensitivity and specificity (gold standard)...
December 1, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29206233/genome-wide-admixture-and-association-study-of-subclinical-atherosclerosis-in-the-women-s-interagency-hiv-study-wihs
#17
Aditi Shendre, Howard W Wiener, Marguerite R Irvin, Bradley E Aouizerat, Edgar T Overton, Jason Lazar, Chenglong Liu, Howard N Hodis, Nita A Limdi, Kathleen M Weber, Stephen J Gange, Degui Zhi, Michelle A Floris-Moore, Ighovwerha Ofotokun, Qibin Qi, David B Hanna, Robert C Kaplan, Sadeep Shrestha
Cardiovascular disease (CVD) is a major comorbidity among HIV-infected individuals. Common carotid artery intima-media thickness (cCIMT) is a valid and reliable subclinical measure of atherosclerosis and is known to predict CVD. We performed genome-wide association (GWA) and admixture analysis among 682 HIV-positive and 288 HIV-negative Black, non-Hispanic women from the Women's Interagency HIV study (WIHS) cohort using a combined and stratified analysis approach. We found some suggestive associations but none of the SNPs reached genome-wide statistical significance in our GWAS analysis...
2017: PloS One
https://www.readbyqxmd.com/read/29205451/subdermal-ultrasound-contrast-agent-injection-for-sentinel-lymph-node-identification-an-analysis-of-safety-and-contrast-agent-dose-in-healthy-volunteers
#18
Priscilla Machado, Maria Stanczak, Ji-Bin Liu, Jason N Moore, John R Eisenbrey, Laurence Needleman, Walter K Kraft, Flemming Forsberg
OBJECTIVES: Mapping of the lymphatic chain for identification of the sentinel lymph node (SLN) is an important aspect of predicting outcomes for patients with breast cancer, and it is usually performed as an intraoperative procedure using blue dye and/or radiopharmaceutical agents. Recently, the use of contrast-enhanced ultrasound (CEUS) has been proposed as an alternative imaging technique for this mapping. The objective of this study was to evaluate the use of subdermal administration of the ultrasound (US) contrast agent Sonazoid (GE Healthcare, Oslo, Norway) in terms of patient safety and to select the dose to be used for lymphatic applications in humans...
December 5, 2017: Journal of Ultrasound in Medicine: Official Journal of the American Institute of Ultrasound in Medicine
https://www.readbyqxmd.com/read/29187732/structural-basis-of-respiratory-syncytial-virus-subtype-dependent-neutralization-by-an-antibody-targeting-the-fusion-glycoprotein
#19
Daiyin Tian, Michael B Battles, Syed M Moin, Man Chen, Kayvon Modjarrad, Azad Kumar, Masaru Kanekiyo, Kevin W Graepel, Noor M Taher, Anne L Hotard, Martin L Moore, Min Zhao, Zi-Zheng Zheng, Ning-Shao Xia, Jason S McLellan, Barney S Graham
A licensed vaccine for respiratory syncytial virus (RSV) is unavailable, and passive prophylaxis with the antibody palivizumab is restricted to high-risk infants. Recently isolated antibodies 5C4 and D25 are substantially more potent than palivizumab, and a derivative of D25 is in clinical trials. Here we show that unlike D25, 5C4 preferentially neutralizes subtype A viruses. The crystal structure of 5C4 bound to the RSV fusion (F) protein reveals that the overall binding mode of 5C4 is similar to that of D25, but their angles of approach are substantially different...
November 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/29163476/induction-of-peripheral-tolerance-in-ongoing-autoimmune-inflammation-requires-interleukin-27-signaling-in-dendritic-cells
#20
Rodolfo Thomé, Jason N Moore, Elisabeth R Mari, Javad Rasouli, Daniel Hwang, Satoshi Yoshimura, Bogoljub Ciric, Guang-Xian Zhang, Abdolmohamad M Rostami
Peripheral tolerance to autoantigens is induced via suppression of self-reactive lymphocytes, stimulation of tolerogenic dendritic cells (DCs) and regulatory T (Treg) cells. Interleukin (IL)-27 induces tolerogenic DCs and Treg cells; however, it is not known whether IL-27 is important for tolerance induction. We immunized wild-type (WT) and IL-27 receptor (WSX-1) knockout mice with MOG35-55 for induction of experimental autoimmune encephalomyelitis and intravenously (i.v.) injected them with MOG35-55 after onset of disease to induce i...
2017: Frontiers in Immunology
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