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https://www.readbyqxmd.com/read/29777750/post-a-framework-for-set-based-association-analysis-in-high-dimensional-data
#1
Xueyuan Cao, E Olusegun George, Mingjuan Wang, Dale B Armstrong, Cheng Cheng, Susana Raimondi, Jeffrey E Rubnitz, James R Downing, Mondira Kundu, Stanley B Pounds
Evaluating the differential expression of a set of genes belonging to a common biological process or ontology has proven to be a very useful tool for biological discovery. However, existing gene-set association methods are limited to applications that evaluate differential expression across k⩾2 treatment groups or biological categories. This limitation precludes researchers from most effectively evaluating the association with other phenotypes that may be more clinically meaningful, such as quantitative variables or censored survival time variables...
May 16, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29777596/morphological-analysis-of-pore-size-and-connectivity-in-a-thick-mixed-culture-biofilm
#2
Alex F Rosenthal, James S Griffin, Michael Wagner, Aaron I Packman, Oluwaseyi Balogun, George F Wells
Morphological parameters are commonly used to predict transport and metabolic kinetics in biofilms. Yet, quantification of biofilm morphology remains challenging due to imaging technology limitations and lack of robust analytical approaches. We present a novel set of imaging and image analysis techniques to estimate internal porosity, pore size distributions, and pore network connectivity to a depth of 1 mm at a resolution of 10 µm in a biofilm exhibiting both heterotrophic and nitrifying activity. Optical coherence tomography (OCT) scans revealed an extensive pore network with diameters as large as 110 µm directly connected to the biofilm surface and surrounding fluid...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777230/serum-biomarkers-of-inflammation-and-adiposity-in-the-labs-cohort-associations-with-metabolic-disease-and-surgical-outcomes
#3
Robert W O'Rourke, Geoffrey S Johnson, Jonathan Q Purnell, Anita P Courcoulas, Gregory F Dakin, Luis Garcia, Marcelo Hinojosa, James E Mitchell, Alfons Pomp, Walter J Pories, Konstantinos Spaniolas, David R Flum, Abdus S Wahed, Bruce M Wolfe
BACKGROUND: The utility of serum biomarkers related to inflammation and adiposity as predictors of metabolic disease prevalence and outcomes after bariatric surgery are not well-defined. METHODS: Associations between pre- and post-operative serum levels of four biomarkers (C-reactive protein (CRP), cystatin C (CC), leptin, and ghrelin) with baseline measures of adiposity and metabolic disease prevalence (asthma, diabetes, sleep apnea), and weight loss and metabolic disease remission after bariatric surgery were studied in the Longitudinal Assessment of Bariatric Surgery (LABS) cohort...
May 17, 2018: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/29776994/first-demonstration-of-olfactory-learning-and-long-term-memory-in-honey-bee-queens
#4
Zhiwen Gong, Ken Tan, James C Nieh
As the primary source of colony reproduction, social insect queens play a vital role. However, the cognitive abilities of queens are not well understood, although queen learning and memory are essential in multiple species such as honey bees, in which virgin queens must leave the nest and then successful learn to navigate back over repeated nuptial flights. Honey bee queen learning has never been previously demonstrated. We therefore tested olfactory learning in queens and workers and examined the role of DNA methylation, which plays a key role in long term memory formation...
May 18, 2018: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29775542/exercise-and-circulating-bdnf-mechanisms-of-release-and-implications-for-the-design-of-exercise-interventions
#5
Jeremy James Walsh, Michael E Tschakovsky
Engagement in regular bouts of exercise confers numerous positive effects on brain health across the lifespan. Acute bouts of exercise transiently improve cognitive function, while long-term exercise training stimulates brain plasticity, improves brain function, and helps to stave off neurological disease. The action of brain-derived neurotrophic factor (BDNF) is a candidate mechanism underlying these exercise-induced benefits and is the subject of considerable attention in the exercise-brain health literature...
May 18, 2018: Applied Physiology, Nutrition, and Metabolism, Physiologie Appliquée, Nutrition et Métabolisme
https://www.readbyqxmd.com/read/29775302/free-base-nicotine-determination-in-electronic-cigarette-liquids-by-1-h-nmr-spectroscopy
#6
Anna K Duell, James F Pankow, David H Peyton
E-liquids usually contain significant nicotine, which will exist primarily in two forms, monoprotonated and free-base the proportions are alterable through the effective pH of the medium. The fraction of nicotine in the free-base form is αfb , with 0 < αfb < 1. When dosed via aerosol, the two nicotine forms have different mechanisms and kinetics of delivery, as well as differing implications for harshness of the inhaled aerosol, so αfb is relevant regarding abuse liability. Previous attempts to determine αfb in electronic cigarette liquids and vapor have been flawed...
May 18, 2018: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/29774967/re-optimization-of-the-organocatalyzed-double-aldol-domino-process-to-a-key-enal-intermediate-and-its-application-to-the-total-synthesis-of-%C3%AE-%C3%A2-%C3%A2-prostaglandin-j%C3%A2
#7
Andrejs Pelss, Narasimhulu Gandhamsetty, James Robin Smith, Damien Mailhol, Mattia Silvi, Andrew Watson, Isabel Perez-Powell, Sébastien Prévost, Nina Schützenmeister, Peter Moore, Varinder Kumar Aggarwal
Re-investigation of the L-proline catalyzed double aldol cascade dimerization of succinaldehyde for the synthesis of a key bicyclic enal intermediate, pertinent in the field of stereoselective prostaglandin synthesis, is reported. The yield of this process has been more than doubled, from 14% to a 29% isolated yield on a multi-gram scale (32% NMR yield), through conducting a detailed study of the reaction solvent, temperature and concentration, as well as a catalyst screen. The synthetic utility of this enal intermediate has been further demonstrated through the total synthesis of Δ¹²-prostaglandin J₃, a compound with known anti-leukemic properties...
May 18, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29773510/implications-of-the-abcd-study-for-developmental-neuroscience
#8
Sarah W Feldstein Ewing, James M Bjork, Monica Luciana
The Adolescent Brain Cognitive Development Study (ABCD) will capture a breadth of multi-faceted biobehavioral, environmental, familial, and genetic longitudinal developmental open-access data from over 11,000 9-10 year olds throughout the United States of America (USA) for an envisioned ten-year span. This will subsequently represent the largest study ever attempted with this level of brain phenotypic detail. This study holds the opportunity for exciting advances in the understanding of typical adolescent neurodevelopment, discovery of neurodevelopmental underpinnings of mental illness, as well as the neurodevelopmental influences of (and on) social factors, substance use, and critically - their interaction...
May 14, 2018: Developmental Cognitive Neuroscience
https://www.readbyqxmd.com/read/29773157/genetic-etiology-for-alcohol-induced-cardiac-toxicity
#9
James S Ware, Almudena Amor-Salamanca, Upasana Tayal, Risha Govind, Isabel Serrano, Joel Salazar-Mendiguchía, Jose Manuel García-Pinilla, Domingo A Pascual-Figal, Julio Nuñez, Gonzalo Guzzo-Merello, Emiliano Gonzalez-Vioque, Alfredo Bardaji, Nicolas Manito, Miguel A López-Garrido, Laura Padron-Barthe, Elizabeth Edwards, Nicola Whiffin, Roddy Walsh, Rachel J Buchan, William Midwinter, Alicja Wilk, Sanjay Prasad, Antonis Pantazis, John Baski, Declan P O'Regan, Luis Alonso-Pulpon, Stuart A Cook, Enrique Lara-Pezzi, Paul J Barton, Pablo Garcia-Pavia
BACKGROUND: Alcoholic cardiomyopathy (ACM) is defined by a dilated and impaired left ventricle due to chronic excess alcohol consumption. It is largely unknown which factors determine cardiac toxicity on exposure to alcohol. OBJECTIVES: This study sought to evaluate the role of variation in cardiomyopathy-associated genes in the pathophysiology of ACM, and to examine the effects of alcohol intake and genotype on dilated cardiomyopathy (DCM) severity. METHODS: The authors characterized 141 ACM cases, 716 DCM cases, and 445 healthy volunteers...
May 22, 2018: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/29772916/home-oxygen-therapy-for-bronchiolitis-an-evaluation-of-the-primary-care-providers-experience-at-sea-level
#10
Erin E Dunbar, Michelle L Macy, James A Cranford, Nicole Sroufe, Marie Lozon, Marisa C Louie
Despite 90% of primary care providers at altitude reporting experience with home oxygen therapy for hypoxemic, otherwise well infants, its use at sea level is not well described. Our objective was to understand experience with home oxygen at sea level and determine potential barriers and benefits of its use. We surveyed all pediatricians and family medicine providers within a 30-mile radius of our pediatric hospital from May 2016 to December 2016. Forty-three percent of providers responded. Few (8%) had any experience with home oxygen therapy for bronchiolitis...
May 1, 2018: Clinical Pediatrics
https://www.readbyqxmd.com/read/29771685/enterotoxigenic-escherichia-coli-blood-group-a-interactions-intensify-diarrheal-severity
#11
Pardeep Kumar, F Matthew Kuhlmann, Subhra Chakroborty, A Louis Bourgeois, Jennifer Foulke-Abel, Brunda Tumala, Tim J Vickers, David A Sack, Barbara DeNearing, Clayton D Harro, W Shea Wright, Jeffrey C Gildersleeve, Matthew A Ciorba, Srikanth Santhanam, Chad K Porter, Ramiro L Gutierrez, Michael G Prouty, Mark S Riddle, Alexander Polino, Alaullah Sheikh, Mark Donowitz, James M Fleckenstein
Enterotoxigenic Escherichia coli (ETEC) infections are highly prevalent in developing countries where clinical presentations range from asymptomatic colonization to severe cholera-like illness. The molecular basis for these varied presentations, that may involve strain-specific virulence features as well as host factors, have not been elucidated. We demonstrate that when challenged with ETEC strain H10407, originally isolated from a case of cholera-like illness, blood group A human volunteers developed severe diarrhea more frequently than individuals from other blood groups...
May 17, 2018: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29770715/enasidenib-for-the-treatment-of-acute-myeloid-leukemia
#12
James Dugan, Daniel Pollyea
In August 2017 the United States Federal Drug Administration (FDA) approved enasidenib (Idhifa, Celgene/Agios) for adults with relapsed and refractory acute myelogenous leukemia (AML) with an IDH2 mutation. Enasidenib targets cells with mutant copies of isocitrate dehydrogenase-2 (IDH2), inhibiting the oncometabolite 2-hydroxyglutarte (2-HG) formed by the mutant IDH2. Areas covered: We review the studies leading to enasidenib's approval, as well as common side effects and safety issues experienced during the clinical trials...
May 17, 2018: Expert Review of Clinical Pharmacology
https://www.readbyqxmd.com/read/29770225/quality-of-life-of-irradiated-brain-tumor-survivors-treated-with-donepezil-or-placebo-results-of-the-wfu-ccop-research-base-protocol-91105
#13
Michelle J Naughton, L Douglas Case, Ann Peiffer, Michael Chan, Volker Stieber, Dennis Moore, Steven Falchuk, James Piephoff, William Edenfield, Jeffrey Giguere, Monica Loghin, Edward G Shaw, Stephen R Rapp
Background: The health-related quality of life (HRQL) and fatigue of brain cancer survivors treated with donepezil or placebo for cognitive symptoms after radiation therapy were examined. Methods: One hundred ninety-eight patients who completed >30 Gy fractionated whole or partial brain irradiation at least 6 months prior to enrollment were randomized to either placebo or donepezil (5 mg for 6 weeks followed by 10 mg for 18 weeks) in a phase 3 trial. A neurocognitive battery, the Functional Assessment of Cancer Therapy-Brain (FACT-Br) and the Functional Assessment of Chronic Illness Therapy (FACIT)-fatigue, was administered at baseline, 12 weeks, and 24 weeks...
May 2018: Neuro-oncology Practice
https://www.readbyqxmd.com/read/29769725/mxra8-is-a-receptor-for-multiple-arthritogenic-alphaviruses
#14
Rong Zhang, Arthur S Kim, Julie M Fox, Sharmila Nair, Katherine Basore, William B Klimstra, Rebecca Rimkunas, Rachel H Fong, Hueylie Lin, Subhajit Poddar, James E Crowe, Benjamin J Doranz, Daved H Fremont, Michael S Diamond
Arthritogenic alphaviruses comprise a group of enveloped RNA viruses that are transmitted to humans by mosquitoes and cause debilitating acute and chronic musculoskeletal disease 1 . The host factors required for alphavirus entry remain poorly characterized 2 . Here we use a genome-wide CRISPR-Cas9-based screen to identify the cell adhesion molecule Mxra8 as an entry mediator for multiple emerging arthritogenic alphaviruses, including chikungunya, Ross River, Mayaro and O'nyong nyong viruses. Gene editing of mouse Mxra8 or human MXRA8 resulted in reduced levels of viral infection of cells and, reciprocally, ectopic expression of these genes resulted in increased infection...
May 16, 2018: Nature
https://www.readbyqxmd.com/read/29769669/diverse-mechanisms-for-endogenous-regeneration-and-repair-in-mammalian-organs
#15
REVIEW
James M Wells, Fiona M Watt
Mammalian organs comprise an extraordinary diversity of cell and tissue types. Regenerative organs, such as the skin and gastrointestinal tract, use resident stem cells to maintain tissue function. Organs with a lower cellular turnover, such as the liver and lungs, mostly rely on proliferation of committed progenitor cells. In many organs, injury reveals the plasticity of both resident stem cells and differentiated cells. The ability of resident cells to maintain and repair organs diminishes with age, whereas, paradoxically, the risk of cancer increases...
May 2018: Nature
https://www.readbyqxmd.com/read/29768634/perceived-burden-of-ehrs-on-physicians-at-different-stages-of-their-career
#16
Saif Khairat, Gary Burke, Heather Archambault, Todd Schwartz, James Larson, Raj M Ratwani
OBJECTIVE:  The purpose of this study was to further explore the effect of EHRs on emergency department (ED) attending and resident physicians' perceived workload, satisfaction, and productivity through the completion of six EHR patient scenarios combined with workload, productivity, and satisfaction surveys. METHODS:  To examine EHR usability, we used a live observational design combined with post observation surveys conducted over 3 days, observing emergency physicians' interactions with the EHR during a 1-hour period...
April 2018: Applied Clinical Informatics
https://www.readbyqxmd.com/read/29768456/the-hidden-costs-identification-of-indirect-costs-associated-with-acute-gastrointestinal-illness-in-an-inuit-community
#17
Nia King, Rachael Vriezen, Victoria L Edge, James Ford, Michele Wood, Sherilee Harper
BACKGROUND: Acute gastrointestinal illness (AGI) incidence and per-capita healthcare expenditures are higher in some Inuit communities as compared to elsewhere in Canada. Consequently, there is a demand for strategies that will reduce the individual-level costs of AGI; this will require a comprehensive understanding of the economic costs of AGI. However, given Inuit communities' unique cultural, economic, and geographic contexts, there is a knowledge gap regarding the context-specific indirect costs of AGI borne by Inuit community members...
2018: PloS One
https://www.readbyqxmd.com/read/29768121/a-biomechanical-comparison-of-initial-sprint-acceleration-performance-and-technique-in-an-elite-athlete-with-cerebral-palsy-and-able-bodied-sprinters
#18
Ian N Bezodis, James Cowburn, Adam Brazil, Rhian Richardson, Cassie Wilson, Timothy A Exell, Gareth Irwin
Cerebral palsy is known to generally limit range of motion and force producing capability during movement. It also limits sprint performance, but the exact mechanisms underpinning this are not well known. One elite male T36 multiple-Paralympic sprint medallist (T36) and 16 well-trained able-bodied (AB) sprinters each performed 5-6 maximal sprints from starting blocks. Whole-body kinematics (250 Hz) in the block phase and first two steps, and synchronised external forces (1,000 Hz) in the first stance phase after block exit were combined to quantify lower limb joint kinetics...
May 16, 2018: Sports Biomechanics
https://www.readbyqxmd.com/read/29768000/monolayer-molybdenum-disulfide-transistors-with-single-atom-thick-gates
#19
Yibo Zhu, Yijun Li, Ghidewon Arefe, Robert A Burke, Cheng Tan, Yufeng Hao, Xiaochi Liu, Xue Liu, Won Jong Yoo, Madan Dubey, Qiao Lin, James C Hone
Two-dimensional transition metal dichalcogenides (TMDs) are unique candidates for development of next-generation electronic devices. However, the large contact resistance between metal and the monolayer TMDs have significantly limited the devices' performance. Also, integration of ultrathin high-k dielectric layer with TMD remains difficult due to the lack of dangling bonds on the surface of TMDs. We present monolayer molybdenum disulfide field effect transistors with bottom local gates consisting of monolayer graphene...
May 16, 2018: Nano Letters
https://www.readbyqxmd.com/read/29767950/different-benzodiazepines-bind-with-distinct-binding-modes-to-gaba-a-receptors
#20
Alshaimaa A Elgarf, David C B Siebert, Friederike Steudle, Angelika Draxler, Guanguan Li, Shengming Huang, James M Cook, Margot Ernst, Petra Scholze
Benzodiazepines are clinically relevant drugs, which bind to GABAA neurotransmitter receptors at the α+/γ2- interfaces and thereby enhance GABA induced chloride ion flux leading to neuronal hyperpolarization. However, the structural basis of benzodiazepine interactions with their high affinity site at GABAA receptors is controversially debated in the literature and in silico studies led to discrepant binding mode hypotheses. In the current study computational docking of diazepam into α+/γ2- homology models suggested that a chiral methyl group, which is known to promote preferred binding to α5-containing GABAA receptors (position 3 of the 7-membered diazepine ring), could possibly provide experimental evidence in favor of or against the so far proposed binding modes...
May 16, 2018: ACS Chemical Biology
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