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https://www.readbyqxmd.com/read/28655203/kronos-a-workflow-assembler-for-genome-analytics-and-informatics
#1
M Jafar Taghiyar, Jamie Rosner, Diljot Grewal, Bruno M Grande, Radhouane Aniba, Jasleen Grewal, Paul C Boutros, Ryan D Morin, Ali Bashashati, Sohrab P Shah
Background: The field of next generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into 'best practices' for automated analysis of NGS datasets) still requires significant programming investment and expertise. Results: We present Kronos , a software platform for facilitating the development and execution of modular, auditable and distributable bioinformatics workflows...
June 26, 2017: GigaScience
https://www.readbyqxmd.com/read/28654939/speech-versus-speaking-the-experiences-of-people-with-parkinson-s-disease-and-implications-for-intervention
#2
Kathryn Yorkston, Carolyn Baylor, Deanna Britton
Purpose: In this project, we explore the experiences of people who report speech changes associated with Parkinson's disease as they describe taking part in everyday communication situations and report impressions related to speech treatment. Method: Twenty-four community-dwelling adults with Parkinson's disease took part in face-to-face, semistructured interviews. Qualitative research methods were used to code and develop themes related to the interviews. Results: Two major themes emerged...
June 22, 2017: American Journal of Speech-language Pathology
https://www.readbyqxmd.com/read/28654930/understanding-the-inter-disciplinary-and-institutional-diversity-of-citizen-science-a-survey-of-current-practice-in-germany-and-austria
#3
Lisa Pettibone, Katrin Vohland, David Ziegler
Citizen science has become more popular in recent years, quickly taking on a variety of potentially conflicting characteristics: a way to collect massive data sets at relatively low cost, a way to break science out of the ivory tower and better engage the public, an approach to educate lay people in scientific methods. But the extent of current citizen science practice-the types of actors and scientific disciplines who take part-is still poorly understood. This article builds on recent surveys of citizen science in PLOS One by analyzing citizen science practice in Germany and Austria through the projects on two online platforms...
2017: PloS One
https://www.readbyqxmd.com/read/28654877/highlighting-the-complexities-of-a-groundwater-pilot-study-during-an-avian-influenza-outbreak-methods-lessons-learned-and-select-contaminant-results
#4
Laura E Hubbard, Dana W Kolpin, Chad L Fields, Michelle L Hladik, Luke R Iwanowicz
The highly pathogenic avian influenza (H5N2) outbreak in the Midwestern United States (US) in 2015 was historic due to the number of birds and poultry operations impacted and the corresponding economic loss to the poultry industry and was the largest animal health emergency in US history. The U.S. Geological Survey (USGS), with the assistance of several state and federal agencies, aided the response to the outbreak by developing a study to determine the extent of virus transport in the environment. The study goals were to: develop the appropriate sampling methods and protocols for measuring avian influenza virus (AIV) in groundwater, provide the first baseline data on AIV and outbreak- and poultry-related contaminant occurrence and movement into groundwater, and document climatological factors that may have affected both survival and transport of AIV to groundwater during the months of the 2015 outbreak...
June 24, 2017: Environmental Research
https://www.readbyqxmd.com/read/28654869/a-review-of-high-performance-liquid-chromatographic-mass-spectrometric-urinary-methods-for-anticancer-drug-exposure-of-health-care-workers
#5
REVIEW
Patricia I Mathias, Thomas H Connor, Clayton B'Hymer
This review describes published high performance liquid chromatography/mass spectrometry (HPLC-MS) methods for the determination of anticancer drugs in human urine as non-invasive tool for monitoring of health care worker exposure to antineoplastic and cytotoxic drugs. HPLC-MS is a sensitive and specific method for analysis of anticancer drugs and their metabolites in biological fluids. In this review, a tabular summary and overview of published HPLC-MS methods are presented, as well as future trends and limitations in this area of research...
June 19, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28654646/developing-and-validating-a-scale-to-measure-food-and-nutrition-literacy-fnlit-in-elementary-school-children-in-iran
#6
Aazam Doustmohammadian, Nasrin Omidvar, Nastaran Keshavarz-Mohammadi, Morteza Abdollahi, Maryam Amini, Hassan Eini-Zinab
BACKGROUND: Food and nutrition literacy is an emerging term which is increasingly used in policy and research. Though research in this area is growing, progression is limited by the lack of an accepted method to measure food and nutrition literacy. The aim of this study is to develop a valid and reliable questionnaire to assess food and nutrition literacy in elementary school children in the city of Tehran. METHODS: The study was conducted in three phases. To develop Food and Nutrition Literacy (FNLIT) questionnaire, a comprehensive literature review and a qualitative study were initially performed to identify food and nutrition literacy dimensions and its components...
2017: PloS One
https://www.readbyqxmd.com/read/28654639/improvement-of-atropine-on-esophagogastric-junction-observation-during-sedative-esophagogastroduodenoscopy
#7
Zhihao Chen, Lingang Liu, Jiangfeng Tu, Guangming Qin, Weiwei Su, Xiaoge Geng, Xiaojun Chen, Hongguang Wu, Wensheng Pan
BACKGROUND AND STUDY AIMS: Although sedation esophagogastroduodenoscopy (EGD) is now widely used, previous research has reported that sedation during EGD exhibits a negative effect on esophagogastric junction (EGJ) exposure. Atropine might improve EGJ exposure, as noted in clinical practice. The aim of this study was to examine whether sedation had a negative effect on EGJ observation in the Chinese population, and whether atropine had some ability to act as an antidote to this unexpected secondary effect of sedation...
2017: PloS One
https://www.readbyqxmd.com/read/28654550/promoters-and-barriers-to-implementation-of-tracheal-intubation-airway-safety-bundle-a-mixed-method-analysis
#8
Katherine Finn Davis, Natalie Napolitano, Simon Li, Hayley Buffman, Kyle Rehder, Matthew Pinto, Sholeen Nett, J Dean Jarvis, Pradip Kamat, Ronald C Sanders, David A Turner, Janice E Sullivan, Kris Bysani, Anthony Lee, Margaret Parker, Michelle Adu-Darko, John Giuliano, Katherine Biagas, Vinay Nadkarni, Akira Nishisaki
OBJECTIVES: To describe promoters and barriers to implementation of an airway safety quality improvement bundle from the perspective of interdisciplinary frontline clinicians and ICU quality improvement leaders. DESIGN: Mixed methods. SETTING: Thirteen PICUs of the National Emergency Airway Registry for Children network. INTERVENTION: Remote or on-site focus groups with interdisciplinary ICU staff. Two semistructured interviews with ICU quality improvement leaders with quantitative and qualitative data-based feedbacks...
June 24, 2017: Pediatric Critical Care Medicine
https://www.readbyqxmd.com/read/28654479/knowledge-translation-in-rehabilitation-a-shared-vision
#9
Jennifer L Moore, Keiko Shikako-Thomas, Deborah Backus
PURPOSE: Advances in rehabilitation provide the infrastructure for research and clinical data to improve care and patient outcomes. However, gaps between research and practice are prevalent. Knowledge translation (KT) aims to decrease the gap between research and its clinical use. This special communication summarizes KT-related proceedings from the 2016 IV STEP conference, describes current KT in rehabilitation science, and provides suggestions for its application in clinical care. SUMMARY OF KEY POINTS: We propose a vision for rehabilitation clinical practice and research that includes the development, adaptation, and implementation of evidence-based practice recommendations, which will contribute to a learning health care system...
July 2017: Pediatric Physical Therapy
https://www.readbyqxmd.com/read/28654262/machine-learning-consensus-scoring-improves-performance-across-targets-in-structure-based-virtual-screening
#10
Spencer S Ericksen, Haozhen Wu, Huikun Zhang, Lauren A Michael, Michael A Newton, F Michael Hoffmann, Scott A Wildman
In structure-based virtual screening, compound ranking through a consensus of scores from a variety of docking programs or scoring functions, rather than ranking by scores from a single program, provides better predictive performance and reduces target performance variability. Here we compare traditional consensus scoring methods with a novel, unsupervised gradient boosting approach. We also observed increased score variation among active ligands and developed a statistical mixture model consensus score based on combining score means and variances...
June 27, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28654231/enhanced-adhesion-of-mosquitoes-to-rough-surfaces
#11
Leila Pashazanusi, Baraka Lwoya, Shreyas Oak, Tushar Khosla, Julie N L Albert, Yu Tian, Geetha Bansal, Nirbhay Kumar, Noshir S Pesika
Insects and small animals capable of adhering reversibly to a variety of surfaces employ the unique design of the distal part of their legs. In the case of mosquitoes, their feet are composed of thousands of micro- and nanoscale protruding structures, which impart superhydrophobic properties. Previous research has shown that the superhydrophobic nature of the feet allows mosquitoes to land on water, which is necessary for their reproduction cycle. Here, we show that van der Waals interactions are the main adhesion mechanism employed by mosquitoes to adhere to various surfaces...
June 27, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28654155/incidence-of-hematologic-malignancy-and-cause-specific-mortality-in-the-women-s-health-initiative-randomized-controlled-trial-of-calcium-and-vitamin-d-supplementation
#12
Eric M Ammann, Matthew T Drake, Bjarni Haraldsson, Robert B Wallace, Karen C Johnson, Pinkal Desai, Emily M Lin, Brian K Link
BACKGROUND: Prior evidence of a possible link between vitamin D status and hematologic malignancy (HM) in humans comes from observational studies, leaving unresolved the question of whether a true causal relationship exists. METHODS: The authors performed a secondary analysis of data from the Women's Health Initiative Calcium/Vitamin D (CaD) trial, a large randomized controlled trial of CaD supplementation compared with placebo in older women. Kaplan-Meier and Cox proportional hazards survival analysis methods were used to evaluate the relationship between treatment assignment and 1) incident HM and 2) HM-specific mortality over 10 years following randomization...
June 27, 2017: Cancer
https://www.readbyqxmd.com/read/28654119/environmentally-sensitive-molecular-probes-reveal-mutations-and-epigenetic-5-methyl-cytosine-in-human-oncogenes
#13
M Taskova, M C Barducci, K Astakhova
There is currently an unmet need for reliable tools that allow for direct detection and quantification of modifications in genomic DNA. For example, in cancer research and clinical diagnostics, target DNA has to be amplified and sequenced in order to reveal mutations. For 5-methylcytosine detection, bisulfite treatment of DNA is applied for the analysis, which often leads to poor specificity and reproducibility of the results. Herein we describe a simple approach that specifically detects clinically significant modifications in the human oncogenes BRAF and KRAS...
June 27, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28654086/a-multiscale-dataset-for-understanding-complex-eco-hydrological-processes-in-a-heterogeneous-oasis-system
#14
Xin Li, Shaomin Liu, Qin Xiao, Mingguo Ma, Rui Jin, Tao Che, Weizhen Wang, Xiaoli Hu, Ziwei Xu, Jianguang Wen, Liangxu Wang
We introduce a multiscale dataset obtained from Heihe Watershed Allied Telemetry Experimental Research (HiWATER) in an oasis-desert area in 2012. Upscaling of eco-hydrological processes on a heterogeneous surface is a grand challenge. Progress in this field is hindered by the poor availability of multiscale observations. HiWATER is an experiment designed to address this challenge through instrumentation on hierarchically nested scales to obtain multiscale and multidisciplinary data. The HiWATER observation system consists of a flux observation matrix of eddy covariance towers, large aperture scintillometers, and automatic meteorological stations; an eco-hydrological sensor network of soil moisture and leaf area index; hyper-resolution airborne remote sensing using LiDAR, imaging spectrometer, multi-angle thermal imager, and L-band microwave radiometer; and synchronical ground measurements of vegetation dynamics, and photosynthesis processes...
June 27, 2017: Scientific Data
https://www.readbyqxmd.com/read/28654076/a-method-to-test-the-efficacy-of-handwashing-for-the-removal-of-emerging-infectious-pathogens
#15
Marlene K Wolfe, Daniele S Lantagne
Handwashing is widely recommended to prevent infectious disease transmission. However, little comparable evidence exists on the efficacy of handwashing methods in general. Additionally, little evidence exists comparing handwashing methods to determine which are most efficacious at removing infectious pathogens. Research is needed to provide evidence for the different approaches to handwashing that may be employed during infectious disease outbreaks. Here, a laboratory method to assess the efficacy of handwashing methods at removing microorganisms from hands and their persistence in rinse water is described...
June 7, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28654069/optimized-protocol-for-the-extraction-of-proteins-from-the-human-mitral-valve
#16
Cristina Banfi, Anna Guarino, Maura Brioschi, Stefania Ghilardi, Valeria Mastrullo, Elena Tremoli, Gianluca Polvani
Analysis of the cellular proteome can help to elucidate the molecular mechanisms underlying diseases due to the development of technologies that permit the large-scale identification and quantification of the proteins present in complex biological systems.The knowledge gained from a proteomic approach can potentially lead to a better understanding of the pathogenic mechanisms underlying diseases, allowing for the identification of novel diagnostic and prognostic disease markers, and, hopefully, of therapeutic targets...
June 14, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28654037/non-invasive-assessments-of-subjective-and-objective-recovery-characteristics-following-an-exhaustive-jump-protocol
#17
Erich Hohenauer, Peter Clarys, Jean-Pierre Baeyens, Ron Clijsen
Fast recovery after strenuous exercise is important in sports and is often studied via cryotherapy applications. Cryotherapy has a significant vasoconstrictive effect, which seems to be the leading factor in its effectiveness. The resulting enhanced recovery can be measured by using both objective and subjective parameters. Two commonly measured subjective characteristics of recovery are delayed-onset muscle soreness (DOMS) and ratings of perceived exertion (RPE). Two important objective recovery characteristics are countermovement jump (CMJ) performance and peak power output (PPO)...
June 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28654036/in-ovo-electroporation-in-the-chicken-auditory-brainstem
#18
Ting Lu, Ariel Loren Cohen, Jason Tait Sanchez
Electroporation is a method that introduces genes of interest into biologically relevant organisms like the chicken embryo. It is long established that the chicken embryo is an effective research model for studying basic biological functions of auditory system development. More recently, the chicken embryo has become particularly valuable in studying gene expression, regulation and function associated with hearing. In ovo electroporation can be used to target auditory brainstem regions responsible for highly specialized auditory functions...
June 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28653973/research-on-a-novel-exciting-method-for-a-sandwich-transducer-operating-in-longitudinal-bending-hybrid-modes
#19
Yingxiang Liu, Qiangqiang Shen, Shengjun Shi, Jie Deng, Weishan Chen, Liang Wang
A novel exciting method for a sandwich type piezoelectric transducer operating in longitudinal-bending hybrid vibration modes is proposed and discussed, in which the piezoelectric elements for the excitations of the longitudinal and bending vibrations share the same axial location, but correspond to different partitions. Whole-piece type piezoelectric plates with three separated partitions are used, in which the center partitions generate the first longitudinal vibration, while the upper and lower partitions produce the second bending vibration...
June 27, 2017: Sensors
https://www.readbyqxmd.com/read/28653921/conservation-of-indigenous-knowledge-of-medicinal-plants-of-western-himalayan-region-rawalakot-azad-kashmir-pakistan
#20
Sajjad Hussain, Ghulam Murtaza, Ansar Mehmood, Rizwana Aleem Qureshi
The aim of present was to document indigenous knowledge of medicinal plants traditionally used by inhabitants of Rawalakot Azad Kashmir and to screen selected medicinal plants for their antibacterial potential. Several field surveys were conducted to document indigenous knowledge of medicinal plants through interviews from local inhabitants during 2010-2013. During the study, 58 plant species, belonging to 37 families, were identified and their medicinal uses were recorded. Ethnobotanical data indicates that inhabitants of Rawalakot use medicinal plant mainly for the treatment of stomach, liver and sexual disorders...
May 2017: Pakistan Journal of Pharmaceutical Sciences
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