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https://www.readbyqxmd.com/read/28545397/jed-a-java-essential-dynamics-program-for-comparative-analysis-of-protein-trajectories
#1
Charles C David, Ettayapuram Ramaprasad Azhagiya Singam, Donald J Jacobs
BACKGROUND: Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two common approaches to determine PCA modes (eigenvectors) and their eigenvalues. Protein dynamics can be characterized in terms of Cartesian coordinates or internal distance pairs. In understanding protein dynamics, a comparison of trajectories taken from a set of proteins for similarity assessment provides insight into conserved mechanisms...
May 25, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28544279/controlled-clinical-trial-exploring-the-impact-of-a-brief-intervention-for-prevention-of-falls-in-an-emergency-department
#2
Kristie J Harper, Annette D Barton, Glenn Arendts, Deborah G Edwards, Antonio C Petta, Antonio Celenza
OBJECTIVE: To establish the effectiveness of a brief intervention to prevent falls in older patients presenting to the ED post-discharge. METHODS: The present study is a prospective single-centre, quasi-randomised controlled clinical trial of a brief targeted educational intervention to prevent falls. The intervention group received brief scripted education and were advised of their percentage probability of falling in the next 6 months. The key message was to reinforce the importance of falls prevention strategies and the seriousness of falls...
May 23, 2017: Emergency Medicine Australasia: EMA
https://www.readbyqxmd.com/read/28544058/beyond-differences-in-means-robust-graphical-methods-to-compare-two-groups-in-neuroscience
#3
Guillaume A Rousselet, Cyril R Pernet, Rand R Wilcox
If many changes are necessary to improve the quality of neuroscience research, one relatively simple step could have great pay-offs: to promote the adoption of detailed graphical methods, combined with robust inferential statistics. Here we illustrate how such methods can lead to a much more detailed understanding of group differences than bar graphs and t-tests on means. To complement the neuroscientist's toolbox, we present two powerful tools that can help us understand how groups of observations differ: the shift function and the difference asymmetry function...
May 24, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/28542514/panweb-a-web-interface-for-pan-genomic-analysis
#4
Yan Pantoja, Kenny Pinheiro, Allan Veras, Fabrício Araújo, Ailton Lopes de Sousa, Luis Carlos Guimarães, Artur Silva, Rommel T J Ramos
With increased production of genomic data since the advent of next-generation sequencing (NGS), there has been a need to develop new bioinformatics tools and areas, such as comparative genomics. In comparative genomics, the genetic material of an organism is directly compared to that of another organism to better understand biological species. Moreover, the exponentially growing number of deposited prokaryote genomes has enabled the investigation of several genomic characteristics that are intrinsic to certain species...
2017: PloS One
https://www.readbyqxmd.com/read/28542180/jupyter-and-galaxy-easing-entry-barriers-into-complex-data-analyses-for-biomedical-researchers
#5
Björn A Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko
What does it take to convert a heap of sequencing data into a publishable result? First, common tools are employed to reduce primary data (sequencing reads) to a form suitable for further analyses (i.e., the list of variable sites). The subsequent exploratory stage is much more ad hoc and requires the development of custom scripts and pipelines, making it problematic for biomedical researchers. Here, we describe a hybrid platform combining common analysis pathways with the ability to explore data interactively...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28541034/microfluidic-capillaric-circuit-for-rapid-and-facile-bacteria-detection
#6
Ayokunle Oluwafemi Olanrewaju, Andy Ng, Philippe Decorwin-Martin, Alessandra Robillard, David Juncker
Urinary tract infections (UTI) are one of the most common bacterial infections and would greatly benefit from a rapid point-of-care diagnostic test. Although significant progress has been made in developing microfluidic systems for nucleic acid and whole bacteria immunoassay tests, their practical application is limited by complex protocols, bulky peripherals, and slow operation. Here we present a microfluidic capillaric circuit (CC) optimized for rapid and automated detection of bacteria in urine. Molds for CCs were constructed using previously-established design rules, then 3D-printed and replicated into poly(dimethylsiloxane)...
May 25, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28540623/qsp-toolbox-computational-implementation-of-integrated-workflow-components-for-deploying-multi-scale-mechanistic-models
#7
Yougan Cheng, Craig J Thalhauser, Shepard Smithline, Jyotsna Pagidala, Marko Miladinov, Heather E Vezina, Manish Gupta, Tarek A Leil, Brian J Schmidt
Quantitative systems pharmacology (QSP) modeling has become increasingly important in pharmaceutical research and development, and is a powerful tool to gain mechanistic insights into the complex dynamics of biological systems in response to drug treatment. However, even once a suitable mathematical framework to describe the pathophysiology and mechanisms of interest is established, final model calibration and the exploration of variability can be challenging and time consuming. QSP models are often formulated as multi-scale, multi-compartment nonlinear systems of ordinary differential equations...
May 24, 2017: AAPS Journal
https://www.readbyqxmd.com/read/28536470/a-temporal-banding-approach-for-consistent-taxonomic-ranking-above-the-species-level
#8
Ekaphan Kraichak, Ana Crespo, Pradeep K Divakar, Steven D Leavitt, H Thorsten Lumbsch
Comparable taxonomic ranks within clades can facilitate more consistent classifications and objective comparisons among taxa. Here we use a temporal approach to identify taxonomic ranks. This is an extension of the temporal banding approach including a Temporal Error Score that finds an objective cut-off for each taxonomic rank using information for the current classification. We illustrate this method using a data set of the lichenized fungal family Parmeliaceae. To assess its performance, we simulated the effect of taxon sampling and compared our method with the other temporal banding method...
May 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28534567/intrinsic-ferromagnetism-and-quantum-anomalous-hall-effect-in-a-cobr2-monolayer
#9
Peng Chen, Jin-Yu Zou, Bang-Gui Liu
The electronic, magnetic, and topological properties of a CoBr2 monolayer are studied in the framework of density-functional theory (DFT) combined with tight-binding (TB) modeling in terms of the Wannier basis. Our DFT investigation and Monte Carlo simulation show that there exists intrinsic two-dimensional ferromagnetism in the CoBr2 monolayer, thanks to the large out-of-plane magnetocrystalline anisotropic energy. Our further study indicates that the spin-orbit coupling makes it become a topologically nontrivial insulator with a quantum anomalous Hall effect and topological Chern number [script C] = 4 and its edge states can be manipulated by changing the width of its nanoribbons and applying strains...
May 23, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28533200/beliefs-about-prescribed-medication-among-older-patients-with-polypharmacy-a-mixed-methods-study-in-primary-care
#10
Barbara Clyne, Janine A Cooper, Fiona Boland, Carmel M Hughes, Tom Fahey, Susan M Smith
BACKGROUND: Polypharmacy (≥5 medications) is common in older patients and is associated with adverse outcomes. Patients' beliefs about medication can influence their expectations for medication, adherence, and willingness to deprescribe. Few studies have examined beliefs about prescribed medication among older patients with polypharmacy in primary care. AIM: To explore medication-related beliefs in older patients with polypharmacy and factors that might influence beliefs...
May 22, 2017: British Journal of General Practice: the Journal of the Royal College of General Practitioners
https://www.readbyqxmd.com/read/28533102/real-time-electronic-dashboard-technology-and-its-use-to-improve-pediatric-radiology-workflow
#11
REVIEW
Randheer Shailam, Ariel Botwin, Markus Stout, Michael S Gee
The purpose of our study was to create a real-time electronic dashboard in the pediatric radiology reading room providing a visual display of updated information regarding scheduled and in-progress radiology examinations that could help radiologists to improve clinical workflow and efficiency. To accomplish this, a script was set up to automatically send real-time HL7 messages from the radiology information system (Epic Systems, Verona, WI) to an Iguana Interface engine, with relevant data regarding examinations stored in an SQL Server database for visual display on the dashboard...
March 19, 2017: Current Problems in Diagnostic Radiology
https://www.readbyqxmd.com/read/28526976/how-to-achieve-patient-centered-testing-role-of-the-protocol-nurse
#12
Patricia N Salimi, Joelyn B Niggel, Friederike K Keating
INTRODUCTION: Patient-centered cardiac testing is predicated on choosing the right test for the right patient. We studied the effects of changing from script-driven scheduling to nurse-driven protocoling of stress tests. METHODS AND RESULTS: A protocol nurse reviewed records before scheduling and communicated with patients and ordering providers if needed. We found that instituting nurse protocolling of all non-imaging (ETT) and nuclear (MPI) stress tests (N = 3071) resulted in protocol changes in 37% of our patients, and reduced the proportion of tests that could not be performed as scheduled by 56% and cancelations by 71% (P < 0...
May 19, 2017: Journal of Nuclear Cardiology: Official Publication of the American Society of Nuclear Cardiology
https://www.readbyqxmd.com/read/28526931/reduced-amygdala-reactivity-and-impaired-working-memory-during-dissociation-in-borderline-personality-disorder
#13
Annegret Krause-Utz, Dorina Winter, Friederike Schriner, Chui-De Chiu, Stefanie Lis, Philip Spinhoven, Martin Bohus, Christian Schmahl, Bernet M Elzinga
Affective hyper-reactivity and impaired cognitive control of emotional material are core features of borderline personality disorder (BPD). A high percentage of individuals with BPD experience stress-related dissociation, including emotional numbing and memory disruptions. So far little is known about how dissociation influences the neural processing of emotional material in the context of a working memory task in BPD. We aimed to investigate whole-brain activity and amygdala functional connectivity (FC) during an Emotional Working Memory Task (EWMT) after dissociation induction in un-medicated BPD patients compared to healthy controls (HC)...
May 19, 2017: European Archives of Psychiatry and Clinical Neuroscience
https://www.readbyqxmd.com/read/28526918/effect-of-problem-and-scripting-based-learning-on-spine-surgical-trainees-learning-outcomes
#14
Lin Cong, Qi Yan, Chenjing Sun, Yue Zhu, Guanjun Tu
PURPOSE: To assess the impact of problem and scripting-based learning (PSBL) on spine surgical trainees' learning outcomes. METHODS: 30 spine surgery postgraduate-year-1 residents (PGY-1s) from the First Hospital of China Medical University were randomly divided into two groups. The first group studied spine surgical skills and developed individual judgment under a conventional didactic model, whereas the PSBL group used PBL and Scripted model. A feedback questionnaire and the satisfaction of residents were evaluated by the first assistant surgeon immediately following each procedure...
May 19, 2017: European Spine Journal
https://www.readbyqxmd.com/read/28526252/determinants-of-sleep-behavior-in-adolescents-a-pilot-study
#15
Reut Gruber, Gail Somerville, Soukaina Paquin, Johanne Boursier
PURPOSE: To identify determinants of sleep behavior in adolescents of middle to high socioeconomic status. METHODS: Eighteen students (9 boys, 9 girls) with a mean age of 14.9±1.5years were interviewed using a standardized script inspired by the theory of planned behavior. Interviews were audio-recorded and anonymously transcribed verbatim. In addition, participants completed a survey assessing demographic and health characteristics and their sleep duration was measured using actigraphy...
June 2017: Sleep Health
https://www.readbyqxmd.com/read/28526219/cardiorespiratory-fitness-and-muscular-strength-as-mediators-of-the-influence-of-fatness-on-academic-achievement
#16
Antonio García-Hermoso, Irene Esteban-Cornejo, Jordi Olloquequi, Robinson Ramírez-Vélez
OBJECTIVE: To examine the combined association of fatness and physical fitness components (cardiorespiratory fitness [CRF] and muscular strength) with academic achievement, and to determine whether CRF and muscular strength are mediators of the association between fatness and academic achievement in a nationally representative sample of adolescents from Chile. STUDY DESIGN: Data were obtained for a sample of 36 870 adolescents (mean age, 13.8 years; 55.2% boys) from the Chilean System for the Assessment of Educational Quality test for eighth grade in 2011, 2013, and 2014...
May 16, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28525607/rna-moip-prediction-of-rna-secondary-structure-and-local-3d-motifs-from-sequence-data
#17
Jason Yao, Vladimir Reinharz, François Major, Jérôme Waldisphül
RNA structures are hierarchically organized. The secondary structure is articulated around sophisticated local three-dimensional (3D) motifs shaping the full 3D architecture of the molecule. Recent contributions have identified and organized recurrent local 3D motifs, but applications of this knowledge for predictive purposes is still in its infancy. We recently developed a computational framework, named RNA-MoIP, to reconcile RNA secondary structure and local 3D motif information available in databases. In this paper, we introduce a web service using our software for predicting RNA hybrid 2D-3D structures from sequence data only...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520987/proteosign-an-end-user-online-differential-proteomics-statistical-analysis-platform
#18
Georgios Efstathiou, Andreas N Antonakis, Georgios A Pavlopoulos, Theodosios Theodosiou, Peter Divanach, David C Trudgian, Benjamin Thomas, Nikolas Papanikolaou, Michalis Aivaliotis, Oreste Acuto, Ioannis Iliopoulos
Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520726/losing-a-jewel-rapid-declines-in-myanmar-s-intact-forests-from-2002-2014
#19
Tejas Bhagwat, Andrea Hess, Ned Horning, Thiri Khaing, Zaw Min Thein, Kyaw Moe Aung, Kyaw Htet Aung, Paing Phyo, Ye Lin Tun, Aung Htat Oo, Anthony Neil, Win Myo Thu, Melissa Songer, Katherine LaJeunesse Connette, Asja Bernd, Qiongyu Huang, Grant Connette, Peter Leimgruber
New and rapid political and economic changes in Myanmar are increasing the pressures on the country's forests. Yet, little is known about the past and current condition of these forests and how fast they are declining. We mapped forest cover in Myanmar through a consortium of international organizations and environmental non-governmental groups, using freely-available public domain data and open source software tools. We used Landsat satellite imagery to assess the condition and spatial distribution of Myanmar's intact and degraded forests with special focus on changes in intact forest between 2002 and 2014...
2017: PloS One
https://www.readbyqxmd.com/read/28511135/solubility-of-organic-compounds-in-octanol-improved-predictions-based-on-the-geometrical-fragment-approach
#20
Didier Mathieu
Two new models are introduced to predict the solubility of chemicals in octanol (Soct), taking advantage of the extensive character of log(Soct) through a decomposition of molecules into so-called geometrical fragments (GF). They are extensively validated and their compliance with regulatory requirements is demonstrated. The first model requires just a molecular formula as input. Despite an extreme simplicity, it performs as well as an advanced random forest model involving 86 descriptors, with a root mean square error (RMSE) of 0...
May 10, 2017: Chemosphere
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