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https://www.readbyqxmd.com/read/28636905/a-kepler-workflow-tool-for-reproducible-amber-gpu-molecular-dynamics
#1
Shweta Purawat, Pek U Ieong, Robert D Malmstrom, Garrett J Chan, Alan K Yeung, Ross C Walker, Ilkay Altintas, Rommie E Amaro
With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636386/msviz-a-graphical-software-tool-for-in-depth-manual-validation-and-quantitation-of-post-translational-modifications
#2
Trinidad Martin Campos, Roman Mylonas, Alexandre Masselot, Patrice Waridel, Tanja Petricevic, Ioannis Xenarios, Manfredo Quadroni
Mass spectrometry (MS) has become the tool of choice for the large scale identification and quantitation of proteins and their post-translational modifications (PTMs). This development has been enabled by powerful software packages for the automated analysis of MS data. While data on PTM's of thousands of proteins can nowadays be readily obtained, fully deciphering the complexity and combinatorics of modification patterns even on a single protein often remains challenging. Moreover, functional investigation of PTMs on a protein of interest requires validation of the localization and the accurate quantitation of its changes across several conditions, tasks that often still require human evaluation...
June 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28633194/moving-forward-in-circles-challenges-and-opportunities-in-modelling-population-cycles
#3
REVIEW
Frédéric Barraquand, Stilianos Louca, Karen C Abbott, Christina A Cobbold, Flora Cordoleani, Donald L DeAngelis, Bret D Elderd, Jeremy W Fox, Priscilla Greenwood, Frank M Hilker, Dennis L Murray, Christopher R Stieha, Rachel A Taylor, Kelsey Vitense, Gail S K Wolkowicz, Rebecca C Tyson
Population cycling is a widespread phenomenon, observed across a multitude of taxa in both laboratory and natural conditions. Historically, the theory associated with population cycles was tightly linked to pairwise consumer-resource interactions and studied via deterministic models, but current empirical and theoretical research reveals a much richer basis for ecological cycles. Stochasticity and seasonality can modulate or create cyclic behaviour in non-intuitive ways, the high-dimensionality in ecological systems can profoundly influence cycling, and so can demographic structure and eco-evolutionary dynamics...
June 20, 2017: Ecology Letters
https://www.readbyqxmd.com/read/28631977/a-profile-based-framework-for-factorial-similarity-and-the-congruence-coefficient
#4
Anselma G Hartley, R Michael Furr
We present a novel profile-based framework for understanding factorial similarity in the context of exploratory factor analysis in general, and for understanding the congruence coefficient (a commonly used index of factor similarity) specifically. First, we introduce the profile-based framework articulating factorial similarity in terms of 3 intuitive components: general saturation similarity, differential saturation similarity, and configural similarity. We then articulate the congruence coefficient in terms of these components, along with 2 additional profile-based components, and we explain how these components resolve ambiguities that can be-and are-found when using the congruence coefficient...
March 2, 2017: Journal of Personality Assessment
https://www.readbyqxmd.com/read/28631297/an-augmented-reality-tool-for-learning-spatial-anatomy-on-mobile-devices
#5
Nishant Jain, Patricia Youngblood, Matthew Hasel, Sakti Srivastava
INTRODUCTION: Augmented Realty (AR) offers a novel method of blending virtual and real anatomy for intuitive spatial learning. Our first aim in the study was to create a prototype AR tool for mobile devices. Our second aim was to complete a technical evaluation of our prototype AR tool focused on measuring the system's ability to accurately render digital content in the real world. MATERIALS AND METHODS: We imported Computed Tomography (CT) data derived virtual surface models into a 3D Unity engine environment and implemented an AR algorithm to display these on mobile devices...
June 20, 2017: Clinical Anatomy
https://www.readbyqxmd.com/read/28630888/gillespy-a-python-package-for-stochastic-model-building-and-simulation
#6
John H Abel, Brian Drawert, Andreas Hellander, Linda R Petzold
GillesPy is an open-source Python package for model construction and simulation of stochastic biochemical systems. GillesPy consists of a Python framework for model building and an interface to the StochKit2 suite of efficient simulation algorithms based on the Gillespie stochastic simulation algorithms (SSA). To enable intuitive model construction and seamless integration into the scientific Python stack, we present an easy to understand, action-oriented programming interface. Here, we describe the components of this package and provide a detailed example relevant to the computational biology community...
September 2016: IEEE Life Sciences Letters
https://www.readbyqxmd.com/read/28630564/cathrob-a-highly-compact-and-versatile-remote-catheter-navigation-system
#7
Laura Cercenelli, Barbara Bortolani, Emanuela Marcelli
Several remote catheter navigation systems have been developed and are now commercially available. However, these systems typically require specialized catheters or equipment, as well as time-consuming operations for the system set-up. In this paper, we present CathROB, a highly compact and versatile robotic system for remote navigation of standard tip-steerable electrophysiology (EP) catheters. Key features of CathROB include an extremely compact design that minimizes encumbrance and time for system set-up in a standard cath lab, a force-sensing mechanism, an intuitive command interface, and functions for automatic catheter navigation and repositioning...
2017: Applied Bionics and Biomechanics
https://www.readbyqxmd.com/read/28630527/a-promising-approach-to-integrally-evaluate-the-disease-outcome-of-cerebral-ischemic-rats-based-on-multiple-biomarker-crosstalk
#8
Guimei Ran, Yixuan Wang, Haochen Liu, Chunxiang Wei, Tao Zhu, Haidong Wang, Hua He, Xiaoquan Liu
PURPOSE: The study was designed to evaluate the disease outcome based on multiple biomarkers related to cerebral ischemia. METHODS: Rats were randomly divided into sham, permanent middle cerebral artery occlusion, and edaravone-treated groups. Cerebral ischemia was induced by permanent middle cerebral artery occlusion surgery in rats. To form a simplified crosstalk network, the related multiple biomarkers were chosen as S100β, HIF-1α, IL-1β, PGI2, TXA2, and GSH-Px...
2017: Disease Markers
https://www.readbyqxmd.com/read/28630467/computational-method-allowing-hydrogen-deuterium-exchange-mass-spectrometry-at-single-amide-resolution
#9
Chris Gessner, Wieland Steinchen, Sabrina Bédard, John J Skinner, Virgil L Woods, Thomas J Walsh, Gert Bange, Dionysios P Pantazatos
Hydrogen-deuterium exchange (HDX) coupled with mass spectrometry (HDXMS) is a rapid and effective method for localizing and determining protein stability and dynamics. Localization is routinely limited to a peptide resolution of 5 to 20 amino acid residues. HDXMS data can contain information beyond that needed for defining protein stability at single amide resolution. Here we present a method for extracting this information from an HDX dataset to generate a HDXMS protein stability fingerprint. High resolution (HR)-HDXMS was applied to the analysis of a model protein of a spectrin tandem repeat that exemplified an intuitive stability profile based on the linkage of two triple helical repeats connected by a helical linker...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28629668/underestimating-the-size-of-the-problem-uk-anaesthesia-for-patients-with-obesity
#10
James Palmer, Mike Sury, Claire Nightingale, Jaideep Pandit, Tim Cook
We analysed data from 14,000 patients in the 2013 United Kingdom Anaesthesia Activity Survey of the Fifth National Audit Project of the Royal College of Anaesthetists and Association of Anaesthetists of Great Britain and Ireland to examine anaesthetic, organisational and clinical practice for patients with obesity. We compared practice then with current guidance on management of this patient group. Obesity was reported in 22%, mainly Black, Afro-Caribbean and White Caucasian patients. There was minimal variation in surgical timing, anaesthetic seniority, induction location or day-case procedure rates...
June 16, 2017: Obesity Research & Clinical Practice
https://www.readbyqxmd.com/read/28629648/ten-reasons-to-embrace-scientism
#11
Rik Peels
A strong version of scientism, such as that of Alex Rosenberg, says, roughly, that natural science reliably delivers rational belief or knowledge, whereas common sense sources of belief, such as moral intuition, memory, and introspection, do not. In this paper I discuss ten reasons that adherents of scientism have or might put forward in defence of scientism. The aim is to show which considerations could plausibly count in favour of scientism and what this implies for the way scientism ought to be formulated...
June 2017: Studies in History and Philosophy of Science
https://www.readbyqxmd.com/read/28629436/disease-compass-a-navigation-system-for-disease-knowledge-based-on-ontology-and-linked-data-techniques
#12
Kouji Kozaki, Yuki Yamagata, Riichiro Mizoguchi, Takeshi Imai, Kazuhiko Ohe
BACKGROUND: Medical ontologies are expected to contribute to the effective use of medical information resources that store considerable amount of data. In this study, we focused on disease ontology because the complicated mechanisms of diseases are related to concepts across various medical domains. The authors developed a River Flow Model (RFM) of diseases, which captures diseases as the causal chains of abnormal states. It represents causes of diseases, disease progression, and downstream consequences of diseases, which is compliant with the intuition of medical experts...
June 19, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28628952/seeking-comfort-in-an-uncomfortable-chair
#13
Elena Molinari
The author explores the concept of comfort in relation to the setting. The concept of comfort, an unusual word in the psychoanalytic lexicon, describes the intuitive and complex experience of patient and analyst being together in the analytic office. The couch and the chair are not the only tools of the setting, but they are potential instruments with which to study the therapeutic process, both in high-frequency therapy and in lower-frequency treatments. To describe the transformations that an alternative experience of comfort can promote, the author looks at the intersection of this concept with the body-mind relationship and with the Bionian concept of binocular vision...
April 2017: Psychoanalytic Quarterly
https://www.readbyqxmd.com/read/28628714/advanced-real-time-multi-display-educational-system-armes-an-innovative-real-time-audiovisual-mentoring-tool-for-complex-robotic-surgery
#14
Joong Ho Lee, Eiji Tanaka, Yanghee Woo, Güner Ali, Taeil Son, Hyoung-Il Kim, Woo Jin Hyung
INTRODUCTION: The recent scientific and technologic advances have profoundly affected the training of surgeons worldwide. We describe a novel intraoperative real-time training module, the Advanced Robotic Multi-display Educational System (ARMES). METHODS: We created a real-time training module, which can provide a standardized step by step guidance to robotic distal subtotal gastrectomy with D2 lymphadenectomy procedures, ARMES. The short video clips of 20 key steps in the standardized procedure for robotic gastrectomy were created and integrated with TilePro™ software to delivery on da Vinci Surgical Systems (Intuitive Surgical, Sunnyvale, CA)...
June 19, 2017: Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28627916/individual-differences-in-reliance-on-intuition-predict-harsher-moral-judgments
#15
Sarah J Ward, Laura A King
The notion that intuition guides moral judgment is widely accepted. Yet, there is a dearth of research examining whether individual differences in reliance on intuition influence moral judgment. Five studies provided evidence that faith in intuition (FI) predicts higher condemnation of moral transgressions. Studies 1 and 2 (combined N = 543) demonstrated that FI predicted higher moral condemnation of strange actions characterized by ambiguous harm. This association maintained controlling for a host of relevant ideological and emotional "third" variables...
June 19, 2017: Journal of Personality and Social Psychology
https://www.readbyqxmd.com/read/28627841/clinical-decision-making-from-theory-to-practice%C3%A2-and-backward
#16
Lionel De Alencastro, Carole Clair, Isabella Locatelli, Mark H Ebell, Nicolas Senn
Being able to analyze all the successive steps of decision making from the first contact with the patient to the final diagnosis is complex because it refers sometimes to intuitive elements proper to each clinician. However, understanding how they integrate probabilities of diseases into their clinical practice and manage diagnostic uncertainties is crucial. This allows a more rational practice of medicine and identifying factors related to the patient, physician or context that may modify the clinical decision making...
May 2017: Revue Médicale Suisse
https://www.readbyqxmd.com/read/28626978/a-fast-multi-target-inverse-treatment-planning-strategy-optimizing-dosimetric-measures-for-high-dose-rate-hdr-brachytherapy
#17
Christian V Guthier, Antonio L Damato, Akila N Viswanathan, Juergen W Hesser, Robert A Cormack
PURPOSE: In this study, we introduce a novel, fast, inverse treatment planning strategy for interstitial high-dose-rate (HDR) brachytherapy with multiple regions of interest solely based on dose-volume-histogram-related dosimetric measures (DMs). METHODS: We present a new problem formulation of the objective function that approximates the indicator variables of the standard DM optimization problem with a smooth logistic function. This problem is optimized by standard gradient-based methods...
June 19, 2017: Medical Physics
https://www.readbyqxmd.com/read/28626903/economical-sponge-phantom-for-teaching-understanding-and-researching-a-and-b-line-reverberation-artifacts-in-lung-ultrasound
#18
Christian Blüthgen, Sergio Sanabria, Thomas Frauenfelder, Volker Klingmüller, Marga Rominger
This project evaluated a low-cost sponge phantom setup for its capability to teach and study A- and B-line reverberation artifacts known from lung ultrasound and to numerically simulate sound wave interaction with the phantom using a finite-difference time-domain (FDTD) model. Both A- and B-line artifacts were reproducible on B-mode ultrasound imaging as well as in the FDTD-based simulation. The phantom was found to be an easy-to-set up and economical tool for understanding, teaching, and researching A- and B-line artifacts occurring in lung ultrasound...
June 19, 2017: Journal of Ultrasound in Medicine: Official Journal of the American Institute of Ultrasound in Medicine
https://www.readbyqxmd.com/read/28625755/multilevel-engineering-of-the-upstream-module-of-aromatic-amino-acid-biosynthesis-in-saccharomyces-cerevisiae-for-high-production-of-polymer-and-drug-precursors
#19
Miguel Suástegui, Chiam Yu Ng, Anupam Chowdhury, Wan Sun, Mingfeng Cao, Emma House, Costas D Maranas, Zengyi Shao
A multilevel approach was implemented in Saccharomyces cerevisiae to optimize the precursor module of the aromatic amino acid biosynthesis pathway, which is a rich resource for synthesizing a great variety of chemicals ranging from polymer precursor, to nutraceuticals and pain-relief drugs. To facilitate the discovery of novel targets to enhance the pathway flux, we incorporated the computational tool YEASTRACT for predicting novel transcriptional repressors and OptForce strain-design for identifying non-intuitive pathway interventions...
June 15, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28625267/-application-of-quality-control-chart-in-quality-control-for-nosocomial-infection-in-intensive-care-unit
#20
Yumei Cheng, Yuanyi Liu, Difen Wang
OBJECTIVE: To explore the application value of control chart in the management of nosocomial infection in intensive care unit (ICU) by using quality control chart to monitor the infections in ICU. METHODS: From October 2011 to June 2016, ventilator-associated pneumonia (VAP), central line-associated bloodstream infection (CLABSI) and catheter-associated urinary tract infection (CAUTI), namely the three catheters, occurred in ICU of the Affiliated Hospital of Guizhou Medical University were monitored and recorded monthly, then the data was imput into the Excel, and the data was analyzed using SPSS...
February 2017: Zhonghua Wei Zhong Bing Ji Jiu Yi Xue
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