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https://www.readbyqxmd.com/read/28641267/a-cpu-mic-collaborated-parallel-framework-for-gromacs-on-tianhe-2-supercomputer
#1
Shaoliang Peng, Shunyun Yang, Wenhe Su, Xiaoyu Zhang, Tenglilang Zhang, Weiguo Liu, Xingming Zhao
Molecular Dynamics (MD) is the simulation of the dynamic behavior of atoms and molecules. As the most popular software for molecular dynamics, GROMACS cannot work on large-scale data because of limit computing resources. In this paper, we propose a CPU and Intel® Xeon Phi Many Integrated Core (MIC) collaborated parallel framework to accelerate GROMACS using the offload mode on a MIC coprocessor, with which the performance of GROMACS is improved significantly, especially with the utility of Tianhe-2 supercomputer...
June 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28636905/a-kepler-workflow-tool-for-reproducible-amber-gpu-molecular-dynamics
#2
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/28636434/selective-breeding-and-short-term-access-to-a-running-wheel-alter-stride-characteristics-in-house-mice
#3
Gerald C Claghorn, Zoe Thompson, Jarren C Kay, Genesis Ordonez, Thomas G Hampton, Theodore Garland
Postural and kinematic aspects of running may have evolved to support high runner (HR) mice to run approximately threefold farther than control mice. Mice from four replicate HR lines selectively bred for high levels of voluntary wheel running show many differences in locomotor behavior and morphology as compared with four nonselected control (C) lines. We hypothesized that HR mice would show stride alterations that have coadapted with locomotor behavior, morphology, and physiology. More specifically, we predicted that HR mice would have stride characteristics that differed from those of C mice in ways that parallel some of the adaptations seen in highly cursorial animals...
September 2017: Physiological and Biochemical Zoology: PBZ
https://www.readbyqxmd.com/read/28636351/heats-of-formation-of-medium-size-organic-compounds-from-contemporary-electronic-structure-methods
#4
Yury Minenkov, Heng Wang, Zhandong Wang, S Mani Sarathy, Luigi Cavallo
Computational electronic structure calculations are routinely undertaken to predict thermodynamic properties of the various species. However, the application of highly accurate wave function theory methods, such as the "gold standard" coupled cluster approach including single, double and partly triple excitations in perturbative fashion, CCSD(T), to large molecules is limited due to high computational cost. In this work, the promising domain based local pair natural orbital coupled cluster approach, DLPNO-CCSD(T), has been tested to reproduce 113 accurate formation enthalpies of medium-size molecules (few dozens heavy atoms) important for bio- and combustion chemistry via the reaction based Feller-Peterson-Dixon approach...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636204/aerobic-exercise-training-for-adults-with-fibromyalgia
#5
REVIEW
Julia Bidonde, Angela J Busch, Candice L Schachter, Tom J Overend, Soo Y Kim, Suelen M Góes, Catherine Boden, Heather Ja Foulds
BACKGROUND: Exercise training is commonly recommended for individuals with fibromyalgia. This review is one of a series of reviews about exercise training for people with fibromyalgia that will replace the "Exercise for treating fibromyalgia syndrome" review first published in 2002. OBJECTIVES: • To evaluate the benefits and harms of aerobic exercise training for adults with fibromyalgia• To assess the following specific comparisons ० Aerobic versus control conditions (eg, treatment as usual, wait list control, physical activity as usual) ० Aerobic versus aerobic interventions (eg, running vs brisk walking) ० Aerobic versus non-exercise interventions (eg, medications, education) We did not assess specific comparisons involving aerobic exercise versus other exercise interventions (eg, resistance exercise, aquatic exercise, flexibility exercise, mixed exercise)...
June 21, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/28635533/the-burden-of-endometriosis-symptoms-on-health-related-quality-of-life-in-women-in-the-united-states-a-cross-sectional-study
#6
Ahmed M Soliman, Karin S Coyne, Erica Zaiser, Jane Castelli-Haley, Mahesh J Fuldeore
INTRODUCTION: To examine the symptomatic burden of endometriosis on health-related quality of life (HRQL) in women in the United States (US). METHODS: A cross sectional web-based survey study was conducted among women using survey panels. The survey included study-specific questions and standardized HRQL questionnaires. Participants reviewed a list of endometriosis symptoms and selected all symptoms they had ever or were currently experiencing. For current symptoms, participants rated the severity and bothersomeness of each symptom...
February 21, 2017: Journal of Psychosomatic Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/28634794/evaluation-in-situ-of-genotoxicity-and-stress-in-south-american-common-toad-rhinella-arenarum-in-environments-related-to-fluorite-mine
#7
Favio E Pollo, Pablo R Grenat, Zulma A Salinas, Manuel A Otero, Nancy E Salas, Adolfo L Martino
Little attention has been paid to the impact of wastewater generated by mining activities on fluoride. In this study, we evaluated the hematology responses of common South American toad Rhinella arenarum inhabiting natural and artificial environments associated with a fluorite mine from central Argentina. We analyzed three sampling stations associated with the fluorite mine: (I) Los Cerros Negros stream (CN), which runs on granitic rock with a high fluorite content; (II) Los Vallecitos stream (LV), which runs on metamorphic rock with low fluorite content; and (III) artificial decantation ponds (DP) containing sediments produced by fluorite flotation process...
June 20, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28634757/a-uhplc-ms-ms-method-for-profiling-multifunctional-steroids-in-human-hair
#8
Zhen Dong, Caihong Wang, Jinlan Zhang, Zhe Wang
It is important to profile steroids in many physiological and pathological processes. Recently, hair has been used for the long-term measurement of endogenous steroid hormones. Analyzing hair has advantages of being noninvasive and time sequential compared with other bio-specimens. Liquid chromatography-mass spectrometry (LC-MS) techniques have been widely used over the past decades; however, it is challenging to profile estrogens in hair by LC-MS, and more comprehensive steroid profiling is required. In this paper, an ultra high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method was developed to simultaneously profile 28 multifunctional steroids, including corticosteroids (n = 6), estrogens (n = 13), androgens (n = 5) and progestogens (n = 4), in human scalp hair in a single run...
June 20, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28634458/phone-conversation-while-processing-information-chronometric-analysis-of-load-effects-in-everyday-media-multitasking
#9
Michael B Steinborn, Lynn Huestegge
This is a pilot study that examined the effect of cell-phone conversation on cognition using a continuous multitasking paradigm. Current theorizing argues that phone conversation affects behavior (e.g., driving) by interfering at a level of cognitive processes (not peripheral activity) and by implying an attentional-failure account. Within the framework of an intermittent spare-utilized capacity threading model, we examined the effect of aspects of (secondary-task) phone conversation on (primary-task) continuous arithmetic performance, asking whether phone use makes components of automatic and controlled information-processing (i...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28633971/manganese-enhanced-magnetic-resonance-imaging-depicts-brain-activity-in-models-of-acute-and-chronic-pain-a-new-window-to-study-experimental-spontaneous-pain
#10
I M Devonshire, J J Burston, L Xu, A Lillywhite, M J Prior, D J G Watson, C M Greenspon, S J Iwabuchi, D P Auer, V Chapman
Application of functional imaging techniques to animal models is vital to understand pain mechanisms, but is often confounded by the need to limit movement artefacts with anaesthesia, and a focus on evoked responses rather than clinically relevant spontaneous pain and related hyperalgesia. The aim of the present study was to investigate the potential of manganese-enhanced magnetic resonance imaging (MEMRI) to measure neural responses during on-going pain that underpins hyperalgesia in pre-clinical models of nociception...
June 17, 2017: NeuroImage
https://www.readbyqxmd.com/read/28633795/valgus-ankle-degenerative-arthritis-with-an-isolated-deltoid-insufficiency-and-tibial-varus-a-case-report
#11
Joo-Yul Bae, Hee-Jae Won, Dong-Kyo Seo
We report a case of valgus ankle degenerative arthritis due to chronic isolated deltoid insufficiency combined with tibial varus that was treated successfully with ankle joint preserving surgery. A 63-year-old male complained of right lateral ankle pain with 10 minutes of maximal pain-free walking time. The assessed American Orthopaedic Foot and Ankle ankle-hindfoot scale score was 33 points. The ankle joint showed 18° of valgus deformity with 6° of tibia varus. Medial displacement calcaneal osteotomy, supramalleolar open wedge osteotomy, and deltoid ligament imbrication were performed...
July 2017: Journal of Foot and Ankle Surgery: Official Publication of the American College of Foot and Ankle Surgeons
https://www.readbyqxmd.com/read/28633617/simultaneous-determination-of-primary-and-secondary-d-and-l-amino-acids-by-reversed-phase-high-performance-liquid-chromatography-using-pre-column-derivatization-with-two-step-labelling-method
#12
Takehiko Yokoyama, Masaharu Tokuda, Masafumi Amano, Koji Mikami
This work describes a method for the simultaneous determination of primary d- and l-amino acids and secondary amino acids such as d- and l-proline. In order to remove interferences in the simultaneous determination of primary and secondary amines, the primary amines were derivatized with o-phthalaldehyde/N-acetyl-l-cysteine (OPA/NAC) and subsequently with 1-(9-fluorenyl)ethyl chloroformate (FLEC) for secondary amines, in a pre-column separation derivatization technique. These fluorescent diastereomers of the amino acids were obtained within 3 min at room temperature and determined simultaneously by changing wavelengths during analysis in a single eluting run in the high-performance liquid chromatography column...
June 21, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28632550/suture-choice-in-lumbar-dural-closure-contributes-to-variation-in-leak-pressures-experimental-model
#13
George M Ghobrial, Christopher M Maulucci, Matthew J Viereck, Sara Beygi, Ameet Chitale, Srinivas Prasad, Jack Jallo, Joshua Heller, Ashwini D Sharan, James S Harrop
STUDY DESIGN: Open-label laboratory investigational study; non-animal surgical simulation. OBJECTIVE: The authors perform a comparison of dural closure strength in a durotomy simulator across 2 different suture materials. SUMMARY OF BACKGROUND DATA: Incidental durotomy leading to persistent cerebrospinal fluid leak adds considerable morbidity to spinal procedures, often complicating routine elective lumbar spinal procedures. Using an experimental durotomy simulation, the authors compare the strength of closure using Gore-Tex with other suture types and sizes, using various closure techniques...
July 2017: Clinical Spine Surgery
https://www.readbyqxmd.com/read/28632457/the-bevps-a-new-test-battery-to-assess-visual-perceptual-and-spatial-processing-abilities-in-5-14-year-old-children
#14
Emilie Schmetz, Laurence Rousselle, Cécile Ballaz, Jean-Jacques Detraux, Koviljka Barisnikov
This study aims to examine the different levels of visual perceptual object recognition (early, intermediate, and late) defined in Humphreys and Riddoch's model as well as basic visual spatial processing in children using a new test battery (BEVPS). It focuses on the age sensitivity, internal coherence, theoretical validity, and convergent validity of this battery. French-speaking, typically developing children (n = 179; 5 to 14 years) were assessed using 15 new computerized subtests. After selecting the most age-sensitive tasks though ceiling effect and correlation analyses, an exploratory factorial analysis was run with the 12 remaining subtests to examine the BEVPS' theoretical validity...
June 20, 2017: Applied Neuropsychology. Child
https://www.readbyqxmd.com/read/28632158/on-the-application-of-image-processing-methods-for-bubble-recognition-to-the-study-of-subcooled-flow-boiling-of-water-in-rectangular-channels
#15
Concepción Paz, Marcos Conde, Jacobo Porteiro, Miguel Concheiro
This work introduces the use of machine vision in the massive bubble recognition process, which supports the validation of boiling models involving bubble dynamics, as well as nucleation frequency, active site density and size of the bubbles. The two algorithms presented are meant to be run employing quite standard images of the bubbling process, recorded in general-purpose boiling facilities. The recognition routines are easily adaptable to other facilities if a minimum number of precautions are taken in the setup and in the treatment of the information...
June 20, 2017: Sensors
https://www.readbyqxmd.com/read/28632055/muscle-activity-in-sprinting-a-review
#16
Róisín M Howard, Richard Conway, Andrew J Harrison
The use of electromyography (EMG) is widely recognised as a valuable tool for enhancing the understanding of performance drivers and potential injury risk in sprinting. The timings of muscle activations relative to running gait cycle phases and the technology used to obtain muscle activation data during sprinting are of particular interest to scientists and coaches. This review examined the main muscles being analysed by surface EMG (sEMG), their activations and timing, and the technologies used to gather sEMG during sprinting...
February 28, 2017: Sports Biomechanics
https://www.readbyqxmd.com/read/28630733/return-to-running-after-arthroscopic-hip-surgery-literature-review-and-proposal-of-a-physical-therapy-protocol
#17
REVIEW
Matthew J Kraeutler, Joy Anderson, Jorge Chahla, Justin J Mitchell, Robyn Thompson-Etzel, Omer Mei-Dan, Cecilia Pascual-Garrido
The number of hip arthroscopy procedures has significantly increased in the last several years, thereby necessitating individualized rehabilitation protocols for patients following hip arthroscopy. The purpose of this article is to review the literature on rehabilitation protocols for patients following hip arthroscopy and to describe a new protocol specifically designed for patients to return to running following hip arthroscopy. A search of PubMed was performed through October 2016 to locate studies of rehabilitation protocols for patients wishing to return to sport/general activity following hip arthroscopy...
July 2017: Journal of Hip Preservation Surgery
https://www.readbyqxmd.com/read/28630722/hip-arthroscopy-protocol-expert-opinions-on-post-operative-weight-bearing-and-return-to-sports-guidelines
#18
Ehud Rath, Zachary T Sharfman, Matan Paret, Eyal Amar, Michael Drexler, Nicolas Bonin
The objectives of this study are to survey the weight-bearing limitation practices and delay for returning to running and impact sports of high volume hip arthroscopy orthopedic surgeons. The study was designed in the form of expert survey questionnaire. Evidence-based data are scares regarding hip arthroscopy post-operative weight-bearing protocols. An international cross-sectional anonymous Internet survey of 26 high-volume hip arthroscopy specialized surgeons was conducted to report their weight-bearing limitations and rehabilitation protocols after various arthroscopic hip procedures...
January 2017: Journal of Hip Preservation Surgery
https://www.readbyqxmd.com/read/28630702/evaluation-of-an-in-vitro-fibre-fermentation-method-using-feline-faecal-inocula-repeatability-and-reproducibility
#19
Guido Bosch, Lisa Heesen, Karine de Melo Santos, Wilbert F Pellikaan, John W Cone, Wouter H Hendriks
To gain knowledge on the precision of an in vitro method for characterisation of the fermentability of dietary fibres, this study aimed to evaluate the repeatability and reproducibility of such a method. Substrates used were citrus pectin (CP), fructo-oligosaccharides (FOS), guar gum (GG), sugar beet pulp (SBP) and wheat middlings (WM). Each substrate was incubated with faecal inoculum from five cats with three replicates for each substrate-cat combination. Gas production was measured continuously during the 48 h incubation and SCFA and organic matter disappearance (only SBP and WM) were determined after incubation...
2017: Journal of Nutritional Science
https://www.readbyqxmd.com/read/28630581/5000-meter-run-performance-is-not-enhanced-24-hrs-after-an-intense-exercise-bout-and-cold-water-immersion
#20
Mary C Stenson, Matthew R Stenson, Tracey D Matthews, Vincent J Paolone
Cold water immersion (CWI) is used by endurance athletes to speed recovery between exercise bouts, but little evidence is available on the effects of CWI on subsequent endurance performance. The purpose of this study was to investigate the effects of CWI following an acute bout of interval training on 5000 m run performance 24 hrs after interval training, perceived muscle soreness (PMS), range of motion (ROM), thigh circumference (TC), and perceived exertion (RPE). Nine endurance-trained males completed 2 trials, each consisting of an interval training session of 8 repetitions of 1200 m at a running pace equal to 75% of VO2peak, either a control or CWI treatment, and a timed 5000 m run 24 hrs post interval training session...
June 2017: Journal of Sports Science & Medicine
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