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https://www.readbyqxmd.com/read/29764422/hmmibd-software-to-infer-pairwise-identity-by-descent-between-haploid-genotypes
#1
Stephen F Schaffner, Aimee R Taylor, Wesley Wong, Dyann F Wirth, Daniel E Neafsey
BACKGROUND: A number of recent malaria studies have used identity by descent (IBD) to study epidemiological processes relevant to malaria control. In this paper, a software package, hmmIBD, is introduced for estimating pairwise IBD between haploid genomes, such as those of the malaria parasite, sampled from one or two populations. Source code is freely available. METHODS: The performance of hmmIBD was verified using simulated data and benchmarked against an existing method for detecting IBD within populations...
May 15, 2018: Malaria Journal
https://www.readbyqxmd.com/read/29762644/indexed-variation-graphs-for-efficient-and-accurate-resistome-profiling
#2
Will P M Rowe, Martyn D Winn
Motivation: Antimicrobial resistance remains a major threat to global health. Profiling the collective antimicrobial resistance genes within a metagenome (the "resistome") facilitates greater understanding of antimicrobial resistance gene diversity and dynamics. In turn, this can allow for gene surveillance, individualised treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows...
May 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29755927/deep-data-analysis-via-physically-constrained-linear-unmixing-universal-framework-domain-examples-and-a-community-wide-platform
#3
REVIEW
R Kannan, A V Ievlev, N Laanait, M A Ziatdinov, R K Vasudevan, S Jesse, S V Kalinin
Many spectral responses in materials science, physics, and chemistry experiments can be characterized as resulting from the superposition of a number of more basic individual spectra. In this context, unmixing is defined as the problem of determining the individual spectra, given measurements of multiple spectra that are spatially resolved across samples, as well as the determination of the corresponding abundance maps indicating the local weighting of each individual spectrum. Matrix factorization is a popular linear unmixing technique that considers that the mixture model between the individual spectra and the spatial maps is linear...
2018: Advanced Structural and Chemical Imaging
https://www.readbyqxmd.com/read/29731401/adverse-effects-of-common-sports-and-recreational-activities-on-male-reproduction
#4
REVIEW
Kush Panara, John M Masterson, Luis F Savio, Ranjith Ramasamy
CONTEXT: Male factor infertility plays a significant role in infertility. Many factors have been associated with male infertility; however, the link between many sports and recreational factors and male reproduction remains poorly characterized. OBJECTIVE: To evaluate the current literature regarding the impact of many common sports and recreational factors on male reproduction. EVIDENCE ACQUISITION: A comprehensive PubMed and Embase search for relevant articles published between 1970 and 2017 was performed by combining the following search terms: male, sports (including individual sports), traumatic brain injury, sauna, hot tub, fertility, erectile dysfunction, varicocele, environment, cell phone, and laptop computer...
May 3, 2018: European Urology Focus
https://www.readbyqxmd.com/read/29722952/a-nursing-student-s-reflective-account-of-decision-making-in-a-school-nursing-setting
#5
Bethaney Squirrell, Jane Hunt
Reflection is integral to professional revalidation and enhancing nursing practice; it is an art and a science to be learned. Learning the art of reflection begins as a student in clinical placement settings. Drawing on a reflective model, this article presents an account of one second-year children's nursing student's experiences in a community-based placement with a school nursing team. A school nurse appointment was reflected on where advice was offered to a 13-year-old student with sleep difficulties, low affect and lethargy, which included avoiding caffeinated drinks, reducing use of a laptop and mobile phone before going to sleep, and establishing a regular bedtime routine...
May 3, 2018: Nursing Children and Young People
https://www.readbyqxmd.com/read/29719699/the-tensormol-0-1-model-chemistry-a-neural-network-augmented-with-long-range-physics
#6
Kun Yao, John E Herr, David W Toth, Ryker Mckintyre, John Parkhill
Traditional force fields cannot model chemical reactivity, and suffer from low generality without re-fitting. Neural network potentials promise to address these problems, offering energies and forces with near ab initio accuracy at low cost. However a data-driven approach is naturally inefficient for long-range interatomic forces that have simple physical formulas. In this manuscript we construct a hybrid model chemistry consisting of a nearsighted neural network potential with screened long-range electrostatic and van der Waals physics...
February 28, 2018: Chemical Science
https://www.readbyqxmd.com/read/29709072/numerical-evaluation-of-human-exposure-to-wimax-patch-antenna-in-tablet-or-laptop
#7
Beatrice Siervo, Maria Sole Morelli, Luigi Landini, Valentina Hartwig
The use of wireless communication devices, such as tablets or laptops, is increasing among children. Only a few studies assess specific energy absorption rate (SAR) due to exposure from wireless-enabled tablets and laptops, in particular with Worldwide Interoperability for Microwave Access (WiMax) technology. This paper reports the estimation of the interaction between an E-shaped patch antenna (3.5 GHz) and human models, by means of finite-difference time-domain (FDTD) method. Specifically, four different human models (young adult male, young adult female, pre-teenager female, male child) in different exposure conditions (antenna at different distances from the human model, in different positions, and orientations) were considered and whole-body, 10 and 1 g local SAR and magnetic field value (Bmax) were evaluated...
April 30, 2018: Bioelectromagnetics
https://www.readbyqxmd.com/read/29679703/pc-pvt-2-0-an-updated-platform-for-psychomotor-vigilance-task-testing-analysis-prediction-and-visualization
#8
Jaques Reifman, Kamal Kumar, Maxim Y Khitrov, Jianbo Liu, Sridhar Ramakrishnan
BACKGROUND: The psychomotor vigilance task (PVT) has been widely used to assess the effects of sleep deprivation on human neurobehavioral performance. To facilitate research in this field, we previously developed the PC-PVT, a freely available software system analogous to the "gold-standard" PVT-192 that, in addition to allowing for simple visual reaction time (RT) tests, also allows for near real-time PVT analysis, predictions, and visualization in a personal computer (PC)...
April 18, 2018: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/29662525/video-conferencing-telehealth-linkage-attempts-to-schools-to-facilitate-mental-health-consultation
#9
John D McLennan
Objective: Telehealth to schools may be a strategic approach to expand child mental health service delivery, however, there are only a few published examples. This report describes video-conferencing telehealth linkage attempts to schools to facilitate mental health consultation. Methods: A series of synchronous video-conferencing linkage strategies were attempted to connect a mental health consultation service to multiple schools in a Canadian setting. Consultation to support the implementation of the Daily Report Card, for students with attentional and behavioural problems, was the core content of this pilot linkage attempt...
April 2018: Journal of the Canadian Academy of Child and Adolescent Psychiatry
https://www.readbyqxmd.com/read/29621716/assessment-of-dermal-exposure-to-halogenated-flame-retardants-comparison-using-direct-measurements-from-hand-wipes-with-an-indirect-estimation-from-settled-dust-concentrations
#10
Joo Hui Tay, Ulla Sellström, Eleni Papadopoulou, Juan Antonio Padilla-Sánchez, Line Småstuen Haug, Cynthia A de Wit
There are few studies estimating dermal exposure to halogenated flame retardants in adults. To fill this gap, sixty-one hand wipe samples were collected from a Norwegian adult cohort using gauze pads immersed in isopropanol. BDE-47, BDE-209, bis(2‑ethyl‑hexyl)‑3,4,5,6‑tetrabromophthalate (BEH-TEBP) and decabromodiphenylethane (DBDPE) were the most frequently detected chemicals. The highest median mass in hand wipes was that of sumEHFR (570 ng), followed by sumHBCDD (180 ng) and sumPBDE (2.9 ng)...
April 2, 2018: Environment International
https://www.readbyqxmd.com/read/29618053/g-anchor-a-novel-approach-for-whole-genome-comparative-mapping-utilising-evolutionary-conserved-dna-sequences
#11
Vasileios Panagiotis E Lenis, Martin Swain, Denis M Larkin
Background: Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available now from multiple projects there is an increasing demand for genome comparative analyses...
April 3, 2018: GigaScience
https://www.readbyqxmd.com/read/29603963/age-pupil-size-differences-and-color-choices-for-the-dress-and-the-jacket
#12
Kavita Vemuri, Akanksha Srivastava, Saksham Agrawal, Mithra Anand
The color identification responses to photographs of #thedress (white/gold and blue/black) and a jacket (white/blue and green/black, and teal) reveal obvious individual differences in color perception. To explore possible association between pupil size/retinal illuminance and color perception, we recorded the pupil diameters of participants shown 22 uniformly colored (generated from the RGB values using a laptop LCD display) screens followed by photographs of #thedress and jacket. We analyzed (a) pupil size difference in the color groups and (b) age-related pupil size and/or reflex change and its influence on color perception...
April 1, 2018: Journal of the Optical Society of America. A, Optics, Image Science, and Vision
https://www.readbyqxmd.com/read/29597013/a-new-telemetry-based-system-for-assessing-cardiovascular-function-in-group-housed-large-animals-taking-the-3rs-to-a-new-level-with-the-evaluation-of-remote-measurement-via-cloud-data-transmission
#13
Michael Markert, Thomas Trautmann, Florian Krause, Marius Cioaga, Sebastien Mouriot, Miriam Wetzel, Brian D Guth
INTRODUCTION: A newly developed total implant telemetry system for cardiovascular (CV), electrophysiological and body temperature measurement was evaluated. A cloud-based transmission of the physiological signals allowed an assessment of the quality of the physiological signals despite the physical separation between the instrumented animals and the evaluating home laboratory. The new system is intended to be used for safety pharmacological evaluations of drug candidates in various species...
March 26, 2018: Journal of Pharmacological and Toxicological Methods
https://www.readbyqxmd.com/read/29590168/just-ask-siri-a-pilot-study-comparing-smartphone-digital-assistants-and-laptop-google-searches-for-smoking-cessation-advice
#14
Matt Boyd, Nick Wilson
OBJECTIVE: To compare voice-activated internet searches by smartphone (two digital assistants) with laptop ones for information and advice related to smoking cessation. DESIGN: Responses to 80 questions on a range of topics related to smoking cessation (including the FAQ from a NHS website), compared for quality. SETTING: Smartphone and internet searches as performed in New Zealand. MAIN OUTCOME MEASURES: Ranked responses to the questions...
2018: PloS One
https://www.readbyqxmd.com/read/29581634/adaptive-learning-in-medical-education-the-final-piece-of-technology-enhanced-learning
#15
Neel Sharma, Iain Doherty, Chaoyan Dong
Technology enhanced learning (TEL) is now common practice in the field of medical education. One of the primary examples of its use is that of high fidelity simulation and computerised mannequins. Further examples include online learning modules, electronic portfolios, virtual patient interactions, massive open online courses and the flipped classroom movement. The rise of TEL has occurred primarily due to the ease of internet access enabling the retrieval and sharing of information in an instant. Furthermore, the compact nature of internet ready devices such as smartphones and laptops has meant that access to information can occur anytime and anywhere...
September 2017: Ulster Medical Journal
https://www.readbyqxmd.com/read/29581092/detecting-motor-impairment-in-early-parkinson-s-disease-via-natural-typing-interaction-with-keyboards-validation-of-the-neuroqwerty-approach-in-an-uncontrolled-at-home-setting
#16
Teresa Arroyo-Gallego, María J Ledesma-Carbayo, Ian Butterworth, Michele Matarazzo, Paloma Montero-Escribano, Verónica Puertas-Martín, Martha L Gray, Luca Giancardo, Álvaro Sánchez-Ferro
BACKGROUND: Parkinson's disease (PD) is the second most prevalent neurodegenerative disease and one of the most common forms of movement disorder. Although there is no known cure for PD, existing therapies can provide effective symptomatic relief. However, optimal titration is crucial to avoid adverse effects. Today, decision making for PD management is challenging because it relies on subjective clinical evaluations that require a visit to the clinic. This challenge has motivated recent research initiatives to develop tools that can be used by nonspecialists to assess psychomotor impairment...
March 26, 2018: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/29572866/topoms-comprehensive-topological-exploration-for-molecular-and-condensed-matter-systems
#17
Harsh Bhatia, Attila G Gyulassy, Vincenzo Lordi, John E Pask, Valerio Pascucci, Peer-Timo Bremer
We introduce TopoMS, a computational tool enabling detailed topological analysis of molecular and condensed-matter systems, including the computation of atomic volumes and charges through the quantum theory of atoms in molecules, as well as the complete molecular graph. With roots in techniques from computational topology, and using a shared-memory parallel approach, TopoMS provides scalable, numerically robust, and topologically consistent analysis. TopoMS can be used as a command-line tool or with a GUI (graphical user interface), where the latter also enables an interactive exploration of the molecular graph...
March 23, 2018: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29568688/a-low-cost-multimodal-head-mounted-display-system-for-neuroendoscopic-surgery
#18
Xinghua Xu, Yi Zheng, Shujing Yao, Guochen Sun, Bainan Xu, Xiaolei Chen
Background: With rapid advances in technology, wearable devices as head-mounted display (HMD) have been adopted for various uses in medical science, ranging from simply aiding in fitness to assisting surgery. We aimed to investigate the feasibility and practicability of a low-cost multimodal HMD system in neuroendoscopic surgery. Methods: A multimodal HMD system, mainly consisted of a HMD with two built-in displays, an action camera, and a laptop computer displaying reconstructed medical images, was developed to assist neuroendoscopic surgery...
January 2018: Brain and Behavior
https://www.readbyqxmd.com/read/29543149/chewbbaca-a-complete-suite-for-gene-by-gene-schema-creation-and-strain-identification
#19
Mickael Silva, Miguel P Machado, Diogo N Silva, Mirko Rossi, Jacob Moran-Gilad, Sergio Santos, Mario Ramirez, João André Carriço
Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers...
March 15, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29540968/effective-office-ergonomics-awareness-experiences-from-global-corporates
#20
Kishore P Madhwani, P K Nag
Background: Use of laptops and hand-held devices increase the risk of musculoskeletal disorders (MSDs). More time spent on this activity adopting faulty postures, higher the risk of developing such injuries. This study addresses training on office ergonomics with emphasis on sustainable behavior change among employees to work in safe postures, as this is a top priority in the corporate environment, today. Aim: To explore training intervention methods that ensure wider coverage of awareness on office ergonomics, thereby promoting safer working and suggesting sustainable programs for behavior change and job enrichment...
May 2017: Indian Journal of Occupational and Environmental Medicine
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