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https://www.readbyqxmd.com/read/28829778/chimericseq-an-open-source-user-friendly-interface-for-analyzing-ngs-data-to-identify-and-characterize-viral-host-chimeric-sequences
#1
Fwu-Shan Shieh, Patrick Jongeneel, Jamin D Steffen, Selena Lin, Surbhi Jain, Wei Song, Ying-Hsiu Su
Identification of viral integration sites has been important in understanding the pathogenesis and progression of diseases associated with particular viral infections. The advent of next-generation sequencing (NGS) has enabled researchers to understand the impact that viral integration has on the host, such as tumorigenesis. Current computational methods to analyze NGS data of virus-host junction sites have been limited in terms of their accessibility to a broad user base. In this study, we developed a software application (named ChimericSeq), that is the first program of its kind to offer a graphical user interface, compatibility with both Windows and Mac operating systems, and optimized for effectively identifying and annotating virus-host chimeric reads within NGS data...
2017: PloS One
https://www.readbyqxmd.com/read/28829372/rudo-a-home-ambient-intelligence-system-for-blind-people
#2
Milan Hudec, Zdenek Smutny
The article introduces an ambient intelligence system for blind people which besides providing assistance in home environment also helps with various situations and roles in which blind people may find themselves involved. RUDO, the designed system, comprises several modules that mainly support or ensure recognition of approaching people, alerting to other household members' movement in the flat, work on a computer, supervision of (sighted) children, cooperation of a sighted and a blind person (e.g., when studying), control of heating and zonal regulation by a blind person...
August 22, 2017: Sensors
https://www.readbyqxmd.com/read/28828272/genet-a-web-application-to-explore-and-share-gene-co-expression-network-analysis-data
#3
Amit P Desai, Mehdi Razeghin, Oscar Meruvia-Pastor, Lourdes Peña-Castillo
Gene Co-expression Network Analysis (GCNA) is a popular approach to analyze a collection of gene expression profiles. GCNA yields an assignment of genes to gene co-expression modules, a list of gene sets statistically over-represented in these modules, and a gene-to-gene network. There are several computer programs for gene-to-gene network visualization, but these programs have limitations in terms of integrating all the data generated by a GCNA and making these data available online. To facilitate sharing and study of GCNA data, we developed GeNET...
2017: PeerJ
https://www.readbyqxmd.com/read/28822820/utility-of-3d-reconstruction-of-2d-liver-computed-tomography-magnetic-resonance-images-as-a-surgical-planning-tool-for-residents-in-liver-resection-surgery
#4
Caitlin T Yeo, Andrew MacDonald, Tamas Ungi, Andras Lasso, Diederick Jalink, Boris Zevin, Gabor Fichtinger, Sulaiman Nanji
OBJECTIVE: A fundamental aspect of surgical planning in liver resections is the identification of key vessel tributaries to preserve healthy liver tissue while fully resecting the tumor(s). Current surgical planning relies primarily on the surgeon's ability to mentally reconstruct 2D computed tomography/magnetic resonance (CT/MR) images into 3D and plan resection margins. This creates significant cognitive load, especially for trainees, as it relies on image interpretation, anatomical and surgical knowledge, experience, and spatial sense...
August 16, 2017: Journal of Surgical Education
https://www.readbyqxmd.com/read/28822042/implementation-of-a-big-data-accessing-and-processing-platform-for-medical-records-in-cloud
#5
Chao-Tung Yang, Jung-Chun Liu, Shuo-Tsung Chen, Hsin-Wen Lu
Big Data analysis has become a key factor of being innovative and competitive. Along with population growth worldwide and the trend aging of population in developed countries, the rate of the national medical care usage has been increasing. Due to the fact that individual medical data are usually scattered in different institutions and their data formats are varied, to integrate those data that continue increasing is challenging. In order to have scalable load capacity for these data platforms, we must build them in good platform architecture...
August 18, 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28820652/decreasing-stroke-code-to-ct-time-in-patients-presenting-with-stroke-symptoms
#6
Aleksandrs Kalnins, L Jake Mickelsen, Daisha Marsh, Christoph Zorich, Stephanie Casal, Waimei Amy Tai, Nirali Vora, Gennette Olalia, Max Wintermark, David B Larson
Guided quality improvement (QI) programs present an effective means to streamline stroke code to computed tomography (CT) times in a comprehensive stroke center. Applying QI methods and a multidisciplinary team approach may decrease the stroke code to CT time in non-prenotified emergency department (ED) patients presenting with symptoms of stroke. The aim of this project was to decrease this time for non-prenotified stroke code patients from a baseline mean of 20 minutes to one less than 15 minutes during an 18-week period by applying QI methods in the context of a structured QI program...
August 18, 2017: Radiographics: a Review Publication of the Radiological Society of North America, Inc
https://www.readbyqxmd.com/read/28820354/validity-of-screening-for-psychiatric-disorders-in-unaccompanied-minor-asylum-seekers-use-of-computer-based-assessment
#7
Marianne Jakobsen, Melinda A Meyer DeMott, Trond Heir
Self-report screening is an important element of transcultural research. Problems concerning illiteracy, cultural sensitivity, and possible misunderstandings have been handled differently in different settings. The aim of this study was to evaluate the validity of two well-known instruments: the Hopkins Symptoms Check List (HSCL-25), and the Harvard Trauma Questionnaire (HTQ, Part IV), with a sample of 160 unaccompanied asylum-seeking adolescents from Afghanistan and Somalia. Assessments were performed 4 months after arrival in Norway, and the screening instruments were presented to the informants on computers with touch-screen function, using the program MultiCASI...
January 1, 2017: Transcultural Psychiatry
https://www.readbyqxmd.com/read/28820140/clarity-of-objectives-and-working-principles-enhances-the-success-of-biomimetic-programs
#8
Jonas Wolff, David Wells, Chris Reid, Sean John Blamires
Biomimetics, the transfer of functional principles from living systems into product designs, is increasingly being utilized by engineers. Nevertheless, recurring problems must be overcome if it is to avoid becoming a short-lived fad. Here we assess the efficiency and suitability of methods typically employed by examining three flagship examples of biomimetic design approaches from different disciplines: (1) the creation of gecko-inspired adhesives; (2) the synthesis of spider silk, and (3) the derivation of computer algorithms from natural self-organizing systems...
August 18, 2017: Bioinspiration & Biomimetics
https://www.readbyqxmd.com/read/28819746/the-effects-of-resistance-exercise-training-on-anxiety-a-meta-analysis-and-meta-regression-analysis-of-randomized-controlled-trials
#9
REVIEW
Brett R Gordon, Cillian P McDowell, Mark Lyons, Matthew P Herring
BACKGROUND: The salutary effects of resistance exercise training (RET) are well established, including increased strength and function; however, less is known regarding the effects of RET on mental health outcomes. Aerobic exercise has well-documented positive effects on anxiety, but a quantitative synthesis of RET effects on anxiety is needed. OBJECTIVES: To estimate the population effect size for resistance exercise training (RET) effects on anxiety and to determine whether variables of logical, theoretical, and/or prior empirical relation to anxiety moderate the overall effect...
August 17, 2017: Sports Medicine
https://www.readbyqxmd.com/read/28818647/malocclusion-class-ii-division-1-skeletal-and-dental-relationships-measured-by-cone-beam-computed-tomography
#10
Yiling Xu, Heesoo Oh, Manuel O Lagravère
OBJECTIVES: The purpose of this study was to locate traditionally-used landmarks in two-dimensional (2D) images and newly-suggested ones in three-dimensional (3D) images (cone-beam computer tomographies [CBCTs]) and determine possible relationships between them to categorize patients with Class II-1 malocclusion. METHODS: CBCTs from 30 patients diagnosed with Class II-1 malocclusion were obtained from the University of Alberta Graduate Orthodontic Program database...
August 14, 2017: International Orthodontics
https://www.readbyqxmd.com/read/28818165/effectiveness-and-safety-of-sofosbuvir-in-treatment-n%C3%A3-ivechildren-with-hepatitis-c-infection
#11
Muhammad Almas Hashmi, Huma Arshad Cheema
OBJECTIVE: To determine the effectiveness and safety of Sofosbuvir and Ribavirin combination in treatment-näivechildren with HCV infection. STUDY DESIGN: An experimental study. PLACE AND DURATION OF STUDY: Gastroentrology, Hepatology Department, The Children's Hospital and The Institute of Child Health, Lahore, from January to December 2016. METHODOLOGY: HCV PCR positive treatment-näivepatients, 5 to 18 years of age, were enrolled by consecutive nonprobability sampling...
July 2017: Journal of the College of Physicians and Surgeons—Pakistan: JCPSP
https://www.readbyqxmd.com/read/28816681/augmented-lagrange-programming-neural-network-for-localization-using-time-difference-of-arrival-measurements
#12
Zifa Han, Chi Sing Leung, Hing Cheung So, Anthony George Constantinides
A commonly used measurement model for locating a mobile source is time-difference-of-arrival (TDOA). As each TDOA measurement defines a hyperbola, it is not straightforward to compute the mobile source position due to the nonlinear relationship in the measurements. This brief exploits the Lagrange programming neural network (LPNN), which provides a general framework to solve nonlinear constrained optimization problems, for the TDOA-based localization. The local stability of the proposed LPNN solution is also analyzed...
August 15, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28816292/-precision-of-three-dimensional-printed-brackets
#13
D Zhang, L C Wang, Y H Zhou, X M Liu, J Li
OBJECTIVE: This study was based on digital orthodontic diagnosis work flow for indirect bonding transfer tray model design and three-dimensional (3D) printing, and the aim of this paper was to inspect the dimensional accuracyof 3D printed brackets, which is the foundation of the follow up work and hoped that will illuminate the clinical application of the digital orthodontics work flow. METHODS: The samples which consisted of 14 cases of patients with malocclusion from Department of Orthodontics Peking University were selected, including 8 cases with tooth extraction and 6 cases without tooth extraction...
August 18, 2017: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
https://www.readbyqxmd.com/read/28816025/aromatic-interactions-at-the-ligand-protein-interface-implications-for-the-development-of-docking-scoring-functions
#14
Michal Brylinski
The ability to design and fine-tune non-covalent interactions between organic ligands and proteins is indispensable to rational drug development. Aromatic stacking has long been recognized as one of the key constituents of ligand-protein interfaces. In this communication, we employ a two-parameter geometric model to conduct a large-scale statistical analysis of aromatic contacts in the experimental and computer-generated structures of ligand-protein complexes, considering various combinations of aromatic amino acid residues and ligand rings...
August 17, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28815397/detecting-and-accounting-for-multiple-sources-of-positional-variance-in-peak-list-registration-analysis-and-spin-system-grouping
#15
Andrey Smelter, Eric C Rouchka, Hunter N B Moseley
Peak lists derived from nuclear magnetic resonance (NMR) spectra are commonly used as input data for a variety of computer assisted and automated analyses. These include automated protein resonance assignment and protein structure calculation software tools. Prior to these analyses, peak lists must be aligned to each other and sets of related peaks must be grouped based on common chemical shift dimensions. Even when programs can perform peak grouping, they require the user to provide uniform match tolerances or use default values...
August 16, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28814968/asp-based-method-for-the-enumeration-of-attractors-in-non-deterministic-synchronous-and-asynchronous-multi-valued-networks
#16
Emna Ben Abdallah, Maxime Folschette, Olivier Roux, Morgan Magnin
BACKGROUND: This paper addresses the problem of finding attractors in biological regulatory networks. We focus here on non-deterministic synchronous and asynchronous multi-valued networks, modeled using automata networks (AN). AN is a general and well-suited formalism to study complex interactions between different components (genes, proteins,...). An attractor is a minimal trap domain, that is, a part of the state-transition graph that cannot be escaped. Such structures are terminal components of the dynamics and take the form of steady states (singleton) or complex compositions of cycles (non-singleton)...
2017: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/28814133/behavioral-and-psychosocial-characteristics-among-head-start-childcare-providers
#17
Jiying Ling
The aim of the study was twofold: (a) describe behavioral and psychosocial characteristics of Head Start childcare providers including technology use, physical activity, nutrition, depression, and quality of life and (b) examine associations among these characteristics. Using a cross-sectional design, a nonrandom sample of 80 Head Start childcare providers completed an online survey via SurveyMonkey. About 80.1% were overweight or obese. Nearly all had a computer or smartphone. About 55% met the national physical activity recommendation of 150 min/week...
January 1, 2017: Journal of School Nursing: the Official Publication of the National Association of School Nurses
https://www.readbyqxmd.com/read/28813870/upper-limb-training-assessment-program-using-passive-force-controllable-rehabilitation-system
#18
Takehito Kikuchi, Chihiro Sato, Kazuki Yamabe, Isao Abe, Tetsuya Ohno, Shintaro Kugimiya, Akio Inoue
Upper limb rehabilitation training for Hemiplegie patients has been conducted mainly by human therapists. Training methods and conditions depend strongly on their experience because of the wide range of individual differences between patients. The force control and sensing functions of rehabilitation robots are expected to be used for the qualitative assessment of next-generation computational rehabilitation. In this study, we developed a simple exercise machine for upper limbs (SEMUL) using an electro-rheological fluid brake, as a safe brake-type robotic rehabilitation system...
July 2017: IEEE ... International Conference on Rehabilitation Robotics: [proceedings]
https://www.readbyqxmd.com/read/28813151/the-medicinal-and-biological-chemistry-mbc-library-an-efficient-source-on-new-hits
#19
Víctor Sebastián Pérez, Carlos Roca, Mahendra Awale, Jean-Louis Reymond, Ana Martínez, Carmen Gil, Nuria E Campillo
Identification of new hits is one of the biggest challenges in drug discovery. Creating a library of well-characterized drug-like compounds is a key step in this process. Our group has developed an in-house chemical library called Medicinal and Biological Chemistry (MBC) library. This collection has been successfully used to start several medicinal chemistry programs and developed in an accumulation of more than thirty years of experience in drug design and discovery of new drugs for unmet diseases. It contains over 1,000 compounds, mainly heterocyclic scaffolds...
August 16, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28811609/rapid-and-accurate-in-silico-solubility-screening-of-a-monoclonal-antibody-library
#20
Pietro Sormanni, Leanne Amery, Sofia Ekizoglou, Michele Vendruscolo, Bojana Popovic
Antibodies represent essential tools in research and diagnostics and are rapidly growing in importance as therapeutics. Commonly used methods to obtain novel antibodies typically yield several candidates capable of engaging a given target. The development steps that follow, however, are usually performed with only one or few candidates since they can be resource demanding, thereby increasing the risk of failure of the overall antibody discovery program. In particular, insufficient solubility, which may lead to aggregation under typical storage conditions, often hinders the ability of a candidate antibody to be developed and manufactured...
August 15, 2017: Scientific Reports
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