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https://www.readbyqxmd.com/read/29348708/hybphylomaker-target-enrichment-data-analysis-from-raw-reads-to-species-trees
#1
Tomáš Fér, Roswitha E Schmickl
Summary: Hybridization-based target enrichment in combination with genome skimming (Hyb-Seq) is becoming a standard method of phylogenomics. We developed HybPhyloMaker, a bioinformatics pipeline that performs target enrichment data analysis from raw reads to supermatrix-, supertree-, and multispecies coalescent-based species tree reconstruction. HybPhyloMaker is written in BASH and integrates common bioinformatics tools. It can be launched both locally and on a high-performance computer cluster...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29295773/a-comprehensive-approach-to-convert-a-radiology-department-from-coding-based-on-international-classification-of-diseases-ninth-revision-to-coding-based-on-international-classification-of-diseases-tenth-revision
#2
Morgan P McBee, Tal Laor, Rebecca M Pryor, Rachel Smith, Judy Hardin, Lisa Ulland, Sally May, Bin Zhang, Alexander J Towbin
PURPOSE: The purpose of this study was to adapt our radiology reports to provide the documentation required for specific International Classification of Diseases, tenth rev (ICD-10) diagnosis coding. MATERIALS AND METHODS: Baseline data were analyzed to identify the reports with the greatest number of unspecified ICD-10 codes assigned by computer-assisted coding software. A two-part quality improvement initiative was subsequently implemented. The first component involved improving clinical histories by utilizing technologists to obtain information directly from the patients or caregivers, which was then imported into the radiologist's report within the speech recognition software...
December 30, 2017: Journal of the American College of Radiology: JACR
https://www.readbyqxmd.com/read/29223404/computer-assisted-total-knee-arthroplasty-is-there-a-difference-between-image-based-and-imageless-techniques
#3
Reza M Tabatabaee, Mohammad R Rasouli, Mitchell G Maltenfort, Robert Fuino, Camilo Restrepo, Ali Oliashirazi
BACKGROUND: Image-based and imageless computer-assisted total knee arthroplasty (CATKA) has become increasingly popular. This study aims to compare outcomes, including perioperative complications and transfusion rate, between CATKA and conventional total knee arthroplasty (TKA), as well as between image-based and imageless CATKA. METHODS: Using the 9th revision of the International Classification of Diseases codes, we queried the Nationwide Inpatient Sample database from 2005 to 2011 to identify unilateral conventional TKA, image-based, and imageless CATKAs as well as in-hospital complications and transfusion rates...
November 21, 2017: Journal of Arthroplasty
https://www.readbyqxmd.com/read/29192293/digital-evaluation-of-the-fit-of-zirconia-reinforced-lithium-silicate-crowns-with-a-new-three-dimensional-approach
#4
Moritz Zimmermann, Andre Valcanaia, Gisele Neiva, Albert Mehl, Dennis Fasbinder
OBJECTIVE: Several methods for the evaluation of fit of computer-aided design/computer-assisted manufacture (CAD/CAM)-fabricated restorations have been described. In the study, digital models were recorded with an intraoral scanning device and were measured using a new three-dimensional (3D) computer technique to evaluate restoration internal fit. The aim of the study was to evaluate the internal adaptation and fit of chairside CAD/CAM-fabricated zirconia-reinforced lithium silicate ceramic crowns fabricated with different post-milling protocols...
November 30, 2017: Quintessence International
https://www.readbyqxmd.com/read/29175248/a-data-extraction-algorithm-for-assessment-of-contraceptive-counseling-and-provision
#5
Brittany J Roser, Susan E Rubin, Nisha Nagarajan, Daryl L Wieland, Nerys C Benfield
BACKGROUND: Contraception counseling and provision is an essential preventative service. Real-time assessment of these services is critical for quality improvement and comparative study. Direct observation is not feasible on a large scale so indirect measures, such as chart review, have been determined to be acceptable tools for this assessment. Computer-aided chart review has significant benefits over manual chart review as far as greater efficiency and ease of repeated measurements...
November 23, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/29133713/three-dimensional-model-printing-for-surgery-on-arteriovenous-malformations
#6
Abhidha Shah, Bhavin Jankharia, Atul Goel
AIM: Surgery for intracranial complex vascular malformations can be quite exigent and involves considerable preoperative planning. Here, we present the advantages of using three-dimensional (3D) printed models as a preoperative investigational modality. MATERIAL AND METHODS: 3D printed models were made from thin-slice computed tomography (CT) angiography scans of 6 patients with arteriovenous malformations over an18-month period from August 2015 to December 2016...
November 2017: Neurology India
https://www.readbyqxmd.com/read/29124548/development-of-an-experimental-and-digital-cardiovascular-arterial-model-for-transient-hemodynamic-and-postural-change-studies-a-preliminary-framework-analysis
#7
Rodward L Hewlin, John P Kizito
The ultimate goal of the present work is to aid in the development of tools to assist in the treatment of cardiovascular disease. Gaining an understanding of hemodynamic parameters for medical implants allow clinicians to have some patient-specific proposals for intervention planning. In the present work an experimental and digital computational fluid dynamics (CFD) arterial model consisting of a number of major arteries (aorta, carotid bifurcation, cranial, femoral, jejunal, and subclavian arteries) were fabricated to study: (1) the effects of local hemodynamics (flow parameters) on global hemodynamics (2) the effects of transition from bedrest to upright position (postural change) on hemodynamics, and (3) diffusion of dye (medical drug diffusion simulation) in the arterial system via experimental and numerical techniques...
November 9, 2017: Cardiovascular Engineering and Technology
https://www.readbyqxmd.com/read/29065524/parents-perceived-barriers-to-accessing-sports-and-recreation-facilities-in-ontario-canada-exploring-the-relationships-between-income-neighbourhood-deprivation-and-community
#8
Daniel W Harrington, Jocelyn W Jarvis, Heather Manson
Sports and recreation facilities provide places where children can be physically active. Previous research has shown that availability is often worse in lower-socioeconomic status (SES) areas, yet others have found inverse relationships, no relationships, or mixed findings. Since children's health behaviours are influenced by their parents, it is important to understand parents' perceived barriers to accessing sports and recreation facilities. Data from computer assisted telephone interviews with parents living in Ontario, Canada were merged via postal codes with neighbourhood deprivation data...
October 23, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29050896/intraoperative-pedicle-screw-navigation-does-not-significantly-affect-complication-rates-after-spine-surgery
#9
Scott C Wagner, Patrick B Morrissey, Ian D Kaye, Arjun Sebastian, Joseph S Butler, Christopher K Kepler
Various forms of intraoperative computer-assisted navigation technologies exist, and have consistently been shown to improve pedicle screw accuracy. However, the overall clinical effects of inaccurate pedicle screw placement have been debated. We examined the clinical effects of improved pedicle screw accuracy with computer navigation technology in reducing complication rates in patients undergoing multi-level spinal fusion. We retrospectively reviewed the ACS-NSQIP registry utilizing Current Procedural Terminology (CPT) codes 22843 + 22844 to identify patients undergoing spinal instrumentation of greater than 7 levels, as well as the CPT code 61783 to denote the use of intraoperative computer-assisted navigation...
October 16, 2017: Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia
https://www.readbyqxmd.com/read/28968779/a-graph-regularized-non-negative-matrix-factorization-method-for-identifying-microrna-disease-associations
#10
Qiu Xiao, Jiawei Luo, Cheng Liang, Jie Cai, Pingjian Ding
Motivation: MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulations and various cellular processes. The identification of disease-related miRNAs provides great insights into the underlying pathogenesis of diseases at a system level. However, most existing computational approaches are biased towards known miRNA-disease associations, which is inappropriate for those new diseases or miRNAs without any known association information. Results: In this study, we propose a new method with graph regularized non-negative matrix factorization in heterogeneous omics data, called GRNMF, to discover potential associations between miRNAs and diseases, especially for new diseases and miRNAs or those diseases and miRNAs with sparse known associations...
September 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28968637/dugong-a-docker-image-based-on-ubuntu-linux-focused-on-reproducibility-and-replicability-for-bioinformatics-analyses
#11
Fabiano B Menegidio, Daniela L Jabes, Regina Costa de Oliveira, Luiz R Nunes
Summary: This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects...
September 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28883671/a-three-phase-decision-model-of-computer-aided-coding-for-the-iranian-classification-of-health-interventions-irchi
#12
Zahra Azadmanjir, Reza Safdari, Marjan Ghazisaeedi, Mehrshad Mokhtaran, Mohammad Esmail Kameli
INTRODUCTION: Accurate coded data in the healthcare are critical. Computer-Assisted Coding (CAC) is an effective tool to improve clinical coding in particular when a new classification will be developed and implemented. But determine the appropriate method for development need to consider the specifications of existing CAC systems, requirements for each type, our infrastructure and also, the classification scheme. AIM: The aim of the study was the development of a decision model for determining accurate code of each medical intervention in Iranian Classification of Health Interventions (IRCHI) that can be implemented as a suitable CAC system...
June 2017: Acta Informatica Medica: AIM
https://www.readbyqxmd.com/read/28843166/occupation-and-mammographic-density-a-population-based-study-ddm-occup
#13
MULTICENTER STUDY
Javier García-Pérez, Marina Pollán, Beatriz Pérez-Gómez, Mario González-Sánchez, Rosa Ana Cortés Barragán, Jerónimo Maqueda Blasco, María Carmen González-Galarzo, Miguel Ángel Alba, Rudolf van der Haar, Silvia Casas, Cándida Vicente, Pilar Medina, María Ederra, Carmen Santamariña, María Pilar Moreno, Francisco Casanova, Carmen Pedraz-Pingarrón, Pilar Moreo, Nieves Ascunce, Montse García, Dolores Salas-Trejo, Carmen Sánchez-Contador, Rafael Llobet, Virginia Lope
INTRODUCTION: High mammographic density is one of the main risk factors for breast cancer. Although several occupations have been associated with breast cancer, there are no previous occupational studies exploring the association with mammographic density. Our objective was to identify occupations associated with high mammographic density in Spanish female workers. METHODS: We conducted a population-based cross-sectional study of occupational determinants of high mammographic density in Spain, based on 1476 women, aged 45-68 years, recruited from seven screening centers within the Spanish Breast Cancer Screening Program network...
November 2017: Environmental Research
https://www.readbyqxmd.com/read/28818053/the-impact-of-self-interviews-on-response-patterns-for-sensitive-topics-a-randomized-trial-of-electronic-delivery-methods-for-a-sexual-behaviour-questionnaire-in-rural-south-africa
#14
Guy Harling, Dumile Gumede, Tinofa Mutevedzi, Nuala McGrath, Janet Seeley, Deenan Pillay, Till W Bärnighausen, Abraham J Herbst
BACKGROUND: Self-interviews, where the respondent rather than the interviewer enters answers to questions, have been proposed as a way to reduce social desirability bias associated with interviewer-led interviews. Computer-assisted self-interviews (CASI) are commonly proposed since the computer programme can guide respondents; however they require both language and computer literacy. We evaluated the feasibility and acceptability of using electronic methods to administer quantitative sexual behaviour questionnaires in the Somkhele demographic surveillance area (DSA) in rural KwaZulu-Natal, South Africa...
August 17, 2017: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/28814023/representing-high-dimensional-data-to-intelligent-prostheses-and-other-wearable-assistive-robots-a-first-comparison-of-tile-coding-and-selective-kanerva-coding
#15
Jaden B Travnik, Patrick M Pilarski
Prosthetic devices have advanced in their capabilities and in the number and type of sensors included in their design. As the space of sensorimotor data available to a conventional or machine learning prosthetic control system increases in dimensionality and complexity, it becomes increasingly important that this data be represented in a useful and computationally efficient way. Well structured sensory data allows prosthetic control systems to make informed, appropriate control decisions. In this study, we explore the impact that increased sensorimotor information has on current machine learning prosthetic control approaches...
July 2017: IEEE ... International Conference on Rehabilitation Robotics: [proceedings]
https://www.readbyqxmd.com/read/28813447/the-use-of-high-throughput-small-rna-sequencing-reveals-differentially-expressed-micrornas-in-response-to-aster-yellows-phytoplasma-infection-in-vitis-vinifera-cv-chardonnay
#16
Marius C Snyman, Marie-Chrystine Solofoharivelo, Rose Souza-Richards, Dirk Stephan, Shane Murray, Johan T Burger
Phytoplasmas are cell wall-less plant pathogenic bacteria responsible for major crop losses throughout the world. In grapevine they cause grapevine yellows, a detrimental disease associated with a variety of symptoms. The high economic impact of this disease has sparked considerable interest among researchers to understand molecular mechanisms related to pathogenesis. Increasing evidence exist that a class of small non-coding endogenous RNAs, known as microRNAs (miRNAs), play an important role in post-transcriptional gene regulation during plant development and responses to biotic and abiotic stresses...
2017: PloS One
https://www.readbyqxmd.com/read/28748430/inicu-integrated-neonatal-care-unit-capturing-neonatal-journey-in-an-intelligent-data-way
#17
Harpreet Singh, Gautam Yadav, Raghuram Mallaiah, Preetha Joshi, Vinay Joshi, Ravneet Kaur, Suneyna Bansal, Samir K Brahmachari
Neonatal period represents first 28 days of life, which is the most vulnerable time for a child's survival especially for the preterm babies. High neonatal mortality is a prominent and persistent problem across the globe. Non-availability of trained staff and infrastructure are the major recognized hurdles in the quality care of these neonates. Hourly progress growth charts and reports are still maintained manually by nurses along with continuous calculation of drug dosage and nutrition as per the changing weight of the baby...
August 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28732163/diamines-can-initiate-new-particle-formation-in-the-atmosphere
#18
Jonas Elm, Monica Passananti, Theo Kurtén, Hanna Vehkamäki
Recent experimental evidence suggests that diamines can enhance atmospheric new particle formation more efficiently compared to monoamines such as dimethylamine. Here we investigate the molecular interactions between sulfuric acid (sa) and the diamine putrescine (put) using computational methods. The molecular structure of up to four sulfuric acid molecules and up to four putrescine molecules were obtained at the ωB97X-D/6-31++G(d,p) level of theory. We utilized a domain local pair natural orbital coupled cluster method (DLPNO-CCSD(T)/aug-cc-pVTZ) to obtain highly accurate binding energies of the clusters...
August 4, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28730433/computational-prediction-of-the-immunomodulatory-potential-of-rna-sequences
#19
Gandharva Nagpal, Kumardeep Chaudhary, Sandeep Kumar Dhanda, Gajendra Pal Singh Raghava
Advances in the knowledge of various roles played by non-coding RNAs have stimulated the application of RNA molecules as therapeutics. Among these molecules, miRNA, siRNA, and CRISPR-Cas9 associated gRNA have been identified as the most potent RNA molecule classes with diverse therapeutic applications. One of the major limitations of RNA-based therapeutics is immunotoxicity of RNA molecules as it may induce the innate immune system. In contrast, RNA molecules that are potent immunostimulators are strong candidates for use in vaccine adjuvants...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28623846/sonocad-a-software-to-solve-the-dilemma-of-the-prenatal-diagnosis-of-fetal-syndromes
#20
Mahmoud Abdelnaby, Abdulmeneam Fawzi, Manal Swelem, Hisham Elgammal, Hamdy Elgammal
OBJECTIVE: The aim of this work is to develop an efficient, user-friendly, time-saving computer software program specified with prenatal diagnosis, based solely on ultrasound findings provided by the sonographer. MATERIALS AND METHOD: Sonographyic computer-assisted diagnosis (SonoCAD) program was developed in four phases. Phase I: data gathering phase. Phase II: the software development phase in which the source code of the software was developed. Phase III: system testing phase that was divided into two steps: alpha testing phase, in which 20 syndromic scenarios were supplied to the software and the beta testing phase, in which the performance of SonoCAD was compared with the performance of the already established web site phenotip...
June 17, 2017: Prenatal Diagnosis
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