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https://www.readbyqxmd.com/read/29036683/cr2cancer-a-database-for-chromatin-regulators-in-human-cancer
#1
Beibei Ru, Jianlong Sun, Yin Tong, Ching Ngar Wong, Aditi Chandra, Acacia Tsz So Tang, Larry Ka Yue Chow, Wai Lam Wun, Zarina Levitskaya, Jiangwen Zhang
Chromatin regulators (CRs) can dynamically modulate chromatin architecture to epigenetically regulate gene expression in response to intrinsic and extrinsic signalling cues. Somatic alterations or misexpression of CRs might reprogram the epigenomic landscape of chromatin, which in turn lead to a wide range of common diseases, notably cancer. Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036546/crocoblast-running-blast-efficiently-in-the-age-of-next-generation-sequencing
#2
Ravi José Tristão Ramos, Allan Cézar de Azevedo Martins, Gabrielle da Silva Delgado, Crina-Maria Ionescu, Turán Peter Ürményi, Rosane Silva, Jaroslav Koca
Summary: CrocoBLAST is a tool for dramatically speeding up BLAST+ execution on any computer. Alignments that would take days or weeks with NCBI BLAST+ can be run overnight with CrocoBLAST. Additionally, CrocoBLAST provides features critical for NGS data analysis, including: results identical to those of BLAST+; compatibility with any BLAST+ version; real-time information regarding calculation progress and remaining run time; access to partial alignment results; queueing, pausing, and resuming BLAST+ calculations without information loss...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036533/gvolante-for-standardizing-completeness-assessment-of-genome-and-transcriptome-assemblies
#3
Osamu Nishimura, Yuichiro Hara, Shigehiro Kuraku
Motivation: Along with the increasing accessibility to comprehensive sequence information, such as whole genomes and transcriptomes, the demand for assessing their quality has been multiplied. To this end, metrics based on sequence lengths, such as N50, have become a standard, but they only evaluate one aspect of assembly quality. Conversely, analyzing the coverage of pre-selected reference protein-coding genes provides essential content-based quality assessment, but the currently available pipelines for this purpose, CEGMA and BUSCO, do not have a user-friendly interface to serve as a uniform environment for assembly completeness assessment...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036529/itsonedb-a-comprehensive-collection-of-eukaryotic-ribosomal-rna-internal-transcribed-spacer-1-its1-sequences
#4
Monica Santamaria, Bruno Fosso, Flavio Licciulli, Bachir Balech, Ilaria Larini, Giorgio Grillo, Giorgio De Caro, Sabino Liuni, Graziano Pesole
A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036527/isyte-2-0-a-database-for-expression-based-gene-discovery-in-the-eye
#5
Atul Kakrana, Andrian Yang, Deepti Anand, Djordje Djordjevic, Deepti Ramachandruni, Abhyudai Singh, Hongzhan Huang, Joshua W K Ho, Salil A Lachke
Although successful in identifying new cataract-linked genes, the previous version of the database iSyTE (integrated Systems Tool for Eye gene discovery) was based on expression information on just three mouse lens stages and was functionally limited to visualization by only UCSC-Genome Browser tracks. To increase its efficacy, here we provide an enhanced iSyTE version 2.0 (URL: http://research.bioinformatics.udel.edu/iSyTE) based on well-curated, comprehensive genome-level lens expression data as a one-stop portal for the effective visualization and analysis of candidate genes in lens development and disease...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036445/development-validation-and-demonstration-of-the-nthu-flight-dose-calculator
#6
An-Lun Li, Wei-Fan Pan, Rong-Jiun Sheu
Galactic cosmic-ray-induced air showers constitute the largest source of radiation exposure for aircrew and passengers. To facilitate the evaluation of effective doses received by this population, a database containing dose rates of various radiation components in the atmosphere was established; the parameterization accounted for altitude, geomagnetic rigidity and solar modulation. Energy spectra of secondary cosmic rays and effective dose rates were calculated using the FLUKA Monte Carlo code. An auxiliary MATLAB program with a graphical user interface was developed to estimate the aviation route dose through interpolation and integration...
September 23, 2017: Radiation Protection Dosimetry
https://www.readbyqxmd.com/read/29036351/mirandola-2017-a-curated-knowledge-base-of-non-invasive-biomarkers
#7
Francesco Russo, Sebastiano Di Bella, Federica Vannini, Gabriele Berti, Flavia Scoyni, Helen V Cook, Alberto Santos, Giovanni Nigita, Vincenzo Bonnici, Alessandro Laganà, Filippo Geraci, Alfredo Pulvirenti, Rosalba Giugno, Federico De Masi, Kirstine Belling, Lars J Jensen, S Ren Brunak, Marco Pellegrini, Alfredo Ferro
miRandola (http://mirandola.iit.cnr.it/) is a database of extracellular non-coding RNAs (ncRNAs) that was initially published in 2012, foreseeing the relevance of ncRNAs as non-invasive biomarkers. An increasing amount of experimental evidence shows that ncRNAs are frequently dysregulated in diseases. Further, ncRNAs have been discovered in different extracellular forms, such as exosomes, which circulate in human body fluids. Thus, miRandola 2017 is an effort to update and collect the accumulating information on extracellular ncRNAs that is spread across scientific publications and different databases...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036298/myvcf-a-desktop-application-for-high-throughput-mutations-data-management
#8
Alessandro Pietrelli, Luca Valenti
Summary: Next-generation sequencing technologies have become the most powerful tool to discover genetic variants associated with human diseases. Although the dramatic reductions in the costs facilitate the use in the wet-lab and clinics, the huge amount of data generated renders their management by non-expert researchers and physicians extremely difficult. Therefore, there is an urgent need of novel approaches and tools aimed at getting the 'end-users' closer to the sequencing data, facilitating the access by non-bioinformaticians, and to speed-up the functional interpretation of genetic variants...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29035624/nurses-perceptions-and-problems-in-the-usability-of-a-medication-safety-app
#9
Kalyani Ankem, Sookyung Cho, Diana Simpson
INTRODUCTION: The majority of medication apps support medication adherence. Equally, if not more important, is medication safety. Few apps report on medication safety, and fewer studies have been conducted with these apps. OBJECTIVES: The usability of a medication safety app was tested with nurses to reveal their perceptions of the graphical user interface and to discover problems they encountered in using the app. METHODS: Usability testing of the app was conducted with RN-BSN students and informatics students (n = 18)...
October 16, 2017: Informatics for Health & Social Care
https://www.readbyqxmd.com/read/29035160/towards-malaria-control-and-elimination-in-ghana-challenges-and-decision-making-tools-to-guide-planning
#10
Timothy Awine, Keziah Malm, Constance Bart-Plange, Sheetal P Silal
Ghana is classified as being in the malaria control phase, according to the global malaria elimination program. With many years of policy development and control interventions, malaria specific mortality among children less than 5 years old has declined from 14.4% in 2000 to 0.6% in 2012. However, the same level of success has not been achieved with malaria morbidity. The recently adopted 2015-2020 Ghana strategic action plan aims to reduce the burden of malaria by 75.0%. Planning and policy development has always been guided by evidence from field studies, and mathematical models that are able to investigate malaria transmission dynamics have not played a significant role in supporting policy development...
2017: Global Health Action
https://www.readbyqxmd.com/read/29031082/quantum-associative-memory-with-linear-and-non-linear-algorithms-for-the-diagnosis-of-some-tropical-diseases
#11
J-P Tchapet Njafa, S G Nana Engo
This paper presents the QAMDiagnos, a model of Quantum Associative Memory (QAM) that can be a helpful tool for medical staff without experience or laboratory facilities, for the diagnosis of four tropical diseases (malaria, typhoid fever, yellow fever and dengue) which have several similar signs and symptoms. The memory can distinguish a single infection from a polyinfection. Our model is a combination of the improved versions of the original linear quantum retrieving algorithm proposed by Ventura and the non-linear quantum search algorithm of Abrams and Lloyd...
September 21, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/29029024/diversepathsj-diverse-shortest-paths-for-bioimage-analysis
#12
Virginie Uhlmann, Carsten Haubold, Fred A Hamprecht, Michael Unser
Motivation: We introduce a formulation for the general task of finding diverse shortest paths between two end-points. Our approach is not linked to a specific biological problem and can be applied to a large variety of images thanks to its generic implementation as a user-friendly ImageJ/Fiji plugin. It relies on the introduction of additional layers in a Viterbi path graph, which requires slight modifications to the standard Viterbi algorithm rules. This layered graph construction allows for the specification of various constraints imposing diversity between solutions...
September 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028989/phast-phaster-and-phastest-tools-for-finding-prophage-in-bacterial-genomes
#13
David Arndt, Ana Marcu, Yongjie Liang, David S Wishart
PHAST (PHAge Search Tool) and its successor PHASTER (PHAge Search Tool - Enhanced Release) have become two of the most widely used web servers for identifying putative prophages in bacterial genomes. Here we review the main capabilities of these web resources, provide some practical guidance regarding their use and discuss possible future improvements. PHAST, which was first described in 2011, made its debut just as whole bacterial genome sequencing and was becoming inexpensive and relatively routine. PHAST quickly gained popularity among bacterial genome researchers because of its web accessibility, its ease of use along with its enhanced accuracy and rapid processing times...
September 25, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29028917/comparative-usability-of-modern-anaesthesia-ventilators-a-human-factors-study
#14
J Spaeth, T Schweizer, A Schmutz, H Buerkle, S Schumann
Background: The anaesthesia ventilator represents the key equipment for intraoperative respiratory care. Improper operation of this device may threaten a patient's health. A self-explanatory interface facilitates handling and decreases the risk of operating errors. This study systematically evaluates the usability of user interfaces in four modern anaesthesia ventilators. Methods: Twenty naïve operators were asked to execute 20 tasks on each of four different anaesthesia ventilators (Avance CS2™, GE Healthcare; Flow-i™, Maquet; and Perseus™ and Primus™, Dräger) in a randomized order...
October 3, 2017: British Journal of Anaesthesia
https://www.readbyqxmd.com/read/29028878/web-based-drug-repurposing-tools-a-survey
#15
Elizabeth Sam, Prashanth Athri
Drug repurposing (a.k.a. drug repositioning) is the search for new indications or molecular targets distinct from a drug's putative activity, pharmacological effect or binding specificities. With the ever-increasing rates of termination of drugs in clinical trials, drug repositioning has risen as one of the effective solutions against the risk of drug failures. Repositioning finds a way to reverse the grim but real trend that Eroom's law portends for the pharmaceutical and biotech industry, and drug discovery in general...
October 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29026438/mental-health-assessments-in-refugees-and-asylum-seekers-evaluation-of-a-tablet-assisted-screening-software
#16
Naser Morina, Simon M Ewers, Sandra Passardi, Ulrich Schnyder, Christine Knaevelsrud, Julia Müller, Richard A Bryant, Angela Nickerson, Matthis Schick
BACKGROUND: Mental health problems resulting from persecution and forced migration are very common among refugees and asylum seekers and evolve into a major public health challenge in hosting societies. Language barriers often prevent timely access to appropriate health care, leading to chronic trajectories and abortive social integration. Tools for multilingual screening and assessment could be of great benefit for this particularly vulnerable population as well as for policy makers...
2017: Conflict and Health
https://www.readbyqxmd.com/read/29025696/usability-test-of-exercise-games-designed-for-rehabilitation-of-elderly-patients-after-hip-replacement-surgery-pilot-study
#17
Yun Ling, Louis P Ter Meer, Zerrin Yumak, Remco C Veltkamp
BACKGROUND: Patients who receive rehabilitation after hip replacement surgery are shown to have increased muscle strength and better functional performance. However, traditional physiotherapy is often tedious and leads to poor adherence. Exercise games, provide ways for increasing the engagement of elderly patients and increase the uptake of rehabilitation exercises. OBJECTIVE: The objective of this study was to evaluate Fietsgame (Dutch for cycling game), which translates existing rehabilitation exercises into fun exercise games...
October 12, 2017: JMIR Serious Games
https://www.readbyqxmd.com/read/29025144/synthea-an-approach-method-and-software-mechanism-for-generating-synthetic-patients-and-the-synthetic-electronic-health-care-record
#18
Jason Walonoski, Mark Kramer, Joseph Nichols, Andre Quina, Chris Moesel, Dylan Hall, Carlton Duffett, Kudakwashe Dube, Thomas Gallagher, Scott McLachlan
Objective: Our objective is to create a source of synthetic electronic health records that is readily available; suited to industrial, innovation, research, and educational uses; and free of legal, privacy, security, and intellectual property restrictions. Materials and Methods: We developed Synthea, an open-source software package that simulates the lifespans of synthetic patients, modeling the 10 most frequent reasons for primary care encounters and the 10 chronic conditions with the highest morbidity in the United States...
August 30, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/29025122/software-application-profile-opal-and-mica-open-source-software-solutions-for-epidemiological-data-management-harmonization-and-dissemination
#19
Dany Doiron, Yannick Marcon, Isabel Fortier, Paul Burton, Vincent Ferretti
Motivation: Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination. Implementation: Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP...
September 2, 2017: International Journal of Epidemiology
https://www.readbyqxmd.com/read/29024413/deep-tissue-loads-in-the-seated-buttocks-on-an-off-loading-wheelchair-cushion-versus-air-cell-based-and-foam-cushions-finite-element-studies
#20
Lea Peko Cohen, Amit Gefen
For wheelchair users, a common injury is a sitting-acquired pressure ulcer (PU) which typically onsets near the interface between the ischial tuberosity (IT) and the overlying soft tissues. The risk of developing PUs can be reduced considerably if an adequate cushion is placed on the wheelchair in order to protect tissues from PUs by minimising interface mechanical loads between the body and cushion and also, exposure to internal soft tissue loads. In this work, we studied the biomechanical performances of an off-loading (OL) cushion with limited adjustability, in comparison to a standard foam cushion and a fully adjustable air-cell-based (ACB) cushion...
September 6, 2017: International Wound Journal
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