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https://www.readbyqxmd.com/read/28441656/development-of-a-smartphone-app-for-visualizing-heart-sounds-and-murmurs
#1
Noritaka Mamorita, Naoya Arisaka, Risa Isonaka, Tadashi Kawakami, Akihiro Takeuchi
BACKGROUND: Auscultation is one of the basic techniques for the diagnosis of heart disease. However, the interpretation of heart sounds and murmurs is a highly subjective and difficult skill. OBJECTIVES: To assist the auscultation skill at the bedside, a handy phonocardiogram was developed using a smartphone (Samsung Galaxy J, Android OS 4.4.2) and an external microphone attached to a stethoscope. METHODS AND RESULTS: The Android app used Java classes, "AudioRecord," "AudioTrack," and "View," that recorded sounds, replayed sounds, and plotted sound waves, respectively...
April 26, 2017: Cardiology
https://www.readbyqxmd.com/read/28438318/the-affinities-of-homo-floresiensis-based-on-phylogenetic-analyses-of%C3%A2-cranial-dental-and-postcranial-characters
#2
Debbie Argue, Colin P Groves, Michael S Y Lee, William L Jungers
Although the diminutive Homo floresiensis has been known for a decade, its phylogenetic status remains highly contentious. A broad range of potential explanations for the evolution of this species has been explored. One view is that H. floresiensis is derived from Asian Homo erectus that arrived on Flores and subsequently evolved a smaller body size, perhaps to survive the constrained resources they faced in a new island environment. Fossil remains of H. erectus, well known from Java, have not yet been discovered on Flores...
April 19, 2017: Journal of Human Evolution
https://www.readbyqxmd.com/read/28430977/deep-mining-heterogeneous-networks-of-biomedical-linked-data-to-predict-novel-drug-target-associations
#3
Nansu Zong, Hyeoneui Kim, Victoria Ngo, Olivier Harismendy
Motivation: A heterogeneous network topology possessing abundant interactions between biomedical entities has yet to be utilized in similarity-based methods for predicting drug-target associations based on the array of varying features of drugs and their targets. Deep learning reveals features of vertices of a large network that can be adapted in accommodating the similarity-based solutions to provide a flexible method of drug-target prediction. Results: We propose a similarity-based drug-target prediction method that enhances existing association discovery methods by using a topology-based similarity measure...
April 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28428139/use-and-reporting-of-bayesian-methods-for-primary-data-analysis-in-epidemiological-research-a-systematic-review
#4
REVIEW
Charlotte Rietbergen, Thomas Pa Debray, Irene Klugkist, Kristel Jm Janssen, Karel Gm Moons
BACKGROUND: The objective of this systematic review is to investigate the use of Bayesian data analysis in epidemiology in the past decade, and particularly to evaluate the quality of research papers reporting the results of these analyses. METHODS: Complete volumes of five major epidemiological journals in the period 2005-2015 were searched via Pubmed. In addition we performed an extensive within-manuscript search using a specialized Java application. Details of reporting on Bayesian statistics were examined in original research papers with primary Bayesian data analyses...
April 17, 2017: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/28427373/a-protocol-for-a-cluster-randomized-controlled-trial-of-a-self-help-psycho-education-programme-to-reduce-diagnosis-delay-in-women-with-breast-cancer-symptoms-in-indonesia
#5
Hari Setyowibowo, Marit Sijbrandij, Aulia Iskandarsyah, Joke A M Hunfeld, Sawitri S Sadarjoen, Dharmayanti F Badudu, Drajat R Suardi, Jan Passchier
BACKGROUND: Breast cancer (BC) is the most frequent cancer occurring in women across the world. Its mortality rate in low-middle income countries (LMICs) is higher than in high-income countries (HICs), and in Indonesia BC is the leading cause of cancer deaths among women. Delay in breast cancer diagnosis negatively impacts cancer prognosis. Only about 30% of patients who come to the hospital to check on their breast abnormalities, continue thorough examination to biopsy to get a diagnosis based on the results of anatomical pathology...
April 20, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28423853/square
#6
Carsten Oliver Schmidt, Christine Krabbe, Janka Schössow, Martin Albers, Dörte Radke, Jörg Henke
Valid scientific inferences from epidemiological and clinical studies require high data quality. Data generating departments therefore aim to detect data irregularities as early as possible in order to guide quality management processes. In addition, after the completion of data collections the obtained data quality must be evaluated. This can be challenging in complex studies due to a wide scope of examinations, numerous study variables, multiple examiners, devices, and examination centers. This paper describes a Java EE web application used to monitor and evaluate data quality in institutions with complex and multiple studies, named Square<sup>2</sup>...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28413078/evaluation-of-immunochromatographic-test-ict-strips-for-the-serological-detection-of-babesia-bovis-and-babesia-bigemina-infection-in-cattle-from-western-java-indonesia
#7
Azirwan Guswanto, Puttik Allamanda, Euis Siti Mariamah, Tserendorf Munkjargal, Bumduuren Tuvshintulga, Hitoshi Takemae, Thillaiampalam Sivakumar, Mahmoud AbouLaila, Mohamad Alaa Terkawi, Madoka Ichikawa-Seki, Yoshifumi Nishikawa, Naoaki Yokoyama, Ikuo Igarashi
Three types of immunochromatographic test (ICT) strips were prepared for the detection of an antibody response against spherical body protein 4 (SBP-4) of Babesia bovis (bovICT), C-terminal-truncated rhoptry-associated protein 1 (rRAP1/CT17) of B. bigemina (bigICT), and the combination of both proteins (dual-ICT). The evaluation of their performance was conducted using a confirmed positive and negative serum panel for B. bovis and B. bigemina. Together with ELISA, the ICT strips were applied to determine the seroprevalence of bovine babesiosis in Western Java, Indonesia...
April 10, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28399028/pathologic-and-treatment-outcomes-among-a-geriatric-population-of-endometrial-cancer-patients-an-nrg-oncology-gynecologic-oncology-group-ancillary-data-analysis-of-lap2
#8
Erin A Bishop, James J Java, Kathleen N Moore, Joan L Walker
OBJECTIVES: Elderly endometrial cancer patients have worse disease-specific survival than their younger counterparts, but the cause for this discrepancy is unknown. The goal of this analysis is to compare outcomes by age in a fully staged elderly endometrial cancer population. METHODS/MATERIALS: This is an analysis of patients on Gynecologic Oncology Group Study (GOG) LAP2, which included clinically early stage endometrial cancer patients randomized to laparotomy versus laparoscopy for surgical staging...
May 2017: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/28398456/garn2-coarse-grained-prediction-of-3d-structure-of-large-rna-molecules-by-regret-minimization
#9
Mélanie Boudard, Dominique Barth, Julie Bernauer, Alain Denise, Johanne Cohen
Motivation: Predicting the 3D structure of RNA molecules is a key feature towards predicting their functions. Methods which work at atomic or nucleotide level are not suitable for large molecules. In these cases, coarse-grained prediction methods aim to predict a shape which could be refined later by using more precise methods on smaller parts of the molecule. Results: We developed a complete method for sampling 3D RNA structure at a coarse-grained model, taking a secondary structure as input...
April 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28397710/comparison-of-computed-tomography-shielding-design-methods-using-radshield
#10
Matthew DeLorenzo, Kai Yang, Dee Wu, Weiyuan Wang, I Rutel
PURPOSE: To comprehensively compare four computed tomography (CT) scanner shielding design methods using RadShield, a Java-based Graphical User Interface (GUI). METHODS: RadShield, a floor plan based graphical user interface (GUI), was extended to calculate air kerma and barrier thickness using accepted methods from the National Council on Radiation Protection and Measurements (NCRP), the British Institute of Radiology (BIR), and a method using isodose maps, for spatially distributed points beyond user defined barriers...
April 11, 2017: Journal of Radiological Protection: Official Journal of the Society for Radiological Protection
https://www.readbyqxmd.com/read/28392477/lirex-a-package-for-identification-of-long-inverted-repeats-in-genomes
#11
Yong Wang, Jiao-Mei Huang
Long inverted repeats (LIRs) are evolutionarily and functionally important structures in genomes because of their involvement in RNA interference, DNA recombination, and gene duplication. Identification of LIRs is highly complicated when mismatches and indels between the repeats are permitted. Long inverted repeat explorer (Lirex) was developed and introduced in this report. Written in Java, Lirex provides a user-friendly interface and allows users to specify LIR searching criteria, such as length of the region, as well as pattern and size of the repeats...
April 7, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28391814/antibiogramj-a-tool-for-analysing-images-from-disk-diffusion-tests
#12
C A Alonso, C Domínguez, J Heras, E Mata, V Pascual, C Torres, M Zarazaga
BACKGROUND AND OBJECTIVES: Disk diffusion testing, known as antibiogram, is widely applied in microbiology to determine the antimicrobial susceptibility of microorganisms. The measurement of the diameter of the zone of growth inhibition of microorganisms around the antimicrobial disks in the antibiogram is frequently performed manually by specialists using a ruler. This is a time-consuming and error-prone task that might be simplified using automated or semi-automated inhibition zone readers...
May 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28383659/the-proteins-api-accessing-key-integrated-protein-and-genome-information
#13
Andrew Nightingale, Ricardo Antunes, Emanuele Alpi, Borisas Bursteinas, Leonardo Gonzales, Wudong Liu, Jie Luo, Guoying Qi, Edd Turner, Maria Martin
The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to 'talk' to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby...
April 5, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28379351/sqc-secure-quality-control-for-meta-analysis-of-genome-wide-association-studies
#14
Zhicong Huang, Huang Lin, Jacques Fellay, Zoltán Kutalik, Jean-Pierre Hubaux
Motivation: Due to the limited power of small-scale genome-wide association studies (GWAS), researchers tend to collaborate and establish a larger consortium in order to perform large-scale GWAS. Genome-wide association meta-analysis (GWAMA) is a statistical tool that aims to synthesize results from multiple independent studies to increase the statistical power and reduce false-positive findings of GWAS. However, it has been demonstrated that the aggregate data of individual studies are subject to inference attacks, hence privacy concerns arise when researchers share study data in GWAMA...
April 4, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28369225/aozan-an-automated-post-sequencing-data-processing-pipeline
#15
Sandrine Perrin, Cyril Firmo, Sophie Lemoine, Stéphane Le Crom, Laurent Jourdren
Motivation: Data management and quality control of output from Illumina sequencers is a disk space- and time-consuming task. Thus, we developed Aozan to automatically handle data transfer, demultiplexing, conversion, and quality control once a run has finished. This software greatly improves run data management and the monitoring of run statistics via automatic emails and HTML web reports. Availability and Implementation: Aozan is implemented in Java and Python, supported on Linux systems, and distributed under the GPLv3 License at: http://www...
March 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28369214/constructing-linkage-maps-in-the-genomics-era-with-mapdisto-2-0
#16
Christopher Heffelfinger, Christopher A Fragoso, Mathias Lorieux
Motivation: Genotyping by sequencing (GBS) generates datasets that are challenging to handle by current genetic mapping software with graphical interface. Geneticists need new user-friendly computer programs that can analyze GBS data on desktop computers. This requires improvements in computation efficiency, both in terms of speed and use of random-access memory (RAM). Results: MapDisto v.2.0 is a user-friendly computer program for construction of genetic linkage maps...
March 28, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28368739/training-in-readmission-reduction-in-an-indonesian-hospital
#17
Hasiholan Simorangkir, Stephen J J McGuire
The authors implemented a new discharge protocol to reduce readmission rates in a hospital in West Java, Indonesia. Forty nurses were trained in the use of the protocol. Results indicate that posttest group readmission rates were significantly lower after the implementation of protocol, from 6.11% to 4.21%. The protocol was effective in reducing readmissions for patients discharged from internal medicine, pulmonology, and women. Differences were also found by type of insurance or payment method, generally suggesting that the lower the socioeconomic status of the patients was, the more effective the discharge protocol was...
April 3, 2017: Hospital Topics
https://www.readbyqxmd.com/read/28358893/halvade-rna-parallel-variant-calling-from-transcriptomic-data-using-mapreduce
#18
Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier
Given the current cost-effectiveness of next-generation sequencing, the amount of DNA-seq and RNA-seq data generated is ever increasing. One of the primary objectives of NGS experiments is calling genetic variants. While highly accurate, most variant calling pipelines are not optimized to run efficiently on large data sets. However, as variant calling in genomic data has become common practice, several methods have been proposed to reduce runtime for DNA-seq analysis through the use of parallel computing. Determining the effectively expressed variants from transcriptomics (RNA-seq) data has only recently become possible, and as such does not yet benefit from efficiently parallelized workflows...
2017: PloS One
https://www.readbyqxmd.com/read/28351384/maternal-characteristics-and-obstetrical-complications-impact-neonatal-outcomes-in-indonesia-a-prospective-study
#19
Trisari Anggondowati, Ayman A E El-Mohandes, S Nurul Qomariyah, Michele Kiely, Judith J Ryon, Reginald F Gipson, Benjamin Zinner, Anhari Achadi, Linda L Wright
BACKGROUND: We investigated associations between maternal characteristics, access to care, and obstetrical complications including near miss status on admission or during hospitalization on perinatal outcomes among Indonesian singletons. METHODS: We prospectively collected data on inborn singletons at two hospitals in East Java. Data included socio-demographics, reproductive, obstetric and neonatal variables. Reduced multivariable models were constructed. Outcomes of interest included low and very low birthweight (LBW/VLBW), asphyxia and death...
March 28, 2017: BMC Pregnancy and Childbirth
https://www.readbyqxmd.com/read/28334306/peptidemapper-efficient-and-versatile-amino-acid-sequence-and-tag-mapping
#20
Dominik Kopczynski, Harald Barsnes, Pål R Njølstad, Albert Sickmann, Marc Vaudel, Robert Ahrends
Summary: The mapping of amino acid sequences is an essential task in bioinformatics. Notably, the mapping of peptide sequences on a proteome is required for the post-processing of proteomics results. However, this step can quickly become a bottleneck when working with extensive numbers of peptides or large protein sequence databases. Here, we present PeptideMapper, a novel amino acid sequence mapper for both peptide sequences and de novo sequencing identification results. By taking advantage of the latest advances in pattern matching, PeptideMapper achieves unprecedented performance (i...
March 2, 2017: Bioinformatics
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