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Java Walladbegi, Sarah A Smith, Amy Grayson, Craig Murdoch, Mats Jontell, Helen E Colley
BACKGROUND: The cytotoxic effect of chemotherapeutic agents to the oral mucosa, as a side-effect of cancer treatment, is a major problem. Cooling the oral mucosa using ice chips in conjunction with chemotherapy is known to reduce the severity of oral mucositis. However, although the use of ice chips is of clinical value, this method of cooling has inherent problems including discomfort for the patient, non-uniformity and fluctuations in cooling temperature throughout the oral cavity. Furthermore, despite being used clinically, it is not known what reduction in temperature is required to prevent oral mucositis...
February 22, 2018: Journal of Oral Pathology & Medicine
Yenita Agus, Shigeko Horiuchi, Mariko Iida
BACKGROUND: In the 1990s, the Indonesian government launched programmes to train traditional birth attendants (TBAs) and increase the number of midwives. AIM: To identify and compare the factors that influence women's choice of a midwife or a TBA for maternal healthcare in Indonesia. METHODS: This study used a descriptive design for comparing women's choice of maternal healthcare. The participants were (1) married women, (2) experienced birth within two years, (3) living in a rural or urban village, and (4) capable of communicating in the Indonesia language...
February 14, 2018: Women and Birth: Journal of the Australian College of Midwives
Alexander Bergmayr, Michael Grossniklaus, Manuel Wimmer, Gerti Kappel
The capability of UML profiles to serve as annotation mechanism has been recognized in both research and industry. Today's modeling tools offer profiles specific to platforms, such as Java, as they facilitate model-based engineering approaches. However, considering the large number of possible annotations in Java, manually developing the corresponding profiles would only be achievable by huge development and maintenance efforts. Thus, leveraging annotation-based modeling requires an automated approach capable of generating platform-specific profiles from Java libraries...
2018: Software and Systems Modeling
Raza-Ur Rahman, Abhivyakti Gautam, Jörn Bethune, Abdul Sattar, Maksims Fiosins, Daniel Sumner Magruder, Vincenzo Capece, Orr Shomroni, Stefan Bonn
BACKGROUND: Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep sequencing. RESULTS: Here we present Oasis 2, which is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy...
February 14, 2018: BMC Bioinformatics
Renata F Martins, Anke Schmidt, Dorina Lenz, Andreas Wilting, Joerns Fickel
In this study we compared the phylogeographic patterns of two Rusa species, Rusa unicolor and Rusa timorensis, in order to understand what drove and maintained differentiation between these two geographically and genetically close species and investigated the route of introduction of individuals to the islands outside of the Sunda Shelf. We analyzed full mitogenomes from 56 archival samples from the distribution areas of the two species and 18 microsatellite loci in a subset of 16 individuals to generate the phylogeographic patterns of both species...
February 2018: Ecology and Evolution
Piotr Madanecki, Magdalena Bałut, Patrick G Buckley, J Renata Ochocka, Rafał Bartoszewski, David K Crossman, Ludwine M Messiaen, Arkadiusz Piotrowski
High-throughput technologies generate considerable amount of data which often requires bioinformatic expertise to analyze. Here we present High-Throughput Tabular Data Processor (HTDP), a platform independent Java program. HTDP works on any character-delimited column data (e.g. BED, GFF, GTF, PSL, WIG, VCF) from multiple text files and supports merging, filtering and converting of data that is produced in the course of high-throughput experiments. HTDP can also utilize itemized sets of conditions from external files for complex or repetitive filtering/merging tasks...
2018: PloS One
Andrew Collins, Andrew R Jones
The recent establishment of cloud computing, high throughput networking, and more versatile web standards and browsers has led to a renewed interest in web-based applications. While traditionally big data has been the domain of optimised desktop and server applications, it is now possible to store vast amounts of data and perform the necessary calculations offsite in cloud storage and computing providers, with the results visualised in a high quality cross-platform interface via a web browser. There are number of emerging platforms for cloud based mass spectrometry data analysis, however, there is limited pre-existing code accessible to web developers, especially for those that are constrained to a shared hosting environment where Java and C applications are often forbidden from use by the hosting provider...
February 5, 2018: Journal of Proteome Research
Amit P Java, Kevin L Greason, Angela Dispenzieri, Martha Grogan, Katherine S King, Joseph J Maleszewski, Richard C Daly, Mackram F Eleid, Alberto Pochettino, Hartzell V Schaff
BACKGROUND: Outcome data on aortic valve replacement in patients with amyloidosis are limited. To address this issue, we reviewed our experience of patients with amyloidosis who underwent aortic valve replacement. METHODS: We retrospectively reviewed the records of 16 patients with amyloidosis who underwent aortic valve replacement between May 2000 and February 2017. RESULTS: The cohort comprised 11 males (69%) and 5 females (31%). The median patient age was 76 years (interquartile range [IQR], 71-82 years), and Society of Thoracic Surgeons predicted rate of mortality was 5...
December 19, 2017: Journal of Thoracic and Cardiovascular Surgery
Tomohiro Ono, Yuki Miyabe, Mami Akimoto, Nobutaka Mukumoto, Yoshitomo Ishihara, Mitsuhiro Nakamura, Takashi Mizowaki
PURPOSE: Our aim was to develop a portable quality control (QC) application using a thermometer, a barometer, an angle gauge, and a range finder implemented in a tablet-type consumer electronic device (CED) and to assess the accuracies of the measurements made. METHODS: The QC application was programmed using Java and OpenCV libraries. First, temperature and atmospheric pressure were measured over 30 days using the temperature and pressure sensors of the CED and compared with those measured by a double-tube thermometer and a digital barometer...
February 2, 2018: Medical Physics
Conrad Voelker, Hayder Alsaad
This study aims to develop an approach to couple a computational fluid dynamics (CFD) solver to the University of California, Berkeley (UCB) thermal comfort model to accurately evaluate thermal comfort. The coupling was made using an iterative Java script to automatically transfer data for each individual segment of the human body back and forth between the CFD solver and the UCB model until reaching convergence defined by a stopping criterion. The location from which data are transferred to the UCB model was determined using a new approach based on the temperature difference between subsequent points on the temperature profile curve in the vicinity of the body surface...
February 2, 2018: Indoor Air
Jaima Hillary Smith, Tony King, Clare Campbell, Susan M Cheyne, Vincent Nijman
Population viability analysis is a predictive procedure that uses a combination of different modelling approaches to estimate species vulnerability to extinction. Javan gibbons (Hylobates moloch) are vulnerable to local extinction primarily due to loss of habitat and hunting for the illegal pet trade. Using the modelling software VORTEX, we assessed the status of Javan gibbons in 3 areas (Ujung Kulon National Park, Halimun-Salak National Park, and Dieng Mountains) which hold over half of the remaining estimated number of gibbons on Java...
January 25, 2018: Folia Primatologica; International Journal of Primatology
N Terranova, P Girard, K Ioannou, U Klinkhardt, A Munafo
Mathematical models of tumor dynamics generally omit information on individual target lesions (iTLs), and consider the most important variable to be the sum of tumor sizes (TS). However, differences in lesion dynamics might be predictive of tumor progression. To exploit this information, we have developed a novel and flexible approach for the non-parametric analysis of iTLs, which integrates knowledge from signal processing and machine learning. We called this new methodology ClassIfication Clustering of Individual Lesions (CICIL)...
February 1, 2018: CPT: Pharmacometrics & Systems Pharmacology
Diego Darriba, Tomáš Flouri, Alexandros Stamatakis
With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users...
January 29, 2018: Molecular Biology and Evolution
Rubiatul Adawiyah Bokhari, Nur Adeelah Che Ahmad Tantowi, Seng Fong Lau, Suhaila Mohamed
The effect of Orthosiphon stamineus aqueous (OSA) extract against osteoarthritis (OA) was investigated in explant cartilage culture and in postmenopausal OA rat model. Female rats were bilaterally ovariectomized (OVX). Osteoarthritis was induced after surgical recovery, by intra-articular injection of monosodium iodoacetate (MIA) into the right knee. Rats were grouped (n = 8) into: healthy sham control; non-treated OA; OA + diclofenac (positive control 5 mg/kg); and two doses OSA (150-300 mg/kg). After 4 weeks' treatment, rats were evaluated for OA-related parameters and biomarkers...
January 29, 2018: Inflammopharmacology
Wei Zhang, Zhaohua Deng, Ziying Hong, Richard Evans, Jingdong Ma, Hui Zhang
BACKGROUND: With the rise in popularity of Web 2.0 technologies, the sharing of patient experiences about physicians on online forums and medical websites has become a common practice. However, negative comments posted by patients are considered to be more influential by other patients and physicians than those that are satisfactory. OBJECTIVE: The aim of this study was to analyze negative comments posted online about physicians and to identify possible solutions to improve patient satisfaction, as well as their relationship with physicians...
January 25, 2018: Journal of Medical Internet Research
Dmitry Suplatov, Yana Sharapova, Daria Timonina, Kirill Kopylov, Vytas Švedas
The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e...
December 28, 2017: Journal of Bioinformatics and Computational Biology
C C Chamon, T N A Pereira, M B Mendonça, A Akama
A new species of Spectracanthicus is described from the Rio Javaés, Rio Araguaia basin. The new species is distinguished from its congeners (except Spectracanthicus immaculatus) by colour pattern: body dark grey to dark brown without dots or blotches (v. body colour with yellowish small dots in Spectracanthicus murinus, Spectracanthicus punctatissimus and Spectracanthicus tocantinensis and large white dots in Spectracanthicus zuanoni). It can be further distinguished from S. immaculatus by having thicker and less numerous teeth, with up to eight premaxillary and 20 dentary teeth (v...
January 18, 2018: Journal of Fish Biology
Marius Wöste, Martin Dugas
Summary: With the rapid development in next-generation sequencing, cost and time requirements for genomic sequencing are decreasing, enabling applications in many areas such as cancer research. Many tools have been developed to analyze genomic variation ranging from single nucleotide variants to whole chromosomal aberrations. As sequencing throughput increases, the number of variants called by such tools also grows. Often employed manual inspection of such calls is thus becoming a time-consuming procedure...
January 15, 2018: Bioinformatics
Herfina Y Nababan, Md Hasan, Tiara Marthias, Rolina Dhital, Aminur Rahman, Iqbal Anwar
Purpose: Overall health status indicators have improved significantly over the past three decades in Indonesia. However, the country's maternal mortality ratio remains high with a stark inequality by region. Fewer studies have explored access inequity in maternal health care service over time using multiple inequality markers. In this study, we analyzed Indonesian Demographic and Health Survey (DHS) data to explore trends and inequities in use of any antenatal care (ANC), four or more ANC (ANC4+), institutional birth, and cesarean section (c-section) birth in Indonesia during 1986-2012 to inform policy for future strategies ending preventable maternal deaths...
2018: International Journal of Women's Health
Chunpeng James Chen, Zhiwu Zhang
Summary: The ultimate goal of genomic research is to effectively predict phenotypes from genotypes so that medical management can improve human health and molecular breeding can increase agricultural production. Genomic prediction or selection (GS) plays a complementary role to genome-wide association studies (GWAS), which is the primary method to identify genes underlying phenotypes. Unfortunately, most computing tools cannot perform data analyses for both GWAS and GS. Furthermore, the majority of these tools are executed through a command-line interface (CLI), which requires programming skills...
January 11, 2018: Bioinformatics
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