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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
Chi-Jung Chung, Yu-Chen Kuo, Yun-Yu Hsieh, Tsai-Chung Li, Cheng-Chieh Lin, Wen-Miin Liang, Li-Na Liao, Chia-Ing Li, Hsueh-Chun Lin
PURPOSE: This study applied open source technology to establish a subject-enabled analytics model that can enhance measurement statistics of case studies with the public health data in cloud computing. METHODS: The infrastructure of the proposed model comprises three domains: 1) the health measurement data warehouse (HMDW) for the case study repository, 2) the self-developed modules of online health risk information statistics (HRIStat) for cloud computing, and 3) the prototype of a Web-based process automation system in statistics (PASIS) for the health risk assessment of case studies with subject-enabled evaluation...
November 2017: International Journal of Medical Informatics
Piotr Dzwiniel, Mateusz Gola, Anna Wójcik-Gryciuk, Wioletta J Waleszczyk
Visual field impairment affects more than 100 million people globally. However, due to the lack of the access to appropriate ophthalmic healthcare in undeveloped regions as a result of associated costs and expertise this number may be an underestimate. Improved access to affordable diagnostic software designed for visual field examination could slow the progression of diseases, such as glaucoma, allowing for early diagnosis and intervention. We have developed Specvis, a free and open-source application written in Java programming language that can run on any personal computer to meet this requirement (http://www...
2017: PloS One
Sainan An, Xiaoping Feng, Yue Dai, Hongli Bo, Xiuqing Wang, Mu Li, John Zhuohao Woo, Xingmei Liang, Cheng Guo, Charles Xingchao Liu, Liping Wei
BACKGROUND: Mobile touchscreen devices are currently being used as speech-generating devices (SGDs) and have been shown to promote the communication skills, particularly the requesting skills of children with autism spectrum disorders (ASD) who have limited spoken language. However, no augmentative and alternative communication (AAC) mobile app has been developed and evaluated in the Chinese language in Mainland China. METHODS: We developed an AAC mobile app, which is the first in Mainland China, to our knowledge, named Yuudee (Chinese name (xiaoyudi))...
2017: Molecular Autism
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
Dewi Santosaningsih, Sanarto Santoso, Henri A Verbrugh, Juliëtte A Severin
This study aimed to identify risk factors for methicillin-resistant Staphylococcus aureus (MRSA) carriage among patients at admission to the surgery ward in a resource-limited hospital in Indonesia. A case-control study was performed including 65 MRSA carriage patients and 132 non-MRSA carriage patients screened at admission to surgery wards in a hospital in Malang, East Java. For MRSA screening, swabs were obtained from nares and throat, cultured in an enrichment broth followed by subculturing onto CHROMagar(™) MRSA; suspected colonies were confirmed by polymerase chain reaction...
September 18, 2017: American Journal of Tropical Medicine and Hygiene
Manmohan Pandey, Ravindra Kumar, Prachi Srivastava, Suyash Agarwal, Shreya Srivastava, N S Nagpure, J K Jena, Basdeo Kushwaha
Mining and characterization of SSR markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. WGS-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, ncRNA, core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic and core gene region) along with primer identification and mining of cross-species markers...
September 16, 2017: Journal of Heredity
Nurfika Asmaningrum, Yun-Fang Tsai
AIM: To gain an understanding towards the perspectives of hospitalized inpatients in Indonesia regarding maintaining dignity during clinical care. BACKGROUND: Dignity is a basic human right that is crucial for an individual's well-being. Respect for a person as a valuable human is a concept that is comparable to treating a person with dignity. Maintaining patient's dignity is an ethical goal of nursing care. Nevertheless, the concept is highly dependent on cultural context...
October 5, 2017: Journal of Advanced Nursing
Java Walladbegi, Martin Gellerstedt, Anncarin Svanberg, Mats Jontell
PURPOSE: Most of the patients who receive myeloablative therapy prior to stem cell transplantation develop oral mucositis (OM). This adverse reaction manifests as oral mucosal erythema and ulcerations and may require high doses of morphine for pain alleviation. OM may also interfere with food intake and result in weight loss, a need for parenteral nutrition, and impaired quality of life. To date, there have been very few studies of evidence-based interventions for the prevention of OM...
October 3, 2017: Cancer Chemotherapy and Pharmacology
Kristoffer Bernhem, Hjalmar Brismar
Summary: SMLocalizer combines the availability of ImageJ with the power of GPU processing for fast and accurate analysis of single molecule localization microscopy data. Analysis of 2D and 3D data in multiple channels is supported. Availability and Implementation: Plugin freely available for Fiji and ImageJ2.0 through . Plugin also available for continuous updates through ImageJ update system, add http://sites.imagej...
September 4, 2017: Bioinformatics
Lydia Ninan Lestario, Luke R Howard, Cindi Brownmiller, Nathan B Stebbins, Rohana Liyanage, Jackson O Lay
Java plum (Syzygium cumini Lam.) is a rich source of polyphenolics with many purported health benefits, but the effect of maturation on polyphenolic content is unknown. Freeze-dried samples of Java plum from seven different maturity stages were analyzed for anthocyanin, flavonol, flavanonol and hydrolysable tannin composition by HPLC. Anthocyanins were first detected at the green-pink stage of maturity and increased throughout maturation with the largest increase occurring from the dark purple to black stages of maturation...
October 2017: Food Research International
Son Hoang Nguyen, Tania Duarte, Lachlan Coin, Minh Duc Cao
Motivation: The recent introduction of a barcoding protocol for Oxford Nanopore sequencing has increased the versatility of the technology. Several bioinformatics tools have been developed to demultiplex barcoded reads, but none of them support streaming analysis. This limits the use of multiplexed sequencing in real- time applications, which is one of the main advantages of the technology. Results: We introduced npBarcode, an open source and cross platform tool for barcode demultiplexing in streaming fashion that can be used to pipe data to further real-time analyses...
August 24, 2017: Bioinformatics
Aravind Sankar, Sayan Ranu, Karthik Raman
Motivation: The ability to predict pathways for biosynthesis of metabolites is very important in metabolic engineering. It is possible to mine the repertoire of biochemical transformations from reaction databases, and apply the knowledge to predict reactions to synthesise new molecules. However, this usually involves a careful understanding of the mechanism and the knowledge of the exact bonds being created and broken. There is a need for a method to rapidly predict reactions for synthesising new molecules, which relies only on the structures of the molecules, without demanding additional information such as thermodynamics or hand-curated reactant mapping, which are often hard to obtain accurately...
July 27, 2017: Bioinformatics
Christopher Churas, Alex J Perez, Hiroyuki Hakozaki, Willy Wong, David Lee, Steven T Peltier, Mark H Ellisman
Summary: To expedite the review of semi-automated probability maps of organelles and other features from 3D electron microscopy data we have developed Probability Map Viewer, a Java-based web application that enables the computation and visualization of probability map generation results in near real-time as the data are being collected from the microscope. Probability Map Viewer allows the user to select one or more voxel classifiers, apply them on a sub-region of an active collection, and visualize the results as overlays on the raw data via any web browser using a personal computer or mobile device...
October 1, 2017: Bioinformatics
M Queißer, M R Burton, F Arzilli, A Chiarugi, G I Marliyani, F Anggara, A Harijoko
Studying the quantity and origin of CO2 emitted by back-arc mud volcanoes is critical to correctly model fluid-dynamical, thermodynamical, and geochemical processes that drive their activity and to constrain their role in the global geochemical carbon cycle. We measured CO2 fluxes of the Bledug Kuwu mud volcano on the Kendeng Fold and thrust belt in the back arc of Central Java, Indonesia, using scanning remote sensing absorption spectroscopy. The data show that the expelled gas is rich in CO2 with a volume fraction of at least 16 vol %...
June 2017: Journal of Geophysical Research. Solid Earth
Rubiatul Adawiyah Bokhari, Seng Fong Lau, Suhaila Mohamed
OBJECTIVE: Orthosiphon stamineus (OS) or Misai Kucing (Java tea) is a popular herbal supplement from Southeast Asia for various metabolic, age-related diseases. This study investigated the potential use of OS leaf extracts to ameliorate osteoporosis in ovariectomized rats. METHODS: Fifty-six female Sprague-Dawley rats were randomly allocated into eight groups (n = 7): SHAM (healthy sham control); OVX (ovarietomized) nontreated rats (negative control); OVX + Remifemin (100 mg/kg body weight), and 2% green tea extract (positive controls); OVX + OS 50% ethanolic and aqueous extracts, both at either 150 or 300 mg/kg...
September 18, 2017: Menopause: the Journal of the North American Menopause Society
Ryuichi Kobayashi, Atit Kanti, Hiroko Kawasaki
This study describes three novel xylose-assimilating yeasts, which were isolated from decayed wood collected from Bung Hatta Botanical Garden in West Sumatra and Cibodas Botanic Garden in West Java, or from litter from Eka Karya Bali Botanic Garden in Bali, Indonesia. Phylogenetic analysis was performed based on the sequences of the D1/D2 domains of the large ribosomal subunit (LSU), the small ribosomal subunit (SSU), the internal transcribed spacer (ITS) and elongation factor-1α (EF-1α), and the three strains were found to represent three novel species belonging to genera Barnettozyma or Wickerhamomyces...
September 12, 2017: International Journal of Systematic and Evolutionary Microbiology
Georg Fette, Mathias Kaspar, Georg Dietrich, Maximilian Ertl, Jonathan Krebs, Stefan Stoerk, Frank Puppe
In recent years, clinical data warehouses (CDW) storing routine patient data have become more and more popular to support scientific work in the medical domain. Although CDW systems provide interfaces to import new data, these interfaces have to be used by processing tools that are often not included in the systems themselves. In order to establish an extraction-transformation-load (ETL) workflow, already existing components have to be taken or new components have to be developed to perform the load part of the ETL...
2017: Studies in Health Technology and Informatics
Yoichiro Nakatani, Aoife McLysaght
Motivation: It has been argued that whole-genome duplication (WGD) exerted a profound influence on the course of evolution. For the purpose of fully understanding the impact of WGD, several formal algorithms have been developed for reconstructing pre-WGD gene order in yeast and plant. However, to the best of our knowledge, those algorithms have never been successfully applied to WGD events in teleost and vertebrate, impeded by extensive gene shuffling and gene losses. Results: Here, we present a probabilistic model of macrosynteny (i...
July 15, 2017: Bioinformatics
Stefan Theisen, Harry W Palm, Sarah H Al-Jufaili, Sonja Kleinertz
An endoparasitic monogenean was identified for the first time from Indonesia. The oesophagus and anterior stomach of the croakers Nibea soldado (Lacépède) and Otolithes ruber (Bloch & Schneider) (n = 35 each) sampled from the South Java coast in May 2011 and Johnius amblycephalus (Bleeker) (n = 2) (all Sciaenidae) from Kedonganan fish market, South Bali coast, in November 2016, were infected with Pseudempleurosoma haywardi sp. nov. Prevalences in the first two croakers were 63% and 46%, respectively, and the two J...
2017: PloS One
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