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https://www.readbyqxmd.com/read/28302930/molecular-characterization-of-an-akabane-virus-isolate-from-west-java-indonesia
#1
Suryo Purnomo Edi, Afif Ibrahim, Rinto Sukoco, Lukman Bunali, Masaji Taguchi, Tomoko Kato, Tohru Yanase, Hiroaki Shirafuji
We isolated an arbovirus from bovine blood in Indonesia. The arbovirus was obtained from the plasma of a cow showing no clinical symptoms in West Java in February 2014, and was identified as Akabane virus (AKAV) by AKAV-specific RT-PCR and subsequent sequence analysis. Phylogenetic analysis based on partial S segment indicated the AKAV isolate, WJ-1SA/P/2014, was most closely related with two isolates from Israel and Turkey reported in 2001 and 2015, respectively, and that WJ-1SA/P/2014 isolate belongs to AKAV genogroup Ib...
March 8, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28297451/radshield-semiautomated-shielding-design-using-a-floor-plan-driven-graphical-user-interface
#2
Matthew C DeLorenzo, Dee H Wu, Kai Yang, Isaac B Rutel
The purpose of this study was to introduce and describe the development of RadShield, a Java-based graphical user interface (GUI), which provides a base design that uniquely performs thorough, spatially distributed calculations at many points and reports the maximum air-kerma rate and barrier thickness for each barrier pursuant to NCRP Report 147 methodology. Semiautomated shielding design calculations are validated by two approaches: a geometry-based approach and a manual approach. A series of geometry-based equations were derived giving the maximum air-kerma rate magnitude and location through a first derivative root finding approach...
September 2016: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28293298/rapid-development-of-entity-based-data-models-for-bioinformatics-with-persistence-object-oriented-design-and-structured-interfaces
#3
Elishai Ezra Tsur
Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed...
2017: BioData Mining
https://www.readbyqxmd.com/read/28284194/clonocalc-and-clonoplot-immune-repertoire-analysis-from-raw-files-to-publication-figures-with-graphical-user-interface
#4
Anke Fähnrich, Moritz Krebbel, Normann Decker, Martin Leucker, Felix D Lange, Kathrin Kalies, Steffen Möller
BACKGROUND: Next generation sequencing (NGS) technologies enable studies and analyses of the diversity of both T and B cell receptors (TCR and BCR) in human and animal systems to elucidate immune functions in health and disease. Over the last few years, several algorithms and tools have been developed to support respective analyses of raw sequencing data of the immune repertoire. These tools focus on distinct aspects of the data processing and require a strong bioinformatics background...
March 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28282767/pulmonary-edema-in-preeclampsia-an-indonesian-case-control-study
#5
Manggala Pasca Wardhana, Erry Gumilar Dachlan, Gustaaf Dekker
OBJECTIVE: To analyze risk factors, obstetric outcome and the need for mechanical ventilation in preeclampsia complicated by pulmonary edema. MATERIALS AND METHODS: Case-control study using medical record on preeclampsia complicated by pulmonary edema patients in East Java tertiary referral hospital over 2 years. A simple scoring system was developed to predict the need for mechanical ventilation, using logistic regression. RESULTS: 1106 cases of preeclampsia were admitted, with 62 cases (5...
March 1, 2017: Journal of Maternal-fetal & Neonatal Medicine
https://www.readbyqxmd.com/read/28280770/a-tool-to-simulate-the-transmission-reception-and-execution-of-interactive-tv-applications
#6
Manoel Carvalho Marques Neto, Raoni Kulesza, Thiago Rodrigues, Felipe A L Machado, Celso A S Santos
The emergence of Interactive Digital Television (iDTV) opened a set of technological possibilities that go beyond those offered by conventional TV. Among these opportunities we can highlight interactive contents that run together with linear TV program (television service where the viewer has to watch a scheduled TV program at the particular time it is offered and on the particular channel it is presented on). However, developing interactive contents for this new platform is not as straightforward as, for example, developing Internet applications...
2017: International Scholarly Research Notices
https://www.readbyqxmd.com/read/28280367/clarifying-the-molecular-mechanism-associated-with-carfilzomib-resistance-in-human-multiple-myeloma-using-microarray-gene-expression-profile-and-genetic-interaction-network
#7
Zhihong Zheng, Tingbo Liu, Jing Zheng, Jianda Hu
Carfilzomib is a Food and Drug Administration-approved selective proteasome inhibitor for patients with multiple myeloma (MM). However, recent studies indicate that MM cells still develop resistance to carfilzomib, and the molecular mechanisms associated with carfilzomib resistance have not been studied in detail. In this study, to better understand its potential resistant effect and its underlying mechanisms in MM, microarray gene expression profile associated with carfilzomib-resistant KMS-11 and its parental cell line was downloaded from Gene Expression Omnibus database...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28273111/mating-success-follows-duet-dancing-in-the-java-sparrow
#8
Masayo Soma, Midori Iwama
Mutual interactions between sexes have multiple signalling functions. Duet singing in songbirds is related to mutual mate guarding, joint resource defence, and signalling commitment. Coordinated visual displays of mating pairs are thought to perform similar functions, but are less well understood. The current study evaluated mutual interactions in an Estrildid species to explore the relative importance of duet dancing and male singing in mating success of pairs in a first encounter. When Java sparrows (Lonchura oryzivora) court prospective mates, only males sing...
2017: PloS One
https://www.readbyqxmd.com/read/28257078/google-earth-based-visualizations-for-environmental-flows-and-pollutant-dispersion-in-urban-areas
#9
Daoming Liu, Sasa Kenjeres
In the present study, we address the development and application of an efficient tool for conversion of results obtained by an integrated computational fluid dynamics (CFD) and computational reaction dynamics (CRD) approach and their visualization in the Google Earth. We focus on results typical for environmental fluid mechanics studies at a city scale that include characteristic wind flow patterns and dispersion of reactive scalars. This is achieved by developing a code based on the Java language, which converts the typical four-dimensional structure (spatial and temporal dependency) of data results in the Keyhole Markup Language (KML) format...
March 2, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28255262/new-early-cenozoic-ghost-shrimps-decapoda-axiidea-callianassidae-from-pakistan-and-their-palaeobiogeographic-implications
#10
Matúš Hyžný, Sylvain Charbonnier, Didier Merle, Rafique Ahmed Lashari, Annachiara Bartolini, Grégoire Mètais
A new set of Paleocene and Eocene decapod crustaceans is described from the Kirthar Range of Pakistan. Two new ghost shrimps (Crustacea, Decapoda, Callianassidae) are described: Neocallichirus khadroensis Hyžný & Charbonnier, n. sp. from the Paleocene (Danian, Khadro Formation) of Gawar Band, Ranikot District, and Neocallichirus lakhraensis Hyžný & Charbonnier, n. sp. from the Early Eocene (Ypresian, Lakhra Formation) of Rbod Nala, Jhirak District. Both new species exhibit chelipeds which are morphologically surprisingly close to extant Neocallichirus karumba (Poore & Griffin, 1979) from the Indo-West Pacific...
September 2016: Geodiversitas
https://www.readbyqxmd.com/read/28252219/the-bandung-neurosurgery-patient-outcomes-project-indonesia-part-ii-patient-pathways-and-feasibility-and-acceptability-of-telephone-follow-up
#11
Agung Budi Sutiono, Ahmad Faried, Susan McAllister, Amelia Ganefianty, Kalih Sarjono, Muhammad Zafrullah Arifin, Sarah Derrett
INTRODUCTION: Support of neurosurgery patients following discharge from hospital is important. Currently, little is known about patients' in low- and middle-income countries before and after their hospital treatment. This companion paper reports patients' pathways before and after hospital admission and the feasibility of following up this ill-patient population by telephone. METHODS: Eligible patients were aged ≥18 years admitted to the Neurosurgery Department in Dr...
March 2, 2017: International Journal of Health Planning and Management
https://www.readbyqxmd.com/read/28244712/household-dietary-diversity-and-child-stunting-in-east-java-indonesia
#12
Trias Mahmudiono, Sri Sumarmi, Richard R Rosenkranz
BACKGROUND AND OBJECTIVES: More than one-quarter of under-five children in the developing world are stunted, and those with poor nutrient intake are at risk of irreversible cognitive impairment. The purpose of this study was to determine the relationship between dietary diversity and child stunting in an Indonesian context. METHODS AND STUDY DESIGN: Dietary diversity was assessed using a maternal-reported checklist of 12 food groups, summed as a Household Dietary Diversity Score...
March 2017: Asia Pacific Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28238112/development-of-a-framework-for-metabolic-pathway-analysis-driven-strain-optimization-methods
#13
Vitor Vieira, Paulo Maia, Isabel Rocha, Miguel Rocha
Genome-scale metabolic models (GSMMs) have become important assets for rational design of compound overproduction using microbial cell factories. Most computational strain optimization methods (CSOM) using GSMMs, while useful in metabolic engineering, rely on the definition of questionable cell objectives, leading to some bias. Metabolic pathway analysis approaches do not require an objective function. Though their use brings immediate advantages, it has mostly been restricted to small scale models due to computational demands...
February 25, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28233579/human-survival-in-volcanic-eruptions-thermal-injuries-in-pyroclastic-surges-their-causes-prognosis-and-emergency-management
#14
Peter J Baxter, Susanna Jenkins, Rosadi Seswandhana, Jean-Christophe Komorowski, Ken Dunn, David Purser, Barry Voight, Ian Shelley
This study of burns patients from two eruptions of Merapi volcano, Java, in 1994 and 2010, is the first detailed analysis to be reported of thermal injuries in a large series of hospitalised victims of pyroclastic surges, one of the most devastating phenomena in explosive eruptions. Emergency planners in volcanic crises in populated areas have to integrate the health sector into disaster management and be aware of the nature of the surge impacts and the types of burns victims to be expected in a worst scenario, potentially in numbers and in severity that would overwhelm normal treatment facilities...
February 20, 2017: Burns: Journal of the International Society for Burn Injuries
https://www.readbyqxmd.com/read/28233369/identification-of-the-compositional-changes-in-orthosiphon-stamineus-leaves-triggered-by-different-drying-techniques-using-1-h-nmr-metabolomics
#15
Raghunath Pariyani, Intan Safinar Ismail, Amalina Ahmad Azam, Faridah Abas, Khozirah Shaari
BACKGROUND: Java tea is a well-known herbal infusion prepared from the leaves of Orthosiphon stamineus (OS). The biological properties of tea are in direct correlation with the primary and secondary metabolite composition, which in turn largely depends on the choice of drying methods. Herein, the impact of three commonly used drying methods, i.e., shade, microwave and freeze drying on the metabolite composition and the antioxidant activity of OS leaves were investigated using (1) H NMR spectroscopy combined with multivariate classification and regression analysis tools...
February 23, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28228919/variation-in-morphometric-characters-in-four-sand-crab-albunea-symmysta-populations-collected-from-sumatra-and-java-island-indonesia
#16
Febi Ayu Pramithasari, Nurlisa Alias Butet, Yusli Wardiatno
Variation in morphometric characters in four sand crab (Albunea symmysta) populations from four intertidal areas in Sumatra (Aceh and Bengkulu) and Java (Cilacap and Yogyakarta) were studied. Crabs collected from the four sites were measured to obtain 10 morphometric characters, i.e., carapace length (CL), carapace width (CW), ocular peduncle length and width (LOP and WOP), telson length and width (LT and WT), merus length (ML), carpus length (CaL), propodus length (PL), and dactylus length (DL). Allometric relationships were established among three morphometric characters (CW, PL, and DL) for each site, in which CL was fixed on the abscissa as a reference variable...
January 2017: Tropical Life Sciences Research
https://www.readbyqxmd.com/read/28210467/diversity-and-distribution-of-culturable-lactic-acid-bacterial-species-in-indonesian-sayur-asin
#17
Wibowo Mangunwardoyo, Abinawanto, Andi Salamah, Endang Sukara, Sulistiani, Achmad Dinoto
BACKGROUND AND OBJECTIVES: Lactic acid bacteria (LAB) play important roles in processing of Sayur Asin (spontaneously fermented mustard). Unfortunately, information about LAB in Indonesian Sayur Asin, prepared by traditional manufactures which is important as baseline data for maintenance of food quality and safety, is unclear. The aim of this study was to describe the diversity and distribution of culturable lactic acid bacteria in Sayur Asin of Indonesia. MATERIALS AND METHODS: Four Sayur Asin samples (fermentation liquor and fermented mustard) were collected at harvesting times (3-7 days after fermentation) from two traditional manufactures in Tulung Agung (TA) and Kediri (KDR), East Java provinces, Indonesia...
August 2016: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/28204908/a-large-scale-evaluation-of-algorithms-to-calculate-average-nucleotide-identity
#18
Seok-Hwan Yoon, Sung-Min Ha, Jeongmin Lim, Soonjae Kwon, Jongsik Chun
Average nucleotide identity (ANI) is a category of computational analysis that can be used to define species boundaries of Archaea and Bacteria. Calculating ANI usually involves the fragmentation of genome sequences, followed by nucleotide sequence search, alignment, and identity calculation. The original algorithm to calculate ANI used the BLAST program as its search engine. An improved ANI algorithm, called OrthoANI, was developed to accommodate the concept of orthology. Here, we compared four algorithms to compute ANI, namely ANIb (ANI algorithm using BLAST), ANIm (ANI using MUMmer), OrthoANIb (OrthoANI using BLAST) and OrthoANIu (OrthoANI using USEARCH) using >100,000 pairs of genomes with various genome sizes...
February 15, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28187711/poppante-population-and-pedigree-association-testing-for-quantitative-data
#19
Alessia Visconti, Mashael Al-Shafai, Wadha A Al Muftah, Shaza B Zaghlool, Massimo Mangino, Karsten Suhre, Mario Falchi
BACKGROUND: Family-based designs, from twin studies to isolated populations with their complex genealogical data, are a valuable resource for genetic studies of heritable molecular biomarkers. Existing software for family-based studies have mainly focused on facilitating association between response phenotypes and genetic markers, and no user-friendly tools are at present available to straightforwardly extend association studies in related samples to large datasets of generic quantitative data, as those generated by current -omics technologies...
February 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28187681/revision-and-cladistic-analysis-of-the-southeast-asian-leaf-dwelling-spider-genus-i-calapnita-i-simon-araneae-pholcidae
#20
Bernhard A Huber
The Southeast Asian pholcid genus Calapnita Simon, 1892 is revised, with descriptions of 17 new species, five of them in the phyllicola group (Borneo: C. lehi, C. kubah, C. bidayuh, C. bankirai; Malay Peninsula, Sumatra, Java: C. anai), 12 in the vermiformis group (Borneo: C. bario, C. bariengi, C. magaseng, C. dayak, C. lawangan, C. loksado; Sulawesi: C. bugis; Philippines: C. bohol, C. dinagat, C. mae, C. nunezae, C. maragusan). New records are listed for six of the eight previously described species. A morphological cladistic analysis supports the monophyly of Calapnita and of its two previously proposed species groups and presents several new phylogenetically informative characters...
January 13, 2017: Zootaxa
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