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Kazufumi Shimizu, Laksmi Wulandari, Emmanuel D Poetranto, Retno A Setyoningrum, Resti Yudhawati, Amelia Sholikhah, Aldise M Nastri, Anna L Poetranto, Adithya Y R Candra, Edith F Puruhito, Yusuke Takahara, Yoshiaki Yamagishi, Masaoki Yamaoka, Hak Hotta, Takako Ustumi, Maria I Lusida, Soetjipto, Yohko K Shimizu, Gatot Soegiarto, Yasuko Mori
BACKGROUND:  In Indonesia, highly pathogenic avian influenza A(H5N1) virus has become endemic in poultry and has caused sporadic deadly infections in human. Since 2012, we have conducted fixed-point surveillance of avian influenza viruses at a live-poultry market in East Java, Indonesia. In this study, we examined the seroprevalence of avian influenza A(H5N1) virus infection among market workers. METHODS:  Sera were collected from 101 workers in early 2014 and examined for antibody activity against avian A(H5N1) Eurasian lineage virus by a hemagglutination-inhibition (HI) assay...
December 15, 2016: Journal of Infectious Diseases
Vasundra Touré, Alexander Mazein, Dagmar Waltemath, Irina Balaur, Mansoor Saqi, Ron Henkel, Johann Pellet, Charles Auffray
BACKGROUND: When modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient storage and processing of the encoded biological relationships. They furthermore support queries on the structure of biological networks. RESULTS: We present the Java-based framework STON (SBGN TO Neo4j). STON imports and translates metabolic, signalling and gene regulatory pathways represented in the Systems Biology Graphical Notation into a graph-oriented format compatible with the Neo4j graph database...
December 5, 2016: BMC Bioinformatics
Charlotte Faurie, Clement Mettling, Mohamed Ali Bchir, Danang Sri Hadmoko, Carine Heitz, Evi Dwi Lestari, Michel Raymond, Marc Willinger
Humans have colonized and adapted to extremely diverse environments, and the genetic basis of some such adaptations, for example to high altitude, is understood. In some cases, local or regional variation in selection pressure could also cause behavioural adaptations. Numerous genes influence behaviour, such as alleles at the dopamine receptor locus D4 (DRD4), which are associated with attitude toward risk in experimental settings. We demonstrate genetic differentiation for this gene, but not for five unlinked microsatellite loci, between high- and low risk environments around Mount Merapi, an active volcano in Java, Indonesia...
December 1, 2016: Scientific Reports
Huiqin Jiang, Di Wu, Liuwei Song, Quan Yuan, Shengxiang Ge, Xiaoping Min, Ningshao Xia, Shizhi Qian, Xianbo Qiu
We reported a rapid, convenient, and easy-to-use genotyping method for hepatitis B virus (HBV) based on the smartphone at point-of-care (POC) settings. To perform HBV genotyping especially for genotypes A, B, C, and D, a smartphone is used to image and analyze a one-step immunoassay lateral flow strip functionalized with genotype-specific monoclonal antibodies (mAbs) on multiple capture lines. A light-emitting diode (LED) positioned on the top of the lateral flow strip is used to shine the multiple capture lines for excitation...
November 29, 2016: Journal of Laboratory Automation
Yongjun Piao, Minghao Piao, Keun Ho Ryu
Cancer classification has been a crucial topic of research in cancer treatment. In the last decade, messenger RNA (mRNA) expression profiles have been widely used to classify different types of cancers. With the discovery of a new class of small non-coding RNAs; known as microRNAs (miRNAs), various studies have shown that the expression patterns of miRNA can also accurately classify human cancers. Therefore, there is a great demand for the development of machine learning approaches to accurately classify various types of cancers using miRNA expression data...
November 21, 2016: Computers in Biology and Medicine
Guo-Liang Zhang, Chao Li
The Ontong Java-Manihiki-Hikurangi plateau (OJMHP) is considered to have originated from a starting mantle plume, and have been rifted apart by two spreading ridges. However, the ages of these spreading ridges and their possible interactions with the presumed mantle plume are unclear. The Manihiki-Hikurangi plateau has been rifted apart by the Osbourn Trough which formed the southwestern Pacific crust to the east of the Tonga-Kermadec trench. Here we report Pb-Hf-Os isotopes of the basaltic crust (Site U1365 of IODP Expedition 329) formed by the Osbourn Trough...
November 21, 2016: Scientific Reports
Jeffrey A Smith, James Moody, Jonathan Morgan
Missing data is an important, but often ignored, aspect of a network study. Measurement validity is affected by missing data, but the level of bias can be difficult to gauge. Here, we describe the effect of missing data on network measurement across widely different circumstances. In Part I of this study (Smith and Moody, 2013), we explored the effect of measurement bias due to randomly missing nodes. Here, we drop the assumption that data are missing at random: what happens to estimates of key network statistics when central nodes are more/less likely to be missing? We answer this question using a wide range of empirical networks and network measures...
January 2017: Social Networks
Oscar Martínez-Santiago, Reisel Millán Cabrera, Yovani Marrero-Ponce, Stephen J Barigye, Huong Le-Thi-Thu, F Javier Torres, Cesar H Zambrano, Ivan Yaber-Goenaga, Maykel Cruz-Monteagudo, Yoan Martínez López, Facundo Pérez Giménez, Francisco Torrens
In the present study, a generalized approach for molecular structure characterization is introduced, based on the relation frequency matrix (F) representation of the molecular graph and the subsequent calculation of the corresponding discrete derivative (finite difference) over a pair of elements (atoms). In earlier publications (22- 24), an unique event, named connected subgraphs, (based on the Kier-Hall's subgraphs) was systematically employed for the computation of the matrix F. The present report is a generalization of this notion, in which eleven additional events are introduced, classified in three categories, namely, topological (terminal paths, vertex path incidence, quantum subgraphs, walks of length k, Sach's subgraphs), fingerprints (MACCs, E-state and substructure fingerprints) and atomic contributions (Ghose and Crippen atom-types for hydrophobicity and refractivity) for F generation...
2016: Current Pharmaceutical Design
Daniel LaFave, Duncan Thomas
Taller workers earn more, particularly in lower income settings. It has been argued that adult height is a marker of strength which is rewarded in the labor market; a proxy for cognitive performance or other dimensions of human capital such as school quality; a proxy for health status; and a proxy for family background and genetic characteristics. As a result, the argument goes, height is rewarded in the labor market because it is an informative signal of worker quality to an employer. It has also been argued that the height premium is driven by occupational and sectoral choice...
November 5, 2016: Economics and Human Biology
Yuchen Yang, Norman C Duke, Fangfang Peng, Jianfang Li, Shuhuan Yang, Cairong Zhong, Renchao Zhou, Suhua Shi
Glacial vicariance is thought to influence population dynamics and speciation of many marine organisms. Mangroves, a plant group inhabiting intertidal zones, were also profoundly influenced by Pleistocene glaciations. In this study, we investigated phylogeographic patterns of a widespread mangrove species Sonneratia caseolaris and a narrowly distributed, closely related species S. lanceolata to infer their divergence histories and related it to historical geological events. We sequenced two chloroplast fragments and five nuclear genes for one population of S...
2016: Frontiers in Plant Science
Takashi Tomiyasu, Hitoshi Kodamatani, Yuriko Kono Hamada, Akito Matsuyama, Ryusuke Imura, Yoko Taniguchi, Nuril Hidayati, Joeni Setijo Rahajoe
This study investigates the distribution of total mercury (T-Hg) and methylmercury (MeHg) in the soil and water around the artisanal and small-scale gold mining (ASGM) area along the Cikaniki River, West Java, Indonesia. The concentration of T-Hg and MeHg in the forest soil ranged from 0.07 to 16.7 mg kg(-1) and from <0.07 to 2.0 μg kg(-1), respectively, whereas it ranged from 0.40 to 24.9 mg kg(-1) and from <0.07 to 56.3 μg kg(-1), respectively, in the paddy field soil. In the vertical variation of the T-Hg of forest soil, the highest values were observed at the soil surface, and these values were found to decrease with increasing depth...
November 9, 2016: Environmental Science and Pollution Research International
Annisa Retmanasari, Barandi Sapta Widartono, Mahardika Agus Wijayanti, Wayan Tunas Artama
Toxoplasmosis is a zoonosis caused by Toxoplasma gondii. Risk factors include consumption of undercooked meat, raw vegetables, and unfiltered water. This study aims to determine the seroprevalence and spatial distribution of toxoplasmosis in Middle Java, Indonesia, using an EcoHealth approach, combined with geographic information system (GIS). A total of 630 participants were randomly selected from seven districts. Each participant completed a questionnaire and provided a blood sample. The seroprevalence of toxoplasmosis was 62...
November 9, 2016: EcoHealth
Xavier Aubriot, Caroline Loup, Sandra Knapp
Taxonomic revision of the tropical Asian species of Solanum revealed two names, Solanum poka Dunal and Solanum graciliflorum Dunal, whose identities were uncertain and whose application has always been tentative. Material collected in Java at the beginning of the 19(th) century by Jean-Baptiste Leschenault de la Tour and used to describe these taxa has not been found, despite extensive searches in European herbaria. We here stabilise use of these names by comparing herbarium specimens and drawings of original material made by the artist Toussaint François Node-Véran...
2016: PhytoKeys
Stefan Koch, Christoph Bueschl, Maria Doppler, Alexandra Simader, Jacqueline Meng-Reiterer, Marc Lemmens, Rainer Schuhmacher
Due to its unsurpassed sensitivity and selectivity, LC-HRMS is one of the major analytical techniques in metabolomics research. However, limited stability of experimental and instrument parameters may cause shifts and drifts of retention time and mass accuracy or the formation of different ion species, thus complicating conclusive interpretation of the raw data, especially when generated in different analytical batches. Here, a novel software tool for the semi-automated alignment of different measurement sequences is presented...
November 2, 2016: Metabolites
Geoffrey A Boxshall
A new species of the cyclopoid copepod genus Ergasilus von Nordmann, 1832 is described based on material collected from the gills of an elasmobranch, Himantura oxyrhyncha (Sauvage, 1878), collected in the Java Sea off the coast of West Kalimantan, Indonesia. To justify the establishment of the new species, Ergasilus kimi sp. nov., detailed comparisons are made with the 28 congeneric species that share the combination of a 3-segmented leg 1 endopod and the presence of 2 setae on the free exopodal segment of leg 5...
October 11, 2016: Zootaxa
Sven Mecke, Max Kieckbusch, Lukas Hartmann, Hinrich Kaiser
Cyrtodactylus marmoratus Gray, 1831, a species of bent-toed gecko exhibiting a precloacal groove in males, was described on the basis of specimens collected by Heinrich Kuhl and Johan Conrad van Hasselt in Java, Greater Sunda Islands, Indonesia. Kluge (1985) subsequently designated a lectotype for C. marmoratus from a series of these specimens (i.e., syntypes), now housed in the herpetological collection at Naturalis (formerly the Rijksmuseum van Natuurlijke Historie; RMNH), Leiden, the Netherlands. Our work at Naturalis shows that the type series of C...
October 17, 2016: Zootaxa
Rahul Joshi, Jagbir S Kirti, Navneet Singh
: Genus Nishada Moore (1878) was proposed as a monotypic genus, under subfamily Lithosiinae, family Lithosiidae (now Lithosiini), including only Nishada flabrifera Moore (1878) from Calcutta (now as Kolkata), India. The genus is distributed from China to India, Thailand, Malaysia and up to Australia. The Indian fauna of Nishada is reported from North-East Himalayas, West Bengal (Kolkata) and South India. Members of this genus are unmarked, yellow to brown with short and broad wings. Genus Nishada has been taxonomically dealt by many authors but awaits thorough revision...
October 28, 2016: Zootaxa
Mohammed-Abbas Fazal, Sarah Alexander, Edward Burnett, Ana Deheer-Graham, Karen Oliver, Nancy Holroyd, Julian Parkhill, Julie E Russell
Salmonellae are a significant cause of morbidity and mortality globally. Here, we report the first complete genome sequence for Salmonella enterica subsp. enterica serovar Java strain NCTC5706. This strain is of historical significance, having been isolated in the pre-antibiotic era and was deposited into the National Collection of Type Cultures in 1939.
November 3, 2016: Genome Announcements
Isaías González, Antonio José Calderón, Andrés Mejías, José Manuel Andújar
In this paper the design and implementation of a network for integrating Programmable Logic Controllers (PLC), the Object-Linking and Embedding for Process Control protocol (OPC) and the open-source Easy Java Simulations (EJS) package is presented. A LabVIEW interface and the Java-Internet-LabVIEW (JIL) server complete the scheme for data exchange. This configuration allows the user to remotely interact with the PLC. Such integration can be considered a novelty in scientific literature for remote control and sensor data acquisition of industrial plants...
October 31, 2016: Sensors
Indah Waty Bong, Mary Elizabeth Felker, Ahmad Maryudi
Deforestation and forest degradation are complex and dynamic processes that vary from place to place. They are driven by multiple causes. Local communities are, to some extent, driving and also affected by some of these processes. Can their knowledge aid and add to place-specific assessment and monitoring of Deforestation and forest Degradation (DD) drivers? Our research was conducted in seven villages across three provinces of Indonesia (Papua, West Kalimantan and Central Java). Household surveys and focus group discussions were used to investigate how local community knowledge of DD drivers contributes to place-specific assessment and monitoring of DD drivers...
2016: PloS One
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