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https://www.readbyqxmd.com/read/28633344/pheno4j-a-gene-to-phenotype-graph-database
#1
Sajid Mughal, Ismail Moghul, Jing Yu, Tristan Clark, David S Gregory, Nikolas Pontikos
Summary: Efficient storage and querying of large amounts of genetic and phenotypic data is crucial to contemporary clinical genetic research. This introduces computational challenges for classical relational databases, due to the sparsity and sheer volume of the data. Our Java based solution loads annotated genetic variants and well phenotyped patients into a graph database to allow fast efficient storage and querying of large volumes of structured genetic and phenotypic data. This abstracts technical problems away and lets researchers focus on the science rather than the implementation...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28614807/pregnant-and-breastfeeding-women-drinking-for-two
#2
Saptawati Bardosono, Clémentine Morin, Isabelle Guelinckx, Rizki Pohan
The primary aim of this cross-sectional survey was to assess the total fluid intake (TFI; sum of drinking water and all other fluids) and the intake of water and all other types of beverages in a sample of pregnant and breastfeeding women representative of Java-Island, Indonesia. Therefore, 299 pregnant and 296 breastfeeding women completed a 7-day fluid-specific record. A secondary aim was to estimate the total water intake (TWI; sum of water from fluids and food moisture), and one 24-h recall was performed to determine water intake from food moisture...
2017: Annals of Nutrition & Metabolism
https://www.readbyqxmd.com/read/28610304/systematics-of-eutropis-rugifera-stoliczka-1870-squamata-scincidae-including-the-redescription-of-the-holotype
#3
A A Thasun Amarasinghe, Nikolay A Poyarkov, Patrick D Campbell, Sandy Leo, Jatna Supriatna, Jakob Hallermann
Eutropis rugifera has long been identified as a widespread species complex distributed in Nicobar, Peninsular Malaysia, Greater Sundaic Islands, Bali, Sulawesi and the Philippines. This skink was described by Stoliczka in 1870 from Nicobar Island based on a single specimen (holotype by monotypy). Later, Peters (1871), Bartlett (1895) and Werner (1896) described three more species which were morphologically similar to Euprepes percarinatus (from Java), Mabuia rubricollis (Borneo) and M. quinquecarinata (Sumatra) respectively, which are currently considered junior objective synonyms of Eutropis rugifera...
May 26, 2017: Zootaxa
https://www.readbyqxmd.com/read/28610206/a-new-species-of-i-pseudocalotes-i-squamata-agamidae-from-the-bukit-barisan-range-of-sumatra-with-an-estimation-of-its-phylogeny
#4
Michael B Harvey, Kyle Shaney, Amir Hamidy, Nia Kurniawan, Eric N Smith
We describe a new species of Pseudocalotes from montane forests of the central, western coast of Sumatra. The combination of 3 or 4 interoculabials, slightly enlarged and heavily keeled scales on the lower flanks, a white scapular spot, a relatively long fifth toe, bicarinate lamellae at the base of Toe III, absence of a postrictal modified scale, and three rows of paravertebrals directed dorsally and posteriorly distinguishes the new species from its congeners on Sumatra and Java. Among the new characters defined in this study, counts of subdigital lamellae within the "span of Toe V" proved particularly useful for diagnosing species of Pseudocalotes...
June 11, 2017: Zootaxa
https://www.readbyqxmd.com/read/28609999/speciation-in-indo-pacific-swiftlets-aves-apodidae-integrating-molecular-and-phenotypic-data-for-a-new-provisional-taxonomy-of-the-i-collocalia-i-i-esculenta-i-complex
#5
Frank E Rheindt, Les Christidis, Janette A Norman, James A Eaton, Keren R Sadanandan, Richard Schodde
White-bellied swiftlets of the Collocalia esculenta complex constitute a radiation of colony-breeding swifts distributed throughout the tropical Indo-Pacific region. Resolution of their taxonomy is challenging due to their morphological uniformity. To analyze the evolutionary history of this complex, we combine new biometric measurements and results from plumage assessment of museum specimens with novel as well as previously published molecular data. Together, this body of information constitutes the largest systematic dataset for white-bellied swiftlets yet compiled, drawn from 809 individuals belonging to 32 taxa for which new molecular, biometric, and/or plumage data are presented...
April 7, 2017: Zootaxa
https://www.readbyqxmd.com/read/28605835/predicting-island-biosecurity-risk-from-introduced-fauna-using-bayesian-belief-networks
#6
Cheryl Lohr, Amelia Wenger, Owen Woodberry, Robert L Pressey, Keith Morris
Around the globe, islands are the last refuge for many threatened and endemic species. Islands are frequently also important sites for recreation, cultural activities, and industrial development, all of which facilitate the establishment of invasive species. Surveillance is employed on islands to detect the establishment of invasive species after their arrival, leading to decisions about follow-up actions. Unless surveillance is prioritised according to risk of establishment of invasives, it may be infeasible to implement efficiently over large tracts of publicly accessible land, especially in data-deficient areas...
June 6, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28603640/prevalence-and-molecular-epidemiology-of-clostridium-difficile-infection-in-indonesia
#7
D A Collins, M H Gasem, T H Habibie, I G Arinton, P Hendriyanto, A P Hartana, T V Riley
Clostridium difficile has not been studied in detail in Asia, particularly Southeast Asia. We thus performed a prevalence study across four hospitals in Central Java province, Indonesia. Stool samples were collected from patients with diarrhoea and tested by enzyme immunoassay for glutamate dehydrogenase (GDH) and toxin A/B (C DIFF QUIK CHEK COMPLETE, TechLab). Specimens were cultured and molecular typing was performed. In total, 340 samples were tested, of which 70 (20.6%) were GDH positive, with toxin detected in 19 (5...
July 2017: New Microbes and New Infections
https://www.readbyqxmd.com/read/28572707/thermostable-phycocyanin-from-the-red-microalga-cyanidioschyzon-merolae-a-new-natural-blue-food-colorant
#8
D Y Rahman, F D Sarian, A van Wijk, M Martinez-Garcia, M J E C van der Maarel
The demand for natural food colorants is growing as consumers question the use of artificial colorants more and more. The phycobiliprotein C-phycocyanin of Arthospira platensis is used as a natural blue colorant in certain food products. The thermoacidophilic red microalga Cyanidioschyzon merolae might provide an alternative source of phycocyanin. Cyanidioschyzon merolae belongs to the order Cyanidiophyceae of the phylum Rhodophyta. Its natural habitat are sulfuric hot springs and geysers found near volcanic areas in, e...
2017: Journal of Applied Phycology
https://www.readbyqxmd.com/read/28549446/-gnparser-a-powerful-parser-for-scientific-names-based-on-parsing-expression-grammar
#9
Dmitry Y Mozzherin, Alexander A Myltsev, David J Patterson
BACKGROUND: Scientific names in biology act as universal links. They allow us to cross-reference information about organisms globally. However variations in spelling of scientific names greatly diminish their ability to interconnect data. Such variations may include abbreviations, annotations, misspellings, etc. Authorship is a part of a scientific name and may also differ significantly. To match all possible variations of a name we need to divide them into their elements and classify each element according to its role...
May 26, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28548302/fast-computation-of-full-density-matrix-of-multispin-systems-for-spatially-localized-in-vivo-magnetic-resonance-spectroscopy
#10
Yan Zhang, Li An, Jun Shen
PURPOSE: Numerical simulations of three-dimensionally localized MRS spectra have been very time-consuming for multi-spin systems because the current state-of-the-art requires computation of a large ensemble of spins pixel-by-pixel in three dimensional space. This paper describes a highly accelerated technique for computing spatially localized MRS spectra using the full solution to the Liouville-von Neumann equation. METHODS: The time evolution of spatially localized multispin density matrix as the full solution to the Liouville-von Neumann equation was analyzed...
May 26, 2017: Medical Physics
https://www.readbyqxmd.com/read/28545397/jed-a-java-essential-dynamics-program-for-comparative-analysis-of-protein-trajectories
#11
Charles C David, Ettayapuram Ramaprasad Azhagiya Singam, Donald J Jacobs
BACKGROUND: Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two common approaches to determine PCA modes (eigenvectors) and their eigenvalues. Protein dynamics can be characterized in terms of Cartesian coordinates or internal distance pairs. In understanding protein dynamics, a comparison of trajectories taken from a set of proteins for similarity assessment provides insight into conserved mechanisms...
May 25, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28540698/introduction-on-using-the-fastpcr-software-and-the-related-java-web-tools-for-pcr-and-oligonucleotide-assembly-and-analysis
#12
Ruslan Kalendar, Timofey V Tselykh, Bekbolat Khassenov, Erlan M Ramanculov
This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-distance, inverse, real-time, group-specific, unique, overlap extension PCR for multi-fragments assembling cloning and loop-mediated isothermal amplification (LAMP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540697/in-silico-pcr-tools-for-a-fast-primer-probe-and-advanced-searching
#13
Ruslan Kalendar, Alexandr Muterko, Malika Shamekova, Kabyl Zhambakin
The polymerase chain reaction (PCR) is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. The principle of this technique has been further used and applied in plenty of other simple or complex nucleic acid amplification technologies (NAAT). In parallel to laboratory "wet bench" experiments for nucleic acid amplification technologies, in silico or virtual (bioinformatics) approaches have been developed, among which in silico PCR analysis. In silico NAAT analysis is a useful and efficient complementary method to ensure the specificity of primers or probes for an extensive range of PCR applications from homology gene discovery, molecular diagnosis, DNA fingerprinting, and repeat searching...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28535294/hgva-the-human-genome-variation-archive
#14
Javier Lopez, Jacobo Coll, Matthias Haimel, Swaathi Kandasamy, Joaquin Tarraga, Pedro Furio-Tari, Wasim Bari, Marta Bleda, Antonio Rueda, Stefan Gräf, Augusto Rendon, Joaquin Dopazo, Ignacio Medina
High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion...
May 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28534871/development-of-a-gridded-meteorological-dataset-over-java-island-indonesia-1985-2014
#15
Yanto, Ben Livneh, Balaji Rajagopalan
We describe a gridded daily meteorology dataset consisting of precipitation, minimum and maximum temperature over Java Island, Indonesia at 0.125°×0.125° (~14 km) resolution spanning 30 years from 1985-2014. Importantly, this data set represents a marked improvement from existing gridded data sets over Java with higher spatial resolution, derived exclusively from ground-based observations unlike existing satellite or reanalysis-based products. Gap-infilling and gridding were performed via the Inverse Distance Weighting (IDW) interpolation method (radius, r, of 25 km and power of influence, α, of 3 as optimal parameters) restricted to only those stations including at least 3,650 days (~10 years) of valid data...
May 23, 2017: Scientific Data
https://www.readbyqxmd.com/read/28520890/vcf-filter-interactive-prioritization-of-disease-linked-genetic-variants-from-sequencing-data
#16
Heiko Müller, Raul Jimenez-Heredia, Ana Krolo, Tatjana Hirschmugl, Jasmin Dmytrus, Kaan Boztug, Christoph Bock
Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28508804/ehealth-networking-information-systems-the-new-quality-of-information-exchange
#17
Karin Messer-Misak, Christoph Reiter
BACKGROUND: The development and introduction of platforms that enable interdisciplinary exchange on current developments and projects in the area of eHealth have been stimulated by different authorities. OBJECTIVES: The aim of this project was to develop a repository of eHealth projects that will make the wealth of eHealth projects visible and enable mutual learning through the sharing of experiences and good practice. METHODS: The content of the database and search criteria as well as their categories were determined in close co-ordination and cooperation with stakeholders from the specialist areas...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28508782/the-use-of-restful-web-services-in-medical-informatics-and-clinical-research-and-its-implementation-in-europe
#18
Jozef Aerts
BACKGROUND: RESTful web services nowadays are state-of-the-art in business transactions over the internet. They are however not very much used in medical informatics and in clinical research, especially not in Europe. OBJECTIVES: To make an inventory of RESTful web services that can be used in medical informatics and clinical research, including those that can help in patient empowerment in the DACH region and in Europe, and to develop some new RESTful web services for use in clinical research and regulatory review...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28508774/arden-syntax-mlm-building-blocks-for-microbiological-concepts-and-their-application-in-infection-surveillance
#19
Jeroen S de Bruin, Walter Koller, Julia Zeckl, Alexander Blacky, Andrea Rappelsberger, Klaus-Peter Adlassnig
BACKGROUND: The diagnosis - and hence definitions - of healthcare-associated infections (HAIs) rely on microbiological laboratory test results in specific constellations. OBJECTIVES: To construct a library that provides interoperable building blocks for the analysis of microbiological laboratory test results. METHODS: We used Java for preprocessing raw microbiological laboratory test results and Arden Syntax for knowledge-based querying of data based on microbiology information elements used in European surveillance criteria for HAIs...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28507416/pathotypic-characterization-of-newcastle-disease-virus-isolated-from-vaccinated-chicken-in-west-java-indonesia
#20
Dwi Desmiyeni Putri, Ekowati Handharyani, Retno Damajanti Soejoedono, Agus Setiyono, Ni Luh Putu Ika Mayasari, Okti Nadia Poetri
AIM: This research was conducted to differentiate and characterize eight Newcastle disease virus (NDV) isolates collected from vaccinated chicken at commercial flocks in West Java, Indonesia, in 2011, 2014 and 2015 by pathotype specific primers. MATERIALS AND METHODS: A total of eight NDV isolates collected from clinical outbreaks among commercial vaccinated flocks in West Java, Indonesia, in 2011, 2014, and 2015 were used in this study. Reverse transcription-polymerase chain reaction was used to detect and differentiate virulence of NDV strains, using three sets of primers targeting their M and F gene...
April 2017: Veterinary World
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