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https://www.readbyqxmd.com/read/28077566/duplicates-redundancies-and-inconsistencies-in-the-primary-nucleotide-databases-a-descriptive-study
#1
Qingyu Chen, Justin Zobel, Karin Verspoor
GenBank, the EMBL European Nucleotide Archive and the DNA DataBank of Japan, known collectively as the International Nucleotide Sequence Database Collaboration or INSDC, are the three most significant nucleotide sequence databases. Their records are derived from laboratory work undertaken by different individuals, by different teams, with a range of technologies and assumptions and over a period of decades. As a consequence, they contain a great many duplicates, redundancies and inconsistencies, but neither the prevalence nor the characteristics of various types of duplicates have been rigorously assessed...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28077564/blend4php-a-php-api-for-galaxy
#2
Connor Wytko, Brian Soto, Stephen P Ficklin
Galaxy is a popular framework for execution of complex analytical pipelines typically for large data sets, and is a commonly used for (but not limited to) genomic, genetic and related biological analysis. It provides a web front-end and integrates with high performance computing resources. Here we report the development of the blend4php library that wraps Galaxy's RESTful API into a PHP-based library. PHP-based web applications can use blend4php to automate execution, monitoring and management of a remote Galaxy server, including its users, workflows, jobs and more...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28077280/engineering-out-the-noise
#3
Kurt Yankaskas, Raymond Fischer, Jesse Spence, Jeff Komrower
The US Navy, through an Office of Naval Research (ONR) lead effort on Noise Induced Hearing Loss (NIHL), is investigating methods and techniques to mitigate hearing loss for the crews and warfighters. Hearing protection is a viable and increasingly popular method of reducing hearing exposure for many ship crewmembers; however, it has limitations on comfort and low frequency effectiveness. Furthermore, Personal Hearing Protection (PHP) is often used improperly. Proper vessel planning, programmatic changes and advances in noise control engineering can also have significant impacts by inherently reducing noise exposure through ship design and use of noise control treatments...
January 7, 2017: Hearing Research
https://www.readbyqxmd.com/read/28075249/cost-effectiveness-analysis-of-as04-adjuvanted-human-papillomavirus-16-18-vaccine-compared-with-human-papillomavirus-6-11-16-18-vaccine-in-the-philippines-with-the-new-2-dose-schedule
#4
Maria Julieta Germar, Carrie Purugganan, Ma Socorro Bernardino, Benjamin Cuenca, Y-Chen Chen, Xiao Li, Georges Van Kriekinge, I-Heng Lee
Cervical cancer (CC) is the second leading cause of cancer death among Filipino women. Human papillomavirus (HPV) vaccination protects against CC. Two vaccines (AS04-HPV-16/18 and 4vHPV) are approved in the Philippines; they were originally developed for a 3-dose (3 D) administration and have recently been approved in a 2-dose schedule (2 D). This study aims to evaluate the cost-effectiveness and budget impact of HPV vaccination of 13-year-old Filipino girls, in addition to current screening, in the new 2 D schedule...
January 11, 2017: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/28073758/resolution-and-reconciliation-of-non-binary-gene-trees-with-transfers-duplications-and-losses
#5
Edwin Jacox, Mathias Weller, Eric Tannier, Celine Scornavacca
: Gene trees reconstructed from sequence alignments contain poorly supported branches when the phylogenetic signal in the sequences is insufficient to determine them all. When a species tree is available, the signal of gains and losses of genes can be used to correctly resolve the unsupported parts of the gene history. However finding a most parsimonious binary resolution of a non-binary tree obtained by contracting the unsupported branches is NP-hard if transfer events are considered as possible gene scale events, in addition to gene origination, duplication and loss...
January 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28073746/mirdis-a-web-tool-for-endogenous-and-exogenous-microrna-discovery-based-on-deep-sequencing-data-analysis
#6
Hanyuan Zhang, Bruno Vieira Resende E Silva, Juan Cui
Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes...
January 10, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28069649/antimicrobial-activity-of-ceftazidime-avibactam-when-tested-against-gram-negative-bacteria-isolated-from-patients-hospitalized-with-pneumonia-in-united-states-medical-centers-2011-2015
#7
Helio S Sader, Mariana Castanheira, Robert K Flamm
Bacterial isolates were collected from patients hospitalized with pneumonia (PHP), including ventilator-associated (VAP), from 76 USA medical centers in 2011-2015. The Gram-negative organisms (n=11,185; including 1,097 from VAP) were tested for susceptibility against ceftazidime-avibactam and comparators by broth microdilution method. β-lactamase-encoding genes were screened using a microarray based assay on selected isolates. Pseudomonas aeruginosa and Klebsiella spp. were the most common Gram-negatives isolated from PHP and VAP...
January 9, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28059929/hepatic-progression-free-and-overall-survival-after-regional-therapy-to-the-liver-for-metastatic-melanoma
#8
Andrea M Abbott, Matthew P Doepker, Youngchul Kim, Matthew C Perez, Cassandra Gandle, Kerry L Thomas, Junsung Choi, Ravi Shridhar, Jonathan S Zager
OBJECTIVES: Regional therapy for metastatic melanoma to the liver represents an alternative to systemic therapy. Hepatic progression-free survival (HPFS), progression-free survival (PFS), and overall survival (OS) were evaluated. MATERIALS AND METHODS: A retrospective review of patients with liver metastases from cutaneous or uveal melanoma treated with yttrium-90 (Y90), chemoembolization (CE), or percutaneous hepatic perfusion (PHP) was conducted. RESULTS: Thirty patients (6 Y90, 10 PHP, 12 CE, 1 PHP then Y90, 1 CE then PHP) were included...
January 4, 2017: American Journal of Clinical Oncology
https://www.readbyqxmd.com/read/28056767/bacterial-whole-genome-based-phylogeny-construction-of-a-new-benchmarking-dataset-and-assessment-of-some-existing-methods
#9
Johanne Ahrenfeldt, Carina Skaarup, Henrik Hasman, Anders Gorm Pedersen, Frank Møller Aarestrup, Ole Lund
BACKGROUND: Whole genome sequencing (WGS) is increasingly used in diagnostics and surveillance of infectious diseases. A major application for WGS is to use the data for identifying outbreak clusters, and there is therefore a need for methods that can accurately and efficiently infer phylogenies from sequencing reads. In the present study we describe a new dataset that we have created for the purpose of benchmarking such WGS-based methods for epidemiological data, and also present an analysis where we use the data to compare the performance of some current methods...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28045758/a-virtual-reality-simulation-model-of-spinal-ultrasound-role-in-teaching-spinal-sonoanatomy
#10
Reva Ramlogan, Ahtsham U Niazi, Rongyu Jin, James Johnson, Vincent W Chan, Anahi Perlas
BACKGROUND AND OBJECTIVES: Ultrasound assessment of the lumbar spine improves the success of spinal and epidural anesthesia, especially for patients with underlying difficult anatomy. To assist with the teaching and learning of ultrasound-guided neuraxial anesthesia, we have created an online interactive educational model (http://www.usra.ca/vspine.php and http://pie.med.utoronto.ca/vspine). The aim of the current study was to determine whether the virtual spine model improved the knowledge of neuraxial anatomy and sonoanatomy...
December 29, 2016: Regional Anesthesia and Pain Medicine
https://www.readbyqxmd.com/read/28035428/raised-intracranial-pressure-as-a-result-of-pansynostosis-in-a-child-with-albright-s-hereditary-osteodystrophy
#11
Sepehr Mamoei, Søren Cortnum
CASE: The authors describe the case of an 8-year-old boy with pansynostosis in the context of Albright's hereditary osteodystrophy (AHO). This condition had lead to raised intracranial pressure (ICP). The elevated ICP was a consequence of the rigid skull impeding brain growth. Therefore, a decompressive cranioplasty was performed successfully, leaving further space for the growing brain. Affection of the central nervous system has been documented in AHO. However, affection of the skull bones has rarely been described in literature...
December 29, 2016: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://www.readbyqxmd.com/read/28035026/inmode-tools-for-learning-and-visualizing-intra-motif-dependencies-of-dna-binding-sites
#12
Ralf Eggeling, Ivo Grosse, Jan Grau
: Recent studies have shown that the traditional position weight matrix model is often insufficient for modeling transcription factor binding sites, as intra-motif dependencies play a significant role for an accurate description of binding motifs. Here, we present the Java application InMoDe, a collection of tools for learning, leveraging and visualizing such dependencies of putative higher order. The distinguishing feature of InMoDe is a robust model selection from a class of parsimonious models, taking into account dependencies only if justified by the data while choosing for simplicity otherwise...
December 28, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28025335/caspneurod-a-knowledgebase-of-predicted-caspase-cleavage-sites-in-human-proteins-related-to-neurodegenerative-diseases
#13
Sonu Kumar, Piotr Cieplak
BACKGROUND: A variety of neurodegenerative diseases (NDs) have been associated with deregulated caspase activation that leads to neuronal death. Caspases appear to be involved in the molecular pathology of NDs by directly cleaving important proteins. For instance, several proteins involved in Alzheimer's disease, including β-amyloid precursor protein (APP) and presenilins, are known to be cleaved by caspases. Therefore, cell death pathway may play a central role in many neurological diseases, and targeting the important proteins that control the cell survival and death may potentially represent a therapeutic approach for chronic neurodegenerative disorders...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28013277/enhancing-the-gabi-kat-arabidopsis-thaliana-t-dna-insertion-mutant-database-by-incorporating-araport11-annotation
#14
Nils Kleinboelting, Gunnar Huep, Bernd Weisshaar
SimpleSearch provides access to a database containing information about T-DNA insertion lines of the GABI-Kat collection of Arabidopsis thaliana mutants. These mutants are an important tool for reverse genetics, and GABI-Kat is the 2(nd) largest collection of such T-DNA insertion mutants. Insertion sites were deduced from flanking sequence tags (FSTs), and the database contains information about mutant plant lines as well as insertion alleles. Here, we describe improvements within the interface (available at http://www...
December 23, 2016: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28011771/improving-protein-disorder-prediction-by-deep-bidirectional-long-short-term-memory-recurrent-neural-networks
#15
Jack Hanson, Yuedong Yang, Kuldip Paliwal, Yaoqi Zhou
MOTIVATION: Capturing long-range interactions between structural but not sequence neighbors of proteins is a long-standing challenging problem in bioinformatics. Recently, long short-term memory (LSTM) networks have significantly improved the accuracy of speech and image classification problems by remembering useful past information in long sequential events. Here, we have implemented deep bidirectional LSTM recurrent neural networks in the problem of protein intrinsic disorder prediction...
December 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28008310/corrigendum-better-targeting-better-efficiency-for-wide-scale-neuronal-transduction-with-the-synapsin-promoter-and-aav-php-b
#16
Kasey L Jackson, Robert D Dayton, Benjamin E Deverman, Ronald L Klein
[This corrects the article on p. 116 in vol. 9, PMID: 27867348.].
2016: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28007960/prendb-a-substrate-prediction-database-to-enable-biocatalytic-use-of-prenyltransferases
#17
Jakub Gunera, Florian Kindinger, Shu-Ming Li, Peter Kolb
Prenyltransferases of the dimethylallyltryptophan synthase (DMATS 1 ) superfamily catalyze the attachment of prenyl or prenyl-like moieties to diverse acceptor compounds. These acceptor molecules are generally aromatic in nature and mostly indole or indole-like. Their catalytical transformation represent a major skeletal diversification step in the biosynthesis of secondary metabolites including the indole alkaloids. DMATS enzymes thus contribute significantly to the biological and pharmacological diversity of small molecule metabolites...
December 22, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27995443/pseudohypoparathyroidism-one-gene-several-syndromes
#18
REVIEW
O Tafaj, H Jüppner
Pseudohypoparathyroidism (PHP) and pseudopseudohypoparathyroidism (PPHP) are caused by mutations and/or epigenetic changes at the complex GNAS locus on chromosome 20q13.3 that undergoes parent-specific methylation changes at several sites. GNAS encodes the alpha-subunit of the stimulatory G protein (Gsα) and several splice variants thereof. Heterozygous inactivating mutations involving the maternal GNAS exons 1-13 cause PHP type Ia (PHP1A). Because of much reduced paternal Gsα expression in certain tissues, such as the proximal renal tubules, thyroid, and pituitary, there is little or no Gsα protein in the presence of maternal GNAS mutations, thus leading to PTH-resistant hypocalcemia and hyperphosphatemia...
December 19, 2016: Journal of Endocrinological Investigation
https://www.readbyqxmd.com/read/27993788/mruninovo-an-efficient-tool-for-de-novo-peptide-sequencing-utilizing-the-hadoop-distributed-computing-framework
#19
Chuang Li, Tao Chen, Qiang He, Yunping Zhu, Kenli Li
: Tandem mass spectrometry-based de novo peptide sequencing is a complex and time-consuming process. The current algorithms for de novo peptide sequencing cannot rapidly and thoroughly process large mass spectrometry datasets. In this paper, we propose MRUniNovo, a novel tool for parallel de novo peptide sequencing. MRUniNovo parallelizes UniNovo based on the Hadoop compute platform. Our experimental results demonstrate that MRUniNovo significantly reduces the computation time of de novo peptide sequencing without sacrificing the correctness and accuracy of the results, and thus can process very large datasets that UniNovo cannot...
December 19, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27988776/-i-alloionema-i-i-californicum-i-n-sp-nematoda-alloionematidae-a-new-alloionematid-from-usa
#20
Jiří Nermuť, Vladimír Půža, Zdeněk Mráček, Edwin Lewis
A new species of the family Alloionematidae was isolated from a rotten winged gourd at White Crane Garden, San Francisco, USA, sampled by Christopher Nelson in November 2010, and a live culture is deposited in Félix Lab Strain Database (http://www.justbio.com/worms/index.php), IBENS, Paris, France. Specimens from the culture have been examined. Both morphologically and molecularly, the nematode described herein as Alloionema californicum n. sp. differs from the other alloionematid species, A. appendiculatum and Neoalloionema tricaudatum...
November 7, 2016: Zootaxa
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