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https://www.readbyqxmd.com/read/29143619/diagnostic-accuracy-of-tests-to-detect-hepatitis-b-surface-antigen-a-systematic-review-of-the-literature-and-meta-analysis
#1
Ali Amini, Olivia Varsaneux, Helen Kelly, Weiming Tang, Wen Chen, Debrah I Boeras, Jane Falconer, Joseph D Tucker, Roger Chou, Azumi Ishizaki, Philippa Easterbrook, Rosanna W Peeling
BACKGROUND: Chronic Hepatitis B Virus (HBV) infection is characterised by the persistence of hepatitis B surface antigen (HBsAg). Expanding HBV diagnosis and treatment programmes into low resource settings will require high quality but inexpensive rapid diagnostic tests (RDTs) in addition to laboratory-based enzyme immunoassays (EIAs) to detect HBsAg. The purpose of this review is to assess the clinical accuracy of available diagnostic tests to detect HBsAg to inform recommendations on testing strategies in 2017 WHO hepatitis testing guidelines...
November 1, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29143615/diagnostic-accuracy-of-tests-to-detect-hepatitis-c-antibody-a-meta-analysis-and-review-of-the-literature
#2
Weiming Tang, Wen Chen, Ali Amini, Debi Boeras, Jane Falconer, Helen Kelly, Rosanna Peeling, Olivia Varsaneux, Joseph D Tucker, Philippa Easterbrook
BACKGROUND: Although direct-acting antivirals can achieve sustained virological response rates greater than 90% in Hepatitis C Virus (HCV) infected persons, at present the majority of HCV-infected individuals remain undiagnosed and therefore untreated. While there are a wide range of HCV serological tests available, there is a lack of formal assessment of their diagnostic performance. We undertook a systematic review and meta-analysis to evaluate he diagnostic accuracy of available rapid diagnostic tests (RDT) and laboratory based EIA assays in detecting antibodies to HCV...
November 1, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29143609/survey-of-programmatic-experiences-and-challenges-in-delivery-of-hepatitis-b-and-c-testing-in-low-and-middle-income-countries
#3
Azumi Ishizaki, Julie Bouscaillou, Niklas Luhmann, Stephanie Liu, Raissa Chua, Nick Walsh, Sarah Hess, Elena Ivanova, Teri Roberts, Philippa Easterbrook
BACKGROUND: There have been few reports on programmatic experience of viral hepatitis testing and treatment in resource-limited settings. To inform the development of the 2017 World Health Organization (WHO) viral hepatitis testing guidance and in particular the feasibility of proposed recommendations, we undertook a survey across a range of organisations engaged with hepatitis testing in low- and middle-income countries (LMICs). Our objective was to describe current hepatitis B and C testing practices across a range of settings in different countries, as well as key barriers or challenges encountered and proposed solutions to promote testing scale-up...
November 1, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29140470/database-resources-of-the-national-center-for-biotechnology-information
#4
(no author information available yet)
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 39 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29134598/annotation-of-bacteriophage-genome-sequences-using-dna-master-an-overview
#5
Welkin H Pope, Deborah Jacobs-Sera
Current sequencing technologies allow for the rapid and inexpensive sequencing of complete bacteriophage genomes, using small quantities of nucleic acid as starting material. Determination of the location and function of the gene features within the genome sequence, or annotation, is a necessary next step prior to submission to a public database, publication in a scientific journal, or advanced comparative genomic and proteomic studies. Gene prediction can be largely accomplished through the use of several freely available programs...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29126312/met-db-v2-0-elucidating-context-specific-functions-of-n6-methyl-adenosine-methyltranscriptome
#6
Hui Liu, Huaizhi Wang, Zhen Wei, Songyao Zhang, Gang Hua, Shao-Wu Zhang, Lin Zhang, Shou-Jiang Gao, Jia Meng, Xing Chen, Yufei Huang
Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. A knowledge base with the systematic collection and curation of context specific transcriptome-wide methylations is critical for elucidating their biological functions as well as for developing bioinformatics tools. Since its inception in 2014, the Met-DB (Liu, H., Flores, M.A., Meng, J., Zhang, L., Zhao, X., Rao, M.K., Chen, Y. and Huang, Y. (2015) MeT-DB: a database of transcriptome methylation in mammalian cells...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29126295/moonprot-2-0-an-expansion-and-update-of-the-moonlighting-proteins-database
#7
Chang Chen, Shadi Zabad, Haipeng Liu, Wangfei Wang, Constance Jeffery
MoonProt 2.0 (http://moonlightingproteins.org) is an updated, comprehensive and open-access database storing expert-curated annotations for moonlighting proteins. Moonlighting proteins contain two or more physiologically relevant distinct functions performed by a single polypeptide chain. Here, we describe developments in the MoonProt website and database since our previous report in the Database Issue of Nucleic Acids Research. For this V 2.0 release, we expanded the number of proteins annotated to 370 and modified several dozen protein annotations with additional or updated information, including more links to protein structures in the Protein Data Bank, compared with the previous release...
November 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29104564/high-throughput-sequencing-for-detection-of-foodborne-pathogens
#8
REVIEW
Camilla Sekse, Arne Holst-Jensen, Ulrich Dobrindt, Gro S Johannessen, Weihua Li, Bjørn Spilsberg, Jianxin Shi
High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29092055/sabio-rk-an-updated-resource-for-manually-curated-biochemical-reaction-kinetics
#9
Ulrike Wittig, Maja Rey, Andreas Weidemann, Renate Kania, Wolfgang Müller
SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature and stored in a relational database. The content comprises both naturally occurring and alternatively measured biochemical reactions and is not restricted to any organism class. The data are made available to the public by a web-based search interface and by web services for programmatic access. In this update we describe major improvements and extensions of SABIO-RK since our last publication in the database issue of Nucleic Acid Research (2012)...
October 30, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29069347/vecscreen_plus_taxonomy-imposing-a-tax-onomy-increase-on-vector-contamination-screening
#10
Alejandro A Schäffer, Eric P Nawrocki, Yoon Choi, Paul A Kitts, Ilene Karsch-Mizrachi, Richard McVeigh
Motivation: Nucleic acid sequences in public databases should not contain vector contamination, but many sequences in GenBank do (or did) contain vectors. The National Center for Biotechnology Information (NCBI) uses the program VecScreen to screen submitted sequences for contamination. Additional tools are needed to distinguish true positive (contamination) from false positive (not contamination) VecScreen matches. Results: A principal reason for false positive VecScreen matches is that the sequence and the matching vector subsequence originate from closely related or identical organisms (for example, both originate in E...
October 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29057964/hiv-1-sequences-in-the-epidemic-suggest-an-alternative-pathway-for-the-generation-of-the-long-terminal-repeats
#11
Pierre Cappy, Alice Moisan, Fabienne De Oliveira, Jean-Christophe Plantier, Matteo Negroni
To generate the long-terminal repeats (LTR) that border the integrated viral genome, two-strand transfer steps must occur during reverse transcription. Analysis of the genetic polymorphisms that are present in the LTR of HIV-1 heterozygous virions in single infection cycle studies has revealed which of the two copies of genomic RNAs is used for each transfer event. Thus, the first event of strand transfer has been described to be either intra- or intermolecular, while the second event is generally intramolecular...
October 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29052403/-serum-metabonomics-in-mice-infected-with-mycoplasma-pneumoniae-by-uplc-q-tof-ms
#12
Wen-Feng Wei, Yan-Tao Chu, Ye Liu, Jin-Hai Huo, Wei-Ming Wang
Ultra high performance liquid chromatography coupled with tandem quadrupole time of flight mass spectrometry(UPLC-Q-TOF-MS) was applied to metabonomics study in BALB/c mice infected with mycoplasma pneumoniae(MP) to analyze the changes in serum endogenous metabolites, identify potential biomarkers associated with mycoplasma pneumoniae pneumonia(MPP), analyze the metabolic pathway and explore the pathogenic mechanism of MPP. The BALB/c mice were inoculated with MP by repeated intranasal infectious routes to establish MPP models, and the results of the lung tissue biopsy, IgM and mycoplasma nucleic acid content determination showed that the models of MP in BALB/c mice were successfully established...
April 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28994164/utilization-of-increased-risk-for-transmission-of-infectious-disease-donor-organs-in-solid-organ-transplantation-retrospective-analysis-of-disease-transmission-and-safety
#13
Linda Irwin, Camille N Kotton, Nahel Elias, Julie Palafox, Debra Basler, Sarah H Shao, William Lester, Xiaofeng Zhang, Brendan Kimball, Carrie Trencher, Jay A Fishman
The inadequate supply of transplantable organs necessitates new approaches to organ availability. Serologies and nucleic acid testing (NAT) for hepatitis C virus (HCV), hepatitis B virus (HBV), and human immunodeficiency virus (HIV) are used in microbiologic screening of potential organ donors. Organs from donors considered at "high risk" (Centers for Disease Control and Prevention, CDC 1994) or "increased risk" (U.S. Public Health Service, PHS 2013) for transmission of viral infection to recipients may provide an expanded source of organs for transplantation...
October 10, 2017: Transplant Infectious Disease: An Official Journal of the Transplantation Society
https://www.readbyqxmd.com/read/28990083/confirmation-and-preliminary-analysis-of-circrnas-potentially-involved-in-human-intervertebral-disc-degeneration
#14
Fei Zou, Zhiwen Ding, Jianyuan Jiang, Feizhou Lu, Xinlei Xia, Xiaosheng Ma
Circular RNAs (circRNAs) are relatively recently identified noncoding RNAs that are ubiquitously expressed in human tissues and serve key functions in regulating gene expression. However, few studies have focused on human intervertebral disc degeneration (IDD) circRNAs, and the potential role of circRNAs in IDD has not been described in detail. In the present study, circRNA expression data was downloaded from the Gene Expression Omnibus database, and circRNAs in the human intervertebral disc were classified according to their length, indicating their uniform distribution of circRNAs of different lengths...
December 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28981193/organ-utilization-from-increased-infectious-risk-donors-an-observational-study
#15
Arnaud G L'Huillier, Atul Humar, Clare Payne, Deepali Kumar
BACKGROUND: Donors with an increased risk of transmitting human immunodeficiency virus (HIV), hepatitis B virus (HBV), or hepatitis C virus (HCV) (increased risk donors [IRDs]) are a potential source of organs for transplant. Organs from IRDs can be utilized with appropriate recipient consent and post-transplant follow-up. We reviewed the characteristics and utilization of IRDs in our Organ Procurement Organization (OPO) over a 2-year period. METHODS: Donor information from April 1, 2013 to March 31, 2015 was obtained through the OPO database...
October 5, 2017: Transplant Infectious Disease: An Official Journal of the Transplantation Society
https://www.readbyqxmd.com/read/28937364/nucleic-acid-amplification-testing-in-indian-blood-banks-a-review-with-perspectives
#16
Kanjaksha Ghosh, Kanchan Mishra
BACKGROUND: Nucleic acid amplification testing (NAT) is restricted to a few blood banks in India since 2008. This review was directed toward understanding NAT yield in different parts of the country and prevalence in the NAT of different types of virus. MATERIALS AND METHODS: English literature was searched from 1990 to 2016 in PubMed, Scopus, Ind med, and Google database using properly constructed key words. Literature was collected and finally the data were synthesized...
July 2017: Indian Journal of Pathology & Microbiology
https://www.readbyqxmd.com/read/28932815/a-multicenter-study-to-evaluate-the-performance-of-high-throughput-sequencing-for-virus-detection
#17
Arifa S Khan, Siemon H S Ng, Olivier Vandeputte, Aisha Aljanahi, Avisek Deyati, Jean-Pol Cassart, Robert L Charlebois, Lanyn P Taliaferro
The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses makes it a powerful tool for broad microbial investigations, such as evaluation of novel cell substrates that may be used for the development of new biological products. However, like any new assay, regulatory applications of HTS need method standardization. Therefore, our three laboratories initiated a study to evaluate performance of HTS for potential detection of viral adventitious agents by spiking model viruses in different cellular matrices to mimic putative materials for manufacturing of biologics...
September 2017: MSphere
https://www.readbyqxmd.com/read/28910345/circulating-mrnas-and-mirnas-as-candidate-markers-for-the-diagnosis-and-prognosis-of-prostate-cancer
#18
MULTICENTER STUDY
Marilesia Ferreira de Souza, Hellen Kuasne, Mateus de Camargo Barros-Filho, Heloísa Lizotti Cilião, Fabio Albuquerque Marchi, Paulo Emilio Fuganti, Alexandre Rossi Paschoal, Silvia Regina Rogatto, Ilce Mara de Syllos Cólus
Circulating nucleic acids are found in free form in body fluids and may serve as minimally invasive tools for cancer diagnosis and prognosis. Only a few studies have investigated the potential application of circulating mRNAs and microRNAs (miRNAs) in prostate cancer (PCa). The Cancer Genome Atlas (TCGA) database was used for an in silico analysis to identify circulating mRNA and miRNA as potential markers of PCa. A total of 2,267 genes and 49 miRNAs were differentially expressed between normal and tumor samples...
2017: PloS One
https://www.readbyqxmd.com/read/28905886/time-series-oligonucleotide-count-to-assign-antiviral-sirnas-with-long-utility-fit-in-the-big-data-era
#19
K Wada, Y Wada, Y Iwasaki, T Ikemura
Oligonucleotides are key elements of nucleic acid therapeutics such as small interfering RNAs (siRNAs). Influenza and Ebolaviruses are zoonotic RNA viruses mutating very rapidly, and their sequence changes must be characterized intensively to design therapeutic oligonucleotides with long utility. Focusing on a total of 182 experimentally validated siRNAs for influenza A, B and Ebolaviruses compiled by the siRNA database, we conducted time-series analyses of occurrences of siRNA targets in these viral genomes...
October 2017: Gene Therapy
https://www.readbyqxmd.com/read/28887714/is-it-time-for-one-step-nucleic-acid-amplification-osna-in-colorectal-cancer-a-systematic-review-and-meta-analysis
#20
J B Wild, N Iqbal, J Francombe, T Papettas, D S Sanders, S Ramcharan
BACKGROUND: Lymph node metastasis (LNM) is prognostic in colorectal cancer (CRC). However, evaluation by routine haematoxylin and eosin histology (HE) limits nodal examination and is subjective. Missed LNMs from tissue allocation bias (TAB) might under-stage disease, leading to under-treatment. One-step nucleic acid amplification (OSNA) for CK19 messenger ribonucleic acid (mRNA), a marker of LNM, analyses the whole node. The aim of the present systematic review and meta-analysis was to assess recent studies on OSNA versus HE and its implications for CRC staging and treatment...
September 2017: Techniques in Coloproctology
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