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https://www.readbyqxmd.com/read/28338677/integrated-metabolism-in-sponge-microbe-symbiosis-revealed-by-genome-centered-metatranscriptomics
#1
Lucas Moitinho-Silva, Cristina Díez-Vives, Giampiero Batani, Ana Is Esteves, Martin T Jahn, Torsten Thomas
Despite an increased understanding of functions in sponge microbiomes, the interactions among the symbionts and between symbionts and host are not well characterized. Here we reconstructed the metabolic interactions within the sponge Cymbastela concentrica microbiome in the context of functional features of symbiotic diatoms and the host. Three genome bins (CcPhy, CcNi and CcThau) were recovered from metagenomic data of C. concentrica, belonging to the proteobacterial family Phyllobacteriaceae, the Nitrospira genus and the thaumarchaeal order Nitrosopumilales...
March 24, 2017: ISME Journal
https://www.readbyqxmd.com/read/28334218/reconciliation-between-operational-taxonomic-units-and-species-boundaries
#2
Mohamed Mysara, Peter Vandamme, Ruben Props, Frederiek-Maarten Kerckhof, Natalie Leys, Nico Boon, Jeroen Raes, Pieter Monsieurs
The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into Operational Taxonomic Units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for a bacterial species. Our results show that the robustness of such a generalized cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene...
March 10, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28330138/vdap-gui-a-user-friendly-pipeline-for-variant-discovery-and-annotation-of-raw-next-generation-sequencing-data
#3
Ramesh Menon, Namrata V Patel, Amitbikram Mohapatra, Chaitanya G Joshi
Even though next-generation sequencing (NGS) has become an invaluable tool in molecular biology, several laboratories with NGS facilities lack trained Bioinformaticians for data analysis. Here, focusing on the variant detection application of NGS analysis, we have developed a fully automated pipeline, namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI), which detects and annotates single nucleotide polymorphisms and insertions/deletions from raw sequence reads. VDAP-GUI consolidates several proven methods in each step such as quality control, trimming, mapping, variant detection and annotation...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329450/public-views-on-pulse-oximetry-screening-for-critical-congenital-heart-disease
#4
Praveen Kumar, Hari Iyengar, Prerna Kumar
OBJECTIVES: To understand public views on pulse oximetry screening for critical congenital heart disease. METHODS: Two hundred thirteen adults read a brief vignette describing the importance of early detection of critical congenital heart disease and then answered five questions on a five-point scale of how likely or unlikely they were to support pulse oximetry screening. Responses were tabulated and analyzed using a Fisher exact test, and logistic regression was used to estimate odds ratios for adjusted associations using generalized estimating equations...
March 2017: World Journal for Pediatric & Congenital Heart Surgery
https://www.readbyqxmd.com/read/28327957/nanosim-nanopore-sequence-read-simulator-based-on-statistical-characterization
#5
Chen Yang, Justin Chu, René L Warren, Inanç Birol
Background: The MinION sequencing instrument from Oxford Nanopore Technologies (ONT) produces long read lengths from single-molecule sequencing - valuable features for detailed genome characterization. To realize the potential of this platform, a number of groups are developing bioinformatics tools tuned for the unique characteristics of its data. We note that these development efforts would benefit from a simulator software, output of which could be used to benchmark analysis tools. Findings: Here, we introduce NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data, and allows for adjustments upon improvement of nanopore sequencing technology...
February 24, 2017: GigaScience
https://www.readbyqxmd.com/read/28327849/-effect-of-free-roaming-dogs-culling-on-the-control-of-canine-rabies
#6
Ricardo Castillo-Neyra, Michael Z Levy, Cesar Náquira
In the Peruvian city of Arequipa, rabid dogs have been detected since March 2015, signaling the reintroduction of the rabies virus (RV) in this previously officially-declared rabies free zone. High dog density is considered one of the causes for the continuous transmission of the RV in the outbreak in the city of Arequipa, which seemingly lends support to the culling of dogs as a public health measure. However, the effectiveness of culling free-roaming dogs to control urban rabies has not been evaluated. Objective to determine the effectiveness of free-roaming dog culling as a control measure of urban rabies...
October 2016: Revista Peruana de Medicina Experimental y Salud Pública
https://www.readbyqxmd.com/read/28327296/local-diagnostic-reference-levels-for-intraoral-dental-radiography-in-the-public-hospitals-of-cyprus
#7
Stelios Christofides, Elina Pitri, Marios Lampaskis, Christos Papaefstathiou
PURPOSE: The purpose of this study was to determine local DRLs for children and adults undergoing intraoral dental examinations at the intraoral radiology units of the public hospitals in Cyprus. METHODS: Measurements were made on all the twenty intraoral X-ray units of the public hospitals in Cyprus with the intention to establish the local DRLs for all the possible intraoral X-ray examinations for children and adults. All units are film based. The measurements were made by a Dose Area Product (DAP) meter (GAMMEX RMI 841-RD) placed at the surface of the dental unit's X-ray shaping cone (FSD 20cm)...
November 2016: Physica Medica: PM
https://www.readbyqxmd.com/read/28323747/supporting-a-youth-with-cerebellar-ataxia-into-adolescence
#8
Veronica Meneses, Zurisadai Gonzalez-Castillo, Veronica B Edgar, Marilyn Augustyn
Zoe, a 13-year-old white girl, presents as a new patient to your pediatric clinic with complaints of frequent emesis, anxiety, and learning problems, and previous diagnosis of cerebellar ataxia. Parents accompany Zoe and state, "it is really hard for her to go out, she gets sick and falls easily." She was born full term by vaginal delivery without complications. Given globally delayed milestones, she received early intervention services. Feeding problems began at infancy, including gastroesophageal reflux and aspiration pneumonia...
March 17, 2017: Journal of Developmental and Behavioral Pediatrics: JDBP
https://www.readbyqxmd.com/read/28322691/discussion-of-average-versus-extreme-case-severity-in-pandemic-risk-communications
#9
Brian J Zikmund-Fisher, Aaron M Scherer, Megan Knaus, Enny Das, Angela Fagerlin
To investigate determinants of the public's perceptions of disease threat, in 2015 we conducted a randomized survey experiment in the Netherlands. Adults who read a mock news article describing average +or extreme outcomes from a hypothetical influenza pandemic were more influenced by average than by extreme case information. Presenting both types of information simultaneously appeared counterproductive.
April 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28321845/hidradenitis-suppurativa-gains-increasing-interest-on-world-wide-web-a-source-for-patient-information
#10
Schapoor Hessam, Johannes Salem, Falk G Bechara, Axel Haferkamp, Axel Heidenreich, Pia Paffenholz, Michael Sand, Igor Tsaur, Hendrik Borgmann
BACKGROUND: Gathering health information from Internet websites is increasingly utilized by patients. No data exist about hidradenitis suppurativa (HS)-related online health information. Thus, we aimed to study the quality, popularity, readability, and timeliness of the most frequented websites on HS. METHODS: Google Trends was used to evaluate the public interest in HS. An Internet search on Google was performed for the terms "hidradenitis suppurativa," "acne inversa," and "Verneuil's disease...
March 21, 2017: International Journal of Dermatology
https://www.readbyqxmd.com/read/28321295/getting-started-with-tables
#11
Hazel Inskip, Georgia Ntani, Leo Westbury, Chiara Di Gravio, Stefania D'Angelo, Camille Parsons, Janis Baird
BACKGROUND: Tables are often overlooked by many readers of papers who tend to focus on the text. Good tables tell much of the story of a paper and give a richer insight into the details of the study participants and the main research findings. Being confident in reading tables and constructing clear tables are important skills for researchers to master. METHOD: Common forms of tables were considered, along with the standard statistics used in them. Papers in the Archives of Public Health published during 2015 and 2016 were hand-searched for examples to illustrate the points being made...
2017: Archives of Public Health, Archives Belges de Santé Publique
https://www.readbyqxmd.com/read/28320324/quickmirseq-a-pipeline-for-quick-and-accurate-quantification-of-both-known-mirnas-and-isomirs-by-jointly-processing-multiple-samples-from-microrna-sequencing
#12
Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang, Wen He, Li Xi, Sachin Mathur, Michael Agostino, Theresa Paradis, David von Schack, Michael Vincent, Baohong Zhang
BACKGROUND: Genome-wide miRNA expression data can be used to study miRNA dysregulation comprehensively. Although many open-source tools for microRNA (miRNA)-seq data analyses are available, challenges remain in accurate miRNA quantification from large-scale miRNA-seq dataset. We implemented a pipeline called QuickMIRSeq for accurate quantification of known miRNAs and miRNA isoforms (isomiRs) from multiple samples simultaneously. RESULTS: QuickMIRSeq considers the unique nature of miRNAs and combines many important features into its implementation...
March 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28320310/treetoreads-a-pipeline-for-simulating-raw-reads-from-phylogenies
#13
Emily Jane McTavish, James Pettengill, Steven Davis, Hugh Rand, Errol Strain, Marc Allard, Ruth E Timme
BACKGROUND: Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several different approaches being used to infer phylogenetic tree. These include many different SNP pipelines, wgMLST approaches, k-mer algorithms, whole genome alignment and others; each of these has advantages and disadvantages, some have been extensively validated, some are faster, some have higher resolution...
March 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28315213/enzyme-linked-immunosorbent-assay-elisa
#14
George N Konstantinou
Food allergy is a public health concern especially after recognizing its constantly increased prevalence and severity. Despite careful reading of food ingredient statements, food allergic individuals may experience reactions caused by "hidden", "masked", or "contaminated" proteins that are known major allergens. Many techniques have been developed to detect even small traces of food allergens, for clinical or laboratory purposes. Enzyme-linked immunosorbent assay (ELISA) is one of the best validated and most routinely used immunoassay in allergy research, in allergy diagnosis in allergy-related quality control in various industries...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28303391/transcriptional-sequencing-and-analysis-of-major-genes-involved-in-the-adventitious-root-formation-of-mango-cotyledon-segments
#15
Yun-He Li, Hong-Na Zhang, Qing-Song Wu, Gloria K Muday
A total of 74,745 unigenes were generated and 1975 DEGs were identified. Candidate genes that may be involved in the adventitious root formation of mango cotyledon segment were revealed. Adventitious root formation is a crucial step in plant vegetative propagation, but the molecular mechanism of adventitious root formation remains unclear. Adventitious roots formed only at the proximal cut surface (PCS) of mango cotyledon segments, whereas no roots were formed on the opposite, distal cut surface (DCS). To identify the transcript abundance changes linked to adventitious root development, RNA was isolated from PCS and DCS at 0, 4 and 7 days after culture, respectively...
March 16, 2017: Planta
https://www.readbyqxmd.com/read/28302053/a-fast-and-efficient-python-library-for-interfacing-with-the-biological-magnetic-resonance-data-bank
#16
Andrey Smelter, Morgan Astra, Hunter N B Moseley
BACKGROUND: The Biological Magnetic Resonance Data Bank (BMRB) is a public repository of Nuclear Magnetic Resonance (NMR) spectroscopic data of biological macromolecules. It is an important resource for many researchers using NMR to study structural, biophysical, and biochemical properties of biological macromolecules. It is primarily maintained and accessed in a flat file ASCII format known as NMR-STAR. While the format is human readable, the size of most BMRB entries makes computer readability and explicit representation a practical requirement for almost any rigorous systematic analysis...
March 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28300993/the-use-of-the-primary-care-assessment-tool-pcat-an-integrative-review-and-proposed-update
#17
Otávio Pereira D'Avila, Luiz Felipe da Silva Pinto, Lisiane Hauser, Marcelo Rodrigues Gonçalves, Erno Harzheim
This study proposes an integrative review of the literature based on articles and publications on the use of the Primary Care Assessment Tool (PCAT) as a tool for evaluating these services, discussing the results found in Brazil and in other countries of the world, from the initial matrix conceived by Professor Barbara Starfield's team and proposing updates for the Brazilian version. We identified 124 studies, of which 42 were selected after full reading and according to the established inclusion criteria. Of this subtotal, 17 (40...
March 2017: Ciência & Saúde Coletiva
https://www.readbyqxmd.com/read/28295162/evaluation-of-two-public-genome-references-for-chinese-hamster-ovary-cells-in-the-context-of-rna-seq-based-gene-expression-analysis
#18
Chun Chen, Huong Le, Chetan T Goudar
RNA-Seq is a powerful transcriptomics tool for mammalian cell culture process development. Successful RNA-Seq data analysis requires a high quality reference for read mapping and gene expression quantification. Currently, there are two public genome references for Chinese hamster ovary (CHO) cells, the predominant mammalian cell line in the biopharmaceutical industry. In this study, we compared these two references by analyzing 60 RNA-Seq samples from a variety of CHO cell culture conditions. Among the 20,891 common genes in both references, we observed that 31...
March 15, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28294034/the-holistic-guide-for-cancer-survivors-greener-mark-the-holistic-guide-for-cancer-survivors-168pp-%C3%A2-7-99-sheldon-press-9781847093325-1847093329-formula-see-text
#19
(no author information available yet)
I found this publication easy to read, with excellent content relevant to clinical practice. It has a nursing focus and would be of value to all nurses caring for patients with cancer. I would particularly recommend it to nurses new to the specialty.
March 15, 2017: Nursing Standard
https://www.readbyqxmd.com/read/28293034/characterization-of-bafilomycin-biosynthesis-in-kitasatospora-setae-km-6054-and-comparative-analysis-of-gene-clusters-in-actinomycetales-microorganisms
#20
Ayako Nara, Takuya Hashimoto, Mamoru Komatsu, Makoto Nishiyama, Tomohisa Kuzuyama, Haruo Ikeda
Bafilomycins A1, C1 and B1 (setamycin) produced by Kitasatospora setae KM-6054 belong to the plecomacrolide family, which exhibit antibacterial, antifungal, antineoplastic and immunosuppressive activities. An analysis of gene clusters from K. setae KM-6054 governing the biosynthesis of bafilomycins revealed that it contains five large open reading frames (ORFs) encoding the multifunctional polypeptides of bafilomycin polyketide synthases (PKSs). These clustered PKS genes, which are responsible for bafilomycin biosynthesis, together encode 11 homologous sets of enzyme activities, each catalyzing a specific round of polyketide chain elongation...
March 15, 2017: Journal of Antibiotics
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