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https://www.readbyqxmd.com/read/28335477/association-between-circulating-vitamin-d-level-and-urolithiasis-a-systematic-review-and-meta-analysis
#1
REVIEW
Henglong Hu, Jiaqiao Zhang, Yuchao Lu, Zongbiao Zhang, Baolong Qin, Hongbin Gao, Yufeng Wang, Jianning Zhu, Qing Wang, Yunpeng Zhu, Yang Xun, Shaogang Wang
Many studies compared the serum/plasma 1,25 dihydroxyvitamin D₃ (1,25(OH)₂D) and 25 hydroxyvitamin D₃ (25(OH)D) between people with and without nephrolithiasis, and their results were conflicting. After systematically searching PubMed, Web of Science, The Cochrane Library, CNKI, and the Wanfang Database, we conducted a meta-analysis. Thirty-two observational studies involving 23,228 participants were included. Meta-analysis of these studies showed that of stone formers (SFs), calcium SFs had significantly higher concentrations of 1,25(OH)₂D (weighted mean difference (WMD), 10...
March 18, 2017: Nutrients
https://www.readbyqxmd.com/read/28335433/evaluation-and-adaptation-of-a-laboratory-based-cdna-library-preparation-protocol-for-retrospective-sequencing-of-archived-micrornas-from-up-to-35-year-old-clinical-ffpe-specimens
#2
Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert Greenlee, Deborah Multerer, Stacey Honda, Yihe Daida, Heather Spencer Feigelson, Andrew Glass, Fergus J Couch, Thomas Rohan, Iddo Z Ben-Dov
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years...
March 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335400/online-classification-of-contaminants-based-on-multi-classification-support-vector-machine-using-conventional-water-quality-sensors
#3
Pingjie Huang, Yu Jin, Dibo Hou, Jie Yu, Dezhan Tu, Yitong Cao, Guangxin Zhang
Water quality early warning system is mainly used to detect deliberate or accidental water pollution events in water distribution systems. Identifying the types of pollutants is necessary after detecting the presence of pollutants to provide warning information about pollutant characteristics and emergency solutions. Thus, a real-time contaminant classification methodology, which uses the multi-classification support vector machine (SVM), is proposed in this study to obtain the probability for contaminants belonging to a category...
March 13, 2017: Sensors
https://www.readbyqxmd.com/read/28335389/characteristics%C3%A2-and%C3%A2-lethality%C3%A2-of%C3%A2-a%C3%A2-novel%C3%A2-recombinant%C3%A2-dermonecrotic%C3%A2-venom%C3%A2-phospholipase%C3%A2-d%C3%A2-from%C3%A2-hemiscorpius%C3%A2-lepturus
#4
Elham Torabi, Mahdi Behdani, Mohammad Hosseininejad Chafi, Reza Moazzami, Jean-Marc Sabatier, Vahid Khalaj, Delavar Shahbazzadeh, Kamran Pooshang Bagheri
Hemoscorpius lepturus is the most medically important scorpion in Iran. The clinical signs of H. lepturus envenomation are remarkably similar to those reported for brown spiders, including dermonecrosis, hematuria, renal failure and even death. The lethality and toxicity of brown spiders' venom have been attributed to its phospholipase D activity. This study aims to identify a phospholipase D with possible lethality and dermonecrotic activity in H. lepturus venom. In this study, a cDNA library of the venom glands was generated by Illumina RNA sequencing...
March 13, 2017: Toxins
https://www.readbyqxmd.com/read/28335031/ethics-of-health-policy-and-systems-research-a-scoping-review-of-the-literature
#5
Bridget Pratt, Amy Paul, Adnan A Hyder, Joseph Ali
Health policy and systems research (HPSR) is increasingly funded and undertaken as part of health system strengthening efforts worldwide. HPSR ethics is also a relatively new and emerging field, with numerous normative and descriptive questions that have largely not been considered. Normative questions include what ethical principles and values should guide HPSR. Descriptive questions include what ethical concerns arise when conducting HPSR. A small but growing body of scholarly work characterizes the various ethics issues inherent in HPSR...
March 15, 2017: Health Policy and Planning
https://www.readbyqxmd.com/read/28335006/a-platform-for-functional-assessment-of-large-variant-libraries-in-mammalian-cells
#6
Kenneth A Matreyek, Jason J Stephany, Douglas M Fowler
Sequencing-based, massively parallel genetic assays have revolutionized our ability to quantify the relationship between many genotypes and a phenotype of interest. Unfortunately, variant library expression platforms in mammalian cells are far from ideal, hindering the study of human gene variants in their physiologically relevant cellular contexts. Here, we describe a platform for phenotyping variant libraries in transfectable mammalian cell lines in two steps. First, a landing pad cell line with a genomically integrated, Tet-inducible cassette containing a Bxb1 recombination site is created...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334977/sclip-an-integrated-platform-to-study-rna-protein-interactomes-in-biomedical-research-identification-of-cstf2tau-in-alternative-processing-of-small-nuclear-rnas
#7
Yulia Kargapolova, Michal Levin, Karl Lackner, Sven Danckwardt
RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here, we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing...
February 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334848/systematic-review-of-surveillance-by-social-media-platforms-for-illicit-drug-use
#8
Donna M Kazemi, Brian Borsari, Maureen J Levine, Beau Dooley
Background: The use of social media (SM) as a surveillance tool of global illicit drug use is limited. To address this limitation, a systematic review of literature focused on the ability of SM to better recognize illicit drug use trends was addressed. Methods: A search was conducted in databases: PubMed, CINAHL via Ebsco, PsychINFO via Ebsco, Medline via Ebsco, ERIC, Cochrane Library, Science Direct, ABI/INFORM Complete and Communication and Mass Media Complete...
March 14, 2017: Journal of Public Health
https://www.readbyqxmd.com/read/28334828/flexible-crispr-library-construction-using-parallel-oligonucleotide-retrieval
#9
Abigail Read, Shaojian Gao, Eric Batchelor, Ji Luo
CRISPR/Cas9-based gene knockout libraries have emerged as a powerful tool for functional screens. We present here a set of pre-designed human and mouse sgRNA sequences that are optimized for both high on-target potency and low off-target effect. To maximize the chance of target gene inactivation, sgRNAs were curated to target both 5΄ constitutive exons and exons that encode conserved protein domains. We describe here a robust and cost-effective method to construct multiple small sized CRISPR library from a single oligo pool generated by array synthesis using parallel oligonucleotide retrieval...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334803/statistical-analysis-of-genetic-interactions-in-tn-seq-data
#10
Michael A DeJesus, Subhalaxmi Nambi, Clare M Smith, Richard E Baker, Christopher M Sassetti, Thomas R Ioerger
Tn-Seq is an experimental method for probing the functions of genes through construction of complex random transposon insertion libraries and quantification of each mutant's abundance using next-generation sequencing. An important emerging application of Tn-Seq is for identifying genetic interactions, which involves comparing Tn mutant libraries generated in different genetic backgrounds (e.g. wild-type strain versus knockout strain). Several analytical methods have been proposed for analyzing Tn-Seq data to identify genetic interactions, including estimating relative fitness ratios and fitting a generalized linear model...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334798/risk-factors-for-postoperative-delirium-in-patients-undergoing-major-head-and-neck-cancer-surgery-a-meta-analysis
#11
Yun Zhu, Gangpu Wang, Shengwen Liu, Shanghui Zhou, Ying Lian, Chenping Zhang, Wenjun Yang
Objective: Postoperative delirium is common after extensive surgery. This study aimed to collate and synthesize published literature on risk factors for delirium in patients with head and neck cancer surgery. Methods: Three databases were searched (MEDLINE, Embase, and Cochrane Library) between January 1987 and July 2016. The Newcastle Ottawa Scale (NOS) was adopted to evaluate the study quality. Pooled odds ratios or mean differences for individual risk factors were estimated using the Mantel-Haenszel and inverse-variance methods...
February 24, 2017: Japanese Journal of Clinical Oncology
https://www.readbyqxmd.com/read/28334713/pulsed-dose-rate-brachytherapy-for-the-treatment-of-endometrial-cancer
#12
Francesca De Felice, Rossella Caiazzo, Ilaria Benevento, Daniela Musio, Filippo Rubini, Vincenzo Tombolini
Endometrial cancer (EC) is the most frequent gynecologic malignancy. The aim of this review is to outline clinical practice recommendations, to suggest a technical solution, and to advise doses selection for pulsed-dose rate (PDR) brachytherapy in EC. Electronic bibliographic databases, including PubMed, clinicaltrials.gov, and the American Society of Clinical Oncology (ASCO) Meeting Library, were searched for articles in English. Clinical guidelines and systematic reviews were also considered. The appropriate therapeutic approach should consider risk factors for tumor relapse and PDR brachytherapy and have a convincing role in this multidisciplinary scenario...
March 24, 2017: Oncology
https://www.readbyqxmd.com/read/28334434/withdrawn-nutrition-support-for-bone-marrow-transplant-patients
#13
REVIEW
Susan M Murray, Sima Pindoria
BACKGROUND: This is an update of the original Cochrane review published in Issue 2, 2002. Bone marrow transplantation involves administration of toxic chemotherapy and infusion of marrow cells. After treatment, patients can develop poor appetite, mucositis and gastrointestinal failure, leading to malnutrition. To prevent this, parenteral nutrition (PN) support is often first choice but is associated with increased risk of infection. Enteral nutrition (EN) is an alternative, as is addition of substrates...
March 23, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/28334409/siapopr-a-computational-method-to-simulate-evolutionary-branching-trees-for-analysis-of-tumor-clonal-evolution
#14
Thomas O McDonald, Franziska Michor
Summary: SIApopr (Simulating Infinite-Allele populations) is an R package to simulate homogeneous and inhomogeneous stochastic branching processes under a very flexible set of assumptions using the speed of C ++. The software simulates clonal evolution with the emergence of driver and passenger mutations under the infinite-allele assumption. The software is an application of the Gillespie Stochastic Simulation Algorithm expanded to a large number of cell types and scenarios, with the intention of allowing users to easily modify existing models or create their own...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334393/adjuvant-human-papillomavirus-vaccination-for-secondary-prevention-a-systematic-review
#15
Gregory R Dion, Stephanie Teng, Leslie R Boyd, Antonia Northam, Charlotte Mason-Apps, Dorice Vieira, Milan R Amin, Ryan C Branski
Importance: Human papillomavirus (HPV) vaccination is recommended for children and younger adults but not older adults or those with prior HPV exposure, leaving a large portion of the population at risk for HPV-mediated disease. Emerging data suggest a possible role for vaccination as an adjuvant treatment for individuals with HPV-related clinical disease. Objective: To systematically review the literature regarding HPV vaccination for secondary disease prevention after treatment of active clinical disease across disease sites to serve as a platform for the management of HPV-related disease of the head and neck...
March 23, 2017: JAMA Otolaryngology—Head & Neck Surgery
https://www.readbyqxmd.com/read/28334390/seqarray-a-storage-efficient-high-performance-data-format-for-wgs-variant-calls
#16
Xiuwen Zheng, Stephanie M Gogarten, Michael Lawrence, Adrienne Stilp, Matthew P Conomos, Bruce S Weir, Cathy Laurie, David Levine
Motivation: Whole-genome sequencing (WGS) data is being generated at an unprecedented rate. Analysis of WGS data requires a flexible data format to store the different types of DNA variation. Variant call format (VCF) is a general text-based format developed to store variant genotypes and their annotations. However, VCF files are large and data retrieval is relatively slow. Here we introduce a new WGS variant data format implemented in the R/Bioconductor package "SeqArray" for storing variant calls in an arrayoriented manner which provides the same capabilities as VCF, but with multiple high compression options and data access using high-performance parallel computing...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334373/estimating-error-models-for-whole-genome-sequencing-using-mixtures-of-dirichlet-multinomial-distributions
#17
Steven H Wu, Rachel S Schwartz, David J Winter, Donald F Conrad, Reed A Cartwright
Motivation: Accurate identification of genotypes is an essential part of the analysis of genomic data, including in identification of sequence polymorphisms, linking mutations with disease, and determining mutation rates. Biological and technical processes that adversely affect genotyping include copy-numbervariation, paralogous sequences, library preparation, sequencing error, and reference-mapping biases, among others. Results: We modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models...
March 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334274/interactive-effects-of-multiple-climate-change-factors-on-ammonia-oxidizers-and-denitrifiers-in-a-temperate-steppe
#18
Cuijing Zhang, Jupei Shen, Yifei Sun, Juntao Wang, Limei Zhang, Zhongling Yang, Hongyan Han, Shiqiang Wan, Jizheng He
Global climate change could have profound effects on belowground microbial communities and subsequently affect soil biogeochemical processes. The interactive effects of multiple co-occurring climate change factors on microbially-mediated processes are not well understood. A four-factorial field experiment with elevated CO2, watering, nitrogen (N) addition and night warming was conducted in a temperate steppe of northern China. Real-time polymerase chain reaction and terminal-restriction fragment length polymorphism, combined with clone library techniques were applied to examine the effects of those climate change factors on N-related microbial abundance and community composition...
March 15, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334079/how-do-cold-adapted-plants-respond-to-climatic-cycles-interglacial-expansion-explains-current-distribution-and-genomic-diversity-in-primula-farinosa-l
#19
Spyros Theodoridis, Christophe Randin, Peter Szövényi, Florian C Boucher, Theofania S Patsiou, Elena Conti
Understanding the effects of past climatic fluctuations on the distribution and population-size dynamics of cold-adapted species is essential for predicting their responses to ongoing global climate change. In spite of the heterogeneity of cold-adapted species, two main contrasting hypotheses have been proposed to explain their responses to Late Quaternary glacial cycles, namely, the interglacial contraction versus the interglacial expansion hypotheses. Here, we use the cold-adapted plant Primula farinosa to test two demographic models under each of the two alternative hypotheses and a fifth, null model...
December 21, 2016: Systematic Biology
https://www.readbyqxmd.com/read/28334071/on-the-design-and-prospects-of-direct-rna-sequencing
#20
Georgi K Marinov
Throughout the past nearly a decade, the application of high-throughput sequencing to RNA molecules in the form of RNA sequencing (RNA-seq) and its many variations has revolutionized transcriptomic studies by enabling researchers to take a simultaneously deep and truly global look into the transcriptome. However, there is still considerable scope for improvement on RNA-seq data in its current form, primarily because of the short-read nature of the dominant sequencing technologies, which prevents the completely reliable reconstruction and quantification of full-length transcripts, and the sequencing library building protocols used, which introduce various distortions in the final data sets...
February 17, 2017: Briefings in Functional Genomics
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