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https://www.readbyqxmd.com/read/28330138/vdap-gui-a-user-friendly-pipeline-for-variant-discovery-and-annotation-of-raw-next-generation-sequencing-data
#1
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/28328654/outcomes-for-children-receiving-noninvasive-ventilation-as-the-first-line-mode-of-mechanical-ventilation-at-intensive-care-admission-a-propensity-score-matched-cohort-study
#2
Jenny V Morris, Padmanabhan Ramnarayan, Roger C Parslow, Sarah J Fleming
OBJECTIVES: To compare outcomes of children receiving noninvasive ventilation with those receiving invasive ventilation as first-line mode of mechanical ventilation following unplanned intensive care admission. DESIGN: Propensity score-matched cohort study analyzing data prospectively collected by the Pediatric Intensive Care Audit Network over 8 years (2007-2014). SETTING: Thirty-one PICUs in the United Kingdom and Ireland; twenty-one of whom submitted Pediatric Critical Care Minimum Dataset data for the entire study period...
March 21, 2017: Critical Care Medicine
https://www.readbyqxmd.com/read/28316907/sleep-apps-and-behavioral-constructs-a-content-analysis
#3
Diana S Grigsby-Toussaint, Jong Cheol Shin, Dayanna M Reeves, Ariana Beattie, Evan Auguste, Girardin Jean-Louis
Although sleep apps are among the most popular commercially available health apps, little is known about how well these apps are grounded in behavioral theory. Three-hundred and sixty-nine apps were initially identified using the term "sleep" from the Google play store and Apple iTunes in September 2015. The final sample consisted of 35 apps that met the following inclusion criteria: 1) Stand-alone functionality; 2) Sleep tracker or monitor apps ranked by 100 + users; 3) Sleep Alarm apps ranked by 1000 + users; and 4) English language...
June 2017: Preventive Medicine Reports
https://www.readbyqxmd.com/read/28314164/calculation-spreadsheet-for-uncertainty-estimation-of-measurement-results-in-gamma-ray-spectrometry-and-its-validation-for-quality-assurance-purpose
#4
Alessia Ceccatelli, Ashild Dybdal, Ales Fajgelj, Aurelien Pitois
An Excel calculation spreadsheet has been developed to estimate the uncertainty of measurement results in γ-ray spectrometry. It considers all relevant uncertainty components and calculates the combined standard uncertainty of the measurement result. The calculation spreadsheet has been validated using two independent open access software and is available for download free of charge at: https://nucleus.iaea.org/rpst/ReferenceProducts/Analytical_Methods/index.htm. It provides a simple and easy-to-use template for estimating the uncertainty of γ-ray spectrometry measurement results and supports the radioanalytical laboratories seeking accreditation for their measurements using γ-ray spectrometry...
March 3, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28293619/the-fitness-of-apps-a-theory-based-examination-of-mobile-fitness-app-usage-over-5-months
#5
Lynn Katherine Herrmann, Jinsook Kim
BACKGROUND: There are thousands of fitness-related smartphone applications ("apps") available for free and purchase, but there is uncertainty if these apps help individuals achieve and maintain personal fitness. Technology usage attrition is also a concern among research studies on health technologies. METHODS: Usage of three fitness apps was examined over 5 months to assess adherence and effectiveness. Initially, 64 participants downloaded three free apps available on Android and iOS and 47 remained in the study until posttest...
2017: MHealth
https://www.readbyqxmd.com/read/28289731/deblur-rapidly-resolves-single-nucleotide-community-sequence-patterns
#6
Amnon Amir, Daniel McDonald, Jose A Navas-Molina, Evguenia Kopylova, James T Morton, Zhenjiang Zech Xu, Eric P Kightley, Luke R Thompson, Embriette R Hyde, Antonio Gonzalez, Rob Knight
High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits differentiation of closely related bacteria. Although many scientific questions can be addressed with broad taxonomic profiles, clinical, food safety, and some ecological applications require higher specificity. Here we introduce a novel sub-operational-taxonomic-unit (sOTU) approach, Deblur, that uses error profiles to obtain putative error-free sequences from Illumina MiSeq and HiSeq sequencing platforms...
March 2017: MSystems
https://www.readbyqxmd.com/read/28288057/mesorectal-excision-with-or-without-lateral-lymph-node-dissection-for-clinical-stage-ii-iii-lower-rectal-cancer-jcog0212-a-multicenter-randomized-controlled-noninferiority-trial
#7
Shin Fujita, Junki Mizusawa, Yukihide Kanemitsu, Masaaki Ito, Yusuke Kinugasa, Koji Komori, Masayuki Ohue, Mitsuyoshi Ota, Yoshihiro Akazai, Manabu Shiozawa, Takashi Yamaguchi, Hiroyuki Bandou, Kenji Katsumata, Kohei Murata, Yoshihito Akagi, Nobuhiro Takiguchi, Yoshihisa Saida, Kenichi Nakamura, Haruhiko Fukuda, Takayuki Akasu, Yoshihiro Moriya
OBJECTIVE: The aim of the study was to confirm the noninferiority of mesorectal excision (ME) alone to ME with lateral lymph node dissection (LLND) in terms of efficacy. BACKGROUND: Lateral pelvic lymph node metastasis is occasionally found in clinical stage II or III lower rectal cancer, and ME with LLND is the standard procedure in Japan. ME alone, however, is the international standard surgical procedure for rectal cancer. METHODS: Eligibility criteria included histologically proven rectal cancer at clinical stage II/III; main lesion located in the rectum, with the lower margin below the peritoneal reflection; no lateral pelvic lymph node enlargement; Peformance Status of 0 or 1; and age 20 to 75 years...
March 10, 2017: Annals of Surgery
https://www.readbyqxmd.com/read/28263232/phase-ii-study-of-adjuvant-chemoradiotherapy-using-docetaxel-cisplatin-5-fluorouracil-before-and-after-intensity-modulated-radiotherapy-with-concurrent-docetaxel-in-patients-with-completely-r0-resected-gastric-carcinoma
#8
Yong Liu, Guoqi Zhao, Yi Xu, Tiening Zhang, Zhixiao Chen, Ge Yan, Wenzhi Tu, Ye Hu, Ying Chen, Xia He, Xiaodong Li, Hui Chen, Shengyu Yao, Zhekai Hu, Xuming Chen, Tingfeng Chen
OBJECTIVES: The Intergroup 0116 study has demonstrated a significant survival benefit for completely resected (R0) gastric cancer patients treated with a fluorouracil/leucovorin chemoradiotherapy regimen. However, this regimen is also toxic and less effective in terms of distant disease control. Therefore, a more efficacious and safer regimen is urgently needed. METHODS: Patients with R0 resected gastric carcinoma received up to two 21-day cycles of postoperative adjuvant preradiation and postradiation DCF chemotherapy (docetaxel 37...
March 3, 2017: American Journal of Clinical Oncology
https://www.readbyqxmd.com/read/28263205/long-term-follow-up-of-men1-patients-who-do-not-have-initial-surgery-for-small-%C3%A2-2-cm-nonfunctioning-pancreatic-neuroendocrine-tumors-an-afce-and-gte-study-association-francophone-de-chirurgie-endocrinienne-groupe-d-etude-des-tumeurs-endocrines
#9
Frederic Triponez, Samira M Sadowski, François Pattou, Catherine Cardot-Bauters, Eric Mirallié, Maëlle Le Bras, Frédéric Sebag, Patricia Niccoli, Sophie Deguelte, Guillaume Cadiot, Gilles Poncet, Jean-Christophe Lifante, Françoise Borson-Chazot, Philippe Chaffanjon, Olivier Chabre, Fabrice Menegaux, Eric Baudin, Philippe Ruszniewski, Hélène Du Boullay, Pierre Goudet
OBJECTIVE: To report long-term follow-up of patients with multiple endocrine neoplasia type 1 (MEN1) and nonfunctioning pancreatic neuroendocrine tumors (NF-PET). BACKGROUND: Pancreaticoduodenal tumors occur in almost all patients with MEN1 and are a major cause of death. The natural history and clinical outcome are poorly defined, and management is still controversial for small NF-PET. METHODS: Clinical outcome and tumor progression were analyzed in 46 patients with MEN1 with 2 cm or smaller NF-PET who did not have surgery at the time of initial diagnosis...
March 15, 2017: Annals of Surgery
https://www.readbyqxmd.com/read/28263191/coronary-artery-bypass-graft-surgery-and-dementia-risk-in-the-cardiovascular-health-study
#10
Elżbieta Kuźma, Jac Airdrie, Thomas J Littlejohns, Ilianna Lourida, Jo Thompson-Coon, Iain A Lang, Monica Scrobotovici, Evan L Thacker, Annette Fitzpatrick, Lewis H Kuller, Oscar L Lopez, William T Longstreth, Obioha C Ukoumunne, David J Llewellyn
INTRODUCTION: The association between history of coronary artery bypass graft surgery (CABG) and dementia risk remains unclear. METHODS: We conducted a prospective cohort analysis using data on 3155 elderly adults free from prevalent dementia from the US population-based Cardiovascular Health Study (CHS) with adjudicated incident all-cause dementia, Alzheimer disease (AD), vascular dementia (VaD), and mixed dementia. RESULTS: In the CHS, the hazard ratio (HR) for all-cause dementia was 1...
March 3, 2017: Alzheimer Disease and Associated Disorders
https://www.readbyqxmd.com/read/28259147/proteomodlr-for-functional-proteomic-analysis
#11
Paolo Cifani, Mojdeh Shakiba, Sagar Chhangawala, Alex Kentsis
BACKGROUND: High-accuracy mass spectrometry enables near comprehensive quantification of the components of the cellular proteomes, increasingly including their chemically modified variants. Likewise, large-scale libraries of quantified synthetic peptides are becoming available, enabling absolute quantification of chemically modified proteoforms, and therefore systems-level analyses of changes of their absolute abundance and stoichiometry. Existing computational methods provide advanced tools for mass spectral analysis and statistical inference, but lack integrated functions for quantitative analysis of post-translationally modified proteins and their modification stoichiometry...
March 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28245685/-characteristics-of-clinical-trials-in-hungary-based-on-the-analysis-of-an-international-database
#12
Tamás Tóth, Péter Pollner, Gergely Palla, Elek Dinya
Intorduction: The ClinicalTrials.gov website, which is operated by the US government, collects data about clinical trials. AIM: We have processed data related to Hungary by downloading from the website as XML files. METHOD: Most of the data describe trials performed after 2000, so we got an overview about the clinical research of the last 10 to 15 years. As the majority of the data fields are collected as free text, significant data cleaning was needed. RESULTS: The database contained 2863 trials related to Hungary from 189 settlements...
March 2017: Orvosi Hetilap
https://www.readbyqxmd.com/read/28235750/the-state-of-open-source-electronic-health-record-projects-a-software-anthropology-study
#13
Mona Alsaffar, Peter Yellowlees, Alberto Odor, Michael Hogarth
BACKGROUND: Electronic health records (EHR) are a key tool in managing and storing patients' information. Currently, there are over 50 open source EHR systems available. Functionality and usability are important factors for determining the success of any system. These factors are often a direct reflection of the domain knowledge and developers' motivations. However, few published studies have focused on the characteristics of free and open source software (F/OSS) EHR systems and none to date have discussed the motivation, knowledge background, and demographic characteristics of the developers involved in open source EHR projects...
February 24, 2017: JMIR Medical Informatics
https://www.readbyqxmd.com/read/28230254/resistance-to-valproic-acid-as-predictor-of-treatment-resistance-in-genetic-generalized-epilepsies
#14
Joanna Gesche, Marina Khanevski, Carl Solberg, Christoph Patrick Beier
This study aimed at defining clinical predictors of drug resistance in adults with genetic generalized epilepsy (GGE) who were treated with a broad spectrum of antiepileptic drugs. Of a cohort of 137 unselected adult GGE patients with long-term follow up, clinical and demographic data, putative prognostic factors (e.g., psychiatric comorbidities, electroencephalography [EEG]), treatment response, and data indicative of social status were collected. Fifty-eight patients had seizures within the past year. Thirty-three patients met the definition of "drug-resistant epilepsy" according to the International League Against Epilepsy (ILAE) definition...
February 23, 2017: Epilepsia
https://www.readbyqxmd.com/read/28222477/checklists-for-the-assessment-of-correct-inhalation-therapy
#15
V Knipel, S Schwarz, F S Magnet, J H Storre, C P Criée, W Windisch
Introduction For the long-term treatment of obstructive lung diseases inhalation therapy with drugs being delivered directly to the lungs as an aerosol has become the method of choice. However, patient-related mistakes in inhalation techniques are frequent and recognized to be associated with reduced disease control. Since the assessment of patient-mistakes in inhalation has yet not been standardized, the present study was aimed at developing checklists for the assessment of correct inhalation. Methods Checklists were developed in German by an expert panel of pneumologists and professionally translated into English following back-translation procedures...
February 2017: Pneumologie
https://www.readbyqxmd.com/read/28207831/the-relationship-between-rassf1a-gene-promoter-methylation-and-the-susceptibility-and-prognosis-of-melanoma-a-meta-analysis-and-bioinformatics
#16
Chihao Shao, Wenzhu Dai, Haili Li, Wenru Tang, Shuting Jia, Xiaoming Wu, Ying Luo
BACKGROUND: The function of the tumor suppressor gene RASSF1A in cancer cells has been detailed in many studies. However, due to the methylation of its promoter, the expression of RASSF1A is missing in most cancers. In the literature, we found that the conclusion regarding the relationship between RASSF1A gene promoter methylation and the susceptibility and prognosis of melanoma was not unified. This study adopts the use of a meta-analysis and bioinformatics to explore the relationship between RASSF1A gene promoter methylation and the susceptibility and prognosis of melanoma...
2017: PloS One
https://www.readbyqxmd.com/read/28207723/unhealthy-food-marketing-to-new-zealand-children-and-adolescents-through-the-internet
#17
Stefanie Vandevijvere, Karuna Sagar, Bridget Kelly, Boyd Swinburn
AIM: To assess the extent and nature of unhealthy food marketing to New Zealand children and adolescents through the internet. METHODS: Internet traffic data for January 2014 was purchased from AC Nielsen to identify the most popular websites (n=110) among children and adolescents aged 6-17 years. In addition, websites (n=70) of food and beverage brands most frequently marketed to children through television, sports, magazines and Facebook were included. Marketing techniques and features on those websites were analysed...
February 17, 2017: New Zealand Medical Journal
https://www.readbyqxmd.com/read/28198670/metatopics-an-integration-tool-to-analyze-microbial-community-profile-by-topic-model
#18
Jifang Yan, Guohui Chuai, Tao Qi, Fangyang Shao, Chi Zhou, Chenyu Zhu, Jing Yang, Yifei Yu, Cong Shi, Ning Kang, Yuan He, Qi Liu
BACKGROUND: Deciphering taxonomical structures based on high dimensional sequencing data is still challenging in metagenomics study. Moreover, the common workflow processed in this field fails to identify microbial communities and their effect on a specific disease status. Even the relationships and interactions between different bacteria in a microbial community keep unknown. RESULTS: MetaTopics can efficiently extract the latent microbial communities which reflect the intrinsic relations or interactions among several major microbes...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28196507/vrex-an-open-source-toolbox-for-creating-3d-virtual-reality-experiments
#19
Madis Vasser, Markus Kängsepp, Murad Magomedkerimov, Kälver Kilvits, Vladislav Stafinjak, Taavi Kivisik, Raul Vicente, Jaan Aru
BACKGROUND: We present VREX, a free open-source Unity toolbox for virtual reality research in the fields of experimental psychology and neuroscience. RESULTS: Different study protocols about perception, attention, cognition and memory can be constructed using the toolbox. VREX provides a procedural generation of (interconnected) rooms that can be automatically furnished with a click of a button. VREX includes a menu system for creating and storing experiments with different stages...
February 14, 2017: BMC Psychology
https://www.readbyqxmd.com/read/28187712/vmcmc-a-graphical-and-statistical-analysis-tool-for-markov-chain-monte-carlo-traces
#20
Raja H Ali, Mikael Bark, Jorge Miró, Sayyed A Muhammad, Joel Sjöstrand, Syed M Zubair, Raja M Abbas, Lars Arvestad
BACKGROUND: MCMC-based methods are important for Bayesian inference of phylogeny and related parameters. Although being computationally expensive, MCMC yields estimates of posterior distributions that are useful for estimating parameter values and are easy to use in subsequent analysis. There are, however, sometimes practical difficulties with MCMC, relating to convergence assessment and determining burn-in, especially in large-scale analyses. Currently, multiple software are required to perform, e...
February 10, 2017: BMC Bioinformatics
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