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https://www.readbyqxmd.com/read/28549078/herod-a-human-ethnic-and-regional-specific-omics-database
#1
Xian Zeng, Lin Tao, Zhang Peng, Chu Qin, Shangying Chen, Weidong He, Ying Tan, Hong Xia Liu, Sheng Yong Yang, Zhe Chen, Yu Yang Jiang, Yu Zong Chen
Motivation: Genetic and gene expression variations within and between populations and across geographical regions have substantial effects on the biological phenotypes, diseases, and therapeutic response. The development of precision medicines can be facilitated by the OMICS studies of the patients of specific ethnicity and geographic region. However, there is an inadequate facility for broadly and conveniently accessing the ethnic and regional specific OMICS data. Results: Here, we introduced a new free database, HEROD, a human ethnic and regional specific OMICS database...
May 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28548922/development-of-ergonomics-audits-for-bagging-haul-truck-and-maintenance-and-repair-operations-in-mining
#2
Patrick G Dempsey, Jonisha Pollard, William L Porter, Alan Mayton, John R Heberger, Sean Gallagher, Leanna Reardon, Colin G Drury
The development and testing of ergonomics and safety audits for small and bulk bag filling, haul truck, and maintenance and repair operations in coal preparation and mineral processing plants found at surface mine sites is described. The content for the audits was derived from diverse sources of information on ergonomics and safety deficiencies including: analysis of injury, illness, and fatality data and reports; task analysis; empirical laboratory studies of particular tasks; field studies and observations at mine sites; and maintenance records...
May 26, 2017: Ergonomics
https://www.readbyqxmd.com/read/28537669/e2f2-induces-mcm4-ccne2-and-whsc1-upregulation-in-ovarian-cancer-and-predicts-poor-overall-survival
#3
L Xie, T Li, L-H Yang
OBJECTIVE: To explore the genes co-upregulated with E2F2 in ovarian cancer and their association with survival outcomes in ovarian cancer patients. MATERIALS AND METHODS: The raw data of GDS3592 was downloaded from GEO datasets for reanalysis. The overlapping subset between the top 150 upregulated genes in ovarian cancer epithelial cells (CEPIs) and the E2F2 positively correlated genes (Pearson's r≥0.5) in ovarian cancer cohort in TCGA was identified. The association between E2F2, MCM4, CCNE2 and WHSC1 and overall survival (OS) and recurrence-free survival (RFS) in ovarian cancer patients were assessed using Kaplan-Meier plotter...
May 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28537202/self-assessment-of-independence-in-older-people
#4
Pierre Koskas, B Wolfowicz
BACKGROUND: E-health initiatives on the Internet can be used to provide support to people with chronic diseases and to their caregivers. In 2014/2015, we created a free website called jesuisautonome.fr where older people, or their carers on their behalf, can assess their independence in daily living by filling out a simple questionnaire. OBJECTIVES: To evaluate the interest of the public in websites of this kind, by analysing home care plans obtained via the self-assessment questionnaire...
January 1, 2017: HIM Journal
https://www.readbyqxmd.com/read/28535189/predicting-accurate-contacts-in-thousands-of-pfam-domain-families-using-pconsc3
#5
Mirco Michel, Marcin J Skwark, David Menéndez Hurtado, Magnus Ekeberg, Arne Elofsson
Motivation: A fewyears ago it was shown that by using amaximumentropy approach to describe couplings between columns in a multiple sequence alignment it is possible to significantly increase the accuracy of residue contact predictions. For very large protein families with more than 1000 effective sequences the accuracy is sufficient to produce accurate models of proteins as well as complexes. Today, for about half of all Pfam domain families no structure is known, but unfortunately most of these families have at most a few hundred members, i...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28529712/looking-into-pandora-s-box-the-content-of-sci-hub-and-its-usage
#6
Bastian Greshake
Despite the growth of Open Access, potentially illegally circumventing paywalls to access scholarly publications is becoming a more mainstream phenomenon. The web service Sci-Hub is amongst the biggest facilitators of this, offering free access to around 62 million publications. So far it is not well studied how and why its users are accessing publications through Sci-Hub. By utilizing the recently released corpus of Sci-Hub and comparing it to the data of  ~28 million downloads done through the service, this study tries to address some of these questions...
2017: F1000Research
https://www.readbyqxmd.com/read/28518173/simultaneous-quantification-of-n-and-o-glycans-using-a-solid-phase-method
#7
Shuang Yang, Yingwei Hu, Lori Sokoll, Hui Zhang
Glycosylation has a pivotal role in a diverse range of biological activities, modulating the structure and function of proteins. Glycogens coupled to the nitrogen atom (N-linked) of asparagine side chains or to the oxygen atom (O-linked) of serine and threonine side chains represent the two major protein glycosylation forms. N-glycans can be released by glycosidases, whereas O-glycans are often cleaved by chemical reaction. However, it is challenging to combine these enzymatic and chemical reactions in order to analyze both N- and O-glycans...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28509812/ospemifene-s-effects-on-lipids-and-coagulation-factors-a-post-hoc-analysis-of-phase-2-and-3-clinical-trial-data
#8
David F Archer, Corrado Altomare, Wei Jiang, Susannah Cort
OBJECTIVE: To evaluate the effect of ospemifene 60 mg on the lipid and coagulation parameters of postmenopausal women using data from five phase 2 and 3 clinical trials. METHODS: Data for lipids and coagulation factors for 2,166 postmenopausal women were pooled from five randomized, placebo-controlled studies. Lipid and coagulation parameters included in this analysis were total cholesterol, high-density lipoproteins (HDL), low-density lipoproteins (LDL), triglycerides, activated partial thromboplastin time (aPTT), fibrinogen, antithrombin antigen, protein C Ag, and protein S Ag free...
May 15, 2017: Menopause: the Journal of the North American Menopause Society
https://www.readbyqxmd.com/read/28509710/ultrasound-guided-pericardiocentesis-a-novel-parasternal-approach
#9
Adi Osman, Tan Wan Chuan, Jamalludin Ab Rahman, Gabriele Via, Guido Tavazzi
OBJECTIVE: The aim of this study was to evaluate a novel pericardiocentesis technique using an in-plane parasternal medial-to-lateral approach with the use of a high-frequency probe in patients with cardiac tamponade. BACKGROUND: Echocardiography is pivotal in the diagnosis of pericardial effusion and tamponade physiology. Ultrasound guidance for pericardiocentesis is currently considered the standard of care. Several approaches have been described recently, which differ mainly on the site of puncture (subxiphoid, apical, or parasternal)...
May 15, 2017: European Journal of Emergency Medicine: Official Journal of the European Society for Emergency Medicine
https://www.readbyqxmd.com/read/28505005/gastric-cancer-with-primitive-enterocyte-phenotype-an-aggressive-subgroup-of-intestinal-type-adenocarcinoma
#10
Sho Yamazawa, Tetsuo Ushiku, Aya Shinozaki-Ushiku, Akimasa Hayashi, Akiko Iwasaki, Hiroyuki Abe, Amane Tagashira, Hiroharu Yamashita, Yasuyuki Seto, Hiroyuki Aburatani, Masashi Fukayama
A primitive cell-like gene expression signature is associated with aggressive phenotypes of various cancers. We assessed the expression of phenotypic markers characterizing primitive cells and its correlation with clinicopathologic and molecular characteristics in gastric cancer. Immunohistochemical analysis of a panel of primitive phenotypic markers, including embryonic stem cell markers (OCT4, NANOG, SALL4, CLDN6, and LIN28) and known oncofetal proteins (AFP and GPC3), was performed using tissue microarray on 386 gastric cancers...
May 12, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28503199/the-aachen-fall-prevention-app-a-smartphone-application-app-for-the-self-assessment-of-elderly-patients-at-risk-for-ground-level-falls
#11
Peter Rasche, Alexander Mertens, Christina Bröhl, Sabine Theis, Tobias Seinsch, Matthias Wille, Hans-Christoph Pape, Matthias Knobe
BACKGROUND: Fall incidents are a major problem for patients and healthcare. The "Aachen Fall Prevention App" (AFPA) represents the first mobile Health (mHealth) application (app) empowering older patients (persons 50+ years) to self-assess and monitor their individual fall risk. Self-assessment is based on the "Aachen Fall Prevention Scale," which consists of three steps. First, patients answer ten standardized yes-no questions (positive criterion ≥ 5 "Yes" responses). Second, a ten-second test of free standing without compensatory movement is performed (positive criterion: compensatory movement)...
2017: Patient Safety in Surgery
https://www.readbyqxmd.com/read/28481970/foldit-standalone-a-video-game-derived-protein-structure-manipulation-interface-using-rosetta
#12
Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B Siegel, Firas Khatib, Seth Cooper
Summary: Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements...
May 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28481779/claudin-4-expression-is-associated-with-survival-in-ovarian-cancer-but-not-with-chemotherapy-response
#13
Laura Martín de la Fuente, Susanne Malander, Linda Hartman, Jenny-Maria Jönsson, Anna Ebbesson, Mef Nilbert, Anna Måsbäck, Ingrid Hedenfalk
The tight junction protein claudin-4 has been reported to be overexpressed in advanced ovarian cancer. We investigated the prognostic significance of claudin-4 overexpression and whether claudin-4 expression could predict platinum response in primary ovarian carcinoma (OC). Claudin-4 expression was evaluated by immunohistochemistry in a tissue microarray of 140 OCs. Multivariable Cox-regression models were used to assess the effect of claudin-4 overexpression on progression-free survival and overall survival (OS)...
May 5, 2017: International Journal of Gynecological Pathology
https://www.readbyqxmd.com/read/28475830/bayeswham-a-bayesian-approach-for-free-energy-estimation-reweighting-and-uncertainty-quantification-in-the-weighted-histogram-analysis-method
#14
Andrew L Ferguson
The weighted histogram analysis method (WHAM) is a powerful approach to estimate molecular free energy surfaces (FES) from biased simulation data. Bayesian reformulations of WHAM are valuable in proving statistically optimal use of the data and providing a transparent means to incorporate regularizing priors and estimate statistical uncertainties. In this work, we develop a fully Bayesian treatment of WHAM to generate statistically optimal FES estimates in any number of biasing dimensions under arbitrary choices of the Bayes prior...
May 5, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28474220/the-quality-of-patient-information-booklets-for-cancer-patients-an-evaluation-of-free-accessible-material-in-german-language
#15
Christian Keinki, Ivonne Rudolph, Dana Ruetters, Ulrike Kuenzel, Jessica Lobitz, Maike Schaefer, Hani Hanaya, Jutta Huebner
According to the information-seeking behaviors of patients, booklets which can be downloaded from the Internet for free are an important source of information notably for patients with cancer. This study investigated whether information booklets for patients with cancer available at German websites are in accordance with the formal and content criteria of evidence-based information. We compared and compiled both content and formal criteria by matching different national and international standards for written patient information using a merged instrument...
May 4, 2017: Journal of Cancer Education: the Official Journal of the American Association for Cancer Education
https://www.readbyqxmd.com/read/28472495/c-spade-a-web-tool-for-interactive-analysis-and-visualization-of-drug-screening-experiments-through-compound-specific-bioactivity-dendrograms
#16
Balaguru Ravikumar, Zaid Alam, Gopal Peddinti, Tero Aittokallio
The advent of polypharmacology paradigm in drug discovery calls for novel chemoinformatic tools for analyzing compounds' multi-targeting activities. Such tools should provide an intuitive representation of the chemical space through capturing and visualizing underlying patterns of compound similarities linked to their polypharmacological effects. Most of the existing compound-centric chemoinformatics tools lack interactive options and user interfaces that are critical for the real-time needs of chemical biologists carrying out compound screening experiments...
May 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28472085/transcriptomic-immunologic-signature-associated-with-favorable-clinical-outcome-in-basal-like-breast-tumors
#17
Sandra Martínez-Canales, Francisco Cifuentes, Miguel López De Rodas Gregorio, Leticia Serrano-Oviedo, Eva María Galán-Moya, Eitan Amir, Atanasio Pandiella, Balázs Győrffy, Alberto Ocaña
BACKGROUND: Most patients with early stage triple negative breast cancer (TNBC) receive adjuvant chemotherapy. Activation of the immune system is associated with tumor response and may help identify TNBC with favorable outcome. METHODS: Gene expression data were obtained from the GEO Dataset GDS2250/GSE3744. Affymetrix CEL files were downloaded and analyzed with Affymetrix Transcriptome Analysis Console 3.0. Functional genomics was implemented with David Bioinformatics Resources 6...
2017: PloS One
https://www.readbyqxmd.com/read/28454901/a-computational-model-for-predicting-integrase-catalytic-domain-of-retrovirus
#18
Sijia Wu, Jiuqiang Han, Xinman Zhang, Dexing Zhong, Ruiling Liu
Integrase catalytic domain (ICD) is an essential part in the retrovirus for integration reaction, which enables its newly synthesized DNA to be incorporated into the DNA of infected cells. Owing to the crucial role of ICD for the retroviral replication and the absence of an equivalent of integrase in host cells, it is comprehensible that ICD is a promising drug target for therapeutic intervention. However, annotated ICDs in UniProtKB database have still been insufficient for a good understanding of their statistical characteristics so far...
April 26, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28449639/clovr-comparative-automated-cloud-enabled-comparative-microbial-genome-sequence-analysis-pipeline
#19
Sonia Agrawal, Cesar Arze, Ricky S Adkins, Jonathan Crabtree, David Riley, Mahesh Vangala, Kevin Galens, Claire M Fraser, Hervé Tettelin, Owen White, Samuel V Angiuoli, Anup Mahurkar, W Florian Fricke
BACKGROUND: The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. RESULTS: CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI...
April 27, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28431175/minepath-org-a-free-interactive-pathway-analysis-web-server
#20
Lefteris Koumakis, Panos Roussos, George Potamias
Minepath (www.minepath.org) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles...
April 20, 2017: Nucleic Acids Research
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