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Data linkage

Ivan Yu Chernyshov, Philip V Toukach
Motivation: Glycans and glycoconjugates are usually recorded in dedicated databases in residue-based notations. Only a few of them can be converted into chemical (atom-based) formats highly demanded in conformational and biochemical studies. In this work, we present a tool for translation from a residue-based glycan notation to SMILES. Results: The REStLESS algorithm for translation from the CSDB Linear notation to SMILES was developed. REStLESS stands for ResiduEs as Smiles and LinkagEs as SmartS, where SMARTS reaction expressions are used to merge pre-encoded residues into a molecule...
March 14, 2018: Bioinformatics
Rogério M Pinto, Susan S Witte, Prema L Filippone, C Jean Choi, Melanie Wall
The U.S. Centers for Disease Control and Prevention (CDC) Diffusion of Effective Behavioral Interventions project has disseminated HIV behavioral interventions (EBIs) across the United States since the 1990s. In 2011, the CDC launched the High-Impact HIV Prevention (HIP) project, providing EBIs plus high-impact services (HIV testing, primary care, and support services). Providers (nurses, social workers, educators) are unable to consistently make linkages; thus, numerous at-risk individuals are not benefitting from HIP...
March 1, 2018: Health Education & Behavior: the Official Publication of the Society for Public Health Education
Helen Bould, Bianca De Stavola, Glyn Lewis, Nadia Micali
Previous research on eating disorders, disordered eating behaviours, and whether their prevalence varies across schools, has produced inconsistent results. Our previous work using Swedish record-linkage data found that rates of diagnosed eating disorders vary between schools, with higher proportions of girls and higher proportions of highly educated parents within a school being associated with greater numbers of diagnosed eating disorders. We aimed to extend these findings to a UK population-based sample and hypothesised that a similar association would be evident when studying disordered eating behaviours...
March 15, 2018: European Child & Adolescent Psychiatry
Jie-Li Lv, Zhou Li, Li-Min Guo, Lai-Bin Zhang
Two new sesquiterpene lactones, artelavanolides A (1) and B (2), and four known sesquiterpene lactones (3-6) were isolated from the leaves of Artemisia lavandulaefolia. Their structures were elucidated based on the analysis of spectroscopic data (1D, 2D NMR and HRESIMS). The absolute configuration of 1 was determined by the analysis of single-crystal X-ray diffraction data. Artelavanolide A (1) is a rare sesquiterpene lactone possessing an unusual skeleton with the linkage of Me(14)-C(1) that is probably formed through a rearrangement of the guaiane-type sesquiterpenoids...
March 15, 2018: Chemistry & Biodiversity
Hui Yu, Xinxin You, Jia Li, Xinhui Zhang, Shuai Zhang, Shoujia Jiang, Xueqiang Lin, Hao-Ran Lin, Zining Meng, Qiong Shi
The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing...
March 12, 2018: Science China. Life Sciences
Anne Liu, An Le, Jian Zhang, Chris Wong, Clifford Wong, Linda Henry, Mindie H Nguyen
OBJECTIVES: Data on liver and non-liver co-morbidities in chronic hepatitis B (CHB) patients are limited. This study analyzes the prevalence of co-morbidities in a multicenter CHB cohort evaluated over 15 years. METHODS: This study included 2734 consecutive adult American CHB patients from a university medical center and several community primary care clinics. Data were analyzed by time periods (patients in each time period were unique without overlapping): 2000-2005 (n = 885), 2006-2010 (n = 888), and 2011-2015 (n = 961)...
March 14, 2018: Clinical and Translational Gastroenterology
Ray Hu, Michael P Morley, Jeffrey Brandimarto, Nathan R Tucker, Victoria A Parsons, Sihai D Zhao, Benjamin Meder, Hugo A Katus, Frank Rühle, Monika Stoll, Eric Villard, François Cambien, Honghuang Lin, Nicholas L Smith, Janine F Felix, Ramachandran S Vasan, Pim van der Harst, Christopher Newton-Cheh, Jin Li, Cecilia E Kim, Hakon Hakonarson, Sridhar Hannenhalli, Euan A Ashley, Christine S Moravec, W H Wilson Tang, Marjorie Maillet, Jeffery D Molkentin, Patrick T Ellinor, Kenneth B Margulies, Thomas P Cappola
BACKGROUND: Inhibition of PKC-α (protein kinase C-α) enhances contractility and cardioprotection in animal models, but effects in humans are unknown. Genotypes at rs9912468 strongly associate with PRKCA expression in the left ventricle, enabling genetic approaches to measure effects of reduced PKC-α in human populations. METHODS AND RESULTS: We analyzed the cis expression quantitative trait locus for PRKCA marked by rs9912468 using 313 left ventricular specimens from European Ancestry patients...
March 2018: Circ Genom Precis Med
Catherine M Olsen, Nirmala Pandeya, Bridie S Thompson, Jean Claude Dusingize, Penelope M Webb, Adele C Green, Rachel E Neale, David C Whiteman
Background: Risk stratification can improve the efficacy and cost-efficiency of screening programs for early detection of cancer. We sought to derive a risk stratification tool for melanoma that was suitable for the general population using only self-reported information. Methods: We used melanoma risk factor information collected at baseline from QSKIN, a prospective cohort study of Queensland adults age 40 to 69 years at recruitment (n = 41 954). We examined two separate outcomes: 1) invasive melanomas and 2) all melanomas (invasive + in situ) obtained through data linkage to the cancer registry...
March 11, 2018: Journal of the National Cancer Institute
Hanh Ngo, Roberto Forero, David Mountain, Daniel Fatovich, Wing Nicola Man, Peter Sprivulis, Mohammed Mohsin, Sam Toloo, Antonio Celenza, Gerard Fitzgerald, Sally McCarthy, Ken Hillman
BACKGROUND: In 2009, the Western Australian (WA) Government introduced the Four-Hour Rule (FHR) program. The policy stated that most patients presenting to Emergency Departments (EDs) were to be seen and either admitted, transferred, or discharged within 4 hours. This study utilised de-identified data from five participating hospitals, before and after FHR implementation, to assess the impact of the FHR on several areas of ED functioning. METHODS: A state (WA) population-based intervention study design, using longitudinal data obtained from administrative health databases via record linkage methodology, and interrupted time series analysis technique...
2018: PloS One
Jade M S Delevaux, Robert Whittier, Kostantinos A Stamoulis, Leah L Bremer, Stacy Jupiter, Alan M Friedlander, Matthew Poti, Greg Guannel, Natalie Kurashima, Kawika B Winter, Robert Toonen, Eric Conklin, Chad Wiggins, Anders Knudby, Whitney Goodell, Kimberly Burnett, Susan Yee, Hla Htun, Kirsten L L Oleson, Tracy Wiegner, Tamara Ticktin
Declining natural resources have led to a cultural renaissance across the Pacific that seeks to revive customary ridge-to-reef management approaches to protect freshwater and restore abundant coral reef fisheries. Effective ridge-to-reef management requires improved understanding of land-sea linkages and decision-support tools to simultaneously evaluate the effects of terrestrial and marine drivers on coral reefs, mediated by anthropogenic activities. Although a few applications have linked the effects of land cover to coral reefs, these are too coarse in resolution to inform watershed-scale management for Pacific Islands...
2018: PloS One
Fenglong Xie, Lisandro D Colantonio, Jeffrey R Curtis, Meredith L Kilgore, Emily B Levitan, Keri L Monda, Monika M Safford, Ben Taylor, Mark Woodward, Paul Muntner
BACKGROUND: Cause of death is often not available in administrative claims data. OBJECTIVE: To develop claims-based algorithms to identify deaths due to fatal cardiovascular disease (CVD; ie, fatal coronary heart disease [CHD] or stroke), CHD, and stroke. METHODS: Reasons for Geographic and Racial Differences in Stroke (REGARDS) study data were linked with Medicare claims to develop the algorithms. Events adjudicated by REGARDS study investigators were used as the gold standard...
March 14, 2018: Pharmacoepidemiology and Drug Safety
Christina M Nagle, Tracy A O'Mara, Yen Tan, Daniel D Buchanan, Andreas Obermair, Penny Blomfield, Michael A Quinn, Penelope M Webb, Amanda B Spurdle
OBJECTIVE: The risk of developing endometrial cancer (EC) and/or survival following a diagnosis of EC might differ by tumor DNA mismatch repair (MMR) status. We assessed the association between tumor MMR status (classified as MMR-proficient, somatic MMR-deficient, germline MMR-deficient) and the risk of developing EC and survival following a diagnosis of EC. METHODS: We analyzed data from women who participated in the Australian National Endometrial Cancer Study (ANECS) conducted between 2005 and 2007...
February 23, 2018: Journal of Gynecologic Oncology
Emily Baker, Karl Michael Schmidt, Rebecca Sims, Michael C O'Donovan, Julie Williams, Peter Holmans, Valentina Escott-Price, With The Gerad Consortium
Polygenic risk scores (PRSs) are a method to summarize the additive trait variance captured by a set of SNPs, and can increase the power of set-based analyses by leveraging public genome-wide association study (GWAS) datasets. PRS aims to assess the genetic liability to some phenotype on the basis of polygenic risk for the same or different phenotype estimated from independent data. We propose the application of PRSs as a set-based method with an additional component of adjustment for linkage disequilibrium (LD), with potential extension of the PRS approach to analyze biologically meaningful SNP sets...
March 12, 2018: Genetic Epidemiology
Úna C Mc Menamin, Andrew T Kunzmann, Michael B Cook, Brian T Johnston, Liam J Murray, Andrew D Spence, Marie M Cantwell, Chris R Cardwell
Incidence of upper gastrointestinal cancers of the oesophagus and stomach show a strong unexplained male predominance. Hormonal and reproductive factors have been associated with upper gastrointestinal cancers in women but there is little available data on men. To investigate this, we included 219,425 men enrolled in the UK Biobank in 2006-2010. Baseline assessments provided information on hormonal and reproductive factors (specifically hair baldness, number of children fathered, relative age at first facial hair and relative age voice broke) and incident oesophageal or gastric cancers were identified through linkage to UK cancer registries...
March 13, 2018: International Journal of Cancer. Journal International du Cancer
Rebecca Miller, Clifford Akateh, Noelle Thompson, Dmitry Tumin, Don Hayes, Sylvester M Black, Joseph D Tobias
BACKGROUND: Existing risk adjustment models for solid organ transplantation omit socioeconomic status (SES). With limited data available on transplant candidates' SES, linkage of transplant outcomes data to geographic SES measures has been proposed. We investigate the utility of county SES for understanding differences in pediatric kidney transplantation (KTx) outcomes. METHODS: We identified patients < 18 years of age receiving first-time KTx using United Network for Organ Sharing registry data in two eras: 2006-2010 and 2011-2015, corresponding to periods of county SES data collection...
March 12, 2018: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
Claudio Toma, Alex D Shaw, Richard J N Allcock, Anna Heath, Kerrie D Pierce, Philip B Mitchell, Peter R Schofield, Janice M Fullerton
Bipolar disorder (BD) is a complex psychiatric condition with high heritability, the genetic architecture of which likely comprises both common variants of small effect and rare variants of higher penetrance, the latter of which are largely unknown. Extended families with high density of illness provide an opportunity to map novel risk genes or consolidate evidence for existing candidates, by identifying genes carrying pathogenic rare variants. We performed whole-exome sequencing (WES) in 15 BD families (117 subjects, of whom 72 were affected), augmented with copy number variant (CNV) microarray data, to examine contributions of multiple classes of rare genetic variants within a familial context...
March 13, 2018: Translational Psychiatry
Donghyun Shin, Sung-Hoon Kim, Joowan Park, Hak-Kyo Lee, Ki-Duk Song
Objective: The genetic diversity of the Landrace population, a representative maternal pig breeds in Korea, is important for genetic improvement. Previously, the effective population size (Ne) has been used to infer the genetic diversity of a population of interest. In this study, we aimed to use single nucleotide polymorphism (SNP) data to characterize linkage disequilibrium (LD) and the Ne of the Korean Landrace population. Methods: We genotyped 1,128 Landrace individuals from three representative Korean major grand-grand-parent (GGP) farms using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 SNPs located across all autosomes and mitochondrial and sex chromosomes...
March 13, 2018: Asian-Australasian Journal of Animal Sciences
Anthony J Greenberg
Explosive growth in the amount of genomic data is matched by increasing power of consumer grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative samples from large data sets. I describe a fast and memory efficient implementation of an on-line sampling method developed for tape drives 30 years ago. Focusing on genotype files, I test the performance of this technique on modern solid-state and spinning hard drives, and show that it performs well compared to a simple sampling scheme...
March 12, 2018: G3: Genes—Genomes—Genetics
Heng Yao, Xiaoxuan Wang, Pengcheng Chen, Ling Hai, Kang Jin, Lixia Yao, Chuanzao Mao, Xin Chen
An advanced functional understanding of omics data is important for elucidating the design logic of physiological processes in plants and effectively controlling desired traits in plants. We present the latest version of the predicted Arabidopsis interactome resource (PAIR) and of the gene set linkage analysis (GSLA) tool, which enable the interpretation of an observed transcriptomic change (differentially expressed genes, DEGs) in Arabidopsis with respect to its functional impact for biological processes. PAIR v5...
March 12, 2018: Plant Physiology
Yu-Na Im, Yu-Dong Lee, Jeong-Soo Park, Hae-Kyoung Kim, Suhn-Young Im, Hwa-Ryung Song, Hern-Ku Lee, Myung-Kwan Han
Many itch mediators activate G-protein coupled receptor (GPCR), and trigger itch via activation of GPCR-mediated signaling pathways. GPCRs are desensitized by G protein-coupled receptor kinases (GRKs). The aim of this study is to explore the role of GRKs in itch response and the linkage between GRKs and glutamine (Gln), an amino acid previously demonstrated as an itching reliever. Itch responses were evoked by histamine, chloroquine (CQ), and dinitrochlorobenzene (DNCB)-induced contact dermatitis (CD). Phosphorylation and protein expression were detected by immunofluorescent staining and Western blotting...
March 9, 2018: Journal of Investigative Dermatology
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