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https://www.readbyqxmd.com/read/27913357/introducing-a-stable-bootstrap-validation-framework-for-reliable-genomic-signature-extraction
#1
Nikolaos-Kosmas Chlis, Ekaterini S Bei, Michael Zervakis
The application of machine learning methods for the identification of candidate genes responsible for phenotypes of interest, such as cancer, is a major challenge in the field of bioinformatics. These lists of genes are often called genomic signatures and their linkage to phenotype associations may form a significant step in discovering the causation between genotypes and phenotypes. Traditional methods that produce genomic signatures from DNA Microarray data tend to extract significantly different lists under relatively small variations of the training data...
November 29, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27911320/ethnic-variations-in-prognosis-of-patients-with-dementia-a-prospective-nationwide-registry-linkage-study-in-the-netherlands
#2
Charles Agyemang, Irene E van de Vorst, Huiberdina L Koek, Michiel L Bots, Azizi Sexas, Marie Norredam, Umar Ikram, Karien Stronks, Ilonca Vaartjes
BACKGROUND: Data on dementia prognosis among ethnic minority groups are limited in Europe. OBJECTIVE: We assessed differences in short-term (1-year) and long-term (3-year) mortality and readmission risk after a first hospitalization or first ever referral to a day clinic for dementia between ethnic minority groups and the ethnic Dutch population in the NetherlandsMethods: Nationwide prospective cohorts of first hospitalized dementia patients (N = 55,827) from January 1, 2000 to December 31, 2010 were constructed...
November 29, 2016: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/27911129/socioeconomic-position-and-mortality-among-patients-with-prostate-cancer-influence-of-mediating-factors
#3
Signe Benzon Larsen, Klaus Brasso, Jane Christensen, Christoffer Johansen, Anne Tjønneland, Søren Friis, Peter Iversen, Susanne Oksbjerg Dalton
INTRODUCTION: Men with low socioeconomic position experience higher mortality after a prostate cancer diagnosis compared to men with a higher socioeconomic position, however, the specific mediators of this association are unclear. We therefore evaluated the influence of potential mediators on the association between socioeconomic position, and prostate cancer-specific and all-cause death in prostate cancer patients. MATERIALS AND METHODS: We conducted a cohort study of prostate cancer patients in the Danish Diet, Cancer and Health study...
December 2, 2016: Acta Oncologica
https://www.readbyqxmd.com/read/27910110/runs-of-homozygosity-current-knowledge-and-applications-in-livestock
#4
REVIEW
E Peripolli, D P Munari, M V G B Silva, A L F Lima, R Irgang, F Baldi
This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome...
December 1, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27909260/prioritizing-and-funding-nepal-s-multisector-nutrition-plan
#5
Amanda Pomeroy-Stevens, Madhukar B Shrestha, Monica Biradavolu, Kusum Hachhethu, Robin Houston, Indu Sharma, Jolene Wun
BACKGROUND: Nepal has a long tradition of designing good multisectoral nutrition policy. However, success of policy implementation has varied. More evidence on how to successfully carry out multisector nutrition policy is needed. OBJECTIVE: We tracked the influence of Nepal's multisectoral nutrition plan (MSNP) on the process of priority setting and budgeting from 2014 to 2016. METHODS: This study used a mixed-method longitudinal design to track qualitative and budgetary changes related to MSNP processes nationally as well as in 3 districts...
December 2016: Food and Nutrition Bulletin
https://www.readbyqxmd.com/read/27909040/association-between-organisational-and-workplace-cultures-and-patient-outcomes-systematic-review-protocol
#6
J Braithwaite, J Herkes, K Ludlow, G Lamprell, L Testa
INTRODUCTION: Despite widespread interest in the topic, no current synthesis of research is available analysing the linkages between organisational or workplace cultures on the one hand, and patient outcomes on the other. This protocol proposes a systematic review to analyse and synthesise the literature to date on this topic. The resulting review will discuss characteristics of included studies in terms of the type of healthcare settings researched, the measurements of organisational and workplace culture, patient outcomes measured and the influence of these cultures on patient outcomes...
December 1, 2016: BMJ Open
https://www.readbyqxmd.com/read/27909039/algorithm-for-predicting-death-among-older-adults-in-the-home-care-setting-study-protocol-for-the-risk-evaluation-for-support-predictions-for-elder-life-in-the-community-tool-respect
#7
Amy T Hsu, Douglas G Manuel, Monica Taljaard, Mathieu Chalifoux, Carol Bennett, Andrew P Costa, Susan Bronskill, Daniel Kobewka, Peter Tanuseputro
INTRODUCTION: Older adults living in the community often have multiple, chronic conditions and functional impairments. A challenge for healthcare providers working in the community is the lack of a predictive tool that can be applied to the broad spectrum of mortality risks observed and may be used to inform care planning. OBJECTIVE: To predict survival time for older adults in the home care setting. The final mortality risk algorithm will be implemented as a web-based calculator that can be used by older adults needing care and by their caregivers...
December 1, 2016: BMJ Open
https://www.readbyqxmd.com/read/27909036/defining-adolescent-common-mental-disorders-using-electronic-primary-care-data-a-comparison-with-outcomes-measured-using-the-cis-r
#8
Rosie P Cornish, Ann John, Andy Boyd, Kate Tilling, John Macleod
OBJECTIVE: To compare the prevalence of common mental disorders (CMDs) derived from data held in primary care records with that measured using the revised Clinical Interview Schedule (CIS-R) in order to assess the potential robustness of findings based only on routinely collected data. DESIGN AND SETTING: Comparison study using linkage between the Avon Longitudinal Study of Parents and Children (ALSPAC) and electronic primary care records. PARTICIPANTS: We studied 1562 adolescents who had completed the CIS-R in ALSPAC at age 17-18 years and had linkage established to their primary care records...
December 1, 2016: BMJ Open
https://www.readbyqxmd.com/read/27906046/chromatin-landscapes-and-genetic-risk-in-systemic-lupus
#9
Joyce S Hui-Yuen, Lisha Zhu, Lai Ping Wong, Kaiyu Jiang, Yanmin Chen, Tao Liu, James N Jarvis
BACKGROUND: Systemic lupus erythematosus (SLE) is a multi-system, complex disease in which the environment interacts with inherited genes to produce broad phenotypes with inter-individual variability. Of 46 single nucleotide polymorphisms (SNPs) shown to confer genetic risk for SLE in recent genome-wide association studies, 30 lie within noncoding regions of the human genome. We therefore sought to identify and describe the functional elements (aside from genes) located within these regions of interest...
December 1, 2016: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/27906029/trends-in-clinical-characteristics-and-outcomes-of-pre-art-care-at-a-large-hiv-clinic-in-nairobi-kenya-a-retrospective-cohort-study
#10
Jared O Mecha, Elizabeth N Kubo, Lucy W Nganga, Peter N Muiruri, Lilian N Njagi, Immaculate N Mutisya, Justine J Odionyi, Syokau C Ilovi, Mary Wambui, Christopher Githu, Richard Ngethe, Elizabeth M Obimbo, Zipporah W Ngumi
BACKGROUND: The success of antiretroviral therapy in resource-scarce settings is an illustration that complex healthcare interventions can be successfully delivered even in fragile health systems. Documenting the success factors in the scale-up of HIV care and treatment in resource constrained settings will enable health systems to prepare for changing population health needs. This study describes changing demographic and clinical characteristics of adult pre-ART cohorts, and identifies predictors of pre-ART attrition at a large urban HIV clinic in Nairobi, Kenya...
November 14, 2016: AIDS Research and Therapy
https://www.readbyqxmd.com/read/27906012/determinants-of-time-to-antiretroviral-treatment-initiation-and-subsequent-mortality-on-treatment-in-a-cohort-in-rural-northern-malawi
#11
Jeremy Philip Brown, Bagrey Ngwira, Terence Tafatatha, Amelia Catharine Crampin, Neil French, Olivier Koole
BACKGROUND: To optimise care HIV patients need to be promptly initiated on antiretroviral therapy (ART) and subsequently retained on treatment. In this study we report on the interval between enrolment and treatment initiation, and investigate subsequent attrition and mortality of patients on ART at a rural clinic in Malawi. METHODS: HIV-positive individuals were recruited to a cohort study between January 2008 and August 2011 at Chilumba Rural Hospital (CRH). Outcomes were ascertained, up to 7 years after enrolment, through follow-up and by linkage to ART registers and the Karonga Health and Demographic Surveillance System (KHDSS)...
July 8, 2016: AIDS Research and Therapy
https://www.readbyqxmd.com/read/27905951/expansion-or-compression-of-long-term-care-in-germany-between-2001-and-2009-a-small-area-decomposition-study-based-on-administrative-health-data
#12
Daniel Kreft, Gabriele Doblhammer
BACKGROUND: Studies state profound cross-country differences in healthy life years and its time trends, suggesting either the health scenario of expansion or compression of morbidity. A much-discussed question in public health research is whether the health scenarios are heterogeneous or homogeneous on the subnational level as well. Furthermore, the question arises whether the morbidity trends or the mortality trends are the decisive drivers of the care need-free life years (CFLY), the life years with care need (CLY), and, ultimately, the health scenarios...
July 13, 2016: Population Health Metrics
https://www.readbyqxmd.com/read/27905878/genomic-prediction-using-preselected-dna-variants-from-a-gwas-with-whole-genome-sequence-data-in-holstein-friesian-cattle
#13
Roel F Veerkamp, Aniek C Bouwman, Chris Schrooten, Mario P L Calus
BACKGROUND: Whole-genome sequence data is expected to capture genetic variation more completely than common genotyping panels. Our objective was to compare the proportion of variance explained and the accuracy of genomic prediction by using imputed sequence data or preselected SNPs from a genome-wide association study (GWAS) with imputed whole-genome sequence data. METHODS: Phenotypes were available for 5503 Holstein-Friesian bulls. Genotypes were imputed up to whole-genome sequence (13,789,029 segregating DNA variants) by using run 4 of the 1000 bull genomes project...
December 1, 2016: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/27903950/shout-it-now-a-mobile-hct-model-employing-technology-and-edutainment-in-south-africa
#14
Joseph Daniels, Arnost Komarek, Bruce Forgreive, Kathryn Pahl, Stephen Stafford, Laurie Campbell Bruns, Thomas Coates
BACKGROUND: Mobile HIV counseling and testing (HCT) has been effective in reaching men, women, and adolescents in South Africa. However, there is limited understanding of effective mobile HCT programs utilizing tools like technology and edutainment to increase HIV counseling and testing rates. The authors examine data from the Shout-It-Now (S-N) program that uses such tools in South Africa. METHODS: The S-N program utilizes various forms of technology and ongoing telephonic counseling within a 6-step program of HIV testing and linkage-to-care support, and program data were analyzed over an 18-month period...
November 30, 2016: Journal of the International Association of Providers of AIDS Care
https://www.readbyqxmd.com/read/27902806/orthology-guided-transcriptome-assembly-of-italian-ryegrass-and-meadow-fescue-for-single-nucleotide-polymorphism-discovery
#15
Štěpán Stočes, Tom Ruttink, Jan Bartoš, Bruno Studer, Steven Yates, Zbigniew Zwierzykowski, Michael Abrouk, Isabel Roldán-Ruiz, Tomasz Książczyk, Elodie Rey, Jaroslav Doležel, David Kopecký
Single-nucleotide polymorphisms (SNPs) represent natural DNA sequence variation. They can be used for various applications including the construction of high-density genetic maps, analysis of genetic variability, genome-wide association studies, and map-based cloning. Here we report on transcriptome sequencing in the two forage grasses, meadow fescue ( Huds.) and Italian ryegrass ( Lam.), and identification of various classes of SNPs. Using the Orthology Guided Assembly (OGA) strategy, we assembled and annotated a total of 18,952 and 19,036 transcripts for Italian ryegrass and meadow fescue, respectively...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902793/snp-discovery-and-qtl-mapping-of-sclerotinia-basal-stalk-rot-resistance-in-sunflower-using-genotyping-by-sequencing
#16
Zahirul I Talukder, Gerald J Seiler, Qijian Song, Guojia Ma, Lili Qi
Basal stalk rot (BSR), caused by the ascomycete fungus (Lib.) de Bary, is a serious disease of sunflower ( L.) in the cool and humid production areas of the world. Quantitative trait loci (QTL) for BSR resistance were identified in a sunflower recombinant inbred line (RIL) population derived from the cross HA 441 × RHA 439. A genotyping-by-sequencing (GBS) approach was adapted to discover single nucleotide polymorphism (SNP) markers. A genetic linkage map was developed comprised of 1053 SNP markers on 17 linkage groups (LGs) spanning 1401...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902594/combined-genotype-and-haplotype-distributions-of-mthfr-c677t-and-a1298c-polymorphisms-a-cross-sectional-descriptive-study-of-13-473-chinese-adult-women
#17
Shujun Fan, Boyi Yang, Xueyuan Zhi, Yanxun Wang, Quanmei Zheng, Guifan Sun
Methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C polymorphisms are, independently and/or in combination, associated with many disorders. However, data on the combined genotype and haplotype distributions of the 2 polymorphisms in Chinese population were limited.We recruited 13,473 adult women from 9 Chinese provinces, collected buccal cell samples, and determined genotypes, to estimate the combined genotype and haplotype distributions of the MTHFR C677T and A1298C polymorphisms.In the total sample, the 6 common combined genotypes were CT/AA (29...
November 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27901467/structural-basis-for-the-disaggregase-activity-and-regulation-of-hsp104
#18
Alexander Heuck, Sonja Schitter-Sollner, Marcin Józef Suskiewicz, Robert Kurzbauer, Juliane Kley, Alexander Schleiffer, Pascaline Rombaut, Franz Herzog, Tim Clausen
The Hsp104 disaggregase is a two-ring ATPase machine that rescues various forms of non-native proteins including the highly resistant amyloid fibers. The structural-mechanistic underpinnings of how the recovery of toxic protein aggregates is promoted and how this potent unfolding activity is prevented from doing collateral damage to cellular proteins are not well understood. Here, we present structural and biochemical data revealing the organization of Hsp104 from Chaetomium thermophilum at 3.7 Å resolution...
November 30, 2016: ELife
https://www.readbyqxmd.com/read/27900808/genetic-and-developmental-basis-for-fin-shape-variation-in-african-cichlid-fishes
#19
Dina Navon, Nathan Olearczyk, R Craig Albertson
Adaptive radiations are often characterized by the rapid evolution of traits associated with divergent feeding modes. For example, the evolutionary history of African cichlids is marked by repeated and coordinated shifts in skull, trophic, fin and body shape. Here, we seek to explore the molecular basis for fin shape variation in Lake Malawi cichlids. We first described variation within an F2 mapping population derived by crossing two cichlid species with divergent morphologies including fin shape. We then used this population to genetically map loci that influence variation in this trait...
November 4, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27900776/hospital-admissions-in-children-with-cerebral-palsy-a-data-linkage-study
#20
Elaine Meehan, Susan M Reid, Katrina Williams, Gary L Freed, Jillian R Sewell, Suzanna Vidmar, Susan Donath, Dinah S Reddihough
AIM: The overall aim was to investigate the feasibility and utility of linking a cerebral palsy (CP) register to an administrative data set for health services research purposes. We sought to compare CP hospital admissions to general childhood population admissions, and identify factors associated with type and frequency of admissions in a CP cohort. METHOD: The CP register for Victoria, Australia was linked to the state's hospital admissions database. Data pertaining to the admissions of a CP cohort (n=1748) that took place between 2007 and 2014 were extracted...
November 30, 2016: Developmental Medicine and Child Neurology
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