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https://www.readbyqxmd.com/read/28643617/preselection-statistics-and-random-forest-classification-identify-population-informative-single-nucleotide-polymorphisms-in-cosmopolitan-and-autochthonous-cattle-breeds
#1
F Bertolini, G Galimberti, G Schiavo, S Mastrangelo, R Di Gerlando, M G Strillacci, A Bagnato, B Portolano, L Fontanesi
Commercial single nucleotide polymorphism (SNP) arrays have been recently developed for several species and can be used to identify informative markers to differentiate breeds or populations for several downstream applications. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this work, we compared several methods of SNPs preselection (Delta, F st and principal component analyses (PCA)) in addition to Random Forest classifications to analyse SNP data from six dairy cattle breeds, including cosmopolitan (Holstein, Brown and Simmental) and autochthonous Italian breeds raised in two different regions and subjected to limited or no breeding programmes (Cinisara, Modicana, raised only in Sicily and Reggiana, raised only in Emilia Romagna)...
June 23, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28641361/maternal-alcohol-use-disorder-and-risk-of-child-contact-with-the-justice-system-in-western-australia-a-population-cohort-record-linkage-study
#2
Katherine Hafekost, David Lawrence, Colleen O'Leary, Carol Bower, James Semmens, Stephen R Zubrick
BACKGROUND: Early contact with the justice system is associated with a multitude of negative outcomes across the life course. This includes an increased risk of ongoing justice contact, social disadvantage and marginalization, and mental health and substance use issues. Children whose mothers have an alcohol use disorder may be at risk of early justice system contact, and we sought to quantify this relationship in a Western Australian cohort. METHODS: This population cohort study made use of linked administrative data...
June 22, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28641316/a-cancer-geography-paradox-poorer-cancer-outcomes-with-longer-travelling-times-to-healthcare-facilities-despite-prompter-diagnosis-and-treatment-a-data-linkage-study
#3
Melanie Turner, Shona Fielding, Yuhan Ong, Chris Dibben, Zhiqianq Feng, David H Brewster, Corri Black, Amanda Lee, Peter Murchie
BACKGROUND: Rurality and distance from cancer treatment centres have been shown to negatively impact cancer outcomes, but the mechanisms remain obscure. METHODS: We analysed the impact of travel time to key healthcare facilities and mainland/island residency on the cancer diagnostic pathway (treatment within 62 days of referral, and within 31 days of diagnosis) and 1-year mortality using a data-linkage study with 12 339 patients. RESULTS: After controlling for important confounders, mainland patients with more than 60 min of travelling time to their cancer treatment centre ((OR 1...
June 22, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28640800/hiv-testing-linkage-to-hiv-medical-care-and-interviews-for-partner-services-among-youths-61-health-department-jurisdictions-united-states-puerto-rico-and-the-u-s-virgin-islands-2015
#4
Renee Stein, Wei Song, Mariette Marano, Heta Patel, Shubha Rao, Elana Morris
Identifying persons living with human immunodeficiency virus (HIV) who are unaware of their infection, linking them to HIV medical care, and reducing health disparities are important national goals (1). Of the 8,841 teens and young adults aged 13-24 years (collectively referred to as youths in this report) who received a diagnosis of HIV in 2014, 70% were young men who have sex with men (MSM) (2). In the same year, an estimated 52% of young MSM living with HIV were unaware of their infection compared with 15% among all persons living with HIV (3)...
June 23, 2017: MMWR. Morbidity and Mortality Weekly Report
https://www.readbyqxmd.com/read/28639989/use-of-expenditure-analysis-to-enhance-returns-on-investments-in-hiv-services
#5
Brian Honermann, Richael O'Hagan
PURPOSE OF REVIEW: Globally, the response to the HIV epidemic is at a crisis point. International investments in the HIV response have been essentially flat for 8 years and domestic budgets in low and middle-income countries - still recovering from the global recession - have not been able to fill the resource gap to drive a full-fledged HIV response. Still, efficiencies and prioritization of evidence-based interventions enable a significant scale-up of treatment, but millions more people remain without treatment...
July 20, 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/28639741/the-impact-of-comorbidity-on-mortality-in-multiple-myeloma-a-danish-nationwide-population-based-study
#6
Henrik Gregersen, Annette Juul Vangsted, Niels Abildgaard, Niels Frost Andersen, Robert Schou Pedersen, Ulf Christian Frølund, Carsten Helleberg, Bettina Broch, Per Trøllund Pedersen, Peter Gimsing, Tobias Wirenfeldt Klausen
To describe the prevalence of comorbidity and its impact on survival in newly diagnosed multiple myeloma patients compared with population controls. Cases of newly diagnosed symptomatic multiple myeloma during the 2005-2012 period were identified in the Danish National Multiple Myeloma Registry. For each myeloma patient, 10 members of the general population matched by age and sex were chosen from the national Civil Registration System. Data on comorbidity in the myeloma patients and the general population comparison cohort were collected by linkage to the Danish National Patient Registry (DNPR)...
June 22, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28639698/definitional-elasticity-in-the-measurement-of-intergenerational-continuity-in-substance-use
#7
Thomas A Loughran, Pilar Larroulet, Terence P Thornberry
Increasingly, three generation studies have investigated intergenerational (IG) continuity and discontinuity in substance use and related problem behaviors. However, surprisingly little attention has been paid to the conceptual definition of continuity or to different types of discontinuity (resilience and escalation) or to measurement sensitivity, which affects not only the magnitudes of observed continuity but also factors that correlate with this linkage. This study uses longitudinal data on 427 parent-child dyads from the Rochester IG Study to study continuity and discontinuity in substance use over ages 14-18...
June 22, 2017: Child Development
https://www.readbyqxmd.com/read/28639471/an-enhancer-haplotype-may-influence-bcl11a-expression-levels-and-the-response-to-hydroxyurea-in-%C3%AE-thalassemia-patients
#8
Nahal Maroofi, Azita Azarkeivan, Soosan Banihashemi, Saeid Mohammadparast, Ali Aghajanirefah, Mehdi Banan
AIM: To identify the BCL11A intron-2 enhancer linkage disequilibrium (LD) block, harboring two previously identified SNPs, associating with the hydroxyurea response in β-thalassemia patients and the functional significance of this region. MATERIALS & METHODS: Several neighboring SNPs were genotyped in our cohort. The associating LD block was identified, and its function studied in K562 erythroid cells via CRISPR/Cas9 genome editing. RESULTS: A haplotype harboring three tag SNPs correlated significantly with the HU-response and BCL11A transcript levels in the patients' reticulocytes...
June 22, 2017: Pharmacogenomics
https://www.readbyqxmd.com/read/28638316/a-new-generation-of-brain-computer-interfaces-driven-by-discovery-of-latent-eeg-fmri-linkages-using-tensor-decomposition
#9
Gopikrishna Deshpande, D Rangaprakash, Luke Oeding, Andrzej Cichocki, Xiaoping P Hu
A Brain-Computer Interface (BCI) is a setup permitting the control of external devices by decoding brain activity. Electroencephalography (EEG) has been extensively used for decoding brain activity since it is non-invasive, cheap, portable, and has high temporal resolution to allow real-time operation. Due to its poor spatial specificity, BCIs based on EEG can require extensive training and multiple trials to decode brain activity (consequently slowing down the operation of the BCI). On the other hand, BCIs based on functional magnetic resonance imaging (fMRI) are more accurate owing to its superior spatial resolution and sensitivity to underlying neuronal processes which are functionally localized...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28637865/an-evolutionarily-distinct-family-of-polysaccharide-lyases-removes-rhamnose-capping-of-complex-arabinogalactan-proteins
#10
José Munoz-Munoz, Alan Cartmell, Nicolas Terrapon, Arnaud Baslé, Bernard Henrissat, Harry J Gilbert
The human gut microbiota utilizes complex carbohydrates as major nutrients. The requirement for efficient glycan degrading systems exerts a major selective selection pressure on this microbial community. Thus, we propose that this microbial ecosystem represents a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis we screened the potential enzymatic functions of hypothetical proteins encoded by genes of Bacteroides thetaiotaomicron that were upregulated by arabinogalactan arabinogalactan proteins or AGPs...
June 21, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28637725/filling-the-gaps-in-sards-research-collection-and-linkage-of-administrative-health-data-and-self-reported-survey-data-for-a-general-population-based-cohort-of-individuals-with-and-without-diagnoses-of-systemic-autoimmune-rheumatic-disease-sards-from-british
#11
Natalie McCormick, Kathryn Reimer, Ali Famouri, Carlo A Marra, J Antonio Aviña-Zubieta
PURPOSE: Systemic autoimmune rheumatic diseases (SARDs) are a group of debilitating autoimmune diseases, including systemic lupus erythematosus and related disorders. Assessing the healthcare and economic burden of SARDs has been challenging: while administrative databases can be used to determine healthcare utilisation and costs with minimal selection and recall bias, other health, sociodemographic and economic data have typically been sourced from highly selected, clinic-based cohorts...
June 21, 2017: BMJ Open
https://www.readbyqxmd.com/read/28637661/the-full-transforming-capacity-of-mll-af4-is-interlinked-with-lymphoid-lineage-commitment
#12
Shan Lin, Roger T Luo, Mahesh Shrestha, Michael J Thirman, James C Mulloy
Chromosome rearrangements involving mixed-lineage leukemia gene (MLL) create MLL-fusion proteins, which could drive both acute lymphoblastic and myeloid leukemia (ALL and AML). The lineage decision of MLL-fusion leukemia is influenced by the fusion partner and microenvironment. To investigate the interplay of fusion proteins and microenvironment in lineage choice, we transplanted human hematopoietic stem and progenitor cells (HSPC) expressing MLL-AF9 or MLL-Af4 into immunodeficient NSGS mice, which strongly promote myeloid development...
June 21, 2017: Blood
https://www.readbyqxmd.com/read/28636419/poison-or-prevention-understanding-the-linkages-between-vaccine-negative-individuals-knowledge-deficiency-motivations-and-active-communication-behaviors
#13
Arunima Krishna
The last few decades have seen growing concerns among parents regarding the safety of childhood vaccines, arguably leading to the rise of the anti-vaccine movement. This study is an effort to understand situational and cross-situational factors that influence individuals' negative attitudes toward vaccines, referred to as vaccine negativity. In doing so, this study elucidated how situational and cross-situational factors influence vaccine negativity. Specifically, this study tested how knowledge deficiency, or acceptance of scientifically inaccurate data about vaccines, and institutional trust influenced negative attitudes toward vaccines...
June 21, 2017: Health Communication
https://www.readbyqxmd.com/read/28635630/development-of-a-high-density-snp-based-linkage-map-and-detection-of-qtl-for-%C3%AE-glucans-protein-content-grain-yield-per-spike-and-heading-time-in-durum-wheat
#14
Ilaria Marcotuli, Agata Gadaleta, Giacomo Mangini, Antonio Massimo Signorile, Silvana Addolorata Zacheo, Antonio Blanco, Rosanna Simeone, Pasqualina Colasuonno
High-density genetic linkage maps of crop species are particularly useful in detecting qualitative and quantitative trait loci for important agronomic traits and in improving the power of classical approaches to identify candidate genes. The aim of this study was to develop a high-density genetic linkage map in a durum wheat recombinant inbred lines population (RIL) derived from two elite wheat cultivars and to identify, characterize and correlate Quantitative Trait Loci (QTL) for β-glucan, protein content, grain yield per spike and heading time...
June 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28634199/characterising-cis-regulatory-variation-in-the-transcriptome-of-histologically-normal-and-tumour-derived-pancreatic-tissues
#15
Mingfeng Zhang, Soren Lykke-Andersen, Bin Zhu, Wenming Xiao, Jason W Hoskins, Xijun Zhang, Lauren M Rost, Irene Collins, Martijn van de Bunt, Jinping Jia, Hemang Parikh, Tongwu Zhang, Lei Song, Ashley Jermusyk, Charles C Chung, Bin Zhu, Weiyin Zhou, Gail L Matters, Robert C Kurtz, Meredith Yeager, Torben Heick Jensen, Kevin M Brown, Halit Ongen, William R Bamlet, Bradley A Murray, Mark I McCarthy, Stephen J Chanock, Nilanjan Chatterjee, Brian M Wolpin, Jill P Smith, Sara H Olson, Gloria M Petersen, Jianxin Shi, Laufey Amundadottir
OBJECTIVE: To elucidate the genetic architecture of gene expression in pancreatic tissues. DESIGN: We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. RESULTS: We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0...
June 20, 2017: Gut
https://www.readbyqxmd.com/read/28633571/the-role-of-peri-traumatic-stress-and-disruption-distress-in-predicting-symptoms-of-major-depression-following-exposure-to-a-natural-disaster
#16
Caroline J Bell, Joseph M Boden, L John Horwood, Roger T Mulder
OBJECTIVE: Few studies have examined the contribution of specific disaster-related experiences to symptoms of depression. The aims of this study were to do this by examining the roles of peri-traumatic stress and distress due to lingering disaster-related disruption in explaining linkages between disaster exposure and major depressive disorder symptoms among a cohort exposed to the 2010-2011 Canterbury (New Zealand) earthquakes. METHODS: Structural equation models were fitted to data obtained from the Christchurch Health and Development Study at age 35 ( n = 495), 20-24 months following the onset of the disaster...
July 2017: Australian and New Zealand Journal of Psychiatry
https://www.readbyqxmd.com/read/28630467/computational-method-allowing-hydrogen-deuterium-exchange-mass-spectrometry-at-single-amide-resolution
#17
Chris Gessner, Wieland Steinchen, Sabrina Bédard, John J Skinner, Virgil L Woods, Thomas J Walsh, Gert Bange, Dionysios P Pantazatos
Hydrogen-deuterium exchange (HDX) coupled with mass spectrometry (HDXMS) is a rapid and effective method for localizing and determining protein stability and dynamics. Localization is routinely limited to a peptide resolution of 5 to 20 amino acid residues. HDXMS data can contain information beyond that needed for defining protein stability at single amide resolution. Here we present a method for extracting this information from an HDX dataset to generate a HDXMS protein stability fingerprint. High resolution (HR)-HDXMS was applied to the analysis of a model protein of a spectrin tandem repeat that exemplified an intuitive stability profile based on the linkage of two triple helical repeats connected by a helical linker...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28628480/kernel-based-measure-of-variable-importance-for-genetic-association-studies
#18
Vicente Gallego, M Luz Calle, Ramon Oller
The identification of genetic variants that are associated with disease risk is an important goal of genetic association studies. Standard approaches perform univariate analysis where each genetic variant, usually Single Nucleotide Polymorphisms (SNPs), is tested for association with disease status. Though many genetic variants have been identified and validated so far using this univariate approach, for most complex diseases a large part of their genetic component is still unknown, the so called missing heritability...
June 17, 2017: International Journal of Biostatistics
https://www.readbyqxmd.com/read/28628399/polymorphisms-in-lep-and-lepr-genes-in-infants-correlation-with-serum-leptin-values-in-the-first-6-months-of-life
#19
Francesco Savino, Allegra Sardo, Paola Montanari, Ilaria Galliano, Liliana Di Stasio, Massimiliano Bergallo, Leandra Silvestro
OBJECTIVE: Because several studies indicate that polymorphisms in leptin (Lep) and leptin receptor (Lepr) genes play a central role in determining obesity, we analyzed 2 single nucleotide polymorphisms (SNPs) in the Lep gene (Lep G2548A and A19G) and one in the Lepr gene (Lepr A668G) to verify the effect of the 3 SNPs on leptin concentrations in infancy. METHODS: We enrolled 80 healthy Caucasian infants under 6 months of age, who were genotyped for the 3 SNPs with amplification refractory mutation system-mismatch amplification mutation assay (ARMS-MAMA) real-time polymerase chain reaction (PCR)...
June 19, 2017: Journal of the American College of Nutrition
https://www.readbyqxmd.com/read/28628238/a-genome-wide-association-study-of-23-agronomic-traits-in-chinese-wheat-landraces
#20
Yaxi Liu, Yu Lin, Shang Gao, Zhanyi Li, Jian Ma, Mei Deng, Guoyue Chen, Yuming Wei, Youliang Zheng
Uncovering the genetic basis of agronomic traits in wheat landraces is important for ensuring global food security via the development of improved varieties. Here, 723 wheat landraces from 10 Chinese agro-ecological zones were evaluated for 23 agronomic traits in six environments. All accessions could be clustered into five subgroups based on phenotypic data via discriminant function analysis, which was highly consistent with genotypic classification. A genome-wide association study was conducted for these traits using 52,303 DArT-seq markers to identify marker-trait associations and candidate genes...
June 19, 2017: Plant Journal: for Cell and Molecular Biology
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