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https://www.readbyqxmd.com/read/28917120/automated-arteriole-and-venule-classification-using-deep-learning-for-retinal-images-from-the-uk-biobank-cohort
#1
R A Welikala, P J Foster, P H Whincup, A R Rudnicka, C G Owen, D P Strachan, S A Barman
The morphometric characteristics of the retinal vasculature are associated with future risk of many systemic and vascular diseases. However, analysis of data from large population based studies is needed to help resolve uncertainties in some of these associations. This requires automated systems that extract quantitative measures of vessel morphology from large numbers of retinal images. Associations between retinal vessel morphology and disease precursors/outcomes may be similar or opposing for arterioles and venules...
September 8, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28912709/extending-xnat-platform-with-an-incremental-semantic-framework
#2
Santiago Timón, Mariano Rincón, Rafael Martínez-Tomás
Informatics increases the yield from neuroscience due to improved data. Data sharing and accessibility enable joint efforts between different research groups, as well as replication studies, pivotal for progress in the field. Research data archiving solutions are evolving rapidly to address these necessities, however, distributed data integration is still difficult because of the need of explicit agreements for disparate data models. To address these problems, ontologies are widely used in biomedical research to obtain common vocabularies and logical descriptions, but its application may suffer from scalability issues, domain bias, and loss of low-level data access...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28912672/maximizing-the-potential-of-longitudinal-cohorts-for-research-in-neurodegenerative-diseases-a-community-perspective
#3
Catherine J Moody, Derick Mitchell, Grace Kiser, Dag Aarsland, Daniela Berg, Carol Brayne, Alberto Costa, Mohammad A Ikram, Gail Mountain, Jonathan D Rohrer, Charlotte E Teunissen, Leonard H van den Berg, Joanna M Wardlaw
Despite a wealth of activity across the globe in the area of longitudinal population cohorts, surprisingly little information is available on the natural biomedical history of a number of age-related neurodegenerative diseases (ND), and the scope for intervention studies based on these cohorts is only just beginning to be explored. The Joint Programming Initiative on Neurodegenerative Disease Research (JPND) recently developed a novel funding mechanism to rapidly mobilize scientists to address these issues from a broad, international community perspective...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28910820/prospective-investigation-of-risk-factors-for-prostate-cancer-in-the-uk-biobank-cohort-study
#4
Aurora Perez-Cornago, Timothy J Key, Naomi E Allen, Georgina K Fensom, Kathryn E Bradbury, Richard M Martin, Ruth C Travis
BACKGROUND: Prostate cancer is the most common cancer in British men but its aetiology is not well understood. We aimed to identify risk factors for prostate cancer in British males. METHODS: We studied 219 335 men from the UK Biobank study who were free from cancer at baseline. Exposure data were collected at recruitment. Prostate cancer risk by the different exposures was estimated using multivariable-adjusted Cox proportional hazards models. RESULTS: In all, 4575 incident cases of prostate cancer occurred during 5...
September 14, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28903566/biobanking-the-first-step-to-successful-liquid-biopsy-experiments
#5
M Almasi, S Sevcikova, M Penka, M Krejci, Z Adam, P Vrublova, T Jelínek, R Hájek
BACKGROUND: Archiving of biological materials in biobanks is considered to be the initial crucial part of research activities. Most often, biobanks are founded for research purposes since they allow collection of sufficient material for analysis of new or testing of previously identified biomarkers. Biobanking needs to quickly react to current needs of researchers as well as clinicians, it is not a rigid system. Laboratory analyses of monoclonal gammopathies are based on separation of plasma cells from bone marrow of patients...
2017: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
https://www.readbyqxmd.com/read/28900884/the-social-dimension-of-biobanking-objectives-and-challenges
#6
E V Bryzgalina, K Y Alasania, T A Varkhotov, S M Gavrilenko, E M Shkomova
The present article allows to explore, analyze and reflect on the consequences and problems posed by biobanks and attempts to prove the need of social and humanitarian support in establishing and functioning of biobanks as a new type of scientific institutions. The basis of the article is the latest publications devoted to social and humanitarian aspects of biobanking and Russian experience of the initial formation of this subject domain (before the first professional biobanks were established in Russia in the 2010-s, the only highly specialized collections of bio-samples had been registered)...
September 13, 2017: Life Sciences, Society and Policy
https://www.readbyqxmd.com/read/28900029/young-adulthood-and-adulthood-adiposity-in-relation-to-incidence-of-pancreatic-cancer-a-prospective-study-of-0-5-million-chinese-adults-and-a-meta-analysis
#7
Yuanjie Pang, Michael V Holmes, Christiana Kartsonaki, Yu Guo, Ling Yang, Zheng Bian, Yiping Chen, Fiona Bragg, Andri Iona, Iona Y Millwood, Junshi Chen, Liming Li, Zhengming Chen
BACKGROUND: Adult adiposity is positively associated with pancreatic cancer in Western populations. Little is known, however, about the association in China where many have lower body mass index (BMI) or about the relevance of young adulthood adiposity for pancreatic cancer in both Western and East Asian populations. METHODS: The China Kadoorie Biobank (CKB) recruited 512 891 adults aged 30-79 years during 2004-2008, recording 595 incident cases of pancreatic cancer during 8-year follow-up...
September 12, 2017: Journal of Epidemiology and Community Health
https://www.readbyqxmd.com/read/28895531/genetic-identification-of-a-common-collagen-disease-in-puerto-ricans-via-identity-by-descent-mapping-in-a-health-system
#8
Gillian Morven Belbin, Jacqueline Odgis, Elena P Sorokin, Muh-Ching Yee, Sumita Kohli, Benjamin S Glicksberg, Christopher R Gignoux, Genevieve L Wojcik, Tielman Van Vleck, Janina M Jeff, Michael Linderman, Claudia Schurmann, Douglas Ruderfer, Xiaoqiang Cai, Amanda Merkelson, Anne E Justice, Kristin L Young, Misa Graff, Kari E North, Ulrike Peters, Regina James, Lucia Hindorff, Ruth Kornreich, Lisa Edelmann, Omri Gottesman, Eli Ea Stahl, Judy H Cho, Ruth Jf Loos, Erwin P Bottinger, Girish N Nadkarni, Noura S Abul-Husn, Eimear E Kenny
Achieving confidence in the causality of a disease locus is a complex task that often requires supporting data from both statistical genetics and clinical genomics. Here we describe a combined approach to identify and characterize a genetic disorder that leverages distantly related patients in a health system and population-scale mapping. We utilize genomic data to uncover components of distant pedigrees, in the absence of recorded pedigree information, in the multi-ethnic BioMe biobank in New York City. By linking to medical records, we discover a locus associated with both elevated genetic relatedness and extreme short stature...
September 12, 2017: ELife
https://www.readbyqxmd.com/read/28893854/will-big-data-close-the-missing-heritability-gap
#9
Hwasoon Kim, Alexander Grueneberg, Ana I Vazquez, Stephen Hsu, Gustavo de Los Campos
Despite the important discoveries reported by Genome-Wide Association studies, for most traits and diseases the prediction R-squared (R-sq.) achieved with genetic scores remains considerably lower than the trait heritability. Modern biobanks will soon deliver unprecedentedly large biomedical data sets: Will the advent of Big Data close the gap between the trait heritability and the proportion of variance that can be explained by a genomic predictor? We addressed this question using Bayesian methods and a data analysis approach that produces a surface response relating prediction R-sq...
September 11, 2017: Genetics
https://www.readbyqxmd.com/read/28893184/the-canadian-hiv-and-aging-cohort-study-determinants-of-increased-risk-of-cardio-vascular-diseases-in-hiv-infected-individuals-rationale-and-study-protocol
#10
Madeleine Durand, Carl Chartrand-Lefebvre, Jean-Guy Baril, Sylvie Trottier, Benoit Trottier, Marianne Harris, Sharon Walmsley, Brian Conway, Alexander Wong, Jean-Pierre Routy, Colin Kovacs, Paul A MacPherson, Kenneth Marc Monteith, Samer Mansour, George Thanassoulis, Michal Abrahamowicz, Zhitong Zhu, Christos Tsoukas, Petronela Ancuta, Nicole Bernard, Cécile L Tremblay
BACKGROUND: With potent antiretroviral drugs, HIV infection is becoming a chronic disease. Emergence of comorbidities, particularly cardiovascular disease (CVD) has become a leading concern for patients living with the infection. We hypothesized that the chronic and persistent inflammation and immune activation associated with HIV disease leads to accelerated aging, characterized by CVD. This will translate into higher incidence rates of CVD in HIV infected participants, when compared to HIV negative participants, after adjustment for traditional CVD risk factors...
September 11, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28883179/proof-of-concept-integration-of-heterogeneous-biobank-it-infrastructures-into-a-hybrid-biobanking-network
#11
Sebastian Mate, Dennis Kadioglu, Raphael W Majeed, Mark R Stöhr, Michael Folz, Patric Vormstein, Holger Storf, Daniel P Brucker, Dietmar Keune, Norman Zerbe, Michael Hummel, Karsten Senghas, Hans-Ulrich Prokosch, Martin Lablans
Cross-institutional biobank networks hold the promise of supporting medicine by enabling the exchange of associated samples for research purposes. Various initiatives, such as BBMRI-ERIC and German Biobank Node (GBN), aim to interconnect biobanks for enabling the compilation of joint biomaterial collections. However, building software platforms to facilitate such collaboration is challenging due to the heterogeneity of existing biobank IT infrastructures and the necessary efforts for installing and maintaining additional software components...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28883174/a-decentralized-it-architecture-for-locating-and-negotiating-access-to-biobank-samples
#12
Rumyana Proynova, Diogo Alexandre, Martin Lablans, David Van Enckevort, Sebastian Mate, Niina Eklund, Kaisa Silander, Michael Hummel, Petr Holub, Frank Ückert
There is a need among researchers for the easy discoverability of biobank samples. Currently, there is no uniform way for finding samples and negotiate access. Instead, researchers have to communicate with each biobank separately. We present the architecture for the BBMRI-CS IT platform, whose goal is to facilitate sample location and access. We chose a decentral approach, which allows for strong data protection and provides the high flexibility needed in the highly heterogeneous landscape of European biobanks...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28883167/on-the-fly-query-translation-between-i2b2-and-samply-in-the-german-biobank-node-gbn-prototypes
#13
Sebastian Mate, Patric Vormstein, Dennis Kadioglu, Raphael W Majeed, Martin Lablans, Hans-Ulrich Prokosch, Holger Storf
Information retrieval is a major challenge in medical informatics. Various research projects have worked on this task in recent years on an institutional level by developing tools to integrate and retrieve information. However, when it comes down to querying such data across institutions, the challenge persists due to the high heterogeneity of data and differences in software systems. The German Biobank Node (GBN) project faced this challenge when trying to interconnect four biobanks to enable distributed queries for biospecimens...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28882820/high-levels-of-un-switched-memory-b-cells-are-associated-with-better-outcome-in-patients-with-advanced-atherosclerotic-disease
#14
John A L Meeuwsen, Amerik van Duijvenvoorde, Aisha Gohar, Maria O Kozma, Sander M van de Weg, Crystel M Gijsberts, Saskia Haitjema, Harry Björkbacka, Gunilla N Fredrikson, Gert J de Borst, Hester M den Ruijter, Gerard Pasterkamp, Christoph J Binder, Imo E Hoefer, Saskia C A de Jager
BACKGROUND: Atherosclerosis is an inflammatory lipid disorder and the main underlying pathology of acute ischemic events. Despite a vast amount of data from murine atherosclerosis models, evidence of B-cell involvement in human atherosclerotic disease is limited. We therefore investigated the association of circulating B-cell subtypes with the occurrence of secondary cardiovascular events in advanced atherosclerotic disease. METHODS AND RESULTS: This cohort study consists of 168 patients who were included in the Athero-Express biobank between 2009 and 2011...
September 7, 2017: Journal of the American Heart Association
https://www.readbyqxmd.com/read/28881265/new-variants-near-rhoj-and-c2-hla-dra-region-and-susceptibility-to-endometriosis-in-the-polish-population-the-genome-wide-association-study
#15
Marta Sobalska-Kwapis, Beata Smolarz, Marcin Słomka, Tomasz Szaflik, Ewa Kępka, Bartosz Kulig, Anna Siewierska-Górska, Grzegorz Polak, Hanna Romanowicz, Dominik Strapagiel, Krzysztof Szyłło
OBJECTIVE: Endometriosis is a common gynaecological disease, associated with severe pelvic pain and reduced fertility; however, molecular mechanisms remain largely unknown. Genome-wide association studies (GWAS) are able to identify genetic loci, which can play significant role during endometriosis development. AIM: The study aimed at localisation of new genes and chromosomal loci, the nucleotide variants of which determine the level of susceptibility to endometriosis...
September 1, 2017: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/28881048/a-novel-technique-for-biobanking-of-large-sections-of-radical-prostatectomy-specimens
#16
Claes Lindh, Brett Delahunt, Hemamali Samaratunga, John Yaxley, Jóna Gudjónsdóttir, Mark Clements, Johan Lindberg, Lars Egevad
AIMS: Harvesting of unfixed tissue from radical prostatectomy specimens for research purposes is challenging. Many prostate cancers cannot be identified at gross inspection and this tumour is notoriously multifocal and heterogeneous. We aimed to develop a technique to allow detailed topographic analysis and the sampling of sufficient amount of tumour without jeopardizing clinical reporting. METHODS AND RESULTS: A custom-made double-bladed knife was utilized for cutting a 4 mm thick horizontal section of the prostate...
September 7, 2017: Histopathology
https://www.readbyqxmd.com/read/28877583/leaf-lims-a-flexible-laboratory-information-management-system-with-a-synthetic-biology-focus
#17
Thomas Craig, Richard Holland, Rosalinda D'Amore, James Johnson, Hannah V McCue, Anthony West, Valentin Zulkower, Hille Tekotte, Yizhi Cai, Daniel Swan, Robert P Davey, Christiane Hertz-Fowler, Anthony Hall, Mark Caddick
This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most LIMS systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture...
September 6, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28876137/penetrance-and-the-healthy-elderly
#18
Paul Lacaze, Ingrid Winship, John McNeil
The variable penetrance of pathogenic variants (PVs) represents a major challenge to the field of human genetics, often complicating clinical decision-making and risk management. Nonpenetrance, the detection of PVs in the absence of disease manifestation, is a common phenomenon, yet, we know very little about the underlying factors, which may protect some individuals and not others. Placing a new focus on the genomic study of the healthy elderly may be pivotal for advancing our understanding of penetrance. Studying those who remain unaffected late into life, despite harboring known genetic risk variants, could provide important insights into disease mechanisms and ultimately inform clinical care, yet, it has received relatively little attention as a research strategy...
September 6, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28873402/gene-environment-interaction-study-for-bmi-reveals-interactions-between-genetic-factors-and-physical-activity-alcohol-consumption-and-socioeconomic-status
#19
Mathias Rask-Andersen, Torgny Karlsson, Weronica E Ek, Åsa Johansson
Previous genome-wide association studies (GWAS) have identified hundreds of genetic loci to be associated with body mass index (BMI) and risk of obesity. Genetic effects can differ between individuals depending on lifestyle or environmental factors due to gene-environment interactions. In this study, we examine gene-environment interactions in 362,496 unrelated participants with Caucasian ancestry from the UK Biobank resource. A total of 94 BMI-associated SNPs, selected from a previous GWAS on BMI, were used to construct weighted genetic scores for BMI (GSBMI)...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28873397/long-term-intra-individual-reproducibility-of-heart-rate-dynamics-during-exercise-and-recovery-in-the-uk-biobank-cohort
#20
Michele Orini, Andrew Tinker, Patricia B Munroe, Pier D Lambiase
BACKGROUND: The heart rate (HR) response to exercise provides useful information about the autonomic function and has prognostic value, but its reproducibility over a long period of time, a critical requirement for using it as a clinical biomarker, is undetermined. AIM: To determine the intra-individual reproducibility of HR dynamics during sub-maximum exercise and one minute recovery. METHODS: 1187 individuals from the Cardio physical fitness assessment test of the UK Biobank repeated a standard exercise stress test twice (recall time 34...
2017: PloS One
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