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https://www.readbyqxmd.com/read/28642364/the-accuracy-and-bias-of-single-step-genomic-prediction-for-populations-under-selection
#1
Wan-Ling Hsu, Dorian J Garrick, Rohan Luigi Fernando
In single-step analyses, missing genotypes are explicitly or implicitly imputed, and this requires centering the observed genotypes, using the means of the unselected founders. If genotypes are only available on selected individuals, centering on the unselected founder mean is not straightforward. Here, computer simulation is used to study an alternative analysis that does not require centering genotypes but fits the mean μg of unselected individuals as a fixed effect. Centering the entire matrix of observed and imputed genotypes using their sample means can be done to improve numerical properties of the analysis, in addition to fitting μg...
June 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28641921/genome-wide-association-and-interaction-studies-of-csf-t-tau-a%C3%AE-42-ratio-in-adni-cohort
#2
Jin Li, Qiushi Zhang, Feng Chen, Xianglian Meng, Wenjie Liu, Dandan Chen, Jingwen Yan, Sungeun Kim, Lei Wang, Weixing Feng, Andrew J Saykin, Hong Liang, Li Shen
The pathogenic relevance in Alzheimer's disease (AD) presents a decrease of cerebrospinal fluid amyloid-ß42 (Aß42) burden and an increase in cerebrospinal fluid total tau (T-tau) levels. In this work, we performed genome-wide association study (GWAS) and genome-wide interaction study of T-tau/Aß42 ratio as an AD imaging quantitative trait on 843 subjects and 563,980 single-nucleotide polymorphisms (SNPs) in ADNI cohort. We aim to identify not only SNPs with significant main effects but also SNPs with interaction effects to help explain "missing heritability"...
May 15, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28635678/evaluation-of-classifier-performance-for-multiclass-phenotype-discrimination-in-untargeted-metabolomics
#3
Patrick J Trainor, Andrew P DeFilippis, Shesh N Rai
Statistical classification is a critical component of utilizing metabolomics data for examining the molecular determinants of phenotypes. Despite this, a comprehensive and rigorous evaluation of the accuracy of classification techniques for phenotype discrimination given metabolomics data has not been conducted. We conducted such an evaluation using both simulated and real metabolomics datasets, comparing Partial Least Squares-Discriminant Analysis (PLS-DA), Sparse PLS-DA, Random Forests, Support Vector Machines (SVM), Artificial Neural Network, k-Nearest Neighbors (k-NN), and Naïve Bayes classification techniques for discrimination...
June 21, 2017: Metabolites
https://www.readbyqxmd.com/read/28632787/risk-of-alzheimer-s-disease-or-dementia-following-a-cancer-diagnosis
#4
Erin J Aiello Bowles, Rod L Walker, Melissa L Anderson, Sascha Dublin, Paul K Crane, Eric B Larson
OBJECTIVE: We evaluated dementia and Alzheimer's disease (AD) risks after a cancer diagnosis in a population-based prospective cohort, the Adult Changes in Thought (ACT) study. METHODS: We followed community-dwelling people aged ≥65 years without dementia at study entry for incident dementia and AD from 1994-2015. We linked study data with cancer registry data and categorized cancer diagnoses as prevalent (diagnosed before ACT study enrollment) or incident (diagnosed during follow-up)...
2017: PloS One
https://www.readbyqxmd.com/read/28631331/missing-data-in-clinical-trials-control-based-mean-imputation-and-sensitivity-analysis
#5
Devan V Mehrotra, Fang Liu, Thomas Permutt
In some randomized (drug versus placebo) clinical trials, the estimand of interest is the between-treatment difference in population means of a clinical endpoint that is free from the confounding effects of "rescue" medication (e.g., HbA1c change from baseline at 24 weeks that would be observed without rescue medication regardless of whether or when the assigned treatment was discontinued). In such settings, a missing data problem arises if some patients prematurely discontinue from the trial or initiate rescue medication while in the trial, the latter necessitating the discarding of post-rescue data...
June 20, 2017: Pharmaceutical Statistics
https://www.readbyqxmd.com/read/28629879/prediction-of-cognition-in-parkinson-s-disease-with-a-clinical-genetic-score-a-longitudinal-analysis-of-nine-cohorts
#6
Ganqiang Liu, Joseph J Locascio, Jean-Christophe Corvol, Brendon Boot, Zhixiang Liao, Kara Page, Daly Franco, Kyle Burke, Iris E Jansen, Ana Trisini-Lipsanopoulos, Sophie Winder-Rhodes, Caroline M Tanner, Anthony E Lang, Shirley Eberly, Alexis Elbaz, Alexis Brice, Graziella Mangone, Bernard Ravina, Ira Shoulson, Florence Cormier-Dequaire, Peter Heutink, Jacobus J van Hilten, Roger A Barker, Caroline H Williams-Gray, Johan Marinus, Clemens R Scherzer
BACKGROUND: Cognitive decline is a debilitating manifestation of disease progression in Parkinson's disease. We aimed to develop a clinical-genetic score to predict global cognitive impairment in patients with the disease. METHODS: In this longitudinal analysis, we built a prediction algorithm for global cognitive impairment (defined as Mini Mental State Examination [MMSE] ≤25) using data from nine cohorts of patients with Parkinson's disease from North America and Europe assessed between 1986 and 2016...
June 16, 2017: Lancet Neurology
https://www.readbyqxmd.com/read/28606970/the-dynamics-of-response-as-measured-by-multiple-composite-outcome-tools-in-the-tight-control-of-inflammation-in-early-psoriatic-arthritis-ticopa-trial
#7
Laura C Coates, Farrouq Mahmood, Paul Emery, Philip G Conaghan, Philip S Helliwell
BACKGROUND: We aimed to evaluate the dynamics of treatment response with different composite measures in the TIght COntrol of inflammation in early Psoriatic Arthritis (TICOPA) trial. METHODS: Participants with early disease-modifying antirheumatic drug-naïve psoriatic arthritis (PsA) were randomised 1:1 to either tight control (TC; 4 weekly review with therapy escalation if criteria not met) or standard care (SC; 12 weekly review). We calculated modified versions of the Psoriatic ArthritiS Disease Activity Score (PASDAS), Group for Research and Assessment of Psoriasis and Psoriatic Arthritis (GRAPPA) Composite scorE (GRACE) and Composite Psoriatic Disease Activity Index (CPDAI) at baseline and 12 weekly to 48 weeks by blinded assessor...
June 12, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/28599749/statin-prescribing-for-prevention-of-cardiovascular-disease-amongst-people-with-severe-mental-illness-cohort-study-in-uk-primary-care
#8
R Blackburn, D Osborn, K Walters, I Nazareth, I Petersen
BACKGROUND: Severe mental illness (SMI) is associated with excess cardiovascular disease (CVD) morbidity, but little is known on provision of preventative interventions. We investigated statin initiation for primary CVD prevention in individuals with and without SMI. METHODS: We used primary care data from The Health Improvement Network from 2006 to 2015 for UK patients aged 30-99years with no pre-existing CVD conditions and selected individuals with schizophrenia (n=13,252) or bipolar disorder (n=11,994)...
June 6, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28584366/biostatistics-series-module-9-survival-analysis
#9
Avijit Hazra, Nithya Gogtay
Survival analysis is concerned with "time to event" data. Conventionally, it dealt with cancer death as the event in question, but it can handle any event occurring over a time frame, and this need not be always adverse in nature. When the outcome of a study is the time to an event, it is often not possible to wait until the event in question has happened to all the subjects, for example, until all are dead. In addition, subjects may leave the study prematurely. Such situations lead to what is called censored observations as complete information is not available for these subjects...
May 2017: Indian Journal of Dermatology
https://www.readbyqxmd.com/read/28573919/propensity-score-analysis-with-partially-observed-covariates-how-should-multiple-imputation-be-used
#10
Clémence Leyrat, Shaun R Seaman, Ian R White, Ian Douglas, Liam Smeeth, Joseph Kim, Matthieu Resche-Rigon, James R Carpenter, Elizabeth J Williamson
Inverse probability of treatment weighting is a popular propensity score-based approach to estimate marginal treatment effects in observational studies at risk of confounding bias. A major issue when estimating the propensity score is the presence of partially observed covariates. Multiple imputation is a natural approach to handle missing data on covariates: covariates are imputed and a propensity score analysis is performed in each imputed dataset to estimate the treatment effect. The treatment effect estimates from each imputed dataset are then combined to obtain an overall estimate...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28572146/investigating-parent-needs-participation-and-psychological-distress-in-the-children-s-hospital
#11
Jessica Jones, Amy S Nowacki, Amy Greene, Christine Traul, Johanna Goldfarb
BACKGROUND AND OBJECTIVES: Greater parent participation in a child's hospital care is associated with better child outcomes in the hospital and after discharge. This study examined the relationships between perceived need fulfillment for parents, parent participation in hospital care, and parent psychological distress. We hypothesized that greater perceived need fulfillment would be associated with greater participation in hospital care and decreased psychological distress. METHODS: In this prospective cohort study, 166 parents completed questionnaires on a pediatric (nonintensive care) floor...
June 1, 2017: Hospital Pediatrics
https://www.readbyqxmd.com/read/28559587/urban-eddy-covariance-measurements-reveal-significant-missing-nox-emissions-in-central-europe
#12
T Karl, M Graus, M Striednig, C Lamprecht, A Hammerle, G Wohlfahrt, A Held, L von der Heyden, M J Deventer, A Krismer, C Haun, R Feichter, J Lee
Nitrogen oxide (NOx) pollution is emerging as a primary environmental concern across Europe. While some large European metropolitan areas are already in breach of EU safety limits for NO2, this phenomenon does not seem to be only restricted to large industrialized areas anymore. Many smaller scale populated agglomerations including their surrounding rural areas are seeing frequent NO2 concentration violations. The question of a quantitative understanding of different NOx emission sources is therefore of immanent relevance for climate and air chemistry models as well as air pollution management and health...
May 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28557022/missing-binary-outcomes-under-covariate-dependent-missingness-in-cluster-randomised-trials
#13
Anower Hossain, Karla DiazOrdaz, Jonathan W Bartlett
Missing outcomes are a commonly occurring problem for cluster randomised trials, which can lead to biased and inefficient inference if ignored or handled inappropriately. Two approaches for analysing such trials are cluster-level analysis and individual-level analysis. In this study, we assessed the performance of unadjusted cluster-level analysis, baseline covariate-adjusted cluster-level analysis, random effects logistic regression and generalised estimating equations when binary outcomes are missing under a baseline covariate-dependent missingness mechanism...
May 29, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/28554159/health-system-responsiveness-and-chronic-disease-care-what-is-the-role-of-disease-management-programs-an-analysis-based-on-cross-sectional-survey-and-administrative-claims-data
#14
Julia Röttger, Miriam Blümel, Roland Linder, Reinhard Busse
Health system responsiveness is an important aspect of health systems performance. The concept of responsiveness relates to the interpersonal and contextual aspects of health care. While disease management programs (DMPs) aim to improve the quality of health care (e.g. by improving the coordination of care), it has not been analyzed yet whether these programs improve the perceived health system responsiveness. Our study aims to close this gap by analyzing the differences in the perceived health system responsiveness between DMP-participants and non-participants...
May 17, 2017: Social Science & Medicine
https://www.readbyqxmd.com/read/28545423/determinants-of-tuberculosis-transmission-and-treatment-abandonment-in-fortaleza-brazil
#15
Guy Harling, Antonio S Lima Neto, Geziel S Sousa, Marcia M T Machado, Marcia C Castro
BACKGROUND: Tuberculosis (TB) remains a public health problem, despite recent achievements in reducing incidence and mortality rates. In Brazil, these achievements were above the worldwide average, but marked by large regional heterogeneities. In Fortaleza (5th largest city in Brazil), the tuberculosis cure rate has been declining and treatment abandonment has been increasing in the past decade, despite a reduction in incidence and an increase in directly observed therapy (DOT). These trends put efforts to eliminate tuberculosis at risk...
May 25, 2017: BMC Public Health
https://www.readbyqxmd.com/read/28544919/risk-factors-for-patient-reported-errors-during-cancer-follow-up-results-from-a-national-survey-in-denmark
#16
Anne Hjøllund Christiansen, Henriette Lipczak, Janne Lehmann Knudsen, Anne Mette Tranberg Kejs
Due to an increased cancer survival, more cancer patients are referred to follow-up after primary treatment. Knowledge of patient safety during follow-up is sparse. OBJECTIVE: To examine patient-reported errors during cancer follow-up and identify factors associated with errors. DESIGN: A national survey on cancer patients' experiences of treatment and aftercare was conducted in 2012, about two years following cancer diagnosis (N=6914). Associations between patient-reported errors during follow-up and covariates were examined using multiple logistic regression...
May 22, 2017: Cancer Epidemiology
https://www.readbyqxmd.com/read/28541924/characterizing-highly-benefited-patients-in-randomized-clinical-trials
#17
Vivek Charu, Paul B Rosenberg, Lon S Schneider, Lea T Drye, Lisa Rein, David Shade, Constantine G Lyketsos, Constantine E Frangakis
Physicians and patients may choose a certain treatment only if it is predicted to have a large effect for the profile of that patient. We consider randomized controlled trials in which the clinical goal is to identify as many patients as possible that can highly benefit from the treatment. This is challenging with large numbers of covariate profiles, first, because the theoretical, exact method is not feasible, and, second, because usual model-based methods typically give incorrect results. Better, more recent methods use a two-stage approach, where a first stage estimates a working model to produce a scalar predictor of the treatment effect for each covariate profile; and a second stage estimates empirically a high-benefit group based on the first-stage predictor...
May 20, 2017: International Journal of Biostatistics
https://www.readbyqxmd.com/read/28535776/the-role-of-anti-ige-omalizumab-xolair-in-the-management-of-severe-recalcitrant-paediatric-atopic-eczema-adapt-statistical-analysis-plan
#18
Tao Chen, Susan Chan, Gideon Lack, Suzie Cro, Victoria R Cornelius
BACKGROUND: The Atopic Dermatitis Anti-IgE Paediatric Trial (ADAPT) is a trial to determine the clinical efficacy and safety of omalizumab for children with severe atopic eczema. This article describes the detailed statistical analysis plan for the ADAPT as an update to the published protocol and is submitted prior to knowing all outcomes. METHOD AND DESIGN: The ADAPT is a randomised, double-blind, placebo-controlled trial with a primary objective to determine whether anti-IgE reduces eczema severity as assessed by the validated eczema score (objective SCORAD) after 24 weeks of treatment in children with severe eczema...
May 23, 2017: Trials
https://www.readbyqxmd.com/read/28530430/subjective-social-status-life-course-ses-and-bmi-in-young-adulthood
#19
Matt Bradshaw, Blake Victor Kent, W Matthew Henderson, Anna Catherine Setar
OBJECTIVE: Socioeconomic status (SES) is associated with many aspects of health and well-being, including body mass index (BMI). Most research in this area has focused on objective indicators of SES such as education and income, but recent work suggests that subjective social status (SSS) is also important. This study contributes to a growing body of research on SSS and BMI. METHOD: Data from Waves I and IV the National Longitudinal Study of Adolescent to Adult Health (Add Health), a study of 14,780 individuals followed from adolescence to young adulthood, were analyzed...
May 22, 2017: Health Psychology: Official Journal of the Division of Health Psychology, American Psychological Association
https://www.readbyqxmd.com/read/28529839/estimating-effects-with-rare-outcomes-and-high-dimensional-covariates-knowledge-is-power
#20
Laura Balzer, Jennifer Ahern, Sandro Galea, Mark van der Laan
Many of the secondary outcomes in observational studies and randomized trials are rare. Methods for estimating causal effects and associations with rare outcomes, however, are limited, and this represents a missed opportunity for investigation. In this article, we construct a new targeted minimum loss-based estimator (TMLE) for the effect or association of an exposure on a rare outcome. We focus on the causal risk difference and statistical models incorporating bounds on the conditional mean of the outcome, given the exposure and measured confounders...
December 2016: Epidemiologic Methods
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