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Simone Wahl, Anne-Laure Boulesteix, Astrid Zierer, Barbara Thorand, Mark Avan de Wiel
BACKGROUND: Missing values are a frequent issue in human studies. In many situations, multiple imputation (MI) is an appropriate missing data handling strategy, whereby missing values are imputed multiple times, the analysis is performed in every imputed data set, and the obtained estimates are pooled. If the aim is to estimate (added) predictive performance measures, such as (change in) the area under the receiver-operating characteristic curve (AUC), internal validation strategies become desirable in order to correct for optimism...
October 26, 2016: BMC Medical Research Methodology
Alexander Rozental, Kristoffer Magnusson, Johanna Boettcher, Gerhard Andersson, Per Carlbring
Objective: Psychological treatments can relieve mental distress and improve well-being, and the dissemination of evidence-based methods can help patients gain access to the right type of aid. Meanwhile, Internet-based cognitive-behavioral therapy (ICBT) has shown promising results for many psychiatric disorders. However, research on the potential for negative effects of psychological treatments has been lacking. Method: An individual patient data meta-analysis of 29 clinical trials of ICBT (N = 2,866) was performed using the Reliable Change Index for each primary outcome measures to distinguish deterioration rates among patients in treatment and control conditions...
October 24, 2016: Journal of Consulting and Clinical Psychology
Katarina Cheng, Ribal Bassil, Raphael Carandang, Wiley Hall, Susanne Muehlschlegel
The Glasgow Coma Scale (GCS) has limited utility in intubated patients due to the inability to assign verbal sub-scores. The verbal sub-score can be derived from the eye and motor sub-scores using a mathematical model, but the advantage of this method and its use in outcome prognostication in traumatic brain injury (TBI) patients remains unknown. We compared the validated "Core+CT"-IMPACT-model performance in 251 intubated TBI patients prospectively enrolled in the longitudinal OPTIMISM-study between November 2009 and May 2015 when substituting the original motor GCS with the total estimated GCS (teGCS; with estimated verbal sub-score)...
October 22, 2016: Journal of Neurotrauma
M H Kuniholm, X Xie, K Anastos, X Xue, L Reimers, A L French, S J Gange, S G Kassaye, A Kovacs, T Wang, B E Aouizerat, H D Strickler
Human leucocyte antigen (HLA) genes play a central role in response to pathogens and in autoimmunity. Research to understand the effects of HLA genes on health has been limited because HLA genotyping protocols are labour intensive and expensive. Recently, algorithms to impute HLA genotype data using genome-wide association study (GWAS) data have been published. However, imputation accuracy for most of these algorithms was based primarily on training data sets of European ancestry individuals. We considered performance of two HLA-dedicated imputation algorithms - SNP2HLA and HIBAG - in a multiracial population of n = 1587 women with HLA genotyping data by gold standard methods...
October 24, 2016: International Journal of Immunogenetics
Ludi Simpson, Stephen Jivraj, James Warren
The instability of ethnicity measured in the national census is found to have doubled from the period 1991-2001 to the period 2001-2011, using the Longitudinal Study that links a sample of individuals' census records across time. From internal evidence and comparison with results from the Census Quality Survey and the Labour Force Survey, estimates are made of instability due to changing question wording, imputation of missing answers, proxy reporting, recording errors and changes in the allocation of write-in answers...
October 2016: Journal of the Royal Statistical Society. Series A, (Statistics in Society)
Ling Chen, Jianguo Sun, Chengjie Xiong
Clustered interval-censored failure time data can occur when the failure time of interest is collected from several clusters and known only within certain time intervals. Regression analysis of clustered interval-censored failure time data is discussed assuming that the data arise from the semiparametric additive hazards model. A multiple imputation approach is proposed for inference. A major advantage of the approach is its simplicity because it avoids estimating the correlation within clusters by implementing a resampling-based method...
November 2016: Computational Statistics & Data Analysis
Marc Aerts, Girma Minalu, Stefan Bösner, Frank Buntinx, Bernard Burnand, Jörg Haasenritter, Lilli Herzig, J André Knottnerus, Staffan Nilsson, Walter Renier, Carol Sox, Harold Sox, Norbert Donner-Banzhoff
OBJECTIVE: To construct a clinical prediction rule for coronary artery disease (CAD) presenting with chest pain in primary care. STUDY DESIGN: Meta-Analysis using 3099 patients from 5 studies. To identify candidate predictors, we used random forest trees, multiple imputation of missing values and logistic regression within individual studies. To generate a prediction rule on the pooled data, we applied a regression model that took account of the differing standard data sets collected by the 5 studies...
October 20, 2016: Journal of Clinical Epidemiology
Melanie L Bell, Diane L Fairclough, Mallorie H Fiero, Phyllis N Butow
BACKGROUND: The Hospital Anxiety and Depression Scale (HADS) is a widely used questionnaire in health research, but there is little guidance on how to handle missing items. We aimed to investigate approaches to handling item non-response, varying sample size, proportion of subjects with missing items, proportion of missing items per subject, and the missingness mechanism. METHODS: We performed a simulation study based on anxiety and depression data among cancer survivors and patients...
October 22, 2016: BMC Research Notes
Susanna Lemmelä, Svetlana Solovieva, Rahman Shiri, Christian Benner, Markku Heliövaara, Johannes Kettunen, Verneri Anttila, Samuli Ripatti, Markus Perola, Ilkka Seppälä, Markus Juonala, Mika Kähönen, Veikko Salomaa, Jorma Viikari, Olli T Raitakari, Terho Lehtimäki, Aarno Palotie, Eira Viikari-Juntura, Kirsti Husgafvel-Pursiainen
Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS) and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291 Finnish sciatica cases and 3671 controls genotyped and imputed at 7...
2016: PloS One
Bo Jiang, Shiqian Ma, Jason Causey, Linbo Qiao, Matthew Price Hardin, Ian Bitts, Daniel Johnson, Shuzhong Zhang, Xiuzhen Huang
Genome-wide association studies present computational challenges for missing data imputation, while the advances of genotype technologies are generating datasets of large sample sizes with sample sets genotyped on multiple SNP chips. We present a new framework SparRec (Sparse Recovery) for imputation, with the following properties: (1) The optimization models of SparRec, based on low-rank and low number of co-clusters of matrices, are different from current statistics methods. While our low-rank matrix completion (LRMC) model is similar to Mendel-Impute, our matrix co-clustering factorization (MCCF) model is completely new...
October 20, 2016: Scientific Reports
I Mancini, I Ricaño-Ponce, E Pappalardo, A Cairo, M M Gorski, G Casoli, B Ferrari, M Alberti, D Mikovic, M Noris, C Wijmenga, F Peyvandi
BACKGROUND: Acquired thrombotic thrombocytopenic purpura (TTP) is a rare, life-threatening thrombotic microangiopathy associated with the development of autoantibodies against the von Willebrand factor cleaving protease, ADAMTS13. Similarly to other autoimmune disorders, evidences of a genetic contribution have been reported, including the association of the human leukocyte antigen (HLA) class II complex with disease risk OBJECTIVE: To identify novel genetic risk factors in acquired TTP...
October 20, 2016: Journal of Thrombosis and Haemostasis: JTH
Miguel Ceballos, Gail Wallace, Glenda Goodwin
BACKGROUND: The presence of postpartum depression can lead to poor maternal-child attachment, failure to thrive, and even infant death. Postpartum depression affects 13-19 % of parturients. However, among racial and ethnic minority parturients, postpartum depression rates have been shown to reach up to 35-67 % (as reported by O'Hara and McCabe, Annu Rev Clin Psychol 9:379-407, 2013; Boury et al., Women Health. 39(3):19-34, 2004; Ramos-Marcuse et al.. J Affect Disord. 122(1-2):68-75, 2010; Lucero et al...
October 19, 2016: Journal of Racial and Ethnic Health Disparities
A K Taylor, E Netsi, H O'Mahen, A Stein, J Evans, R M Pearson
BACKGROUND: Sleep problems are associated with increased risk of physical and mental illness. Identifying risk factors is an important method of reducing public health impact. We examined the association between maternal postnatal depression (PND) and offspring adolescent sleep problems. METHOD: The sample was derived from Avon Longitudinal Study of Parents and Children (ALSPAC) participants. A sample with complete data across all variables was used, with four outcome variables...
October 20, 2016: Psychological Medicine
Hanne Gro Olsen, Tim Martin Knutsen, Anna M Lewandowska-Sabat, Harald Grove, Torfinn Nome, Morten Svendsen, Mariann Arnyasi, Marte Sodeland, Kristil K Sundsaasen, Sandra Rinne Dahl, Bjørg Heringstad, Hanne H Hansen, Ingrid Olsaker, Matthew Peter Kent, Sigbjørn Lien
BACKGROUND: Clinical mastitis is an inflammation of the mammary gland and causes significant costs to dairy production. It is unfavourably genetically correlated to milk production, and, thus, knowledge of the mechanisms that underlie these traits would be valuable to improve both of them simultaneously through breeding. A quantitative trait locus (QTL) that affects both clinical mastitis and milk production has recently been fine-mapped to around 89 Mb on bovine chromosome 6 (BTA6), but identification of the gene that underlies this QTL was not possible due to the strong linkage disequilibrium between single nucleotide polymorphisms (SNPs) within this region...
October 19, 2016: Genetics, Selection, Evolution: GSE
Daniel R Ripoll, Ilja Khavrutskii, Anders Wallqvist, Sidhartha Chaudhury
Cryo-electron-microscopy (cryo-EM) structures of flaviviruses reveal significant variation in epitope occupancy across different monoclonal antibodies that have largely been attributed to epitope-level differences in conformation or accessibility that affect antibody binding. The consequences of these variations for macroscopic properties such as antibody binding and neutralization are the results of the law of mass action-a stochastic process of innumerable binding and unbinding events between antibodies and the multiple binding sites on the flavivirus in equilibrium-that cannot be directly imputed from structure alone...
October 18, 2016: Biophysical Journal
Louis R Pasquale, Hugues Aschard, Jae H Kang, Jessica N Cooke Bailey, Sara Lindström, Daniel I Chasman, William G Christen, R Rand Allingham, Allison Ashley-Koch, Richard K Lee, Sayoko E Moroi, Murray H Brilliant, Gadi Wollstein, Joel S Schuman, John Fingert, Donald L Budenz, Tony Realini, Terry Gaasterland, Douglas Gaasterland, William K Scott, Kuldev Singh, Arthur J Sit, Robert P Igo, Yeunjoo E Song, Lisa Hark, Robert Ritch, Douglas J Rhee, Vikas Gulati, Shane Havens, Douglas Vollrath, Donald J Zack, Felipe Medeiros, Robert N Weinreb, Margaret A Pericak-Vance, Yutao Liu, Peter Kraft, Julia E Richards, Bernard A Rosner, Michael A Hauser, Jonathan L Haines, Janey L Wiggs
OBJECTIVE: Several attributes of female reproductive history, including age at natural menopause (ANM), have been related to primary open-angle glaucoma (POAG). We assembled 18 previously reported common genetic variants that predict ANM to determine their association with ANM or POAG. METHODS: Using data from the Nurses' Health Study (7,143 women), we validated the ANM weighted genetic risk score in relation to self-reported ANM. Subsequently, to assess the relation with POAG, we used data from 2,160 female POAG cases and 29,110 controls in the National Eye Institute Glaucoma Human Genetics Collaboration Heritable Overall Operational Database (NEIGHBORHOOD), which consists of 8 datasets with imputed genotypes to 5...
October 10, 2016: Menopause: the Journal of the North American Menopause Society
Joachim D Pleil
Biomarker datasets often include entries 'below the level of quantitation' (LoQ) wherein the instrumentation is no longer able to provide values that meet required analytical quality standards, a phenomenon referred to as 'left-censored' data. Generally, some form of imputation for missing values is required to allow calculating distributions and summary statistics for comparing datasets to each other. This article discusses the available options for imputing (modeling) left-censored data, presents the methods for implementing different procedures, and provides examples and guidelines using realistic data to assess relative performance...
October 18, 2016: Journal of Breath Research
Chenguang Wang, Daniel O Scharfstein, Elizabeth Colantuoni, Timothy D Girard, Ying Yan
In randomized studies involving severely ill patients, functional outcomes are often unobserved due to missed clinic visits, premature withdrawal, or death. It is well known that if these unobserved functional outcomes are not handled properly, biased treatment comparisons can be produced. In this article, we propose a procedure for comparing treatments that is based on a composite endpoint that combines information on both the functional outcome and survival. We further propose a missing data imputation scheme and sensitivity analysis strategy to handle the unobserved functional outcomes not due to death...
October 17, 2016: Biometrics
Sarah Batson, Hannah Burton
AIMS: Meta-analysis is of critical importance to decision makers to assess the comparative efficacy and safety of interventions and is integral to health technology assessment. A major problem for the meta-analysis of continuous outcomes is that associated variance data are not consistently reported in trial publications. The omission of studies from a meta-analysis due to incomplete reporting may introduce bias. The objectives of this study are to summarise and describe the methods used for handling missing variance data in meta-analyses in populations with type 2 diabetes mellitus (T2DM)...
2016: PloS One
Corina Lesseur, Brenda Diergaarde, Andrew F Olshan, Victor Wünsch-Filho, Andrew R Ness, Geoffrey Liu, Martin Lacko, José Eluf-Neto, Silvia Franceschi, Pagona Lagiou, Gary J Macfarlane, Lorenzo Richiardi, Stefania Boccia, Jerry Polesel, Kristina Kjaerheim, David Zaridze, Mattias Johansson, Ana M Menezes, Maria Paula Curado, Max Robinson, Wolfgang Ahrens, Cristina Canova, Ariana Znaor, Xavier Castellsagué, David I Conway, Ivana Holcátová, Dana Mates, Marta Vilensky, Claire M Healy, Neonila Szeszenia-Dąbrowska, Eleonóra Fabiánová, Jolanta Lissowska, Jennifer R Grandis, Mark C Weissler, Eloiza H Tajara, Fabio D Nunes, Marcos B de Carvalho, Steve Thomas, Rayjean J Hung, Wilbert H M Peters, Rolando Herrero, Gabriella Cadoni, H Bas Bueno-de-Mesquita, Annika Steffen, Antonio Agudo, Oxana Shangina, Xiangjun Xiao, Valérie Gaborieau, Amélie Chabrier, Devasena Anantharaman, Paolo Boffetta, Christopher I Amos, James D McKay, Paul Brennan
We conducted a genome-wide association study of oral cavity and pharyngeal cancer in 6,034 cases and 6,585 controls from Europe, North America and South America. We detected eight significantly associated loci (P < 5 × 10(-8)), seven of which are new for these cancer sites. Oral and pharyngeal cancers combined were associated with loci at 6p21.32 (rs3828805, HLA-DQB1), 10q26.13 (rs201982221, LHPP) and 11p15.4 (rs1453414, OR52N2-TRIM5). Oral cancer was associated with two new regions, 2p23.3 (rs6547741, GPN1) and 9q34...
October 17, 2016: Nature Genetics
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