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https://www.readbyqxmd.com/read/29352324/efficient-genome-wide-genotyping-strategies-and-data-integration-in-crop-plants
#1
REVIEW
Davoud Torkamaneh, Brian Boyle, François Belzile
Next-generation sequencing (NGS) has revolutionized plant and animal research by providing powerful genotyping methods. This review describes and discusses the advantages, challenges and, most importantly, solutions to facilitate data processing, the handling of missing data, and cross-platform data integration. Next-generation sequencing technologies provide powerful and flexible genotyping methods to plant breeders and researchers. These methods offer a wide range of applications from genome-wide analysis to routine screening with a high level of accuracy and reproducibility...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29350878/perfusion-ct-in-posterior-circulation-stroke-predictors-and-prognostic-implications-of-focal-hypoperfusion
#2
Lars-Peder Pallesen, Dimitris Lambrou, Ashraf Eskandari, Jessica Barlinn, Kristian Barlinn, Heinz Reichmann, Vincent Dunet, Philippe Maeder, Volker Puetz, Patrik Michel
BACKGROUND: We aimed to determine predictors of focal hypoperfusion on CT Perfusion (CTP) in patients with acute posterior circulation stroke and its association with long-term outcome. METHODS: We selected patients with posterior circulation stroke from the Acute STroke Registry and Analysis of Lausanne (ASTRAL) who underwent CTP within 24 hours of stroke onset as part of the stroke imaging protocol. Hypoperfusion was defined as an area of visually well demarcated mean-transit-time (MTT) prolongation corresponding to an arterial territory on standard reconstruction CTP imaging maps...
January 19, 2018: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
https://www.readbyqxmd.com/read/29350345/measurement-invariance-and-general-population-reference-values-of-the-promis-profile-29-in-the-uk-france-and-germany
#3
Felix Fischer, Chris Gibbons, Joël Coste, Jose M Valderas, Matthias Rose, Alain Leplège
PURPOSE: Comparability of patient-reported outcome measures over different languages is essential to allow cross-national research. We investigate the comparability of the PROMIS Profile 29, a generic health-related quality of life measure, in general population samples in the UK, France, and Germany and present general population reference values. METHODS: A web-based survey was simultaneously conducted in the UK (n = 1509), France (1501), and Germany (1502)...
January 19, 2018: Quality of Life Research
https://www.readbyqxmd.com/read/29349773/progestin-only-and-combined-oral-contraceptives-and-receptor-defined-premenopausal-breast-cancer-risk-the-norwegian-women-and-cancer-study
#4
Marit Busund, Nora S Bugge, Tonje Braaten, Marit Waaseth, Charlotta Rylander, Eiliv Lund
Receptor-defined subtypes of breast cancer represent distinct cancer types and have differences in risk factors. Whether the two main hormonal forms of oral contraceptives (OCs); i.e. progestin-only (POC) and combined oral contraceptives (COC), are differentially associated with these subtypes are not well known. The aim of this study was to assess the effect of POC and COC use on hormone receptor-defined breast cancer risk in premenopausal women in a prospective population-based cohort - The Norwegian Women and Cancer study (NOWAC)...
January 19, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29348432/genome-wide-association-study-of-self-reported-food-reactions-in-japanese-identifies-shrimp-and-peach-specific-loci-in-the-hla-dr-dq-gene-region
#5
Seik-Soon Khor, Ryoko Morino, Kazuyuki Nakazono, Shigeo Kamitsuji, Masanori Akita, Maiko Kawajiri, Tatsuya Yamasaki, Azusa Kami, Yuria Hoshi, Asami Tada, Kenichi Ishikawa, Maaya Hine, Miki Kobayashi, Nami Kurume, Naoyuki Kamatani, Katsushi Tokunaga, Todd A Johnson
Food allergy is an increasingly important health problem in the world. Several genome-wide association studies (GWAS) focused on European ancestry samples have identified food allergy-specific loci in the HLA class II region. We conducted GWAS of self-reported reactivity with common foods using the data from 11011 Japanese women and identified shrimp and peach allergy-specific loci in the HLA-DR/DQ gene region tagged by rs74995702 (P = 6.30 × 10-17, OR = 1.91) and rs28359884 (P = 2.3 × 10-12, OR = 1...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348415/trends-in-fetal-growth-between-2000-to-2014-in-singleton-live-births-from-israel
#6
Keren Agay-Shay, Mary Rudolf, Lisa Rubin, Ziona Haklai, Itamar Grotto
Trends in birthweight and abnormal fetal growth, namely term low birthweight (LBW), macrosomia, small-for-gestational age (SGA) and large-for-gestational age (LGA), are important indicators of changes in the health of populations. We performed this epidemiological study to evaluate these trends among 2,039,415 singleton live births from Israel over a period of 15 years. Birth certificate data was obtained from the Ministry of Health. Multivariable linear and logistic regression models were used to evaluate crude and adjusted estimates compared to the baseline of 2000 and polynomial trends...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29346621/assessing-polymyalgia-rheumatica-activity-when-c-reactive-protein-is-unavailable-or-uninterpretable
#7
Valérie Devauchelle-Pensec, Lea Saraux, Jean Marie Berthelot, Michel De Bandt, Divi Cornec, Dewi Guellec, Thierry Marhadour, Sandrine Jousse-Joulin, Maelenn Gouillou, Alain Saraux
Objective: The PMR activity score (PMR-AS) includes the CRP value, which may be lacking or invalid owing to anti-IL-6 therapy. Our objective was to develop alternatives to PMR-AS that do not require CRP. Methods: We used the Club Rhumatisme et Inflammation (CRI; 89 patients with PMR) and the Tolerance and Efficacy of tocilizumab iN pOlymyalgia Rheumatica (TENOR; 20 patients with recent-onset PMR naive to glucocorticoid who received three tocilizumab infusions, at weeks 0, 4 and 8, followed by prednisone from weeks 12 to 24) cohorts...
January 15, 2018: Rheumatology
https://www.readbyqxmd.com/read/29345073/improving-accuracy-of-genomic-prediction-in-brangus-cattle-by-adding-animals-with-imputed-low-density-snp-genotypes
#8
F B Lopes, X-L Wu, H Li, J Xu, T Perkins, J Genho, R Ferretti, R G Tait, S Bauck, G J M Rosa
Reliable genomic prediction of breeding values for quantitative traits requires the availability of sufficient number of animals with genotypes and phenotypes in the training set. As of 31 October 2016, there were 3,797 Brangus animals with genotypes and phenotypes. These Brangus animals were genotyped using different commercial SNP chips. Of them, the largest group consisted of 1,535 animals genotyped by the GGP-LDV4 SNP chip. The remaining 2,262 genotypes were imputed to the SNP content of the GGP-LDV4 chip, so that the number of animals available for training the genomic prediction models was more than doubled...
February 2018: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29342163/doxylamine-pyridoxine-for-nausea-and-vomiting-of-pregnancy-randomized-placebo-controlled-trial-prespecified-analyses-and-reanalysis
#9
Navindra Persaud, Christopher Meaney, Khaled El-Emam, Rahim Moineddin, Kevin Thorpe
BACKGROUND: Doxylamine-pyridoxine is recommended as a first line treatment for nausea and vomiting during pregnancy and it is commonly prescribed. We re-analysed the findings of a previously reported superiority trial of doxylamine-pyridoxine for the treatment of nausea and vomiting during pregnancy using the clinical study report obtained from Health Canada. METHODS AND FINDINGS: We re-analysed individual level data for a parallel arm randomized controlled trial that was conducted in six outpatient obstetrical practices in the United States...
2018: PloS One
https://www.readbyqxmd.com/read/29335598/gene-and-microrna-perturbations-of-cellular-response-to-pemetrexed-implicate-biological-networks-and-enable-imputation-of-response-in-lung-adenocarcinoma
#10
Eric R Gamazon, Matthew R Trendowski, Yujia Wen, Claudia Wing, Shannon M Delaney, Won Huh, Shan Wong, Nancy J Cox, M Eileen Dolan
Pemetrexed is indicated for non-small cell lung carcinoma and mesothelioma, but often has limited efficacy due to drug resistance. To probe the molecular mechanisms underlying chemotherapeutic response, we performed mRNA and microRNA (miRNA) expression profiling of pemetrexed treated and untreated lymphoblastoid cell lines (LCLs) and applied a hierarchical Bayesian method. We identified genetic variation associated with gene expression in human lung tissue for the most significant differentially expressed genes (Benjamini-Hochberg [BH] adjusted p < 0...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29335448/regional-evaluation-of-childhood-acute-lymphoblastic-leukemia-genetic-susceptibility-loci-among-japanese
#11
Kevin Y Urayama, Masatoshi Takagi, Takahisa Kawaguchi, Keitaro Matsuo, Yoichi Tanaka, Yoko Ayukawa, Yuki Arakawa, Daisuke Hasegawa, Yuki Yuza, Takashi Kaneko, Yasushi Noguchi, Yuichi Taneyama, Setsuo Ota, Takeshi Inukai, Masakatsu Yanagimachi, Dai Keino, Kazutoshi Koike, Daisuke Toyama, Yozo Nakazawa, Hidemitsu Kurosawa, Kozue Nakamura, Koichi Moriwaki, Hiroaki Goto, Yujin Sekinaka, Daisuke Morita, Motohiro Kato, Junko Takita, Toshihiro Tanaka, Johji Inazawa, Katsuyoshi Koh, Yasushi Ishida, Akira Ohara, Shuki Mizutani, Fumihiko Matsuda, Atsushi Manabe
Genome-wide association studies (GWAS) performed mostly in populations of European and Hispanic ancestry have confirmed an inherited genetic basis for childhood acute lymphoblastic leukemia (ALL), but these associations are less clear in other races/ethnicities. DNA samples from ALL patients (aged 0-19 years) previously enrolled onto a Tokyo Children's Cancer Study Group trial were collected during 2013-2015, and underwent single nucleotide polymorphism (SNP) microarray genotyping resulting in 527 B-cell ALL for analysis...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29335023/early-neonatal-glutaric-aciduria-type-i-hidden-by-perinatal-asphyxia-a-case-report
#12
Giacomo Biasucci, Nicola Morelli, Federica Natacci, Massimo Mastrangelo
BACKGROUND: Perinatal asphyxia (PA) occurs in about 2 to 10 per 1000 live full-term births. Although neonatal epileptic seizures are observed in up to 60% of cases, PA may mimic or subtend other conditions. Hypoxia related brain injury is particularly relevant, as it may have permanent effects on neuropsychomotor development. Antepartum obstetric conditions, may, in turn, lead to hypoxic-ischemic damage to the fetus and the newborn, often underlying PA. Herein, a case of PA that hid and triggered signs and symptoms of Glutaric Aciduria type I (GA-I), is reported...
January 15, 2018: Italian Journal of Pediatrics
https://www.readbyqxmd.com/read/29333672/controlled-pattern-imputation-for-sensitivity-analysis-of-longitudinal-binary-and-ordinal-outcomes-with-nonignorable-dropout
#13
Yongqiang Tang
The controlled imputation method refers to a class of pattern mixture models that have been commonly used as sensitivity analyses of longitudinal clinical trials with nonignorable dropout in recent years. These pattern mixture models assume that participants in the experimental arm after dropout have similar response profiles to the control participants or have worse outcomes than otherwise similar participants who remain on the experimental treatment. In spite of its popularity, the controlled imputation has not been formally developed for longitudinal binary and ordinal outcomes partially due to the lack of a natural multivariate distribution for such endpoints...
January 15, 2018: Statistics in Medicine
https://www.readbyqxmd.com/read/29330539/missing-value-imputation-approach-for-mass-spectrometry-based-metabolomics-data
#14
Runmin Wei, Jingye Wang, Mingming Su, Erik Jia, Shaoqiu Chen, Tianlu Chen, Yan Ni
Missing values exist widely in mass-spectrometry (MS) based metabolomics data. Various methods have been applied for handling missing values, but the selection can significantly affect following data analyses. Typically, there are three types of missing values, missing not at random (MNAR), missing at random (MAR), and missing completely at random (MCAR). Our study comprehensively compared eight imputation methods (zero, half minimum (HM), mean, median, random forest (RF), singular value decomposition (SVD), k-nearest neighbors (kNN), and quantile regression imputation of left-censored data (QRILC)) for different types of missing values using four metabolomics datasets...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29329993/pulmonary-arterial-hypertension-in-four-patients-treated-by-leflunomide
#15
Valentin Coirier, Alain Lescoat, Céline Chabanne, Maxime Fournet, Guillaume Coiffier, Stéphane Jouneau, Elisabeth Polard, Patrick Jégo
Pulmonary arterial hypertension (PAH) is a rare disorder that can be drug-induced, mostly following treatment by appetite-suppressant drugs. We report four cases of patients who developed PAH following a treatment by leflunomide for rheumatoid arthritis, psoriatic arthritis or undetermined connective tissue disease. All patients described a progressive dyspnea from grade II to IV of NYHA classification; clinical examination found signs of heart failure. PAH was finally diagnosed and confirmed by right heart catheterisation...
January 9, 2018: Joint, Bone, Spine: Revue du Rhumatisme
https://www.readbyqxmd.com/read/29329371/alcohol-use-in-adolescence-and-later-working-memory-findings-from-a-large-population-based-birth-cohort
#16
Liam Mahedy, Matt Field, Suzanne Gage, Gemma Hammerton, Jon Heron, Matt Hickman, Marcus R Munafò
Aims: The study aimed to examine the association between adolescent alcohol use and working memory (WM) using a large population sample. Methods: Data from the Avon Longitudinal Study of Parents and Children were used to investigate the association between alcohol use at age 15 years and WM 3 years later, assessed using the N-back task (N ~ 3300). A three-category ordinal variable captured mutually exclusive alcohol groupings ranging in order of severity (i.e. low alcohol users, frequent drinkers and frequent/binge drinkers)...
January 10, 2018: Alcohol and Alcoholism: International Journal of the Medical Council on Alcoholism
https://www.readbyqxmd.com/read/29329022/impact-of-non-anticoagulant-therapy-on-patients-with-sepsis-induced-disseminated-intravascular-coagulation-a-multicenter-case-control-study
#17
Daisuke Kudo, Mineji Hayakawa, Kota Ono, Kazuma Yamakawa
INTRODUCTION: Anticoagulant therapy for patients with sepsis is not recommended in the latest Surviving Sepsis Campaign guidelines, and non-anticoagulant therapy is the global standard treatment approach at present. We aimed at elucidating the effect of non-anticoagulant therapy on patients with sepsis-induced disseminated intravascular coagulation (DIC), as evidence on this topic has remained inconclusive. MATERIALS AND METHODS: Data from 3195 consecutive adult patients admitted to 42 intensive care units for the treatment of severe sepsis were retrospectively analyzed via propensity score analyses with and without multiple imputation...
January 3, 2018: Thrombosis Research
https://www.readbyqxmd.com/read/29325529/a-multiple-imputation-method-based-on-weighted-quantile-regression-models-for-longitudinal-censored-biomarker-data-with-missing-values-at-early-visits
#18
MinJae Lee, Mohammad H Rahbar, Matthew Brown, Lianne Gensler, Michael Weisman, Laura Diekman, John D Reveille
BACKGROUND: In patient-based studies, biomarker data are often subject to left censoring due to the detection limits, or to incomplete sample or data collection. In the context of longitudinal regression analysis, inappropriate handling of these issues could lead to biased parameter estimates. We developed a specific multiple imputation (MI) strategy based on weighted censored quantile regression (CQR) that not only accounts for censoring, but also missing data at early visits when longitudinal biomarker data are modeled as a covariate...
January 11, 2018: BMC Medical Research Methodology
https://www.readbyqxmd.com/read/29324972/prognostic-and-predictive-role-of-neutrophil-lymphocytes-ratio-in-metastatic-colorectal-cancer-a-retrospective-analysis-of-the-tribe-study-by-gono
#19
E Dell'Aquila, C Cremolini, T Zeppola, S Lonardi, F Bergamo, G Masi, M Stellato, F Marmorino, M Schirripa, F Urbano, M Ronzoni, G Tomasello, A Zaniboni, P Racca, A Buonadonna, G Allegrini, E Fea, S Di Donato, S Chiara, G Tonini, D Tomcikova, L Boni, A Falcone, D Santini
Background: Neutrophil/Lymphocyte ratio (NLR), defined as absolute neutrophils count divided by absolute lymphocytes count, has been reported as poor prognostic factor in several neoplastic diseases but only a few data are available about unresectable metastatic colorectal cancer (mCRC) patients (pts). The aim of our study was to evaluate the prognostic and predictive role of NLR in the TRIBE trial. Patients and Methods: Pts enrolled in TRIBE trial were included...
January 8, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29321673/genomic-analysis-of-family-data-reveals-additional-genetic-effects-on-intelligence-and-personality
#20
W David Hill, Ruben C Arslan, Charley Xia, Michelle Luciano, Carmen Amador, Pau Navarro, Caroline Hayward, Reka Nagy, David J Porteous, Andrew M McIntosh, Ian J Deary, Chris S Haley, Lars Penke
Pedigree-based analyses of intelligence have reported that genetic differences account for 50-80% of the phenotypic variation. For personality traits these effects are smaller, with 34-48% of the variance being explained by genetic differences. However, molecular genetic studies using unrelated individuals typically report a heritability estimate of around 30% for intelligence and between 0 and 15% for personality variables. Pedigree-based estimates and molecular genetic estimates may differ because current genotyping platforms are poor at tagging causal variants, variants with low minor allele frequency, copy number variants, and structural variants...
January 10, 2018: Molecular Psychiatry
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