We evaluated via a simulation study several strategies for imputing missing ordinal outcomes in a longitudinal clinical trial, contrasting methods that involve truncation of imputed values outside plausible ranges with those that do not. Our aim was to identify a preferred imputation strategy for estimating treatment difference at study endpoint. Plausible data were simulated via resampling of existing placebo data sets and adding treatment effect; then different imputation strategies were evaluated under missingness at random (MAR) and varying dropout rates. Our conclusion is that imputation methods based on rounding and truncation lead to larger bias than strategies based on simple methods based on (nontruncated) multivariate normal distribution.
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http://dx.doi.org/10.1080/10543406.2014.901344 | DOI Listing |
J Chem Theory Comput
December 2024
Department of Polymer Materials and Engineering, College of Materials and Metallurgy, Guizhou University, Guiyang 550025, P. R. China.
Missing data in tabular data sets is ubiquitous in statistical analysis, big data analysis, and machine learning studies. Many strategies have been proposed to impute missing data, but their reliability has not been stringently assessed in materials science. Here, we carried out a benchmark test for six imputation strategies: Mean, MissForest, HyperImpute, Gain, Sinkhorn, and a newly proposed MatImpute on seven representative data sets in materials science.
View Article and Find Full Text PDFVirus Evol
November 2024
Department of Biology, University of Maryland, College Park, MD 20742, USA.
The enormous diversity of bacteriophages and their bacterial hosts presents a significant challenge to predict which phages infect a focal set of bacteria. Infection is largely determined by complementary-and largely uncharacterized-genetics of adsorption, injection, cell take-over, and lysis. Here we present a machine learning approach to predict phage-bacteria interactions trained on genome sequences of and phenotypic interactions among 51 strains and 45 phage λ strains that coevolved in laboratory conditions for 37 days.
View Article and Find Full Text PDFTherap Adv Gastroenterol
December 2024
Department of Gastroenterology, Second Medical Center of Chinese PLA General Hospital, Beijing 100853, China.
Background: Colorectal adenomas (CAs) represent a significant global health issue, particularly in China, where lifestyle modifications have contributed to their increased prevalence. These adenomas are precursors to colorectal cancer. While high-fiber diets have been shown to decrease risk, the implications of food-specific serum immunoglobulin G reactivity (FSsIgGR) on CAs remain uncertain and warrant further investigation.
View Article and Find Full Text PDFMetabolism
December 2024
Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. Electronic address:
Background: Delineating the shared genetic architecture of type 2 diabetes with muscle mass and function and frailty is essential for unraveling the common etiology and developing holistic therapeutic strategies for these co-existing conditions.
Methods: In this genome-wide pleiotropic association study, we performed multi-level pairwise trait pleiotropic analyses using genome-wide association study summary statistics from up to 461,026 European ancestry individuals to dissect the shared genetic factors and causal relationships of type 2 diabetes and seven glycemic traits with four muscle mass- and function-related phenotypes and the frailty index.
Results: We first identified 27 pairs with significant genetic correlations through the linkage disequilibrium score regression and high-definition likelihood analysis.
Animal
November 2024
Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China. Electronic address:
Genomic prediction has been widely applied to the pig industry and has greatly accelerated the progress of genetic improvement in pigs. With the development of sequencing technology and price reduction, more and more genotype imputation panels of pig have been investigated, providing an effective and economical method to further study the genetic variation of pig economic traits. In this study, the imputation from 80 k Single Nucleotide Polymorphism chip data of 832 Large White pigs to whole-genome sequencing genotypes was performed by Swine Imputation Server, Pig Haplotypes Reference Panel (PHARP), Animal Genotype Imputation Database and 1k-pig-genomes four thousand-pig imputation panels.
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