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metamicrobiomeR: an R package for analysis of microbiome relative abundance data using zero-inflated beta GAMLSS and meta-analysis across studies using random effects models
BackgroundThe rapid growth of high-throughput sequencing-based microbiome profiling has yielded tremendous insights into human health and physiology....
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Muscle Strength Reference Values and Correlation with Appendicular Muscle Mass in Mexican Children and Adolescents
Strength and muscle mass are important determinants of health status, and reference values for pediatric populations from every country or geographic...
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Disentangling landscape features and vegetation composition effects on wild ungulate use of hay meadows in high Pyrenees
Wild ungulates seek out food resources at the bottom of mountain valleys in winter and spring, where their high density can negatively impact the...
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Age-related decline in thickness and surface area in the cortical surface and hippocampus: lifespan trajectories and decade-by-decade analyses
Previous studies on age-related changes in cortical and hippocampal morphology were not designed or able to reveal the complex spatial patterns of...
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A supervised learning method for classifying methylation disorders
BackgroundDNA methylation is one of the most stable and well-characterized epigenetic alterations in humans. Accordingly, it has already found...
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Adaptive phenotypic plasticity of mandibles with respect to host plants
Polyphagous butterflies, i.e., those that feed on multiple host plants, need to evolve adaptations against the defenses of many plants. Studies have...
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Growth charts for small sample sizes using unsupervised clustering: Application to canine early growth
Breed-specific growth curves (GCs) are needed for neonatal puppies, but breed-specific data may be insufficient. We investigated an unsupervised...
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Meta-analysis of 16S rRNA microbial data identified alterations of the gut microbiota in COVID-19 patients during the acute and recovery phases
BackgroundDozens of studies have demonstrated gut dysbiosis in COVID-19 patients during the acute and recovery phases. However, a consensus on the...
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Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios
BackgroundSingle-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life...
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Abiotic factors predict taxonomic composition and genetic admixture in populations of hybridizing white oak species (Quercus sect. Quercus) on regional scale
Knowing which drivers affect the spatial distribution of hybridizing species and their admixed individuals on local or regional scale can leverage...
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Pollen dispersal distance is determined by phenology and ancillary traits but not floral gender in an andromonoecious, fly-pollinated alpine herb
Pollen-mediated gene flow and spatial genetic structure have rarely been studied in alpine plants that are pollinated by dipteran insects. In...
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Zero-Inflated Beta Models for Microbiome Data
This chapter introduces two specifically designed zero-inflated beta regression models for analyzing zero-inflated count microbiome data. First, it...
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Is the amount of parenchyma in storage organs a good predictor of non-structural carbohydrate storage in herbs?
Background and AimsNon-structural carbohydrates (NSC) are stored in plants for osmoregulation or resprouting after seasonal rest or damage. In trees,...
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The composition of lung microbiome in lung cancer: a systematic review and meta-analysis
BackgroundAlthough recent studies have indicated that imbalance in the respiratory microbiome composition is linked to several chronic respiratory...
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Mixture density networks for the indirect estimation of reference intervals
BackgroundReference intervals represent the expected range of physiological test results in a healthy population and are essential to support medical...
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Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease
BackgroundX-chromosome inactivation (XCI) is an epigenetic process that occurs during early development in mammalian females by randomly silencing...
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Agaricus subrufescens fermented rye affects the development of intestinal microbiota, local intestinal and innate immunity in suckling-to-nursery pigs
BackgroundAgaricus subrufescens is considered as one of the most important culinary-medicinal mushrooms around the world. It has been widely...
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Characterization of the genetic architecture of infant and early childhood body mass index
Early childhood obesity is a growing global concern; however, the role of common genetic variation on infant and child weight development is unclear....
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scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental...
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Oral iron supplementation after antibiotic exposure induces a deleterious recovery of the gut microbiota
BackgroundOral iron supplementation is commonly prescribed for anemia and may play an important role in the gut microbiota recovery of anemic...
