Search results for "MULT"

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning

2020

Genome-wide association studies (GWAS) identify genetic variants associated with traits or diseases. GWAS never directly link variants to regulatory mechanisms. Instead, the functional annotation of variants is typically inferred by post hoc analyses. A specific class of deep learning-based methods allows for the prediction of regulatory effects per variant on several cell type-specific chromatin features. We here describe “DeepWAS”, a new approach that integrates these regulatory effect predictions of single variants into a multivariate GWAS setting. Thereby, single variants associated with a trait or disease are directly coupled to their impact on a chromatin feature in a cell type. Up to…

Identifying Prognostic SNPs in Clinical Cohorts: Complementing Univariate Analyses by Resampling and Multivariable Modeling

2016

Clinical cohorts with time-to-event endpoints are increasingly characterized by measurements of a number of single nucleotide polymorphisms that is by a magnitude larger than the number of measurements typically considered at the gene level. At the same time, the size of clinical cohorts often is still limited, calling for novel analysis strategies for identifying potentially prognostic SNPs that can help to better characterize disease processes. We propose such a strategy, drawing on univariate testing ideas from epidemiological case-controls studies on the one hand, and multivariable regression techniques as developed for gene expression data on the other hand. In particular, we focus on …

2020

Background Small sample sizes combined with multiple correlated endpoints pose a major challenge in the statistical analysis of preclinical neurotrauma studies. The standard approach of applying univariate tests on individual response variables has the advantage of simplicity of interpretation, but it fails to account for the covariance/correlation in the data. In contrast, multivariate statistical techniques might more adequately capture the multi-dimensional pathophysiological pattern of neurotrauma and therefore provide increased sensitivity to detect treatment effects. Results We systematically evaluated the performance of univariate ANOVA, Welch’s ANOVA and linear mixed effects models …

Lipid levels, atrial fibrillation and the impact of age:Results from the LIPIDOGRAM2015 study

2020

Background and aims: An inverse relationship between lipid levels and atrial fibrillation (AF) has been suggested, but whether the association is upheld for all age groups remains unclear. The aim of the study was to examine associations between lipid levels and AF by age groups in a nationwide study in Poland. Methods: Multivariate Poisson regression models were used to estimate prevalence ratios (PRs) for AF by lipid levels. Low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), triglycerides (TG), total cholesterol (TC), non-HDL-C and LDL-C/HDL-C ratios were grouped into quartiles. Results: Of the 13,724 participants, 5.2% (n = 708) had AF. People with…

Simple Muscle Architecture Analysis (SMA): An ImageJ macro tool to automate measurements in B-mode ultrasound scans

2020

In vivo measurements of muscle architecture (i.e. the spatial arrangement of muscle fascicles) are routinely included in research and clinical settings to monitor muscle structure, function and plasticity. However, in most cases such measurements are performed manually, and more reliable and time-efficient automated methods are either lacking completely, or are inaccessible to those without expertise in image analysis. In this work, we propose an ImageJ script to automate the entire analysis process of muscle architecture in ultrasound images: Simple Muscle Architecture Analysis (SMA). Images are filtered in the spatial and frequency domains with built-in commands and external plugins to hi…

Influence of middle-distance running on muscular micro RNAs

2018

A specific subset of micro RNAs (miRs), including miR-133 and miR-206, is specifically expressed in muscle tissue, so that they are currently defined as muscular miRs (myomiRs). To further elucidate the role of myomiRs in muscle biology, we measured miR-133a and miR-206 in plasma of 28 middle-age recreational athletes. The study population consisted of 28 middle aged, recreation athletes (11 women and 17 men; mean age, 46 years) who completed a 21.1 km, half-marathon. The plasma concentration of miR-133a and miR-206, the serum concentration of creatine kinase (CK) and high-sensitivity (HS) cardiac troponin T (cTnT), as well as capillary lactate, were measured before and immediately after th…

The shared frameshift mutation landscape of microsatellite-unstable cancers suggests immunoediting during tumor evolution

2020

The immune system can recognize and attack cancer cells, especially those with a high load of mutation-induced neoantigens. Such neoantigens are abundant in DNA mismatch repair (MMR)-deficient, microsatellite-unstable (MSI) cancers. MMR deficiency leads to insertion/deletion (indel) mutations at coding microsatellites (cMS) and to neoantigen-inducing translational frameshifts. Here, we develop a tool to quantify frameshift mutations in MSI colorectal and endometrial cancer. Our results show that frameshift mutation frequency is negatively correlated to the predicted immunogenicity of the resulting peptides, suggesting counterselection of cell clones with highly immunogenic frameshift peptid…

2018

Evoked potentials (EPs) are well established in clinical practice for diagnosis and prognosis in multiple sclerosis (MS). However, their value is limited to the assessment of their respective functional systems. Here, we used transcranial magnetic stimulation (TMS) coupled with electroencephalography (TMS-EEG) to investigate cortical excitability and spatiotemporal dynamics of TMS-evoked neural activity in MS patients. Thirteen patients with early relapsing-remitting MS (RRMS) with a median Expanded Disability Status Scale (EDSS) of 1.0 (range 0-2.5) and 16 age- and gender-matched healthy controls received single-pulse TMS of left and right primary motor cortex (L-M1 and R-M1), respectively…

Evaluation of permeability applicability based on continuum mechanics law in fluid flow through graphene membrane

2019

AbstractGraphene is expected to be used in separation applications such as desalination. However, it is difficult to predict the flow phenomena at the nanoscale using the conventional continuum law. Particularly at a Knudsen number (Kn) of >0.1, which is applied in filtration, it has been reported that not even slip boundary conditions can be applied. In this study, to identify the parameters that affect the applicability of the continuum law, we conducted a fluid permeation simulation using graphene. The deviation of the permeability from that of the continuum model was calculated by changing the channel width, fluid temperature, and fluid type. The result showed that the channel width …

Effect of graphene substrate type on formation of Bi2Se3 nanoplates

2019

AbstractKnowledge of nucleation and further growth of Bi2Se3 nanoplates on different substrates is crucial for obtaining ultrathin nanostructures and films of this material by physical vapour deposition technique. In this work, Bi2Se3 nanoplates were deposited under the same experimental conditions on different types of graphene substrates (as-transferred and post-annealed chemical vapour deposition grown monolayer graphene, monolayer graphene grown on silicon carbide substrate). Dimensions of the nanoplates deposited on graphene substrates were compared with the dimensions of the nanoplates deposited on mechanically exfoliated mica and highly ordered pyrolytic graphite flakes used as refer…