Search results for "Data"
showing 10 items of 12992 documents
SWhybrid: A Hybrid-Parallel Framework for Large-Scale Protein Sequence Database Search
2017
Computer architectures continue to develop rapidly towards massively parallel and heterogeneous systems. Thus, easily extensible yet highly efficient parallelization approaches for a variety of platforms are urgently needed. In this paper, we present SWhybrid, a hybrid computing framework for large-scale biological sequence database search on heterogeneous computing environments with multi-core or many-core processing units (PUs) based on the Smith- Waterman (SW) algorithm. To incorporate a diverse set of PUs such as combinations of CPUs, GPUs and Xeon Phis, we abstract them as SIMD vector execution units with different number of lanes. We propose a machine model, associated with a unified …
Human-based evidence for the therapeutic potential of arginase inhibitors in cardiovascular diseases
2020
Arginase is a ubiquitous enzyme that regulates polyamine- and nitric-oxide-requiring vascular functions. It is well-established that, in mammals, arginase overactivation contributes to endothelial dysfunction, a hallmark of cardiovascular diseases. The pharmacological potential of arginase inhibition for improving vascular function is largely supported by a wide range of data from animal studies. However, caution is required before extrapolating animal data to humans because interspecies differences in arginase expression and localization have been observed. For this reason, this review presents the existing arguments from human data in favor of a role of arginase in cardiovascular diseases…
Functional comparison of bacteria from the human gut and closely related non-gut bacteria reveals the importance of conjugation and a paucity of moti…
2016
International audience; The human GI tract is a complex and still poorly understood environment, inhabited by one of the densest microbial communities on earth. The gut microbiota is shaped by millennia of evolution to co-exist with the host in commensal or symbiotic relationships. Members of the gut microbiota perform specific molecular functions important in the human gut environment. This can be illustrated by the presence of a highly expanded repertoire of proteins involved in carbohydrate metabolism, in phase with the large diversity of polysaccharides originating from the diet or from the host itself that can be encountered in this environment. In order to identify other bacterial fun…
An Integrative Framework for the Construction of Big Functional Networks
2018
We present a methodology for biological data integration, aiming at building and analysing large functional networks which model complex genotype-phenotype associations. A functional network is a graph where nodes represent cellular components (e.g., genes, proteins, mRNA, etc.) and edges represent associations among such molecules. Different types of components may cohesist in the same network, and associations may be related to physical[biochemical interactions or functional/phenotipic relationships. Due to both the large amount of involved information and the computational complexity typical of the problems in this domain, the proposed framework is based on big data technologies (Spark a…
Effect of processing on the bioaccessibility of bioactive compounds – A review focusing on carotenoids, minerals, ascorbic acid, tocopherols and poly…
2018
Health benefits of bioactive compounds depend not only on the intake levels but also on their bioavailability (BAv). In vitro methods to simulate gastro-intestinal digestion allow to determine the bioaccessibility (BAcs) of these compounds, as a first step of BAv, and can be used to evaluate the effect of processing on them to design functional foods with increased health-promoting effects. The impact of traditional processing technologies such as thermal treatment and novel emerging non-thermal technologies such as high pressure processing, high-intensity pulsed electric fields and ultrasound on BAcs of bioactive compounds as carotenoids, minerals, ascorbic acid, tocopherols, polyphenols a…
Revealing the relationship between vegetable oil composition and oxidative stability: A multifactorial approach
2018
Abstract A detailed composition analysis was performed for 22 diverse oils and fats and included determination of tocopherols (α, γ and δ), β-carotene, chlorophyll, total phenolic compounds (TPC) and fatty acid (FA) composition, as well as the determination of their oxidative stability (Rancimat test). Principal components analysis was applied to obtain an overview of the sample variations and to identify behavioural patterns. Linear regression correlations and a multiple linear regression model were performed to quantify the relationship between the composition of oils and fats and their oxidative stability. The TPC and saturated FA were the main individual factors that correlated positive…
The still under-investigated role of cognitive deficits in PML diagnosis
2017
Background: Despite cognitive deficits frequently represent the first clinical manifestations of Progressive Multifocal Leukoencephalopathy (PML) in Natalizumab-treated MS patients, the importance of cognitive deficits in PML diagnosis is still under-investigated. The aim of the current study is to investigate the cognitive deficits at PML diagnosis in a group of Italian patients with PML. Methods: Thirty-four PML patients were included in the study. The demographic and clinical data, the lesion load and localization, and the longitudinal clinical course was compared between patients with (n = 13) and without (n = 15) cognitive deficit upon PML suspicion (the remaining six patients were asy…
SNPs in bone-related miRNAs are associated with the osteoporotic phenotype
2017
AbstractBiogenesis and function of microRNAs can be influenced by genetic variants in the pri-miRNA sequences leading to phenotypic variability. This study aims to identify single nucleotide polymorphisms (SNPs) affecting the expression levels of bone-related mature microRNAs and thus, triggering an osteoporotic phenotype. An association analysis of SNPs located in pri-miRNA sequences with bone mineral density (BMD) was performed in the OSTEOMED2 cohort (n = 2183). Functional studies were performed for assessing the role of BMD-associated miRNAs in bone cells. Two SNPs, rs6430498 in the miR-3679 and rs12512664 in the miR-4274, were significantly associated with femoral neck BMD. Further, we…
FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.
2021
International audience; Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever- increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among d…
Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive err…
2020
Corneal curvature, a highly heritable trait, is a key clinical endophenotype for myopia - a major cause of visual impairment and blindness in the world. Here we present a trans-ethnic meta-analysis of corneal curvature GWAS in 44,042 individuals of Caucasian and Asian with replication in 88,218 UK Biobank data. We identified 47 loci (of which 26 are novel), with population-specific signals as well as shared signals across ethnicities. Some identified variants showed precise scaling in corneal curvature and eye elongation (i.e. axial length) to maintain eyes in emmetropia (i.e. HDAC11/FBLN2 rs2630445, RBP3 rs11204213); others exhibited association with myopia with little pleiotropic effects …