Search results for " data"

Enabling openness of valuable information resources: Curbing data subtractability and exclusion

2019

In this paper we investigate how data openness can be made possible in communal settings. We adopt a utility perspective that foregrounds the use value of data, conceptualizing them as “goods.” On the basis of this conceptualization we explore 2 key goods' attributes: subtractability and exclusion. Our theoretical basis is built upon concepts from the theory of the commons, power theorizing, and notions related to data and information. Empirically, we investigate openness in the genetics domain through a longitudinal study of the evolving communal infrastructure for data related to 2 genes influencing women's susceptibility to breast and ovarian cancer (BRCA1 and BRCA2). We follow the conti…

Next-generation sequencing: big data meets high performance computing

2017

The progress of next-generation sequencing has a major impact on medical and genomic research. This high-throughput technology can now produce billions of short DNA or RNA fragments in excess of a few terabytes of data in a single run. This leads to massive datasets used by a wide range of applications including personalized cancer treatment and precision medicine. In addition to the hugely increased throughput, the cost of using high-throughput technologies has been dramatically decreasing. A low sequencing cost of around US$1000 per genome has now rendered large population-scale projects feasible. However, to make effective use of the produced data, the design of big data algorithms and t…

2019

As rats learn to search for multiple sources of food or water in a complex environment, they generate increasingly efficient trajectories between reward sites. Such spatial navigation capacity involves the replay of hippocampal place-cells during awake states, generating small sequences of spatially related place-cell activity that we call "snippets". These snippets occur primarily during sharp-wave-ripples (SWRs). Here we focus on the role of such replay events, as the animal is learning a traveling salesperson task (TSP) across multiple trials. We hypothesize that snippet replay generates synthetic data that can substantially expand and restructure the experience available and make learni…

Principal components analysis: theory and application to gene expression data analysis

2018

Advances in computational power have enabled research to generate significant amounts of data related to complex biological problems. Consequently, applying appropriate data analysis techniques has become paramount to tackle this complexity. However, theoretical understanding of statistical methods is necessary to ensure that the correct method is used and that sound inferences are made based on the analysis. In this article, we elaborate on the theory behind principal components analysis (PCA), which has become a favoured multivariate statistical tool in the field of omics-data analysis. We discuss the necessary prerequisites and steps to produce statistically valid results and provide gui…

Analysis of Microstructure of the Cardiac Conduction System Based on Three-Dimensional Confocal Microscopy

2016

The specialised conducting tissues present in the ventricles are responsible for the fast distribution of the electrical impulse from the atrio-ventricular node to regions in the subendocardial myocardium. Characterisation of anatomical features of the specialised conducting tissues in the ventricles is highly challenging, in particular its most distal section, which is connected to the working myocardium via Purkinje-myocardial junctions. The goal of this work is to characterise the architecture of the distal section of the Purkinje network by differentiating Purkinje cells from surrounding tissue, performing a segmentation of Purkinje fibres at cellular scale, and mathematically describin…

Allele frequencies distribution of 16 forensic STR loci in a Western Sicilian population sample

2017

Abstract The PowerPlex® ESI 17 Fast and ESX 17 Fast Systems represent faster cycling versions released by Promega® to follow the requirements of ENFSI and EDNAP groups’ for new STR genotyping systems in Europe. Allele frequencies and forensic parameters were estimated in a population sample of 120 unrelated healthy individuals living in Sicily (Western Sicilian population sample) using PowerPlex® ESI 17 Fast and PowerPlex® 17 Fast Systems. Full concordance of the results for both systems was observed. No significant deviation from Hardy-Weinberg equilibrium was detected. The observed heterozygosity changed from 0.85833 for FGA to 0.95 for TH01. The combined power of discrimination for the 1…

Marinomonas spartinae sp. nov., a novel species with plant-beneficial properties.

2016

Two strains of Gram-stain-negative, chemo-organotrophic, aerobic and halophilic gammaproteobacteria, isolated from within the stem and roots of Spartina maritima in salt marshes from the south Atlantic Spanish coast, were found to represent a novel species in the genus Marinomonas through phylogenetic analysis of their 16S rRNA genes and phenotypic characterization. 16S rRNA gene sequences of the two strains shared < 96.2 % similarity with other Marinomonas species, with Marimonas alcarazii being the most similar in sequence. They required sodium ions for growth, were able to thrive at low (4 °C) temperatures and at salinities of 12–15 %, were unable to hydrolyse any tested macromolecule ex…

Reactome pathway analysis: a high-performance in-memory approach

2016

Reactome aims to provide bioinformatics tools for visualisation, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education. Pathway analysis methods have a broad range of applications in physiological and biomedical research; one of the main problems, from the analysis methods performance point of view, is the constantly increasing size of the data samples. Here, we present a new high-performance in-memory implementation of the well-established over-representation analysis method. To achieve the target, the over-representation analysis method is divided in four different steps and, for each of them, specific data st…

Fruit and vegetable consumption and health outcomes: an umbrella review of observational studies

2019

The aim of this study was to provide a comprehensive evaluation of current evidence on fruit and vegetable consumption and health outcomes. A systematic search for quantitative syntheses was performed. Several criteria, including study design, dose-response relationship, heterogeneity and agreement of results over time, and identification of potential confounding factors, were used to assess the level of evidence. The strongest (probable) evidence was found for cardiovascular disease protection; possible evidence for decreased risk of colon cancer, depression and pancreatic diseases was found for fruit intake; and colon and rectal cancer, hip fracture, stroke, depression and pancreatic dise…

Reactome graph database: Efficient access to complex pathway data

2018

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its qu…