Search results for " Medical Informatics"
showing 10 items of 335 documents
Modality-specific dysfunctional neural processing of social-abstract and non-social-concrete information in schizophrenia
2021
Highlights • Social/non-social information processing in three modalities was investigated in SZ. • SZ showed reduced activation for social information only in gesture modality. • Reduced activation in SZ was observed for non-social information only in speech. • Neural Neural processing in bimodal condition is not different between patients and controls.
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
2009
Abstract Background ESTs or variable sequence reads can be available in prokaryotic studies well before a complete genome is known. Use cases include (i) transcriptome studies or (ii) single cell sequencing of bacteria. Without suitable software their further analysis and mapping would have to await finalization of the corresponding genome. Results The tool JANE rapidly maps ESTs or variable sequence reads in prokaryotic sequencing and transcriptome efforts to related template genomes. It provides an easy-to-use graphics interface for information retrieval and a toolkit for EST or nucleotide sequence function prediction. Furthermore, we developed for rapid mapping an enhanced sequence align…
Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.
2007
Abstract Background Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric) has gained prominence. It is based on the deep theory of Kolmogorov Complexity and universality is its most novel striking feature. Since it can only be approximated via data compression, USM is a methodology rath…
CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification
2020
Abstract Background Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that nucleosomes are determined by the combined effects of several factors, including DNA sequence organization. Interestingly, the identification of nucleosomes on a genomic scale has been successfully performed by computational methods using DNA sequence as input data. Results In this work, we propose CORENup, a deep learning model for nucleosome identification. CORENup processes a DNA sequence as input using one-hot representation and combines in a parallel fashion a fully convolutional neural network and a recurrent layer. These two parallel …
PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing
2019
Abstract Background The detection of known human papillomaviruses (PVs) from targeted wet-lab approaches has traditionally used PCR-based methods coupled with Sanger sequencing. With the introduction of next-generation sequencing (NGS), these approaches can be revisited to integrate the sequencing power of NGS. Although computational tools have been developed for metagenomic approaches to search for known or novel viruses in NGS data, no appropriate tool is available for the classification and identification of novel viral sequences from data produced by amplicon-based methods. Results We have developed PVAmpliconFinder, a data analysis workflow designed to rapidly identify and classify kno…
pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
2019
AbstractBackgroundPrincipal component analysis (PCA) is frequently useentirely written ind in genomics applications for quality assessment and exploratory analysis in high-dimensional data, such as RNA sequencing (RNA-seq) gene expression assays. Despite the availability of many software packages developed for this purpose, an interactive and comprehensive interface for performing these operations is lacking.ResultsWe developed the pcaExplorer software package to enhance commonly performed analysis steps with an interactive and user-friendly application, which provides state saving as well as the automated creation of reproducible reports. pcaExplorer is implemented in R using the Shiny fra…
Job strain in public transport drivers: Data to assess the relationship between demand-control model indicators, traffic accidents and sanctions
2018
This Data in Brief (DiB) article examines the association between the Job Demand-Control (JDC) model of stress and traffic safety outcomes (accidents and sanctions) in public transport drivers (n = 780). The data was collected using a structured self-administrable questionnaire composed of measurements of work stress (Job Content Questionnaire), and demographics (professional driving experience, hours and days working/driving per week). The data contains 4 parts: descriptive statistics, bivariate correlations between the study variables, analysis of variance (ANOVA) and Post-Hoc comparisons between drivers classified different quadrants of the JDC model. For further information, it is conve…
Telemedicine Follow Up of Chronic Obstructive Pulmonary Disease Integrated into a Patient-Centered Health Care Team-Setting Impacts on Patient Empowe…
2017
Health care services are facing challenges with a growing ageing population prone to chronic conditions and multi-morbidities. Telemedicine applications have the potential to enhance patient’s safety at home by monitoring of chronic diseases, promoting coping and independence. The research project Patients and Professionals in Productive Teams aims to study patient-centered teamwork across organizational borders, supported by technology. This paper describes the research agenda for a study on how telemedicine follow-up impacts on chronic obstructive pulmonary disease patients’ quality of life and possible effects on patient empowerment, in the health region of Southern Norway. The outcome i…
DESIGUALDAD DE GÉNERO EN LA INVESTIGACIÓN MÉDICA ESPAÑOLA: UN CASO PARADIGMÁTICO
2021
Resumen Con el objeto de evaluar la desigualdad de género en la investigación científica médica, se analizan las bases de datos institucionales de investigación de la Universidad de Valencia (2000-2018), de las facultades de ciencias de la salud (Medicina y Odontología, Farmacia, Enfermería y Fisioterapia), considerando sexo, categoría académica, edad y especialidad clínica de los investigadores/as. Los académicos son responsables de un número abrumador de proyectos y contratos de investigación, de importes mucho más elevados que los dirigidos por sus colegas mujeres. El estudio revela también segregación horizontal y una brecha salarial de género significativa, subrayando la necesidad de p…
UVPAR: fast detection of functional shifts in duplicate genes.
2006
Abstract Background The imprint of natural selection on gene sequences is often difficult to detect. A plethora of methods have been devised to detect genetic changes due to selective processes. However, many of those methods depend heavily on underlying assumptions regarding the mode of change of DNA sequences and often require sophisticated mathematical treatments that made them computationally slow. The development of fast and effective methods to detect modifications in the selective constraints of genes is therefore of great interest. Results We describe UVPAR, a program designed to quickly test for changes in the functional constraints of duplicate genes. Starting with alignments of t…