Search results for "Corrigendum"
showing 10 items of 34 documents
Drosophila Evolution over Space and Time (DEST) : A New Population Genomics Resource
2021
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a…
A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning
2020
ABSTRACT Background Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. F…
Identification of a new locus and validation of previously reported loci showing differential methylation associated with smoking. The REGICOR study.
2015
Smoking increases the risk of many diseases and could act through changes in DNA methylation patterns. The aims of this study were to determine the association between smoking and DNA methylation throughout the genome at cytosine-phosphate-guanine (CpG) site level and genomic regions. A discovery cross-sectional epigenome-wide association study nested in the follow-up of the REGICOR cohort was designed and included 645 individuals. Blood DNA methylation was assessed using the Illumina HumanMethylation450 BeadChip. Smoking status was self-reported using a standardized questionnaire. We identified 66 differentially methylated CpG sites associated with smoking, located in 38 genes. In most of …
Comparative protein profiling of B16 mouse melanoma cells susceptible and non-susceptible to alphavirus infection: Effect of the tumor microenvironme…
2016
Alphavirus vectors are promising tools for cancer treatment. However, relevant entry mechanisms and interactions with host cells are still not clearly understood. The first step toward a more effective therapy is the identification of novel intracellular alterations that could be associated with cancer aggressiveness and could affect the therapeutic potential of these vectors. In this study, we observed that alphaviruses efficiently infected B16 mouse melanoma tumors/tumor cells in vivo, whereas their transduction efficiency in B16 cells under in vitro conditions was blocked. Therefore, we further aimed to understand the mechanisms pertaining to the differential transduction efficacy of alp…
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures
2017
RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ∼5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method over the entire Protein Data Bank, with data quality is guaranteed by a…
gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms
2020
The study of bacterial symbioses has grown exponentially in the recent past. However, existing bioinformatic workflows of microbiome data analysis do commonly not integrate multiple meta-omics levels and are mainly geared toward human microbiomes. Microbiota are better understood when analyzed in their biological context; that is together with their host or environment. Nevertheless, this is a limitation when studying non-model organisms mainly due to the lack of well-annotated sequence references. Here, we present gNOMO, a bioinformatic pipeline that is specifically designed to process and analyze non-model organism samples of up to three meta-omics levels: metagenomics, metatranscriptomic…
The Perception of Psychosocial Risks and Work-Related Stress in Relation to Job Insecurity and Gender Differences: A Cross-Sectional Study
2018
Introduction. The perception of psychosocial risks exposes workers to develop work-related stress. Recently the attention of scientific research has focused on a psychosocial risk already identified as “job insecurity” that regards the “overall concern about the continued existence of the job in the future” and that also depends on worker’s perception, different for each gender. Aim of the Study. The aim of this cross sectional study is to show if job insecurity, in the form of temporary contracts, can influence the perception of psychosocial risks and therefore increase worker’s vulnerability to work-related stress and how the magnitude of this effect differs between genders. Materials and…
Corrigendum to “Short-term changes in light distortion in orthokeratology subjects"
2015
Artigo completo publicado na revista "BioMed Research International, (2015), 1-7" e disponível no RepositóriUM em: http://hdl.handle.net/1822/33375
Comparison of physical activity levels in Spanish adults with chronic conditions before and during COVID-19 quarantine
2020
Abstract Background This is the first study analyzing levels of physical activity in a sample of quarantined adults with chronic conditions. The aim of this study was to compare moderate- and vigorous-intensity physical activity levels in Spanish adults with chronic conditions before and during coronavirus disease 2019 (COVID-19) quarantine. Methods A cross-sectional online survey was administered during the COVID-19 quarantine in Spain. A total of 163 participants with chronic conditions (113 females and 47 males; age range 18–64 years) completed the survey. A total of 26 chronic conditions were included. Participants self-reported average minutes/day of moderate and vigorous physical acti…
Localization of Brain Networks Engaged by the Sustained Attention to Response Task Provides Quantitative Markers of Executive Impairment in Amyotroph…
2020
Abstract Objective: To identify cortical regions engaged during the sustained attention to response task (SART) and characterize changes in their activity associated with the neurodegenerative condition amyotrophic lateral sclerosis (ALS). Methods: High-density electroencephalography (EEG) was recorded from 33 controls and 23 ALS patients during a SART paradigm. Differences in associated event-related potential peaks were measured for Go and NoGo trials. Sources active during these peaks were localized, and ALS-associated differences were quantified. Results: Go and NoGo N2 and P3 peak sources were localized to the left primary motor cortex, bilateral dorsolateral prefrontal cortex (DLPFC),…