PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies

Next-generation sequencing (NGS) technologies are making sequence data available on an unprecedented scale. In this context, new catalogs of Single Nucleotide Polymorphism and mutations generated by resequencing studies are usually stored in genome position files (e.g. Variant Call Format, SAMTools pileup, BED, GFF) comprising of large lists of genomic positions, which are difficult to handle by researchers. Here, we present PileLineGUI, a novel desktop application primarily designed for manipulating, browsing and analysing genome position files (GPF), with specific support to somatic mutation finding studies. The developed tool also integrates a new genome browser module specially designed for inspecting GPFs. PileLineGUI is free, multiplatform and designed to be intuitively used by biomedical researchers. PileLineGUI is available at: http://sing.ei.uvigo.es/pileline/pilelinegui.html

WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis

WhichGenes is a web-based interactive gene set building tool offering a very simple interface to extract always-updated gene lists from multiple databases and unstructured biological data sources. While the user can specify new gene sets of interest by following a simple four-step wizard, the tool is able to run several queries in parallel. Every time a new set is generated, it is automatically added to the private gene-set cart and the user is notified by an e-mail containing a direct link to the new set stored in the server. WhichGenes provides functionalities to edit, delete and rename existing sets as well as the capability of generating new ones by combining previous existing sets (intersection, union and difference operators). The user can export his sets configuring the output format and selecting among multiple gene identifiers. In addition to the user-friendly environment, WhichGenes allows programmers to access its functionalities in a programmatic way through a Representational State Transfer web service. WhichGenes front-end is freely available at http://www.whichgenes.org/, WhichGenes API is accessible at http://www.whichgenes.org/api/

A Brief Review on the Regulatory Roles of MicroRNAs in Cystic Diseases and Their Use as Potential Biomarkers

miRNAs are small endogenous conserved non-coding RNA molecules that regulate post-transcriptional gene expression through mRNA degradation or translational inhibition, modulating nearly 60% of human genes. Cystic diseases are characterized by the presence of abnormal fluid-filled sacs in the body, and though most cysts are benign, they can grow inside tumors and turn malignant. Recent evidence has revealed that the aberrant expression of a number of miRNAs present in extracellular fluids, including plasma or serum, urine, saliva, follicular fluid, and semen, contribute to different cystic pathologies. This review aims to describe the role of different miRNAs in three worldwide relevant cystic diseases: polycystic ovarian syndrome (PCOS), polycystic kidney disease (PKD), and pancreatic cyst tumors (PCTs), as well as their potential use as novel biomarkers.publishedVersio

Endometrial area of the blood flow as a marker of endometritis in equine

In this study, uterine blood flow area (BFA) has been evaluated for the first time using power Doppler ultrasound (PD) as a marker of endometritis in mares and jennies. The uterine BFA in healthy mares was greater in oestrus than in diestrus (p <.001). However, differences in endometrial blood flow between oestrus and diestrus were not observed in mares with endometritis. The uterine blood flow in healthy jennies is not affected by the oestrus cycle. Both species showed an increase in endometrial BFA in pathological uterine conditions compared to controls. BFA was a good marker of endometritis with an area under curve (AUC) (estrus:0.94 (p <.001) diestrus:0.98 (p <.001) in mares and AUC (0.91 (p <.0001) in jennies. The results of this preliminary study suggest that PD ultrasound in combination with computerized image analysis has the potential to be a very useful tool in the diagnosis of endometritis

Increased Serum Levels of sCD14 and sCD163 Indicate a Preponderant Role for Monocytes in COVID-19 Immunopathology

Background: Emerging evidence indicates a potential role for monocytes in COVID-19 immunopathology. We investigated two soluble markers of monocyte activation, sCD14 and sCD163, in COVID-19 patients, with the aim of characterizing their potential role in monocyte-macrophage disease immunopathology. To the best of our knowledge, this is the first study of its kind. Methods: Fifty-nine SARS-Cov-2 positive hospitalized patients, classified according to ICU or non-ICU admission requirement, were prospectively recruited and analyzed by ELISA for levels of sCD14 and sCD163, along with other laboratory parameters, and compared to a healthy control group. Results: sCD14 and sCD163 levels were significantly higher among COVID-19 patients, independently of ICU admission requirement, compared to the control group. We found a significant correlation between sCD14 levels and other inflammatory markers, particularly Interleukin-6, in the non-ICU patients group. sCD163 showed a moderate positive correlation with the time lapsed from admission to sampling, independently of severity group. Treatment with corticoids showed an interference with sCD14 levels, whereas hydroxychloroquine and tocilizumab did not. Conclusions: Monocyte-macrophage activation markers are increased and correlate with other inflammatory markers in SARS-Cov-2 infection, in association to hospital admission. These data suggest a preponderant role for monocyte-macrophage activation in the development of immunopathology of COVID-19 patients

BLISS: an artificial language for learnability studies

To explore neurocognitive mechanisms underlying the human language faculty, cognitive scientists use artificial languages to control more precisely the language learning environment and to study selected aspects of natural languages. Artificial languages applied in cognitive studies are usually designed ad hoc, to only probe a specific hypothesis, and they include a miniature grammar and a very small vocabulary. The aim of the present study is the construction of an artificial language incorporating both syntax and semantics, BLISS. Of intermediate complexity, BLISS mimics natural languages by having a vocabulary, syntax, and some semantics, as defined by a degree of non-syntactic statistical dependence between words. We quantify, using information theoretical measures, dependencies between words in BLISS sentences as well as differences between the distinct models we introduce for semantics. While modeling English syntax in its basic version, BLISS can be easily varied in its internal parametric structure, thus allowing studies of the relative learnability of different parameter sets

Premissas para a compreensão da saúde dos trabalhadores no setor serviço

O setor serviço ou terciário responde atualmente por mais de dois terços do PIB nos países desenvolvidos e, no Brasil, emprega cerca de três quartos da população economicamente ativa. Muitos autores consideram que esse fenômeno expressa uma transição da sociedade industrial para a sociedade de serviços. Entretanto, os estudos sobre a saúde do trabalhador, mesmo atentos às mutações tecnológicas e à reestruturação produtiva, não se aprofundam suficientemente no conhecimento das características do setor serviço, persistindo em referências aos processos industriais. O presente ensaio tem por objetivo analisar determinados conceitos sobre os processos de trabalho no setor serviço considerados importantes para compreensão da saúde dos trabalhadores desse setor. Formula-se a hipótese da proximidade entre trabalhador e consumidor como uma das principais características das relações de trabalho desse setor com possibilidades de repercussões específicas nos processos saúde e doença. Sob essa perspectiva de análise são incorporados os conceitos de simultaneidade, co-presença, co-produção, autosserviço e gestão emocional. Conclui-se que essas peculiaridades, além de permitirem uma compreensão mais adequada do processo saúde/doença dos trabalhadores no setor serviço, indicam a necessidade da construção de uma nova interface entre a saúde do trabalhador e as práticas emergentes de proteção à saúde do consumidor.At the present time the service sector is responsible for over two thirds of the GNP in developed countries and, in Brazil, it employs nearly 75% of the economically active population. Many authors view this phenomenon as a manifestation of the transition from industrial society to a service society. Yet, in spite of considering technological changes and the restructuring of production, studies on workers' health do not search far enough for a comprehension of the characteristics of the service sector, basically keeping to references to industrial processes. The present study analyzes specific concepts related to work processes in the service sector, which are considered important for an understanding of workers' health in this sector. This analysis puts forward the hypothesis that worker-consumer physical proximity is one of the main characteristics of work relations in that sector, leading to potential impacts on health and disease processes. From this perspective, the concepts of simultaneousness, co-presence, co-production, self-service and emotional management are incorporated. Such peculiarities, besides allowing a better understanding of workers' health/illness processes in the service sector, point to the need to create a new interface between workers' health and the emerging consumer health protection practices

The Effect of Viticultural Climate on Red and White Wine Typicity - Characterization in Ibero-American grape-growing regions

Aim: This study is part of a CYTED (Ibero-American Program for Science, Technology and Development) project on vitivinicultural zoning. The objective was to characterize the effect of viticultural climate on red and white wine typicity in the macro Ibero-American viticultural region. Methods and results: The climate of 46 grape-growing regions in 6 Ibero-American countries (Argentina, Bolivia, Brazil, Chile, Spain and Portugal) was characterized using the three viticultural climate index of the Geoviticulture MCC System: the Heliothermal index HI, the Cool Night index CI and the Dryness index DI. The main sensory characteristics frequently observed in representative red and white wines of each of these regions were described by enology experts in the respective countries: intensity of colour, aroma, aroma-ripe fruit, body-palate concentration, alcohol, tannins (for red wines) and acidity as well as persistence on the palate. The data were submitted to a correlation analysis of the variables and Principal Component Analysis (PCA). Conclusion: The typicity of red and white wines was correlated with the HI, CI and DI viticultural climate indexes from the MCC System. The main wine sensory variables affected by viticultural climate were identified. Significance and impact of the study : The results can be used to project the potential impacts of climate change on wine sensory characteristics

Comparative analysis of distinct phenotypes in gambling disorder based on gambling preferences

Background: Studies examining gambling preferences have identified the importance of the type of gambling practiced on distinct individual profiles. The objectives were to compare clinical, psychopathological and personality variables between two different groups of individuals with a gambling disorder (strategic and non-strategic gamblers) and to evaluate the statistical prediction capacity of these preferences with respect to the severity of the disorder. Method: A total sample of 2010 treatment-seeking patients with a gambling disorder participated in this stand-alone study. All were recruited from a single Pathological Gambling Unit in Spain (1709 strategic and 301 non-strategic gamblers). The design of the study was cross-sectional and data were collected at the start of treatment. Data was analysed using logistic regression for binary outcomes and analysis of variance (ANOVA) for quantitative responses. Results: There were significant differences in several socio-demographic and clinical variables, as well as in personality traits (novelty seeking and cooperativeness). Multiple regression analysis showed harm avoidance and self-directedness were the main predictors of gambling severity and psychopathology, while age at assessment and age of onset of gambling behaviour were predictive of gambling severity. Strategic gambling (as opposed to non-strategic) was significantly associated with clinical outcomes, but the effect size of the relationships was small. Conclusions: It is possible to identify distinct phenotypes depending on the preference of gambling. While these phenotypes differ in relation to the severity of the gambling disorder, psychopathology and personality traits, they can be useful from a clinical and therapeutic perspective in enabling risk factors to be identified and prevention programs targeting specific individual profiles to be developed