Vitamin D-related polymorphisms and vitamin D levels as risk biomarkers of COVID-19 disease severity.

Vitamin D is a fundamental regulator of host defences by activating genes related to innate and adaptive immunity. Previous research shows a correlation between the levels of vitamin D in patients infected with SARS-CoV-2 and the degree of disease severity. This work investigates the impact of the genetic background related to vitamin D pathways on COVID-19 severity.

Short-term intradialytic NMES targeting muscles of the legs improves the phase angle: A pilot randomized clinical trial.

Purpose: Neuromuscular electrical stimulation (NMES) elicits muscle contraction and has been shown to attenuate muscle atrophy when physical activity is not possible. Thus, we hypothesized that intradialytic NMES would attenuate the loss leg lean mass and improve the phase angle in patients undergoing hemodialysis (HD).

Methods: A randomized controlled trial was performed with twenty-one adult HD patients (n = 8 F, n = 13 M; 45.

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.

Background: Shotgun metagenomes contain a sample of all the genomic material in an environment, allowing for the characterization of a microbial community. In order to understand these communities, bioinformatics methods are crucial. A common first step in processing metagenomes is to compute abundance estimates of different taxonomic or functional groups from the raw sequencing data.

Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation.

Drill cuttings leave behind thousands of tons of residues without adequate treatment, generating a large environmental liability. Therefore knowledge about the microbial community of drilling residue may be useful for developing bioremediation strategies. In this work, samples of drilling residue were enriched in different culture media in the presence of petroleum, aiming to select potentially oil-degrading bacteria and biosurfactant producers.

Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near-equatorial biomes have higher abundance of genes with potential for bioremediation.

Background: Bacterial and Archaeal communities have a complex, symbiotic role in crude oil bioremediation. Their biosurfactants and degradation enzymes have been in the spotlight, mainly due to the awareness of ecosystem pollution caused by crude oil accidents and their use. Initially, the scientific community studied the role of individual microbial species by characterizing and optimizing their biosurfactant and oil degradation genes, studying their individual distribution.

Is energy intake underreported in hemodialysis patients?

Introduction: Underreporting of energy intake is not much studied in hemodialysis population.

Objective: To evaluate the underreporting of energy intake and associated factors in hemodialysis patients.

Methods: A cross-sectional study, with 344 patients stable adults, of ten hemodialysis centers in Goiânia-GO.

Nutritional status and interdialytic weight gain of chronic hemodialysis patients.

Introduction: The nutritional status (NS) of patients on hemodialysis (HD) is a major concern and challenge. Malnutrition is common in these patients and is related to poorer clinical outcomes.

Objectives: To assess the association between the NS and the interdialytic weight gain (IDWG) of patients with chronic kidney disease (CKD) on HD.

BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies.

Crude oil extraction, transportation and use provoke the contamination of countless ecosystems. Therefore, bioremediation through surfactants mobilization or biodegradation is an important subject, both economically and environmentally. Bioremediation research had a great boost with the recent advances in Metagenomics, as it enabled the sequencing of uncultured microorganisms providing new insights on surfactant-producing and/or oil-degrading bacteria.

Significant Differences Characterise the Correlation Coefficients between Biocide and Antibiotic Susceptibility Profiles in Staphylococcus aureus.

There is a growing concern by regulatory authorities for the selection of antibiotic resistance caused by the use of biocidal products. We aimed to complete the detailed information on large surveys by investigating the relationship between biocide and antibiotic susceptibility profiles of a large number of Staphylococcus aureus isolates using four biocides and antibiotics commonly used in clinical practice. The minimal inhibitory concentration (MIC) for most clinically-relevant antibiotics was determined according to the standardized methodology for over 1600 clinical S.

Nutritional assessment and hand grip strength of candidates for surgery of the gastrointestinal tract.

Background: The assessment of nutritional status in clinical practice must be done with simple, reliable, low cost and easy performance methods. The power of handshake is recognized as a useful tool to evaluate muscle strength, and therefore, it is suggested that can detect malnutrition.

Aim: To evaluate the nutritional status by subjective global assessment and power of handshake preoperatively in patients going to gastrointestinal surgeries and to compare the diagnosis obtained by subjective global assessment with traditional anthropometric methods and power of handshake.

Prevalence and associated factors with abdominal obesity in hemodialysis patients in Goiânia--GO.

Introduction: The presence of excess weight, especially visceral obesity contributes to the increased risk of metabolic and cardiovascular complications in patients with chronic kidney disease.

Objective: To determine the prevalence and associated factors with abdominal obesity in patients on hemodialysis (HD).

Methods: Cross-sectional study with 344 patients older than 18 years.

slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array.

Motivation: Maximal exact matches, or just MEMs, are a powerful tool in the context of multiple sequence alignment and approximate string matching. The most efficient algorithms to collect them are based on compressed indexes that rely on longest common prefix array-centered data structures. However, their space-efficient representations make use of encoding techniques that are expensive from a computational point of view.

The semantic web in translational medicine: current applications and future directions.

Semantic web technologies offer an approach to data integration and sharing, even for resources developed independently or broadly distributed across the web. This approach is particularly suitable for scientific domains that profit from large amounts of data that reside in the public domain and that have to be exploited in combination. Translational medicine is such a domain, which in addition has to integrate private data from the clinical domain with proprietary data from the pharmaceutical domain.

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae.

The YEASTRACT (http://www.yeastract.com) information system is a tool for the analysis and prediction of transcription regulatory associations in Saccharomyces cerevisiae.

Enrichment analysis applied to disease prognosis.

: Enrichment analysis is well established in the field of transcriptomics, where it is used to identify relevant biological features that characterize a set of genes obtained in an experiment.This article proposes the application of enrichment analysis as a first step in a disease prognosis methodology, in particular of diseases with a strong genetic component. With this analysis the objective is to identify clinical and biological features that characterize groups of patients with a common disease, and that can be used to distinguish between groups of patients associated with disease-related events.

Evaluation of reduced susceptibility to quaternary ammonium compounds and bisbiguanides in clinical isolates and laboratory-generated mutants of Staphylococcus aureus.

The MICs and minimum bactericidal concentrations (MBCs) for the biocides benzalkonium chloride and chlorhexidine were determined against 1,602 clinical isolates of Staphylococcus aureus. Both compounds showed unimodal MIC and MBC distributions (2 and 4 or 8 mg/liter, respectively) with no apparent subpopulation with reduced susceptibility. To investigate further, all isolates were screened for qac genes, and 39 of these also had the promoter region of the NorA multidrug-resistant (MDR) efflux pump sequenced.

The use of machine learning methodologies to analyse antibiotic and biocide susceptibility in Staphylococcus aureus.

Background: The rise of antibiotic resistance in pathogenic bacteria is a significant problem for the treatment of infectious diseases. Resistance is usually selected by the antibiotic itself; however, biocides might also co-select for resistance to antibiotics. Although resistance to biocides is poorly defined, different in vitro studies have shown that mutants presenting low susceptibility to biocides also have reduced susceptibility to antibiotics.

Empirical assessment of sequencing errors for high throughput pyrosequencing data.

Background: Sequencing-by-synthesis technologies significantly improve over the Sanger method in terms of speed and cost per base. However, they still usually fail to compete in terms of read length and quality. Current high-throughput implementations of the pyrosequencing technique yield reads whose length approach those of the capillary electrophoresis method.

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.

Motivation: The computational search for novel microRNA (miRNA) precursors often involves some sort of structural analysis with the aim of identifying which type of structures are prone to being recognized and processed by the cellular miRNA-maturation machinery. A natural way to tackle this problem is to perform clustering over the candidate structures along with known miRNA precursor structures. Mixed clusters allow then the identification of candidates that are similar to known precursors.

A novel resistance mechanism to triclosan that suggests horizontal gene transfer and demonstrates a potential selective pressure for reduced biocide susceptibility in clinical strains of Staphylococcus aureus.

The widely used biocide triclosan selectively targets FabI, the NADH-dependent trans-2-enoyl-acyl carrier protein reductase, which is an important target for narrow-spectrum antimicrobial drug development. In relation to the growing concern about biocide resistance, we compared in vitro mutants and clinical isolates of Staphylococcus aureus with reduced triclosan susceptibility. Clinical isolates of S.

Quantitative modeling of the Saccharomyces cerevisiae FLR1 regulatory network using an S-system formalism.

In this study we address the problem of finding a quantitative mathematical model for the genetic network regulating the stress response of the yeast Saccharomyces cerevisiae to the agricultural fungicide mancozeb. An S-system formalism was used to model the interactions of a five-gene network encoding four transcription factors (Yap1, Yrr1, Rpn4 and Pdr3) regulating the transcriptional activation of the FLR1 gene. Parameter estimation was accomplished by decoupling the resulting system of nonlinear ordinary differential equations into a larger nonlinear algebraic system, and using the Levenberg-Marquardt algorithm to fit the models predictions to experimental data.

Efficient alignment of pyrosequencing reads for re-sequencing applications.

Background: Over the past few years, new massively parallel DNA sequencing technologies have emerged. These platforms generate massive amounts of data per run, greatly reducing the cost of DNA sequencing. However, these techniques also raise important computational difficulties mostly due to the huge volume of data produced, but also because of some of their specific characteristics such as read length and sequencing errors.

Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries.

Background: Eucalyptus species are among the most planted hardwoods in the world because of their rapid growth, adaptability and valuable wood properties. The development and integration of genomic resources into breeding practice will be increasingly important in the decades to come. Bacterial artificial chromosome (BAC) libraries are key genomic tools that enable positional cloning of important traits, synteny evaluation, and the development of genome framework physical maps for genetic linkage and genome sequencing.

YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface.

The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT) information system (http://www.yeastract.com) was developed to support the analysis of transcription regulatory associations in Saccharomyces cerevisiae.