NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins

<p>Abstract</p> <p>Background</p> <p>Most predictive methods currently available for the identification of protein secretion mechanisms have focused on classically secreted proteins. In fact, only two methods have been reported for predicting non-classically secreted proteins of Gram-positive bacteria. This study describes the implementation of a sequence-based classifier, denoted as NClassG+, for identifying non-classically secreted Gram-positive bacterial proteins.</p> <p>Results</p> <p>Several feature-based classifiers were trained using different sequence transformation vectors (frequencies, dipeptides, physicochemical factors and PSSM) and Support Vector Machines (SVMs) with Linear, Polynomial and Gaussian kernel functions. Nested <it>k</it>-fold cross-validation (CV) was applied to select the best models, using the inner CV loop to tune the model parameters and the outer CV group to compute the error. The parameters and Kernel functions and the combinations between all possible feature vectors were optimized using grid search.</p> <p>Conclusions</p> <p>The final model was tested against an independent set not previously seen by the model, obtaining better predictive performance compared to SecretomeP V2.0 and SecretPV2.0 for the identification of non-classically secreted proteins. NClassG+ is freely available on the web at <url>http://www.biolisi.unal.edu.co/web-servers/nclassgpositive/</url></p

Successful strategies implemented towards the elimination of canine rabies in the Western Hemisphere

Almost all cases of human rabies result from dog bites, making the elimination of canine rabies a global priority. During recent decades, many countries in the Western Hemisphere have carried out large-scale dog vaccination campaigns, controlled their free-ranging dog populations and enforced legislation for responsible pet ownership. This article reviews progress in eliminating canine rabies from the Western Hemisphere. After briefly summarizing the history of control efforts and describing the approaches listed above, we note that programs in some countries have been hindered by societal attitudes and severe economic disparities, which underlines the need to discuss measures that will be required to complete the elimination of canine rabies throughout the region. We also note that there is a constant threat for dog-maintained epizootics to re-occur, so as long as dog-maintained rabies "hot spots" are still present, free-roaming dog populations remain large, herd immunity becomes low and dog-derived rabies lyssavirus (RABLV) variants continue to circulate in close proximity to rabies-naïve dog populations. The elimination of dog-maintained rabies will be only feasible if both dog-maintained and dog-derived RABLV lineages and variants are permanently eliminated. This may be possible by keeping dog herd immunity above 70% at all times, fostering sustained laboratory-based surveillance through reliable rabies diagnosis and RABLV genetic typing in dogs, domestic animals and wildlife, as well as continuing to educate the population on the risk of rabies transmission, prevention and responsible pet ownership. Complete elimination of canine rabies requires permanent funding, with governments and people committed to make it a reality. An accompanying article reviews the history and epidemiology of canine rabies in the Western Hemisphere, beginning with its introduction during the period of European colonization, and discusses how spillovers of viruses between dogs and various wild carnivores will affect future eradication efforts (Velasco-Villa et al., 2017)

Hyperplasia of alveolar neuroendocrine cells in rat lung carcinogenesis by silica with selective expression of proadrenomedullin-derived peptides and amidating enzymes

Pulmonary neuroendocrine (NE) cells are found as clusters called neuroepithelial bodies (NEBs) or as single cells scattered in the respiratory epithelium. They express a variety of bioactive peptides, and they are thought to be the origin of NE lung tumors. Proadrenomedullin N-terminal 20 peptide (PAMP) is a peptide derived from the same precursor as adrenomedullin (AM). AM and PAMP are C-terminally amidated during their processing by a well-characterized amidating enzyme, peptidylglycine alpha-amidating monooxygenase (PAM). We explored AM, PAMP, and PAM expression as markers for NE hyperplasia in three rodent species (Fischer 344 rats, Syrian golden hamsters, and A/J mice) after a single intratracheal instillation of crystalline silica (quartz), which was previously found to induce different reactions in the three species. Rats developed a marked silicosis, with alveolar and bronchiolar hyperplasia and formation of peripheral lung epithelial tumors. Mice developed a moderate degree of silicosis, but not epithelial hyperplasia or tumors. Hamsters showed dust-storage lesions, but not silicosis or tumors. NE cells were immunolabeled for calcitonin gene-related peptide (CGRP), AM, PAMP, and PAM in serial sections of each lung. The numbers of positive NEBs per lung area and positive cells per NEB were quantified. A marked hyperplastic reaction in the NEBs of silica treated rats occurred only in alveolar NEBs, but not in bronchiolar NEBs. From Month 11 onwards, there were marked differences in the number of alveolar NEBs per section and in the number of cells per alveolar NEB immunoreactive for CGRP. No hyperplastic NE cell reaction was observed in silica-treated mice and hamsters. Significant PAMP and PAM expression was seen only in rat hyperplastic alveolar and in bronchiolar NEBs from Month 11 onwards. In E18, rat fetal lung NEBs were found to be strongly positive for PAMP and PAM

Special fast diffusion with slow asymptotics. Entropy method and flow on a Riemannian manifold

We consider the asymptotic behaviour of positive solutions $u(t,x)$ of the fast diffusion equation $u_t=\Delta (u^{m}/m)={\rm div} (u^{m-1}\nabla u)$ posed for x\in\RR^d, $t>0$, with a precise value for the exponent $m=(d-4)/(d-2)$. The space dimension is $d\ge 3$ so that $m<1$, and even $m=-1$ for $d=3$. This case had been left open in the general study \cite{BBDGV} since it requires quite different functional analytic methods, due in particular to the absence of a spectral gap for the operator generating the linearized evolution. The linearization of this flow is interpreted here as the heat flow of the Laplace-Beltrami operator of a suitable Riemannian Manifold (\RR^d,{\bf g}), with a metric ${\bf g}$ which is conformal to the standard \RR^d metric. Studying the pointwise heat kernel behaviour allows to prove {suitable Gagliardo-Nirenberg} inequalities associated to the generator. Such inequalities in turn allow to study the nonlinear evolution as well, and to determine its asymptotics, which is identical to the one satisfied by the linearization. In terms of the rescaled representation, which is a nonlinear Fokker--Planck equation, the convergence rate turns out to be polynomial in time. This result is in contrast with the known exponential decay of such representation for all other values of $m$.Comment: 37 page

Hydrogen as energy storage for wind energy

Nowadays, problems associated with greenhouse gases emission and fuel ending, makes that renewable energy sources and hydrogen technology have high interest for governments and researchers, and become an option for an environmentaly sustainable world. Renewable energy sources, like solar energy and wind energy, have been used for the last three decades to produce electricity. Researchers and companies have improved the efficiency of this kind of systems, but they have a problem due to energy source temporality that does a fluctuation in systems power output. This fluctuation makes sometimes energy demand is higher than energy produced by the system and vice versa. Hydrogen Technology, actuating as energy storage, may solve this problem. In this paper, a wind-hydrogen installation will be described. Also, its behavior in relation to different electric demand will be analysed

Incidence of Dementia in Elderly Latin Americans: Results of the Maracaibo Aging Study

Introduction—There are few longitudinal studies of dementia in developing countries. We used longitudinal data from the Maracaibo Aging Study (MAS) to accurately determine the age- and sex-specific incidence of dementia in elderly Latin Americans. Methods—The DSM IV-R was used to diagnose dementia, which was classified as Alzheimer’s disease (AD), vascular dementia (VaD), or other. Age- and sex-specific incidence was estimated as the number of new cases of dementia divided by person-years of follow-up (p-y). Results—The incidence of all dementia diagnoses was 9.10 per 1000 p-y (95% CI 7.13–11.44; 8026 total p-y), 5.18 for AD (95% CI 3.72–7.03; 7916 total p-y), and 3.35 for VaD (95% CI 2.19–4.91; 7757 total p-y). Discussion—Among MAS participants under 65 years of age, the incidence of dementia was higher than that of US whites. Among individuals over 65 years of age, the incidence was comparable to the mean of previous incidence estimates for other populations worldwide

Altered expression of adhesion molecules and epithelial-mesenchymal transition in silica-induced rat lung carcinogenesis

Loss of the epithelial phenotype and disruption of adhesion molecules is a hallmark in the epithelial-mesenchymal transition (EMT) reported in several types of cancer. Most of the studies about the relevance of adhesion and junction molecules in lung cancer have been performed using established tumors or in vitro models. The sequential molecular events leading to EMT during lung cancer progression are still not well understood. We have used a rat model for multistep lung carcinogenesis to study the status of adherens and tight junction proteins and mesenchymal markers during EMT. After silica-induced chronic inflammation, rats sequentially develop epithelial hyperplasia, preneoplastic lesions, and tumors such as adenocarcinomas and squamous cell carcinomas. In comparison with normal and hyperplastic bronchiolar epithelium and with hyperplastic alveolar type II cells, the expression levels of E-cadherin, alpha-catenin and beta-catenin were significantly reduced in adenomatoid preneoplastic lesions and in late tumors. The loss of E-cadherin in tumors was associated with its promoter hypermethylation. alpha- and beta-catenin dysregulation lead to cytoplasmic accumulation in some carcinomas. No nuclear beta-catenin localization was found at any stage of any preneoplastic or neoplastic lesion. Zonula occludens protein-1 was markedly decreased in 66% of adenocarcinomas and in 100% squamous cell carcinomas. The mesenchymal-associated proteins N-cadherin and vimentin were analyzed as markers for EMT. N-cadherin was de novo expressed in 32% of adenocarcinomas and 33% of squamous cell carcinomas. Vimentin-positive tumor cells were found in 35% of adenocarcinomas and 88% of squamous cell carcinomas. Mesenchymal markers were absent in precursor lesions, both hyperplastic and adenomatoid. The present results show that silica-induced rat lung carcinogenesis is a good model to study EMT in vivo, and also provide in vivo evidence suggesting that the changes in cell-cell adhesion molecules are an early event in lung carcinogenesis, while EMT occurs at a later stage

Mortality and Advanced Support Requirement for Patients With Cancer With COVID-19 : A Mathematical Dynamic Model for Latin America

PURPOSE: In the midst of a global pandemic, evidence suggests that similar to other severe respiratory viral infections, patients with cancer are at higher risk of becoming infected by COVID-19 and have a poorer prognosis. METHODS: We have modeled the mortality and the intensive care unit (ICU) requirement for the care of patients with cancer infected with COVID-19 in Latin America. A dynamic multistate Markov model was constructed. Transition probabilities were estimated on the basis of published reports for cumulative probability of complications. Basic reproductive number (R0) values were modeled with R using the EpiEstim package. Estimations of days of ICU requirement and absolute mortality were calculated by imputing number of cumulative cases in the Markov model. RESULTS: Estimated median time of ICU requirement was 12.7 days, median time to mortality was 16.3 days after infection, and median time to severe event was 8.1 days. Peak ICU occupancy for patients with cancer was calculated at 16 days after infection. Deterministic sensitivity analysis revealed an interval for mortality between 18.5% and 30.4%. With the actual incidence tendency, Latin America would be expected to lose approximately 111,725 patients with cancer to SARS-CoV-2 (range, 87,116-143,154 patients) by the 60th day since the start of the outbreak. Losses calculated vary between < 1% to 17.6% of all patients with cancer in the region. CONCLUSION: Cancer-related cases and deaths attributable to SARS-CoV-2 will put a great strain on health care systems in Latin America. Early implementation of interventions on the basis of data given by disease modeling could mitigate both infections and deaths among patients with cancer