New insights about host response to smallpox using microarray data

<p>Abstract</p> <p>Background</p> <p>Smallpox is a lethal disease that was endemic in many parts of the world until eradicated by massive immunization. Due to its lethality, there are serious concerns about its use as a bioweapon. Here we analyze publicly available microarray data to further understand survival of smallpox infected macaques, using systems biology approaches. Our goal is to improve the knowledge about the progression of this disease.</p> <p>Results</p> <p>We used KEGG pathways annotations to define groups of genes (or modules), and subsequently compared them to macaque survival times. This technique provided additional insights about the host response to this disease, such as increased expression of the cytokines and ECM receptors in the individuals with higher survival times. These results could indicate that these gene groups could influence an effective response from the host to smallpox.</p> <p>Conclusion</p> <p>Macaques with higher survival times clearly express some specific pathways previously unidentified using regular gene-by-gene approaches. Our work also shows how third party analysis of public datasets can be important to support new hypotheses to relevant biological problems.</p

Casos autoctones de esquistossomose mansonica em criancas de Recife, PE

OBJETIVO : Investigar criadouros com moluscos hospedeiros e casos humanos autóctones para esquistossomose. MÉTODOS : Entre julho de 2010 e setembro de 2012 foram realizados: (1) levantamento malacológico para busca ativa de criadouros, coleta e identificação de caramujos Biomphalaria positivos para Schistosoma mansoni em Recife, PE; (2) inquérito de prevalência com 2.718 escolares, de sete a 14 anos, para diagnóstico de casos de esquistossomose; (3) exame clínico e ultrassonografia nos casos positivos para S. mansoni. Os casos foram investigados quanto à sua autoctonia e avaliados clinicamente. Os casos e criadouros foram georreferenciados e espacializados. RESULTADOS : Foram identificados 30 criadouros de B. straminea , quatro deles potenciais focos de transmissão, uma vez que os testes moleculares identificaram DNA de S. mansoni nos caramujos coletados. Foram diagnosticadas 14 crianças com esquistossomose; entre elas, cinco foram consideradas casos autóctones da doença. CONCLUSÕES : Ações emergenciais pela vigilância em saúde são necessárias para evitar que a esquistossomose se endemize em Recife, como acontece em localidades litorâneas do estado de Pernambuco

New Insights into the Evolution of Wolbachia Infections in Filarial Nematodes Inferred from a Large Range of Screened Species

Wolbachia are intriguing symbiotic endobacteria with a peculiar host range that includes arthropods and a single nematode family, the Onchocercidae encompassing agents of filariases. This raises the question of the origin of infection in filariae. Wolbachia infect the female germline and the hypodermis. Some evidences lead to the theory that Wolbachia act as mutualist and coevolved with filariae from one infection event: their removal sterilizes female filariae; all the specimens of a positive species are infected; Wolbachia are vertically inherited; a few species lost the symbiont. However, most data on Wolbachia and filaria relationships derive from studies on few species of Onchocercinae and Dirofilariinae, from mammals.We investigated the Wolbachia distribution testing 35 filarial species, including 28 species and 7 genera and/or subgenera newly screened, using PCR, immunohistochemical staining, whole mount fluorescent analysis, and cocladogenesis analysis. (i) Among the newly screened Onchocercinae from mammals eight species harbour Wolbachia but for some of them, bacteria are absent in the hypodermis, or in variable density. (ii) Wolbachia are not detected in the pathological model Monanema martini and in 8, upon 9, species of Cercopithifilaria. (iii) Supergroup F Wolbachia is identified in two newly screened Mansonella species and in Cercopithifilaria japonica. (iv) Type F Wolbachia infect the intestinal cells and somatic female genital tract. (v) Among Oswaldofilariinae, Waltonellinae and Splendidofilariinae, from saurian, anuran and bird respectively, Wolbachia are not detected.The absence of Wolbachia in 63% of onchocercids, notably in the ancestral Oswaldofilariinae estimated 140 mya old, the diverse tissues or specimens distribution, and a recent lateral transfer in supergroup F Wolbachia, modify the current view on the role and evolution of the endosymbiont and their hosts. Further genomic analyses on some of the newly sampled species are welcomed to decipher the open questions

Beneficial effects of reading aloud and solving simple arithmetic calculations (learning therapy) on a wide range of cognitive functions in the healthy elderly: study protocol for a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>Almost all cognitive functions decline with age. Results of previous studies have shown that cognitive training related to everyday life (reading aloud and solving simple arithmetic calculations), namely learning therapy, can improve two cognitive function (executive functions and processing speed) in elderly people. However, it remains unclear whether learning therapy engenders improvement of various cognitive functions or not. We investigate the impact of learning therapy on various cognitive functions (executive functions, episodic memory, short-term memory, working memory, attention, reading ability, and processing speed) in healthy older adults.</p> <p>Methods</p> <p>We use a single-blinded intervention with two parallel groups (a learning therapy group and a waiting list control group). Testers are blind to the study hypothesis and the group membership of participants. Through an advertisement in local newspaper, 64 healthy older adults are recruited. They will be assigned randomly to a learning therapy group or a waiting list control group. In the learning therapy group, participants are required to perform two cognitive tasks for 6 months: reading Japanese aloud and solving simple calculations. The waiting list group does not participate in the intervention. The primary outcome measure is the Stroop test score: a measure of executive function. Secondary outcome measures are assessments including the following: verbal fluency task, logical memory, first and second names, digit span forward, digit span backward, Japanese reading test, digit cancellation task, digit symbol coding, and symbol search. We assess these outcome measures before and after the intervention.</p> <p>Discussion</p> <p>This report is the first study which investigates the beneficial effects of learning therapy on a wide range of cognitive functions of elderly people. Our study provides sufficient evidence of learning therapy effectiveness. Most cognitive functions, which are correlated strongly with daily life activities, decrease with age. These study results can elucidate effects of cognitive training on elderly people.</p> <p>Trial registration</p> <p>This trial was registered in The University Hospital Medical Information Network Clinical Trials Registry (No. <a href="http://www.clinicaltrials.gov/ct2/show/UMIN000006998">UMIN000006998</a>).</p

Effects of pre-operative isolation on postoperative pulmonary complications after elective surgery: an international prospective cohort study

We aimed to determine the impact of pre-operative isolation on postoperative pulmonary complications after elective surgery during the global SARS-CoV-2 pandemic. We performed an international prospective cohort study including patients undergoing elective surgery in October 2020. Isolation was defined as the period before surgery during which patients did not leave their house or receive visitors from outside their household. The primary outcome was postoperative pulmonary complications, adjusted in multivariable models for measured confounders. Pre-defined sub-group analyses were performed for the primary outcome. A total of 96,454 patients from 114 countries were included and overall, 26,948 (27.9%) patients isolated before surgery. Postoperative pulmonary complications were recorded in 1947 (2.0%) patients of which 227 (11.7%) were associated with SARS-CoV-2 infection. Patients who isolated pre-operatively were older, had more respiratory comorbidities and were more commonly from areas of high SARS-CoV-2 incidence and high-income countries. Although the overall rates of postoperative pulmonary complications were similar in those that isolated and those that did not (2.1% vs 2.0%, respectively), isolation was associated with higher rates of postoperative pulmonary complications after adjustment (adjusted OR 1.20, 95%CI 1.05-1.36, p = 0.005). Sensitivity analyses revealed no further differences when patients were categorised by: pre-operative testing; use of COVID-19-free pathways; or community SARS-CoV-2 prevalence. The rate of postoperative pulmonary complications increased with periods of isolation longer than 3 days, with an OR (95%CI) at 4-7 days or ≥ 8 days of 1.25 (1.04-1.48), p = 0.015 and 1.31 (1.11-1.55), p = 0.001, respectively. Isolation before elective surgery might be associated with a small but clinically important increased risk of postoperative pulmonary complications. Longer periods of isolation showed no reduction in the risk of postoperative pulmonary complications. These findings have significant implications for global provision of elective surgical care

Theileria annae in a young Swedish dog

A severe regenerative anemia was detected in a 12-week-old mixed breed puppy in Sweden. A small protozoan parasite was observed in erythrocytes on a blood smear. It was initially suspected to be Babesia gibsoni based on its size and because B. gibsoni was previously recorded in Sweden. Surprisingly, specific polymerase chain reaction analysis identified the protozoan as Theileria annae. T. annae is endemic in Northwest Spain, is very uncommonly reported elsewhere and has never been recorded in Scandinavia. T. annae has been identified in dogs used for dog fighting, and it is thought to be transmitted by dog bites. This puppy was a mixed pit bull terrier. Pit bull terriers are sometimes used for dog fighting. T. annae has been reported to be transmitted vertically, and in light of the puppy's age, this transmission was suspected in the present case

NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms

One of the long-standing open challenges in computational systems biology is the topology inference of gene regulatory networks from high-throughput omics data. Recently, two community-wide efforts, DREAM4 and DREAM5, have been established to benchmark network inference techniques using gene expression measurements. In these challenges the overall top performer was the GENIE3 algorithm. This method decomposes the network inference task into separate regression problems for each gene in the network in which the expression values of a particular target gene are predicted using all other genes as possible predictors. Next, using tree-based ensemble methods, an importance measure for each predictor gene is calculated with respect to the target gene and a high feature importance is considered as putative evidence of a regulatory link existing between both genes. The contribution of this work is twofold. First, we generalize the regression decomposition strategy of GENIE3 to other feature importance methods. We compare the performance of support vector regression, the elastic net, random forest regression, symbolic regression and their ensemble variants in this setting to the original GENIE3 algorithm. To create the ensemble variants, we propose a subsampling approach which allows us to cast any feature selection algorithm that produces a feature ranking into an ensemble feature importance algorithm. We demonstrate that the ensemble setting is key to the network inference task, as only ensemble variants achieve top performance. As second contribution, we explore the effect of using rankwise averaged predictions of multiple ensemble algorithms as opposed to only one. We name this approach NIMEFI (Network Inference using Multiple Ensemble Feature Importance algorithms) and show that this approach outperforms all individual methods in general, although on a specific network a single method can perform better. An implementation of NIMEFI has been made publicly available

Restinga and Lowland forests in coastal plain of southeastern Brazil: vegetation and environmental heterogeneity

It was evaluated the floristic similarity between two Atlantic Rainforest physiognomies in Brazilian coast area, herein called Restinga and Lowland forests. The hypothesis was that, due the differences in geomorphologic processes, these forests would differ on soil physical and chemical properties, floristic composition, live above-ground biomass. and litterfall production. It was sampled 1 ha (100 x 100 m) for each site located in Ubatuba, Sao Paulo state, SE Brazil. Within each hectare it was recorded trees with DBH >4.8 cm in all 10 x 10 m contiguous plots, and collected soil and litterfall samples. The cluster and ordination analyses indicated the two communities as distinct groups considering soil and floristic composition, agreeing with the initial hypothesis. Species diversity was higher (p 0.05) between the two forests. This apparent paradox could be explained assuming that, since different species establish themselves in the Restinga or Lowland forests and find a favorable spectrum of conditions and resources, they would tend to persist and to develop in that place; even so the edaphic conditions differ between the Restinga and Lowland forests, each species could respond in a particular way to these variations, and then both forests could reach similar values of biomass and litterfall production. It is probable that the environmental filter conditioned by soils has being important for the strong floristic segregation between these two forests.11210312