Predicting the HMA-LMA status in marine sponges by machine learning

The dichotomy between high microbial abundance (HMA) and low microbial abundance (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized the differences between the microbiomes of HMA (n=19) and LMA (n=17) sponges (575 specimens) present in the Sponge Microbiome Project. HMA sponges were associated with richer and more diverse microbiomes than LMA sponges, as indicated by the comparison of alpha diversity metrics. Microbial community structures differed between HMA and LMA sponges considering Operational Taxonomic Units (OTU) abundances and across microbial taxonomic levels, from phylum to species. The largest proportion of microbiome variation was explained by the host identity. Several phyla, classes, and OTUs were found differentially abundant in either group, which were considered “HMA indicators” and “LMA indicators”. Machine learning algorithms (classifiers) were trained to predict the HMA-LMA status of sponges. Among nine different classifiers, higher performances were achieved by Random Forest trained with phylum and class abundances. Random Forest with optimized parameters predicted the HMA-LMA status of additional 135 sponge species (1,232 specimens) without a priori knowledge. These sponges were grouped in four clusters, from which the largest two were composed of species consistently predicted as HMA (n=44) and LMA (n=74). In summary, our analyses shown distinct features of the microbial communities associated with HMA and LMA sponges. The prediction of the HMA-LMA status based on the microbiome profiles of sponges demonstrates the application of machine learning to explore patterns of host-associated microbial communities

Candidates for Balancing Selection in Leishmania donovani Complex Parasites

The Leishmania donovani species complex is the causative agent of visceral leishmaniasis, which cause 20–40,000 fatalities a year. Here, we conduct a screen for balancing selection in this species complex. We used 384 publicly available L. donovani and L. infantum genomes, and sequence 93 isolates of L. infantum from Brazil to describe the global diversity of this species complex. We identify five genetically distinct populations that are sufficiently represented by genomic data to search for signatures of selection. We find that signals of balancing selection are generally not shared between populations, consistent with transient adaptive events, rather than long-term balancing selection. We then apply multiple diversity metrics to identify candidate genes with robust signatures of balancing selection, identifying a curated set of 24 genes with robust signatures. These include zetatoxin, nodulin-like, and flagellum attachment proteins. This study highlights the extent of genetic divergence between L. donovani complex parasites and provides genes for further stud

Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis.

To visualize the personalized distributions of pathogens and chemical environments, including microbial metabolites, pharmaceuticals, and their metabolic products, within and between human lungs afflicted with cystic fibrosis (CF), we generated three-dimensional (3D) microbiome and metabolome maps of six explanted lungs from three cystic fibrosis patients. These 3D spatial maps revealed that the chemical environments differ between patients and within the lungs of each patient. Although the microbial ecosystems of the patients were defined by the dominant pathogen, their chemical diversity was not. Additionally, the chemical diversity between locales in the lungs of the same individual sometimes exceeded interindividual variation. Thus, the chemistry and microbiome of the explanted lungs appear to be not only personalized but also regiospecific. Previously undescribed analogs of microbial quinolones and antibiotic metabolites were also detected. Furthermore, mapping the chemical and microbial distributions allowed visualization of microbial community interactions, such as increased production of quorum sensing quinolones in locations where Pseudomonas was in contact with Staphylococcus and Granulicatella, consistent with in vitro observations of bacteria isolated from these patients. Visualization of microbe-metabolite associations within a host organ in early-stage CF disease in animal models will help elucidate the complex interplay between the presence of a given microbial structure, antibiotics, metabolism of antibiotics, microbial virulence factors, and host responses.IMPORTANCE Microbial infections are now recognized to be polymicrobial and personalized in nature. Comprehensive analysis and understanding of the factors underlying the polymicrobial and personalized nature of infections remain limited, especially in the context of the host. By visualizing microbiomes and metabolomes of diseased human lungs, we reveal how different the chemical environments are between hosts that are dominated by the same pathogen and how community interactions shape the chemical environment or vice versa. We highlight that three-dimensional organ mapping methods represent hypothesis-building tools that allow us to design mechanistic studies aimed at addressing microbial responses to other microbes, the host, and pharmaceutical drugs

An international network to monitor the structure, composition and dynamics of Amazonian forests (RAINFOR)

The Amazon basin is likely to be increasingly affected by environmental changes: higher temperatures, changes in precipitation, CO2 fertilization and habitat fragmentation. To examine the important ecological and biogeochemical consequences of these changes, we are developing an international network, RAINFOR, which aims to monitor forest biomass and dynamics across Amazonia in a co-ordinated fashion in order to understand their relationship to soil and climate. The network will focus on sample plots established by independent researchers, some providing data extending back several decades. We will also conduct rapid transect studies of poorly monitored regions. Field expeditions analysed local soil and plant properties in the first phase (2001–2002). Initial results suggest that the network has the potential to reveal much information on the continental-scale relations between forest and environment. The network will also serve as a forum for discussion between researchers, with the aim of standardising sampling techniques and methodologies that will enable Amazonian forests to be monitored in a coherent manner in the coming decades

Cranial chordoma heterogeneity : Two case reports

Cordomas são neoplasias raras originadas da notocorda primitiva, que se localizam predominantemente em região sacroccígena e menos freqüentemente intracranianas, correspondendo de 3 a 5% dos tumores primários cerebrais. Os cordomas intracranianos são de manejo difícil, a ressecção cirúrgica geralmente é incompleta e os pacientes podem evoluir para óbito em decorrência do crescimento incontrolável do tumor e/ou compressão de estruturas nobres adjacentes. Neste trabalho os autores relatam dois pacientes com cordoma intracraniano cuja evolução clínica foi absolutamente distinta, dissertando sobre os diversos aspectos relacionados ao diagnóstico, tratamento e evolução dos dois casos.Chordomas are very rare primitive notochord-related tumors localized most frequently in sacrococcygeal and cranial regions. Intracranial lesions correspond to 3-5% of the primary tumors. Clinical management is very difficult; surgical ressection is usually incomplete, and can be associated with rapid tumor growth and multiple neurological involvement. In this study, the authors report on two cases of intracranial chordomas with diverse presentation and evolution, and discuss the diagnosis and the management of these patients

Pliocene deglacial event timelines and the biogeochemical response offshore Wilkes Subglacial Basin, East Antarctica

Significantly reduced ice coverage in Greenland and West Antarctica during the warmer-than-present Pliocene could account for ∼10m of global mean sea level rise. Any sea level increase beyond this would require contributions from the East Antarctic Ice Sheet (EAIS). Previous studies have presented low-resolution geochemical evidence from the geological record, suggesting repeated ice advance and retreat in low-lying areas of the EAIS such as the Wilkes Subglacial Basin. However, the rates and mechanisms of retreat events are less well constrained. Here we present orbitally-resolved marine detrital sediment provenance data, paired with ice-rafted debris and productivity proxies, during three time intervals from the middle to late Pliocene at IODP Site U1361A, offshore of the Wilkes Subglacial Basin. Our new data reveal that Pliocene shifts in sediment provenance were paralleled by increases in marine productivity, while the onset of such changes was marked by peaks in ice-rafted debris mass accumulation rates. The coincidence of sediment provenance and marine productivity change argues against a switch in sediment delivery between ice streams, and instead suggests that deglacial warming triggered increased rates of iceberg calving, followed by inland retreat of the ice margin. Timescales from the onset of deglaciation to an inland retreated ice margin within the Wilkes Subglacial Basin are on the order of several thousand years. This geological evidence corroborates retreat rates determined from ice sheet modeling, and a contribution of ∼3 to 4m of equivalent sea level rise from one of the most vulnerable areas of the East Antarctic Ice Sheet during interglacial intervals throughout the middle to late Pliocene.Provenance analysis was supported by a Kristian Gerhard Jeb-sen PhD Scholarship and NERC UK IODP grants (NE/H025162/1 and NE/H014144/1). Biogenic silica data was supported by a Royal So-ciety of New Zealand Marsden FastStart grant (#UOO-1315) and a University of Otago PhD Scholarship. Support for sedimentol-ogyanalysis was provided by the Royal Society of New ZealandRutherford Discovery Fellowship (RDF-13-VUW-003). XRF work was supported by the Ministry of Science and Innovation Grant CTM2014-60451-C2-1-P co-financed by the European Regional De-velopment Fund (FEDER). Samples were provided by the Integrated Ocean Drilling Program

MicroRNAs of Gallid and Meleagrid herpesviruses show generally conserved genomic locations and are virus-specific

AbstractMany herpesviruses, including Marek's disease viruses (MDV1 and MDV2), encode microRNAs. In this study, we report microRNAs of two related herpesviruses, infectious laryngotracheitis virus (ILTV) and herpesvirus of turkeys (HVT), as well as additional MDV2 microRNAs. The genome locations, but not microRNA sequences, are conserved among all four of these avian herpesviruses. Most are clustered in the repeats flanking the unique long region (I/TRL), except in ILTV which lacks these repeats. Two abundant ILTV microRNAs are antisense to the immediate early gene ICP4. A homologue of host microRNA, gga-miR-221, was found among the HVT microRNAs. Additionally, a cluster of HVT microRNAs was found in a region containing two locally duplicated segments, resulting in paralogous HVT microRNAs with 96–100% identity. The prevalence of microRNAs in the genomic repeat regions as well as in local repeats suggests the importance of genetic plasticity in herpesviruses for microRNA evolution and preservation of function

Treatment outcomes of new tuberculosis patients hospitalized in Kampala, Uganda: a prospective cohort study.

BACKGROUND: In most resource limited settings, new tuberculosis (TB) patients are usually treated as outpatients. We sought to investigate the reasons for hospitalisation and the predictors of poor treatment outcomes and mortality in a cohort of hospitalized new TB patients in Kampala, Uganda. METHODS AND FINDINGS: Ninety-six new TB patients hospitalised between 2003 and 2006 were enrolled and followed for two years. Thirty two were HIV-uninfected and 64 were HIV-infected. Among the HIV-uninfected, the commonest reasons for hospitalization were low Karnofsky score (47%) and need for diagnostic evaluation (25%). HIV-infected patients were commonly hospitalized due to low Karnofsky score (72%), concurrent illness (16%) and diagnostic evaluation (14%). Eleven HIV uninfected patients died (mortality rate 19.7 per 100 person-years) while 41 deaths occurred among the HIV-infected patients (mortality rate 46.9 per 100 person years). In all patients an unsuccessful treatment outcome (treatment failure, death during the treatment period or an unknown outcome) was associated with duration of TB symptoms, with the odds of an unsuccessful outcome decreasing with increasing duration. Among HIV-infected patients, an unsuccessful treatment outcome was also associated with male sex (P = 0.004) and age (P = 0.034). Low Karnofsky score (aHR = 8.93, 95% CI 1.88 - 42.40, P = 0.001) was the only factor significantly associated with mortality among the HIV-uninfected. Mortality among the HIV-infected was associated with the composite variable of CD4 and ART use, with patients with baseline CD4 below 200 cells/µL who were not on ART at a greater risk of death than those who were on ART, and low Karnofsky score (aHR = 2.02, 95% CI 1.02 - 4.01, P = 0.045). CONCLUSION: Poor health status is a common cause of hospitalisation for new TB patients. Mortality in this study was very high and associated with advanced HIV Disease and no use of ART

PERFIL DOS TÉCNICOS QUE DESENVOLVEM PRODUTOS ALIMENTÍCIOS

O sucesso em desenvolvimento de novos produtos (DNP) tem se tornado indicador importante do sucesso organizacional e depende fundamentalmente das pessoas com ele envolvidas. Este trabalho buscou traçar o perfil das pessoas que trabalham com DNP de alimentos no Estado do Paraná e descobrir quais temas podem ser introduzidos no currículo desses profissionais para ajuda-los a desempenhar melhor suas tarefas. TECHNICAL PROFILE OF PEOLE WORKING WITH NEW PRODUCT DEVELOPMENT Abstract The success in new product development (NPD) has become an important indicator of organizational success and it depends primarily upon the people involved on its tasks. The purpose of this work was to identify the profile of people working in food DNP in the Parana State and which subjects could be taught in the Universities in order to help them dealing with the responsibilities of the job

Attenuation of motor deficits by hydroethanolic extract of Poincianella pyramidalis in a Parkinson's disease model

The present study aimed to evaluate the possible neuroprotective effect of the hydroethanolic extract of Poincianella pyramidalis (EFIPp) (Tul.) L. P. Queiroz (Fabaceae), an endemic plant found in Northeastern Brazil, commonly used in folk medicine, on the motor deficits induced by repeated treatment with reserpine (RES) in rats. Adult male Wistar rats received 10 s.c. injections of 0.1 mg/kg RES or vehicle (VR), every 48 h, and daily i.p. injections daily of HEPp (25 mg/kg) or vehicle (VE). Throughout treatment, catalepsy behavior and oral movements were scored. After behavioral tests, superoxide dismutase (SOD) and catalase (CAT) activities were evaluated in the prefrontal cortex, hippocampus and striatum. RES treatment induced a progressive increase of catalepsy time in the treated group compared to control groups starting at day 15. RES also increased the number of vacuous chewing movements, tongue protrusions and duration of facial twitching. Treatment with HEPp attenuated the motor deficit in the catalepsy test and delayed the onset of oral movements induced by RES. No significant changes were observed in the antioxidant assay. Taken together, these results show a beneficial effect of HEPp on motor deficits induced by reserpine, suggesting a neuroprotective effect in a rat model of PD.Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)Fundação de Apoio a Pesquisa e a Inovação Tecnologica do Estado de Sergipe (FAPITEC)Pro-reitoria de Pesquisa da Universidade Federal de Sergipe (POSGRAP/UFS)Univ Fed Sergipe, Dept Physiol, Sao Cristovao, SE, BrazilUniv Massachusetts, Neurosci & Behav Program, Amherst, MA 01003 USAMinist Educ, CAPES Fdn, BR-70040020 Brasilia, DF, BrazilUniv Fed Sao Paulo, Dept Biosci, Santos, SP, BrazilUniv Fed Sao Paulo, Dept Pharmacol, Sao Paulo, SP, BrazilUniv Fed Sergipe, Dept Biosci, Itabaiana, SE, BrazilUniv Fed Sao Paulo, Dept Biosci, Santos, SP, BrazilUniv Fed Sao Paulo, Dept Pharmacol, Sao Paulo, SP, BrazilWeb of Scienc