PSSA - um método de otimização usando a computação paralela

Neste trabalho foi considerado o problema de determinação de todos os minimizantes globais, e alguns locais, de um problema de otimização não linear. Para a resolução deste problema foi considerada uma estratégia multilocal combinada com técnicas de computação paralela. Assim, foram desenvolvidas diferentes variantes paralelas do Stretched Simulated Annealing (SSA) - um algoritmo que combina o método de simulated annealing com a função stretching - baseadas em diferentes estratégias de particionamento do domínio de pesquisa. A abordagem resultante - Parallel SSA (PSSA) - foi testada com diversos problemas onde a função objetivo é multimodal

Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon

The pathogenic role of beta-hemolytic Streptococcus dysgalactiae in the equine host is increasingly recognized. A collection of 108 Lancefield group C (n = 96) or L (n = 12) horse isolates recovered in the United States and in three European countries presented multilocus sequence typing (MLST) alleles, sequence types and emm types (only 56% of the isolates could be emm typed) that were, with few exceptions, distinct from those previously found in human Streptococcus dysgalactiae subsp. equisimilis. Characterization of a subset of horse isolates by multilocus sequence analysis (MLSA) and 16S rRNA gene sequence showed that most equine isolates could also be differentiated from S. dysgalactiae strains from other animal species, supporting the existence of a horse specific genomovar. Draft genome information confirms the distinctiveness of the horse genomovar and indicates the presence of potentially horse-specific virulence factors. While this genomovar represents most of the isolates recovered from horses, a smaller MLST and MLSA defined sub-population seems to be able to cause infections in horses, other animals and humans, indicating that transmission between hosts of strains belonging to this group may occur

Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon

The pathogenic role of beta-hemolytic Streptococcus dysgalactiae in the equine host is increasingly recognized. A collection of 108 Lancefield group C (n=96) or L (n=12) horse isolates recovered in the United States and in three European countries presented multilocus sequence typing (MLST) alleles, sequence types and emm types (only 56% of the isolates could be emm typed) that were, with few exceptions, distinct from those previously found in human Streptococcus dysgalactiae subsp. equisimilis. Characterization of a subset of horse isolates by multilocus sequence analysis (MLSA) and 16S rRNA gene sequence showed that most equine isolates could also be differentiated from S. dysgalactiae strains from other animal species, supporting the existence of a horse specific genomovar. Draft genome information confirms the distinctiveness of the horse genomovar and indicates the presence of potentially horse-specific virulence factors. While this genomovar represents most of the isolates recovered from horses, a smaller MLST and MLSA defined sub-population seems to be able to cause infections in horses, other animals and humans, indicating that transmission between hosts of strains belonging to this group may occur

Cobaltabis(dicarbollide) ([o-COSAN]−) as Multifunctional Chemotherapeutics: A Prospective Application in Boron Neutron Capture Therapy (BNCT) for Glioblastoma

Purpose: The aim of our study was to assess if the sodium salt of cobaltabis(dicarbollide) and its di-iodinated derivative (Na[o-COSAN] and Na[8,8′-I2-o-COSAN]) could be promising agents for dual anti-cancer treatment (chemotherapy + BNCT) for GBM. Methods: The biological activities of the small molecules were evaluated in vitro with glioblastoma cells lines U87 and T98G in 2D and 3D cell models and in vivo in the small model animal Caenorhabditis elegans (C. elegans) at the L4-stage and using the eggs. Results: Our studies indicated that only spheroids from the U87 cell line have impaired growth after treatment with both compounds, suggesting an increased resistance from T98G spheroids, contrary to what was observed in the monolayer culture, which highlights the need to employ 3D models for future GBM studies. In vitro tests in U87 and T98G cells conclude that the amount of 10B inside the cells is enough for BNCT irradiation. BNCT becomes more effective on T98G after their incubation with Na[8,8′-I2-o-COSAN], whereas no apparent cell-killing effect was observed for untreated cells. Conclusions: These small molecules, particularly [8,8′-I2-o-COSAN]−, are serious candidates for BNCT now that the facilities of accelerator-based neutron sources are more accessible, providing an alternative treatment for resistant glioblastoma

Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens

High throughput sequencing has been proposed as a one-stop solution for diagnostics and molecular typing directly from patient samples, allowing timely and appropriate implementation of measures for treatment, infection prevention and control. However, it is unclear how the variety of available methods impacts the end results. We applied shotgun metagenomics on diverse types of patient samples using three different methods to deplete human DNA prior to DNA extraction. Libraries were prepared and sequenced with Illumina chemistry. Data was analyzed using methods likely to be available in clinical microbiology laboratories using genomics. The results of microbial identification were compared to standard culture-based microbiological methods. On average, 75% of the reads corresponded to human DNA, being a major determinant in the analysis outcome. None of the kits was clearly superior suggesting that the initial ratio between host and microbial DNA or other sample characteristics were the major determinants of the proportion of microbial reads. Most pathogens identified by culture were also identified through metagenomics, but substantial differences were noted between the taxonomic classification tools. In two cases the high number of human reads resulted in insufficient sequencing depth of bacterial DNA for identification. In three samples, we could infer the probable multilocus sequence type of the most abundant species. The tools and databases used for taxonomic classification and antimicrobial resistance identification had a key impact on the results, recommending that efforts need to be aimed at standardization of the analysis methods if metagenomics is to be used routinely in clinical microbiology

A Global Comparison of Stream Diatom Beta Diversity on Islands Versus Continents Across Scales

Online version of record before inclusion in an issue[EN] Aim: To evaluate the patterns of stream diatom beta diversity in islands versus continents across scales, to relate community similarities with spatial and environmental distances and to investigate the role of island characteristics in shaping insular diatom beta diversity. Location: Africa, America, Europe and the Pacific. Time Period: Present. Major Taxa Studied: Stream diatoms. Methods: We compared diatom beta diversity between islands and continents at large scales (within biogeographic regions) in two study regions (America and Europe) and at small scales (within islands/equivalent areas in continents) in three regions (Africa, America and Europe) partitioning beta diversity into turnover and nestedness components. We used a partial Mantel test and distance–decay curves to assess how diatom beta diversity on islands and continents is affected by spatial and environmental distances. Finally, using island data from all four regions, we evaluated the relationship between island beta diversity and island latitude, area, age and isolation using linear models. Results: At large scales, mean dissimilarities were higher on islands than in continents in Europe but lower in America. At smaller scales, the differences varied mostly depending on island isolation. Beta diversity was mainly caused by species turnover. Partial Mantel test and distance–decay curves revealed that spatial and environmental distances shaped diatom beta diversity at large, but not at small scales. Moreover, diatom beta diversity on islands was affected by island latitude, age and isolation, but not by island area. Main Conclusions: Diatom beta diversity on islands versus continents and its responses to spatial and environmental factors are scale and region dependent. Incomplete colonisation, evolutionary processes and environmental filtering likely contribute to insular beta diversity, which further varies with island latitude, age and isolation. This study sheds new light on beta diversity of microorganisms on islands and suggests that beta diversity should be explicitly considered in island biogeographical researchSIThis work was supported by the Academy of Finland (grant no. 346812 to J.S.); the Institut Français de Finlande; the Embassy of France to Finland; the French Ministry of Education and Higher Education; and the Finnish Society of Sciences and Letters. J. Wang was further supported by the National Natural Science Foundation of China (91851117 and 41871048), CAS Key Research Program of Frontier Sciences (QYZDB- SSW-DQC043) and The National Key Research and Development Program of China (2019YFA0607100

Author Correction: Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens (vol 8, 13767, 2018)

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper

Stream diatom community assembly processes in islands and continents: a global perspective

[EN] Understanding the roles of deterministic and stochastic processes in community assembly is essential for gaining insights into the biogeographical patterns of biodiversity. However, the way community assembly processes operate is still not fully understood, especially in oceanic islands. In this study, we examine the importance of assembly processes in shaping diatom communities in islands and continents, while also investigating the influence of climate and local water chemistry variables on species distributions. Location Global. Taxon Stream benthic diatoms. Methods We used diatom datasets from five continents and 19 islands and applied beta diversity analyses with a null model approach and hierarchical joint species distribution modelling. To facilitate comparisons with continents, we used continental area equivalents (CAEs), which represent continental subsets with comparable areas and the same number of study sites as their corresponding islands counterparts. Results We found that homogeneous selection (i.e., communities being more similar than the random expectation) was the dominant assembly process within islands whereas stochastic processes tended to be more important within continents. In addition, assembly processes were influenced by study scale and island isolation. Climatic variables showed a greater influence on species distribution than local factors. However, in islands, local environmental variables had a greater impact on the distributions of unique taxa as opposed to non-unique taxa. Main Conclusions We observed that the assembly processes of diatom communities were complex and influenced by a combination of deterministic and stochastic forces, which varied across spatial scales. In islands, there was no universal pattern of assembly processes, given that their influence depends on abiotic conditions such as area, isolation, and environmental heterogeneity. In addition, the sensitivity of species occurring uniquely in islands to local environmental variables suggests that they are perhaps less vulnerable to climatic changes but may be more influenced by changes in local physicochemistrySIFor financial support, the authors thank the Academy of Finland (grant nr. 346812 to JS); the Institut Francais de Finlande; the Embassy of France to Finland; the French Ministry of Education and Higher Education; Finnish Society of Sciences and Letters. J.J. Wang was further supported by the National Natural Science Foundation of China (91851117, 41871048), CAS Key Research Program of Frontier Sciences (QYZDB-SSW-DQC043), and The National Key Research and Development Program of China (2019YFA0607100

Population dynamics of synanthropic rodents after a chemical and infrastructural intervention in an urban low-income community.

Synanthropic rodents are ubiquitous in low-income communities and pose risks for human health, as they are generally resistant to control programs. However, few or no studies have evaluated the long-term effect of chemical and infrastructural interventions on rodent population dynamics, especially in urban low-income communities, or evaluated the potential recovery of their population following interventions. We conducted a longitudinal study in a low-income community in the city of Salvador (BA, Brazil) to characterize the effect of interventions (chemical and infrastructural) on the dynamics of rodent population, and documented the post-intervention recovery of their population. We evaluated the degree of rodent infestation in 117 households/sampling points over three years (2014-2017), using tracking plates, a proxy for rodent abundance/activity. We reported a significant lower rodent activity/abundance after the chemical and infrastructural interventions (Z = -4.691 (p < 0.001)), with track plate positivity decreasing to 28% from 70% after and before interventions respectively. Therefore, the combination of chemical and infrastructural interventions significantly decreased the degree of rodent infestation in the study area. In addition, no rodent population rebound was recorded until almost a year post-intervention, and the post-intervention infestation level did not attain the pre-intervention level all through the study. Moreover, among pre-treatment conditions, access to sewer rather than the availability of food was the variable most closely associated with household rodent infestation. Our study indicates that Integrated Pest Management (IPM)-approaches are more effective in reducing rodent infestation than the use of a single method. Our findings will be useful in providing guidance for long-term rodent control programs, especially in urban low-income communities

Unusual circulation patterns of the rias baixas induced by minho freshwater intrusion (NW of the Iberian Peninsula)

The Minho River, situated 30 km south of the Rias Baixas, is the most important freshwater source flowing into the Western Galician coast (NW of the Iberian Peninsula). The buoyancy generated by the Minho estuarine plume can reverse the normal circulation pattern inside the Rias Baixas affecting the exchange between the Rias and the ocean, changing the input of nutrients. Nevertheless, this inversion of the circulation patterns is not a well-monitored phenomenon. The only published results based on in situ data related to the presence of the Minho River plume inside the Rias de Vigo and Pontevedra correspond to an event measured on spring 1998. In this case unexpectedly higher inflow surface current velocities were found at the Ria de Pontevedra, located further away from Minho River. Thus, the main aim of this study is to research the main factors inducing this unusual pattern on the circulation of the Rias de Vigo and Pontevedra. A numerical model implementation of MOHID previously developed, calibrated, and validated for this coastal area was used. Several scenarios were performed in order to explain the individual effect of the Minho River, rivers discharging into each Rias, and estuarine morphology changes. According to the model results, the Minho River discharge is a key factor in the establishment of the negative circulation, while small rivers inside the Rias slightly attenuate this circulation. The negative circulation was stronger in Ria de Pontevedra independently of the distance of this coastal system from the Minho River mouth, showing that morphologic estuarine features are the main factor justifying the different local circulation patterns