Integrating metatranscriptomes and metagenomes for deconvolution of composition and expression in human gut and artificial communities

Over the last 15 years the human microbiome has received increasing attention.During this time, many studies have contributed to shed light on the complex network of interactions both between the microorganisms and their host, and within microbial communities themselves. While traditionally aiming at assessing composition, recent studies have broadened this scope to multi-dimensional aspects, using multi-omics approaches.By integrating information about genomes, transcripts, proteins and metabolites, a holistic understanding of the microbiome is now within reach.However progressive, these studies generally suffer from a lack of closure, as interpretation and integration of this data is all but straightforward. In the particular case of metatranscriptomes, species abundance and gene expression are coupled into a single readout.Consequently, normalization of this data is a crucial but poorly understood and unresolved problem. Here I present different approaches to normalise metatranscriptomes and highlight procedural concerns when obtaining this type of data. Results show that better normalization strategies are necessary when integrating multi-omics data and that controlled pilot experiments are required for a better understanding of the intricate dynamics and interactions between members of these communities. This work further exposes concerns about the interpretation of functional aspects of microbial populations, primarily driven by the many uncontrolled sources of variation herein discussed. As these new data types become more widespread, methods will certainly evolve towards better standardization and controlled procedures. This will help the microbiome field to move beyond its descriptive state into one able to provide a more detailed and mechanistic understanding

Feature learning in feature-sample networks using multi-objective optimization

Data and knowledge representation are fundamental concepts in machine learning. The quality of the representation impacts the performance of the learning model directly. Feature learning transforms or enhances raw data to structures that are effectively exploited by those models. In recent years, several works have been using complex networks for data representation and analysis. However, no feature learning method has been proposed for such category of techniques. Here, we present an unsupervised feature learning mechanism that works on datasets with binary features. First, the dataset is mapped into a feature--sample network. Then, a multi-objective optimization process selects a set of new vertices to produce an enhanced version of the network. The new features depend on a nonlinear function of a combination of preexisting features. Effectively, the process projects the input data into a higher-dimensional space. To solve the optimization problem, we design two metaheuristics based on the lexicographic genetic algorithm and the improved strength Pareto evolutionary algorithm (SPEA2). We show that the enhanced network contains more information and can be exploited to improve the performance of machine learning methods. The advantages and disadvantages of each optimization strategy are discussed.Comment: 7 pages, 4 figure

Control and filtering of time-varying linear systems via parameter dependent Lyapunov functions

The main contribution of this dissertation is to propose conditions for linear filter and controller design, considering both robust and parameter dependent structures, for discrete time-varying systems. The controllers, or filters, are obtained through the solution of optimization problems, formulated in terms of bilinear matrix inequalities, using a method that alternates convex optimization problems described in terms of linear matrix inequalities. Both affine and multi-affine in different instants of time (path dependent) Lyapunov functions were used to obtain the design conditions, as well as extra variables introduced by the Finsler\u27s lemma. Design problems that take into account an H-infinity guaranteed cost were investigated, providing robustness with respect to unstructured uncertainties. Numerical simulations show the efficiency of the proposed methods in terms of H-infinity performance when compared with other strategies from the literature

SEXUAL DIMORPHISM IN A COOPERATIVE BREEDING THRAUPID (WHITE‐BANDED TANAGER, NEOTHRAUPIS FASCIATA): THE RELEVANCEOF THE BLACK MASK

ABSTRACT ∙ Sexual dimorphism is common among birds, and is often caused by sexual selection. The detailed characterization of sexual dimorphism in a species is essential to propose and test hypotheses about the mechanisms responsible for its origin and maintenance. In this context, we examined the sexual size and plumage dimorphism in the White‐banded Tanager (Neothraupis fasciata) based on wild individuals sexed using DNA‐based techniques in seven different localities in the Brazilian savanna (Cerrado). Based on eight morphometric variables, we found that males were on average larger than females, and found statistically significant differences for some morphometric variables in three localities studied. Sexual dimorphism in plumage coloration was restricted to the size of the black mask, which extended to the lores in males and was limited to the auriculars in females. Thus, our results showed that the White‐banded Tanager exhibits dimorphism in size and plumage, indicating that sexual dimorphism in this species seems more intricate than it has been described in literature. We also emphasize that the extension of the black mask is the best trait for sexing this species, and it can also be applied to immatures. Finally, we point out some aspects that should be investigated to better understand the evolution and maintenance of the sexual dimorphism in the White-banded Tanager.RESUMO ∙ Dimorfismo sexual em um traupídeo com reprodução cooperativa (tiê‐do‐cerrado, Neothraupis fasciata): a relevância da máscara preta O dimorfismo sexual é comum entre as aves e é frequentemente causado pela seleção sexual. A caracterização do dimorfismo sexual de uma espécie é essencial para propor e testar hipóteses relacionadas aos mecanismos responsáveis pela sua origem e manutenção. Neste contexto, examinamos o dimorfismo sexual de tamanho e plumagem no tiê‐do‐cerrado (Neothraupis fasciata) em sete localidades diferentes distribuídas nas savanas brasileiras (Cerrado) com base em indivíduos sexados por técnica molecular. Considerando as oito variáveis morfométricas avaliadas, observamos que os machos foram em média maiores do que as fêmeas, e encontramos diferenças estatisticamente significativas para algumas variáveis morfométricas em três localidades amostadas. O dimorfismo sexual de plumagem nessa espécie está relacionado com o tamanho da máscara preta, que se estende até o loro nos machos e está limitada às auriculares nas fêmeas. Os resultados mostram que o tiê‐do‐cerrado apresenta tanto dimorfismo de tamanho quanto de plumagem, indicando que o dimorfismo sexual nessa espécie parece mais complexo do que tem sido descrito na literatura. Ressaltamos ainda que a extensão da máscara preta é a melhor característica para identificar o sexo dos indivíduos desta espécie, inclusive porque esta característica pode ser aplicada em imaturos. Finalmente, nós apontamos alguns aspectos que podem ser investigados para melhor entender a evolução e manutenção do dimorfismo sexual no tiê‐do‐cerrado

A century of research: what have we learned about the interaction of Trypanosoma cruzi with host cells?

Since the discovery of Trypanosoma cruzi and the brilliant description of the then-referred to "new tripanosomiasis" by Carlos Chagas 100 years ago, a great deal of scientific effort and curiosity has been devoted to understanding how this parasite invades and colonises mammalian host cells. This is a key step in the survival of the parasite within the vertebrate host, and although much has been learned over this century, differences in strains or isolates used by different laboratories may have led to conclusions that are not as universal as originally interpreted. Molecular genotyping of the CL-Brener clone confirmed a genetic heterogeneity in the parasite that had been detected previously by other techniques, including zymodeme or schizodeme (kDNA) analysis. T. cruzi can be grouped into at least two major phylogenetic lineages: T. cruzi I, mostly associated with the sylvatic cycle and T. cruzi II, linked to human disease; however, a third lineage, T. cruziIII, has also been proposed. Hybrid isolates, such as the CL-Brener clone, which was chosen for sequencing the genome of the parasite (Elias et al. 2005, El Sayed et al. 2005a), have also been identified. The parasite must be able to invade cells in the mammalian host, and many studies have implicated the flagellated trypomastigotes as the main actor in this process. Several surface components of parasites and some of the host cell receptors with which they interact have been described. Herein, we have attempted to identify milestones in the history of understanding T. cruzi- host cell interactions. Different infective forms of T. cruzi have displayed unexpected requirements for the parasite to attach to the host cell, enter it, and translocate between the parasitophorous vacuole to its final cytoplasmic destination. It is noteworthy that some of the mechanisms originally proposed to be broad in function turned out not to be universal, and multiple interactions involving different repertoires of molecules seem to act in concert to give rise to a rather complex interplay of signalling cascades involving both parasite and cellular components.CNPqCoordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)FAPESPFINE

Summer Thermal Conditions in Outdoor Public Spaces: A Case Study in a Mediterranean Climate

Comfort in public spaces is essential to their attractiveness and continued role in improving human quality of life. Acceptable thermal conditions are determinant to ensuring users' comfort. This study undertakes an assessment of three urban sites in Arouca, in the north of Portugal, using ENVI-met software. Simulations test the influence of pavement and facade covering material, vegetation, and site morphology. The climate of the region is classified as Mediterranean Csb, with rainy winters and dry and mildly warm summers. A typical summer day is considered. The results reveal that a combination of factors might lead to thermal discomfort even in this mild climate on an average day, mainly due to heat exchange by radiation. In addition, the impact of alterations to surface properties depends on the morphological characteristics of the site, e.g., high albedo of the pavement may lead to a decrease or an increase in mean radiant temperature, depending on the space. This variability is present in the effects observed at the studied sites. A high facade albedo always contributes, in these cases, to thermal discomfort. The conclusions of the present study highlight the importance of performing a specific study for each urban site whenever an intervention is to be planned

How to Measure Socioemotional Ties in Workgroups? Validation of Workgroup Socioaffective Interdependence Scale

The main purpose of this study is the validation of the Workgroup Socioaffective Interdependence Scale – WSAIS developed by the authors in a preliminary study. The authors aim is to confirm the multidimensional structure of the measure and to analyse its psychometric properties in a sample of 488 employees from 92 teams. To test construct validity a confirmatory factor analysis was conducted, and social network density of socioemotional ties were calculated to assess convergent and discriminant validity. The findings confirm the underlying factor structure of the scale and provide support for the adequacy of the instrument as a team multidimensional measure of socioaffective interdependence

Filosofia : uma proposta de apresentação para alunos do ensino médio

Orientador : Orientador: Prof. Dr. Edmilson PaschoalMonografia (especialização) - Universidade Federal do Paraná. Coordenação de Integração de Políticas de Educação à Distância, Curso de Especialização em Ensino de Filosofia no MédioInclui referências: p. 51-53Resumo: Este trabalho versa sobre uma possível apresentação da filosofia para estudantes do ensino médio. Partindo das indagações iniciais dos estudantes que travam contato com o campo filosófico pela primeira vez, buscamos pensar em uma compreensão da filosofia que seja significativa para esse sujeito. Desse modo, analisamos a dinâmica da sociedade contemporânea, a partir das análises de Michel Foucault. Essa dinâmica revelará uma sociedade assentada nos signos do neoliberalismo e da disciplina, impedindo o pensamento crítico. Em um segundo momento, pensamos as questões iniciais que estudantes e professores enfrentam em sala de aula. Por fim, e com a intenção de responder a esses questionamentos, oferecemos uma compreensão da filosofia a partir de Michel Foucault e Pierre Hadot. Os dois pensadores tematizam a filosofia como modo de vida, isto é, não simplesmente como teorias que evoluem ao longo do tempo, mas como forma de pensar e construir a própria existência