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The vast amount of genome sequence data that is available, and that is predicted to drastically increase in the near future, can only be efficiently dealt with by building automated pipelines. Indeed, the Earth Biogenome Project will produce high-quality reference genome sequences for all 1.8 million named living eukaryote species, providing unprecedented insight into the evolution of genes and gene families, and thus on biological issues. Here, new modules for gene annotation, further BLAST search algorithms, further multiple sequence alignment methods, the adding of reference sequences, further tree rooting methods, the estimation of rates of synonymous and nonsynonymous substitutions, and the identification of positively selected amino acid sites, have been added to auto-phylo (version 2), a recently developed software to address biological problems using phylogenetic inferences. Additionally, we present auto-phylo-pipeliner, a graphical user interface application that further facilitates the creation and running of auto-phylo pipelines. Inferences on S-RNase specificity, are critical for both cross-based breeding and for the establishment of pollination requirements. Therefore, as a test case, we develop an auto-phylo pipeline to identify amino acid sites under positive selection, that are, in principle, those determining S-RNase specificity, starting from both non-annotated Prunus genomes and sequences available in public databases.

The BA.5 lineage of the SARS-CoV-2 Omicron variant emerged in South Africa in February 2022 (1) and rapidly spread to other countries (2). In Portugal, the first BA.5 case was [...]

A presente pesquisa teve como objetivo realizar uma revisão de literatura a fim de identificar a produção sobre mídia desenvolvida pela área da psicologia no Brasil. Para tanto, foram feitos levantamentos em bases de dados nacionais, utilizando duas combinações de descritores: mídia e psicologia; comunicação e psicologia. Com os dados obtidos foi possível verificar a exígua produção sobre o tema. Por meio da análise dos artigos foram identificados autores e instituições que se destacam na produção do conhecimento sobre o assunto. Também, verificou-se que a mídia aparece nos artigos tanto como objeto de estudo, quanto como instrumento para coleta de informações. A análise apontou que o interesse pela psicologia em pesquisar a mídia aumentou na última década. Nos últimos anos, o meio digital vem ganhando destaque entre as pesquisas. Por fim, espera-se que esta pesquisa, além de apresentar um panorama da produção acadêmica da psicologia brasileira sobre mídia, possa apontar as lacunas, indicando novas e urgentes possibilidades de investigação sobre a interface mídia e psicologia.

In this work, we present a review of Energy-Momentum Squared Gravity (EMSG)—more specifically, f (R , T μ ν T μ ν) gravity, where R represents the Ricci scalar and T μ ν denotes the energy-momentum tensor. The inclusion of quadratic contributions from the energy-momentum components has intriguing cosmological implications, particularly during the Universe's early epochs. These effects dominate under high-energy conditions, enabling EMSG to potentially address unresolved issues in General Relativity (GR), such as the initial singularity and aspects of big-bang nucleosynthesis in certain models. The theory's explicit non-minimal coupling between matter and geometry leads to the non-conservation of the energy-momentum tensor, which prompts the investigation of cosmological scenarios through the framework of irreversible thermodynamics of open systems. By employing this formalism, we interpret the energy-balance equations within EMSG from a thermodynamic perspective, viewing them as descriptions of irreversible matter creation processes. Since EMSG converges to GR in a vacuum and differences emerge only in the presence of an energy-momentum distribution, these distinctions become significant in high-curvature regions. Therefore, deviations from GR are expected to be pronounced in the dense cores of compact objects. This review delves into these facets of EMSG, highlighting its potential to shed light on some of the fundamental questions in modern cosmology and gravitational theory. [ABSTRACT FROM AUTHOR]

Resumo O presente artigo objetiva compreender como profissionais de psicologia relacionam-se com as mídias. Para tanto, serão apresentados resultados de uma pesquisa realizada com psicólogos residentes no estado de Santa Catarina, a fim de verificar como eles lidam com as mídias, tanto como fonte de informação quanto como objeto e ferramenta de trabalho. Neste estudo, entende-se a mídia como um instrumento de mediação que contribui para o processo de constituição de subjetividades, sendo assim, um campo que merece atenção por parte da Psicologia. Os dados obtidos foram submetidos à análise estatística descritiva e as respostas às questões discursivas foram analisadas por meio do método da análise de conteúdo temática. Entre os resultados encontrados, a mídia figura como um tema raramente discutido durante a formação. Destaca-se, também, a centralidade da internet como meio para obtenção de informações, de modo que o celular é o dispositivo mais acessado para essa finalidade. Além disso, as redes sociais são utilizadas por 65% dos participantes para a troca e compartilhamento de informações profissionais. Tal fato aponta para a importância de pensar os novos modos de interação com a mídia, bem como o alcance das transformações que as mídias já têm operado. Frente a isso, surgem importantes questões éticas que merecem ser alvo de discussão por parte da Psicologia. Diante da escassez de discussões acerca da interface mídia e Psicologia, espera-se que esta pesquisa contribua para a ampliação desse debate e seus desdobramentos práticos.

Este artigo tem a proposta de desenvolver reflexões sobre a relação entre feminismos e as mídias digitais, a partir do atual contexto social e político brasileiro. O artigo explora o modo como o movimento feminista tem se apropriado do meio digital como espaço de divulgação de suas pautas. As discussões apontam para a presença de uma dualidade em relação ao feminismo digital: ao mesmo tempo em que se apresenta como um espaço de militância e de visibilidade, suas pautas são apropriadas e mercantilizadas, tornando-se alvo de disputas mercadológicas. Porém, mesmo em meio a embates políticos, ataques conservadores e fortalecimento de preceitos neoliberais, as ações feministas ligadas à esfera digital têm cumprido um papel central de luta e resistência.

This study extensively analyzed campylobacteriosis surveillance in Portugal from 2009 to 2021, aiming to investigate demographic shifts, seasonal variations, and antimicrobial resistance (AMR) within Campylobacter isolates. Surveillance network and sentinel laboratory-based system data revealed a substantial under-notification of campylobacteriosis cases, suggesting an underestimated disease burden. Notification rates exhibited a paradigm shift, with a notable prevalence among the pediatric population, particularly in children aged 1–4 years, diverging from European reports. Additionally, an emerging trend of Campylobacter infections in younger adults (15–44 years) was observed. The study unveiled a unique seasonal distribution of cases, defying typical summer peaks seen elsewhere. AMR analysis revealed high resistance to ciprofloxacin and tetracycline, in both C. jejuni (93.7% and 79.2%, respectively) and C. coli (96.5% and 93.2%, respectively), stable throughout the studied period (2013–2021). C. coli exhibited significantly higher resistance to erythromycin, gentamicin, ampicillin and ertapenem compared to C. jejuni (p < 0.001). Multilocus Sequence Typing (MLST) data demonstrated the distribution of resistance markers across diverse sequence types, challenging the notion of a clonal origin for multidrug-resistant isolates. In conclusion, the study highlights the need for enhanced surveillance and raises concerns about alarming AMR levels, recommending the implementation of whole-genome sequencing (WGS)-based surveillance for a deeper comprehension of disease patterns and an evolving AMR landscape. [ABSTRACT FROM AUTHOR]

Recently, the scalar–tensor representation of f (R, T) gravity was used to explore gravitationally induced particle production/annihilation. Using the framework of irreversible thermodynamics of open systems in the presence of matter creation/annihilation, the physical and cosmological consequences of this setup were investigated in detail. In this paper, we test observationally the scalar–tensor representation of f (R, T) gravity in the context of the aforementioned framework, using the Hubble and Pantheon + measurements. The best fit parameters are obtained by solving numerically the modified Friedmann equations of two distinct cosmological models in scalar–tensor f (R, T) gravity, corresponding to two different choices of the potential, and by performing a Markov Chain Monte Carlo analysis. The best parameters are used to compute the cosmographic parameters, that is, the deceleration, the jerk, and the snap parameters. Using the output resulting from the Markov Chain Monte Carlo analysis, the cosmological evolution of the creation pressure and of the matter creation rates are presented for both models. To figure out the statistical significance of the studied scalar–tensor f (R, T) gravity, the Bayesian and the corrected Akaike information criteria are used. The latter indicates that the first considered model in scalar–tensor f (R, T) gravity is statistically better than ΛCDM, that is, it is more favoured by observations. Besides, a continuous particle creation process is present in Model 1. Alternatively, for large redshifts, in Model 2 the particle creation rate may become negative, thus indicating the presence of particle annihilation processes. However, both models lead to an accelerating expansion of the universe at late times, with a deceleration parameter equivalent to that of the ΛCDM model. [ABSTRACT FROM AUTHOR]

The Mycobacterium abscessus complex (MABC) is an emerging, difficult to treat, multidrug-resistant nontuberculous mycobacteria responsible for a wide spectrum of infections and associated with an increasing number of cases worldwide. Dominant circulating clones (DCCs) of MABC have been genetically identified as groups of strains associated with higher prevalence, higher levels of antimicrobial resistance, and worse clinical outcomes. To date, little is known about the genomic characteristics of MABC species circulating in Portugal. Here, we examined the genetic diversity and antimicrobial resistance profiles of 30 MABC strains isolated between 2014 and 2022 in Portugal. The genetic diversity of circulating MABC strains was assessed through a gene-by-gene approach (wgMLST), allowing their subspecies differentiation and the classification of isolates into DCCs. Antimicrobial resistance profiles were defined using phenotypic, molecular, and genomic approaches. The majority of isolates were resistant to at least two antimicrobials, although a poor correlation between phenotype and genotype data was observed. Portuguese genomes were highly diverse, and data suggest the existence of MABC lineages with potential international circulation or cross-border transmission. This study highlights the genetic diversity and antimicrobial resistance profile of circulating MABC isolates in Portugal while representing the first step towards the implementation of a genomic-based surveillance system for MABC at the Portuguese NIH. [ABSTRACT FROM AUTHOR]

Understanding the relationship between environmental temperature and the biological traits of organisms is fundamental to inferring the potential impacts of climate change. In the case of marine poikilotherm species, seawater temperature is one of the main driving forces of biological processes, with consequences at higher levels of organization such as population and ecosystem. In this study, we analysed differences in maximum carapace width (CWmax), size at maturation, relative size at maturation, and duration of the reproductive season for the green crab (Carcinus maenas) along a temperature gradient. An extensive review of bibliographic data was performed on studies published between 1962 and 2020, gathering C. maenas data from 55 different populations, spread over 20 degrees of latitude and 14.2 °C of sea surface temperature (SST). In addition, green crab data were collected at five different lagoons and estuaries along the continental Portuguese coast. The relationship between average SST and CWmax, age of maturation, reduction of size at maturation, and duration of egg bearing was analysed to understand the role of SST in driving variation in these C. maenas characteristics across a latitudinal gradient. There was a significant relationship between SST and CWmax for males and SST and CW of females at maturation, respectively. The results extrapolate for each local projected temperature increase caused by climate change and suggest an effect on the morphometric and reproductive traits of C. maenas across regions. These changes comprise an overall reduction in C. maenas body size, an enlargement of the reproductive season, a shortening in the duration of larval developmental time, and a decrease in the relative size of crabs at maturation. Secondary consequences on the fecundity and connectivity of populations are discussed. [ABSTRACT FROM AUTHOR]