The rise of taxon-specific epitope predictors.

Computational predictors of immunogenic peptides, or epitopes, are traditionally built based on data from a broad range of pathogens without consideration for taxonomic information. While this approach may be reasonable if one aims to develop one-size-fits-all models, it may be counterproductive if the proteins for which the model is expected to generalize are known to come from a specific subset of phylogenetically related pathogens. There is mounting evidence that, for these cases, taxon-specific models can outperform generalist ones, even when trained with substantially smaller amounts of data. In this comment, we provide some perspective on the current state of taxon-specific modelling for the prediction of linear B-cell epitopes, and the challenges faced when building and deploying these predictors.

Perceptions of health professionals in providing care for people with anorexia nervosa and bulimia nervosa: a systematic review and meta-synthesis of qualitative studies.

This study sought to synthesize and reinterpret findings from primary qualitative studies on the experience of health professionals in caring for people with anorexia nervosa and bulimia nervosa. We conducted a systematic review of the literature with the SPIDER search strategy assessing six databases. A meta-synthesis was performed with data from qualitative studies. Two independent reviewers screened and assessed the articles, extracted data from the articles and elaborated thematic synthesis. Nineteen articles met the inclusion/exclusion criteria. The meta-synthesis revealed three descriptive themes: Going outside the comfort zone: hard relational experiences of health professionals in providing care for people with anorexia nervosa and bulimia nervosa; Reflecting on treatment: relevance of discussion, communication, and flexibility in health professionals' work with anorexia nervosa and bulimia nervosa; and Dealing with ambivalences: experiences of health professionals with family members of people with anorexia nervosa and bulimia nervosa. We elaborated two analytical themes: Making work with eating disorders palatable: malleability necessary for health professionals in bonding with people with anorexia and bulimia nervosa and their families; and Leaving the professional comfort zone: transition from multi to interdisciplinary. Thus, mental health professionals who work with people diagnosed with anorexia and bulimia nervosa cope with hard emotional experiences that makes them feel out of their comfort zone, requiring flexibility to benefit a good therapeutic alliance, but there are still difficulties in promoting interdisciplinarity.

Lessons from the Evolutionary Computation Bestiary.

The field of metaheuristics has a long history of finding inspiration in natural systems, starting from evolution strategies, genetic algorithms, and ant colony optimization in the second half of the 20th century. In the last decades, however, the field has experienced an explosion of metaphor-centered methods claiming to be inspired by increasingly absurd natural (and even supernatural) phenomena-several different types of birds, mammals, fish and invertebrates, soccer and volleyball, reincarnation, zombies, and gods. Although metaphors can be powerful inspiration tools, the emergence of hundreds of barely discernible algorithmic variants under different labels and nomenclatures has been counterproductive to the scientific progress of the field, as it neither improves our ability to understand and simulate biological systems nor contributes generalizable knowledge or design principles for global optimization approaches. In this article we discuss some of the possible causes of this trend, its negative consequences for the field, and some efforts aimed at moving the area of metaheuristics toward a better balance between inspiration and scientific soundness.

CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species.

Living species vary significantly in phenotype and genomic content. Sophisticated statistical methods linking genes with phenotypes within a species have led to breakthroughs in complex genetic diseases and genetic breeding. Despite the abundance of genomic and phenotypic data available for thousands of species, finding genotype-phenotype associations across species is challenging due to the non-independence of species data resulting from common ancestry. To address this, we present CALANGO (comparative analysis with annotation-based genomic components), a phylogeny-aware comparative genomics tool to find homologous regions and biological roles associated with quantitative phenotypes across species. In two case studies, CALANGO identified both known and previously unidentified genotype-phenotype associations. The first study revealed unknown aspects of the ecological interaction between Escherichia coli, its integrated bacteriophages, and the pathogenicity phenotype. The second identified an association between maximum height in angiosperms and the expansion of a reproductive mechanism that prevents inbreeding and increases genetic diversity, with implications for conservation biology and agriculture.

Why are some plants taller? Researchers on the unveiling of genetic variation associated with complex quantitative phenotypes.

Francisco Pereira Lobo, Giovanni Marques de Castro, and Felipe Campelo are part of an international team of collaborators that developed CALANGO, a comparative genomics tool to investigate quantitative genotype-phenotype relationships. Their Patterns article highlights how the tool integrates species-centric data to perform genome-wide search and detect genes potentially involved in the emergence of complex quantitative traits across species. Here, they talk about their view of data science, their experience with interdisciplinary research, and the potential applications of their tool.

Perceptions of health professionals in providing care for people with anorexia nervosa and bulimia nervosa: a systematic review and meta-synthesis of qualitative studies / Percepções de profissionais de saúde no cuidado a pessoas com anorexia e bulimia nervosa: revisão sistemática e metassíntese de estudos qualitativos / Percepciones de los profesionales de la salud en el cuidado de personas con anorexia y bulimia nerviosa: revisión sistemática y metasíntesis de estudios cualitativos

Abstract: This study sought to synthesize and reinterpret findings from primary qualitative studies on the experience of health professionals in caring for people with anorexia nervosa and bulimia nervosa. We conducted a systematic review of the literature with the SPIDER search strategy assessing six databases. A meta-synthesis was performed with data from qualitative studies. Two independent reviewers screened and assessed the articles, extracted data from the articles and elaborated thematic synthesis. Nineteen articles met the inclusion/exclusion criteria. The meta-synthesis revealed three descriptive themes: Going outside the comfort zone: hard relational experiences of health professionals in providing care for people with anorexia nervosa and bulimia nervosa; Reflecting on treatment: relevance of discussion, communication, and flexibility in health professionals' work with anorexia nervosa and bulimia nervosa; and Dealing with ambivalences: experiences of health professionals with family members of people with anorexia nervosa and bulimia nervosa. We elaborated two analytical themes: Making work with eating disorders palatable: malleability necessary for health professionals in bonding with people with anorexia and bulimia nervosa and their families; and Leaving the professional comfort zone: transition from multi to interdisciplinary. Thus, mental health professionals who work with people diagnosed with anorexia and bulimia nervosa cope with hard emotional experiences that makes them feel out of their comfort zone, requiring flexibility to benefit a good therapeutic alliance, but there are still difficulties in promoting interdisciplinarity.

Resumo: Este estudo buscou sintetizar e reinterpretar os achados de estudos qualitativos primários sobre a experiência de profissionais de saúde no cuidado a pessoas com anorexia e bulimia nervosa. Realizamos uma revisão sistemática da literatura com a estratégia de busca estruturada SPIDER em seis bases de dados. Foi realizada uma metassíntese com dados destes estudos qualitativos. Os artigos foram triados e avaliados por dois revisores independentes que extraíram dados desses artigos e elaboraram uma síntese temática. No total, 19 artigos atenderam nossos critérios de inclusão e exclusão. A metassíntese revelou três temas descritivos: Sair da zona de conforto: profissionais de saúde tiveram vivências relacionais difíceis no cuidado à pessoa com anorexia e bulimia nervosa; Refletir sobre o tratamento: a relevância da discussão, comunicação e flexibilidade no trabalho dos profissionais de saúde; e Lidar com ambivalências: vivências de profissionais de saúde com familiares de pessoas com anorexia e bulimia nervosa. Elaboramos dois temas analíticos: Tornando o trabalho com distúrbios alimentares agradável: maleabilidade necessária para vincular profissionais de saúde à pessoa com anorexia e bulimia nervosa e sua família; e Saindo da zona de conforto profissional: transição do multi para o interdisciplinar. Assim, os profissionais de saúde mental que trabalham com pessoas diagnosticadas com anorexia e bulimia nervosa enfrentam experiências emocionais difíceis que os fazem se sentir fora de sua zona de conforto, exigindo flexibilidade para o benefício de uma boa aliança terapêutica, mas ainda há dificuldades em promover a interdisciplinaridade.

Resumen: Este estudio buscó sintetizar y reinterpretar los hallazgos de estudios cualitativos primarios sobre la experiencia de profesionales de la salud en el cuidado de personas con anorexia y bulimia nerviosa. Realizamos una revisión sistemática de la literatura con la estrategia de búsqueda estructurada SPIDER en seis bases de datos. Se realizó una metasíntesis con los datos de estos estudios cualitativos. Los artículos fueron seleccionados y evaluados por dos revisores independientes que extrajeron datos de estos artículos y elaboraron una síntesis temática. En total, 19 artículos cumplieron con nuestros criterios de inclusión y exclusión. La metasíntesis reveló tres temas descriptivos: Salir de la zona de confort: los profesionales de la salud tuvieron vivencias relacionales difíciles en el cuidado a la persona con anorexia y bulimia nerviosa; Reflexionar sobre el tratamiento: la relevancia de la discusión, la comunicación y la flexibilidad en el trabajo de los profesionales de la salud; y Lidiar con las ambivalencias: experiencias de los profesionales de la salud con familiares de personas con anorexia y bulimia nerviosa. Elaboramos dos temas analíticos: Hacer agradable el trabajo con los trastornos alimentarios: maleabilidad necesaria para vincular a los profesionales de la salud con la persona con anorexia y bulimia nerviosa y su familia; y Salir de la zona de confort profesional: transición de lo múltiple a lo interdisciplinario. Por lo tanto, los profesionales de la salud mental que trabajan con personas diagnosticadas con anorexia y bulimia nerviosa enfrentan experiencias emocionales difíciles que los hacen sentir fuera de su zona de confort, lo que requiere flexibilidad en beneficio de una buena alianza terapéutica, pero aún existen dificultades para promover la interdisciplinariedad.

The role of human bocavirus as an agent of community-acquired pneumonia in children under 5 years of age in Fortaleza, Ceará (Northeast Brazil).

The human bocavirus (HBoV) is an agent of upper and lower respiratory infections, affecting mainly children under 5 years of age. Community-acquired pneumonia (CAP) is an important public health problem in developing countries, representing one of the main causes of hospitalizations and deaths in children. The aim of this study was to describe the prevalence of HBoV and the clinical and epidemiological characteristics in children diagnosed with CAP. For this purpose, nasopharyngeal aspirates were collected from 545 children aged 0 to 60 months diagnosed with CAP between January 2013 and December 2014 in a reference pediatric hospital in Fortaleza, Ceará, Brazil. The samples were subjected to PCR for detection of HBoV and parainfluenza 4 (PIV4) and indirect immunofluorescence for detection of respiratory syncytial virus (RSV), adenovirus (AdV), influenza A and B (FLU A and FLU B), and parainfluenza 1, 2, and 3 (PIV1, PIV2, PIV3). Clinically, most CAP were non-complicated (487/545; 89.3%); however, 10.7% (58/545) of children were treated in the ICU/resuscitation sector. Among the total samples analyzed, 359 (65.8%) were positive for at least one virus surveyed and 105 (19.2%) samples had two or more viruses. HBoV was detected in 87 samples (15.9%), being the second most prevalent virus. RSV, AdV, FLU A, FLU B, and PIV 1-3 were detected in 150 (27.5%), 45 (8.2%), 30 (5.5%), 3 (0.5%), and 131 (24%) samples, respectively. The age average was 12.1 months in children infected with HBoV, and the most frequent symptoms were dyspnea and cough. In addition, 90.6% of HboV-positive children received antibiotics as empirical treatment. HBoV did not show any circulation pattern; however, it seemed to be more frequent in the first half of the year, totaling 68.9% of the cases. HBoV is a frequent agent of pneumonia in the child population studied.

SARS-CoV-2 IgG Seroprevalence among Blood Donors as a Monitor of the COVID-19 Epidemic, Brazil.

During epidemics, data from different sources can provide information on varying aspects of the epidemic process. Serology-based epidemiologic surveys could be used to compose a consistent epidemic scenario. We assessed the seroprevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) IgG in serum samples collected from 7,837 blood donors in 7 cities of Brazil during March-December 2020. Based on our results, we propose a modification in a compartmental model that uses reported number of SARS-CoV-2 cases and serology results from blood donors as inputs and delivers estimates of hidden variables, such as daily values of SARS-CoV-2 transmission rates and cumulative incidence rate of reported and unreported SARS-CoV-2 cases. We concluded that the information about cumulative incidence of a disease in a city's population can be obtained by testing serum samples collected from blood donors. Our proposed method also can be extended to surveillance of other infectious diseases.

Organism-specific training improves performance of linear B-cell epitope prediction.

MOTIVATION: In silico identification of linear B-cell epitopes represents an important step in the development of diagnostic tests and vaccine candidates, by providing potential high-probability targets for experimental investigation. Current predictive tools were developed under a generalist approach, training models with heterogeneous datasets to develop predictors that can be deployed for a wide variety of pathogens. However, continuous advances in processing power and the increasing amount of epitope data for a broad range of pathogens indicate that training organism or taxon-specific models may become a feasible alternative, with unexplored potential gains in predictive performance. RESULTS: This article shows how organism-specific training of epitope prediction models can yield substantial performance gains across several quality metrics when compared to models trained with heterogeneous and hybrid data, and with a variety of widely used predictors from the literature. These results suggest a promising alternative for the development of custom-tailored predictive models with high predictive power, which can be easily implemented and deployed for the investigation of specific pathogens. AVAILABILITY AND IMPLEMENTATION: The data underlying this article, as well as the full reproducibility scripts, are available at https://github.com/fcampelo/OrgSpec-paper. The R package that implements the organism-specific pipeline functions is available at https://github.com/fcampelo/epitopes. SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.