The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors

The function of proteins can often be inferred from their three-dimensional structures. Experimental structural biologists spent decades studying these structures, but the accelerated pace of protein sequencing continuously increases the gaps between sequences and structures. The early 2020s saw the advent of a new generation of deep learning-based protein structure prediction tools that offer the potential to predict structures based on any number of protein sequences. In this review, we give an overview of the impact of this new generation of structure prediction tools, with examples of the impacted field in the life sciences. We discuss the novel opportunities and new scientific and technical challenges these tools present to the broader scientific community. Finally, we highlight some potential directions for the future of computational protein structure prediction

Maternal recognition of child mental health problems in two Brazilian cities

Objective: To identify child behaviors and types of impairment that increase the likelihood of maternal recognition of emotional/behavioral problems (EBP) in children and adolescents. Methods: Maternal-reported data were obtained from two subsamples of 11-to-16-year-olds derived from cross-sectional studies conducted in two Brazilian municipalities: Itaborai, state of Rio de Janeiro (n=480), and Embu, state of Sao Paulo (n=217). The Itaborai study involved a representative sample of 6-to-16-year-olds (n=1,248response rate = 86.0%) selected from the Family Health Program registry, which covered 85.5% of the municipal population. The Embu study was based on a probabilistic sample of clusters of eligible households (women aged 15-49 years, child < 18 years), with one mother-child pair selected randomly per household (n=813response rate = 82.4%). The outcome variable was mother's opinion of whether her child had EBP. Potential correlates included types of child behaviors (hyperactivity/conduct/emotional problems as isolated or combined conditions) and impairment, assessed using the Strengths and Difficulties Questionnaire (SDQ)child's age and gendermaternal education and anxiety/depression (assessed using the Self-Reporting Questionnaire [SRQ]). Results: Multivariate regression models identified the following correlates of maternal perception of child EBP: comorbidity (co-occurring hyperactivity/conduct/emotional problems), emotional problems alone, and interference of problems with classroom learning and friendships. Conclusion: Comorbidity of different problem types, emotional problems alone, and interference with classroom learning and friendships increase the likelihood of maternal recognition of EBP in children.Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPqMCT/CNPq/CT-Saude/MS/SCTIE/DECIT grant) [33/2008]Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [00/14555-4]Univ Fed Sao Paulo UNIFESP, Dept Psiquiatria, Sao Paulo, SP, BrazilUniv Cambridge, Dept Psychiat, Cambridge, EnglandUniv Fed Pelotas, Programa Posgrad Epidemiol, Pelotas, RS, BrazilUniv Fed Sao Paulo UNIFESP, Dept Psiquiatria, Sao Paulo, SP, BrazilCNPqMCT/CNPq/CT-Saude/MS/SCTIE/DECIT grant) [33/2008]FAPESP [00/14555-4]Web of Scienc

Caracterização dos estádios de desenvolvimento do girassol e sua relação com alguns parâmetros climáticos.

bitstream/item/54002/1/29.pd

TrajPy: empowering feature engineering for trajectory analysis across domains

Trajectories, sequentially measured quantities that form a path, are an important presence in many different fields, from hadronic beams in physics to electrocardiograms in medicine. Trajectory anal-ysis requires the quantification and classification of curves either using statistical descriptors or physics-based features. To date, there is no extensive and user-friendly package for trajectory anal-ysis available, despite its importance and potential application across domains. We developed a free open-source python package named TrajPy as a complementary tool to empower trajectory analysis. The package showcases a friendly graphic user interface and provides a set of physical descriptors that help characterizing these intricate structures. In combina-tion with image analysis, it was already successfully applied to the study of mitochondrial motility in neuroblastoma cell lines and to the analysis of in silico models for cell migration. The TrajPy package was developed in Python 3 and released under the GNU GPL-3 license. Easy installation is available through PyPi and the development source code can be found in the repository https://github.com/ocbe-uio/TrajPy/. The package release is automatically archived under the DOI 10.5281/zenodo.3656044.Comment: 4 pages, 1 figur

REGULATION OF MEMBRANE BAND 3 TYR-PHOSPHORYLATION BY PROTEOLYSIS OF P72 AND POSSIBLE INVOLVEMENT IN SENESCENCE PROCESS

Erythrocyte senescence is characterized by exposure of cell surface epitopes on cell membrane proteins leading to immune mediated removal of red blood cells. One mechanism for antigen formation is tyrosine phosphorylation (Tyr-P) of the transmembrane protein band 3 by Syk kinase. Our aim was to test the hypothesis that proteolytic activation of Syk kinase by conversion from 72 kDa (p72Syk) to the 36 kDa (p36Syk) isoform enhances its phosphorylating activity independently of the association of Syk kinase with the cytoskeleton. Tyr-P assay was conducted using quantification of 32P uptake into the cytoplasmic domain of band 3 after addition of p72Syk or p36Syk. Effect of prephosphorylation of erythrocyte membrane band 3 protein by p36Syk on p72Syk-mediated phosphorylation and the effect of addition of a protease inhibitor (leupeptin) on p72Syk-mediated phosphorylation were studied by autoradiographic visualization of 32P uptake. Tyr-P by Syk isoforms of membrane skeletal and soluble fractions of band 3 was visualized by immunoblotting. It was found that p36Syk had a higher band 3 tyrosine phosphorylating activity compared with p72Syk. Pre-phosphorylation with p36Syk or p72Syk increased band 3 phosphorylating activity. Protease inhibition treatment reduced p72Syk but not p36Syk band 3 tyrosine phosphorylating activity significantly. Both soluble and membrane skeletal fractions of band 3 protein were equally tyrosine phosphorylated by each Syk isoform. In conclusion, we confirmed the hypothesis that proteolytic cleavage of p72Syk is an important regulatory step for band 3 Tyr-P and its independence of the association of band 3 with the cytoskeleton

INFLUÊNCIA DO CONSUMO DE ÁGUA EM INDIVÍDUOS DA TERCEIRA IDADE PRATICANTES DE HIDROGINÁSTICA NA ACADEMIA FIT FOZ

Analisou-se 20 praticantes de hidroginástica da terceira idade da academia Fit Foz, na cidade de Foz do Iguaçu, integrantes do grupo “melhor idade”, com a finalidade de verificar o consumo de água em ambos os sexos. Acompanhou-se, durante o período das aulas, o consumo de água ingerido pelos participantes, obtendo também dados sobre o consumo de água durante o dia. As mulheres obtiveram maior porcentagem do que os homens em relação ao seu consumo de água, porém, o grupo masculino obteve maiores resultados nos dados antropométricos. Ao analisar a média de qualidade de vida, observamos que Capacidade Funcional, Estado Geral de Saúde e Vitalidade obtiveram os melhores resultados com as faixas entre 70-79 anos, concluindo que as mesmas têm melhor qualidade de vida que as outras faixas estudadas. Limitação por aspectos Físicos, Limitações por Aspectos Emocionais e Dor estão relacionadas com a restrição à atividade e conseqüentemente alteração negativa na qualidade de vida. A faixa etária que mais reclamou foram as de 60-69 anos, com maiores resultados, as outras, no somatório tiveram menores escores. Na Saúde Mental, duas faixas etárias empataram, as de 50-59 e 70-79 anos, deixando os piores resultados para a faixa etária de 60-69 anos, corroborando o item anterior. Isso nos leva a concluir que as mulheres que pior se relacionam à qualidade de vida estão na faixa etária entre 60-69 anos

Interactional positioning and narrative self-construction in the first session of psychodynamic-interpersonal psychotherapy

The purpose of this study is to identify possible session one indicators of end of treatment psychotherapy outcome using the framework of three types of interactional positioning; client’s self-positioning, client’s positioning between narrated self and different partners, and the positioning between client and therapist. Three successful cases of 8-session psychodynamic-interpersonal (PI) therapy were selected on the basis of client Beck Depression Inventory scores. One unsuccessful case was also selected against which identified patterns could be tested. The successful clients were more descriptive about their problems and demonstrated active rapport-building, while the therapist used positionings expressed by the client in order to explore the positionings developed between them during therapy. The unsuccessful case was characterized by lack of positive self-comment, minimization of agentic self-capacity, and empathy-disrupting narrative confusions. We conclude that the theory of interactional positioning has been useful in identifying patterns worth exploring as early indicators of success in PI therapy

A Component Framework for Java-based Real-time Embedded Systems

Rank (CORE): A.International audienceThe Real-Time Specification for Java (RTSJ) is becoming a popular choice in the world of real-time and embedded programming. However, RTSJ introduces many non-intuitive rules and restrictions which prevent its wide adoption. Moreover, current state-of-the-art frameworks usually fail to alleviate the development process into higher layers of the software development life-cycle. In this paper we extend our philosophy that RTSJ concepts need to be considered at early stages of software development, postulated in our prior work, in a framework that provides continuum between the design and implementation process. A component model designed specially for RTSJ serves here as a cornerstone. As the first contribution of this work, we propose a development process where RTSJ concepts are manipulated independently from functional aspects. Second, we mitigate complexities of RTSJ-development by automatically generating execution infrastructure where real-time concerns are transparently managed. We thus allow developers to create systems for variously constrained real-time and embedded environments. Performed benchmarks show that the overhead of the framework is minimal in comparison to manually written object-oriented approach, while providing more extensive functionality. Finally, the framework is designed with the stress on dynamic adaptability of target systems, a property we envisage as a fundamental in an upcoming era of massively developed real-time systems

Human neutrophil alloantigens systems

Neutrophil alloantigens are involved in a variety of clinical conditions including immune neutropenias, transfusion-related acute lung injury (TRALI), refractoriness to granulocyte transfusions and febrile transfusion reactions. In the last decade, considerable progress has been made in the characterization of the implicated antigens. Currently, seven antigens are assigned to five human neutrophil antigen (HNA) systems. The HNA-1a, HNA-1b and HNA-1c antigens have been identified as polymorphic forms of the neutrophil Fcγ receptor IIIb (CD16b), encoded by three alleles. Recently, the primary structure of the HNA-2a antigen was elucidated and the HNA-2a-bearing glycoprotein was identified as a member of the Ly-6/uPAR superfamily, which has been clustered as CD177. The HNA-3a antigen is located on a 70-95 kDa glycoprotein; however, its molecular basis is still unknown. Finally, the HNA-4a and HNA-5a antigens were found to be caused by single nucleotide mutations in the αM (CD11b) and αL (CD11a) subunits of the leucocyte adhesion molecules (β2 integrins). Molecular and biochemical characterization of neutrophil antigenshave expanded our diagnostic tools by the introduction of genotyping techniques and immunoassays for antibody identification. Further studies in the field of neutrophil immunology will facilitate the prevention and management of transfusion reactions and immune diseases caused by neutrophil antibodies.Os aloantígenos de neutrófilos estão associados a várias condições clínicas como neutropenias imunes, insuficiência pulmonar relacionada à transfusão (TRALI), refratariedade à transfusão de granulócitos, e reações transfusionais febris. Na última década, foi observado considerável progresso na caracterização dos aloantígenos envolvidos nestas condições clínicas. Atualmente sete antígenos estão incluídos em cinco sistemas de antígenos de neutrófilo humano (HNA). Os antígenos HNA-1a, HNA-1b e HNA-1c foram identificados como formas polimórficas do receptor Fcγ RIIIb (CD16b), codificados por três alelos. Recentemente, a estrutura primária do antígeno HNA-2a foi elucidada e a glicoproteína carreadora do antígeno foi identificada como um membro da superfamília Ly-6/uPARe designada como CD177. O antígeno HNA-3a está localizadoem uma glicoproteína de 70-90 kDa, entretanto sua base molecular ainda é desconhecida. Finalmente, os antígenos HNA-4ae HNA-5a são resultantes de mutações de um único nucleotídeo nas subunidades αM (CD11b) and αL (CD11a) das moléculas de adesão de leucócitos (β2 integrinas). A caracterização molecular e bioquímica dos antígenos neutrofílicos permitiu a expansão das ferramentas diagnósticas pela introdução de técnicas de genotipagem e imunoensaios para a identificação de anticorpos. Novos estudos envolvendo a imunologia de granulócitos serão de grande valor para a prevenção e tratamento de reações transfusionais e doenças imunes causadas por aloanticorpos de neutrófilos.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Universidade Federal de São Paulo (UNIFESP)UNIFESPSciEL