a Python interface for SBML compatible hybrid modelling

This work was supported by the Associate Laboratory for Green Chemistry—LAQV which is financed by national funds from FCT/MCTES [UIDB/50006/2020 and UIDP/50006/2020]. This work has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement number [101000733] (PROMICON project). The authors thank H. Mochao for useful implementation ideas. JP and LA acknowledge PhD grants [SFRD/BD14610472019 and 2021.07759.BD], Fundação para a Ciência e Tecnologia (FCT) and RSC the contract [CEECIND/01399/2017].Here we present sbml2hyb, an easy-to-use standalone Python tool that facilitates the conversion of existing mechanistic models of biological systems in Systems Biology Markup Language (SBML) into hybrid semiparametric models that combine mechanistic functions with machine learning (ML). The so-formed hybrid models can be trained and stored back in databases in SBML format. The tool supports a user-friendly export interface with an internal format validator. Two case studies illustrate the use of the sbml2hyb tool. Additionally, we describe HMOD, a new model format designed to support and facilitate hybrid models building. It aggregates the mechanistic model information with the ML information and follows as close as possible the SBML rules. We expect the sbml2hyb tool and HMOD to greatly facilitate the widespread usage of hybrid modeling techniques for biological systems analysis.publishersversionpublishe

INFLUÊNCIA DO DIÂMETRO DE ESTACAS NO DESENVOLVIMENTO DOS BROTOS DE Platanus x acerifolia

O objetivo do presente trabalho foi determinar o diâmetro ideal de estacas para a produção de mudas de Platanus x acerifolia. As estacas utilizadas foram coletadas em árvores cuja a brotação apresentava-se com um ano de idade. Foram comparados três diâmetros de estacas: diâmetros inferiores a 1 cm, diâmetros entre 1 e 2 cm e diâmetros superiores a 2 cm. Todas as estacas possuiam 30 cm de comprimento. Decorridos 90 dias do plantio das estacas, foram medidas as alturas dos brotos, onde na qual o maior desenvolvimento foi observado nas estacas com diâmetro entre 1 e 2 centímetros

Macro- and microstructural descriptions of the zebrafish (Danio rerio) liver

The liver is an essential metabolically active organ, responsible for many vital life functions such as metabolism, synthesis, and storage. This study describes the macroscopic and microscopic zebrafish liver and its temporal changes during a period of 13 weeks. Forty-six adult zebrafish were used (46), of which 27 were females and were 19 males. Seven fish were euthanized initially for macroscopic evaluation and 3 fish were euthanized weekly for 13 weeks for microscopic evaluation. Routine histological technique was performed; the slides were stained with haematoxylin/eosin and periodic acid-Schiff. The volumetric (Vv(h)) and numerical (Nv(h)) densities of hepatocytes and vacuolation intensity were determined weekly. The liver was located in the coelomic cavity ventrally to the swim bladder, slightly brownish and divided into 3 hepatic lobes. Microscopically, it consisted of hepatocytes forming a muralium duplex around the sinusoids. The staining of the cytoplasm of hepatocytes was more eosinophilic and more basophilic in males and females, respectively. There was no formation of portal triads and phagocytic cells. The gallbladder had transitional epithelium, and the bile ducts had simple cuboidal epithelium. The volume and numerical density of hepatocytes during the 13 weeks was not statistically different, but these parameters displayed a positive correlation. The vacuolation was due to the presence of glycogen. The zebrafish liver has macro and micro structural particular features while, quantitatively, the volume and number of hepatocytes showed great capacity to respond to the physiological needs of the animal at the time

PDCA Method for Environmental Management of Pollutants Generated in a Battery Industry in an Amazonian City

The automotive battery industry is a fixed emission source of high pollution potential arising from secondary lead smelting processes pollutants. The management, the quality control standards of air, air pollutant emission limits as well as the allocation and disposal of waste and effluents are provided by legal norms. The objective is to identify management practices and management of atmospheric emissions and the allocation and disposal of waste and effluents in a battery industry that manufactures and reuses materials from reverse logistics to propose a management model based on PDCA- Plan, Do, Check and Act. The specific objectives are:(1)Identify the management and environmental management practices in the industry and relates them with economic development and innovation in industrial processes; (2)Check the procedures adopted for the reverse logistics management and allocation and disposal of wastes, effluents and emissions to mitigate the generation of pollutants; (3)propose management actions and environmental management, according to the PDCA method. It is a descriptive exploratory survey of bibliographical studies and field research with observations of practices in the industry and using the interview questionnaire, to present qualitative and quantitative data. The sample was randomly chosen to focus an industry that generates wastes, effluents and emissions of high polluting potential. Employing the task isintended to answer the question: An environmental management plan based on the PDCA method is able to systematize sustainable actions in an industry that generates highly toxic pollutants? The result is of interest to managers of enterprises that manufacture and reuse of waste battery. This study is important considering thelocus of research, the Amazonian City, which deserves special attention

Se deus me chamar não vou: um olhar para as emoções da infância e da adolescência

This article is characterized as a review of the book Se Deus me Chamar não Vou , by Mariana Salomão Carrara (2019). We aim to perform a critical and reflective review for teachers and educators of Basic Education, especially those who work with Elementary School. The main points that guided our reflections were dilemmas, doubts, fears, and other feelings (shown or not) by the main character in the book, which resembles the reality of pre-teens of contemporary school age, whose discussions lead us to the need to listen and discuss the meaning of life and respect the different emotions in the classroom – an important fact in order to meet the general objectives of the Base Nacional Curricular Comum (BNCC) and engender the exercise of welcoming and dialogue between people. The discussions held between the literary work and education in its emotional bias, allows us to emphasize the importance of educators to broaden the look and the care with the emotions of pre-adolescents, which is permeated with intense feelings, which often involves death or loneliness.Este trabajo se caracteriza por ser una reseña del libro titulado Se Deus me Chamar não Vou, de la escritora Mariana Salomão Carrara (2019). Pretendemos realizar una revisión crítica y reflexiva dirigida a los profesores y educadores de la Educación Básica, especialmente a los que trabajan con la Educación Primaria. Los puntos principales que guiaron nuestras reflexiones fueron los dilemas, las dudas, los miedos y otros sentimientos (mostrados o no) del personaje principal del libro que se asemejan a la realidad de los preadolescentes en edad escolar en la contemporaneidad, cuyas discusiones nos llevan a la necesidad de escuchar y debatir el sentido de la vida y respetar las diferentes emociones en el aula, hecho importante para cumplir los objetivos generales de la Base Nacional Curricular Comum brasileña y engendrar el ejercicio de la acogida y el diálogo entre las personas. Las discusiones mantenidas entre la obra literaria y la educación en su dimensión emocional nos permiten destacar la importancia de que los educadores amplíen la mirada y el cuidado con las emociones de los preadolescentes, que muchas veces implican temas como la muerte o la soledad.Este trabalho caracteriza-se como uma resenha do livro intitulado "Se deus me chamar não vou", da escritora Mariana Salomão Carrara (2019). Temos por objetivo realizar uma resenha crítica e reflexiva, destinada a professores e educadores da Educação Básica, especialmente aqueles que atuam com o Ensino Fundamental. Os principais pontos que nortearam as nossas reflexões foram dilemas, dúvidas, medos e outros sentimentos (demonstrados ou não) pela personagem principal do livro, que se assemelha à realidade de pré-adolescentes em idade escolar da contemporaneidade, cujas discussões nos conduzem à necessidade de ouvir e debater o sentido da vida e respeitar as diferentes emoções em sala de aula – fato importante para que se cumpram os objetivos gerais da Base Nacional Comum Curricular e engendrar o exercício do acolhimento e do diálogo entre as pessoas. As discussões realizadas entre a produção literária e a educação, em seu viés emocional, nos permitem ressaltar a importância de os educadores ampliarem o olhar e o cuidado com as emoções dos pré-adolescentes, que muitas vezes envolvem temas como a morte ou a solidão

Estimating genetic diversity of onion germplasm via morphological, agronomic, and biochemical descriptors

A divergência genética de 64 acessos de cebola (Allium cepa L.) tropicais e subtropicais do banco de germoplasma da Embrapa Hortaliças foi avaliada utilizando 23 descritores morfológicos, bioquímicos e agronômicos. A distância generalizada de Mahalanobis (D²) foi usada como medida de dissimilaridade e os métodos de otimização de Tocher e hierárquico do Vizinho mais Próximo foram empregados para o agrupamento dos acessos. O germoplasma de cebola avaliado apresentou base genética relativamente ampla. As cultivares EX 3000 e Régia foram os acessos geneticamente mais similares. A maior distância genética estimada foi entre os acessos VAL 14 e Beta Cristal. O método de otimização de Tocher proporcionou a formação de treze grupos, enquanto o procedimento hierárquico do vizinho mais próximo possibilitou a formação de doze grupos (corte com 43% de dissimilaridade) A maioria dos acessos dos tipos Grano e Granex, agronomicamente considerados de dias curtos e com ciclo de maturação precoce, se concentraram em mesmo grupo de similaridade genética. À exceção do acesso Tampico White, os demais acessos de bulbos brancos do tipo indústria (Beta Cristal; Dehydrator # 8; Dehydrator # 6; Primero e White Creole) exibiram estreito relacionamento. Os acessos TX 24, Baia Periforme Super Precoce, EX 3001, Excel, Red Creole, H 688, Franciscana IPA 10 e Roxa IPA 3 exibiram alta dissimilaridade genética. Os caracteres teor de açúcares totais, comprimento de bulbo, número de dias para a colheita, porcentagem de bulbos com diâmetro entre 70 e 90 mm e massa média de bulbos foram responsáveis por 58% de toda a variabilidade genética observada entre os acessos. O estudo da divergência entre acessos é importante subsídio na escolha de parentais divergentes e complementares a fim de desenvolver populações segregantes com ampla base genética em programas de melhoramento genético de cebolas tropicais.The genetic diversity of 64 tropical and subtropical onion accessions (Allium cepa L.) belonging to the Embrapa Hortaliças collection was estimated using 23 morphological, agronomic, and biochemical descriptors. Methods of multivariate statistical analysis (Mahalanobis' D² distances, Tocher's cluster analysis and nearest-neighbor method) were employed in order to obtain the average genetic distances among accessions and to perform the clustering. The onion germplasm displayed a relatively large genetic base. Cultivars EX 3000 and Régia were the two most similar accessions. The highest mean genetic distance was observed between cultivars VAL 14 and Beta Cristal. The Tocher's optimization method revealed the formation of 13 groups, whereas the nearest-neighbor method revealed the formation of 12 groups (cutting point of 43% of dissimilarity. The majority of the accessions belonging to Grano and Granex cultivars (agronomically classified as short-day and early-maturing types) clustered together in the same group. The white bulb accessions for processing (Beta Cristal; Dehydrator # 8; Dehydrator # 6; Primero and White Creole), with the exception of Tampico White, displayed a small genetic divergence. The accessions TX 24, Baia Periforme Super Precoce, EX 3001, Excel, Red Creole, H 688, Franciscana IPA 10 and Roxa IPA 3 displayed a large genetic divergence. The descriptors total sugar content, bulb length, number of days from planting to harvesting (i.e. plant cycle), percentage of bulbs with transversal diameter between 70 and 90 mm, and average bulb weight were responsible for 58% of the genetic variability present among accessions. Studies of divergence among accessions are important to choose divergent parentals but complementary genetic materials would allow the development of useful segregating populations with wide genetic basis for tropical onion breeding programs