VALIDAÇÃO DE PROTOCOLO ELETRÔNICO MULTIPROFISSIONAL PARA CIRURGIA DO APARELHO DIGESTIVO

Background: The creation of a computerized clinical database with the ability to collect prospective information from patients and with the possibility of rescue and crossing data enables scientific studies of higher quality and credibility in less time. Aim: To validate, in a single master protocol, the clinical data referring to Surgery of Digestive System in a multidisciplinary way, incorporating it in the SINPEâ platform, and to verify the incidence of digestive diseases based on the prospectively performed collections. Method: Organize in one software, in a standardized structure, all the pre-existing items in the SINPEâ database; the theoretical basis was computerized through the MIGRASINPEâ module creating a single multiprofessional master protocol for use as a whole. Results: The existing specific protocols were created and/or adapted – they correspond to the most prevalent digestive diseases - unifying them. The possibility of multiprofessional use was created by integrating all data collected from Medicine, Nursing, Physiotherapy, Nutrition and Health Management in a prospective way. The total was 4,281 collections, distributed as follows: extrahepatic biliary tract n=1,786; esophagus n=1015; anorectal n=736; colon n=550; small intestine n=86; pancreas n=71; stomach=23; liver n=14. Conclusions: The validation of the unification and structuring in a single master protocol of the clinical data referring to the Surgery of the Digestive System in a multiprofessional and prospective way was possible and the epidemiological study carried out allowed to identify the most prevalent digestive diseases in a tertiary university hospital.Racional: A criação de um banco de dados clínicos informatizado com a capacidade de coletar informações dos pacientes de forma prospectiva e com possibilidade de resgate e cruzamento viabiliza estudos científicos de maior qualidade e credibilidade em menor tempo. Objetivos: Validar em único protocolo mestre os dados clínicos referentes à Cirurgia do Aparelho Digestivo de forma multiprofissional incorporando-o na plataforma SINPEâ, e verificar a incidência das doenças digestivas com base nas coletas prospectivamente realizadas. Método: Organizar no software em estrutura padronizada todos os itens pré-existentes no banco de dados do SINPEâ, informatizou-se a base teórica através do módulo MIGRASINPE© criando-se um único protocolo mestre multiprofissional para uso como um todo. Resultados: Foram criados e/ou adaptados os protocolos específicos existentes - que correspondem às doenças mais prevalentes que assolam este aparelho – unificando-os. Criou-se a possibilidade de uso multiprofissional integrando todos os dados coletados da Medicina, Enfermagem, Fisioterapia, Nutrição e Gestão em Saúde de maneira prospectiva. O total foi de 4.281 coletas assim distribuídas: vias biliares extra-hepáticas n=1.786; esôfago n=1015; anorretais n=736; cólon n=550; intestino delgado n=86; pâncreas n=71; estômago=23; fígado n=14.  Conclusões: A validação da unificação e estruturação em único protocolo mestre dos dados clínicos referentes à Cirurgia do Aparelho Digestivo de forma multiprofissional e prospectiva foi possível e o estudo epidemiológico realizado permitiu identificar as doenças mais prevalentes nesse aparelho em um hospital universitário terciário

Multidrug resistance 1 gene polymorphisms may determine Crohn's disease behavior in patients from Rio de Janeiro

OBJECTIVES: Conflicting data from studies on the potential role of multidrug resistance 1 gene polymorphisms in inflammatory bowel disease may result from the analysis of genetically and geographically distinct populations. Here, we investigated whether multidrug resistance 1 gene polymorphisms are associated with inflammatory bowel diseases in patients from Rio de Janeiro. METHODS: We analyzed 123 Crohn's disease patients and 83 ulcerative colitis patients to determine the presence of the multidrug resistance 1 gene polymorphisms C1236T, G2677T and C3435T. In particular, the genotype frequencies of Crohn's disease and ulcerative colitis patients were analyzed. Genotype-phenotype associations with major clinical characteristics were established, and estimated risks were calculated for the mutations. RESULTS: No significant difference was observed in the genotype frequencies of the multidrug resistance 1 G2677T/A and C3435T polymorphisms between Crohn's disease and ulcerative colitis patients. In contrast, the C1236T polymorphism was significantly more common in Crohn's disease than in ulcerative colitis (p = 0.047). A significant association was also found between the multidrug resistance 1 C3435T polymorphism and the stricturing form of Crohn's disease (OR: 4.13; p = 0.009), whereas no association was found with penetrating behavior (OR: 0.33; p = 0.094). In Crohn's disease, a positive association was also found between the C3435T polymorphism and corticosteroid resistance/refractoriness (OR: 4.14; p = 0.010). However, no significant association was found between multidrug resistance 1 gene polymorphisms and UC subphenotypic categories. CONCLUSION: The multidrug resistance 1 gene polymorphism C3435T is associated with the stricturing phenotype and an inappropriate response to therapy in Crohn's disease. This association with Crohn's disease may support additional pathogenic roles for the multidrug resistance 1 gene in regulating gut-microbiota interactions and in mediating fibrosis. Understanding the effects of several drugs associated with multidrug resistance 1 gene variants may aid in the selection of customized therapeutic regimens

Avaliação da incidência de antracnose, do desempenho e estado nutricional de variedades de mangueira, para cultivo orgânico, na região centro-norte do Estado de São Paulo.

A mudança do perfil do consumidor, aliada aos riscos da contaminação por agrotóxicos, tem levado à busca de alternativas ecologicamente apropriadas para produção de frutas. Os objetivos deste trabalho foram avaliar a incidência de antracnose, o desempenho e estado nutricional de variedades de mangueira conduzidas organicamente na região de Pindorama-SP. Foram utilizadas 17 variedades de mangueira. O experimento foi instalado em delineamento experimental em blocos completos ao acaso, com 17 tratamentos (variedades) e seis repetições. Foi avaliada a severidade de antracnose nas folhas, através de uma escala diagramática, atribuindo-se notas aos sintomas. Foram avaliados o crescimento e o desenvolvimento (altura da planta, perímetro do tronco e da copa) e o estado nutricional, mediante análise foliar, das diferentes variedades utilizadas. Através dos resultados obtidos, podem-se considerar como muito suscetíveis à antracnose as variedades Bourbon, Rocha e Rosa; e resistentes, as variedades IAC 111, Alfa, Beta e Parvin; as variedades de manga apresentaram o mesmo padrão de crescimento; as maiores alturas da planta corresponderam aos maiores diâmetros do tronco e da copa; a variedade Parvin apresentou o melhor desempenho dentre as variedades estudadas, com relação à resistência à antracnose, altura e diâmetro do caule e da copa, podendo ser recomendada ao cultivo orgânico. As variedades Omega e Alfa também apresentaram bom crescimento, podendo ser indicadas para esse cultivo, pelo menos nessa fase inicial; as variedades Surpresa e Rosa não apresentaram bom desempenho, no campo, em relação às demais, não devendo ser recomendadas para o cultivo orgânico, principalmente a variedade Rosa, bastante suscetível à antracnose. As concentrações de N, P e K foram elevadas na fase vegetativa das plantas, comparadas à baixa concentração de Ca; houve carência de Boro em todas as variedades estudadas. A manga Rosa, provavelmente, sofreu toxicidade ao excesso de manganês, ocasionando diminuição em seu desenvolvimento

OptFlux: an open-source software platform for in silico metabolic engineering

<p>Abstract</p> <p>Background</p> <p>Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications.</p> <p>Results</p> <p><it>OptFlux </it>is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes.</p> <p><it>OptFlux </it>also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms.</p> <p>The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. <it>OptFlux </it>has a visualization module that allows the analysis of the model structure that is compatible with the layout information of <it>Cell Designer</it>, allowing the superimposition of simulation results with the model graph.</p> <p>Conclusions</p> <p>The <it>OptFlux </it>software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community.</p> <p>Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models.</p

Country activities of Global Alliance against Chronic Respiratory Diseases (GARD): focus presentations at the 11th GARD General Meeting, Brussels

© Journal of Thoracic Disease. All rights reserved.The Global Alliance against Chronic Respiratory Diseases (GARD) is a voluntary network of national and international organizations, institutions and agencies led by the World Health Organization (WHO), working towards the vision of a world where all people breathe freely (1). GARD is supporting WHO in successfully implementing the WHO’s Global Action Plan for the Prevention and Control of Noncommunicable Diseases (NCDs) 2013–2020. The GARD report on GARD activities is published on a regular basis. Collaboration among GARD countries is critical for sharing experiences and providing technical assistance to developing countries based on each country’s needs (2). The annual GARD meeting is a unique opportunity for assembling all of the GARD participants from developed and developing countries: European countries, North and South American Countries, China, Vietnam as well as Eastern Mediterranean, and African countries. Coordinator for Management of NCDs in the WHO Department for Management of Noncommunicable Diseases, Disability, Violence and Injury Prevention (Cherian Varghese) is present at this meeting. The annual meeting of GARD is a forum for exchanging opinions in order to improve care for chronic respiratory diseases (CRDs) and to achieve the GARD goal—a world where all people breathe freely. Experts—in collaboration with WHO—are helping developing countries to achieve their projects regarding teaching, research and programming for CRD. Each year, there is a poster presentation session on country activities. Each participant is able to present his/her country activities that have been achieved since the last meeting. This is followed by discussion. In this paper, we summarize the posters presented during the 11th GARD general meeting. We hope that this will give readers of the GARD section an opportunity to learn for their countries. We can find all posters on the link: https://gard-breathefreely.org/resources-poster/.info:eu-repo/semantics/publishedVersio

Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme—GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century