merlin v4: an updated platform for reconstructing genome-scale metabolic models

The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) software is an open source user-friendly Java application developed for Windows and Unix, aimed towards the reconstruction of genome-scale metabolic models. The development of merlin follows a design philosophy of automating time-consuming steps in the reconstruction of genome-scale metabolic models, while allowing users to control the parameters of operations and manually curate the results. All major steps involved in the reconstruction of a metabolic model are implemented in merlin, including genome retrieval and its functional annotation, construction of the reactions set and associated entities, model compartmentalization and conversion to standard SBML formats. The fourth iteration of merlin includes a major overhaul of the user interface, implementation of new features, improvements to existing features, and most notably, the implementation of the object-relational mapping framework Hibernate. The graphical layout has been significantly streamlined, while supporting the latest version of AiBench, providing users with an intuitive and responsive interface. Development was also focused at new quality of life improvements, aimed mainly towards importing, exporting and duplicating merlin user projects. The development of the latest version of merlin followed a modular approach, culminating in the implementation of a plugin manager which simplifies and hastens the process of updating and debugging the various features of merlin. In addition, TranSyT, a state-of-the-art genome-wide transmembrane transport system annotation tool has been implemented to overcome the limitations of the previously available TRIAGE module. Finally, it is noteworthy to mention the implementation of BioISO, a tool aimed at evaluating a genome-scale metabolic network or biomass formulation, based on the previously available COBRA and FBA frameworks.info:eu-repo/semantics/publishedVersio

Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database

First Online: 28 August 2021Genome-Scale metabolic models (GEMs) are a relevant tool in systems biology for in silico strain optimisation and drug discovery. An easier way to reconstruct a model is to use available GEMs as templates to create the initial draft, which can be curated up until a simulation-ready model is obtained. This approach is implemented in merlin's BiGG Integration Tool, which reconstructs models from existing GEMs present in the BiGG Models database. This study aims to assess draft models generated using models from BiGG as templates for three distinct organisms, namely, Streptococcus thermophilus, Xylella fastidiosa and Mycobacterium tuberculosis. Several draft models were reconstructed using the BiGG Integration Tool and different templates (all, selected and random). The variability of the models was assessed using the reactions and metabolic functions associated with the model's genes. This analysis showed that, even though the models shared a significant portion of reactions and metabolic functions, models from different organisms are still differentiated. Moreover, there also seems to be variability among the templates used to generate the draft models to a lower extent. This study concluded that the BiGG Integration Tool provides a fast and reliable alternative for draft reconstruction for bacteria.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit. A. Oliveira (DFA/BD/10205/2020), E. Cunha (DFA/BD/8076/2020), F. Cruz (SFRH /BD/139198/2018), J. Sequeira (SFRH/BD/147271/2019), and M. Sampaio (SFRH/BD/144643/2019) hold a doctoral fellowship provided by the FCT. Oscar Dias acknowledge FCT for the Assistant Research contract obtained under CEEC Individual 2018.info:eu-repo/semantics/publishedVersio

Walkability Index for Elderly Health: A Proposal

Nowadays, the elderly tend to make more trips: Health benefits resulting from their daily walking routines are an important topic in the context of urban renewal processes. Many health organizations and researchers have demonstrated the influence of the urban environment on walkability levels. This article aims to design a multifactor Walkability Index for Elderly Health (WIEH), capable of associating both the adequacy level of public spaces to elderly walkability, and physical exercise benefits while walking. The methodological approach comprised two main parts: Firstly, a literature review of main reports, legislation, and scientific articles was conducted at the intersection of 'gerontology and physical exercise' with 'urban design and mobility', leading to the selection of four aging-related studies as main contributors to the design of the WIEH; and, secondly, the development of the WIEH was undertaken, based on two premises and designed according to four steps. The first premise defined three systematic areas (urban tissue, urban scene, and safety), variables, and criteria to classify the pedestrian network; and the second premise focused on slopes and stairs in public spaces. The WIEH is divided in four steps: (1) Analyzing public spaces and characterizing their quality for walking, (2) considering the existence of slopes and stairs, (3) calculating different routes for the elderly in their daily routines, or when going to points of interest, and (4) selecting the "heart-friendly route" for elderly people. Adequate walking paths for the elderly can be identified through this innovative approach, with the aim of achieving direct health benefits during their daily routines. Ultimately, the WIEH is capable of supporting decision makers and designers in creating inclusive and age-friendly spaces

A 2-Year Longitudinal Seroepidemiological Evaluation of Toxoplasma gondii Antibodies in a Cohort of Autochthonous Sheep from Central Portugal

Background: Toxoplasma gondii is an important zoonosis and one of the major causes of abortion in sheep worldwide. (2) Methods: We performed a 2-year longitudinal serological antiT. gondii IgG screening on a cohort of a spatially confined population of a Portuguese autochthonous sheep breed in central Portugal. (3) Results: From the screening of the 2015 and 2016 sera, an increase of seroprevalence was observed (57.7% (95% CI: 49.9–65.3%) versus 69.1% (95% CI: 61.5–75.9), from 2015 and 2016, respectively) (p = 0.031). (4) Conclusions The present study is the first to provide prospective data on the anti-T. gondii serological status of a sheep cohort in Portugal, showing an increase in the occurrence of T. gondii. There is a need to provide a clearer understanding of T. gondii epidemiology in Portugal, ideally by implementing monitoring programs on sentinel herds, not only due to the high impact of T. gondii on animal health but also for it being a zoonosis.info:eu-repo/semantics/publishedVersio

Thrombus aspiration in patients with ST-elevation myocardial infarction: results of a national registry of interventional cardiology

BACKGROUND: We aimed to evaluate the impact of thrombus aspiration (TA) during primary percutaneous coronary intervention (P-PCI) in 'real-world' settings. METHODS: We performed a retrospective study, using data from the National Registry of Interventional Cardiology (RNCI 2006-2012, Portugal) with ST-elevation myocardial infarction (STEMI) patients treated with P-PCI. The primary outcome, in-hospital mortality, was analysed through adjusted odds ratio (aOR) and 95% confidence intervals (95%CI). RESULTS: We assessed data for 9458 STEMI patients that undergone P-PCI (35% treated with TA). The risk of in-hospital mortality with TA (aOR 0.93, 95%CI:0.54-1.60) was not significantly decreased. After matching patients through the propensity score, TA reduced significantly the risk of in-hospital mortality (OR 0.58, 95%CI:0.35-0.98; 3500 patients). CONCLUSIONS: The whole cohort data does not support the routine use of TA in P-PCI, but the results of the propensity-score matched cohort suggests that the use of selective TA may improve the short-term risks of STEMI..info:eu-repo/semantics/publishedVersio

Effects of single low dose of dexamethasone before noncardiac and nonneurologic surgery and general anesthesia on postoperative cognitive dysfunction : a phase III double blind, randomized clinical trial

Postoperative cognitive dysfunction (POCD) is a multifactorial adverse event most frequently in elderly patients. This study evaluated the effect of dexamethasone on POCD incidence after noncardiac and nonneurologic surgery. METHODS: One hundred and forty patients (ASA I-II; age 60–87 years) took part in a prospective phase III, double blind, randomized study involving the administration or not of 8 mg of IV dexamethasone before general anesthesia under bispectral index (BIS) between 35–45 or 46–55. Neuropsychological tests were applied preoperatively and on the 3rd, 7th, 21st, 90th and 180th days after surgery and compared with normative data. S100β was evaluated before and 12 hours after induction of anesthesia. The generalized estimating equations (GEE) method was applied, followed by the posthoc Bonferroni test considering P<0.05 as significant. RESULTS: On the 3rd postoperative day, POCD was diagnosed in 25.2% and 15.3% of patients receiving dexamethasone, BIS 35–45, and BIS 46–55 groups, respectively. Meanwhile, POCD was present in 68.2% and 27.2% of patients without dexamethasone, BIS 35–45 and BIS 46–55 groups (p<0.0001). Neuropsychological tests showed that dexamethasone associated to BIS 46–55 decreased the incidence of POCD, especially memory and executive function. The administration of dexamethasone might have prevented the postoperative increase in S100β serum levels. CONCLUSION: Dexamethasone can reduce the incidence of POCD in elderly patients undergoing surgery, especially when associated with BIS 46–55. The effect of dexamethasone on S100β might be related with some degree of neuroprotection

II Diretriz Brasileira de Transplante Cardíaco

Universidade de São Paulo Faculdade de Medicina Hospital das ClínicasIIHospital de Messejana Dr. Carlos Alberto Studart GomesUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de MedicinaInstituto Dante Pazzanese de CardiologiaUniversidade Federal de Minas Gerais Hospital das ClínicasFaculdade de Medicina de São José do Rio PretoPontifícia Universidade Católica do ParanáIHospital Israelita Albert EinsteinInstituto Nacional de Cardiologia, Fundação Universitária do Rio Grande do Sul Instituto de CardiologiaReal e Benemérita Sociedade de Beneficência Portuguesa, São PauloHospital Pró-Cardíaco do Rio de JaneiroSanta Casa do Rio de JaneiroUNIFESP, EPMSciEL

III Diretriz Brasileira de Insuficiência Cardíaca Crônica

Universidade de São Paulo Faculdade de Medicina Hospital das ClínicasUniversidade Federal do Rio Grande do Sul Hospital de Clínicas de Porto AlegreUniversidade de Pernambuco Faculdade de Ciências Médicas de PernambucoUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de MedicinaUniversidade Federal de Minas Gerais Faculdade de MedicinaFaculdade de Medicina de São José do Rio PretoFundação Universitária de Cardiologia do Rio Grande do Sul Instituto de CardiologiaRede Labs D'OrUniversidade Federal FluminenseUniversidade do Estado do Rio de Janeiro Faculdade de Ciencias MédicasInstituto Dante Pazzanese de CardiologiaSanta Casa de MisericórdiaUniversidade de Pernambuco Pronto Socorro Cardiológico de PernambucoHospital Pró CardíacoHospital de MessejanaPontifícia Universidade Católica do ParanáUniversidade Federal de Goiás Faculdade de MedicinaUniversidade de São Paulo Faculdade de Medicina de Ribeirão PretoReal e Benemerita Sociedade de Beneficência PortuguesaFaculdade de Ciências Médicas de Minas GeraisUNIFESP, EPMSciEL

A list of land plants of Parque Nacional do Caparaó, Brazil, highlights the presence of sampling gaps within this protected area

Brazilian protected areas are essential for plant conservation in the Atlantic Forest domain, one of the 36 global biodiversity hotspots. A major challenge for improving conservation actions is to know the plant richness, protected by these areas. Online databases offer an accessible way to build plant species lists and to provide relevant information about biodiversity. A list of land plants of “Parque Nacional do Caparaó” (PNC) was previously built using online databases and published on the website "Catálogo de Plantas das Unidades de Conservação do Brasil." Here, we provide and discuss additional information about plant species richness, endemism and conservation in the PNC that could not be included in the List. We documented 1,791 species of land plants as occurring in PNC, of which 63 are cited as threatened (CR, EN or VU) by the Brazilian National Red List, seven as data deficient (DD) and five as priorities for conservation. Fifity-one species were possible new ocurrences for ES and MG states