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  1. Article ; Online: Análise sistêmica do município de São Paulo e suas implicações para o avanço dos casos de Covid-19

    JARDIM, VINÍCIUS CARVALHO / BUCKERIDGE, MARCOS SILVEIRA

    Estudos Avançados v.34 n.99 2020

    2020  

    Abstract: RESUMO No primeiro semestre de 2020 a cidade de São Paulo foi assolada pela pandemia da Covid-19. Como uma Cidade Global, São Paulo acabou se tornando o epicentro da pandemia no Brasil. Sendo uma metrópole com alto nível de desigualdade, São Paulo acabou ...

    Abstract RESUMO No primeiro semestre de 2020 a cidade de São Paulo foi assolada pela pandemia da Covid-19. Como uma Cidade Global, São Paulo acabou se tornando o epicentro da pandemia no Brasil. Sendo uma metrópole com alto nível de desigualdade, São Paulo acabou salientando as vulnerabilidades a ela relacionadas. Neste trabalho, aplicamos a ferramenta sistêmica BioNetStat aos dados censitários do município de São Paulo. Basea- mo-nos em trabalho prévio de Nery et al. (2019) que distinguiu oito padrões urbanos. Primeiro mostramos que as análises sistêmicas demonstram que diferentes conjuntos de fatores caracterizam cada um dos padrões urbanos. Mostramos que existem vantagens na análise conjunta de fatores para estudo da estrutura da cidade de São Paulo. Numa segunda análise, aplicamos a abordagem sistêmica com a inclusão de casos e óbitos de Covid-19. Os resultados mostraram que a pandemia levou a uma maior letalidade em regiões com padrão urbano coincidente com baixos níveis de educação e renda, maior número de viagens ao trabalho e com falhas no abastecimento de água. Concluímos que para lidar com a vulnerabilidade de São Paulo a situações extremas - como a pandemia da Covid-19 - políticas públicas sistêmicas deveriam ser utilizadas. Sugerimos que talvez seja o momento de adaptar a gestão urbana aos padrões urbanos ao invés da tradicional abordagem político administrativa.
    Keywords Covid-19 ; Gestão sistêmica ; São Paulo ; Políticas públicas ; covid19
    Language Portuguese
    Publishing date 2020-08-01
    Publisher Instituto de Estudos Avançados da Universidade de São Paulo
    Publishing country br
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Análise sistêmica do município de São Paulo e suas implicações para o avanço dos casos de Covid-19

    Jardim, Vinicius Carvalho / Buckeridge, Marcos Silveira

    Estudos Avançados; v. 34 n.; 157-174 ; 1806-9592 ; 0103-4014

    2020  Volume 99

    Abstract: During the first semester of 2020, the city of São Paulo was ravaged by the covid-19 pandemic 19. As a global city, São Paulo became the epicenter of the pandemic in Brazil. Displaying high levels of inequality, São Paulo ended up exacerbating the ... ...

    Abstract During the first semester of 2020, the city of São Paulo was ravaged by the covid-19 pandemic 19. As a global city, São Paulo became the epicenter of the pandemic in Brazil. Displaying high levels of inequality, São Paulo ended up exacerbating the vulnerabilities related to the outbreak. In this work, we applied the software BioNetStat to census data pertaining to the city of São Paulo. Our analysis was based on the work of Nery et al. (2019), which proposed the existence of eight urban patterns. We first show that the systemic analysis demonstrates that different groups of factors characterize each urban pattern. We also show the advantages of a multiple factors analysis in the study of the city structure of São Paulo. In a second study, we applied the systemic approach with the inclusion of covid-19 cases and deaths in the data. The results show that the pandemic led to higher lethality in regions with urban patterns coinciding with lower levels of education and income, a higher number of trips to work, and failures in the water supply system. We conclude that dealing with São Paulo’s vulnerability to extreme events, such as the covid-19 pandemic, demands the application of systemic public policies. We suggest that this might be the moment to adapt the city’s governance to urban patterns, as opposed to the traditional political-administrative approach.

    No primeiro semestre de 2020 a cidade de São Paulo foi assolada pela pandemia da Covid-19. Como uma Cidade Global, São Paulo acabou se tornando o epicentro da pandemia no Brasil. Sendo uma metrópole com alto nível de desigualdade, São Paulo acabou salientando as vulnerabilidades a ela relacionadas. Neste trabalho, aplicamos a ferramenta sistêmica BioNetStat aos dados censitários do município de São Paulo. Baseamo-nos em trabalho prévio de Nery et al. (2019) que distinguiu oito padrões urbanos. Primeiro mostramos que as análises sistêmicas demonstram que diferentes conjuntos de fatores caracterizam cada um dos padrões urbanos. Mostramos que existem vantagens na análise conjunta de fatores para estudo da estrutura da cidade de São Paulo. Numa segunda análise, aplicamos a abordagem sistêmica com a inclusão de casos e óbitos de Covid-19. Os resultados mostraram que a pandemia levou a uma maior letalidade em regiões com padrão urbano coincidente com baixos níveis de educação e renda, maior número de viagens ao trabalho e com falhas no abastecimento de água. Concluímos que para lidar com a vulnerabilidade de São Paulo a situações extremas – como a pandemia da Covid-19 – políticas públicas sistêmicas deveriam ser utilizadas. Sugerimos que talvez seja o momento de adaptar a gestão urbana aos padrões urbanos ao invés da tradicional abordagem político administrativa.
    Keywords Covid-19 ; Systemic management ; São Paulo ; Public policies ; Gestão sistêmica ; Políticas públicas ; covid19
    Language Portuguese
    Publishing date 2020-08-07
    Publisher Universidade de São Paulo. Instituto de Estudos Avançados
    Publishing country br
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  3. Article: BioNetStat: A Tool for Biological Networks Differential Analysis.

    Jardim, Vinícius Carvalho / Santos, Suzana de Siqueira / Fujita, Andre / Buckeridge, Marcos Silveira

    Frontiers in genetics

    2019  Volume 10, Page(s) 594

    Abstract: The study of interactions among biological components can be carried out by using methods grounded on network theory. Most of these methods focus on the comparison of two biological networks (e.g., control vs. disease). However, biological systems often ... ...

    Abstract The study of interactions among biological components can be carried out by using methods grounded on network theory. Most of these methods focus on the comparison of two biological networks (e.g., control vs. disease). However, biological systems often present more than two biological states (e.g., tumor grades). To compare two or more networks simultaneously, we developed BioNetStat, a Bioconductor package with a user-friendly graphical interface. BioNetStat compares correlation networks based on the probability distribution of a feature of the graph (e.g., centrality measures). The analysis of the structural alterations on the network reveals significant modifications in the system. For example, the analysis of centrality measures provides information about how the relevance of the nodes changes among the biological states. We evaluated the performance of BioNetStat in both, toy models and two case studies. The latter related to gene expression of tumor cells and plant metabolism. Results based on simulated scenarios suggest that the statistical power of BioNetStat is less sensitive to the increase of the number of networks than Gene Set Coexpression Analysis (GSCA). Also, besides being able to identify nodes with modified centralities, BioNetStat identified altered networks associated with signaling pathways that were not identified by other methods.
    Language English
    Publishing date 2019-06-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2019.00594
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Will climate change shift carbon allocation and stem hydraulics? Insights on a systemic view of carbon- and water-related wood traits in an anysohydric tropical tree species (Hymenaea courbaril, Leguminosae)

    Macieira, Bernardo Pretti Becacici / Locosselli, Giuliano Maselli / Buckeridge, Marcos Silveira / Jardim, Vinícius Carvalho / Krottenthaler, Stefan / Anhuf, Dieter / Helle, Gerhard / Cuzzuol, Geraldo Rogério Faustini / Ceccantini, Gregório

    Ecological indicators. 2021 Sept., v. 128

    2021  

    Abstract: Tropical forests uptake more atmospheric CO₂ and transpire more water than any other forest in the world and are critical components of the global carbon and hydrological cycles. Both cycles depend to a great extent on the carbon and water balance of ... ...

    Abstract Tropical forests uptake more atmospheric CO₂ and transpire more water than any other forest in the world and are critical components of the global carbon and hydrological cycles. Both cycles depend to a great extent on the carbon and water balance of individual trees. Such adjustments are usually evaluated through well-established and newly-emerging traits but integrating them for a systemic understanding of trees' responses to climate change can be challenging. We propose using complex correlation networks to integrate and understand how trees coordinate water- and carbon-related traits under changing climate conditions. We built a correlation network based on 20 traits measured in the wood of Hymenaea courbaril (Leguminosae) trees, a species known for its extreme anisohydric water-use strategy, sampled along a climate gradient in Southeastern Brazil. Intercellular to ambient CO₂ concentrations ratio (cᵢ/cₐ, estimated from tree-ring δ¹³C) is a central network trait for being coordinated with several hydraulic and carbon allocation traits. Trees of H. courbaril coordinate these traits along the climate gradient, favoring high cᵢ/cₐ under warm and dry conditions. A high cᵢ/cₐ is only possible through a consistent water supply provided by wider vessels together with the investment on soluble sugars, at the detriment of starch, likely for hydraulic maintenance. Trees also favor heat resistance by investing in cell-wall xylose, another central network trait, from xyloglucans and xylans, at the expense of mannose from glucomannans. Such trade-offs within, and between, structural and non-structural carbon allocation reflect well-known metabolic pathways in plants. In summary, this systemic approach confirms previously reported patterns on leaf physiology, stem hydraulics and carbon adjustments while bringing to light the previously unreported role of cell-wall composition and its fine adjustments to cope with climate change.
    Keywords Hymenaea courbaril ; carbon ; carbon dioxide ; climate change ; fluid mechanics ; glucomannans ; growth rings ; heat tolerance ; leaves ; mannose ; physiology ; starch ; trees ; tropical plants ; water supply ; wood ; xyloglucans ; xylose ; Brazil
    Language English
    Dates of publication 2021-09
    Publishing place Elsevier Ltd
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2036774-0
    ISSN 1872-7034 ; 1470-160X
    ISSN (online) 1872-7034
    ISSN 1470-160X
    DOI 10.1016/j.ecolind.2021.107798
    Database NAL-Catalogue (AGRICOLA)

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  5. Article: Evaluation of Setaria viridis physiological and gene expression responses to distinct water-deficit conditions

    Rodrigues, Tamires de Souza / Lins, João Travassos / Cattem, Marcus Vinicius / Jardim, Vinicius Carvalho / Buckeridge, Marcos Silveira / Sá, Maria Fátima Grossi de / Reinert, Fernanda / Alves-Ferreira, Márcio

    Biotechnology Research and Innovation. 2020 Mar. 23,

    2020  

    Abstract: Setaria viridis, a C4 monocot, was proposed as a model plant for studies on the response to stress conditions. Water-deficit ranks among the top three most devastating stresses and its importance will likely increase in the scenario of climate change. ... ...

    Abstract Setaria viridis, a C4 monocot, was proposed as a model plant for studies on the response to stress conditions. Water-deficit ranks among the top three most devastating stresses and its importance will likely increase in the scenario of climate change. The aim of this work was to evaluate physiological and molecular water-deficit responses of S. viridis subjected to different conditions. Principal component analysis highlighted the physiological differences between vegetative and reproductive stages of S. viridis, as well as the differences between two methods of water deficit induction: polyethylene glycol and air-drying. Network interactions were observed in distinct developmental stages and water-deficit induction methods tested, allowing classification of root and shoot fresh weight and non-photochemical quenching as the best physiological parameters to group the networks. Variations in the gene expression patterns of delta 1-pyrroline-5-carboxylate synthase 2 (SvP5CS2), Dehydrin 1 (SvDHN1) and the transcription factors WRKY DNA-binding domain 1 (SvWRKY1), dehydration-responsive element-binding protein 1 class C (SvDREB1C) and NAC protein 6 (SvNAC6) were observed. Among these genes, it was observed two expression patterns predominant during water deficit: inducible (SvDHN1 and SvNAC6) and repressed (SvP5CS2, SvWRKY1 and SvDREB1C) genes. SvDHN1 showed the highest expression level in all the conditions tested. PEG treatment during the reproductive stage promoted the upregulation of the five marker genes in roots. The discriminative analysis suggested that the physiological and molecular responses in S. viridis adjusted according to the evaluated water-deficit conditions, especially after PEG treatments, indicating that the PEG method of water deficit may better replicate field conditions.
    Keywords DNA-binding domains ; Setaria viridis ; air drying ; biotechnology ; climate change ; dehydrins ; developmental stages ; enzymes ; gene expression ; gene expression regulation ; genes ; genetic markers ; models ; polyethylene glycol ; principal component analysis ; roots ; shoots ; stress response ; transcription factors
    Language English
    Dates of publication 2020-0323
    Publishing place Elsevier Editora Ltda.
    Document type Article
    Note Pre-press version
    ISSN 2452-0721
    DOI 10.1016/j.biori.2020.03.001
    Database NAL-Catalogue (AGRICOLA)

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