Inferência estatística clássica para a confiabilidade de rede de coautoria com enfoque nos vértices

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Investigadores de mayor visibilidad en Organización y Representación del Conocimiento: un estudio desde el análisis de cocitaciones

The most visible researchers in Knowledge Organization and Representation were identified, from the perspective of Brazilian researchers, based on cocitations from the papers presented in the last five meetings of the Encontros Nacionais de Pesquisa of the Associação Nacional de Pesquisa e Pós- Graduação em Ciência da Informação (ENANCIBs) from 2003 to 2008. First, the total number of references was identified, a total of 134 articles. Second, a citation analysis was conducted, being considered the most cited authors those who received 12 citations or more, which resulted in 31 most cited authors. Third, the Pajek software was used for the construction of the co-citation network and, thereafter, some indicators were calculated with the Ucinet software, which describe the structure and cohesion of the generated network, and, particularly, its density, and its degree of centrality, betweenness and proximity. The high cohesion of the network and the compliance between the most co-cited authors and the calculated indicators were verified.

Estudos de Análise de Cocitação de Autores: uma abordagem teórico-metodológica para a compreensão de um domínio

This piece of research aims at analyzing the absolute and relative co-citation indicators, especially Salton’s Cosine and comparing the contribution of these indicators to the understanding of a domain, applying them to the universe of "Metric Studies" at the BRAPCI base. It also aims at presenting the co-citation network generated from the absolute frequencies and highlighting the groupings of co-cited authors, depending on the relative values, integrating and explaining the information from the two indexes. The domain analysis, by means of its 11 approaches, including “Bibliometric Studies”, focuses on the science characterization and evaluation, in that it allows us to identify and to analyze the conditions under which the scientific knowledge is constructed and socialized. In these studies, the contribution of citation and co-citation analysis is highlighted. Of the total of 147 articles retrieved at BRAPCI base, the authors cited in at least 11 articles, in a total of 38 researchers, were selected. The 38 x 38 symmetric matrix with the absolute frequencies of co-citation and the matrix with the relative values of Salton’s Cosine were generated. The co-citation network with absolute frequency values were constructed, through Ucinet software. Cluster analysis of data with relative values wer performed, using the SPSS software. Significant differences between the absolute and relative indexes, with some high absolute values of co-citation were observed; when considered in relation to the presence of each author, their significance is decreased. As to the generated network, seven groups were determined, in which only one is established for close themes and comes from co-citations in the original sense of the term. Five groups present closeness in absolute and relative indicators. It can be concluded about the importance of the studies of authors' co-citation analysis, which associate the two indexes, absolute and relative, in order to visualize and understand the underlying structures of a scientific domain.

Visibilidade dos pesquisadores no periódico Scientometrics a partir da perspectiva brasileira: um estudo de cocitação

This research aims at verifying the authors who have given basis to the brazilian researches internationally inserted in the area of Bibliometrics and Scientometrics through the analysis of citation and co-citation of the brazilian articles published in the journal Scientometrics. We used the Scopus data base, with the terms Scientometrics in source title and Brasil or Brazil in affiliation country. We found 53 articles, with 741 references and 19 authors cited 3 or more times. In general, the researchers come from the biologic and health areas. Using the Ucinet software, we build the co-citation network and calculated its indicators. We calculated the co-citation normalized index. The density and average of normalized degree centrality were 65,5%. We concluded the research highlighting the significant presence of brazilians (32%) and the dialogicity occurring between cited Brazilians and foreigners within a balance, where brazilians already dialog with renowned international researchers of the Bibliometrics and Scientometrics area.

Visibilidade dos pesquisadores no GT7 da ANCIB: um estudo de cocitações

This research aims at analyzing the researchers with major insertion and impact within the GT7 ENANCIB community, through an analysis study of citation and co-citation from 2003 to 2010. We propose to highlight the researchers cited in a greater number of papers, as well as the number of citations received. Also, to describe the co-citation network intending to analyze the interlocution network built by the writers towards the cited ones and calculate the indicators of density and centrality of the network. As for the theoretical-methodological basis, we used the Domain Analysis (D.A.), seen as the reflexion of a discourse community. Among the 11 approaches about D.A, the bibliometric studies stand out. Data from the 124 researches presented in the period of this study showed 1446 cited researches for a total of 2307 citations. From the total number of cited researchers in a greater number of papers, 33 were considered authors of major impact and visibility, being cited in at least 8 papers, thus getting at least 8 citations. The software Ucinet was used to map and visualize the net of interlocution established by the citing papers. As for the results, we could notice that, from the total of 33 researchers, 23 are Brazilian, 20 take part in Post-Graduation Programs and 11 are granted CNPq scholarships of productivity. Furthermore, we highlighted the most cited themes and analyzed the relationship involving the number of citations according to the number of papers in which the researcher was cited and the number of researches cited from each researcher. Regarding the network structure, we could observe that the authors form a single component, indicating that the group of researchers co-cited reveals proximity and theoretical, conceptual and methodological articulations. We concluded that the citing community adopts ordinary theoretical schools; moreover, we might characterize the core of the known researchers as a foundation for the knowledge of the GT7 theme.

Rede de coautoria institucional em Ciência da Informação: uma comparação entre indicadores de rede e os conceitos CAPES

The objective of this is study is to point inter-institutional partnerships in Information Science formed through co-authorship network. More specifically, we calculate indicators of centrality degree, betweenness centrality and closeness centrality, and analyze the relationships between the grades attributed by CAPES - Coordination for the Improvement of Higher Education Personnel - to the institutions and the indicators on the network, checking whether there is proximity and similarity between network indicators and CAPES's grades. Our corpus consisted of all articles published in the four journals in the field of Information Science in Brazil, with regular publications, based in SciVerse Scopus, for the 2010- 2012 period. We retrieved 237 articles, 58 co-authored, with 117 participant institutions. We conducted the analysis of relations between institutions with greater grades by CAPES and the network through centrality indicators. It was concluded that these network indicators and CAPES concepts are articulated, harmonizing these two categories of indicators.

A construção do conhecimento sobre governança corporativa: uma análise bibliométrica

Presents a survey of scientific production about the subject corporate governance, using the Bibliometric analysis of theses and dissertations collected in the digital libraries of the Sao Paulo State University (Unesp), Campinas State University (UNICAMP) and University of Sao Paulo (USP). Through the data collected were identified, based on Bibliometric indicators, the origin of authors, the authors more cited, the thematic area of authors, and the construction of co-citation network.

Investigação da colaboração científica na temática de indexação em periódicos on-line em âmbito nacional

This research seeks to demonstrate the scientific collaboration in the field of Information Science, specifically in the thematic indexing, by analyzing the co-authors network, based on scientific collaboration in Brazilian journals online, according to CAPES. We selected six Brazilian journals online, namely: Ciência da Informação; Transinformação; Perspectivas da Ciência da Informação; Encontros BIBLI: Revista Eletrônica de Biblioteconomia e Ciência da Informação; DataGramaZero and Em Questão, totaling 25 articles. It was built in coauthorship network, using Pajek software in order to evaluate interactions between researchers and cohesion of the network by calculating its density.

Synergism and Antagonism between Bacillus thuringiensis Vip3A and Cry1 Proteins in Heliothis virescens, Diatraea saccharalis and Spodoptera frugiperda

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Identification of sense and antisense transcripts regulated by drought in sugarcane

Sugarcane is an important sugar and energy crop that can be used efficiently for biofuels production. The development of sugarcane cultivars tolerant to drought could allow for the expansion of plantations to sub-prime regions. Knowledge on the mechanisms underlying drought responses and its relationship with carbon partition would greatly help to define routes to increase yield. In this work we studied sugarcane responses to drought using a custom designed oligonucleotide array with 21,901 different probes. The oligoarrays were designed to contain probes that detect transcription in both sense and antisense orientation. We validated the results obtained using quantitative real-time PCR (qPCR). A total of 987 genes were differentially expressed in at least one sample of sugarcane plants submitted to drought for 24, 72 and 120 h. Among them, 928 were sense transcripts and 59 were antisense transcripts. Genes related to Carbohydrate Metabolism, RNA Metabolism and Signal Transduction were selected for gene expression validation by qPCR that indicated a validation percentage of 90 %. From the probes presented on the array, 75 % of the sense probes and 11.9 % of the antisense probes have signal above background and can be classified as expressed sequences. Our custom sugarcane oligonucleotide array provides sensitivity and good coverage of sugarcane transcripts for the identification of a representative proportion of natural antisense transcripts (NATs) and sense-antisense transcript pairs (SATs). The antisense transcriptome showed, in most cases, co-expression with respective sense transcripts.

HPV16 Oncoproteins Induce MMPs/RECK-TIMP-2 Imbalance in Primary Keratinocytes: Possible Implications in Cervical Carcinogenesis

Cervical cancer is the third most common cancer in women worldwide. Persistent infection with high-risk HPV types, principally HPV16 and 18 is the main risk factor for the development of this malignancy. However, the onset of invasive tumor occurs many years after initial exposure in a minority of infected women. This suggests that other factors beyond viral infection are necessary for tumor establishment and progression. Tumor progression is characterized by an increase in secretion and activation of matrix metalloproteinases (MMPs) produced by either the tumor cells themselves or tumor-associated fibroblasts or macrophages. Increased MMPs expression, including MMP-2, MMP-9 and MT1-MMP, has been observed during cervical carcinoma progression. These proteins have been associated with degradation of ECM components, tumor invasion, metastasis and recurrence. However, few studies have evaluated the interplay between HPV infection and the expression and activity of MMPs and their regulators in cervical cancer. We analyzed the effect of HPV16 oncoproteins on the expression and activity of MMP-2, MMP-9, MT1-MMP, and their inhibitors TIMP-2 and RECK in cultures of human keratinocytes. We observed that E7 expression is associated with increased pro-MMP-9 activity in the epithelial component of organotypic cultures, while E6 and E7 oncoproteins co-expression down-regulates RECK and TIMP-2 levels in organotypic and monolayers cultures. Finally, a study conducted in human cervical tissues showed a decrease in RECK expression levels in precancer and cancer lesions. Our results indicate that HPV oncoproteins promote MMPs/ RECK-TIMP-2 imbalance which may be involved in HPV-associated lesions outcome.

Tetracycline-inducible RNAi Knockdown of SCL (Stem Cell Leukaemia) in Mice

RNAi (RNA interference) is a powerful technology for sequence-specific targeting of mRNAs. This thesis was aimed at establishing conditions for conditional RNAi-mediated silencing first in vitro and subsequently also in transgenic mice. As a target the basic helix-loop-helix transcription factor encoding gene SCL (stem cell leukaemia also known as Tal-1 or TCL5) was used. SCL is a key regulator for haematopoietic development and ectopic expression of SCL is correlated with acute T-lymphoblastic leukaemias. Loss of SCL function studies demonstrated that ab initio deletion of SCL resulted in embryonic lethality around day E9 in gestation. To be able to conditionally inactivate SCL, RNAi technology was combined with the tetracycline-dependent regulatory system. This strategy allowed to exogenously control the induction of RNAi in a reversible fashion and consequently the generation of a completely switchable RNAi knockdown. First a suitable vector allowing for co-expression of tetracycline-controlled shRNAs (small hairpin RNAs) and constitutively active EGFP (enhanced green fluorescent protein) was generated. This novel vector, pRNAi-EGFP, was then evaluated for EGFP expression and tetracycline-mediated expression of shRNAs. Four sequences targeting different regions within the SCL mRNA were tested for their efficiency to specifically knockdown SCL. These experiments were performed in M1 murine leukaemia cells and subsequently in the HEK 293 cell line, expressing an engineered HA-tagged SCL protein. The second assay provided a solid experimental method for determining the efficiency of different SCL-siRNA knockdown constructs in tissue culture. Western blotting analyses revealed a down regulation of SCL protein for all four tested SCL-specific target sequences albeit with different knockdown efficiencies (between 25% and 100%). Furthermore, stringent tetracycline-dependent switchability of shRNA expression was confirmed by co-transfecting the SCL-specific pRNAi-EGFP vector (SCL-siRNA) together with the HA-tagged SCL expression plasmid into the HEK 293TR /T-REx cell line constitutively expressing the tetracycline repressor (TetR). These series of experiments demonstrated tight regulation of siRNA expression without background activity. To be able to control the SCL knockdown in vivo and especially to circumvent any possible embryonic lethality a transgenic mouse line with general expression of a tetracycline repressor was needed. Two alternative methods were used to generate TetR mice. The first approach was to co-inject the tetracycline-regulated RNAi vector together with a commercially available and here specifically modified T-REx expression vector (SCL-siRNA T-REx FRT LoxP mouse line). The second method involved the generation of a TetR expressor mouse line, which was then used for donating TetR-positive oocytes for pronuclear injection of the RNAi vector (SCL-siRNA T-REx mouse line). As expected, and in agreement with data from conditional Cre-controlled adult SCL knockout mice, post-transcriptional silencing of SCL by RNAi caused a shift in the maturation of red blood cell populations. This was shown in the bone marrow and peripheral blood by FACS analysis with the red blood cell-specific TER119 and CD71 markers which can be used to define erythrocyte differentiation (Lodish plot technique). In conclusion this study established conditions for effective SCL RNAi-mediated silencing in vitro and in vivo providing an important tool for further investigations into the role of SCL and, more generally, of its in vivo function in haematopoiesis and leukaemia. Most importantly, the here acquired knowledge will now allow the establishment of other completely conditional and reversible knockdown phenotypes in mice.

Funzioni della subunità θ e del dominio PHP della subunità α nel core catalitico della DNA polimerasi III di Escherichia coli

Il core catalitico della DNA polimerasi III, composto dalle tre subunità α, ε e θ, è il complesso minimo responsabile della replicazione del DNA cromosomiale in Escherichia coli. Nell'oloenzima, α ed ε possiedono rispettivamente un'attività 5'-3' polimerasica ed un'attività 3'-5' esonucleasica, mentre θ non ha funzioni enzimatiche. Il presente studio si è concentrato sulle regioni del core che interagiscono direttamente con ε, ovvero θ (interagente all'estremità N-terminale di ε) e il dominio PHP di α (interagente all'estremità C-terminale di ε), delle quali non è stato sinora identificato il ruolo. Al fine di assegnare loro una funzione sono state seguite tre linee di ricerca parallele. Innanzitutto il ruolo di θ è stato studiato utilizzando approcci ex-vivo ed in vivo. I risultati presentati in questo studio mostrano che θ incrementa significativamente la stabilità della subunità ε, intrinsecamente labile. Durante gli esperimenti condotti è stata anche identificata una nuova forma dimerica di ε. Per quanto la funzione del dimero non sia definita, si è dimostrato che esso è attivamente dissociato da θ, che potrebbe quindi fungere da suo regolatore. Inoltre, è stato ritrovato e caratterizzato il primo fenotipo di θ associato alla crescita. Per quanto concerne il dominio PHP, si è dimostrato che esso possiede un'attività pirofosfatasica utilizzando un nuovo saggio, progettato per seguire le cinetiche di reazione catalizzate da enzimi rilascianti fosfato o pirofosfato. L'idrolisi del pirofosfato catalizzata dal PHP è stata dimostrata in grado di sostenere l'attività polimerasica di α in vitro, il che suggerisce il suo possibile ruolo in vivo durante la replicazione del DNA. Infine, è stata messa a punto una nuova procedura per la coespressione e purificazione del complesso α-ε-θ

Der Einfluss von TGF-beta1 auf regulatorische T-Zellen in einem murinen Modell für Asthma

Ziel der vorliegenden Arbeit war es, den Einfluss von regulatorischen T-Zellen (Treg) auf die Pathogenese des Asthmas in einem murinen Modell zu untersuchen. Es konnte gezeigt werden, dass die Co-Expression von TGF-ß1 und IL-10 auf Treg notwendig ist, um im Tiermodell vor einer Atemwegs-Hyperreagibilität (AHR) zu schützen. Natürliche Treg konnten keinen Schutz vermitteln. Weiterhin wurde gezeigt, dass der Schutz vor AHR durch TGF-ß1 über Empfänger T-Zellen vermittelt wird. Dabei reichte die alleinige Anwesenheit von TGF-ß1 nicht aus, vielmehr musste das Zytokin von Treg exprimiert werden. Ein Einfluss von TGF-ß1 überexprimierenden Treg auf die peribronchiale Entzündung konnte nicht festgestellt werden, wohingegen adoptiver Transfer von natürlichen Treg die Eosinophilen Anzahl in der Bronchiallavage signifikant verringern konnte. Dabei korrelierte die Eosinophilie mit den IL-5 Spiegeln in der Bronchiallavage. In dieser Arbeit konnte also eine Entkopplung der Mechanismen von AHR und Entzündung festgestellt werden. Die weitere Aufklärung der Mechanismen der Suppression der AHR durch TGF-ß1 und IL-10 produzierende Treg könnte daher die Entwicklung neuer therapeutischer Ansätze bei Atemwegserkrankungen ermöglichen.

Genetische und funktionelle Analyse von Vesikelmembranprotein-Mutanten in Maus und Caenorhabditis elegans

Tetraspan vesicle membrane proteins (TVPs) sind konservierte, ubiquitär vorkommende Membranproteine synaptischer Vesikel und zytoplasmatischer Transportvesikel. Bei Säugetieren lassen sie sich in die Physine, Gyrine und SCAMPs (secretory carrier-associated membrane proteins) unterteilen, die im Nematoden C. elegans jeweils nur durch ein einzelnes Polypeptid vertreten sind (Synaptophysin-1 [SPH-1], Synaptogyrin-1 [SNG-1] und SCAMP-1 [SCM-1]). Obwohl den TVPs eine Beteiligung bei der Regulation des Vesikelzyklus zugesprochen wurde, sind Synaptophysin-1-Knockout-Mäuse und vollständig TVP-defiziente Würmer gesund und weisen nur geringgradige Veränderungen auf. In dieser Arbeit sollten daher zum einen genomweite komparative Transkriptomanalysen durchgeführt werden, um mögliche Kompensationsmechanismen in der Maus und C. elegans zu finden, zum anderen sollten mit Hilfe pharmakologischer Stressassays und genetischer Verfahren Schwachstellen und Redundanzen identifiziert werden. Erstaunlicherweise konnten durch Affymetrix GeneChip-Analysen der RNA in der Retina von Synaptophysin-1-/--Mäusen keine differenziell exprimierten Gene gefunden werden. Bei der Untersuchung der C. elegans-TVP-Dreifachmutante wurden hingegen 17 Gene mit erhöhter und 3 mit erniedrigter Transkription identifiziert. Die Befunde für 12 hochregulierte Gene wurden durch quantitative Real-Time RT-PCR bestätigt. Das am stärksten hochregulierte Gen arf-1.1 kodiert für eine GTPase, die vermutlich an der Regulation der Vesikelbildung beteiligt ist. Von den ebenso identifizierten Genen cdr-2, cdr-4 und pgp-9 ist bekannt, dass sie in Stresssituationen, z. B. in Gegenwart von Cadmium, verstärkt transkribiert werden. ugt-62 und ugt-19 kodieren für Glucuronosyltransferasen. Für arf-1.1, cdr-2, ugt-62 sowie für das Gen T16G1.6, das für eine coiled-coil-Domäne kodiert, wurden im Folgenden fluoreszierende Promoterkonstrukte hergestellt, um Koexpressionsmuster mit TVPs zu bestimmen. Es stellte sich heraus, dass alle vier Promoterkonstrukte im Darm zusammen mit SPH-1 und SCM-1 im Darm transkribiert werden. Mit fluoreszierenden Translationschimären konnte weiterhin gezeigt werden, dass ARF-1.1 und CDR-2 mit den Darm-spezifischen TVPs im apikalen Bereich der Darmzellen kolokalisieren. Um mehr über die Funktion von TVPs im Vesikelzyklus zu erfahren, wurden pharmakologische und genetische Analysen von Würmern durchgeführt, in denen die Expression des Neuronen-spezifischen SNG-1 verändert ist. Deletion oder Überexpression führte zu einer Resistenz gegenüber dem Acetylcholinesterase-Inhibitor Aldicarb und zu erhöhter Empfindlichkeit gegenüber dem GABA-Rezeptor-Antagonisten Pentylentetrazol. Auf genetischer Ebene zeigte sich, dass sng-1 synthetisch mit den Genen für Synaptotagmin-1, Endophilin A sowie Synaptojanin wirkt. Die beobachteten Effekte weisen auf alternative Funktionen in der synaptischen Übertragung hin und unterstützen zugleich die Hypothese, dass SNG-1 im synaptischen Vesikelzyklus eine wichtige Funktion erfüllt, die möglicherweise einem noch unbekannten redundanten Kompartiment-spezifischen Signalweg der synaptischen Transmission zuzuordnen ist.