Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae.

The Xanthomonadaceae family consists of species of non-pathogenic and pathogenic γ-proteobacteria that infect different hosts, including humans and plants. In this study, we performed a comparative analysis using 69 fully sequenced genomes belonging to this family, with a focus on identifying proteins enriched in phytopathogens that could explain the lifestyle and the ability to infect plants. Using a computational approach, we identified seven phytopathogen-enriched protein families putatively secreted by type II secretory system: PheA (CM-sec), LipA/LesA, VirK, and four families involved in N-glycan degradation, NixE, NixF, NixL, and FucA1. In silico and phylogenetic analyses of these protein families revealed they all have orthologs in other phytopathogenic or symbiotic bacteria, and are involved in the modulation and evasion of the immune system. As a proof of concept, we performed a biochemical characterization of LipA from Xac306 and verified that the mutant strain lost most of its lipase and esterase activities and displayed reduced virulence in citrus. Since this study includes closely related organisms with distinct lifestyles and highlights proteins directly related to adaptation inside plant tissues, novel approaches might use these proteins as biotechnological targets for disease control, and contribute to our understanding of the coevolution of plant-associated bacteria

The First Provenance Challenge

The first Provenance Challenge was set up in order to provide a forum for the community to help understand the capabilities of different provenance systems and the expressiveness of their provenance representations. To this end, a Functional Magnetic Resonance Imaging workflow was defined, which participants had to either simulate or run in order to produce some provenance representation, from which a set of identified queries had to be implemented and executed. Sixteen teams responded to the challenge, and submitted their inputs. In this paper, we present the challenge workflow and queries, and summarise the participants contributions

Characterization of Mycobacterium chelonae-like strains by comparative genomics

Isolates of the Mycobacterium chelonae-M. abscessus complex are subdivided into four clusters (CHI to CHIV) in the INNO-LiPA (R) Mycobacterium spp DNA strip assay. A considerable phenotypic variability was observed among isolates of the CHII cluster. In this study, we examined the diversity of 26 CHII cluster isolates by phenotypic analysis, drug susceptibility testing, whole genome sequencing and single-gene analysis. Pairwise genome comparisons were performed using several approaches, including average nucleotide identity (ANI) and genome-to-genome distance (GGD) among others. Based on ANI and GGD the isolates were identified as M. chelonae (14 isolates), M. franklinii (2 isolates) and M. salmoniphium (1 isolate). The remaining 9 isolates were subdivided into three novel putative genomospecies. Phenotypic analyses including drug susceptibility testing, as well as whole genome comparison by TETRA and delta differences, were not helpful in separating the groups revealed by ANI and GGD. The analysis of standard four conserved genomic regions showed that rpoB alone and the concatenated sequences clearly distinguished the taxonomic groups delimited by whole genome analyses. In conclusion, the CHII INNO-LiPa is not a homogeneous cluster; on the contrary, it is composed of closely related different species belonging to the M. chelonae-M. abscessus complex and also several unidentified isolates. The detection of these isolates, putatively novel species, indicates a wider inner variability than the presently known in this complex

A QUESTÃO DA SUSTENTABILIDADE NOS PERIÓDICOS BRASILEIROS DE TURISMO (1990-2018): DESCRIÇÃO E ANÁLISE DA AUTORIA, ESTRUTURA INTELECTUAL E IMPACTO: THE ISSUE OF SUSTAINABILITY IN BRAZILIAN TOURISM JOURNALS (1990-2018): DESCRIPTION AND ANALYSIS OF AUTHORSHIP, INTELLECTUAL STRUCTURE AND IMPACT

RESUMO: Estuda-se o conjunto de 3.887 artigos publicados em 16 periódicos brasileiros de turismo (1990-2018). Por meio de suas palavras-chave, é descrita e avaliada sua trajetória, com a formação de cinco agrupamentos. Objetiva-se descrever a trajetória do agrupamento de sustentabilidade, por meio de suas palavras-chave e ligações com outros agrupamentos. Busca-se, também, descrever e avaliar sua autoria, impacto e estrutura intelectual. Trata-se de um estudo bibliométrico e de análise de redes sociais, o qual utilizou, para a construção dos agrupamentos e redes de autoria e referências, o método de acoplamento bibliográfico. Privilegiou-se a análise qualitativa dos dados gerados, ao invés de se recorrer a uma miríade de métricas quantitativas. O agrupamento de sustentabilidade é claramente delimitado, com palavras-chave que orbitam em torno de “sustentabilidade”, “turismo rural” e “políticas públicas”. A autoria é fragmentada – não há um autor nem sequer uma instituição que responde por alto número de artigos. O agrupamento não apresenta uma estrutura intelectual particular e bem definida, para além de elementos proeminentes no campo de turismo no Brasil. É o agrupamento com mais alto impacto, com média de citações por artigo superior à do campo. Os resultados atestam o crescimento dos periódicos brasileiros de turismo; o agrupamento de sustentabilidade ocupa espaço central na rede de palavras-chave, tendo a mais alta média de citações por artigo dentre os cinco agrupamentos (1990-2018). Contudo, não apresenta, ainda, estrutura intelectual bem-definida, com a predominância de textos didáticos e/ou introdutórios em suas referências. Palavras-chave: sustentabilidade; bibliometria; autoria; referências bibliográficas; impacto.   ABSTRACT: We study the set of 3,887 articles published in 16 Brazilian tourism journals (1990-2018). With the use of its keywords, we describe and evaluate its trajectory, with the creation of five clusters. We aim to describe the trajectory of the sustainability cluster, by means of its keywords and links with other clusters. We also seek to describe and assess its authorship, impact and intellectual structure. We used bibliometric and social network analysis, with bibliographic coupling for the construction of clusters – keywords, authorship and references. We favored the qualitative analysis of the results (tables and networks), rather than the presentation of a myriad of quantitative metrics. The sustainability cluster is clearly delimited, formed by keywords that orbit around “sustainability”, “rural tourism” and “public policies”. Authorship is fragmented – there is not an author neither an institution that accounts for a high number of articles. The cluster does not have a particular and well-defined intellectual structure, besides the presence of authors, institutions and journals that are prominent in the Brazilian field of tourism. It is the cluster with the highest impact, with a higher average of citations per article than the field. The results show the growth of the Brazilian tourism journals; the sustainability cluster is central in the keyword network, and has the highest average of citations per article among the five clusters (1990-2018). However, it still does not have a well-defined intellectual structure, showing the prominence of didactic and/or introductory texts in its references. Keywords: sustainability; bibliometrics; authorship; references; impact

Combining Artificial Intelligence, Ontology, and Frequency-based Approaches to Recommend Activities in Scientific Workflows

The number of activities provided by scientific workflow management systems is large, which requires scientists to know many of them to take advantage of the reusability of these systems. To minimize this problem, the literature presents some techniques to recommend activities during the scientific workflow construction. In this paper we specified and developed a hybrid activity recommendation system considering information on frequency, input and outputs of activities and ontological annotations. Additionally, this paper presents a modeling of activities recommendation as a classification problem, tested using 5 classifiers; 5 regressors; and a composite approach which uses a Support Vector Machine (SVM) classifier, combining the results of other classifiers and regressors to recommend; and Rotation Forest, an ensemble of classifiers. The proposed technique was compared to related techniques and to classifiers and regressors, using 10-fold-cross-validation, achieving a Mean Reciprocal Rank (MRR) at least 70% greater than those obtained by classical techniques

Produção, centralidade e impacto: correlações entre diferentes métricas no campo de turismo no Brasil

In the last decades, bibliometric metrics have been used to assess the quantity and quality of production in different areas of knowledge. Often, a single metric is used to rank researchers and institutions, without, in some cases, justification for its choice. There are, in literature, studies that build rankings of authors and institutions, using production and impact. However, there are still few surveys that discuss whether the use of different metrics generates rankings that are more similar or different from each other. There is also little use of centrality in the field of tourism in Brazil. We calculate and correlate a set of production, centrality, and impact metrics, which are regularly used to build rankings, through 3,887 articles from 16 Brazilian tourism journals (1990-2018). Depending on the metrics applied, the rankings created are more similar or divergent from each other. The collection of data from primary sources and their review was done manually. The calculation of correlations was made for absolute values and ranking positions. The main result is to show that rankings based on a low number of metrics, mainly from the same group, can ignore important points in the performance of authors, institutions, and countries. It is also shown that several correlations are not as high as expected (e.g., between centrality and impact metrics).En las últimas décadas, se han utilizado medidas bibliométricas para evaluar la cantidad y la calidad de la producción en diferentes áreas del conocimiento. A menudo, se utiliza una única métrica para clasificar a los investigadores y las instituciones, sin, en algunos casos, una justificación para su elección. Hay, en la literatura, estudios que construyen rankings de autores e de instituciones, a través de la producción y del impacto. Sin embargo, todavía hay pocas investigaciones que discutan si el uso de diferentes métricas genera rankings más similares o más diferentes entre sí. También hay poco uso de la centralidad en el campo del turismo en Brasil. En este contexto, el objetivo de esta investigación es calcular y correlacionar un conjunto de métricas de producción, de centralidad e de impacto, que se utilizan regularmente para construir rankings. El estudio concentra sus análisis en 3.887 artículos, publicados en 16 revistas de turismo brasileñas (1990-2018). Se estima que, dependiendo de las métricas aplicadas, acaben creando rankings más parecidos o más divergentes entre sí. La recopilación de datos de fuentes primarias y su revisión se realizó de forma manual. El cálculo de correlaciones se realizó para valores absolutos y para posiciones de rankings. El principal resultado es mostrar que las clasificaciones basadas en un número bajo de métricas, principalmente del mismo grupo, pueden ignorar puntos importantes en el desempeño de autores, de instituciones y de países. También se muestra que varias correlaciones no son tan altas como se creía (por ejemplo, entre las métricas de centralidad y las de impacto).Nas últimas décadas, medidas bibliométricas têm sido utilizadas, para avaliar a quantidade e a qualidade da produção nas diferentes áreas do conhecimento. Muitas vezes, uma única métrica é usada para o ranqueamento de pesquisadores e de instituições, sem que haja, em alguns casos, uma justificativa para sua escolha. Há, na literatura, estudos que constroem rankings de autores e de instituições, por meio da produção e do impacto. Contudo, há, ainda, poucas pesquisas que discutam se a utilização de métricas diferentes gera rankings mais semelhantes ou mais diferentes entre si. Há, também, baixa utilização da centralidade no campo de turismo no Brasil. Dentro desse contexto, o presente artigo, tem como objetivo calcular e correlacionar um conjunto de métricas de produção, de centralidade e de impacto, as quais são, regularmente, utilizadas para a construção de rankings. O estudo concentra suas análises em 3.887 artigos, publicados em 16 periódicos brasileiros de turismo (1990-2018). Avalia-se que, a depender das métricas aplicadas, acabam-se por criar rankings mais similares ou mais divergentes entre si. A coleta de dados de fontes primárias e sua revisão foram feitas manualmente. O cálculo das correlações foi feito para valores absolutos e para posições nos rankings. O principal resultado é mostrar que rankings baseados em baixo número de métricas, principalmente do mesmo grupo, podem ignorar pontos importantes do desempenho de autores, de instituições e de países. Mostra-se, também, que várias correlações não são tão altas quanto o esperado (por exemplo, entre métricas de centralidade e as de impacto)

Characterization of mycobacteria and mycobacteriophages isolated from compost at the São Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U

Background: A large collection of sequenced mycobacteriophages capable of infecting a single host strain of Mycobacterium smegmatis shows considerable genomic diversity with dozens of distinctive types (clusters) and extensive variation within those sharing evident nucleotide sequence similarity. Here we profiled the mycobacterial components of a large composting system at the São Paulo zoo. Results: We isolated and sequenced eight mycobacteriophages using Mycobacterium smegmatis mc2155 as a host. None of these eight phages infected any of mycobacterial strains isolated from the same materials. The phage isolates span considerable genomic diversity, including two phages (Barriga, Nhonho) related to Subcluster A1 phages, two Cluster B phages (Pops, Subcluster B1; Godines, Subcluster B2), three Subcluster F1 phages (Florinda, Girafales, and Quico), and Madruga, a relative of phage Patience with which it constitutes the new Cluster U. Interestingly, the two Subcluster A1 phages and the three Subcluster F1 phages have genomic relationships indicating relatively recent evolution within a geographically isolated niche in the composting system. Conclusions: We predict that composting systems such as those used to obtain these mycobacteriophages will be a rich source for the isolation of additional phages that will expand our view of bacteriophage diversity and evolution

La batalla de las lenguas en la publicación nacional: Un estudio comparativo de las publicaciones del CNPq (Brasil) y Conicet (Argentina)

The predominance of English as an academic language in mainstream journals has been extensively studied. In change, it is difficult to gauge the incidence of publication in this language in the Ibero-American world because there are still few studies of regional databases or based in complete academic trajectories of researchers from the countries of the global South. The reasons are simple: a) there are multiple databases of  Ibero-American journals, but with large overlaps in between; b) there are curriculum systems in most countries, but they are not openly available or professionally curated. Precisely to collaborate in this direction, this comparative work offers an overview of the complete publications of two  scientific communities: researchers from the Conselho Nacional de Pesquisa (CNPq, Brazil) and researchers from the National Council for Scientific and Technical Research (Conicet-Argentina). To focus on the language and country of publication of this scientific production, we used the information uploaded in Sigeva  (Argentina) and Lattes (Brazil)  curricular system. Its use offers  difficulties to bibliometric or citation studies, however, it allows the construction of descriptive statistics of the production of complete production itineraries. A relevant information to  offer an overview of multilingualism, bibliodiversity and the weight of the national publication in these communities.El predominio del inglés como lengua académica en las revistas de corriente principal ha sido profusamente estudiado. En cambio, es difícil calibrar la incidencia de la publicación en esteidioma en el mundo Iberoamericano porque son todavía escasos los  estudios de bases de datos regionales o de trayectorias académicas  completas de investigadores de los países del Sur global. Las razones son sencillas: a) hay múltiples bases de datos de revistas Iberoamericanas, pero con grandes solapamientos; y b) hay sistemas de currículo en la mayoría de los países, pero no están disponibles abiertamente o no están curadas profesionalmente. Precisamente para colaborar en esta dirección, este trabajo comparativo ofrece um panorama de las publicaciones completas de dos  comunidades científicas: los pesquisadores del Conselho Nacional de Pesquisa (CNPq, Brasil) y los investigadores del Consejo Nacional de Investigaciones Científicas y Técnicas (Conicet-Argentina). Para poner el foco en el idioma y el país de edición de la producción científica, utilizamos la información autocargada en el sistema curricular Sigeva (Argentina) y Lattes (Brasil). Su utilización ofrece dificultades a los estudios  bibliométricos o de citaciones, en cambio, permite construir una estadística descriptiva de la producción completa de itinerários completos de producción que es relevante para  frecer un panorama del  multilingüismo, la bibliodiversidady el peso de la publicación nacional en estas comunidades.A predominância do inglês como língua acadêmica nos principais periódicos tem sido amplamente estudada. Por outro lado, é difícil mensurar a incidência da publicação nesse idioma no mundo ibero-americano, porque ainda são poucos os estudos de bases de dados regionais ou baseados em trajetórias acadêmicas completas de pesquisadores dos países do Sul global. As razões são simples: a) existem várias bases de dados de revistas ibero-americanas, mas com grandes sobreposições entre elas; b) existem sistemas curriculares na maioria dos países, mas eles não estão disponíveis abertamente ou com curadoria profissional. Visando a colaborar nessa direção, este trabalho comparativo oferece um panorama das publicações completas de duas comunidades científicas: pesquisadores do Conselho Nacional de Pesquisa (CNPq, Brasil) e pesquisadores do Conselho Nacional de Pesquisas Científicas e Técnicas (Conicet-Argentina). Para focar o idioma e o país de publicação dessa produção científica, utilizamos as informações disponibilizadas nosistema curricular Sigeva (Argentina) e Lattes (Brasil). Seu uso oferece dificuldades para estudos bibliométricos ou de citação, porém permite a construção de estatísticas descritivas da produção de trajetórias completas de produção. Uma informação relevante para oferecer um panorama do multilinguismo, da bibliodiversidade e do peso da publicação nacional nestas comunidades

Classificação de autores, instituições e países, por meio de métricas de produção, centralidade e impacto: o campo de turismo no Brasil (periódicos), 1990-2018

We investigated the set of Brazilian tourism journals, specifically 3,887 articles published in 16 journals, from 1990 to 2018. The three main objectives of this study are: a) to rank authors, institutions, and countries in the field of tourism studies in Brazil, using productivity, centrality, and impact metrics, for 1990-1999, 1990-2009, and 1990-2018; b) to characterize the leading elements – i.e. top-ranked ones; and c) to compare these rankings with h-index based rankings. A bibliometric and social network study was carried out, with manual data collection and revision and disambiguation. Productivity (full and fractional counting), centrality (degree, betweenness, and PageRank), and impact (based on actual citations) metrics were calculated. In summary, the leading authors are affiliated with institutions in the South and Southeast regions of Brazil, and they are linked to graduate programs. For institutions, offering a graduate program in tourism or in a related field seems to be a key factor. The University of São Paulo (USP) and the University of Vale do Itajaí (UNIVALI) clearly stand out in all metrics. Brazil occupies the first position in productivity, centrality, and impact, followed by Spain.We investigated the set of Brazilian tourism journals, specifically 3,887 articles published in 16 journals, from 1990 to 2018. The three main objectives of this study are: a) to rank authors, institutions, and countries in the field of tourism studies in Brazil, using productivity, centrality, and impact metrics, for 1990-1999, 1990-2009, and 1990-2018; b) to characterize the leading elements – i.e. top-ranked ones; and c) to compare these rankings with h-index based rankings. A bibliometric and social network study was carried out, with manual data collection and revision and disambiguation. Productivity (full and fractional counting), centrality (degree, betweenness, and PageRank), and impact (based on actual citations) metrics were calculated. In summary, the leading authors are affiliated with institutions in the South and Southeast regions of Brazil, and they are linked to graduate programs. For institutions, offering a graduate program in tourism or in a related field seems to be a key factor. The University of São Paulo (USP) and the University of Vale do Itajaí (UNIVALI) clearly stand out in all metrics. Brazil occupies the first position in productivity, centrality, and impact, followed by Spain.Trabalha-se com o conjunto de periódicos brasileiros de turismo, mas particularmente com os 3.887 artigos publicados em 16 revistas, no período 1990-2018. Há três objetivos principais, a saber: a) construir rankings de autores, instituições e países do campo de turismo no Brasil, segundo métricas de produção, centralidade e impacto, nos períodos 1990-1999, 1990-2009 e 1990-2018; b) caracterizar os elementos mais importantes – aqueles que aparecem nas primeiras posições desses rankings; e c) comparar os resultados desses rankings aos obtidos com a aplicação do Índice H. Foi feito um estudo bibliométrico e de redes, com coleta de dados e revisão e desambiguação manuais; foram calculadas métricas de produção (contagem simples e fracionada), centralidade (grau, intermediação e Page Rank) e impacto (baseadas nas citações reais). Em resumo, os principais pesquisadores trabalham em instituições do Sul e Sudeste do país, e estão vinculados a programas de pós-graduação stricto sensu. Para as instituições, ter um programa de pós-graduação stricto sensu em turismo ou campo correlato parece ser um fator-chave; a Universidade de São Paulo e a Universidade do Vale do Itajaí claramente se destacam das demais, em toda e qualquer métrica. O Brasil ocupa a primeira posição em produção, centralidade e impacto, seguido sempre pela Espanha