jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web

BackgroundMany software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees. Methods/Principal Findings We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is designed to work across all major browsers and renders an alternative format for those browsers that do not support SVG. The library provides tools for building rectangular and circular phylograms with integrated charting. Interactive features may be integrated and made to respond to events such as clicks on any element of the tree, including labels. Conclusions/Significance jsPhyloSVG is an open-source solution for rendering dynamic phylogenetic trees. It is capable of generating complex and interactive phylogenetic trees across all major browsers without the need for plugins. It is novel in supporting the ability to interpret the tree inference formats directly, exposing the underlying markup to data-mining services. The library source code, extensive documentation and live examples are freely accessible at www.jsphylosvg.com

Single-Cell Enumeration of an Uncultivated TM7 Subgroup in the

Specific oligonucleotide hybridization conditions were established for single-cell enumeration of uncultivated TM7 and IO25 bacteria by using clones expressing heterologous 16S rRNA. In situ analysis of human subgingival crevice specimens revealed that a greater proportion of samples from sites of chronic periodontitis than from healthy sites contained TM7 subgroup IO25. In addition, IO25 bacterial cells from periodontitis site samples were more abundant and fourfold longer than IO25 cells from healthy site samples

Prevalence of Bacteria of Division TM7 in Human Subgingival Plaque and Their Association with Disease

Members of the uncultivated bacterial division TM7 have been detected in the human mouth, but little information is available regarding their prevalence and diversity at this site. Human subgingival plaque samples from healthy sites and sites exhibiting various stages of periodontal disease were analyzed for the presence of TM7 bacteria. TM7 ribosomal DNA (rDNA) was found in 96% of the samples, and it accounted for approximately 0.3%, on average, of all bacterial rDNA in the samples as determined by real-time quantitative PCR. Two new phylotypes of this division were identified, and members of the division were found to exhibit filamentous morphology by fluorescence in situ hybridization. The abundance of TM7 rDNA relative to total bacterial rDNA was higher in sites with mild periodontitis (0.54% ± 0.1%) than in either healthy sites (0.21% ± 0.05%, P \u3c 0.01) or sites with severe periodontitis (0.29% ± 0.06%, P \u3c 0.05). One division subgroup, the I025 phylotype, was detected in 1 of 18 healthy samples and 38 of 58 disease samples. These data suggest that this phylotype, and the TM7 bacterial division in general, may play a role in the multifactorial process leading to periodontitis

Methanogenic \u3cem\u3eArchaea\u3c/em\u3e and human periodontal disease

Archaea have been isolated from the human colon, vagina, and oral cavity, but have not been established as causes of human disease. In this study, we reveal a relationship between the severity of periodontal disease and the relative abundance of archaeal small subunit ribosomal RNA genes (SSU rDNA) in the subgingival crevice by using quantitative PCR. Furthermore, the relative abundance of archaeal small subunit rDNA decreased at treated sites in association with clinical improvement. Archaea were harbored by 36% of periodontitis patients and were restricted to subgingival sites with periodontal disease. The presence of archaeal cells at these sites was confirmed by fluorescent in situ hybridization. The archaeal community at diseased sites was dominated by a Methanobrevibacter oralis-like phylotype and a distinct Methanobrevibacter subpopulation related to archaea that inhabit the gut of numerous animals. We hypothesize that methanogens participate in syntrophic relationships in the subgingival crevice that promote colonization by secondary fermenters during periodontitis. Because they are potential alternative syntrophic partners, our finding of larger Treponema populations sites without archaea provides further support for this hypothesis

Cultivation of \u3cem\u3eTropheryma whipplei\u3c/em\u3e from Cerebrospinal Fluid

Whipple disease (WD) is a systemic disorder caused by the bacterium Tropheryma whipplei. Since the recognition of a bacterial etiology in 1961, many attempts have been made to cultivate this bacterium in vitro. It was eventually isolated, in 2000, from an infected heart valve, in coculture with human fibroblasts. Here we report the isolation of 2 new strains of T. whipplei from cerebrospinal fluid (CSF) of 2 patients with intestinal WD but no neurological signs or symptoms. One culture-positive specimen was obtained before treatment; the other was obtained 12 months after discontinuation of therapy, at a time of intestinal remission. In both cases, 15 passages of the cultures were completed over 17 months. Bacterial growth was measured by quantitative polymerase chain reaction, which suggested a generation time of 4 days. Staining with YO-PRO nucleic-acid dye showed characteristic rod-shaped bacteria arranged in chains. Fluorescent in situ hybridization with a T. whipplei–specific oligonucleotide probe, a broad-range bacterial probe, and a nonspecific nucleicacid stain indicated that all visible bacteria were T. whipplei. Scanning electron microscopy and transmission electron microscopy showed both intracellular and extracellular bacteria. This first isolation of T. whipplei from CSF provides clear evidence of viable bacteria in the central nervous system in individuals with WD, even after prolonged antibiotic therapy

Escape às origens e trajetórias de estrangeiros em João Pessoa

Tese (doutorado) - Universidade Federal de Santa Catarina, Centro de Filosofia e Ciências Humanas, Programa de Pós-Graduação Interdisciplinar em Ciências Humanas, Florianópolis, 2014.A presente incursão investigativa traz à baila as percepções e os sentimentos envolvidos nas trajetórias de sujeitos anglo-americanos, que partem de seus países de origem para João Pessoa, Paraíba. Por ser uma pesquisa que atinge vários campos de conhecimentos, me valho da abordagem interdisciplinar para associá-los. Entrevistei, utilizando a técnica e a metodologia da História Oral, seis sujeitos, entre 35 e 70 anos, de Maio de 2012 a Novembro de 2013, acerca dos seus deslocamentos. Inspiro-me na Análise Crítico-Discursiva para investigar como determinadas escolhas lexicais, práticas discursivas e sociais auxiliam na compreensão das experiências sobre os deslocamentos. As temáticas que orientam o percurso analítico são: o local de fala; as percepções das sociedades de origem e lar; os processos decisórios e as motivações para a mudança; os elementos que promovem a fixação na cidade; a (des)construção das práticas sociais em meio aos processos de identificação e adaptação; as relações de alteridade e diversidade; a formação das díades conjugais entre estrangeiros e brasileiras; e os laços familiares. Nesse sentido, a mudança, embora, às vezes, apontada como obra do acaso, muito deve às necessidades pessoais de aventura daqueles que desejam desviar dos destinos sociais. Fuga às origens, busca pela satisfação pessoal e profissional, pela formação de uma família transcultural, o sonho de um lar próximo a praia, esses são alguns elementos do escapismo urbano e contemporâneo que, se a princípio parecia individual, aos poucos é delineado pelas relações conjugais e familiares, centrais para as mobilidades desses sujeitos.Abstract : This investigational research brings out the perceptions and feelings involved in the trajectories of Anglo-American men that leave their countries of origin for João Pessoa, Paraíba. Due to the fact that this study covers several fields of knowledge I make use of the interdisciplinary approach to bring them together. I interviewed, using Oral History s technique and methodology, six men, aged between 35- 70 years old, from May 2012 to November 2013 about their moving. I take Critical Discourse Analysis as a theoretical source of inspiration aiming at investigating how the lexical choices, the discursive and social practices allow me to understand the experiences within their movements. The thematic elements which guide the analytic trail are: where you speak from; the perceptions of society of origin and homesociety; the decision-making processes and the motivations for moving; the elements that encourage the fixation in the city; the (de)construction of social practices amidst identification and adaptation; the relationships of otherness and diversity; the coupling of foreign men and Brazilian women and consequent family ties. With that in mind, the moving, though sometimes pointed out as predestined by fate, owes much to the personal need for adventure in men who wish to deviate from their social destiny. An escape from origins, a search for personal and professional satisfaction, the constitution of a transcultural family, the dream of a home near the beach, these are some elements in the urban and contemporaneous escapism that may have seemed individual but proved to be outlined by marital and family relationships, key in the mobility of these men

Crise socioambiental: compreensão e combate através de uma visão que conecte as esferas individual e coletiva

Resumo: É inegável que a sociedade moderna vivencia uma crise socioambiental. O presente artigo visa explorar questões acerca de tal crise - como surgiu, como funciona, quais os seus efeitos e como combatê-la. Isso será feito através de uma visão que combina disciplinas diversas, principalmente as Relações Internacionais, conectando conscientização e práticas individuais a políticas públicas e medidas coletivas em prol dos direitos humanos e de um mundo sustentável.Palavras-chave Crise socioambiental; meio ambiente; consumismo; sociedade civil; Relações Internacionais. Abstract: It’s undeniable that the modern society experience a social and environmental crisis. This article aims to explore some questions around the crisis: how it emerged, how it works, which are its efects and how to fight it. This will be done through a vision that connects several disciplines, mainly International Relations, conecting individual awareness and practices to public policies and collective measures in favor of human rights and a sustainable world.Keywords: Social and environmental crisis; environment; consumerism; civil society; International Relations

El proceso de reformas del Seguro Social de la Enfermedad de Alemania durante la década del ‘90: avances e impasses

This article describes the process of health care reform in Germany during the ‘90s which was organized based on corporate interests. We also analyze the impact of the reform on system performance. The results are based on a review of the literature on health care systems. The analysis was based on the methodology proposed by Evans focusing on three dimensions: organization and management, financing, and health care delivery. The analysis suggests that, despite the rigidity of social protection systems based on corporatate interests, it is possible to make changes that result in positive outcomes in terms of efficacy and efficiency. The article also suggests that this process can produce negative effects on equity and population coverage.En este artículo se describen las reformas del Seguro Social de la Enfermedad de Alemania realizadas durante la década del ‘90, organizadas en base a una representación corporativa de intereses, y se analizan los impactos sobre la performance de este sistema de salud. Para la descripción del sistema y el análisis de las reformas, se realizó una investigación bibliográfica y se aplicó la metodología de abordaje integrado de las dimensiones de Organización y Gestión, Financiamiento y Atención y Provisión basada en Evans. Los análisis sugieren que, no obstante la rigidez de los sistemas de seguro social organizados sobre bases corporativas, es posible imprimir transformaciones con resultados positivos con relación a la eficacia y a la eficiencia, aunque podrían darse, a la vez, efectos negativos sobre la equidad y la expansión de la cobertura poblacional

[the Meaning Attributed To 'being Old' By Workers Of Long-term Care Nursing Institutions].

This is a descriptive and explorative study with a quantitative approach aimed at identifying the meaning of 'being old' according to 50 health-care workers responsible for direct nursing care to elderly residents in nursing homes. Data was obtained by means of the Portuguese version of the 'Semantic Differential Scale' validated in Brazil. Subjects were predominantly nursing assistants and 'general services' workers. The majority of them conferred to the elderly the adjectives beautiful, tender, sweet, wise, interesting, with sense of opportunity, humble and resigned. The attributes destructive, insecure, critic and intrusive were also cited. Most subjects selected adjectives that, in spite of being positive, are also related with docility and passivity.4157-6