Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

On the effect of tracer density on axial dispersion in a batch oscillatory baffled column

In this paper, we report our modelling evaluation on the effect of tracer density on axial dispersion in a batch oscillatory baffled column (OBC). Tracer solution of potassium nitrite, its specific density ranged from 1.0 to 1.5, was used in the study, and was injected to the vertical column from either the top or bottom. Local concentration profiles are measured using conductivity probes at two locations along the height of the column. Using the experimental measured concentration profiles together with both 'Tank-in-Series' and 'Plug Flow with Axial Dispersion' models, axial dispersion coefficients were determined and used to describe the effect of specific tracer density on mixing in the OBC. The results showed that the axial dispersion coefficients evaluated by the two models are very similar in both magnitudes and trends, and the range of variations in such coefficients is generally larger for the bottom injection than for the top one. Empirical correlations linking the mechanical energy for mixing, the specific density of tracer and axial dispersion coefficient were established. Using these correlations, we identified the enhancements of up to 269% on axial dispersion for various specific tracer densities. (C) 2002 Elsevier Science B.V. All rights reserved.

The residual effects of cooperative-learning experiences: A two-year follow-up

The author investigated how training in small-group and interpersonal behaviors affected children's behavior and interactions as they worked in small groups 2 years later. The authors assigned 52 fifth graders, who had been trained 2 years previously in cooperative group behaviors, to the trained condition and 36 fifth graders, who had not previously been trained, to the untrained condition. Both were reconstituted from the pool of students who had participated previously in group activities. The results showed a residual training effect, with the children in the trained groups being more cooperative and helpful than their untrained peers.

Young women in conflict: Filipinas growing up in Australia

This paper discusses the tensions of adaptation as experienced by 72 young women, born in the Philippines or to immigrant mothers and resident in southeast, far west and far north Queensland, Australia. As illustrated, these women, aged 14-25 years, often have difficulty balancing their expectations with those of their families and of the society in which they live. Like most young Australians they experience some conflicts with parents, but the intersections of race, gender and culture may make it particularly difficult for young Filipinas to develop a sense of their own identity and place in society. The retention of Filipino values often isolates young women from their peers and excludes them from participating in activities considered an important part of growing up Australian, but the adoption of 'Australian' behaviors such as drinking and smoking is not necessarily accompanied by an enhanced sense of belonging.

Exotic vs endemic biocontrol agents: Would the real stratiolaelaps miles (Berlese) (Acari : Mesostigmata : Laelapidae), please stand up?

The ability of introduced organisms to invade undisturbed native habitats is a major concern in conservation biology and has resulted in a re-evaluation of the introduction of exotic biocontrol agents, especially of generalist predators. One such agent is Stratiolaelaps miles (Berlese), a predatory mite described from Italy, known from throughout the Holarctic, and apparently accidentally introduced to other areas of the world, including Australia. Initial investigations revealed that putative S. miles could be found in both disturbed and relatively pristine habitats in Queensland, Australia. However, analysis of the mitochondrial DNA of five populations showed most to be highly divergent genetically. Subsequent morphological analysis established two species groups: the lamington-group from cool-temperate to subtropical rainforests in Eastern Australia and the more eurytopic miles-group with a cosmopolitan distribution. We describe two new species from each of these complexes (Stratiolaelaps womersleyi, Stratiolaelaps lamington; Stratiolaelaps marilyn, Stratiolaelaps lorna, respectively), and resurrect Stratiolaelaps scimitus (Womersley), a species which often appears to have been confused with S. miles. Additionally, the large genetic distances among morphologically homogenous species in the miles-group suggest that the apparently cosmopolitan S. miles may be composed of a suite of cryptic species of potentially varying utility in biological control. (C) 2002 Elsevier Science (USA). All rights reserved.

Living with 'difference': growing up Chinese in white Australia

This Article does not have an abstract.

Measuring the accumulated hazards of smoking: global and regional estimates for 2000

Objective: Current prevalence of smoking, even where data are available, is a poor proxy for cumulative hazards of smoking, which depend on several factors including the age at which smoking began, duration of smoking, number of cigarettes smoked per day, degree of inhalation, and cigarette characteristics such as tar and nicotine content or filter type. Methods: We extended the Peto-Lopez smoking impact ratio method to estimate accumulated hazards of smoking for different regions of the world. Lung cancer mortality data were obtained from the Global Burden of Disease mortality database. The American Cancer Society Cancer Prevention Study, phase 11 (CPS-II) with follow up for the years 1982 to 1988 was the reference population. For the global application of the method, never-smoker lung cancer mortality rates were chosen based on the estimated use of coal for household energy in each region. Results: Men in industrialised countries of Europe, North America, and the Western Pacific had the largest accumulated hazards of smoking. Young and middle age males in many regions of the developing world also had large smoking risks. The accumulated hazards of smoking for women were highest in North America followed by Europe. Conclusions: In the absence of detailed data on smoking prevalence and history, lung cancer mortality provides a robust indicator of the accumulated hazards of smoking. These hazards in developing countries are currently more concentrated among young and middle aged males.

"Up the bay, down the docks": Desenhos e memórias de uma comunidade das docas

“A memória não é um instrumento para explorar o passado, mas o seu teatro” (Walter Benjamin), cujos actores são pessoas comuns que recordam e recriam eventos passados através de diferentes formas de representação. Assim sendo, a memória é dinâmica e reconstrutiva e permite perpetuar a experiência, bem como criar e legitimar a identidade de cada um (Eber and Neal, 2001:37). O objectivo deste artigo é analisar os desenhos de Jack Sullivan sobre a comunidade das docas de Cardiff, conhecida como Butetown ou “Tiger Bay”, e a sua importância enquanto prática cultural na (re)construção de uma memória colectiva e imaginada. De que forma é que esta comunidade das docas é recordada e de que modo são as suas práticas quotidianas representadas através de desenhos? Quem e o que é que Sullivan representa? O que deixa na obscuridade? Como é que a memória individual se torna em memória colectiva? A este artigo subjaz a ideia de que os desenhos de Jack Sullivan, que estiveram na origem dos seus reconhecidos quadros compilados em Tramp Steamers, Seamen & Sailor Town, se apresentam como uma “forma de lembrança” de eventos passados, tanto para aqueles que viveram nesta área de Cardiff, como para aqueles que lhe eram espacial e temporalmente alheios. Estes desenhos constroem as memórias individuais e colectiva, tornando esta comunidade das docas acessível a todos.

"Waking up from Medieval Slumber"

When the book Medieval Goa first appeared three decades ago (Delhi: Concept, 1979), it represented a significant break in the tradition of Indo-Portuguese historiography, until then markedly Luso-Indian, even when Goan native historians were the authors. This was acknowledged by prominent historians like C R Boxer, M N Pearson, A Disney, J Wicki and others who reviewed the book in international journals of history. The colonial culture and the political climate were not helpful for the promotion of a critical approach.

Estratégias de inovação de catching-up: as ligações de aprendizagem entre um instituto de P&D e pequenas empresas

Considerando que diferentes estratégias são utilizadas pelas organizações para potencializar seu desempenho por meio da inovação, este estudo teve como objetivo identificar as ligações de aprendizagem entre um instituto de P&D e pequenas empresas da cadeia produtiva da caprinocultura inserida no sistema de inovação local, tendo como base a seguinte questão: os institutos de P&D podem funcionar como porteiro tecnológico (gatekeepers) provendo conhecimento novo às pequenas empresas em estudo? Para isso foi elaborado o marco teórico do estudo baseado nas discussões referentes às estratégias e aos sistemas de inovação, articulando ainda as temáticas sobre pesquisa e desenvolvimento - P&D e os processos de aprendizagem correspondentes. A metodologia está baseada na estratégia do estudo multicaso. Os dados empíricos foram examinados segundo a abordagem qualitativa, sendo coletados através de entrevistas semiestruturadas, durante participações em reuniões e análises documentais. Nas empresas pesquisadas, observou-se que, apesar de essas manterem ligações de aprendizagem ainda incipientes com o instituto de P&D, evidências mostraram que estas estão incidindo na ampliação da base de conhecimento das pequenas empresas. Relevou-se ainda que estas ligações de aprendizagem estejam sendo ampliadas e potencializadas através das fontes externas e abertas entre as empresas e as demais instituições do sistema e que tiveram como base estratégias de inovação do tipo catching-up.

Do down ao up… : contributos do envolvimento familiar na estimulação precoce de uma criança com Trissomia 21

Do Down ao UP… Percurso de sentimentos, emoções, procuras e certezas, por vezes, incertas mas alegre e esperançosamente desafiantes… O itinerário de investigação, e consequente formação, que foi encetado procurou, com o envolvimento familiar, as estratégias e dinâmicas mais eficazes para a promoção de aquisições relevantes e significativas para uma criança, filha do próprio investigador, com necessidades educativas especiais decorrentes do quadro de Trissomia 21. Através da procura objectiva de dados contextualizadores, foi delineado um programa de estimulação precoce aplicado nas rotinas familiares, as quais se constituíram como reais oportunidades/meios de um envolvimento familiar participante e corresponsável, facilitador e promotor de desenvolvimento das potencialidades e capacidades da própria criança. Com esta investigação pretendeu-se destacar a importância da intervenção/estimulação nas rotinas familiares constituídas ou a potencializar, como forma de obtenção de prometedores resultados em todas as áreas de desenvolvimento, veiculando os princípios da normalização, da funcionalidade, da contextualização e do envolvimento convergente de todo o agregado familiar.