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.

Effect of manual hyperinflation on hemodynamics, gas exchange, and respiratory mechanics in ventilated patients

The authors investigated the effect of manual hyperinflation (MHI) with set parameters applied to patients on mechanical ventilation on hemodynamics, respiratory mechanics, and gas exchange. Sixteen critically ill patients post-septic shock, with acute lung injury, were studied. Heart rate, arterial pressure, and mean pulmonary artery pressure were recorded every minute. pulmonary artery occlusion pressure, cardiac output, arterial blood gases, and dynamic compliance (C-dyn) were recorded pre- and post-MHI. From this, systemic vascular resistance index (SVRI), cardiac index, oxygen delivery, and partial pressure of oxygen:fraction of inspired oxygen (PaO2:FiO(2)) ratio were calculated. There were significant increases in SVRI (P < 0.05) post-MHI and diastolic arterial pressure (P < 0.01)during MHI. C-dyn increased post-MHI (P < 0.01) and was sustained at 20 minutes post-MHI (P < 0.01). Subjects with an intrapulmonary cause of lung disease had a significant decrease (P = 0.02) in PaO2:FiO(2), and those with extrapulmonary causes of lung disease had a significant increase (P < 0.001) in PaO2:FiO(2) post-MHI. In critically ill patients, MHI resulted in an improvement in lung mechanics and an improvement in gas exchange in patients with lung disease due to extrapulmonary events and did not result in impairment of the cardiovascular system.

Exchange rate sensitivity of Australian international equity funds

This paper analyses the exchange rate exposure displayed by a sample of Australian international equity trusts (IET). Exchange rate exposure is also examined in the context of differing economic climates with particular emphasis on the Asian crisis in mid-1997. It is found that there is evidence of exchange rate exposure particularly in the context of a multiple exchange rate model. Exposure varies substantially between three alternative time periods with different exposure apparent subsequent to the Asian crisis than prior to this event.

Broadening conceptions of curriculum for young people: Reports from three student-teachers on exchange

Research reports prepared by three Australian preservice teachers--Paula Shaw, Chris Sharp and Scott McDonald--undertaking their teacher education practicum in Canada, form the basis of this paper. The reports provide critical insights into three aspects of education for young people in both Canada and Australia. They also provide critical insight into the ways in which a practicum research project, along with the opportunities afforded through an international experience, enabled the preservice teachers to broaden their understanding of the curriculum for young people, of issues relevant to the diverse needs of young people, and of themselves and their priorities as teachers. The preservice teachers investigated three topics: attempts to reduce homophobia in schools; the presence or absence of Aboriginal content in the school curricula in British Columbia and Queensland; and "schools-within-schools" as a means to meet the needs of diverse student populations. Linda Farr Darling from the University of British Columbia provides a response to the three reports.

Codon usage bias and A+T content variation in human papillomavirus genomes

We analyzed the codon usage bias of eight open reading frames (ORFs) across up to 79 human papillomavirus (HPV) genotypes from three distinct phylogenetic groups. All eight ORFs across HPV genotypes show a strong codon usage bias, amongst degenerately encoded amino acids, toward 18 codons mainly with T at the 3rd position. For all 18 degenerately encoded amino acids, codon preferences amongst human and animal PV ORFs are significantly different from those averaged across mammalian genes. Across the HPV types, the L2 ORFs show the highest codon usage bias (73.2 +/- 1.6% and the E4 ORFs the lowest (51.1 +/- 0.5%), reflecting as similar bias in codon 3rd position A + T content (L2: 76.1 +/- 4.2%; E4: 58.6 +/- 4.5%). The E4 ORF, uniquely amongst the HPV ORFs, is G + C rich, while the other ORFs are A + T rich. Codon usage bias correlates positively with A + T content at the codon 3rd position in the E2, E6, L1 and L2 ORFs, but negatively in the E4 ORFs. A general conservation of preferred codon usage across human and non-human PV genotypes whether they originate from a same supergroup or not, together with observed difference between the preferred codon usage for HPV ORFs and for genes of the cells they infect, suggests that specific codon usage bias and A + T content variation may somehow increase the replicational fitness of HPVs in mammalian epithelial cells, and have practical implications for gene therapy of HPV infection. (C) 2003 Elsevier B.V. All rights reserved.

STOCK EXCHANGE LISTING INDUCES SOPHISTICATION OF CAPITAL BUDGETING

This article compares capital budgeting techniques employed in listed and unlisted companies in Brazil. We surveyed the Chief Financial Officers (CFOs) of 398 listed companies and 300 large unlisted companies, and based on 91 respondents, the results suggest that the CFOs of listed companies tend to use less simplistic methods more often, for example: NPV and CAPM, and that CFOs of unlisted companies are less likely to estimate the cost of equity, despite being large companies. These findings indicate that stock exchange listing may require greater sophistication of the capital budgeting process.

"Caindo na cana" com Marilyn Monroe: tempo, espaço e "bóias-frias"

Neste artigo pretendo discutir um drama social ("cair na cana") que marca a passagem para uma condição ambígua, liminar. Se uma das experiências associadas ao "modernismo" é a de vivermos simultaneamente em tempos e espaços diferentes, certamente os "bóias-frias" são nossos contemporâneos modernistas. Paradoxalmente, em se tratando de uma imagem que certamente seduziu alguns campos intelectuais durante os anos 70 e 80, teriam as tentativas de definir o "bóia-fria", transformando imagem em categoria, contribuindo para a sua constituição em uma espécie de fóssil recente da produção academica?

Bias dependent photocurrent collection in p-i-n a-Si : EVSiC : H heterojunction

A series of large area single layers and heterojunction cells in the assembly glass/ZnO:Al/p (SixC1-x:H)/i (Si:H)/n (SixC1-x:H)/Al (0

Bias-dependent photocurrent collection in p-i-n a-Si : H/SiC : H heterojunction

A series of large area single layers and glass/ZnO:AVp(SixC1-x:H)/i(Si:H)/n(SixC1-x:H)/AI (0 < x < 1) heterojunction cells were produced by plasma-enhanced chemical vapour deposition (PE-CVD) at low temperature. Junction properties, carrier transport and photogeneration are investigated from dark and illuminated current-voltage (J-V) and capacitance-voltage (C-V) characteristics. For the heterojunction cells atypical J-V characteristics under different illumination conditions are observed leading to poor fill factors. High series resistances around 106 Q are also measured. These experimental results were used as a basis for the numerical simulation of the energy band diagram, and the electrical field distribution of the structures. Further comparison with the sensor performance gave satisfactory agreement. Results show that the conduction band offset is the most limiting parameter for the optimal collection of the photogenerated carriers. As the optical gap increases and the conductivity of the doped layers decreases, the transport mechanism changes from a drift to a diffusion-limited process.

Colour filtering in a-SiC : H based p-i-n-p-i-n cells: A trade-off between bias polarity and absorption regions

A large area colour imager optically addressed is presented. The colour imager consists of a thin wide band gap p-i-n a-SiC:H filtering element deposited on the top of a thick large area a-SiC:H(-p)/a-Si:H(-i)/a-SiC:H(-n) image sensor, which reveals itself an intrinsic colour filter. In order to tune the external applied voltage for full colour discrimination the photocurrent generated by a modulated red light is measured under different optical and electrical bias. Results reveal that the integrated device behaves itself as an imager and a filter giving information not only on the position where the optical image is absorbed but also on it wavelength and intensity. The amplitude and sign of the image signals are electrically tuneable. In a wide range of incident fluxes and under reverse bias, the red and blue image signals are opposite in sign and the green signal is suppressed allowing blue and red colour recognition. The green information is obtained under forward bias, where the blue signal goes down to zero and the red and green remain constant. Combining the information obtained at this two applied voltages a RGB colour image picture can be acquired without the need of the usual colour filters or pixel architecture. A numerical simulation supports the colour filter analysis.

La social stock exchange au Portugal: un nouvel allié de l'économie sociale

Résumé Cet article vise à contribuer à la connaissance de la Bolsa de Valores Sociais (BVS) — Social Stock Exchange — récemment créé au Portugal, dont le but primatial était de permettre la prise de moyens de financement des entités de l'Économie Sociale engagées dans des projets d'éducation et d'entreprenariat. Il se penchera sur la qualification juridique des divers types d'entités cotées dans la BVS, sur le concept d'investisseur social et sur la protection dont il jouira, vis-à-vis des exigences de transparence et de gouvernance qui incombent à ces entités. Le thème proposé sera examiné en soulignant les virtualités et le potentiel de la BVS, faisant référence à l'un ou à l'autre sujet qui viennent à effet, avec un accent particulier sur l'avantage d'élaborer un code de gouvernance corporative pour les entités de l'Économie Sociale. Abstract This article aims to contribute to the knowledge of the Bolsa de Valores Sociais (BVS) — Social Stock Exchange — recently created in Portugal, whose primatial purpose was to allow the taking of means of financing the Social Economy entities, engaged in projects in education and entrepreneurship. It will reflect on the legal classification of the various types of entities rated in the BVS, on the concept of social investor and on the protection he will enjoy, leading to the consequent demands for transparency and governance that falls upon those entities. The proposed theme will be discussed highlighting the virtues and potential of BVS, playing in one or two topics that comes to purpose, with particular emphasis on the relevance of drawing up a code of corporate governance for entities of the Social Economy. Resumen Este artículo tiene como objetivo contribuir al conocimiento de la Bolsa de Valores Sociales (BVS), recientemente creada en Portugal, cuya finalidad principal es que las entidades de la economía social dedicadas a proyectos en las áreas de educación y de iniciativa empresarial puedan obtener medios financieros. Se abordará la calificación jurídica de los diversos tipos de entidades que cotizan en la BVS, así como el concepto de inversor social y la protección de que éste goza, con las consiguientes exigencias en materia de transparencia y de gobierno que recaen sobre esas entidades. Se analizará la temática propuesta destacando las virtudes y potencialidades de la BVS, sin omitir algún otro tópico adyacente que resulte relevante, en especial la conveniencia de que sea elaborado un código de gobernanza corporativa para las entidades de la economía social.

: SiC Multilayer Photonic Structures with Self Optical Bias Amplification

Characteristics of tunable wavelength pi'n/pin filters based on a-SiC:H multilayered stacked cells are studied both experimental and theoretically. Results show that the device combines the demultiplexing operation with the simultaneous photodetection and self amplification of the signal. An algorithm to decode the multiplex signal is established. A capacitive active band-pass filter model is presented and supported by an electrical simulation of the state variable filter circuit. Experimental and simulated results show that the device acts as a state variable filter. It combines the properties of active high-pass and low-pass filter sections into a capacitive active band-pass filter using a changing photo capacitance to control the power delivered to the load.