The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

Incremental parsing in language-based editors: user needs and how to meet them

Incremental parsing has long been recognized as a technique of great utility in the construction of language-based editors, and correspondingly, the area currently enjoys a mature theory. Unfortunately, many practical considerations have been largely overlooked in previously published algorithms. Many user requirements for an editing system necessarily impact on the design of its incremental parser, but most approaches focus only on one: response time. This paper details an incremental parser based on LR parsing techniques and designed for use in a modeless syntax recognition editor. The nature of this editor places significant demands on the structure and quality of the document representation it uses, and hence, on the parser. The strategy presented here is novel in that both the parser and the representation it constructs are tolerant of the inevitable and frequent syntax errors that arise during editing. This is achieved by a method that differs from conventional error repair techniques, and that is more appropriate for use in an interactive context. Furthermore, the parser aims to minimize disturbance to this representation, not only to ensure other system components can operate incrementally, but also to avoid unfortunate consequences for certain user-oriented services. The algorithm is augmented with a limited form of predictive tree-building, and a technique is presented for the determination of valid symbols for menu-based insertion. Copyright (C) 2001 John Wiley & Sons, Ltd.

Core outcome domains for chronic pain clinical trials: IMMPACT recommendations

Objective. To provide recommendations for the core outcome domains that should be considered by investigators conducting clinical trials of the efficacy and effectiveness of treatments for chronic pain. Development of a core set of outcome domains would facilitate comparison and pooling of data, encourage more complete reporting of outcomes, simplify the preparation and review of research proposals and manuscripts, and allow clinicians to make informed decisions regarding the risks and benefits of treatment. Methods. Under the auspices of the Initiative on Methods, Measurement, and Pain Assessment in Clinical Trials (IMMPACT), 27 specialists from academia. governmental agencies, and the pharmaceutical industry participated in a consensus meeting and identified core outcome domains that should be considered in clinical trials of treatments for chronic pain. Conclusions. There was a consensus that chronic pain clinical trials should assess outcomes representing six core domains: (1) pain, (2) physical functioning, (3) emotional functioning, (4) participant ratings of improvement and satisfaction with treatment, (5) symptoms and adverse events, (6) participant disposition (e.g. adherence to the treatment regimen and reasons for premature withdrawal from the trial). Although consideration should be given to the assessment of each of these domains, there may be exceptions to the general recommendation to include all of these domains in chronic pain trials. When this occurs, the rationale for not including domains should be provided. It is not the intention of these recommendations that assessment of the core domains should be considered a requirement for approval of product applications by regulatory agencies or that a treatment must demonstrate statistically significant effects for all of the relevant core domains to establish evidence of its efficacy. (C) 2003 International Association for the Study of Pain.

Quality of scientific articles

The paper discusses the difficulties in judging the quality of scientific manuscripts and describes some common pitfalls that should be avoided when preparing a paper for submission to a peer-reviewed journal. Peer review is an imperfect system, with less than optimal reliability and uncertain validity. However, as it is likely that it will remain as the principal process of screening papers for publication, authors should avoid some common mistakes when preparing a report based on empirical findings of human research. Among these are: excessively long abstracts, extensive use of abbreviations, failure to report results of parsimonious data analyses, and misinterpretation of statistical associations identified in observational studies as causal. Another common problem in many manuscripts is their excessive length, which makes them more difficult to be evaluated or read by the intended readers, if published. The evaluation of papers after their publication with a view towards their inclusion in a systematic review is also discussed. The limitations of the impact factor as a criterion to judge the quality of a paper are reviewed.

D. João de Magalhães e Avelar e a Fundação da Real Biblioteca Pública Municipal do Porto (1833)

D. João de Magalhães e Avelar (1754-1833) formou aquela que, ao tempo, era a maior biblioteca privada portuguesa. Com cerca de 36000 volumes, foi elogiada por personalidades nacionais e estrangeiras, por aliar à quantidade de volumes inúmeros e valiosíssimos manuscritos. Formada ao longo dos séculos XVIII e XIX, durante mais de 30 anos, originou, em 1833, o primeiro núcleo da actual Biblioteca Pública Municipal do Porto. Numa época em que possuir livros era sinónimo de prestígio social mas num período em que quase não havia tradição de bibliotecas públicas no nosso país, contrariamente ao que acontecia noutras realidades, a livraria privada de Avelar formou, com outras, a Real Biblioteca Pública da Cidade do Porto. Em 1833, aquando do primeiro aniversário da entrada do exército liberal no Porto, por decreto, criou-se a biblioteca portuense. Estabelecida na casa que servia de Hospício dos Religiosos de Santo António do Val da Piedade, à praça da Cordoaria, tinha como objectivo satisfazer a utilidade pública, estando aberta todos os dias, excepto domingos e feriados. Propriedade da cidade do Porto, ficava sujeita à administração da Câmara que se obrigava à sua guarda, manutenção, conservação, bem como à constante aquisição de espólio. Como veremos, tratou-se de um processo conflituoso mas o Porto obtinha, definitivamente, a sua biblioteca pública.

An interdisciplinary approach to the study of colour in portuguese manuscript illuminations

Dissertação apresentada para obtenção do Grau de Doutor em Conservação e Restauro, especialidade Teoria, História e Técnicas, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Predictive Biomarkers of Bacillus Calmette-Gu´erin Immunotherapy Response in Bladder Cancer: Where AreWe Now?

The most effective therapeutic option for managing nonmuscle invasive bladder cancer (NMIBC), over the last 30 years, consists of intravesical instillations with the attenuated strain Bacillus Calmette-Gu´erin (the BCG vaccine). This has been performed as an adjuvant therapeutic to transurethral resection of bladder tumour (TURBT) and mostly directed towards patients with highgrade tumours, T1 tumours, and in situ carcinomas. However, from 20% to 40% of the patients do not respond and frequently present tumour progression. Since BCG effectiveness is unpredictable, it is important to find consistent biomarkers that can aid either in the prediction of the outcome and/or side effects development. Accordingly, we conducted a systematic critical review to identify themost preeminent predictive molecular markers associated with BCG response. To the best of our knowledge, this is the first review exclusively focusing on predictive biomarkers for BCG treatment outcome. Using a specific query, 1324 abstracts were gathered, then inclusion/exclusion criteria were applied, and finally 87 manuscripts were included. Several molecules, including CD68 and genetic polymorphisms, have been identified as promising surrogate biomarkers. Combinatory analysis of the candidate predictive markers is a crucial step to create a predictive profile of treatment response.

Atypical Case of Mediterranean Spotted Fever

The authors present a case of atypical severe (malignant) Mediterranean spotted fever, with a brief review on the subject. Although not previously described in Brazil, the possibility of imported cases, especially from Portuguese tourists, is real. This case report highlights the severe form of the disease and the possibility of atypical presentation with confounding differential diagnosis. A brief review of classical presentation is also done. The authors believe it is a valid paper and a good contribution to your Journal of Infectious Diseases. The content of the manuscript represents the views of the coauthors, and neither the corresponding author nor the coauthors have submitted duplicate or overlapping manuscripts elsewhere.

HUMAN T-LYMPHOTROPIC VIRUS 1 (HTLV-1) AND HUMAN T-LYMPHOTROPIC VIRUS 2 (HTLV-2): GEOGRAPHICAL RESEARCH TRENDS AND COLLABORATION NETWORKS (1989-2012)

Publications are often used as a measure of research work success. Human T-lymphotropic virus (HTLV) type 1 and 2 are human retroviruses, which were discovered in the early 1980s, and it is estimated that 15-20 million people are infected worldwide. This article describes a bibliometric review and a coauthorship network analysis of literature on HTLV indexed in PubMed in a 24-year period. A total of 7,564 documents were retrieved, showing a decrease in the number of documents from 1996 to 2007. HTLV manuscripts were published in 1,074 journals. Japan and USA were the countries with the highest contribution in this field (61%) followed by France (8%). Production ranking changed when the number of publications was normalized by population (Dominican Republic and Japan), by gross domestic product (Guinea-Bissau and Gambia), and by gross national income per capita (Brazil and Japan). The present study has shed light on some of the defining features of scientific collaboration performed by HTLV research community, such as the existence of core researchers responsible for articulating the development of research in the area, facilitating wider collaborative relationships and the integration of new authors in the research groups.

Effectiveness of the Dexamethasone Intravitreal Implant for Treatment of Patients with Diabetic Macular Oedema

Diabetic macular oedema (DMO) is a leading cause of vision loss in the working-age population worldwide. Corticosteroid drugs have been demonstrated to inhibit the expression of both the vascular endothelial growth factor (VEGF) gene and other anti-inflammatory mediators, such as prostaglandins. Triamcinolone, fluocinolone and dexamethasone are the main steroids that have been studied for the treatment of macular oedema. Over the last few years, several studies have suggested an important role for dexamethasone in the management of DMO. The dexamethasone intravitreal implant (DEX implant) (Ozurdex®; Allergan, Inc., Irvine, CA) is a novel approach approved by the US Food and Drug Administration (FDA) and by the EU for the intravitreal treatment of macular oedema after branch or central retinal vein occlusion, and for the treatment of non-infectious uveitis affecting the posterior segment of the eye. We reviewed manuscripts that had investigated the pharmacokinetics, efficacy and safety of the DEX implant regarding DMO treatment.

Old cellulose for new multifunctional networks

Dissertação para obtenção do Grau de Doutor em Ciência e Engenharia de Materiais

Some Notes on the Reception of Josquin and of Northern Idioms in Portuguese Music and Culture

Although Josquin is by far the best-represented foreign composer in Gonçalo de Baena's Arte novamente inventada pera aprender a tanger (Lisbon, 1540), his music is undeniably under-represented both in the extant sixteenth-century Portuguese manuscripts containing Franco-Flemish polyphony and in volumes imported from the Netherlands such as Coimbra MM 2 and VienNB 1783. Josquin’s reputation made him, along with Ockeghem, a symbol in Portuguese humanistic culture, but up to at least the late 1530s his name seems to have been much better known than his music. Nevertheless, possible allusions to specific works by Josquin can be found in early- and mid-sixteenth-century Portuguese polyphony. By the 1520s, the general technical and stylistic characteristics of his and the following generation of northerners had begun to permeate locally produced polyphony. This eventually replaced the late-fifteenth- and early-sixteenth-century pan-consonant and homorythmic style associated with the Aragonese and the so-called Spanish court repertory.

Staging the Scientist: The Representation of Science and its Processes in American and British Drama

Dissertação apresentada para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Estudos Ingleses e Norte Americanos

Spectroscopic characterization of natural dyes by their non-invasive identification on pre-Columbian codices: the Maya yellow

Mesoamerican cultures had a strong tradition of written and pictorial manuscripts, called the codices. In studies already performed it was found the use of Maya Blue, made from a mixture of indigo and a clay called palygorskite, forming an incredibly stable material where the dye is trapped inside the nanotubes of the clay, after heating. However, a bigger challenge lies in the study of the yellows used, for these civilizations might have used this clay-dye mixture to produce their yellow colorants. As a first step, it was possible to provide identification, by non-invasive methods, of two colorants (a flavonoid and a carotenoid). While the flavonoid absorbed between 368-379 nm, the carotenoid would absorb around 455 nm. A temperature study also conducted allowed to set 140ºC as the desirable temperature to heat the samples without degrading them. FT-IR, conventional Raman and SERS allowed us to understand the existence of a reaction between the dyes and the clays (palygorskite and kaolinite), however it is difficult to understand it in a molecular point of view. As a second step, five species of Mexican dyes were selected on the basis of historical sources. The Maya yellow samples were produced adapting the recipe proposed by Reyes-Valerio, supporting the yellow dyes extracted from the dried plants on the clays, with addition of water, and then heated at 140ºC. It was found that the addition of water in palygorskite would increase the pH, hence deprotonating the molecules having a clear negative effect in the color. A second recipe was developed, without the addition of water; however, it was found that the use of water based binders would still alter the color of the samples with palygorskite. In this case, kaolinite without heating yield better results as a Maya yellow hybrid. It was found that the Maya chemistry might not have been the same for all the colors. The Mesoamericans might have found that different dyes could work better to their desires if matched with different clays. It was noticeable that for a clear distinction between flavonoids and carotenoids the reflectance and emission studies suffice, but when clay is added, Raman techniques will perform better. For this reason, conventional Raman and SERS were employed in order to create a database for the Mesoamerican dyestuffs for a future identification.

O Corpo e o Gesto na Tapeçaria de Bayeux (séc. XI)

Como responsáveis pela leccionação da disciplina de História da Inglaterra medieval, temos não raro sugerido aos alunos, para fins puramente lúdicos, a leitura da obra clássica de Sellar e Yeatman; no entanto, a sua condição de ‘História de Inglaterra em disparates’ faz com que de imediato aconselhemos no sentido de evitar sincronias com os períodos de avaliação escolar. Ora é precisamente de Sellar e Yeatman que citamos, em jeito de abertura, o seguinte passo: “With Edward the Confessor [1042-1066] perished the last English King [...], since he was succeeded by Waves of Norman Kings (French), Tudors (Welsh), Stuarts (Scottish), and Hanoverians (German) […]. The Norman Conquest was a Good Thing, as from this time onwards England stopped being conquered and thus was able to become top nation.” Descontada a caricatura, estas palavras e o próprio título espelham, afinal, a centralidade de 1066, parecendo reduzir todos os acontecimentos posteriores a um mero posfácio ou epílogo histórico. Esta perspectiva, manifestamente insustentável, em nada contradiz ou anula os sortilégios literário-ficcionais da data, patentes, por exemplo, num romance notável de Julian Rathbone, várias vezes reimpresso desde o seu aparecimento e amplamente merecedor de adaptação cinematográfica.