Chicken BAFF--a highly conserved cytokine that mediates B cell survival.

Members of the tumor necrosis factor (TNF) family play key roles in the regulation of inflammation, immune responses and tissue homeostasis. Here we describe the identification of the chicken homologue of mammalian B cell activating factor of the TNF family (BAFF/BLyS). By searching a chicken EST database we identified two overlapping cDNA clones that code for the entire open reading frame of chicken BAFF (chBAFF), which contains a predicted transmembrane domain and a putative furin protease cleavage site like its mammalian counterparts. The amino acid identity between soluble chicken and human BAFF is 76%, considerably higher than for most other known cytokines. The chBAFF gene is most strongly expressed in the bursa of Fabricius. Soluble recombinant chBAFF produced by human 293T cells interacted with the mammalian cell-surface receptors TACI, BCMA and BAFF-R. It bound to chicken B cells, but not to other lymphocytes, and it promoted the survival of splenic chicken B cells in culture. Furthermore, bacterially expressed chBAFF induced the selective expansion of B cells in the spleen and cecal tonsils when administered to young chicks. Our results suggest that like its mammalian counterpart, chBAFF plays an important role in survival and/or proliferation of chicken B cells.

Técnicas de Data e Text Mining Para Anotação de Um Arquivo Digital

O presente trabalho cujo Título é técnicas de Data e Text Mining para a anotação dum Arquivo Digital, tem como objectivo testar a viabilidade da utilização de técnicas de processamento automático de texto para a anotação das sessões dos debates parlamentares da Assembleia da República de Portugal. Ao longo do trabalho abordaram-se conceitos como tecnologias de descoberta do conhecimento (KDD), o processo da descoberta do conhecimento em texto, a caracterização das várias etapas do processamento de texto e a descrição de algumas ferramentas open souce para a mineração de texto. A metodologia utilizada baseou-se na experimentação de várias técnicas de processamento textual utilizando a open source R/tm. Apresentam-se, como resultados, a influência do pré-processamento, tamanho dos documentos e tamanhos dos corpora no resultado do processamento utilizando o algoritmo knnflex.

Mutations leading to X-linked hypohidrotic ectodermal dysplasia affect three major functional domains in the tumor necrosis factor family member ectodysplasin-A.

Mutations in the epithelial morphogen ectodysplasin-A (EDA), a member of the tumor necrosis factor (TNF) family, are responsible for the human disorder X-linked hypohidrotic ectodermal dysplasia (XLHED) characterized by impaired development of hair, eccrine sweat glands, and teeth. EDA-A1 and EDA-A2 are two splice variants of EDA, which bind distinct EDA-A1 and X-linked EDA-A2 receptors. We identified a series of novel EDA mutations in families with XLHED, allowing the identification of the following three functionally important regions in EDA: a C-terminal TNF homology domain, a collagen domain, and a furin protease recognition sequence. Mutations in the TNF homology domain impair binding of both splice variants to their receptors. Mutations in the collagen domain can inhibit multimerization of the TNF homology region, whereas those in the consensus furin recognition sequence prevent proteolytic cleavage of EDA. Finally, a mutation affecting an intron splice donor site is predicted to eliminate specifically the EDA-A1 but not the EDA-A2 splice variant. Thus a proteolytically processed, oligomeric form of EDA-A1 is required in vivo for proper morphogenesis.

PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data

Despite the advancement of phylogenetic methods to estimate speciation and extinction rates, their power can be limited under variable rates, in particular for clades with high extinction rates and small number of extant species. Fossil data can provide a powerful alternative source of information to investigate diversification processes. Here, we present PyRate, a computer program to estimate speciation and extinction rates and their temporal dynamics from fossil occurrence data. The rates are inferred in a Bayesian framework and are comparable to those estimated from phylogenetic trees. We describe how PyRate can be used to explore different models of diversification. In addition to the diversification rates, it provides estimates of the parameters of the preservation process (fossilization and sampling) and the times of speciation and extinction of each species in the data set. Moreover, we develop a new birth-death model to correlate the variation of speciation/extinction rates with changes of a continuous trait. Finally, we demonstrate the use of Bayes factors for model selection and show how the posterior estimates of a PyRate analysis can be used to generate calibration densities for Bayesian molecular clock analysis. PyRate is an open-source command-line Python program available at http://sourceforge.net/projects/pyrate/.

Laparoscopic and open colorectal surgery in everyday practice : retrospective study

Résumé Introduction: La plupart des études disponibles sur la chirurgie colorectale par laparoscopie concernent des patients hautement sélectionnés. Le but de cette étude est d'analyser les résultats à court et à long terme de l'ensemble des patients traités dans un service de chirurgie générale. Méthodes: Il s'agit d'une analyse rétrospective d'un registre prospectif interne au service, dans lequel tous les patients consécutifs opérés pour la première fois du colon et du rectum entre mars 1993 et décembre 1997 ont été enregistrés. Les informations concernant le suivi ont été collectées par questionnaire. Résultats: Un total de 187 patients ont été opérés par laparoscopie et 215 patients par chirurgie ouverte durant la période d'étude. Les informations concernant le suivi ont pu être collectées dans 95% des cas avec une évolution de 1-107 mois (médiane 59 mois), respectivement de 1-104 mois (médiane 53 mois). Une conversion fut nécessaire dans 28 cas (15%) mais ceux-ci restent inclus dans le groupe laparoscopie pour l'analyse par intention de traitement. Dans le groupe laparoscopie, les opérations ont duré plus longtemps (205 vs 150 min, p<0.001) mais l'hospitalisation a été plus courte (8 vs 13 jours, p<0.001). La reprise du transit a été plus rapide après laparoscopie, mais uniquement après intervention sur le colon gauche (3 vs 4 jours, p<0.01). Cependant, la sélection préopératoire (nombre plus élevé d'urgences et de patients avec un risque anesthésiologique élevé dans le groupe de la chirurgie ouverte) a été favorable à la laparoscopie. Le taux de complications (global ainsi que pour chaque complication chirurgicale) a été similaire dans les deux groupes, avec un taux global de 20% environ. Conclusions: Malgré une sélection favorable des cas, uniquement très peu d'avantages à la laparoscopie sur la chirurgie ouverte ont pu être observés. Abstract Background: Most studies available on laparoscopic colorectal surgery focus on highly selected patient groups. The aim of the present study was to review short- and long-term outcome of everyday patients treated in a general surgery department. Methods: Retrospective review was carried out of a prospective database of all consecutive patients having undergone primary laparoscopic (LAP) or open colorectal surgery between March 1993 and December 1997. Follow-up data were completed via questionnaire. Results: A total of 187 patients underwent LAP resection and 215 patients underwent open surgery. Follow up was complete in 95% with a median of 59 months (range, 1-107 months) and 53 months (range, 1-104 months), respectively. There were 28 conversions (15%) in the LAP group and these remained in the LAP group in an intention-to-treat analysis. The LAP operations lasted significantly longer for all types of resections (205 vs 150 min, P<0.001) and hospital stay was shorter (8 vs 13 days, P<0.001). Recovery of intestinal function was faster in the LAP group, but only after left-sided procedures (3 vs 4days, P<0.01). However, preoperative patient selection (more emergency operations and patients with higher American Society of Anesthesiologists (ASA) score in the open group) had a major influence on these elements and favours the LAP group. Surprisingly, the overall surgical complication rate (including long-term complications such as wound hernia) was 20% in both groups with rates of individual complications also being comparable in both groups. Conclusion: Despite a patient selection favourable to the laparoscopy group, only little advantage in postoperative outcome could be shown for the minimally invasive over the open approach in the everyday patient.

How do very open economies adjust to large immigration flows? Recent evidence from Spanish regions

In recent years, Spain has received unprecedented immigration flows. Between 2001 and 2006 the fraction of the population born abroad more than doubled, increasing from4.8% to 10.8%. For Spanish provinces with above-median inflows (relative to population),immigration increased by 24% the number of high school dropouts while only increasingcollege graduates by 11%. We study different channels by which regional labor markets haveabsorbed the large increase in relative supply of low educated workers. We identify theexogenous supply shock using historical immigrant settlement patterns by country of origin.Using data from the Labor Force Survey and the decennial Census, we find a large expansion ofemployment in high immigration regions. Disaggregating by industry, the absorption operatedthrough large increases in the share of low-educated workers, compared to the same industry inlow-immigration regions. We do not find changes in sectoral specialization. Overall, andperhaps surprisingly, the pattern of absorption is very similar to the one found in the US.

Independent evolution of hypervariable regions of HIV-1 gp120: V4 as a swarm of N-Linked glycosylation variants

In this study we have characterized intra-patient length polymorphism in V4 by cloning and sequencing a C2-C4 fragment from HIV plasma RNA in patients at different stages of HIV disease. Clonal analysis of clade B, G, and CRF02 isolates during early infection shows extensive intra-patient V4 variability, due to the presence of indel-associated polymorphism. Indels, coupled to amino acid substitution events, affect the number and distribution of potential N-glycosylation sites, resulting in the coexistence, within the same patient, of V4 subsets, each characterized by different sizes, amino acid sequences, and potential N-glycosylation patterns. In contrast, V3 appears to be relatively homogeneous, with similar V3 associated to significantly different V4 within the same clinical specimen. Based on these data, we propose that during early chronic infection V4 is present as a highly divergent quasispecies, enabling the virus to adopt different conformational structures according to immune constrains and other selective pressures

Cognitive efficacy of quetiapine in early-onset first-episode psychosis: a 12-week open label trial.

Twenty-three adolescents with psychotic disorders, aged from 13 to 18 years, participated in a 12-week open label trial (17 adolescents completed the study) in order to examine the impact of quetiapine on clinical status and cognitive functions (encompassing processing speed, attention, short-term memory, long-term memory and executive function). An improvement in Clinical Global Impression and Positive and Negative Symptom Scale (P's ≤ 0.001) was observed. In addition, after controlling for amelioration of symptoms, a significant improvement was observed on one executive function (P = 0.044; Trail Making Part B). The remaining cognitive abilities showed stability. In addition, we observed an interaction between quetiapine doses (>300 mg/day or <300 mg/day) and time, where lower doses showed more improvement in verbal short-term memory (P = 0.048), inhibition abilities (P = 0.038) and positive symptoms (P = 0.020). The neuropsychological functioning of adolescents with psychotic disorders remained mainly stable after 12 weeks of treatment with quetiapine. However, lower doses seemed to have a better impact on two components of cognition (inhibition abilities and verbal short-term memory) and on positive symptoms.

Open to closed system transition traced through the TDIC isotopic signature at the aquifer recharge stage, implications for groundwater 14C dating

14C dating models are limited when considering recent groundwater for which the carbon isotopic signature of the total dissolved inorganic carbon (TDIC) is mainly acquired in the unsaturated zone. Reducing the uncertainties of dating thus implies a better identification of the processes controlling the carbon isotopic composition of the TDIC during groundwater recharge. Geochemical interactions between gas, water and carbonates in the unsaturated zone were investigated for two aquifers (the carbonate-free Fontainebleau sands and carbonate-bearing Astian sands, France) in order to identify the respective roles of CO2 and carbonates on the carbon isotopic signatures of the TDIC; this analysis is usually approached using open or closed system terms. Under fully open system conditions, the seasonality of the 13C values in the soil CO2 can lead to important uncertainties regarding the so-called "initial 14C activity" used in 14C correction models. In a carbonate-bearing unsaturated zone such as in the Astian aquifer, we show that an approach based on fully open or closed system conditions is not appropriate. Although the chemical saturation between water and calcite occurs rapidly within the first metre of the unsaturated zone, the carbon isotopic contents (δ13C) of the CO2 and the TDIC evolve downward, impacted by the dissolution-precipitation of the carbonates. In this study, we propose a numerical approach to describe this evolution. The δ13C and the A 14C (radiocarbon activity) of the TDIC at the base of the carbonate-hearing unsaturated zone depends on (i) the δ13C and the A 14C of the TDIC in the soil determined by the soil CO2, (ii) the water's residence time in the unsaturated zone and (iii) the carbonate precipitation-dissolution fluxes. In this type of situation, the carbonate δ13C-A 14C evolutions indicate the presence of secondary calcite and permit the calculation of its accretion flux, equal to ~ 4.5 ± 0.5 x 10-9 mol grock-1 yr-1. More generally, for other sites under temperate climate and with similar properties to the Astian sands site, this approach allows for a reliable determination of the carbon isotopic composition at the base of the unsaturated zone as the indispensable "input function" data of the carbon cycle into the aquifer.

Impact of bedside open lung biopsies on the management of mechanically ventilated immunocompromised patients with acute respiratory distress syndrome of unknown etiology.

BACKGROUND: Open lung biopsy (OLB) is helpful in the management of patients with acute respiratory distress syndrome (ARDS) of unknown etiology. We determine the impact of surgical lung biopsies performed at the bedside on the management of patients with ARDS. METHODS: We reviewed all consecutive cases of patients with ARDS who underwent a surgical OLB at the bedside in a medical intensive care unit between 1993 and 2005. RESULTS: Biopsies were performed in 19 patients mechanically ventilated for ARDS of unknown etiology despite extensive diagnostic process and empirical therapeutic trials. Among them, 17 (89%) were immunocompromised and 10 patients experienced hematological malignancies. Surgical biopsies were obtained after a median (25%-75%) mechanical ventilation of 5 (2-11) days; mean (+/-SD) Pao(2)/Fio(2) ratio was 119.3 (+/-34.2) mm Hg. Histologic diagnoses were obtained in all cases and were specific in 13 patients (68%), including 9 (47%) not previously suspected. Immediate complications (26%) were local (pneumothorax, minimal bleeding) without general or respiratory consequences. The biopsy resulted in major changes in management in 17 patients (89%). It contributed to a decision to limit care in 12 of 17 patients who died. CONCLUSION: Our data confirm that surgical OLB may have an important impact on the management of patients with ARDS of unknown etiology after extensive diagnostic process. The procedure can be performed at the bedside, is safe, and has a high diagnostic yield leading to major changes in management, including withdrawal of vital support, in the majority of patients.

MIAR: hacia un entorno colaborativo de editores, autores y evaluadores de revistas

Se describe la evolución del proyecto MIAR (Matriu d'Informació per l'Avaluació de Revistes), un sistema originalmente diseñado para cuantificar la indización en bases de datos de revistas de humanidades y ciencias sociales. Sin embargo, a la vista del panorama de recursos de evaluación actualmente disponibles en España, los autores plantean la transformación de MIAR hacia un portal colaborativo en el que todos los interesados puedan difundir las principales características de las revistas en las que participan directa o indirectamente. Se estudia una transformación del proyecto contemplando el uso de redes sociales, sistemas de votación y de sugerencia, y la aplicación de tecnologías como open linked data que permiten una mayor difusión y socialización de los datos recogidos para cada publicación. De esta manera los datos podrían ser mejor aprovechados por los tres colectivos más directamente interesados: evaluadores, editores y autores/lectores.

Measuring researchers' use of scholarly information through social bookmarking data: a case study of BibSonomy

This paper explores the possibility of using data from social bookmarking services to measure the use of information by academic researchers. Social bookmarking data can be used to augment participative methods (e.g. interviews and surveys) and other, non-participative methods (e.g. citation analysis and transaction logs) to measure the use of scholarly information. We use BibSonomy, a free resource-sharing system, as a case study. Results show that published journal articles are by far the most popular type of source bookmarked, followed by conference proceedings and books. Commercial journal publisher platforms are the most popular type of information resource bookmarked, followed by websites, records in databases and digital repositories. Usage of open access information resources is low in comparison with toll access journals. In the case of open access repositories, there is a marked preference for the use of subject-based repositories over institutional repositories. The results are consistent with those observed in related studies based on surveys and citation analysis, confirming the possible use of bookmarking data in studies of information behaviour in academic settings. The main advantages of using social bookmarking data are that is an unobtrusive approach, it captures the reading habits of researchers who are not necessarily authors, and data are readily available. The main limitation is that a significant amount of human resources is required in cleaning and standardizing the data.

The situation of open access institutional repositories in Spain: 2009 report

Introduction. The DRIVER I project drew up a detailed report of European repositories based on data gathered in a survey in which Spain's participation was very low. This created a highly distorted image of the implementation of repositories in Spain. This study aims to analyse the current state of Spanish open-access institutional repositories and to describe their characteristics. Method. The data were gathered through a Web survey. The questionnaire was based on that used by DRIVER I: coverage; technical infrastructure and technical issues; institutional policies; services created; and stimulators and inhibitors for establishing, filling and maintaining their digital institutional repositories. Analysis. Data were tabulated and analysed systematically according responses obtained from the questionnaire and grouped by coverage. Results. Responses were obtained from 38 of the 104 institutions contacted, which had 29 institutional repositories. This represents 78.3% of the Spanish repositories according to the BuscaRepositorios directory. Spanish repositories contained mainly full-text materials (journal articles and doctoral theses) together with metadata. The software most used was DSpace, followed by EPrints. The metadata standard most used was Dublin Core. Spanish repositories offered more usage statistics and fewer author-oriented services than the European average. The priorities for the future development of the repositories are the need for clear policies on access to scientific production based on public funding and the need for quality control indicators. Conclusions.This is the first detailed study of Spanish institutional repositories. The key stimulants for establishing, filling and maintaining were, in order of importance, the increase of visibility and citation, the interest of decision-makers, simplicity of use and search services. On the other hand the main inhibitors identified were the absence of policies, the lack of integration with other national and international systems and the lack of awareness efforts among academia.

Mutation hot spots in 5q31-linked corneal dystrophies.

Mutations in the BIGH3 gene on chromosome 5q31 cause four distinct autosomal dominant diseases of the human cornea: granular (Groenouw type I), Reis-Bücklers, lattice type I, and Avellino corneal dystrophies. All four diseases are characterized by both progressive accumulation of corneal deposits and eventual loss of vision. We have identified a specific recurrent missense mutation for each type of dystrophy, in 10 independently ascertained families. Genotype analysis with microsatellite markers surrounding the BIGH3 locus was performed in these 10 families and in 5 families reported previously. The affected haplotype could be determined in 10 of the 15 families and was different in each family. These data indicate that R555W, R124C, and R124H mutations occurred independently in several ethnic groups and that these mutations do not reflect a putative founder effect. Furthermore, this study confirms the specific importance of the R124 and R555 amino acids in the pathogenesis of autosomal dominant corneal dystrophies linked to 5q.

Metallogenic model of the Trepca Pb-Zn-Ag skarn deposit, Kosovo: Evidence from fluid inclusions, Rare Earth Elements, and stable isotope data

The Trepca Pb-Zn-Ag skarn deposit (29 Mt of ore at 3.45% Pb, 2.30% Zn, and 80 g/t Ag) is located in the Kopaonik block of the western Vardar zone, Kosovo. The mineralization, hosted by recrystallized limestone of Upper Triassic age, was structurally and lithologically controlled. Ore deposition is spatially and temporally related with the postcollisional magmatism of Oligocene age (23-26 Ma). The deposit was formed during two distinct mineralization stages: an early prograde closed-system and a later retrograde open-system stage. The prograde mineralization consisting mainly of pyroxenes (Hd(54-100)Jo(0-45)Di(0-45)) resulted from the interaction of magmatic fluids associated with Oligocene (23-26 Ma) postcollisional magmatism. Whereas there is no direct contact between magmatic rocks and the mineralization, the deposit is classified as a distal Pb-Zn-Ag skarn. Abundant pyroxene reflects low oxygen fugacity (<10(-31) bar) and anhydrous environment. Fluid inclusion data and mineral assemblage limit the prograde stage within a temperature range between 390 degrees and 475 degrees C. Formation pressure is estimated below 900 bars. Isotopic composition of aqueous fluid, inclusions hosted by hedenbergite (delta D = -108 to -130 parts per thousand; delta O-18 = 7.5-8.0 parts per thousand), Mn-enriched mineralogy and high REE content of the host carbonates at the contact with the skarn mineralization suggest that a magmatic fluid was modified during its infiltration through the country rocks. The retrograde mineral assemblage comprises ilvaite, magnetite, arsenopyrite, pyrrhotite, marcasite, pyrite, quartz, and various carbonates. Increases in oxygen and sulfur fugacities, as well as a hydrous character of mineralization, require an open-system model. The opening of the system is related to phreatomagmatic explosion and formation of the breccia. Arsenopyrite geothermometer limits the retrograde stage within the temperature range between 350 degrees and 380 degrees C and sulfur fugacity between 10(-8.8) and 10(-7.2) bars. The principal ore minerals, galena, sphalerite, pyrite, and minor chalcopyrite, were deposited from a moderately saline Ca-Na chloride fluid at around 350 degrees C. According to the isotopic composition of fluid inclusions hosted by sphalerite (delta D = -55 to -74 parts per thousand; delta O-18 = -9.6 to -13.6 parts per thousand), the fluid responsible for ore deposition was dominantly meteoric in origin. The delta S-31 values of the sulfides spanning between -5.5 and +10 parts per thousand point to a magmatic origin of sulfur. Ore deposition appears to have been largely contemporaneous with the retrograde stage of the skarn development. Postore stage accompanied the precipitation of significant amount of carbonates including the travertine deposits at the deposit surface. Mineralogical composition of travertine varies from calcite to siderite and all carbonates contain significant amounts of Mn. Decreased formation temperature and depletion in the REE content point to an influence of pH-neutralized cold ground water and dying magmatic system.