iProClass: an integrated, comprehensive and annotated protein classification database

The iProClass database is an integrated resource that provides comprehensive family relationships and structural and functional features of proteins, with rich links to various databases. It is extended from ProClass, a protein family database that integrates PIR superfamilies and PROSITE motifs. The iProClass currently consists of more than 200 000 non-redundant PIR and SWISS-PROT proteins organized with more than 28 000 superfamilies, 2600 domains, 1300 motifs, 280 post-translational modification sites and links to more than 30 databases of protein families, structures, functions, genes, genomes, literature and taxonomy. Protein and family summary reports provide rich annotations, including membership information with length, taxonomy and keyword statistics, full family relationships, comprehensive enzyme and PDB cross-references and graphical feature display. The database facilitates classification-driven annotation for protein sequence databases and complete genomes, and supports structural and functional genomic research. The iProClass is implemented in Oracle 8i object-relational system and available for sequence search and report retrieval at http://pir.georgetow n.edu/iproclass/.

Antiviral activities of the soluble extracellular domains of type I interferon receptors

Alternative splicing leads to the expression of multiple isoforms of the subunits (IFNAR1 and IFNAR2) of the type I IFN receptor. Here we describe two transcripts representing extracellular forms of ovine IFNAR1 and show that soluble extracellular forms of both IFNAR2 and IFNAR1, prepared in recombinant form in Escherichia coli, have antiviral (AV) activity in the absence of IFN. Exposure of Madin-Darby bovine kidney cells to the extracellular domain (R2E) of IFNAR2 at concentrations as low as 10 nM afforded complete protection against vesicular stomatitis virus and led to the rapid activation of the transcription factors ISGF3 and GAF. Although R2E can bind IFN (Kd ≈70 nM), activity was observed irrespective of whether or not ligand was present. R2E was inactive on mouse L929 cells but active on L929 cells expressing a membraneanchored, ovine/human chimeric IFNAR2 with an ovine extracellular domain. The data suggest that AV activity is conferred by the ability of soluble R2E to associate with the transfected IFNAR2 subunit rather than resident murine IFNAR1. Soluble extracellular forms of IFNAR1 have lower AV activity than R2E on Madin-Darby bovine kidney cells but are less species-specific and protect wild-type L929 cells as efficiently as the transfected cell line, presumably by interacting with one of the murine receptor subunits.

Timing of metamorphosis and the onset of the negative feedback loop between the thyroid gland and the pituitary is controlled by type II iodothyronine deiodinase in Xenopus laevis

Two important features of amphibian metamorphosis are the sequential response of tissues to different concentrations of thyroid hormone (TH) and the development of the negative feedback loop between the pituitary and the thyroid gland that regulates TH synthesis by the thyroid gland. At the climax of metamorphosis in Xenopus laevis (when the TH level is highest), the ratio of the circulating precursor thyroxine (T4) to the active form 3,5,3′-triiodothyronine (T3) in the blood is many times higher than it is in tissues. This difference is because of the conversion of T4 to T3 in target cells of the tadpole catalyzed by the enzyme type II iodothyronine deiodinase (D2) and the local effect (cell autonomy) of this activity. Limb buds and tails express D2 early and late in metamorphosis, respectively, correlating with the time that these organs undergo TH-induced change. T3 is required to complete metamorphosis because the peak concentration of T4 that is reached at metamorphic climax cannot induce the final morphological changes. At the climax of metamorphosis, D2 expression is activated specifically in the anterior pituitary cells that express the genes for thyroid-stimulating hormone but not in the cells that express proopiomelanocortin. Physiological concentrations of T3 but not T4 can suppress thyrotropin subunit β gene expression. The timing and the remarkable specificity of D2 expression in the thyrotrophs of the anterior pituitary coupled with the requirement for locally synthesized T3 strongly support a role for D2 in the onset of the negative feedback loop at the climax of metamorphosis.

Complete Cytolysis and Neonatal Lethality in Keratin 5 Knockout Mice Reveal Its Fundamental Role in Skin Integrity and in Epidermolysis Bullosa Simplex

In human patients, a wide range of mutations in keratin (K) 5 or K14 lead to the blistering skin disorder epidermolysis bullosa simplex. Given that K14 deficiency does not lead to the ablation of a basal cell cytoskeleton because of a compensatory role of K15, we have investigated the requirement for the keratin cytoskeleton in basal cells by inactivating the K5 gene in mice. We report that the K5−/− mice die shortly after birth, lack keratin filaments in the basal epidermis, and are more severely affected than K14−/− mice. In contrast to the K14−/− mice, we detected a strong induction of the wound-healing keratin K6 in the suprabasal epidermis of cytolyzed areas of postnatal K5−/− mice. In addition, K5 and K14 mice differed with respect to tongue lesions. Moreover, we show that in the absence of K5 and other type II keratins, residual K14 and K15 aggregated along hemidesmosomes, demonstrating that individual keratins without a partner are stable in vivo. Our data indicate that K5 may be the natural partner of K15 and K17. We suggest that K5 null mutations may be lethal in human epidermolysis bullosa simplex patients.

A minimal gene set for cellular life derived by comparison of complete bacterial genomes.

The recently sequenced genome of the parasitic bacterium Mycoplasma genitalium contains only 468 identified protein-coding genes that have been dubbed a minimal gene complement [Fraser, C.M., Gocayne, J.D., White, O., Adams, M.D., Clayton, R.A., et al. (1995) Science 270, 397-403]. Although the M. genitalium gene complement is indeed the smallest among known cellular life forms, there is no evidence that it is the minimal self-sufficient gene set. To derive such a set, we compared the 468 predicted M. genitalium protein sequences with the 1703 protein sequences encoded by the other completely sequenced small bacterial genome, that of Haemophilus influenzae. M. genitalium and H. influenzae belong to two ancient bacterial lineages, i.e., Gram-positive and Gram-negative bacteria, respectively. Therefore, the genes that are conserved in these two bacteria are almost certainly essential for cellular function. It is this category of genes that is most likely to approximate the minimal gene set. We found that 240 M. genitalium genes have orthologs among the genes of H. influenzae. This collection of genes falls short of comprising the minimal set as some enzymes responsible for intermediate steps in essential pathways are missing. The apparent reason for this is the phenomenon that we call nonorthologous gene displacement when the same function is fulfilled by nonorthologous proteins in two organisms. We identified 22 nonorthologous displacements and supplemented the set of orthologs with the respective M. genitalium genes. After examining the resulting list of 262 genes for possible functional redundancy and for the presence of apparently parasite-specific genes, 6 genes were removed. We suggest that the remaining 256 genes are close to the minimal gene set that is necessary and sufficient to sustain the existence of a modern-type cell. Most of the proteins encoded by the genes from the minimal set have eukaryotic or archaeal homologs but seven key proteins of DNA replication do not. We speculate that the last common ancestor of the three primary kingdoms had an RNA genome. Possibilities are explored to further reduce the minimal set to model a primitive cell that might have existed at a very early stage of life evolution.

Administration of interleukin 12 in combination with type II collagen induces severe arthritis in DBA/1 mice.

The induction of arthritis in DBA/1 mice usually requires immunization with the antigen type II collagen emulsified with Mycobacterium tuberculosis in oil. Here we describe that interleukin 12 (IL-12) can replace mycobacteria and cause severe arthritis of DBA/1 mice when administered in combination with type II collagen. Immunization of DBA/1 mice with type II collagen emulsified in oil alone resulted in a weak immune response, and only a few animals (10-30%) developed arthritis. Administration of IL-12 for 5 days simultaneously with each immunization strongly enhanced the anti-type II collagen immune response. Collagen-specific interferon gamma (IFN-gamma) synthesis by ex vivo activated spleen cells was enhanced 3- to 10-fold. IFN-gamma was almost completely produced by CD4+ T cells. Furthermore, the production of collagen-specific IgG2a and IgG2b antibodies was upregulated 10- to 100-fold. As a consequence, the incidence of arthritis in the group of mice immunized with collagen plus IL-12 was very high (80-100%). The developing arthritis was severe, involving approximately 50% of all limbs with strongly increased footpad thickness in most cases. Furthermore, histological examination revealed massive, mainly polymorphonuclear cell infiltration, synovial hyperplasia, cartilage and bone destruction, as well as new bone formation. In many cases, this resulted in the complete loss of joint structure. Neutralization of IFN-gamma in vivo prevented the development of arthritis in collagen-immunized and IL-12-treated mice. In conclusion, our data show that in vivo administered IL-12 can profoundly upregulate a T helper I-type autoimmune response, resulting in severe joint disease in DBA/1 mice.

A serine proteinase inhibitor locus at 18q21.3 contains a tandem duplication of the human squamous cell carcinoma antigen gene.

The squamous cell carcinoma antigen (SCCA) is a member of the ovalbumin family of serine proteinase inhibitors (serpins). A neutral form of the protein is found in normal and some malignant squamous cells, whereas an acidic form is detected exclusively in tumor cells and in the circulation of patients with squamous cell tumors. In this report, we describe the cloning of the SCCA gene from normal genomic DNA. Surprisingly, two genes were found. They were tandemly arrayed and flanked by two other closely related serpins, plasminogen activator inhibitor type 2 (PAI2) and maspin at 18q21.3. The genomic structure of the two genes, SCCA1 and SCCA2, was highly conserved. The predicted amino acid sequences were 92% identical and suggested that the neutral form of the protein was encoded by SCCA1 and the acidic form was encoded by SCCA2. Further characterization of the region should determine whether the differential expression of the SCCA genes plays a causal role in development of more aggressive squamous cell carcinomas.

Avaliação da capacidade funcional de pacientes vítimas de trauma um ano após alta hospitalar

Objetivos: Avaliar a capacidade funcional de pacientes vítimas de trauma um ano após alta hospitalar e verificar associação da capacidade funcional com fatores relacionados ao trauma e à internação hospitalar. Metodologia: Estudo de coorte prospectivo, com pacientes vítimas de trauma grave (Injury Severity Score - ISS >=16), internados entre Junho e Setembro de 2010 em unidade de terapia intensiva (UTI) cirúrgica especializada em paciente politraumatizado de um hospital público de grande porte na cidade de São Paulo, Brasil. Variáveis de interesse como idade, sexo, escore de Glasgow, Acute Physiology and Chronic Health Disease Classification System II (APACHE II), mecanismos de trauma, número de lesões, região corpórea afetada, número de cirurgias, duração da ventilação mecânica (VM) e tempo de internação hospitalar foram coletadas dos prontuários médicos. A capacidade funcional foi avaliada um ano após alta hospitalar utilizando as escalas Glasgow Outcome Scale (GOS) e Escala de Atividades Instrumentais de Vida Diária de Lawton (AIVDL). Os pacientes também foram questionados se haviam retornado ao trabalho ou estudo. Resultados: O seguimento um ano após trauma foi completo em 49 indivíduos, a maioria composta por jovens (36±11 anos), do sexo masculino (81,6%) e vítimas de acidentes de trânsito (71,5%). Cada indivíduo sofreu aproximadamente 4 lesões corporais, acarretando uma média no ISS de 31 ± 14,4. O traumatismo cranioencefálico foi o tipo de lesão mais comum (65,3%). De acordo com a GOS, a maioria dos pacientes apresentou disfunção moderada (43%) ou disfunção leve ou ausente (37%) um ano após o trauma. A escala AIVDL apresentou pontuação média de 12±4 com aproximadamente 60- 70% dos indivíduos capazes de realizar de forma independente a maioria das atividades avaliadas. Escore de Glasgow, APACHE II, duração da VM e tempo de internação hospitalar foram associadas com a capacidade funcional um ano após lesão. A regressão linear múltipla considerando todas as variáveis significativas revelou associação entre a pontuação da escala AIVDL e o tempo de internação hospitalar. Apenas 32,6% dos indivíduos retornaram ao trabalho ou estudo. Conclusões: A maioria dos pacientes vítimas de trauma grave foi capaz de realizar as atividades avaliadas com independência; apenas um terço deles retornou ao trabalho e/ou estudo um ano após alta hospitalar. O tempo de internação hospitalar foi revelado como preditor significativo para a recuperação da capacidade funcional um ano após lesão grave

Sentiment classification for early detection of health alerts in the chemical textile domain

In the chemical textile domain experts have to analyse chemical components and substances that might be harmful for their usage in clothing and textiles. Part of this analysis is performed searching opinions and reports people have expressed concerning these products in the Social Web. However, this type of information on the Internet is not as frequent for this domain as for others, so its detection and classification is difficult and time-consuming. Consequently, problems associated to the use of chemical substances in textiles may not be detected early enough, and could lead to health problems, such as allergies or burns. In this paper, we propose a framework able to detect, retrieve, and classify subjective sentences related to the chemical textile domain, that could be integrated into a wider health surveillance system. We also describe the creation of several datasets with opinions from this domain, the experiments performed using machine learning techniques and different lexical resources such as WordNet, and the evaluation focusing on the sentiment classification, and complaint detection (i.e., negativity). Despite the challenges involved in this domain, our approach obtains promising results with an F-score of 65% for polarity classification and 82% for complaint detection.

A Be-type star with a black-hole companion

Stellar-mass black holes have all been discovered through X-ray emission, which arises from the accretion of gas from their binary companions (this gas is either stripped from low-mass stars or supplied as winds from massive ones). Binary evolution models also predict the existence of black holes accreting from the equatorial envelope of rapidly spinning Be-type stars1, 2, 3 (stars of the Be type are hot blue irregular variables showing characteristic spectral emission lines of hydrogen). Of the approximately 80 Be X-ray binaries known in the Galaxy, however, only pulsating neutron stars have been found as companions2, 3, 4. A black hole was formally allowed as a solution for the companion to the Be star MWC 656 (ref. 5; also known as HD 215227), although that conclusion was based on a single radial velocity curve of the Be star, a mistaken spectral classification6 and rough estimates of the inclination angle. Here we report observations of an accretion disk line mirroring the orbit of MWC 656. This, together with an improved radial velocity curve of the Be star through fitting sharp Fe ii profiles from the equatorial disk, and a refined Be classification (to that of a B1.5–B2 III star), indicates that a black hole of 3.8 to 6.9 solar masses orbits MWC 656, the candidate counterpart of the γ-ray source AGL J2241+4454 (refs 5, 6). The black hole is X-ray quiescent and fed by a radiatively inefficient accretion flow giving a luminosity less than 1.6 × 10−7 times the Eddington luminosity. This implies that Be binaries with black-hole companions are difficult to detect in conventional X-ray surveys.

Evaluation of an integrated system for classification, assessment and comparison of services for long-term care in Europe: the eDESDE-LTC study

Background: The harmonization of European health systems brings with it a need for tools to allow the standardized collection of information about medical care. A common coding system and standards for the description of services are needed to allow local data to be incorporated into evidence-informed policy, and to permit equity and mobility to be assessed. The aim of this project has been to design such a classification and a related tool for the coding of services for Long Term Care (DESDE-LTC), based on the European Service Mapping Schedule (ESMS). Methods: The development of DESDE-LTC followed an iterative process using nominal groups in 6 European countries. 54 researchers and stakeholders in health and social services contributed to this process. In order to classify services, we use the minimal organization unit or “Basic Stable Input of Care” (BSIC), coded by its principal function or “Main Type of Care” (MTC). The evaluation of the tool included an analysis of feasibility, consistency, ontology, inter-rater reliability, Boolean Factor Analysis, and a preliminary impact analysis (screening, scoping and appraisal). Results: DESDE-LTC includes an alpha-numerical coding system, a glossary and an assessment instrument for mapping and counting LTC. It shows high feasibility, consistency, inter-rater reliability and face, content and construct validity. DESDE-LTC is ontologically consistent. It is regarded by experts as useful and relevant for evidence-informed decision making. Conclusion: DESDE-LTC contributes to establishing a common terminology, taxonomy and coding of LTC services in a European context, and a standard procedure for data collection and international comparison.

Morphological classification of microtidal sand and gravel beaches

A new classification of microtidal sand and gravel beaches with very different morphologies is presented below. In 557 studied transects, 14 variables were used. Among the variables to be emphasized is the depth of the Posidonia oceanica. The classification was performed for 9 types of beaches: Type 1: Sand and gravel beaches, Type 2: Sand and gravel separated beaches, Type 3: Gravel and sand beaches, Type 4: Gravel and sand separated beaches, Type 5: Pure gravel beaches, Type 6: Open sand beaches, Type 7: Supported sand beaches, Type 8: Bisupported sand beaches and Type 9: Enclosed beaches. For the classification, several tools were used: discriminant analysis, neural networks and Support Vector Machines (SVM), the results were then compared. As there is no theory for deciding which is the most convenient neural network architecture to deal with a particular data set, an experimental study was performed with different numbers of neuron in the hidden layer. Finally, an architecture with 30 neurons was chosen. Different kernels were employed for SVM (Linear, Polynomial, Radial basis function and Sigmoid). The results obtained for the discriminant analysis were not as good as those obtained for the other two methods (ANN and SVM) which showed similar success.

Fraturas do rádio distal : revisão bibliográfica

Trabalho Final do Curso de Mestrado Integrado em Medicina, Faculdade de Medicina, Universidade de Lisboa, 2014

Une nouvelle méthode pour estimer la torsion géométrique en scoliose idiopathique de l’adolescent

La scoliose idiopathique de l’adolescent (SIA) est une déformation tridimensionnelle (3D) de la colonne vertébrale. Pour la plupart des patients atteints de SIA, aucun traitement chirurgical n’est nécessaire. Lorsque la déformation devient sévère, un traitement chirurgical visant à réduire la déformation est recommandé. Pour déterminer la sévérité de la SIA, l’imagerie la plus utilisée est une radiographie postéroantérieure (PA) ou antéro-postérieure (AP) du rachis. Plusieurs indices sont disponibles à partir de cette modalité d’imagerie afin de quantifier la déformation de la SIA, dont l’angle de Cobb. La conduite thérapeutique est généralement basée sur cet indice. Cependant, les indices disponibles à cette modalité d’imagerie sont de nature bidimensionnelle (2D). Celles-ci ne décrivent donc pas entièrement la déformation dans la SIA dû à sa nature tridimensionnelle (3D). Conséquemment, les classifications basées sur les indices 2D souffrent des mêmes limitations. Dans le but décrire la SIA en 3D, la torsion géométrique a été étudiée et proposée par Poncet et al. Celle-ci mesure la tendance d’une courbe tridimensionnelle à changer de direction. Cependant, la méthode proposée est susceptible aux erreurs de reconstructions 3D et elle est calculée localement au niveau vertébral. L’objectif de cette étude est d’évaluer une nouvelle méthode d’estimation de la torsion géométrique par l’approximation de longueurs d’arcs locaux et par paramétrisation de courbes dans la SIA. Une première étude visera à étudier la sensibilité de la nouvelle méthode présentée face aux erreurs de reconstructions 3D du rachis. Par la suite, deux études cliniques vont présenter la iv torsion géométrique comme indice global et viseront à démontrer l’existence de sous-groupes non-identifiés dans les classifications actuelles et que ceux-ci ont une pertinence clinique. La première étude a évalué la robustesse de la nouvelle méthode d’estimation de la torsion géométrique chez un groupe de patient atteint de la SIA. Elle a démontré que la nouvelle technique est robuste face aux erreurs de reconstructions 3D du rachis. La deuxième étude a évalué la torsion géométrique utilisant cette nouvelle méthode dans une cohorte de patient avec des déformations de type Lenke 1. Elle a démontré qu’il existe deux sous-groupes, une avec des valeurs de torsion élevées et l’autre avec des valeurs basses. Ces deux sous-groupes possèdent des différences statistiquement significatives, notamment au niveau du rachis lombaire avec le groupe de torsion élevée ayant des valeurs d’orientation des plans de déformation maximales (PMC) en thoraco-lombaire (TLL) plus élevées. La dernière étude a évalué les résultats chirurgicaux de patients ayant une déformation Lenke 1 sous-classifiées selon les valeurs de torsion préalablement. Cette étude a pu démontrer des différences au niveau du PMC au niveau thoraco-lombaire avec des valeurs plus élevées en postopératoire chez les patients ayant une haute torsion. Ces études présentent une nouvelle méthode d’estimation de la torsion géométrique et présentent cet indice quantitativement. Elles ont démontré l’existence de sous-groupes 3D basés sur cet indice ayant une pertinence clinique dans la SIA, qui n’étaient pas identifiés auparavant. Ce projet contribue dans la tendance actuelle vers le développement d’indices 3D et de classifications 3D pour la scoliose idiopathique de l’adolescent.

Type A aortic dissection model to improve endovascular research and technologies.

OBJECTIVE Type A aortic dissection is a life-threatening disease requiring immediate surgical treatment. With emerging catheter-based technologies, endovascular stent-graft implantation to treat aneurysms and dissections has become a standardized procedure. However, endovascular treatment of the ascending aorta remains challenging. Thus we designed an ascending aortic dissection model to allow simulation of endovascular treatment. METHODS Five formalin-fixed human aortas were prepared. The ascending aorta was opened semicircularly in the middle portion and the medial layer was separated from the intima. The intimal tube was readapted using running monofilament sutures. The preparations were assessed by 128-slice computed tomography. A bare-metal stent was implanted for thoracic endovascular aortic repair in 4 of the aortic dissection models. RESULTS Separation of the intimal and medial layer of the aorta was considered to be sufficient because computed tomography showed a clear image of the dissection membrane in each aorta. The dissection was located 3.9 ± 1.4 cm proximally from the aortic annulus, with a length of 4.6 ± 0.9 cm. Before stent implantation, the mean distance from the intimal flap to the aortic wall was measured as 0.63 ± 0.163 cm in the ascending aorta. After stent implantation, this distance decreased to 0.26 ± 0.12 cm. CONCLUSION This model of aortic dissection of the ascending human aorta was reproducible with a comparable pathological and morphological appearance. The technique and model can be used to evaluate new stent-graft technologies to treat type A dissection and facilitate training for surgeons.