Schistosoma mansoni encodes SMT3B and SMT3C molecules responsible for post-translational modification of cellular proteins

The sumoylation pathway is a post-translational modification of nuclear proteins widespread among several organisms. SMT3C is the main protein involved in this process and it is covalently conjugated to a diverse assortment of nuclear protein targets. To date, 3 SUMO paralogues (SMT3C, A/B) have been characterized in mammals and plants. In this work we characterized two SUMO related genes, named SMT3B and SMT3C throughout Schistosoma mansoni life cycle. The SmSMTB/C encodes for proteins sharing significant amino acid homology with SMT3. Phylogenetical analyses revealed that both SmSMT3B/C are distinct proteins. Additionally, SmSMT3B and C are expressed in cercariae, adult worms, eggs and schistosomula however SinSMT3C gene showed an expression level 7 to 9 fold higher than SmSMT3B in eggs, schistosomula and adult worms. The comparison between the SmSMT3C genomic and cDNA sequences established that the encoding sequence is interrupted by 3 introns of 70, 37 and 36 bp. Western Blot has shown SMT3 conjugates are present in nuclear and total protein fractions of adults and cercariae. Therefore our results suggest a functional sumoylation pathway, and the presence of two paralogues also suggests the specificity of substrates for SMT3 in S. mansoni. (c) 2008 Elsevier Ireland Ltd. All rights reserved.

SAGE analysis demonstrates increased expression of TOSO contributing to Fas-mediated resistance in CLL

To identify novel genes involved in the molecular pathogenesis of chronic lymphocytic leukemia (CLL) we performed a serial analysis of gene expression (SAGE) in CLL cells, and compared this with healthy B cells (nCD19(+)). We found a high level of similarity among CLL subtypes, but a comparison of CLL versus nCD19(+) libraries revealed 55 genes that were over-represented and 49 genes that were down-regulated in CLL. A gene ontology analysis revealed that TOSO, which plays a functional role upstream of Fas extrinsic apoptosis pathway, was over-expressed in CLL cells. This finding was confirmed by real-time reverse transcription-polymerase chain reaction in 78 CLL and 12 nCD19(+) cases (P <.001). We validated expression using flow cytometry and tissue microarray and demonstrated a 5.6-fold increase of TOSO protein in circulating CLL cells (P =.013) and lymph nodes (P =.006). Our SAGE results have demonstrated that TOSO is a novel overexpressed antiapoptotic gene in CLL.

Should optional properties be used in conceptual modelling? A theory and three empirical tests

An important feature of some conceptual modelling grammars is the features they provide to allow database designers to show real-world things may or may not possess a particular attribute or relationship. In the entity-relationship model, for example, the fact that a thing may not possess an attribute can be represented by using a special symbol to indicate that the attribute is optional. Similarly, the fact that a thing may or may not be involved in a relationship can be represented by showing the minimum cardinality of the relationship as zero. Whether these practices should be followed, however, is a contentious issue. An alternative approach is to eliminate optional attributes and relationships from conceptual schema diagrams by using subtypes that have only mandatory attributes and relationships. In this paper, we first present a theory that led us to predict that optional attributes and relationships should be used in conceptual schema diagrams only when users of the diagrams require a surface-level understanding of the domain being represented by the diagrams. When users require a deep-level understanding, however, optional attributes and relationships should not be used because they undermine users' abilities to grasp important domain semantics. We describe three experiments which we then undertook to test our predictions. The results of the experiments support our predictions.

Extracting ontological concepts for tendering conceptual structures

It has been argued that beyond software engineering and process engineering, ontological engineering is the third capability needed if successful e-commerce is to be realized. In our experience of building an ontological-based tendering system, we face the problem of building an ontology. In this paper, we demonstrate how to build ontologies in the tendering domain. The ontology life cycle is identified. Extracting concepts from existing resources like on-line catalogs is described. We have reused electronic data interchange (EDI) to build conceptual structures in the tendering domain. An algorithm to extract abstract ontological concepts from these structures is proposed.

Developing a meta model for the Bunge-Wand-Weber ontological constructs

At the core of the analysis task in the development process is information systems requirements modelling, Modelling of requirements has been occurring for many years and the techniques used have progressed from flowcharting through data flow diagrams and entity-relationship diagrams to object-oriented schemas today. Unfortunately, researchers have been able to give little theoretical guidance only to practitioners on which techniques to use and when. In an attempt to address this situation, Wand and Weber have developed a series of models based on the ontological theory of Mario Bunge-the Bunge-Wand-Weber (BWW) models. Two particular criticisms of the models have persisted however-the understandability of the constructs in the BWW models and the difficulty in applying the models to a modelling technique. This paper addresses these issues by presenting a meta model of the BWW constructs using a meta language that is familiar to many IS professionals, more specific than plain English text, but easier to understand than the set-theoretic language of the original BWW models. Such a meta model also facilitates the application of the BWW theory to other modelling techniques that have similar meta models defined. Moreover, this approach supports the identification of patterns of constructs that might be common across meta models for modelling techniques. Such findings are useful in extending and refining the BWW theory. (C) 2002 Elsevier Science Ltd. All rights reserved.

A model of factors affecting an information system's change in state

Management are keen to maximize the life span of an information system because of the high cost, organizational disruption, and risk of failure associated with the re-development or replacement of an information system. This research investigates the effects that various factors have on an information system's life span by understanding how the factors affect an information system's stability. The research builds on a previously developed two-stage model of information system change whereby an information system is either in a stable state of evolution in which the information system's functionality is evolving, or in a state of revolution, in which the information system is being replaced because it is not providing the functionality expected by its users. A case study surveyed a number of systems within one organization. The aim was to test whether a relationship existed between the base value of the volatility index (a measure of the stability of an information system) and certain system characteristics. Data relating to some 3000 user change requests covering 40 systems over a 10-year period were obtained. The following factors were hypothesized to have significant associations with the base value of the volatility index: language level (generation of language of construction), system size, system age, and the timing of changes applied to a system. Significant associations were found in the hypothesized directions except that the timing of user changes was not associated with any change in the value of the volatility index. Copyright (C) 2002 John Wiley Sons, Ltd.

Research commentary: Information systems and conceptual modeling - A research agenda

Within the information systems field, the task of conceptual modeling involves building a representation of selected phenomena in some domain. High-quality conceptual-modeling work is important because it facilitates early detection and correction of system development errors. It also plays an increasingly important role in activities like business process reengineering and documentation of best-practice data and process models in enterprise resource planning systems. Yet little research has been undertaken on many aspects of conceptual modeling. In this paper, we propose a framework to motivate research that addresses the following fundamental question: How can we model the world to better facilitate our developing, implementing, using, and maintaining more valuable information systems? The framework comprises four elements: conceptual-modeling grammars, conceptual-modeling methods, conceptual-modeling scripts, and conceptual-modeling contexts. We provide examples of the types of research that have already been undertaken on each element and illustrate research opportunities that exist.

Service quality and consumers' experience: Towards an interpretive approach

As marketers and researchers we understand quality from the consumer's perspective, and throughout contemporary service quality literature there is an emphasis on what the consumer is looking for, or at least that is the intention. Through examining the underlying assumptions of dominant service quality theories, an implicit dualistic ontology is highlighted (where subject and object are considered independent) and argued to effectively negate the said necessary consumer orientation. This fundamental assumption is discussed, as are the implications, following a critical review of dominant service quality models. Consequently, we propose an alternative approach to service quality research that aims towards a more genuine understanding of the consumer's perspective on quality experienced within a service context. Essentially, contemporary service quality research is suggested to be limited in its inherent third-person perspective and the interpretive, specifically phenomenographic, approach put forward here is suggested as a means of achieving a first-person perspective on service quality.

Mouse proteome analysis

A general overview of the protein sequence set for the mouse transcriptome produced during the FANTOM2 sequencing project is presented here. We applied different algorithms to characterize protein sequences derived from a nonredundant representative protein set (RPS) and a variant protein set (VPS) of the mouse transcriptome. The functional characterization and assignment of Gene Ontology terms was done by analysis of the proteome using InterPro. The Superfamily database analyses gave a detailed structural classification according to SCOP and provide additional evidence for the functional characterization of the proteome data. The MDS database analysis revealed new domains which are not presented in existing protein domain databases. Thus the transcriptome gives us a unique source of data for the detection of new functional groups. The data obtained for the RPS and VPS sets facilitated the comparison of different patterns of protein expression. A comparison of other existing mouse and human protein sequence sets (e.g., the International Protein Index) demonstrates the common patterns in mammalian proteornes. The analysis of the membrane organization within the transcriptome of multiple eukaryotes provides valuable statistics about the distribution of secretory and transmembrane proteins

Document retrieval for e-mail search and discovery using Formal Concept Analysis

This paper discusses a document discovery tool based on Conceptual Clustering by Formal Concept Analysis. The program allows users to navigate e-mail using a visual lattice metaphor rather than a tree. It implements a virtual. le structure over e-mail where files and entire directories can appear in multiple positions. The content and shape of the lattice formed by the conceptual ontology can assist in e-mail discovery. The system described provides more flexibility in retrieving stored e-mails than what is normally available in e-mail clients. The paper discusses how conceptual ontologies can leverage traditional document retrieval systems and aid knowledge discovery in document collections.

Crônica de uma morte anunciada: do suicídio entre os Sorowaha

A prática de suicídio nos Sorowaha, povo de língua Arawa do médio Purus (AM, Brasil), através da ingestão do sumo da raiz de timbó (konaha), mediatiza singularmente as relações entre os indivíduos e a sociedade, projetando uma totalidade social às expensas de um drama ritual individualizador. A relevância do fenômeno é evidenciada tanto pelas taxas de mortalidade que ali se verificam, cerca de cem vezes as médias ocidentais, como também pela inusitada freqüência com que as tentativas, por motivos os mais variados, ocorrem entre eles. O presente ensaio procura examinar as variáveis sociológicas desse padrão de morte voluntária, para em seguida discutir outras dimensões analíticas.

Configuração e interrogação com sistemas federados

Apesar da existência de produtos comerciais e da investigação na área, a construção de sistemas de informação com diversos componentes distribuídos, heterogéneos e autónomos - conhecidos como sistemas de informação federados - é ainda um desafio. Estes sistemas de informação oferecem uma visão global unificada sobre os vários modelos de dados (parciais). No entanto, a modelação destes sistemas é um desafio, já que modelos de dados como o relacional não incluem informação sobre a distribuição e tratamento de heterogeneidade. É também necessário interagir com estes sistemas de informação, através de interrogações sobre os diversos componentes dos sistemas, sem ser necessário conhecer os detalhes dos mesmos. Este trabalho propõe uma abordagem a estes desafios, através da utilização de modelos para descrição semântica, e.g. linguagem OWL (Ontology Web Language), para construir uma descrição unificada dos seus diversos modelos parciais. O modelo criado para dar suporte a esta descrição é, em parte, baseado em ontologias existentes, que foram alteradas e extendidas para resolver diversos desafios de modelação. Sobre este modelo, é criado um componente de software que permite a execução de interrogações SQL (Structured Query Language) sobre o sistema federado, resolvendo os problemas de distribuição e heterogeneidade existentes.

Rede social académica

O processo de Bolonha apresenta directivas para a construção de um espaço europeu de ensino superior. A adopção destas directivas requer uma abordagem que favoreça, na prática, a mobilidade dos estudantes que têm dificuldades em compreenderem as oportunidades que lhes são oferecidas. Neste contexto, esta dissertação explora a hipótese de utilização de uma rede social para apoiar a mobilidade de estudantes no espaço europeu. No âmbito desta dissertação propõe-se um modelo de conhecimento para representar os membros de uma rede social vocacionada para apoiar cenários de mobilidade, designada por rede social académica. Este modelo foi obtido pela fusão da ontologia Academic Ontology to Support the Bologna Mobility Process com a ontologia Friend of a Friend Ontology. Para efeitos de avaliação experimental, foi criado um demonstrador numa rede social disponível publicamente na Internet que utiliza uma versão simplificada do modelo proposto. Os cenários usados nas experiências representam situações reais às quais foi aplicado um processo rudimentar de descoberta de conhecimento

Caracterização biomecânica do gesto de alcançar em individuos pós Acidente Vascular Encefálico

É objectivo deste trabalho caracterizar biomecanicamente o gesto de alcançar em indivíduos pós Acidente Vascular Encefálico. A amostra é constituída por 4 indivíduos sem patologia do foro neuro-músculo-esquelético e 4 indivíduos com confirmação imagiológica do diagnóstico de AVE único e unilateral no território da artéria cerebral média, há pelo menos 3 meses; ausência de neglet; ausência de alterações visuais, perceptivas ou cognitivas e capacidade de realizar movimento activo no membro superior predominantemente afectado de pelo menos 15º no ombro e cotovelo. A partir de uma posição de sentado pré-definida, cada indivíduo foi instruído a executar a tarefa funcional de alcançar um alvo (copo com sumo), colocado sobre uma mesa, no limite anatómico da distância de alcance funcional da mão. Para a análise cinemática foram usadas 4 câmaras dispostas duas a duas para avaliação do movimento de cada um dos membros superiores. Foram colocados marcadores reflectores nas seguintes estruturas ósseas: esterno; acrómio (bilateralmente); epicôndilo lateral; processo estilóide do cúbito, 3º metacarpo e grande trocânter. Foi também colocado um marcador no objecto-alvo. Recorreu-se ao software APAS para análise das seguintes variáveis cinemáticas: tempo de execução do movimento, velocidade máxima da mão, unidades de movimento, trajectória (através do índex de curvatura) e extensão do cotovelo. Verificou-se que no grupo de indivíduos com AVE comparativamente ao grupo de indivíduos sem patologia, o tempo de execução do movimento foi superior (5,8±2,48 e 0,9±0,22 respectivamente), a velocidade máxima da mão foi inferior (101,7±32,62 e 153,3±56,32 respectivamente), o número de unidades de movimento foi superior (6,3±1,50 e 2,5±0,58 respectivamente), o índex de curvatura foi superior (1,8±0,54 e 1,2±0,1 respectivamente) e a amplitude de extensão do cotovelo foi inferior (15,3±16,48 e 50,2±6,72 respectivamente). Os indivíduos com AVE apresentam alterações nos parâmetros cinemáticos analisados, quando comparados com indivíduos sem patologia.

Ontologies for reusing data cleaning knowledge

The emergence of new business models, namely, the establishment of partnerships between organizations, the chance that companies have of adding existing data on the web, especially in the semantic web, to their information, led to the emphasis on some problems existing in databases, particularly related to data quality. Poor data can result in loss of competitiveness of the organizations holding these data, and may even lead to their disappearance, since many of their decision-making processes are based on these data. For this reason, data cleaning is essential. Current approaches to solve these problems are closely linked to database schemas and specific domains. In order that data cleaning can be used in different repositories, it is necessary for computer systems to understand these data, i.e., an associated semantic is needed. The solution presented in this paper includes the use of ontologies: (i) for the specification of data cleaning operations and, (ii) as a way of solving the semantic heterogeneity problems of data stored in different sources. With data cleaning operations defined at a conceptual level and existing mappings between domain ontologies and an ontology that results from a database, they may be instantiated and proposed to the expert/specialist to be executed over that database, thus enabling their interoperability.