XML in Motion from Genome to Drug

Information technology (IT) has emerged as a central to the solution of contemporary genomics and drug discovery problems. Researchers involved in genomics, proteomics, transcriptional profiling, high throughput structure determination, and in other sub-disciplines of bioinformatics have direct impact on this IT revolution. As the full genome sequences of many species, data from structural genomics, micro-arrays, and proteomics became available, integration of these data to a common platform require sophisticated bioinformatics tools. Organizing these data into knowledgeable databases and developing appropriate software tools for analyzing the same are going to be major challenges. XML (eXtensible Markup Language) forms the backbone of biological data representation and exchange over the internet, enabling researchers to aggregate data from various heterogeneous data resources. The present article covers a comprehensive idea of the integration of XML on particular type of biological databases mainly dealing with sequence-structure-function relationship and its application towards drug discovery. This e-medical science approach should be applied to other scientific domains and the latest trend in semantic web applications is also highlighted

Web interaction environments : characterising Web accessibility at the large

Tese de doutoramento, Informática (Engenharia Informática), Universidade de Lisboa, Faculdade de Ciências, 2012Accessibility quality on the Web is essential for providing a good Web experience to people with disabilities. The existence of virtual ramps aid these users grasping and interacting withWeb content, just like the experience of those who are unimpaired. However, more often than not, Web pages impose accessibility barriers, usually centred on the unavailability of tailored content to specific perceptual abilities (e.g., textual description of images, enabling grasping information with assistive technologies), as well as on proper HTML structural elements that adequate the semantics of a Web page. When evaluating the accessibility quality of Web pages, the resulting analysis is often focused on a small sample set (e.g., a single Web page or a selection of pages from a Web site). While this kind of analysis gets the gist of accessibility quality, it misses the big picture on the overall accessibility quality of the Web. This thesis addresses the challenge of observing accessibility phenomena on the Web, through the experimental evaluation of large collections of Web pages. This resulted on new findings about the accessibility quality of the Web, such as its correlation with HTML element count, and the erroneous perception of accessibility quality by developers. Small-scale experiments have been verified also at large scale, such as the correlation between the usage of HTML templates and accessibility quality. Based on the challenges raised by the experimental evaluation, this thesis proposes a novel approach for large scale Web accessibility evaluation based on Linked Data, as well as the establishment of metrics to assess the truthfulness and coverage of automated evaluation methods.A qualidade da acessibilidade é um factor crucial para as pessoas com deficiências terem uma boa experiência de interacção com a Web.A qualidade da acessibilidade é um factor crucial para as pessoas com deficiências terem uma boa experiência de interacção com a Web. A existência de rampas virtuais ajuda estas pessoas a compreender e interagir com conteúdos Web, a par do que o utilizador comum já experiencia. Porém, a maioria das páginas Web ainda contêm barreiras à acessibilidade. Estas barreiras centram-se normalmente na indisponibilidade de conteúdos perceptíveis por diferentes tipos de capacidades (e.g., descrições textuais de imagens), bem como no uso incorrecto de elementos HTML de acordo com a semântica de uma página Web. Nos dias de hoje, a avaliação da qualidade de acessibilidade de páginas Web é ainda efectuada em pequena escala (e.g., uma página Web ou, no melhor caso, um conjunto de páginas representativas de um sítio Web). Apesar deste tipo de avaliações resultarem na compreensão de alguns fenómenos do estado da acessibilidade na Web, ainda não se sabe qual o seu impacto em larga escala. Esta tese discute os principais desafios na observação da acessibilidade da Web, tendo por base um conjunto de avaliações experimentais de colecções de grande dimensão de páginas Web. Destes estudos destacam-se as seguintes contribuições e resultados:a diferença drástica na interpretação dos avisos resultantes de avaliações de acessibilidade Web: um dos resultados principais da avaliação experimental em larga escala destaca a diferença na interpretação dos avisos (warnings) da aplicação de técnicas da norma WCAG, onde a interpretação optimista (i.e., a visão da maioria dos criadores de páginas Web) se distancia amplamente da interpretação conservadora (onde os avisos são interpretados como erros); a correlação entre a qualidade da acessibilidade de uma página Web e a sua complexidade: este mesmo estudo de larga escala revelou uma correlação entre a complexidade de uma página Web (no que diz respeito ao número de elementos HTML que contém) e a qualidade da acessibilidade. Quanto menor a complexidade de uma página Web, mais certa se torna a alta qualidade da acessibilidade dessa página; o benefício do uso de templates e sistemas de gestão de conteúdos na melhoria da acessibilidade de páginas Web: em ambos os estudos experimentais de acessibilidade foi detectada uma correlação entre a qualidade de acessibilidade das páginas Web e o uso de templates e sistemas de gestão de conteúdo. Esta propriedade foi verificada quer em pequena escala (sobre uma colecção de páginas Web da Wikipedia), quer em larga escala; o incumprimento das regras mais elementares e mais conhecidas da acessibilidade: estes estudos experimentais permitiram também verificar que, apesar de toda a envagelização e educação sobre as questões de acessibilidade na Web, a maioria das regras de acessibilidade são incessantemente quebradas pela maioria das páginas Web.Esta problemática verifica-se, em particular, nas regras de cumprimento de acessibilidade mais conhecidas, tal como por exemplo a disponibilidade de textos alternativos a conteúdos multimédia. Com base nestas experiências e resultados, esta tese apresenta um novo modelo de estudo da acessibilidade na Web, tendo por base o ciclo de estudos da Web em larga escala. Deste modelo resultaram as seguintes contribuições: um modelo para a avaliação distribuída de acessibilidade Web, baseado em propriedades tecnológicas e topológicas: foi concebido um modelo de avaliação de acessibilidade Web que permite a concepção de sistemas de avaliação com base em propriedades tecnológicas e topológicas. Este modelo possibilita, entre outras características, o estudo da cobertura de plataformas e avaliadores de acessibilidade, bem como da sua aplicação em larga escala; uma extensão às linguagens e modelos EARL e Linked Data, bem como um conjunto de definições para extrair informação destes: este modelo de avaliação de acessibilidade Web foi sustentado também pela sua concretização em linguagens e modelos já existentes para o estudo de acessibilidade (EARL) e da Web em larga escala (Linked Data), permitindo assim a sua validação; definição dos limites da avaliação de acessibilidade Web: por fim, este modelo de avaliação de acessibilidade permitiu também delinear uma metodologia de meta-avaliação da acessibilidade, na qual se poderão enquadrar as propriedades dos avaliadores de acessibilidade existentes. Todas estas contribuições resultaram também num conjunto de publicações científicas, das quais se destacam: Rui Lopes and Luís Carriço, A Web Science Perspective of Web Accessibility, in submission for the ACM Transactions on Accessible Computing (TACCESS), ACM, 2011; Rui Lopes and Luís Carriço, Macroscopic Characterisations of Web Accessibility, New Review of Hypermedia and Multimedia – Special Issue on Web Accessibility. Taylor & Francis, 2010; Rui Lopes, Karel Van Isacker and Luís Carriço, Redefining Assumptions: Accessibility and Its Stakeholders, The 12th International Conference on Computers Helping People with Special Needs (ICCHP), Vienna, Austria, 14-16 July 2010; Rui Lopes, Daniel Gomes and Luís Carriço, Web Not For All: A Large Scale Study of Web Accessibility, W4A: 7th ACM International Cross-Disciplinary Conference on Web Accessibility, Raleigh, North Carolina, USA, 26-27 April 2010; Rui Lopes, Konstantinos Votis, Luís Carriço, Dimitrios Tzovaras, and Spiridon Likothanassis, The Semantics of Personalised Web Accessibility Assessment, 25th Annual ACM Symposium on Applied Computing (SAC), Sierre, Switzerland, 22-26 March, 2010 Konstantinos Votis, Rui Lopes, Dimitrios Tzovaras, Luís Carriço and Spiridon Likothanassis, A Semantic Accessibility Assessment Environment for Design and Development for the Web, HCI International 2009 (HCII 2009), San Diego, California, USA, 19-24 July 2009 Rui Lopes and Luís Carriço, On the Gap Between Automated and In-Vivo Evaluations of Web Accessibility, HCI International 2009 (HCII 2009), San Diego, California, USA, 19-24 July 2009; Rui Lopes, Konstantinos Votis, Luís Carriço, Spiridon Likothanassis and Dimitrios Tzovaras, Towards the Universal Semantic Assessment of Accessibility, 24th Annual ACM Symposium on Applied Computing (SAC),Waikiki Beach, Honolulu, Hawaii, USA, 8-12 March 2009; Rui Lopes and Luís Carriço, Querying Web Accessibility Knowledge from Web Graphs, Handbook of Research on Social Dimensions of Semantic Technologies, IGI Global, 2009; Rui Lopes, Konstantinos Votis, Luís Carriço, Spiridon Likothanassis and Dimitrios Tzovaras, A Service Oriented Ontological Framework for the Semantic Validation of Web Accessibility, Handbook of Research on Social Dimensions of Semantic Technologies, IGI Global, 2009; Rui Lopes and Luís Carriço, On the Credibility of Wikipedia: an Accessibility Perspective, Second Workshop on Information Credibility on the Web (WICOW 2008), Napa Valley, California, USA, 2008; Rui Lopes, Luís Carriço, A Model for Universal Usability on the Web, WSW 2008: Web Science Workshop, Beijing, China, 22 April 2008; Rui Lopes, Luís Carriço, The Impact of Accessibility Assessment in Macro Scale Universal Usability Studies of the Web, W4A: 5th ACM International Cross-Disciplinary Conference on Web Accessibility, Beijing, China, 21-22 April 2008. Best paper award; Rui Lopes, Luís Carriço, Modelling Web Accessibility for Rich Document Production, Journal on Access Services 6 (1-2), Routledge, Taylor & Francis Group, 2009; Rui Lopes, Luís Carriço, Leveraging Rich Accessible Documents on the Web, W4A: 4th ACM International Cross-Disciplinary Conference on Web Accessibility, Banff, Canada, 7-8 May 2007.Fundação para a Ciência e a Tecnologia (FCT, SFRH/BD/29150/2006

A Systematic Analysis of Accessibility Education Within Computing Disciplines

Accessible technologies improve the usability for all users, including 1 billion people in the world who have a disability. Although there is a demand for accessible technologies, there is currently no requirement for universities to integrate this content within the computing curriculum. A systematic comparison of teaching efficacy is important to effectively prepare future computing professionals with the skills to create accessible technologies. This dissertation contains a mixed-methods cross-sectional and longitudinal analysis of undergraduate Software Engineering and Information Technology students’ learning of accessibility. Four teaching conditions were assessed at Rochester Institute of Technology: content lectures, projects, exposure to stakeholders with a disability, and collaboration with a team member who had a disability. Evidence of student learning was obtained through questionnaires, project reports, and interview data. Student learning was quantified by a knowledge of programming techniques, awareness of accessible technologies, and attitudes towards individuals with a disability. The cross-sectional analysis spanned three years (spring 2016-2019), fourteen courses, and seven distinct professors. We found that students in all conditions gained an increased knowledge of implementation methods. Students who were exposed to a stakeholder with a disability obtained significantly higher scores in their prosocial sympathetic attitudes, awareness of accessible technologies, and knowledge of programming techniques following the course. Students in the other conditions obtained significant changes in only a subset of these measures. While students in all conditions obtained significantly higher knowledge scores in the short term, only students who had a project or a team member with a disability sustained significantly higher knowledge scores two years after exposure. In interviews, senior-level students revealed that there were multiple factors outside the classroom that dissuaded them from furthering their learning of accessibility. Students mentioned a lack of person-centered topics in major software development processes (e.g., agile, waterfall) and workplace tasks. Without direct reinforcement, students focused on functional software requirements and expressed that accessibility would only be necessary in select front-end development career paths or domains. While current work in computer accessibility education evaluates learning during, or immediately following, one course, this dissertation provides a systematic comparison of student learning throughout multiple courses and instructors. The findings within this dissertation may be used to inform future curriculum plans and educational initiatives

NMR and Metabolomics—A Roadmap for the Future

Metabolomics investigates global metabolic alterations associated with chemical, biological, physiological, or pathological processes. These metabolic changes are measured with various analytical platforms including liquid chromatography-mass spectrometry (LC-MS), gas chromatographymass spectrometry (GC-MS) and nuclear magnetic resonance spectroscopy (NMR). While LC-MS methods are becoming increasingly popular in the field of metabolomics (accounting for more than 70% of published metabolomics studies to date), there are considerable benefits and advantages to NMR-based methods for metabolomic studies. In fact, according to PubMed, more than 926 papers on NMR-based metabolomics were published in 2021—the most ever published in a given year. This suggests that NMR-based metabolomics continues to grow and has plenty to offer to the scientific community. This perspective outlines the growing applications of NMR in metabolomics, highlights several recent advances in NMR technologies for metabolomics, and provides a roadmap for future advancements

Strategies for annotation and curation of translational databases: the eTUMOUR project

The eTUMOUR (eT) multi-centre project gathered in vivo and ex vivo magnetic resonance (MR) data, as well as transcriptomic and clinical information from brain tumour patients, with the purpose of improving the diagnostic and prognostic evaluation of future patients. In order to carry this out, among other work, a database—the eTDB—was developed. In addition to complex permission rules and software and management quality control (QC), it was necessary to develop anonymization, processing and data visualization tools for the data uploaded. It was also necessary to develop sophisticated curation strategies that involved on one hand, dedicated fields for QC-generated meta-data and specialized queries and global permissions for senior curators and on the other, to establish a set of metrics to quantify its contents. The indispensable dataset (ID), completeness and pairedness indices were set. The database contains 1317 cases created as a result of the eT project and 304 from a previous project, INTERPRET. The number of cases fulfilling the ID was 656. Completeness and pairedness were heterogeneous, depending on the data type involved

Revealing the Vicious Circle of Disengaged User Acceptance: A SaaS Provider's Perspective

User acceptance tests (UAT) are an integral part of many different software engineering methodologies. In this paper, we examine the influence of UATs on the relationship between users and Software-as-a-Service (SaaS) applications, which are continuously delivered rather than rolled out during a one-off signoff process. Based on an exploratory qualitative field study at a multinational SaaS provider in Denmark, we show that UATs often address the wrong problem in that positive user acceptance may actually indicate a negative user experience. Hence, SaaS providers should be careful not to rest on what we term disengaged user acceptance. Instead, we outline an approach that purposefully queries users for ambivalent emotions that evoke constructive criticism, in order to facilitate a discourse that favors the continuous innovation of a SaaS system. We discuss theoretical and practical implications of our approach for the study of user engagement in testing SaaS applications

Optimizing structural modeling for a specific protein scaffold: knottins or inhibitor cystine knots

<p>Abstract</p> <p>Background</p> <p>Knottins are small, diverse and stable proteins with important drug design potential. They can be classified in 30 families which cover a wide range of sequences (1621 sequenced), three-dimensional structures (155 solved) and functions (> 10). Inter knottin similarity lies mainly between 15% and 40% sequence identity and 1.5 to 4.5 Å backbone deviations although they all share a tightly knotted disulfide core. This important variability is likely to arise from the highly diverse loops which connect the successive knotted cysteines. The prediction of structural models for all knottin sequences would open new directions for the analysis of interaction sites and to provide a better understanding of the structural and functional organization of proteins sharing this scaffold.</p> <p>Results</p> <p>We have designed an automated modeling procedure for predicting the three-dimensionnal structure of knottins. The different steps of the homology modeling pipeline were carefully optimized relatively to a test set of knottins with known structures: template selection and alignment, extraction of structural constraints and model building, model evaluation and refinement. After optimization, the accuracy of predicted models was shown to lie between 1.50 and 1.96 Å from native structures at 50% and 10% maximum sequence identity levels, respectively. These average model deviations represent an improvement varying between 0.74 and 1.17 Å over a basic homology modeling derived from a unique template. A database of 1621 structural models for all known knottin sequences was generated and is freely accessible from our web server at <url>http://knottin.cbs.cnrs.fr</url>. Models can also be interactively constructed from any knottin sequence using the structure prediction module Knoter1D3D available from our protein analysis toolkit PAT at <url>http://pat.cbs.cnrs.fr</url>.</p> <p>Conclusions</p> <p>This work explores different directions for a systematic homology modeling of a diverse family of protein sequences. In particular, we have shown that the accuracy of the models constructed at a low level of sequence identity can be improved by 1) a careful optimization of the modeling procedure, 2) the combination of multiple structural templates and 3) the use of conserved structural features as modeling restraints.</p

Prediction of Protein Domain with mRMR Feature Selection and Analysis

The domains are the structural and functional units of proteins. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to develop effective methods for predicting the protein domains according to the sequences information alone, so as to facilitate the structure prediction of proteins and speed up their functional annotation. However, although many efforts have been made in this regard, prediction of protein domains from the sequence information still remains a challenging and elusive problem. Here, a new method was developed by combing the techniques of RF (random forest), mRMR (maximum relevance minimum redundancy), and IFS (incremental feature selection), as well as by incorporating the features of physicochemical and biochemical properties, sequence conservation, residual disorder, secondary structure, and solvent accessibility. The overall success rate achieved by the new method on an independent dataset was around 73%, which was about 28–40% higher than those by the existing method on the same benchmark dataset. Furthermore, it was revealed by an in-depth analysis that the features of evolution, codon diversity, electrostatic charge, and disorder played more important roles than the others in predicting protein domains, quite consistent with experimental observations. It is anticipated that the new method may become a high-throughput tool in annotating protein domains, or may, at the very least, play a complementary role to the existing domain prediction methods, and that the findings about the key features with high impacts to the domain prediction might provide useful insights or clues for further experimental investigations in this area. Finally, it has not escaped our notice that the current approach can also be utilized to study protein signal peptides, B-cell epitopes, HIV protease cleavage sites, among many other important topics in protein science and biomedicine