Disseny d'ontologia i anàlisi comparatiu de bases de dades semàntiques

Introducció als conceptes bàsics de la web semàntica, disseny d'una ontologia original i anàlisi comparatiu de dos magatzems de dades semàntics: VirtuosoDB i OWLIM.

Modelos teóricos em ciência da informação - abstração e método científico

Analisa a importância dos modelos enquanto recurso metodológico e instrumento de abstração destinado à aquisição de novos conhecimentos, representação e compreensão da realidade, especialmente no contexto das áreas cujo interesse são os fenômenos relacionados à informação, como a informática e a ciência da informação. Examina, na literatura sobre modelos e modelagem, a natureza, características básicas, funções e principais tipos de modelos. Analisa a adequação dos instrumentos de modelagem ao desenvolvimento de sistemas de informação, considerando todo o quadro perceptivo dos usuários e enfatizando a aplicação de modelos aos sistemas de recuperação de informação, principalmente aqueles que privilegiam aspectos cognitivos. Conclui que mais pesquisas sobre a representação de como as pessoas se posicionam diante da informação são extremamente necessárias para a concepção de sistemas de informação que preencham as necessidades de seus usuários.

Addressing trypsin bias in large scale (phospho)proteome analysis by size exclusion chromatography and secondary digestion of large post-trypsin peptides.

In the vast majority of bottom-up proteomics studies, protein digestion is performed using only mammalian trypsin. Although it is clearly the best enzyme available, the sole use of trypsin rarely leads to complete sequence coverage, even for abundant proteins. It is commonly assumed that this is because many tryptic peptides are either too short or too long to be identified by RPLC-MS/MS. We show through in silico analysis that 20-30% of the total sequence of three proteomes (Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Homo sapiens) is expected to be covered by Large post-Trypsin Peptides (LpTPs) with M(r) above 3000 Da. We then established size exclusion chromatography to fractionate complex yeast tryptic digests into pools of peptides based on size. We found that secondary digestion of LpTPs followed by LC-MS/MS analysis leads to a significant increase in identified proteins and a 32-50% relative increase in average sequence coverage compared to trypsin digestion alone. Application of the developed strategy to analyze the phosphoproteomes of S. pombe and of a human cell line identified a significant fraction of novel phosphosites. Overall our data indicate that specific targeting of LpTPs can complement standard bottom-up workflows to reveal a largely neglected portion of the proteome.

Automatic filtering and substantiation of drug safety signals

Drug safety issues pose serious health threats to the population and constitute a major cause of mortality worldwide. Due to the prominent implications to both public health and the pharmaceutical industry, it is of great importance to unravel the molecular mechanisms by which an adverse drug reaction can be potentially elicited. These mechanisms can be investigated by placing the pharmaco-epidemiologically detected adverse drug reaction in an information-rich context and by exploiting all currently available biomedical knowledge to substantiate it. We present a computational framework for the biological annotation of potential adverse drug reactions. First, the proposed framework investigates previous evidences on the drug-event association in the context of biomedical literature (signal filtering). Then, it seeks to provide a biological explanation (signal substantiation) by exploring mechanistic connections that might explain why a drug produces a specific adverse reaction. The mechanistic connections include the activity of the drug, related compounds and drug metabolites on protein targets, the association of protein targets to clinical events, and the annotation of proteins (both protein targets and proteins associated with clinical events) to biological pathways. Hence, the workflows for signal filtering and substantiation integrate modules for literature and database mining, in silico drug-target profiling, and analyses based on gene-disease networks and biological pathways. Application examples of these workflows carried out on selected cases of drug safety signals are discussed. The methodology and workflows presented offer a novel approach to explore the molecular mechanisms underlying adverse drug reactions

Language Resources Factory: case study on the acquisition of Translation Memories

This paper demonstrates a novel distributed architecture to facilitate the acquisition of Language Resources. We build a factory that automates the stages involved in the acquisition, production, updating and maintenance of these resources. The factory is designed as a platform where functionalities are deployed as web services, which can be combined in complex acquisition chains using workflows. We show a case study, which acquires a Translation Memory for a given pair of languages and a domain using web services for crawling, sentence alignment and conversion to TMX.

Electronic Construction Collaboration System – Final Phase, SPR RB02-008, 2014

This phase of the research project involved two major efforts: (1) Complete the implementation of AEC-Sync (formerly known as Attolist) on the Iowa Falls Arch Bridge project and (2) develop a web-based project management system (WPMS) for projects under $10 million. For the first major effort, AEC-Sync was provided for the Iowa Department of Transportation (DOT) in a software as a service agreement, allowing the Iowa DOT to rapidly implement the solution with modest effort. During the 2010 fiscal year, the research team was able to help with the implementation process for the solution. The research team also collected feedback from the Broadway Viaduct project team members before the start of the project and implementation of the solution. For the 2011 fiscal year, the research team collected the post-project surveys from the Broadway Viaduct project members and compared them to the pre-project survey results. The result of the AEC-Sync implementation in the Broadway Viaduct project was a positive one. The project members were satisfied with the performance of AEC-Sync and how it facilitated document management and transparency. In addition, the research team distributed, collected, and analyzed the pre-project surveys for the Iowa Falls Arch Bridge project. During the 2012 fiscal year, the research team analyzed the post-project surveys for the Iowa Falls Arch Bridge project AEC-Sync implementation and found a positive outcome when compared to the pre-project surveys. The second major effort for this project involved the identification and implementation of a WPMS solution for smaller bridge and highway projects. During the 2011 fiscal year, Microsoft SharePoint was selected to be implemented on these smaller highway projects. In this year, workflows for the shop/working drawings for the smaller highway projects specified in Section 1105 of the Iowa DOT Specifications were developed. These workflows will serve as the guide for the development of the SharePoint pages. In order to implement the Microsoft SharePoint pages, the effort of an integrated team proved to be vital because it brought together the expertise required from researchers, programmers, and webpage developers to develop the SharePoint pages.

Accelerated digestion for high-throughput proteomics analysis of whole bacterial proteomes.

In bottom-up proteomics, rapid and efficient protein digestion is crucial for data reliability. However, sample preparation remains one of the rate-limiting steps in proteomics workflows. In this study, we compared the conventional trypsin digestion procedure with two accelerated digestion protocols based on shorter reaction times and microwave-assisted digestion for the preparation of membrane-enriched protein fractions of the human pathogenic bacterium Staphylococcus aureus. Produced peptides were analyzed by Shotgun IPG-IEF, a methodology relying on separation of peptides by IPG-IEF before the conventional LC-MS/MS steps of shotgun proteomics. Data obtained on two LC-MS/MS platforms showed that accelerated digestion protocols, especially the one relying on microwave irradiation, enhanced the cleavage specificity of trypsin and thus improved the digestion efficiency especially for hydrophobic and membrane proteins. The combination of high-throughput proteomics with accelerated and efficient sample preparation should enhance the practicability of proteomics by reducing the time from sample collection to obtaining the results.

Improving globally distributed software development and support processes - A workflow view

We propose a new approach and related indicators for globally distributed software support and development based on a 3-year process improvement project in a globally distributed engineering company. The company develops, delivers and supports a complex software system with tailored hardware components and unique end-customer installations. By applying the domain knowledge from operations management on lead time reduction and its multiple benefits to process performance, the workflows of globally distributed software development and multitier support processes were measured and monitored throughout the company. The results show that the global end-to-end process visibility and centrally managed reporting at all levels of the organization catalyzed a change process toward significantly better performance. Due to the new performance indicators based on lead times and their variation with fixed control procedures, the case company was able to report faster bug-fixing cycle times, improved response times and generally better customer satisfaction in its global operations. In all, lead times to implement new features and to respond to customer issues and requests were reduced by 50%.

Maintenance process development for remote administration of network servers

Maintenance is a part of system development and it is possible to develop operation models for accomplishing maintenance tasks. These models can be applied to individual maintenance tasks, maintenance projects and version management. Beneficial operation models makes maintenance more effective and they assist in managing various changes. The purpose of this thesis was to develop a maintenance process which can be used to remote administer network servers. This consisted of defining those operation models and technical specifications which enable to set up, manage changes, maintain and monitor resources of information systems that are located in several different sites. At first in this thesis the needs of the process were determined and requirements were defined based on those needs. The meaning of processes in maintenance of information systems, maintenance workflows and challenges were studied. Then current practical problems and disadvantages of maintenance work were analyzed in order to focus the development to proper issues. Because available operation models did not cover all the recent needs, new maintenance process which fulfilled the requirements was developed.

La llengua del Collsacabra a partir del diari de Joan Guàrdia : Sincronia i diacronia de la llengua dels pagesos al segle XVII

Aquest treball explora la llengua del diari del pagès Joan de la Guàrdia, de l'Esquirol, escrit al segle XVII durant la guerra dels Segadors. El treball està fet a partir d'una anàlisi dels principals trets morfològics, sintàctics i lexicosemàntics del diari, així com de l'ortografia i de les característiques d'escriptura del document original. Al treball també s'estableix una comparativa d'aquest text amb d'altres del mateix moment, d'abans i de després de la zona, així com amb l'actual parla del Collsacabra.

Interacción, uso lingüístico y construcción del saber gramatical en la educación primaria

Este artículo pone de relieve el papel de la interacción lingüística, entre iguales y con el apoyo del adulto, en la construcción del conocimiento gramatical. Presenta una investigación empírica que explora como 43 parejas de 3º y 6º de educación primaria de Cataluña reconocen tres valores del tiempo verbal del presente: hab itual, atemporal y retrospectivo. En concreto, la investigación explora los obstáculos con que tropiezan los alumnos para reconocer estos valores y las estrategias que usan para superarlos. El estudio demuestra que para ayudar a los alumnos a comprender qu e el tiempo verbal del presente también se usa para expresar otros valores aparte del prototípico (simultaneidad con el acto de habla), es necesario que los aprendices reflexionen sobre estos usos. De los resultados se infiere que la interacción promueve e l desarrollo de actividad metalingüística y que a partir de la reflexión se pueden establecer puentes entre el saber gramatical y los usos lingüísticos. También ponen de manifiesto que un aprendizaje escolar excesivamente formal (que construye el conocimie nto sobre el verbo desde un punto de vista básicamente morfológico) impide a los alumnos interpretar los tiempos verbales de acuerdo con otros criterios (semánticos, sintácticos y pragmáticos). Las conclusiones ratifican que determinadas concepciones de la práctica escolar constituyen un obstáculo para avanzar en la construcción del saber gramatical y apuntan la necesidad de revisar tanto los contenidos como las metodologías para aprender gramática en las aulas de primaria.

Laboratory automation in clinical bacteriology: what system to choose?

Automation was introduced many years ago in several diagnostic disciplines such as chemistry, haematology and molecular biology. The first laboratory automation system for clinical bacteriology was released in 2006, and it rapidly proved its value by increasing productivity, allowing a continuous increase in sample volumes despite limited budgets and personnel shortages. Today, two major manufacturers, BD Kiestra and Copan, are commercializing partial or complete laboratory automation systems for bacteriology. The laboratory automation systems are rapidly evolving to provide improved hardware and software solutions to optimize laboratory efficiency. However, the complex parameters of the laboratory and automation systems must be considered to determine the best system for each given laboratory. We address several topics on laboratory automation that may help clinical bacteriologists to understand the particularities and operative modalities of the different systems. We present (a) a comparison of the engineering and technical features of the various elements composing the two different automated systems currently available, (b) the system workflows of partial and complete laboratory automation, which define the basis for laboratory reorganization required to optimize system efficiency, (c) the concept of digital imaging and telebacteriology, (d) the connectivity of laboratory automation to the laboratory information system, (e) the general advantages and disadvantages as well as the expected impacts provided by laboratory automation and (f) the laboratory data required to conduct a workflow assessment to determine the best configuration of an automated system for the laboratory activities and specificities.

La Relación del lenguaje con la teoría de la mente en edad escolar

In the past years a considerable amount of research has been carried out on the development of theory of mind (ToM) reporting that language and ToM performance are correlated. However it is less clear what aspect of language is related with ToM development. Some studies show a greater influence of semantics aspects, whereas others suggest that sentential complement sentences, a specific aspect of syntax, are crucial for false belief understanding (FB). Yet others argue that pragmatic abilities correlate with FB understanding. The aim of this study is investigate, on the one side, the development of ToM between the ages of 6 and 8 and on the other side, the relationship between some aspects of language and the ToM improvement. Several ToM tasks were administrated to evaluate children’s performance at two different ages (60 participants aged 6 and 8 years) and four tasks to assess language abilities. The results show a significant increase in the understanding of the mind between the ages of 6 and 8. Furthermore, results reveal a significant relationship between syntax and tasks that require FB understanding, while pragmatics is more strongly associated with tasks that involve more complex socio-cognitive understandings

Optimización del framework de paralelización de tareas COMPSs

El propósito de este trabajo es optimizar el sistema de gestión de workflows COMPSs caracterizando el comportamiento de diferentes dispositivos de memoria a nivel de consumo energético y tiempo de ejecución. Para llevar a cabo este propósito, se ha implementado un servicio de caché para COMPSs para conseguir que sea consciente de la jerarquía de memoria y se han realizado múltiples experimentos para caracterizar los dispositivos de memoria y las mejoras en el rendimiento.

Quality and analysis of administration processes in server operations

IT outsourcing refers to the way companies focus on their core competencies and buy the supporting functions from other companies specialized in that area. Service is the total outcome of numerous of activities by employees and other resources to provide solutions to customers' problems. Outsourcing and service business have their unique characteristics. Service Level Agreements quantify the minimum acceptable service to the user. The service quality has to be objectively quantified so that its achievement or non-achievement of it can be monitored. Usually offshoring refers to the transferring of tasks to low-cost nations. Offshoring presents a lot of challenges that require special attention and they need to be assessed thoroughly. IT Infrastructure management refers to installation and basic usability assistance of operating systems, network and server tools and utilities. ITIL defines the industry best practices for organizing IT processes. This thesis did an analysis of server operations service and the customers’ perception of the quality of daily operations. The agreed workflows and processes should be followed better. Service providers’ processes are thoroughly defined but both the customer and the service provider might disobey them. Service provider should review the workflows regarding customer functions. Customer facing functions require persistent skill development, as they communicate the quality to the customer. Service provider needs to provide better organized communication and knowledge exchange methods between the specialists in different geographical locations.