Mining protein structure data

The principal topic of this work is the application of data mining techniques, in particular of machine learning, to the discovery of knowledge in a protein database. In the first chapter a general background is presented. Namely, in section 1.1 we overview the methodology of a Data Mining project and its main algorithms. In section 1.2 an introduction to the proteins and its supporting file formats is outlined. This chapter is concluded with section 1.3 which defines that main problem we pretend to address with this work: determine if an amino acid is exposed or buried in a protein, in a discrete way (i.e.: not continuous), for five exposition levels: 2%, 10%, 20%, 25% and 30%. In the second chapter, following closely the CRISP-DM methodology, whole the process of construction the database that supported this work is presented. Namely, it is described the process of loading data from the Protein Data Bank, DSSP and SCOP. Then an initial data exploration is performed and a simple prediction model (baseline) of the relative solvent accessibility of an amino acid is introduced. It is also introduced the Data Mining Table Creator, a program developed to produce the data mining tables required for this problem. In the third chapter the results obtained are analyzed with statistical significance tests. Initially the several used classifiers (Neural Networks, C5.0, CART and Chaid) are compared and it is concluded that C5.0 is the most suitable for the problem at stake. It is also compared the influence of parameters like the amino acid information level, the amino acid window size and the SCOP class type in the accuracy of the predictive models. The fourth chapter starts with a brief revision of the literature about amino acid relative solvent accessibility. Then, we overview the main results achieved and finally discuss about possible future work. The fifth and last chapter consists of appendices. Appendix A has the schema of the database that supported this thesis. Appendix B has a set of tables with additional information. Appendix C describes the software provided in the DVD accompanying this thesis that allows the reconstruction of the present work.

Preemption-light multiprocessor scheduling of sporadic tasks with high utilisation bound

Known algorithms capable of scheduling implicit-deadline sporadic tasks over identical processors at up to 100% utilisation invariably involve numerous preemptions and migrations. To the challenge of devising a scheduling scheme with as few preemptions and migrations as possible, for a given guaranteed utilisation bound, we respond with the algorithm NPS-F. It is configurable with a parameter, trading off guaranteed schedulable utilisation (up to 100%) vs preemptions. For any possible configuration, NPS-F introduces fewer preemptions than any other known algorithm matching its utilisation bound. A clustered variant of the algorithm, for systems made of multicore chips, eliminates (costly) off-chip task migrations, by dividing processors into disjoint clusters, formed by cores on the same chip (with the cluster size being a parameter). Clusters are independently scheduled (each, using non-clustered NPS-F). The utilisation bound is only moderately affected. We also formulate an important extension (applicable to both clustered and non-clustered NPS-F) which optimises the supply of processing time to executing tasks and makes it more granular. This reduces processing capacity requirements for schedulability without increasing preemptions.

Inter-application redundancy elimination in sensor networks with compiler-assisted scheduling

Most current-generation Wireless Sensor Network (WSN) nodes are equipped with multiple sensors of various types, and therefore support for multi-tasking and multiple concurrent applications is becoming increasingly common. This trend has been fostering the design of WSNs allowing several concurrent users to deploy applications with dissimilar requirements. In this paper, we extend the advantages of a holistic programming scheme by designing a novel compiler-assisted scheduling approach (called REIS) able to identify and eliminate redundancies across applications. To achieve this useful high-level optimization, we model each user application as a linear sequence of executable instructions. We show how well-known string-matching algorithms such as the Longest Common Subsequence (LCS) and the Shortest Common Super-sequence (SCS) can be used to produce an optimal merged monolithic sequence of the deployed applications that takes into account embedded scheduling information. We show that our approach can help in achieving about 60% average energy savings in processor usage compared to the normal execution of concurrent applications.

Caracterização laboratorial de misturas betuminosas com incorporação de agregado siderúrgico inerte para construção (ASIC)

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Civil na Área de Especialização de Vias de Comunicação e Transportes

A CMOS micro power switched-capacitor DC-DC step-up converter for indoor light energy harvesting applications

This paper presents a micro power light energy harvesting system for indoor environments. Light energy is collected by amorphous silicon photovoltaic (a-Si:H PV) cells, processed by a switched capacitor (SC) voltage doubler circuit with maximum power point tracking (MPPT), and finally stored in a large capacitor. The MPPT fractional open circuit voltage (V-OC) technique is implemented by an asynchronous state machine (ASM) that creates and dynamically adjusts the clock frequency of the step-up SC circuit, matching the input impedance of the SC circuit to the maximum power point condition of the PV cells. The ASM has a separate local power supply to make it robust against load variations. In order to reduce the area occupied by the SC circuit, while maintaining an acceptable efficiency value, the SC circuit uses MOSFET capacitors with a charge sharing scheme for the bottom plate parasitic capacitors. The circuit occupies an area of 0.31 mm(2) in a 130 nm CMOS technology. The system was designed in order to work under realistic indoor light intensities. Experimental results show that the proposed system, using PV cells with an area of 14 cm(2), is capable of starting-up from a 0 V condition, with an irradiance of only 0.32 W/m(2). After starting-up, the system requires an irradiance of only 0.18 W/m(2) (18 mu W/cm(2)) to remain operating. The ASM circuit can operate correctly using a local power supply voltage of 453 mV, dissipating only 0.085 mu W. These values are, to the best of the authors' knowledge, the lowest reported in the literature. The maximum efficiency of the SC converter is 70.3 % for an input power of 48 mu W, which is comparable with reported values from circuits operating at similar power levels.

Cyclosporine versus tacrolimus: cost-effectiveness analysis for renal transplantation in Brazil

OBJECTIVE To analyze the cost-effectiveness of treatment regimens with cyclosporine or tacrolimus, five years after renal transplantation.METHODS This cost-effectiveness analysis was based on historical cohort data obtained between 2000 and 2004 and involved 2,022 patients treated with cyclosporine or tacrolimus, matched 1:1 for gender, age, and type and year of transplantation. Graft survival and the direct costs of medical care obtained from the National Health System (SUS) databases were used as outcome results.RESULTS Most of the patients were women, with a mean age of 36.6 years. The most frequent diagnosis of chronic renal failure was glomerulonephritis/nephritis (27.7%). In five years, the tacrolimus group had an average life expectancy gain of 3.96 years at an annual cost of R$78,360.57 compared with the cyclosporine group with a gain of 4.05 years and an annual cost of R$61,350.44.CONCLUSIONS After matching, the study indicated better survival of patients treated with regimens using tacrolimus. However, regimens containing cyclosporine were more cost-effective.

Development of an interface for ontology‐based transformation between features of different types

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

Visualization of clusters in geo-referenced data using three-dimensional self-organizing maps

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação

Integration of e-learning systems with repositories of learning objects

This paper describes a communication model to integrate repositories of programming problems with other e-Learning software components. The motivation for this work comes from the EduJudge project that aims to connect an existing repository of programming problems to learning management systems. When trying to use the existing repositories of learning objects we realized that they are mainly specialized search engines and lack features for integration with other e-Learning systems. With this model we intend to clarify the main features of a programming problem repository, in order to enable the design and development of software components that use it. The two main points of this model are the definition of programming problems as learning objects and the definition of the core functions exposed by the repository. In both cases, this model follows the existing specifications of the IMS standard and proposes extensions to deal with the special requirements of automatic evaluation and grading of programming exercises. In the definition of programming problems as learning objects we introduced a new schema for meta-data. This schema is used to represent meta-data related to automatic evaluation that cannot be conveniently represented using the standard: the type of automatic evaluation; the requirements of the evaluation engine; or the roles of different assets - tests cases, program solutions, etc. In the definition of the core functions we used two different web services flavours - SOAP and REST - and described each function as an operation for each type of interface. We describe also the data types of the arguments of each operation. These data types consist mainly on learning objects and their identifications, but include also usage reports and queries using XQuery.

Extending the learning object definition to represent programming problems

The present generation of eLearning platforms values the interchange of learning objects standards. Nevertheless, for specialized domains these standards are insufficient to fully describe all the assets, especially when they are used as input for other eLearning services. To address this issue we extended an existing learning objects standard to the particular requirements of a specialized domain, namely the automatic evaluation of programming problems. The focus of this paper is the definition of programming problems as learning objects. We introduce a new schema to represent metadata related to automatic evaluation that cannot be conveniently represented using existing standards, such as: the type of automatic evaluation; the requirements of the evaluation engine; or the roles of different assets - tests cases, program solutions, etc. This new schema is being used in an interoperable repository of learning objects, called crimsonHex.

Using mobile device detection approaches to augment the accuracy of web delivery content

Recent studies of mobile Web trends show a continuous explosion of mobile-friendly content. However, the increasing number and heterogeneity of mobile devices poses several challenges for Web programmers who want to automatically get the delivery context and adapt the content to mobile devices. In this process, the devices detection phase assumes an important role where an inaccurate detection could result in a poor mobile experience for the enduser. In this paper we compare the most promising approaches for mobile device detection. Based on this study, we present an architecture for a system to detect and deliver uniform m-Learning content to students in a Higher School. We focus mainly on the devices capabilities repository manageable and accessible through an API. We detail the structure of the capabilities XML Schema that formalizes the data within the devices capabilities XML repository and the REST Web Service API for selecting the correspondent devices capabilities data according to a specific request. Finally, we validate our approach by presenting the access and usage statistics of the mobile web interface of the proposed system such as hits and new visitors, mobile platforms, average time on site and rejection rate.

PExIL: Programming Exercises Interoperability Language

Several standards appeared in recent years to formalize the metadata of learning objects, but they are still insufficient to fully describe a specialized domain. In particular, the programming exercise domain requires interdependent resources (e.g. test cases, solution programs, exercise description) usually processed by different services in the programming exercise life-cycle. Moreover, the manual creation of these resources is time-consuming and error-prone leading to what is an obstacle to the fast development of programming exercises of good quality. This paper focuses on the definition of an XML dialect called PExIL (Programming Exercises Interoperability Language). The aim of PExIL is to consolidate all the data required in the programming exercise life-cycle, from when it is created to when it is graded, covering also the resolution, the evaluation and the feedback. We introduce the XML Schema used to formalize the relevant data of the programming exercise life-cycle. The validation of this approach is made through the evaluation of the usefulness and expressiveness of the PExIL definition. In the former we present the tools that consume the PExIL definition to automatically generate the specialized resources. In the latter we use the PExIL definition to capture all the constraints of a set of programming exercises stored in a learning objects repository.

Using the Common Cartridge profile to enhance learning content interoperability

The concept of Learning Object (LO) is crucial for the standardization on eLearning. The latest LO standard from IMS Global Learning Consortium is the IMS Common Cartridge (IMS CC) that organizes and distributes digital learning content. By analyzing this new specification we considered two interoperability levels: content and communication. A common content format is the backbone of interoperability and is the basis for content exchange among eLearning systems. Communication is more than just exchanging content; it includes also accessing to specialized systems and services and reporting on content usage. This is particularly important when LOs are used for evaluation. In this paper we analyze the Common Cartridge profile based on the two interoperability levels we proposed. We detail its data model that comprises a set of derived schemata referenced on the CC schema and we explore the use of the IMS Learning Tools Interoperability (LTI) to allow remote tools and content to be integrated into a Learning Management System (LMS). In order to test the applicability of IMS CC for automatic evaluation we define a representation of programming exercises using this standard. This representation is intended to be the cornerstone of a network of eLearning systems where students can solve computer programming exercises and obtain feedback automatically. The CC learning object is automatically generated based on a XML dialect called PExIL that aims to consolidate all the data need to describe resources within the programming exercise life-cycle. Finally, we test the generated cartridge on the IMS CC online validator to verify its conformance with the IMS CC specification.

An high-speed parametric ADC and a co-designed mixer for CMOS RF receivers

Dissertação apresentada na faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Using device detection techniques in M-learning scenarios

Recent studies of mobile Web trends show the continued explosion of mobile-friend content. However, the wide number and heterogeneity of mobile devices poses several challenges for Web programmers, who want automatic delivery of context and adaptation of the content to mobile devices. Hence, the device detection phase assumes an important role in this process. In this chapter, the authors compare the most used approaches for mobile device detection. Based on this study, they present an architecture for detecting and delivering uniform m-Learning content to students in a Higher School. The authors focus mainly on the XML device capabilities repository and on the REST API Web Service for dealing with device data. In the former, the authors detail the respective capabilities schema and present a new caching approach. In the latter, they present an extension of the current API for dealing with it. Finally, the authors validate their approach by presenting the overall data and statistics collected through the Google Analytics service, in order to better understand the adherence to the mobile Web interface, its evolution over time, and the main weaknesses.