Zintegrowane kształcenie przedmiotowo-językowe. Dydaktyka zadaniowa a rozwój osobistej kompetencji komunikacyjnej w warunkach półautonomii

Wydział Neofilologii

Gestão do cooperativismo médico no Brasil

Tese apresentada à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Doutor em Ciências Empresariais, especialidade em Gestão

Integration of relational and hierarchical network information for protein function prediction

BACKGROUND:In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most existing technologies pursue this task as a classification problem, on a term-by-term basis, for each term in a database, such as the Gene Ontology (GO) database, a popular rigorous vocabulary for biological functions. However, ontology structures are essentially hierarchies, with certain top to bottom annotation rules which protein function predictions should in principle follow. Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions.RESULTS:We propose a probabilistic framework to integrate information in relational data, in the form of a protein-protein interaction network, and a hierarchically structured database of terms, in the form of the GO database, for the purpose of protein function prediction. At the heart of our framework is a factorization of local neighborhood information in the protein-protein interaction network across successive ancestral terms in the GO hierarchy. We introduce a classifier within this framework, with computationally efficient implementation, that produces GO-term predictions that naturally obey a hierarchical 'true-path' consistency from root to leaves, without the need for further post-processing.CONCLUSION:A cross-validation study, using data from the yeast Saccharomyces cerevisiae, shows our method offers substantial improvements over both standard 'guilt-by-association' (i.e., Nearest-Neighbor) and more refined Markov random field methods, whether in their original form or when post-processed to artificially impose 'true-path' consistency. Further analysis of the results indicates that these improvements are associated with increased predictive capabilities (i.e., increased positive predictive value), and that this increase is consistent uniformly with GO-term depth. Additional in silico validation on a collection of new annotations recently added to GO confirms the advantages suggested by the cross-validation study. Taken as a whole, our results show that a hierarchical approach to network-based protein function prediction, that exploits the ontological structure of protein annotation databases in a principled manner, can offer substantial advantages over the successive application of 'flat' network-based methods.

DSpace Basic Tutorial

PDF of powerpoint slides presented at DSUG 2007 Roma

Resource Management for Responsive Web Computing

The exploding demand for services like the World Wide Web reflects the potential that is presented by globally distributed information systems. The number of WWW servers world-wide has doubled every 3 to 5 months since 1993, outstripping even the growth of the Internet. At each of these self-managed sites, the Common Gateway Interface (CGI) and Hypertext Transfer Protocol (HTTP) already constitute a rudimentary basis for contributing local resources to remote collaborations. However, the Web has serious deficiencies that make it unsuited for use as a true medium for metacomputing --- the process of bringing hardware, software, and expertise from many geographically dispersed sources to bear on large scale problems. These deficiencies are, paradoxically, the direct result of the very simple design principles that enabled its exponential growth. There are many symptoms of the problems exhibited by the Web: disk and network resources are consumed extravagantly; information search and discovery are difficult; protocols are aimed at data movement rather than task migration, and ignore the potential for distributing computation. However, all of these can be seen as aspects of a single problem: as a distributed system for metacomputing, the Web offers unpredictable performance and unreliable results. The goal of our project is to use the Web as a medium (within either the global Internet or an enterprise intranet) for metacomputing in a reliable way with performance guarantees. We attack this problem one four levels: (1) Resource Management Services: Globally distributed computing allows novel approaches to the old problems of performance guarantees and reliability. Our first set of ideas involve setting up a family of real-time resource management models organized by the Web Computing Framework with a standard Resource Management Interface (RMI), a Resource Registry, a Task Registry, and resource management protocols to allow resource needs and availability information be collected and disseminated so that a family of algorithms with varying computational precision and accuracy of representations can be chosen to meet realtime and reliability constraints. (2) Middleware Services: Complementary to techniques for allocating and scheduling available resources to serve application needs under realtime and reliability constraints, the second set of ideas aim at reduce communication latency, traffic congestion, server work load, etc. We develop customizable middleware services to exploit application characteristics in traffic analysis to drive new server/browser design strategies (e.g., exploit self-similarity of Web traffic), derive document access patterns via multiserver cooperation, and use them in speculative prefetching, document caching, and aggressive replication to reduce server load and bandwidth requirements. (3) Communication Infrastructure: Finally, to achieve any guarantee of quality of service or performance, one must get at the network layer that can provide the basic guarantees of bandwidth, latency, and reliability. Therefore, the third area is a set of new techniques in network service and protocol designs. (4) Object-Oriented Web Computing Framework A useful resource management system must deal with job priority, fault-tolerance, quality of service, complex resources such as ATM channels, probabilistic models, etc., and models must be tailored to represent the best tradeoff for a particular setting. This requires a family of models, organized within an object-oriented framework, because no one-size-fits-all approach is appropriate. This presents a software engineering challenge requiring integration of solutions at all levels: algorithms, models, protocols, and profiling and monitoring tools. The framework captures the abstract class interfaces of the collection of cooperating components, but allows the concretization of each component to be driven by the requirements of a specific approach and environment.

Neural Models of Motion Integration, Segmentation, and Probablistic Decision-Making

When brain mechanism carry out motion integration and segmentation processes that compute unambiguous global motion percepts from ambiguous local motion signals? Consider, for example, a deer running at variable speeds behind forest cover. The forest cover is an occluder that creates apertures through which fragments of the deer's motion signals are intermittently experienced. The brain coherently groups these fragments into a trackable percept of the deer in its trajectory. Form and motion processes are needed to accomplish this using feedforward and feedback interactions both within and across cortical processing streams. All the cortical areas V1, V2, MT, and MST are involved in these interactions. Figure-ground processes in the form stream through V2, such as the seperation of occluding boundaries of the forest cover from the boundaries of the deer, select the motion signals which determine global object motion percepts in the motion stream through MT. Sparse, but unambiguous, feauture tracking signals are amplified before they propogate across position and are intergrated with far more numerous ambiguous motion signals. Figure-ground and integration processes together determine the global percept. A neural model predicts the processing stages that embody these form and motion interactions. Model concepts and data are summarized about motion grouping across apertures in response to a wide variety of displays, and probabilistic decision making in parietal cortex in response to random dot displays.

Vector Associative Maps: Unsupervised Real-time Error-based Learning and Control of Movement Trajectories

This article describes neural network models for adaptive control of arm movement trajectories during visually guided reaching and, more generally, a framework for unsupervised real-time error-based learning. The models clarify how a child, or untrained robot, can learn to reach for objects that it sees. Piaget has provided basic insights with his concept of a circular reaction: As an infant makes internally generated movements of its hand, the eyes automatically follow this motion. A transformation is learned between the visual representation of hand position and the motor representation of hand position. Learning of this transformation eventually enables the child to accurately reach for visually detected targets. Grossberg and Kuperstein have shown how the eye movement system can use visual error signals to correct movement parameters via cerebellar learning. Here it is shown how endogenously generated arm movements lead to adaptive tuning of arm control parameters. These movements also activate the target position representations that are used to learn the visuo-motor transformation that controls visually guided reaching. The AVITE model presented here is an adaptive neural circuit based on the Vector Integration to Endpoint (VITE) model for arm and speech trajectory generation of Bullock and Grossberg. In the VITE model, a Target Position Command (TPC) represents the location of the desired target. The Present Position Command (PPC) encodes the present hand-arm configuration. The Difference Vector (DV) population continuously.computes the difference between the PPC and the TPC. A speed-controlling GO signal multiplies DV output. The PPC integrates the (DV)·(GO) product and generates an outflow command to the arm. Integration at the PPC continues at a rate dependent on GO signal size until the DV reaches zero, at which time the PPC equals the TPC. The AVITE model explains how self-consistent TPC and PPC coordinates are autonomously generated and learned. Learning of AVITE parameters is regulated by activation of a self-regulating Endogenous Random Generator (ERG) of training vectors. Each vector is integrated at the PPC, giving rise to a movement command. The generation of each vector induces a complementary postural phase during which ERG output stops and learning occurs. Then a new vector is generated and the cycle is repeated. This cyclic, biphasic behavior is controlled by a specialized gated dipole circuit. ERG output autonomously stops in such a way that, across trials, a broad sample of workspace target positions is generated. When the ERG shuts off, a modulator gate opens, copying the PPC into the TPC. Learning of a transformation from TPC to PPC occurs using the DV as an error signal that is zeroed due to learning. This learning scheme is called a Vector Associative Map, or VAM. The VAM model is a general-purpose device for autonomous real-time error-based learning and performance of associative maps. The DV stage serves the dual function of reading out new TPCs during performance and reading in new adaptive weights during learning, without a disruption of real-time operation. YAMs thus provide an on-line unsupervised alternative to the off-line properties of supervised error-correction learning algorithms. YAMs and VAM cascades for learning motor-to-motor and spatial-to-motor maps are described. YAM models and Adaptive Resonance Theory (ART) models exhibit complementary matching, learning, and performance properties that together provide a foundation for designing a total sensory-cognitive and cognitive-motor autonomous system.

Understanding student stress: a qualitative study of the stress experienced by third level students

Stress can be understood in terms of the meaning of stressful experiences for individuals. The meaning of stressful experiences involves threats to self-adequacy, where self-adequacy is considered a basic human need. Appropriate research methods are required to explore this aspect of stress. The present study is a qualitative exploration of the stress experienced by a group of 27 students at the National Institute of Higher Education, Limerick (since renamed the University of Limerick). The study was carried out by the resident student counsellor at the college. A model of student stress was explored, based on student developmental needs. The data consist of a series of interviews recorded with each of the 27 students over a 3 month period. These interviews were transcribed and the resulting transcripts are the subject of detailed analysis. The analysis of the data is an account of the sense-making process by the student counsellor of the students' reported experiences. The aim of the analysis was to reduce the large amounts of data to their most salient aspects in an ordered fashion, so as to examine the application of a developmental model of stress with this group of students. There were two key elements to the analysis. First, the raw data were edited to identify the key statements contained in the interviews. Second, the statements were categorised, as a means of summarising the data. The results of the qualitative dataanalysis were then applied to the developmental model. The analysis of data revealed a number of patterns of stress amongst the sample of students. Patterns of academic over-identification, parental conflict and social inadequacy were particularly noteworthy. These patterns consisted of an integration of academic, family and social stresses within a developmental framework. Gender differences with regard to the need for separateness and belonging are highlighted. Appropriate student stress intervention strategies are discussed. Based on the present results, the relationship between stress and development has been highlighted and is recommended as a firm basis for future studies of stress in general and student stress in particular.

Police accountability in Ireland: an analysis of the problems posed by the legal, constitutional and political dimensions and how they might be addressed

The concept of police accountability is not susceptible to a universal or concise definition. In the context of this thesis it is treated as embracing two fundamental components. First, it entails an arrangement whereby an individual, a minority and the whole community have the opportunity to participate meaningfully in the formulation of the principles and policies governing police operations. Second, it presupposes that those who have suffered as victims of unacceptable police behaviour should have an effective remedy. These ingredients, however, cannot operate in a vacuum. They must find an accommodation with the equally vital requirement that the burden of accountability should not be so demanding that the delivery of an effective police service is fatally impaired. While much of the current debate on police accountability in Britain and the USA revolves around the issue of where the balance should be struck in this accommodation, Ireland lacks the very foundation for such a debate as it suffers from a serious deficit in research and writing on police generally. This thesis aims to fill that gap by laying the foundations for an informed debate on police accountability and related aspects of police in Ireland. Broadly speaking the thesis contains three major interrelated components. The first is concerned with the concept of police in Ireland and the legal, constitutional and political context in which it operates. This reveals that although the Garda Siochana is established as a national force the legal prescriptions concerning its role and governance are very vague. Although a similar legislative format in Britain, and elsewhere, have been interpreted as conferring operational autonomy on the police it has not stopped successive Irish governments from exercising close control over the police. The second component analyses the structure and operation of the traditional police accountability mechanisms in Ireland; namely the law and the democratic process. It concludes that some basic aspects of the peculiar legal, constitutional and political structures of policing seriously undermine their capacity to deliver effective police accountability. In the case of the law, for example, the status of, and the broad discretion vested in, each individual member of the force ensure that the traditional legal actions cannot always provide redress where individuals or collective groups feel victimised. In the case of the democratic process the integration of the police into the excessively centralised system of executive government, coupled with the refusal of the Minister for Justice to accept responsibility for operational matters, project a barrier between the police and their accountability to the public. The third component details proposals on how the current structures of police accountability in Ireland can be strengthened without interfering with the fundamentals of the law, the democratic process or the legal and constitutional status of the police. The key elements in these proposals are the establishment of an independent administrative procedure for handling citizen complaints against the police and the establishment of a network of local police-community liaison councils throughout the country coupled with a centralised parliamentary committee on the police. While these proposals are analysed from the perspective of maximising the degree of police accountability to the public they also take into account the need to ensure that the police capacity to deliver an effective police service is not unduly impaired as a result.

Grid integration of wave energy & generic modelling of ocean devices for power system studies

The work presented in this thesis covers four major topics of research related to the grid integration of wave energy. More specifically, the grid impact of a wave farm on the power quality of its local network is investigated. Two estimation methods were developed regarding the flicker level Pst generated by a wave farm in relation to its rated power as well as in relation to the impedance angle ψk of the node in the grid to which it is connected. The electrical design of a typical wave farm design is also studied in terms of minimum rating for three types of costly pieces of equipment, namely the VAr compensator, the submarine cables and the overhead line. The power losses dissipated within the farm's electrical network are also evaluated. The feasibility of transforming a test site into a commercial site of greater rated power is investigated from the perspective of power quality and of cables and overhead line thermal loading. Finally, the generic modelling of ocean devices, referring here to both wave and tidal current devices, is investigated.

Hybrid integration and packaging of grating-coupled silicon photonics

This thesis covers both the packaging of silicon photonic devices with fiber inputs and outputs as well as the integration of laser light sources with these same devices. The principal challenge in both of these pursuits is coupling light into the submicrometer waveguides that are the hallmark of silicon-on-insulator (SOI) systems. Previous work on grating couplers is leveraged to design new approaches to bridge the gap between the highly-integrated domain of silicon, the Interconnected world of fiber and the active region of III-V materials. First, a novel process for the planar packaging of grating couplers with fibers is explored in detail. This technology allows the creation of easy-to-use test platforms for laser integration and also stands on its own merits as an enabling technology for next-generation silicon photonics systems. The alignment tolerances of this process are shown to be well-suited to a passive alignment process and for wafer-scale assembly. Furthermore, this technology has already been used to package demonstrators for research partners and is included in the offerings of the ePIXfab silicon photonics foundry and as a design kit for PhoeniX Software’s MaskEngineer product. After this, a process for hybridly integrating a discrete edge-emitting laser with a silicon photonic circuit using near-vertical coupling is developed and characterized. The details of the various steps of the design process are given, including mechanical, thermal, optical and electrical steps. The interrelation of these design domains is also discussed. The construction process for a demonstrator is outlined, and measurements are presented of a series of single-wavelength Fabry-Pérot lasers along with a two-section laser tunable in the telecommunications C-band. The suitability and potential of this technology for mass manufacture is demonstrated, with further opportunities for improvement detailed and discussed in the conclusion.

Development of germanium/silicon integration for near infrared detection

Silicon (Si) is the base material for electronic technologies and is emerging as a very attractive platform for photonic integrated circuits (PICs). PICs allow optical systems to be made more compact with higher performance than discrete optical components. Applications for PICs are in the area of fibre-optic communication, biomedical devices, photovoltaics and imaging. Germanium (Ge), due to its suitable bandgap for telecommunications and its compatibility with Si technology is preferred over III-V compounds as an integrated on-chip detector at near infrared wavelengths. There are two main approaches for Ge/Si integration: through epitaxial growth and through direct wafer bonding. The lattice mismatch of ~4.2% between Ge and Si is the main problem of the former technique which leads to a high density of dislocations while the bond strength and conductivity of the interface are the main challenges of the latter. Both result in trap states which are expected to play a critical role. Understanding the physics of the interface is a key contribution of this thesis. This thesis investigates Ge/Si diodes using these two methods. The effects of interface traps on the static and dynamic performance of Ge/Si avalanche photodetectors have been modelled for the first time. The thesis outlines the original process development and characterization of mesa diodes which were fabricated by transferring a ~700 nm thick layer of p-type Ge onto n-type Si using direct wafer bonding and layer exfoliation. The effects of low temperature annealing on the device performance and on the conductivity of the interface have been investigated. It is shown that the diode ideality factor and the series resistance of the device are reduced after annealing. The carrier transport mechanism is shown to be dominated by generation–recombination before annealing and by direct tunnelling in forward bias and band-to-band tunnelling in reverse bias after annealing. The thesis presents a novel technique to realise photodetectors where one of the substrates is thinned by chemical mechanical polishing (CMP) after bonding the Si-Ge wafers. Based on this technique, Ge/Si detectors with remarkably high responsivities, in excess of 3.5 A/W at 1.55 μm at −2 V, under surface normal illumination have been measured. By performing electrical and optical measurements at various temperatures, the carrier transport through the hetero-interface is analysed by monitoring the Ge band bending from which a detailed band structure of the Ge/Si interface is proposed for the first time. The above unity responsivity of the detectors was explained by light induced potential barrier lowering at the interface. To our knowledge this is the first report of light-gated responsivity for vertically illuminated Ge/Si photodiodes. The wafer bonding approach followed by layer exfoliation or by CMP is a low temperature wafer scale process. In principle, the technique could be extended to other materials such as Ge on GaAs, or Ge on SOI. The unique results reported here are compatible with surface normal illumination and are capable of being integrated with CMOS electronics and readout units in the form of 2D arrays of detectors. One potential future application is a low-cost Si process-compatible near infrared camera.

High-efficiency photovoltaics through mechanically stacked integration of solar cells based on the InP lattice constant

Solar Energy is a clean and abundant energy source that can help reduce reliance on fossil fuels around which questions still persist about their contribution to climate and long-term availability. Monolithic triple-junction solar cells are currently the state of the art photovoltaic devices with champion cell efficiencies exceeding 40%, but their ultimate efficiency is restricted by the current-matching constraint of series-connected cells. The objective of this thesis was to investigate the use of solar cells with lattice constants equal to InP in order to reduce the constraint of current matching in multi-junction solar cells. This was addressed by two approaches: Firstly, the formation of mechanically stacked solar cells (MSSC) was investigated through the addition of separate connections to individual cells that make up a multi-junction device. An electrical and optical modelling approach identified separately connected InGaAs bottom cells stacked under dual-junction GaAs based top cells as a route to high efficiency. An InGaAs solar cell was fabricated on an InP substrate with a measured 1-Sun conversion efficiency of 9.3%. A comparative study of adhesives found benzocyclobutene to be the most suitable for bonding component cells in a mechanically stacked configuration owing to its higher thermal conductivity and refractive index when compared to other candidate adhesives. A flip-chip process was developed to bond single-junction GaAs and InGaAs cells with a measured 4-terminal MSSC efficiency of 25.2% under 1-Sun conditions. Additionally, a novel InAlAs solar cell was identified, which can be used to provide an alternative to the well established GaAs solar cell. As wide bandgap InAlAs solar cells have not been extensively investigated for use in photovoltaics, single-junction cells were fabricated and their properties relevant to PV operation analysed. Minority carrier diffusion lengths in the micrometre range were extracted, confirming InAlAs as a suitable material for use in III-V solar cells, and a 1-Sun conversion efficiency of 6.6% measured for cells with 800 nm thick absorber layers. Given the cost and small diameter of commercially available InP wafers, InGaAs and InAlAs solar cells were fabricated on alternative substrates, namely GaAs. As a first demonstration the lattice constant of a GaAs substrate was graded to InP using an InxGa1-xAs metamorphic buffer layer onto which cells were grown. This was the first demonstration of an InAlAs solar cell on an alternative substrate and an initial step towards fabricating these cells on Si. The results presented offer a route to developing multi-junction solar cell devices based on the InP lattice parameter, thus extending the range of available bandgaps for high efficiency cells.