Development of procedures for the design, optimization and manufacturing of customized orthopaedic and trauma implants: Geometrical/anatomical modelling from 3D medical imaging

Tese de Doutoramento (Programa Doutoral em Engenharia Biomédica)

From software extensions to product lines of dataflow programs

Abstract Dataflow programs are widely used. Each program is a directed graph where nodes are computations and edges indicate the flow of data. In prior work, we reverse-engineered legacy dataflow programs by deriving their optimized implementations from a simple specification graph using graph transformations called refinements and optimizations. In MDE-speak, our derivations were PIM-to-PSM mappings. In this paper, we show how extensions complement refinements, optimizations, and PIM-to-PSM derivations to make the process of reverse engineering complex legacy dataflow programs tractable. We explain how optional functionality in transformations can be encoded, thereby enabling us to encode product lines of transformations as well as product lines of dataflow programs. We describe the implementation of extensions in the ReFlO tool and present two non-trivial case studies as evidence of our work’s generality

Metaphorisms in programming

This paper introduces the metaphorism pattern of relational specification and addresses how specification following this pattern can be refined into recursive programs. Metaphorisms express input-output relationships which preserve relevant information while at the same time some intended optimization takes place. Text processing, sorting, representation changers, etc., are examples of metaphorisms. The kind of metaphorism refinement proposed in this paper is a strategy known as change of virtual data structure. It gives sufficient conditions for such implementations to be calculated using relation algebra and illustrates the strategy with the derivation of quicksort as example.

An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines

The Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef

Training and development in Irish technology companies

The sustained economic growth that has been experienced in the Irish economy in recent years has relied, to a large extent, on the contribution and performance of those industry sectors that possess the ability to provide high-value-added products and services to domestic and international markets. One such contributor has been the Technology sector. However, the performance of this sector relies upon the availability of the necessary capabilities and competencies for Technology companies to remain competitive. The Expert Group on Future Skills Needs have forecasted future skills shortages in this sector. The purpose of this research has been to examine the extent to which Irish Technology companies are taking measures to meet changing skills requirements, through training and development interventions. Survey research methods (in the form of a mail questionnaire, supported by a Web-based questionnaire) have been used to collect information on the expenditure on, and approach to, training and development in these companies, in addition to the methods, techniques and tools/aids that are used to support the delivery of these activities. The contribution of Government intervention has also been examined. The conclusions have been varied. When the activities of the responding companies are considered in isolation, the picture to emerge is primarily positive. Although the expenditure on training and development is slightly lower than that indicated in previous studies, the results vary by company size. Technical employees are clearly the key focus of training provision, while Senior Managers and Directors, Clerical and Administrative staff and Manual workers are a great deal more neglected in training provision. Expenditure on, and use of, computer-based training methods is high, as is the use of most of the specified techniques for facilitating learning. However, when one considers the extent to which external support (in the form of Government interventions and cooperation with other companies and with education and training providers) is integrated into the overall training practices of these companies, significant gaps in practice are identified. The thesis concludes by providing a framework to guide future training and development practices in the Technology sector.

Development of a data acquisition system to characterise sustainable energy technologies and to support Web-Based learning (DAQ-WBL)

Driven by concerns about rising energy costs, security of supply and climate change a new wave of Sustainable Energy Technologies (SET’s) have been embraced by the Irish consumer. Such systems as solar collectors, heat pumps and biomass boilers have become common due to government backed financial incentives and revisions of the building regulations. However, there is a deficit of knowledge and understanding of how these technologies operate and perform under Ireland’s maritime climate. This AQ-WBL project was designed to address both these needs by developing a Data Acquisition (DAQ) system to monitor the performance of such technologies and a web-based learning environment to disseminate performance characteristics and supplementary information about these systems. A DAQ system consisting of 108 sensors was developed as part of Galway-Mayo Institute of Technology’s (GMIT’s) Centre for the Integration of Sustainable EnergyTechnologies (CiSET) in an effort to benchmark the performance of solar thermal collectors and Ground Source Heat Pumps (GSHP’s) under Irish maritime climate, research new methods of integrating these systems within the built environment and raise awareness of SET’s. It has operated reliably for over 2 years and has acquired over 25 million data points. Raising awareness of these SET’s is carried out through the dissemination of the performance data through an online learning environment. A learning environment was created to provide different user groups with a basic understanding of a SET’s with the support of performance data, through a novel 5 step learning process and two examples were developed for the solar thermal collectors and the weather station which can be viewed at http://www.kdp 1 .aquaculture.ie/index.aspx. This online learning environment has been demonstrated to and well received by different groups of GMIT’s undergraduate students and plans have been made to develop it further to support education, awareness, research and regional development.

Design, development and testing of a CAD integrated design for environment software tool.

The research described in this thesis was developed as part o f the Information Management for Green Design (IMA GREE) Project. The 1MAGREE Project was founded by Enterprise Ireland under a Strategic Research Grant Scheme as a partnership project between Galway Mayo Institute o f Technology and C1MRU University College Galway. The project aimed to develop a CAD integrated software tool to support environmental information management for design, particularly for the electronics-manufacturing sector in Ireland.

Development of an integrated approach to reliability management and operation

The research described in this thesis has been developed as a part of the Reliability and Field Data Management for Multi-component Products (REFIDAM) Project. This project was founded under the Applied Research Grants Scheme administered by Enterprise Ireland. The project was a partnership between Galway-Mayo Institute of Technology and Thermo King Europe. The project aimed to develop a system in order to manage the information required for reliability assessment and improvement of multi-component products, by establishing information flows within the company and information exchange with fleet users.

Development and implementation of an integrated technical management system

Quality Management, Integrated Technical Management Systems, ITMS, Technical Elements, Environment, Occupational Health and safety, OH&S, Standards, ISO, General Regulations, Integration, Management Functions, Computer Centre, Suc-cess Concepts, Documentation, PCT, QMS, EMS, OH&S-MS, Portioning, Evaluation, Technical Cycle, Technical Compliance, Framework

Development of a tool for the construction of "ground truth" for complex color images with text

Aquesta memoria resumeix el treball de final de carrera d’Enginyeria Superior d’Informàtica. Explicarà les principals raons que han motivat el projecte així com exemples que il·lustren l’aplicació resultant. En aquest cas el software intentarà resoldre la actual necessitat que hi ha de tenir dades de Ground Truth per als algoritmes de segmentació de text per imatges de color complexes. Tots els procesos seran explicats en els diferents capítols partint de la definició del problema, la planificació, els requeriments i el disseny fins a completar la il·lustració dels resultats del programa i les dades de Ground Truth resultants.

A programme for computer aided identification of Phlebotomine sandflies of the Americas (CIPA): presentation and check-list of American species

The CIPA programme is a collaborative project including two entomologists from France and seven South and Central America countries. Its objective is the development of an expert system for computer aided identification of phlebotomine sandflies from the Americas. It also includes the formation of data bases for bibliographic, taxonomic and biogeographic data. Participant consensus on taxonomic prerequisites, standardization in bibliographic data collections and selection of descriptive variables for the final programme has been established through continous communication among participants and annual meetings. The adopted check-list of American sandflies presented here includes 386 specific taxa, ordered into genera and 28 sub-genera or species groups.

Development of specific ITS markers for plant DNA identification within herbivorous insects

DNA based techniques have proved to be very useful methods to study trophic relationships 17 between pests and their natural enemies. However, most predators are best defined as omnivores, 18 and the identification of plant-specific DNA should also allow the identification of the plant 19 species the predators have been feeding on. In this study, a PCR approach based on the 20 development of specific primers was developed as a self-marking technique to detect plant DNA 21 within the gut of one heteropteran omnivorous predator (Macrolophus pygmaeus) and two 22 lepidopteran pest species (Helicoverpa armigera and Tuta absoluta). Specific tomato primers 23 were designed from the ITS 1-2 region, which allowed the amplification of a tomato DNA 24 fragment of 332 bp within the three insect species tested in all cases (100% of detection at t = 0) 25 and did not detect DNA of other plants nor of the starved insects. Plant DNA half-lives at 25ºC 26 ranged from 5.8h, to 27.7h and 28.7h within M. pygmaeus, H. armigera and T. absoluta, 27 respectively. Tomato DNA detection within field collected M. pygmaeus suggests dietary mixing 28 in this omnivorous predator and showed a higher detection of tomato DNA in females and 29 nymphs than males. This study provides a useful tool to detect and to identify plant food sources 30 of arthropods and to evaluate crop colonization from surrounding vegetation in conservation 31 biological control programs.

Respuesta no lineal y criterios de diseño de puentes arco espaciales

El desarrollo más reciente de los puentes arco ha llevado a una nueva tipología: los “puentes arco espaciales”. Se entiende por puente arco espacial todo puente arco en el que, por su configuración geométrica y estructural, las cargas gravitatorias generan esfuerzos no contenidos en el plano del arco. Por un lado, aparecen para satisfacer las necesidades funcionales cuando estructuras en arco resultan las más adecuadas para sostener tableros curvos y evitar así apoyos intermedios. Desde un punto de vista estético, surgen como demanda de los nuevos puentes en entornos urbanos, buscando, no sólo una forma cuidada, sino persiguiendo convertirse en emblemas de la ciudad a partir de la originalidad y la innovación. Su proyecto y construcción es posible gracias a las grandes posibilidades que ofrecen los nuevos métodos de cálculo y dibujo por ordenador, en los que, a través del incremento de memoria y rapidez, cada vez se emplean programas más completos y nuevas modelizaciones, más cercanas a la realidad. No menos importante es el desarrollo de los medios auxiliares de construcción y de las herramientas de CAD/CAM, que convierte en construibles por control numérico formas de manufactura impensables. Ello trasciende en infinitas posibilidades de diseño y estructura. Sin embargo, el diseño y construcción de estas nuevas tipologías no ha estado acompañado por el avance en el estado del conocimiento fundamentado en la investigación, ya que se han desarrollado pocos estudios que explican parcialmente la respuesta estructural de estos puentes. Existe, por lo tanto, la necesidad de profundizar en el estado del conocimiento y clarificar su respuesta estructural, así como de plantear, finalmente, criterios de diseño que sirvan de apoyo en las fases de concepción y de proyecto a estas nuevas tipologías.

Development and growth of the early juveniles of the spider crab Maja squinado (Brachyura: Majoidea) in an individual culture system

The spider crab Maja squinado is an endangered Mediterranean species; therefore, culturing it successfully is essential for developing restocking programs. The survival, growth and development of post-larval stages (juvenile crabs, C1-C8) were studied using larvae obtained from adult individuals collected in the Catalan Sea. The juvenile crab stages were cultured individually from a megalopal stage using a semi-open recirculation system to obtain the precise growth data of each juvenile crab stage until C8. Development up to C8 at 20ºC lasted 154±10 days. Survival from C1 to C8 was 5.8 %. Moult increment values in cephothoracic length were similar in all the crab stages (21-35 %). Intermoult duration (9±1 in C1-C2 to 51±8 days in C7-C8) increased sharply from juvenile stage 5. Males and females can be distinguished from C4 based on sexual dimorphism in the pleopods and the presence of gonopores. The allometric growth of the pleon is sex-dependent from C4, with females showing positive allometry and males isometric growth. The juvenile growth rate was lower compared with that of the previously studied Atlantic species Maja brachydactyla.