Burrows-wheeler transform in secondary memory

Master’s Thesis in Computer Engineering

A framework for efficient model transformations

The reported productivity gains while using models and model transformations to develop entire systems, after almost a decade of experience applying model-driven approaches for system development, are already undeniable benefits of this approach. However, the slowness of higher-level, rule based model transformation languages hinders the applicability of this approach to industrial scales. Lower-level, and efficient, languages can be used but productivity and easy maintenance seize to exist. The abstraction penalty problem is not new, it also exists for high-level, object oriented languages but everyone is using them now. Why is not everyone using rule based model transformation languages then? In this thesis, we propose a framework, comprised of a language and its respective environment, designed to tackle the most performance critical operation of high-level model transformation languages: the pattern matching. This framework shows that it is possible to mitigate the performance penalty while still using high-level model transformation languages.

Pattern operators for grid

The definition and programming of distributed applications has become a major research issue due to the increasing availability of (large scale) distributed platforms and the requirements posed by the economical globalization. However, such a task requires a huge effort due to the complexity of the distributed environments: large amount of users may communicate and share information across different authority domains; moreover, the “execution environment” or “computations” are dynamic since the number of users and the computational infrastructure change in time. Grid environments, in particular, promise to be an answer to deal with such complexity, by providing high performance execution support to large amount of users, and resource sharing across different organizations. Nevertheless, programming in Grid environments is still a difficult task. There is a lack of high level programming paradigms and support tools that may guide the application developer and allow reusability of state-of-the-art solutions. Specifically, the main goal of the work presented in this thesis is to contribute to the simplification of the development cycle of applications for Grid environments by bringing structure and flexibility to three stages of that cycle through a commonmodel. The stages are: the design phase, the execution phase, and the reconfiguration phase. The common model is based on the manipulation of patterns through pattern operators, and the division of both patterns and operators into two categories, namely structural and behavioural. Moreover, both structural and behavioural patterns are first class entities at each of the aforesaid stages. At the design phase, patterns can be manipulated like other first class entities such as components. This allows a more structured way to build applications by reusing and composing state-of-the-art patterns. At the execution phase, patterns are units of execution control: it is possible, for example, to start or stop and to resume the execution of a pattern as a single entity. At the reconfiguration phase, patterns can also be manipulated as single entities with the additional advantage that it is possible to perform a structural reconfiguration while keeping some of the behavioural constraints, and vice-versa. For example, it is possible to replace a behavioural pattern, which was applied to some structural pattern, with another behavioural pattern. In this thesis, besides the proposal of the methodology for distributed application development, as sketched above, a definition of a relevant set of pattern operators was made. The methodology and the expressivity of the pattern operators were assessed through the development of several representative distributed applications. To support this validation, a prototype was designed and implemented, encompassing some relevant patterns and a significant part of the patterns operators defined. This prototype was based in the Triana environment; Triana supports the development and deployment of distributed applications in the Grid through a dataflow-based programming model. Additionally, this thesis also presents the analysis of a mapping of some operators for execution control onto the Distributed Resource Management Application API (DRMAA). This assessment confirmed the suitability of the proposed model, as well as the generality and flexibility of the defined pattern operators

Matching CO2 large point sources and potential geological storage sites in mainland Portugal

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia do Ambiente, Perfil Gestão e Sistemas Ambientais

A Logic and tool for local reasoning about security protocols

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia Informática

Behavioural development in a matching-to-sample task and token use by an infant chimpanzee reared by his mother

Animal Cognition, V.6, pp. 259–267

A pattern language for parallelizing irregular algorithms

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Informática

Stratigraphic interpretation of Well-Log data of the Athabasca Oil Sands of Alberta Canada through Pattern recognition and Artificial Intelligence

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

Spatial point pattern analysis of gorilla nest sites in the Kagwene Sanctuary, Cameroon: Towards understanding the nesting behavior of a critically endangered subspecies

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

Effects of Spatial Pattern of GreenSpace on Land Surface Temperature: A case study on Oasis City Aksu, northwest China

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

Efeitos da laqueação proximal dos vasos curtos e da fundoplicatura total sobre a microcirculação do fundo gástrico : estudo microvascular em cobaias

RESUMO: A operação de Nissen, por laparoscopia, é considerada a cirurgia antirefluxo mais adequada por ser a que melhor replica a fisiologia normal da válvula gastresofágica na maioria dos doentes com sintomas típicos de doença do refluxo gastresofágico (DRGE). São critérios técnicos o encerramento seguro dos pilares do diafragma e a criação de fundoplicatura completa (360 graus), curta (inferior a dois centímetros), lassa e sem tensão – desiderando para o qual a laqueação proximal dos vasos curtos gástricos é crucial. Realizei a operação de Nissen, por laparoscopia, em sessenta mulheres e quarenta homens com DRGE, sem mortalidade operatória, no Serviço de Cirurgia 6 do Hospital dos Capuchos, CHLC, EPE. Os cem doentes apresentavam média etária de 46 anos e queixas, com tempo de evolução entre 1 e 43 anos, de pirose (90%), regurgitação (80%), azia (73%), epigastralgias (54%). A endoscopia alta revelou esofagite de grau Savary-Miller 0-I (62%), II (23%), III (8%), IV (7%); hérnia de deslizamento (71%), hérnia paraesofágica (8%), sem hérnia (21%); a pHmetria de 24h diagnosticou padrão misto (38%), levantado (20%), deitado (20%), inconclusiva (22%) e a manometria diagnosticou EEI hipotónico (35%), peristálise esofágica normal (88%), hipomotilidade ligeira (5%) e foi omissa (7%). Hérnia hiatal, esofagite grave, ineficácia do controlo sintomático com inibidor da bomba de protões e desejo de descontinuidade terapêutica constituíram as indicações para tratamento cirúrgico. Por celioscopia, efetuei laqueação dos vasos curtos gástricos (70%), cruroplastia e fundoplicatura total (seda 2/0), curta (dimensão média 1,5-2 cm), lassa, sem tensão e sem calibração intraoperatória do esófago. A fundoplicatura de Nissen laparoscópica mostrou-se segura e eficaz no tratamento da DRGE. A sua idoneidade foi ainda comprovada pela normalização da pHmetria de 24 horas e da manometria pós-operatórias, com significado estatístico, num grupo de catorze voluntários assintomáticos. Em catamnese com recuo médio 30,7 meses 94% dos indivíduos persistem assintomáticos. Interrogando-me acerca das repercussões desta operação sobre a microcirculação do fundo gástrico coloquei, como premissa, a possibilidade de na operação de Nissen a laqueação dos vasos curtos poder induzir modificação no diâmetro arteriolar da parede do fundo gástrico. Para pesquisar a influência da laqueação dos vasos curtos gástricos e da fundoplicatura total sobre o calibre arteriolar da parede do estômago no cárdia, no fundo e na região dos vasos curtos gástricos, idealizei um Projeto de investigação experimental em cobaias. O Projeto foi desenvolvido no Centro de Investigação do Departamento de Anatomia da FCM-UNL. Para a sua realização obtive autorização da Comissão Científica e Pedagógica da FCM-UNL, requeri a acreditação como investigador à Direção Geral de Veterinária e, por recorrer à utilização de animais, submeti-o à Comissão de Ética da FCM-UNL, que o aprovou por unanimidade. Para limitar o número de animais utilizados ao mínimo necessário, calculei, por método estatístico, a quantidade de cobaias necessárias. Subdividindo-as num grupo de ensaio (GE), onde realizei a operação de Nissen, e num grupo de controlo (GC), onde apenas procedi a tração gástrica, defini e apliquei protocolos de anestesia, de cirurgia e de eutanásia, segundo os princípios dos 3R – Replacement, Reduction, Refinement da técnica de experimentação humana de Russell e Burch (1959) – uma estrutura ética amplamente aceite para a realização de experimentação científica humanizada com animais. A utilização das técnicas de estudo angiomorfológico permitiu-me analisar e descrever a anatomia normal, a vascularização arterial macroscópica, a microangioarquitetura, por microscopia eletrónica de varrimento de moldes de corrosão vascular, e a histologia da parede do estômago da cobaia. Procedi, também, à definição dos critérios morfológicos que considerei suscetíveis de validação deste modelo animal para o estudo proposto. Por razões académicas, foi necessário abreviar o Projeto encurtando, em cerca de dois anos, o prazo disponível para conclusão do estudo. Apreciando-o com o Gabinete de Análise Epidemiológica e Estatística do Centro de Investigação do CHLC, EPE, optou-se, perante a escassez de elementos após já terem sido recrutados 46 animais, por uma amostra, suplementar, de dimensão de conveniência de oito cobaias (quatro em cada grupo), condicionada pelo limite temporal universitário e pelo respeito pela dignidade dos animais. Neste subgrupo procedi, por microscopia eletrónica de varrimento, à medição dos calibres arteriolares nos moldes vasculares do cárdia, do fundo e da zona dos vasos curtos gástricos tanto no GC como no GE efetuando 469 medições no primeiro e 461 no último. Os dados foram enviados ao Centro de Investigação do CHLC, EPE que procedeu à sua análise estatística (ANOVA). A referida análise revelou que as arteríolas do plexo mucoso e as do plexo submucoso do cárdia, do fundo e da região dos vasos curtos gástricos, mostraram aumento de calibre no GE. O aumento foi, estatisticamente, significativo por ser superior a 50% do calibre do GC. Nos vasos curtos, a diferença foi mais pequena, mas persistiu sendo, estatisticamente, significativa. Os vasos retos dilataram na base, na sua emergência do plexo seroso, apenas no fundo gástrico. Na cobaia a operação de Nissen – fundoplicatura total com laqueação dos vasos curtos gástricos –, provocou vasodilatação arteriolar do fundo gástrico. Considero que essa vasodilatação constituiu acomodação à modificação introduzida e infiro que o mesmo possa acontecer no ser humano. Admito, assim, que também ocorra vasodilatação no ser humano, na sequência da laqueação dos vasos curtos gástricos, pela analogia microvascular entre as duas espécies e que essa vasodilatação corresponda, igualmente, a um mecanismo de adaptação arteriolar visando, por exemplo, suprir a perda incorrida pela laqueação. A associação experimental entre laqueação dos vasos curtos gástricos e realização de fundoplicatura total, que exerce aumento inerente de pressão sobre a JEG, não só não provocou défice da microcirculação do esófago distal ou do estômago proximal como desencadeou um mecanismo de vasodilatação fúndica que reforça o conceito de segurança da operação de Nissen para tratamento da DRGE. -------------- ABSTRACT: The laparoscopic Nissen operation is considered to be the most appropriate antirefluxsurgery because it suitably replicates the standard physiology of the gastroesophageal valve in most patients with typical symptoms of gastroesophageal reflux disease (GERD). The technical criteria includes the safe shutdown of the diafragmatic crura(cruroplasty) and the creation of a complete fundoplication (360 degrees), short (lesser than two inches), floppy and without tension – a goal for which the proximal ligation of the gastric short vessels is crucial. The laparoscopic Nissen operation was performed in sixty women and forty men with GERD, without any operative mortality, at the Surgical Department of the Hospital dos Capuchos, CHLC, EPE. The one hundred patients, averaged 46 years old, complained of heartburn (90%), regurgitation (80%) and upper abdominal pain (54 %). The endoscopy process revealed Savary-Miller esophagitis of grade 0-I (62%), II (23%), III (8%), IV (7%), sliding hernia (71%), paraesophageal hernia (8%) or no herniation (21%). The pHmetry/24h diagnosed mixed pattern (38%), raised (20%), lying (20%) or inconclusive (22%). The manometry diagnosed hypotensive LES (35%), normal esophageal peristalsis (88%), mild hypomotility (5%) and was absent (7%). Hiatal hernia, severe esophagitis, ineffective symptomatic control with proton pump inhibitor and request for treatment discontinuation were the signs for surgical action. A laparoscopic ligation of short gastric vessels (70%), cruroplasty and fundoplication (silk 2/0), short (average size 1.5–2 cm) and floppy, without tension and without intraoperative calibration of the esophagus were thus performed. The laparoscopic Nissen fundoplication behaved safe and effective in treating GERD. In a group of 14 asymptomatic volunteers its reputation was confirmed with statistical significance by normalization of postoperative pHmetry/24h and manometry. 94% of the individuals remained asymptomatic up to 30.7 months (average) in the follow-up. Interrogating myself about the impact of this operation on the microcirculation of the gastric fundus I put premised on the possibility of the ligation of the short gastric vessels in the Nissen procedure can induce changes in the arteriolar diameter in the Wall of the gastric fundus. To explore the influence of ligation of the short gastric vessels and the fundoplication at the arteriolar caliber of the cardia, the fundus and the region of the short vessels of the gastric wall, I designed a project of experimental research in guinea pigs with two interdependent components: one veterinary and another technical where I applied angiomorphological studies. The project was developed at the Research Centre of the Department of Anatomy FCMUNL. For its accomplishment I got permission from the Scientific and Pedagogical Committee of the FCM-UNL, I requested for accreditation as a researcher at the General Directorate of Veterinary and, by resorting to the use of animals I submitted it to the Ethics Committee of the FCM-UNL, which approved it unanimously. The guinea pigs were divided into two experimental groups: an experimental group (EG), in which the Nissen procedure was performed and a control group (CG) in which only a gastric traction was done. Protocols of anesthesia, surgery and euthanasia were applied according to the 3Rs – Replacement, Reduction, Refinement of the technique of human experimentation of Burch and Russell (1959) – a widely accepted ethical framework for conducting scientific experiments using animals humanely. Using histological and angiomorphological techniques, I performed the analysis and the description of the normal, macro and microvascular, anatomy of the guinea pig stomach and I defined the morphological criteria that I considered susceptible for validation of this animal model for the proposed study. By means of scanning electron microscopy I measured the arteriolar calibers of the vascular casts of the cardia, of the fundus and of the short gastric vessels in both CG and EG, making 469 measurements in the former and 461 in the latter. The data were sent to the Research Center of the CHLC which conducted the statistical analysis (ANOVA). The data were sent to the Centre for Research of the CHLC, EPE which proceeded to statistical analysis (ANOVA). This analysis revealed that the arterioles plexus of the mucosal and submucosal plexus of the cardia, fundus and region of the short gastric vessels, showed increased caliber in EG. The increase was statistically significant for being greater than 50% CG gauge. In the short gastric vessels, the difference was smaller, but persisted and statistically significant. Straight vessels were dilated at the base, on its emergence of the plexus serous only in the fundus. In the guinea pig, the Nissen procedure - complete fundoplication with ligation of the short gastric vessels - caused arteriolar vasodilation on the gastric fundus. I believe that this vasodilation constituted some accommodation to the modification introduced and infer that the same might happen in humans. I admit therefore that vasodilation also occurs in humans following the ligation of the short gastric vessels by microvascular analogy between the two species and that this vasodilation corresponds also to na adaptation mechanism arteriolar, for example, to compensate the loss incurred by ligation. The association of experimental ligation of the short gastric vessels with conducting complete fundoplication, which exerts increased pressure on the EGJ, not only did not cause a microcirculation deficit of the distal esophagus or proximal stomach as triggered a mechanism of fundic vasodilation which reinforces the security concept of the Nissen procedure for treatment of GERD.

Planning and verification of multipath routing protocols

Conventionally the problem of the best path in a network refers to the shortest path problem. However, for the vast majority of networks present nowadays this solution has some limitations which directly affect their proper functioning, as well as an inefficient use of their potentialities. Problems at the level of large networks where graphs of high complexity are commonly present as well as the appearing of new services and their respective requirements, are intrinsically related to the inability of this solution. In order to overcome the needs present in these networks, a new approach to the problem of the best path must be explored. One solution that has aroused more interest in the scientific community considers the use of multiple paths between two network nodes, where they can all now be considered as the best path between those nodes. Therefore, the routing will be discontinued only by minimizing one metric, where only one path between nodes is chosen, and shall be made by the selection of one of many paths, thereby allowing the use of a greater diversity of the present paths (obviously, if the network consents). The establishment of multi-path routing in a given network has several advantages for its operation. Its use may well improve the distribution of network traffic, improve recovery time to failure, or it can still offer a greater control of the network by its administrator. These factors still have greater relevance when networks have large dimensions, as well as when their constitution is of high complexity, such as the Internet, where multiple networks managed by different entities are interconnected. A large part of the growing need to use multipath protocols is associated to the routing made based on policies. Therefore, paths with different characteristics can be considered with equal level of preference, and thus be part of the solution for the best way problem. To perform multi-path routing using protocols based only on the destination address has some limitations but it is possible. Concepts of graph theory of algebraic structures can be used to describe how the routes are calculated and classified, enabling to model the routing problem. This thesis studies and analyzes multi-path routing protocols from the known literature and derives a new algebraic condition which allows the correct operation of these protocols without any network restriction. It also develops a range of software tools that allows the planning and the respective verification/validation of new protocols models according to the study made.

Rely-guarantee protocols for safe interference over shared memory

Mutable state can be useful in certain algorithms, to structure programs, or for efficiency purposes. However, when shared mutable state is used in non-local or nonobvious ways, the interactions that can occur via aliases to that shared memory can be a source of program errors. Undisciplined uses of shared state may unsafely interfere with local reasoning as other aliases may interleave their changes to the shared state in unexpected ways. We propose a novel technique, rely-guarantee protocols, that structures the interactions between aliases and ensures that only safe interference is possible. We present a linear type system outfitted with our novel sharing mechanism that enables controlled interference over shared mutable resources. Each alias is assigned separate, local roles encoded in a protocol abstraction that constrains how an alias can legally use that shared state. By following the spirit of rely-guarantee reasoning, our rely-guarantee protocols ensure that only safe interference can occur but still allow many interesting uses of shared state, such as going beyond invariant and monotonic usages. This thesis describes the three core mechanisms that enable our type-based technique to work: 1) we show how a protocol models an alias’s perspective on how the shared state evolves and constrains that alias’s interactions with the shared state; 2) we show how protocols can be used while enforcing the agreed interference contract; and finally, 3) we show how to check that all local protocols to some shared state can be safely composed to ensure globally safe interference over that shared memory. The interference caused by shared state is rooted at how the uses of di↵erent aliases to that state may be interleaved (perhaps even in non-deterministic ways) at run-time. Therefore, our technique is mostly agnostic as to whether this interference was the result of alias interleaving caused by sequential or concurrent semantics. We show implementations of our technique in both settings, and highlight their di↵erences. Because sharing is “first-class” (and not tied to a module), we show a polymorphic procedure that enables abstract compositions of protocols. Thus, protocols can be specialized or extended without requiring specific knowledge of the interference produce by other protocols to that state. We show that protocol composition can ensure safety even when considering abstracted protocols. We show that this core composition mechanism is sound, decidable (without the need for manual intervention), and provide an algorithm implementation.

Breaking the Pattern and Creating New Paths – Feminist Mizrahi Women Artists in Israel

This article addresses the work of Mizrahi women artists, i.e., Israeli-Jewish women of Asian or African ethnic origin, using the artist Vered Nissim as a case study. Nissim seeks to affirm the politics of identity and recognition, as well as feminism in order to create a paradigm shift with regards to the local regime of cultural representations in the Israeli art scene. Endeavouring to find ways of undermining the rigid imbalances between different social groups, she calls for a comprehensive reform of the status quo through artistic activism. Nissim employs a style, content, and medium that disrupts the accepted social order, using humour and irony as unique weapons with which she takes liberties with conventional moral, social, and economic values. Placing issues of race, class and gender at the centre of her work, she seeks to undermine and problematize essentialist attitudes, highlighting the political intersections of different identity categories as the critical analysis of intersectionality unfolds.