Algorithms and methodologies for decision support in energy efficiency on buildings

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

Development of new methodologies in sample treatment for proteomics workflow based on enzymatic probe sonication technology and mass spectrometry

Thesis submitted to the Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia, for the degree of Doctor of Philosophy in Biochemistry

Transparency in project bond ratings: Assessment of rating methodologies and development of a proven rating simulator

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Finance from the NOVA – School of Business and Economics

Marine Protected Areas (MPAs): Methodologies for assessment

Marine Protected Areas are an effective way of protecting biodiversity, with potential socio-economic benefits including the enhancement of local fisheries and maintenance of ecosystem services. However, local fishing communities often fear short-term revenue losses and thus may oppose marine protected areas creation. This work includes a review of the need of having management effectiveness evaluation and its importance in providing useful information for stakeholders. Therefore, evaluation methodologies are presented and assessed in order to suggest possible approaches to the Berlengas MPA. In this case, an indicator-based approach can be relevant as a starting point, providing already some insights about the management effectiveness of Berlengas MPA. It also supports the development of a more ambitious approach such as a bio-economic model.

Integrated methodologies to study human transcriptional regulation from functional genomics data

Abstract : The human body is composed of a huge number of cells acting together in a concerted manner. The current understanding is that proteins perform most of the necessary activities in keeping a cell alive. The DNA, on the other hand, stores the information on how to produce the different proteins in the genome. Regulating gene transcription is the first important step that can thus affect the life of a cell, modify its functions and its responses to the environment. Regulation is a complex operation that involves specialized proteins, the transcription factors. Transcription factors (TFs) can bind to DNA and activate the processes leading to the expression of genes into new proteins. Errors in this process may lead to diseases. In particular, some transcription factors have been associated with a lethal pathological state, commonly known as cancer, associated with uncontrolled cellular proliferation, invasiveness of healthy tissues and abnormal responses to stimuli. Understanding cancer-related regulatory programs is a difficult task, often involving several TFs interacting together and influencing each other's activity. This Thesis presents new computational methodologies to study gene regulation. In addition we present applications of our methods to the understanding of cancer-related regulatory programs. The understanding of transcriptional regulation is a major challenge. We address this difficult question combining computational approaches with large collections of heterogeneous experimental data. In detail, we design signal processing tools to recover transcription factors binding sites on the DNA from genome-wide surveys like chromatin immunoprecipitation assays on tiling arrays (ChIP-chip). We then use the localization about the binding of TFs to explain expression levels of regulated genes. In this way we identify a regulatory synergy between two TFs, the oncogene C-MYC and SP1. C-MYC and SP1 bind preferentially at promoters and when SP1 binds next to C-NIYC on the DNA, the nearby gene is strongly expressed. The association between the two TFs at promoters is reflected by the binding sites conservation across mammals, by the permissive underlying chromatin states 'it represents an important control mechanism involved in cellular proliferation, thereby involved in cancer. Secondly, we identify the characteristics of TF estrogen receptor alpha (hERa) target genes and we study the influence of hERa in regulating transcription. hERa, upon hormone estrogen signaling, binds to DNA to regulate transcription of its targets in concert with its co-factors. To overcome the scarce experimental data about the binding sites of other TFs that may interact with hERa, we conduct in silico analysis of the sequences underlying the ChIP sites using the collection of position weight matrices (PWMs) of hERa partners, TFs FOXA1 and SP1. We combine ChIP-chip and ChIP-paired-end-diTags (ChIP-pet) data about hERa binding on DNA with the sequence information to explain gene expression levels in a large collection of cancer tissue samples and also on studies about the response of cells to estrogen. We confirm that hERa binding sites are distributed anywhere on the genome. However, we distinguish between binding sites near promoters and binding sites along the transcripts. The first group shows weak binding of hERa and high occurrence of SP1 motifs, in particular near estrogen responsive genes. The second group shows strong binding of hERa and significant correlation between the number of binding sites along a gene and the strength of gene induction in presence of estrogen. Some binding sites of the second group also show presence of FOXA1, but the role of this TF still needs to be investigated. Different mechanisms have been proposed to explain hERa-mediated induction of gene expression. Our work supports the model of hERa activating gene expression from distal binding sites by interacting with promoter bound TFs, like SP1. hERa has been associated with survival rates of breast cancer patients, though explanatory models are still incomplete: this result is important to better understand how hERa can control gene expression. Thirdly, we address the difficult question of regulatory network inference. We tackle this problem analyzing time-series of biological measurements such as quantification of mRNA levels or protein concentrations. Our approach uses the well-established penalized linear regression models where we impose sparseness on the connectivity of the regulatory network. We extend this method enforcing the coherence of the regulatory dependencies: a TF must coherently behave as an activator, or a repressor on all its targets. This requirement is implemented as constraints on the signs of the regressed coefficients in the penalized linear regression model. Our approach is better at reconstructing meaningful biological networks than previous methods based on penalized regression. The method is tested on the DREAM2 challenge of reconstructing a five-genes/TFs regulatory network obtaining the best performance in the "undirected signed excitatory" category. Thus, these bioinformatics methods, which are reliable, interpretable and fast enough to cover large biological dataset, have enabled us to better understand gene regulation in humans.

Effects of Road Construction Intensity and Operations on Rural Freeway Work Zone Capacity, TPF-5(081), 2014

Capacity is affected by construction type and its intensity on adjacent open traffic lanes. The effect on capacity is a function of vehicles moving in and out of the closed lanes of the work zone, and the presence of heavy construction vehicles. Construction activity and its intensity, however, are not commonly considered in estimating capacity of a highway lane. The main purpose of this project was to attempt to quantify the effects of construction type and intensity (e.g. maintenance, rehabilitation, reconstruction, and milling) on work zone capacity. The objective of this project is to quantify the effects of construction type and its intensity on work zone capacity and to develop guidelines for MoDOT to estimate the specific operation type and intensity that will improve the traffic flow by reducing the traffic flow and queue length commonly associated with work zones. Despite the effort put into field data collection, the data collected did not show a full speed-flow chart therefore extracting a reliable capacity value was difficult. A statistical comparison between the capacity values found in this study using either methodologies indicates that there is an effect of construction activity on the values work zone capacity. It was found that the heavy construction activity reduces the capacity. It is very beneficial to conduct similar studies on the capacity of work zone with different lane closure barriers, which is also directly related to the type of work zone being short-term or long-term work zones. Also, the effect of different geometric and environmental characteristics of the roadway should be considered in future studies.

Life cycle analysis and life cyle impact assessment methodologies: a state of the art

Life cycle analysis (LCA) is a comprehensive method for assessing the environmental impact of a product or an activity over its entire life cycle. The purpose of conducting LCA studies varies from one application to another. Different applications use LCA for different purposes. In general, the main aim of using LCA is to reduce the environmental impact of products through guiding the decision making process towards more sustainable solutions. The most critical phase in an LCA study is the Life Cycle Impact Assessment (LCIA) where the life cycle inventory (LCI) results of the considered substances related to the study of a certain system are transformed into understandable impact categories that represent the impact on the environment. In this research work, a general structure clarifying the steps that shall be followed ir order to conduct an LCA study effectively is presented. These steps are based on the ISO 14040 standard framework. In addition, a survey is done on the most widely used LCIA methodologies. Recommendations about possible developments and suggetions for further research work regarding the use of LCA and LCIA methodologies are discussed as well.

Chaos in human behavior: the case of work motivation

This study considers the complex dynamics of work motivation. Forty-eight employees completed a work-motivation diary several times per day over a period of four weeks. The obtained time series were analysed using different methodologies derived from chaos theory (i.e. recurrence plots, Lyapunov exponents, correlation dimension and surrogate data). Results showed chaotic dynamics in 75% of cases. The findings confirm the universality of chaotic behavior within human behavior, challenge some of the underlying assumptions on which work motivation theories are based, and suggest that chaos theory may offer useful and relevant information on how this process is managed within organizations.

The reception of Eugen Wüster’s work and the development of terminology

L’objectif principal de cette thèse est d’explorer et d’analyser la réception de l’œuvre d’Eugen Wüster afin d’expliquer comment ses travaux ont influencé le développement disciplinaire de la terminologie. Du point de vue historique, les travaux de Wüster, en particulier la Théorie générale de la terminologie, ont stimulé la recherche en terminologie. Malgré des opinions divergentes, on s’entend pour reconnaître que les travaux de Wüster constituent la pierre angulaire de la terminologie moderne. Notre recherche vise spécifiquement à explorer la réception de l’œuvre wüsterienne en étudiant les écrits relatifs à cette œuvre dans la littérature universitaire en anglais, en espagnol et en français entre 1979 et 2009, en Europe et en Amérique. Réalisée dans le cadre du débat sur la réception de l’œuvre de Wüster, cette étude se concentre exclusivement sur l’analyse des critiques et des commentaires de son œuvre. Pour ce faire, nous avons tenu compte de la production intellectuelle de Wüster, de sa réception positive ou négative, des nouvelles approches théoriques en terminologie ainsi que des études portant sur l’état de la question en terminologie entre 1979 et 2009. Au moyen d’une recherche qualitative de type exploratoire, nous avons analysé un corpus de textes dans lesquels les auteurs : a. ont cité textuellement au moins un extrait d’un texte écrit par Wüster ; b. ont référé aux travaux de Wüster dans la bibliographie de l’article ; ou c. ont fait un commentaire sur ces travaux. De cette manière, nous avons cerné les grandes lignes du débat autour de la réception de son œuvre. Les résultats de notre étude sont éloquents. Ils offrent une idée claire de la réception des travaux de Wüster dans la communauté scientifique. Premièrement, Wüster représente une figure centrale de la terminologie moderne en ce qui concerne la normalisation terminologique. Il fut le premier à proposer une théorie de la terminologie. Deuxièmement, la contextualisation appropriée de son œuvre constitue un point de départ essentiel pour une appréciation éclairée et juste de sa contribution à l’évolution de la discipline. Troisièmement, les résultats de notre recherche dévoilent comment les nouvelles approches théoriques de la terminologie se sont adaptées aux progrès scientifiques et techniques. Quatrièmement, une étude menée sur 166 articles publiés dans des revues savantes confirme que l’œuvre de Wüster a provoqué des réactions variées tant en Europe qu’en Amérique et que sa réception est plutôt positive. Les résultats de notre étude font état d’une tendance qu’ont les auteurs de critiquer les travaux de Wüster avec lesquels, dans la plupart des cas, ils ne semblent cependant pas être bien familiarisés. La « méthodologie des programmes de recherche scientifique », proposée par Lakatos (1978) et appliquée comme un modèle interprétatif, nous a permis de démontrer que Wüster a joué un rôle décisif dans le développement de la terminologie comme discipline et que la terminologie peut être perçue comme un programme de recherche scientifique. La conclusion principale de notre thèse est que la terminologie a vécu des changements considérables et progressifs qui l’ont aidée à devenir, en termes lakatosiens, une discipline forte tant au plan théorique que descriptif.

Vignettes and self-reported work disability in the United States: Correction of report heterogeneity

Subjective measures of health tend to suffer from bias given by reporting heterogeneity. however, some methodologies are used to correct the bias in order to compare self-assessed health for respondents with different sociodemographic characteristics. One of the methods to correct this is the hierarchical ordered probit (hopit), which includes rates of vignettes -hypothetical individuals with a fixed health state- and where two assumptions have to be fulfilled, vignette equivalence and response consistency. this methodology is used for the self-reported work disability for a sample of the united states for 2011. The results show that even though sociodemographic variables influence rating scales, adjusting for this does not change their effect on work disability, which is only influenced by income. the inclusion of variables related with ethnicity or place of birth does not influence the true work disability. however, when only one of them is excluded, it becomes significant and affects the true level of work disability as well as income.

Analytical methodologies based on X-Ray Fluorescence Spectrometry (XRF) and Inductively Couple Plasma Spectroscopy (ICP) for the assessment of metal dispersal around mining environments

La investigació que es presenta en aquesta tesi es centra en l'aplicació i millora de metodologies analítiques existents i el desenvolupament de nous procediments que poden ser utilitzats per a l'estudi dels efectes ambientals de la dispersió dels metalls entorn a les zones mineres abandonades. En primer lloc, es van aplicar diferents procediments d'extracció simple i seqüencial per a estudiar la mobilitat, perillositat i bio-disponibilitat dels metalls continguts en residus miners de característiques diferents. Per altra banda, per a estudiar les fonts potencials de Pb en la vegetació de les zones mineres d'estudi, una metodologia basada en la utilització de les relacions isotòpiques de Pb determinades mitjançant ICP-MS va ser avaluada. Finalment, tenint en compte l'elevat nombre de mostres analitzades per a avaluar l'impacte de les activitats mineres, es va considerar apropiat el desenvolupament de mètodes analítics d'elevada productivitat. En aquest sentit la implementació d'estratègies quantitatives així com l'aplicació de les millores instrumentals en els equips de XRF han estat avaluades per a aconseguir resultats analítics fiables en l'anàlisi de plantes. A més, alguns paràmetres de qualitat com la precisió, l'exactitud i els límits de detecció han estat curosament determinats en les diverses configuracions de espectròmetres de XRF utilitzats en el decurs d'aquest treball (EDXRF, WDXRF i EDPXRF) per a establir la capacitat de la tècnica de XRF com a tècnica alternativa a les clàssiques comunament aplicades en la determinació d'elements en mostres vegetals.

Swarm pattern transformation methodologies

The work reported in this paper is motivated by the need for developing swarm pattern transformation methodologies. Two methods, namely a macroscopic method and a mathematical method are investigated for pattern transformation. The first method is based on macroscopic parameters while the second method is based on both microscopic and macroscopic parameters. A formal definition to pattern transformation considering four special cases of transformation is presented. Simulations on a physics simulation engine are used to confirm the feasibility of the proposed transformation methods. A brief comparison between the two methods is also presented.

A critical review of methodologies for measuring rental depreciation applied to UK commercial real estate

Real estate depreciation continues to be a critical issue for investors and the appraisal profession in the UK in the 1990s. Depreciation-sensitive cash flow models have been developed, but there is a real need to develop further empirical methodologies to determine rental depreciation rates for input into these models. Although building quality has been found to be an important explanatory variable in depreciation it is very difficult to incorporate it into such models or to analyse it retrospectively. It is essential to examine previous depreciation research from real estate and economics in the USA and UK to understand the issues in constructing a valid and pragmatic way of calculating rental depreciation. Distinguishing between 'depreciation' and 'obsolescence' is important, and the pattern of depreciation in any study can be influenced by such factors as the type (longitudinal or crosssectional) and timing of the study, and the market state. Longitudinal studies can analyse change more directly than cross-sectional studies. Any methodology for calculating rental depreciation rate should be formulated in the context of such issues as 'censored sample bias', 'lemons' and 'filtering', which have been highlighted in key US literature from the field of economic depreciation. Property depreciation studies in the UK have tended to overlook this literature, however. Although data limitations and constraints reduce the ability of empirical property depreciation work in the UK to consider these issues fully, 'averaging' techniques and ordinary least squares (OLS) regression can both provide a consistent way of calculating rental depreciation rates within a 'cohort' framework.

'The debatable territory where geology and archaeology meet': reassessing the early archaeobotanical work of Clement Reid and Arthur Lyell at Roman Silchester

The first large-scale archaeobotanical study in Britain, conducted from 1899 to 1909 by Clement Reid and Arthur Lyell at Silchester, provided the first evidence for the introduction of Roman plant foods to Britain, yet the findings have thus far remained unverified. This paper presents a reassessment of these archaeobotanical remains, now stored as part of the Silchester Collection in Reading Museum. The documentary evidence for the Silchester study is summarised, before the results are presented for over a 1000 plant remains including an assessment of preservation, identification and modern contamination. The dataset includes both evidence for the presence of nationally rare plant foods, such as medlar, and several archaeophytes. The methodologies and original interpretations of Reid and Lyell’s study are reassessed in light of current archaeobotanical knowledge. Spatial and contextual patterns in the distribution of plant foods and ornamental taxa are also explored. Finally, the legacy of the study for the development of archaeobotany in the 20th century is evaluated.

The Compromised Researcher : Issues in Feminist Research Methodologies

This article centres on issues of vulnerability and being compromised in feminist research where the focus has frequently been on researching the same. Compromise, here used in its pejorative sense, may for instance occur in terms of one’s research topic, the methods one utilizes, or the participants chosen for a study. Drawing on a range of examples including the methodological work of Ann Oakley (1981, 2000) as well as three articles on researching men that appeared in the journal Signs in 2005, I argue that feminist researchers, possibly because they work in an identity-based discipline, may be diversely vulnerable when researching the same and/or researching the different, and can be compromised both by how they are treated by those whom they encounter in their research and by their own behaviour in that context. I suggest that these concerns are under-articulated in feminist research and conclude with a series of questions that need to be raised.