Dissertations / Theses on the topic 'Discovery and exploration – historiography'

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1990.
Includes bibliographical references (leaves 159-161).
by Kenneth William Haase Jr.
Ph.D.

Entre 1766 et 1769, sur l'Étoile et la Boudeuse, plus de trois cents hommes – et une femme déguisée en homme – ont fait le tour du monde. Il s'agissait d'un des premiers "voyage de découverte", et six marins ont tenu des journaux de bord. Cette thèse propose d'étudier ces journaux, d'analyser les procédés discursifs mis en œuvre dans les descriptions et récits des interactions avec les gens que les marins ont rencontrés lors des escales, là où il s'agissait des 'premiers contacts'. J'étudie d'abord les récits des escales dans le détroit de Magellan, puis, surtout, les récits de l'escale à Tahiti, où les Tahitiens et Tahitiennes ont accueilli les navigateurs d'une manière singulière: ils et elles leur offraient de la nourriture et des boisons en abondance, les invitaient dans leur maisons, et faisaient comprendre aux marins qu'on attendait d'eux qu'ils fassent l'amour avec les femmes tahitiennes... L'irruption des femmes et des corps au premier plan de la rencontre perturbe les marins, bouleverse leurs récits, et permet de mieux saisir – grâce à ce trouble, grâce à ces intrusions qui perturbent le programme scientifique – certains aspects du projet de 'découverte'. J'analyse aussi les interprétations qui ont été faite de ces récits de l'escale à Tahiti, depuis les savants du 18ème siècle jusqu'aux anthropologues du 21ème siècle
Between 1766 and 1769, on the Étoile and the Boudeuse, more than three hundred men – and one woman dressed up as a man – sailed around the world. It was one of the first « discovery voyages ». Six of the sailors held logbooks. This thesis offers a study of these logbooks, in order to analyse the discursive processes at work in the descriptions and narrations of the first contacts between the sailors and the people they had met during their stopovers. I begin with a study of the narratives of the stopovers in the Strait of Magellan, and continue with the narratives of the stopover at Tahiti. There, Tahitian men and women welcomed the sailors in a particular way : they offered them food and drink in abundance, invited them into their houses, and suggested to the sailors that they were expected to make love with Tahitian women… The irruption of women and bodies at the foreground of the encounter disrupts the navigators, disrupts their narratives and allows for a better understanding of certain aspects of the « discovering » project – thanks to this disorder, thanks to these intrusions that disrupt the scientific programm. I also analyse the interpretations of theses narratives of the stopover at Tahiti, from the savants of the 18th century until the anthropologists of the 21 century

El descobriment del bosó de Higgs és la culminació d’una recerca que ha durat 40 anys, i completa un marc teòric sota el qual gairebé totes del dades obtingudes de col·lisionadors de partícules poden ser explicades consistentment. Simultàniament, i paradoxalment, l’aparent con rmació d’una separacó d’escales entre l’electrofeble i la que suposadament estabilitza la masa del bosó de Higgs posa el relleu el problema de la jerarquia. En la recerca d’una descripció del món que simpli qui els patrons i simetries del Model Estàndard, l’exploració de l’escala dels TeVs i en particular l’estudi del bosó de Higgs tindran un paper central. En aquesta tesi presentem les possibilitats que el LHC i futurs col·lisionadors proveiran, amb énfasi en la determinació de l’auto-acoblament del bosó de Higgs. També considerarem l’estudi de la producció de bosons electrofebles com a eina per entendre les interaccions dels bosons de Golstone que formen part del doblet de Higgs, mostrant la seva rellevància al combinar-ho amb les dades del pol de la Z i altres cerques al LHC. Finalment, ens centrem en com el moment dipolar elèctric de l’electró posa fortes restriccions en models on el bosó de Higgs és descrit com un estat compost.
The discovery of the Higgs boson culminates a 40-year long hunt and completes a theoretical framework under which almost all collider data can be consistently explained. At the same time, paradoxically, the con rmation of an apparent mass gap above the electroweak scale exacerbates the problem of the electroweak hierarchy. In the search of a description of the world that simpli es the patterns and symmetries of the Standard Model, the exploration of the TeV scale and in particular the study of the Higgs boson will play a central role. In this thesis we explore the possibilities that the LHC and future colliders will bring, with particular emphasis on the determination of the Higgs self-coupling. We also consider the pair production of electroweak bosons as a probe of the Goldstone interactions in the Higgs doublet, and show its relevance as a way to improve the Z pole measurements and its interplay with other LHC searches. Finally, we focus on how the electron’s electric dipole moment can set strong constraints on models where the Higgs arises as a composite state.

@Aborde trois problématiques dans le contexte de la base de données temporelles. Ils sont le problème de regroupement, la similarité et l'extraction des stratégies. Il reste encore des problèmes pour les travaux futurs. Par exemple, comment réaliser le regroupement graduel pour d'autres algorithmes. Il sera intéressant de grouper des séquences en se basant sur notre nouveau modèle. Mais les questions posées sont le choix d'un algorithme, ou il faut un nouvel algorithme carrément ? Pour construire une stratégie, ce sera aussi possible de pré-définir nos actions. Puis trouver les relations entre les actions et les indicateurs correspondants afin de générer des stratégies. . .

Exploration has been a common literary topic throughout the history of humans. However, much of this historical tradition bas possessed a fairly narrow Ill focus, emphasizing the drama and heroics of an individual explorer or concentrating on a description of a particular exploration. There has been little attempt at understanding the process of exploration and placing this important process in context with the historic and geographic phenomena that both affect and are affected by it. In this thesis, the author has broken the process of exploration down into a theoretical structure that is presented in a holistic model. This model has then been applied to the history of 15th century Portuguese exploration to test its applicability and usefulness.

An agent is placed in an unknown environment and charged with the task of locating a lost object. What can the agent use as an efficient technique to find the object?
We propose a new algorithm for planar search. The algorithm stems from theoretical work on search games, in particular provably optimal search techniques on restricted domains. This thesis addresses the problem of efficiency in robotic search: having a mobile robot find a target object in an unknown environment with obstacles in an efficient manner. As a side-effect, the robot explores the environment.
Based on previous results, a formal description of the problem is presented along with an algorithm to solve it. This algorithm has good worst-case performance, in terms of its competitive ratio. We show experimental data validating the feasibility of our approach and typical results. Quantitative results are demonstrated showing the advantage of modified spiral search versus traditional approaches.

This dissertation focuses on two key issues in text mining, namely unsupervised learning and knowledge acquisition. In spite of their relative maturity, both issues still present some major challenges that need to be addressed. First, for unsupervised learning, a well-known, unresolved challenge is to perform clustering with minimal input parameters. One natural way to reach this is to involve validity indices in the clustering process. Although of great interest, validity indices were not extensively explored in the literature, especially when dealing with high-dimensional data like text. Hence, we make three main contributions: (1) an experimental study comparing extensively 8 validity indices; (2) a context-aware method enhancing validity indices usage as stopping criteria; (3) I-CBC, an Incremental version of the CBC (Clustering By Committee) algorithm. Contributions were validated in two real-world applications: document and word clustering. Second, for knowledge acquisition, we face major issues related to ontology learning from text: low recall of the pattern-based approach, low precision of the distributional approach, context-dependency, and ontology evolution. Thus, we propose a new framework for taxonomy learning from text. The proposal is a hybrid approach which has the following advantages over the other approaches: (1) ability to capture more “flexibly” relations in text; (2) concepts better reflecting the context of the target corpus; (3) more reliable decisions during the learning process; (4) and finally evolution of the learned taxonomy without any manual effort, after its incorporation in a core of an information retrieval system
Cette thèse se focalise sur deux problématiques clés liées à la fouille de texte, à savoir : la classification et l'acquisition des connaissances. En dépit de leur relative maturité, ces deux problématiques présentent encore certains défis majeurs qui doivent être soulevés. En premier lieu, pour la classification, un défi bien connu et non résolu consiste à effectuer des classifications avec un minimum de paramètres en entrée. Une façon naturelle de parvenir à cette fin, est d'utiliser les indices de validité dans le processus de classification. Bien qu'ils soient d'un grand intérêt, les indices de validité n'ont pas été largement explorés dans la littérature, en particulier lorsqu'il s'agit de données de grande dimension, comme c'est le cas des données textuelles. Ainsi, concernant ce volet, nous proposons trois principales contributions : (1) une large étude expérimentale comparant huit indices de validité, (2) une méthode basée sur le contexte améliorant l'utilisation des indices de validité en tant que critère d'arrêt, (3) I-CBC, une version incrémentale de l'algorithme flou CBC (classification par comités). Ces contributions ont été validées sur deux applications du monde réel : la classification de documents et de mots. En deuxième lieu, pour l’acquisition des connaissances, nous nous sommes intéressés à des problématiques importantes liées à la construction d’ontologies à partir de texte : le faible rappel des approches basées sur les patrons, la faible précision de l’approche distributionnelle, la dépendance au contexte et l’évolution des ontologies. Nous proposons ainsi, un nouveau cadre pour l’apprentissage d’ontologies à partir du texte. Notre proposition est une approche hybride qui combine les avantages suivants par rapport aux autres approches : (1) la capacité de capturer avec plus de flexibilité des relations dans le texte, (2) des concepts qui traduisent mieux le contexte du corpus considéré, (3) des décisions plus fiables prises durant le processus d’apprentissage à travers la considération et l’inclusion de plusieurs relations sémantiques, et, enfin, (4) l’évolution de l’ontologie apprise sans aucun effort manuel considérable, après son inclusion au coeurd’un système de recherche d’information

In this thesis we describe an approach to automatically invent/explore new mathematical theories, with the goal of producing results comparable to those produced by humans, as represented, for example, in the libraries of the Isabelle proof assistant. Our approach is based on ‘schemes’, which are formulae in higher-order logic. We show that it is possible to automate the instantiation process of schemes to generate conjectures and definitions. We also show how the new definitions and the lemmata discovered during the exploration of a theory can be used, not only to help with the proof obligations during the exploration, but also to reduce redundancies inherent in most theory-formation systems. We exploit associative-commutative (AC) operators using ordered rewriting to avoid AC variations of the same instantiation. We implemented our ideas in an automated tool, called IsaScheme, which employs Knuth-Bendix completion and recent automatic inductive proof tools. We have evaluated our system in a theory of natural numbers and a theory of lists.

This thesis investigates the computer-based modelling and simulation of complex geospatial phenomena. Geospatial systems are real world processes which extend over some meaningful extent of the Earth's surface, such as cities and fisheries. There are many problems that require urgent attention in this domain (for example relating to sustainability) but despite increasing amounts of data and computational power there is a significant gap between the potential for model-based analyses and their actual impact on real world policy and planning. Analytical methods are confounded by the high dimensionality and nonlinearity of spatio-temporal systems and/or are hard to relate to meaningful policy decisions. Simulation-based approaches on the other hand are more heuristic and policy oriented in nature, but they are difficult to validate and almost always over-fit the data: although a given model can be calibrated on a given set of data, it usually performs very poorly on new unseen data sets. The central contribution of this thesis is a framework which is formally grounded and able to be rigourously validated, yet at the same time is interpretable in terms of real world phenomena and thus has a strong connection to domain knowledge. The scope of the thesis spans both theory and practice, and three specific contributions range along this span. Starting at the theoretical end, the first contribution concerns the conceptual and theoretical basis of the framework, which is a technique known as delay reconstruction. The underlying theory is rooted in the rather technical field of dynamical systems (itself largely based on differential topology), which has hindered its wider application and the formation of strong links with other areas. Therefore, the first contribution is an exposition of delay reconstruction in non-technical language, with a focus on explaining how some recent extensions to this theory make the concept far more widely applicable than is often assumed. The second contribution uses this theoretical foundation to develop a practical, unified framework for pattern discovery and hypothesis exploration in geo-spatial data. The central aspect of this framework is the linking of delay reconstruction with domain knowledge. This is done via the notion that determinism is not an on-off quantity, but rather that a given data set may be ascribed a particular 'degree' of determinism, and that that degree may be increased through manipulation of the data set using domain knowledge. This leads to a framework which can handle spatiotemporally complex (including multi-scale) data sets, is sensitive to the amount of data that is available, and is naturally geared to be used interactively with qualitative feedback conveyed to the user via geometry. The framework is complementary to other techniques in that it forms a scaffold within which almost all modelling approaches - including agent-based modelling - can be cast as particular kinds of 'manipulations' of the data, and as such are easily integrated. The third contribution examines the practical efficacy of the framework in a real world case study. This involves a high resolution spatio-temporal record of fishcatch data from trawlers operating in a large fishery. The study is used to test two fundamental capabilities of the framework: (i) whether real world spatio-temporal phenomena can be identified in the degree-of-determinism signature of the data set, (ii) whether the determinism-level can then be increased by manipulating the data in response to this phenomena. One of the main outcomes of this study is a clear identification of the influence of the lunar cycle on the behaviour of Tiger and Endeavour prawns. The framework allows for this to be 'non-destructively subtracted', increasing the detect-ability of further phenomena.

This thesis investigates the computer-based modelling and simulation of complex geospatial phenomena. Geospatial systems are real world processes which extend over some meaningful extent of the Earth's surface, such as cities and fisheries. There are many problems that require urgent attention in this domain (for example relating to sustainability) but despite increasing amounts of data and computational power there is a significant gap between the potential for model-based analyses and their actual impact on real world policy and planning. Analytical methods are confounded by the high dimensionality and nonlinearity of spatio-temporal systems and/or are hard to relate to meaningful policy decisions. Simulation-based approaches on the other hand are more heuristic and policy oriented in nature, but they are difficult to validate and almost always over-fit the data: although a given model can be calibrated on a given set of data, it usually performs very poorly on new unseen data sets. The central contribution of this thesis is a framework which is formally grounded and able to be rigourously validated, yet at the same time is interpretable in terms of real world phenomena and thus has a strong connection to domain knowledge. The scope of the thesis spans both theory and practice, and three specific contributions range along this span. Starting at the theoretical end, the first contribution concerns the conceptual and theoretical basis of the framework, which is a technique known as delay reconstruction. The underlying theory is rooted in the rather technical field of dynamical systems (itself largely based on differential topology), which has hindered its wider application and the formation of strong links with other areas. Therefore, the first contribution is an exposition of delay reconstruction in non-technical language, with a focus on explaining how some recent extensions to this theory make the concept far more widely applicable than is often assumed. The second contribution uses this theoretical foundation to develop a practical, unified framework for pattern discovery and hypothesis exploration in geo-spatial data. The central aspect of this framework is the linking of delay reconstruction with domain knowledge. This is done via the notion that determinism is not an on-off quantity, but rather that a given data set may be ascribed a particular 'degree' of determinism, and that that degree may be increased through manipulation of the data set using domain knowledge. This leads to a framework which can handle spatiotemporally complex (including multi-scale) data sets, is sensitive to the amount of data that is available, and is naturally geared to be used interactively with qualitative feedback conveyed to the user via geometry. The framework is complementary to other techniques in that it forms a scaffold within which almost all modelling approaches - including agent-based modelling - can be cast as particular kinds of 'manipulations' of the data, and as such are easily integrated. The third contribution examines the practical efficacy of the framework in a real world case study. This involves a high resolution spatio-temporal record of fishcatch data from trawlers operating in a large fishery. The study is used to test two fundamental capabilities of the framework: (i) whether real world spatio-temporal phenomena can be identified in the degree-of-determinism signature of the data set, (ii) whether the determinism-level can then be increased by manipulating the data in response to this phenomena. One of the main outcomes of this study is a clear identification of the influence of the lunar cycle on the behaviour of Tiger and Endeavour prawns. The framework allows for this to be 'non-destructively subtracted', increasing the detect-ability of further phenomena.

This study is an exploration of the making of Xhosa historiography from the end of the eighteenth century to the close of the nineteenth century. Continuity and change are key features that are identifiable in the writing of Xhosa history over the period. Selected documents provide evidence on how different writers built on the works of their predecessors. At the same time, over a period of hundred years, due to changing socio-political contexts, new ideas and perceptions crept into Xhosa history. European writers, who dominated the writing of Xhosa history, were made up of colonial officials, missionaries, and travellers. Sharing a common European Christian background these writers brought along their particular understanding of history, and held assumptions about the indigenous people and their past. However such assumptions were always in a state of flux. South-east Africans were also major contributors to the making of Xhosa history. Their oral traditions were important sources from which Xhosa history was produced. The African and European encounter in the making of Xhosa history meanHhat historioracy and historiography came together in the production of Xhosa history. At the end of the eighteenth century there were a handful of European travellers who explored the interior of southern Africa and recorded their observations of indigenous communities. These observations of south-east Africans, whom they divided into three racial groups, formed the basis of later writings about the indigenous communiti~s. The beginning of the nineteenth century brought the establishment of British rule at the C,ppe. This introduced new players into the African-European drama that was being acted out on the frontier. Colonial officials set out to inform themselves about the indigenous people, and this meant writing up their history. From the 1820s missionaries were a main source of information on amaXhosa. Xhosa history produced under the missionary influence included works by African converts, among whom Noyi was the most noteworthy. As British imperialism gained ground from the middle of the nineteenth century, history was increasingly used by British officials as a tool to justify their colonial expansion. Under Governor Grey there was a deliberate production of a Xhosa history that depicted amaXhosa as having a barbaric past and in need of civilisation. Theal who consulted Dutch and British archives as well as oral tradition made a major contribution to the writing of Xhosa history. But Theal later began to select evidence to show that amaXhosa were recent immigrants into southeast Africa. During the last quarter ofthe nineteenth century a band of literate Africans, using newspapers like Isigidimi and later Imvo Zabantsundu, embarked on writing African history. This study highlights the development of certain themes in Xhosa history, themes which remained central in later years. The royal theme became pivotal and in the process displaced other histories in African communities, like clan histories. This study has also traced the roots of some historical myths. For example claims by early travellers about an empty land fed into the migration theme which sought to explain amaXhosa as recent immigrants into south-east Africa. Xhosa historiography, just like its European counterpart, marginalised ordinary people, especially women, and became primarily an account of the lives and activities of ruling men.

L'extraction de motifs intéressants a connu récemment un développement impressionnant dû à une pression accrue des propriétaires de données sous-exploitées et à la réponse des chercheurs par de nombreux résultats théoriques et pratiques. A l'origine, les données analysées provenaient du domaine de la vente et les motifs intéressants se présentaient sous forme de règles d'association. Des solutions performantes à ce problème pratique ont été élaborées (ex. APRIORI). Puis, les propriétaires d'autres types de données se sont interrogés sur l'utilité de ces premières solutions pour analyser leurs données. Malheureusement, ces données étaient différentes. Souvent, dans ces cas-là, APRIORI était inefficace voire intractable. Nous avons étudié les problèmes liés à l'extraction de motifs intéressants dans des collections de données d'origine différentes, en particulier les problèmes liés au grand nombre de motifs valides dans les données non similaires aux données de ventes. Nos méthodes extraient une collection de motifs qui peut être différente de la collection cible de motifs, en estimant qu'elle sera plus efficace à calculer dans certains types de données. De plus, cette collection, différente de la collection cible de motifs, doit permettre une régénération efficace de la collection cible. Comme la représentation intermédiaire est souvent beaucoup plus petite que la collection cible, nous la désignons sous le terme représentation condensée. Nous avons obtenu des améliorations significatives des performances. L'utilisation de représentations condensées est relativement novatrice dans le domaine. La contribution principale de cette thèse est la proposition de nouvelles représentations condensées pour des motifs élémentaires, ainsi que les algorithmes pour extraire ces représentations condensées et régénérer, à partir d'elles, les collections de motifs cibles. Nous montrons les avantages de ces représentations condensées par rapport aux méthodes existantes
Interesting pattern discovery has recently seen an impressive progress, due to an increasing pressure from owners of large data sets and to the response of scientists by numerous theoretical and practical results. The most of data sets addressed in the beginning of the surge were sales data and the interesting patterns were in form of association rules. Very efficient solutions to this practical problem were elaborated, the root of them was the so-called APRIORI algorithm. Then, the owners of other types of data wondered if these basic methods could help them. Unfortunately, their data were different. Often, these applications could not take advantage of APRIORI. The research following the elaboration of the basic solution addressed the important application areas, where the basic solution could not be used. We addressed the problems with mining frequent patterns in different applicative contexts, especially the problems related to the large number of interesting frequent patterns present in data that are not similar to the sales data. Our methods mine a collection of patterns that may be quite different from the target pattern collection, and hopefully much more efficient to be mined in some types of data. Moreover, that different pattern collection must allow a subsequent "regeneration" of the target collection in a very efficient manner. Since the intermediate representation will be often smaller than the target collection, we call it a condensed representation. We obtained a significant improvement of the performances. The use of condensed representations is relatively novel in the field. Then new major condensed representations of simple frequent patterns are proposed, the algorithms to mine them and derive the target pattern collections. We show the practical advantages of the proposed condensed representations over the past methods, and provide an abstract view of the proposed representations in the unified structure for condensed representations

Thèse doctorat : Informatique : Villeurbanne, INSA : 2002.
Thèse rédigée en anglais. En annexe, résumé étendu en français. Le titre en français "Représentations condensées d'ensembles fréquents : application à la découverte de motifs descriptifs" n'apparait pas sur la thèse. Titre provenant de l'écran-titre. Bibliogr. p. 142-150.

Recent developments spurred on by the Human Genome Project have for the first time permitted genome wide association studies leading to identification of multiple novel variants for complex diseases. This thesis consists of a series of studies exploring recent genetic findings for coronary heart disease (CHD) within the broader context of the promises of the genomic era that new findings would ultimately lead to 1) Identification of new disease mechanisms 2) Permit genotype based risk prediction and 3) Promote development of novel and targeted therapies based on genotype. We sought to address these questions, using the Emory Genebank, a collection of angiographically phenotyped subjects with stored blood samples and long-term follow up. We first refined the phenotype for CHD to help understand underlying mechanism and demonstrated differential associations between 8 novel risk variants including 9p21, and sub-phenotypes of CHD and thereby proposed differing mechanisms of risk for these loci. With two non-CHD cohorts we then demonstrated further association between one particular risk variant at 6p24 and the intermediate phenotype of arterial elasticity and related this to a potential novel mechanism of risk. Despite significant association with first events in population cohorts, we showed that these risk variants including 9p21 have limited value in secondary risk prediction, failing to demonstrate any association with prospective events in our cohort as single markers or when combined into a cumulative genetic risk score. Finally in subjects carrying leukotriene pathway CHD risk variants, we administered an oral leukotriene synthesis inhibitor and after just 4 week of therapy observed significant improvement in their endothelial function. In summary, these studies demonstrate the value of refining the phenotype to understand potential mechanisms, the complexities of genetic risk prediction and the feasibility and benefit of targeting therapy based on risk genotype.

This thesis covers a wide range of research on marine natural products with a focus on their role in drug discovery. Chapter 1 starts with a general introduction to marine natural product chemistry, describing current trends and problems. It gives an insight into the importance of the discovery of new antibiotics in this pressing time where multidrug-resistant bacteria are on the rise. Chapter 2 is a meta-analysis of current trends in marine microbial natural product research and an analysis of how much of their chemistry overlaps with the chemistry of terrestrial microbial natural products. Over the past decade, research has greatly shifted to focus on marine microbial natural products, at the expense of marine macro-organism studies. An assessment of the structural overlap between 55,817 published marine and terrestrial microbe and marine macroorganism natural products, using structural fingerprints and scaffold clustering, was enlightening. The results showed that currently 76.7% of the chemistry found in marine microbes is vastly similar to the chemistry isolated from terrestrial microbes. This overlap is mainly due to the use of terrestrial isolation and culturing methods that select for the growth of terrestrial-like bacteria instead of unique marine bacteria. As a result, the unique chemistry associated with truly marine microbe species that are in close symbiotic relationships with marine macro-organisms is being missed. Chapter 3 describes the antimicrobial assay development and screening of a large collection of Australian marine invertebrate specimens for activity against four different strains of bacteria. It resulted in 12.5% of all the specimens tested, showing activity against the drugresistant strain of Staphylococcus aureus (MRSA) but lower bioactivity rates against Pseudomonas aeruginosa (0.76%) and Escherichia coli (0.76%). This illustrates how much harder it is to find activity against Gram-negative bacteria such as P. aeruginosa and E. coli. To investigate this challenge further, drug combination screening was undertaken to assess the potential of resurrecting antibiotics, for the use against bacterial strains that have developed resistance, by combining the antibiotic with marine invertebrate extracts. The combinatorial assays were unsuccessful, thus for further investigations I concentrated on the specimens that exhibited activity in the main assay. Analysis of the sponge specimen Aaptos aaptos that showed activity against S. aureus resulted in the isolation of demethylaaptamine as the bioactive component. Small quantities of a series of peptides with molecular weights in the range of 3,000- 4,000 Da were also isolated from the sponge. Unfortunately, a detailed structure determination could not be undertaken due to COVID-19 state border restrictions, which prevented recollection of the sponge. The subsequent two chapters report on the chemistry of antimicrobial bioactive marine invertebrate extracts. Chapter 4 describes the structures of two new betaine molecules isolated from the bryozoan Amathia lamourouxi. Their structures were determined through analysis of 1D and 2D NMR and mass spectrometric data. Crude extracts of the specimen showed antimicrobial activity at 2.5 mg/mL. Although the yield of active compounds was too small to be completely isolated and identified they were associated with brominated alkaloids. Unfortunately, recollection of this species was also hindered by state border closure due to the COVID-19 pandemic. Chapter 5 describes the isolation and identification of two new amphiphilic polyamines that together with a mixture of relatives were extracted from the marine sponge Aaptos lobata. The two pure compounds and the mixture of amphiphilic compounds showed moderate bioactivity against both drug sensitive and resistant S. aureus, and P. aeruginosa. Chapter 6 describes a multiplatform investigation of the chemistry of the ascidian B. leachii. This species was targeted because it had a similar chemical profile to Aaptos aaptos, small alkaloid and large (>3500 Da) peptide and was more accessible after the COVID-19 state border closures. The investigation used different analytical tools like LC-MS and advanced NMR techniques, including DOSY to characterise the diversity of compounds found in the mixture, while MALDITOF imaging was used to identify the specific locations of these metabolites within the ascidian tissue. This study demonstrated the power of MALDI imaging to provide an insight into the chemical ecology of marine species and helped to establish relationships between marine invertebrates and their associated microorganisms. This finding will aid future specific targeting of tissue regions within marine invertebrates for symbiotic microbe isolation and identification of natural products. Finally, Chapter 7 combines and discusses all the findings of this thesis and examines the future of marine drug discovery. The research reported here has explored the chemical diversity of microbial natural products, discovered new compounds, some with antimicrobial activity, and investigated the chemistry of marine invertebrates and their interesting symbiotic relationship with microorganisms.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environment and Sc
Science, Environment, Engineering and Technology
Full Text

Despite many medical advances, antibiotic resistant bacteria increasingly plague the modern world, necessitating discovery of new antibiotics. One area of nature that can provide inspiration for antibiotics is antimicrobial peptides. Many of these peptides exist in nature, with some classes that have not been studied or characterized well. One such class is the defensin-like peptides generated by the plant Medicago truncatula as part of their symbiotic relationship with Sinorhizobium meliloti. Nodule-specific Cysteine Rich (NCR) peptides are defined by the presence of multiple cysteines, and regulate the growth of S. meliloti within plant cells. While some of these NCR peptides have been shown to have antimicrobial properties, hundreds of peptides remain uncharacterized. We have developed an assay for further characterization of these peptides in E. coli. Of the seven peptides that have been tested using this assay, three have exhibited definitive antimicrobial properties against both E. coli and S. meliloti. Additionally, we have developed a system for discovering novel antimicrobial peptides. This platform, called PepSeq, uses the expression of random peptides in E. coli combined with deep sequencing to detect antimicrobial activity. This technology is capable of screening through millions of peptide molecules simultaneously. Using this platform, we have discovered and confirmed six novel antimicrobial peptides, with hundreds of additional predicted antimicrobial peptides. In addition to the peptides we have analyzed using PepSeq, additional peptide scaffolds could be used to discover more potent antimicrobial peptides.

This dissertation comprises an introduction, seven previously published papers dealing with aspects of psychodrama and the person-centred approach, criticisms of the person-centred approach, an assessment of my contribution to person-centred theory and practice and an 'afterword' which brings my exploration up to date. Although each of the papers draws on my practical experience as a therapist, researcher and educator, two of them are accounts of research, the others are broadly 'conceptual'. They are presented in the context of an heuristic journey which demonstrates my development as a person-centred thinker and practitioner. The introduction establishes this over-arching heuristic framework and gives my rationale for including these papers. The papers are followed by a consideration of the criticisms of the person-centred approach in which I show (with reference to the literature) how, if I can, I answer these criticisms. In the penultimate chapter I examine my papers in the light of some of the 'critical issues' with respect to the person-centred approach.

La conception des produits implique de grandes quantités de décisions (MQD). Le soutien pertinent et efficace des connaissances est important pour les décisions. La plupart des travaux ont été réalisées sur les connaissances de conception comme support à la conception. Cependant la connaissance de fabrication sur la qualité des produits est également une caractéristique qui n'est pas jugé suffisant. Entre-temps, de grands volumes de données de fabrication sont générés et enregistrés. Des connaissances nécessaires à la production sont implicites dans ces données. Les travaux présentés dans cette thèse se concentre sur l'extraction de connaissances de fabrication de qualité dans ces données en utilisant des méthodes d'exploration de données et de retour d’expérience utiles pour les concepteurs de produits (une ontologie regroupant les éléments importants à la prise de décision a été définie). Des techniques de Data Mining sont ensuite exploitées afin de répondre aux problèmes de qualité de la connaissance en production. Un prototype support à la prise de décision en conception de produits a été défini. Il considère les critères de qualité dans l’extraction et la recherche des connaissances
This work studies knowledge extraction in manufacturing quality data (MQD) for support-ing design decisions. Firstly, an ontological approach for analyzing design decisions and identifying designer’s needs for manufacturing quality knowledge is proposed. The decisions are analyzed ranging from task clarification, conceptual design, embodiment design to detail design. A decision model is proposed in which decisions and its knowledge elements are illustrated. An ontology is constructed to represent the decisions and their knowledge needs. Secondly, MQD preparation for further knowledge discovery is described. The nature of data in manufacturing is described. A GT (group technology) and QBOM (Quality Bill of Material)-based method is proposed to classify and organize MQD. As an important factor, the data quality (DQ) issues related with MQD is also analyzed for data mining (DM) application. A QFD (quality function deployment) based approach is proposed for translating data consumers’ DQ needs into specific DQ dimensions and initiatives. Thirdly, a DM-based manufacturing quality knowledge discovery method is proposed and validated through two popular DM functions and related algorithms. The two DM functions are illustrated through real world data sets from two different production lines. Fourthly, a MQD-based design support proto-type is developed. The prototype includes three major functions such as data input, knowledge extraction and input, knowledge search

Les graphes de connaissances (KG) sont des structures de graphes hétérogènes représentant des faits dans un format lisible par une machine. Ils trouvent des applications dans des tâches telles que la réponse automatique aux questions, la désambiguïsation et liaison d'entités. Cependant, les graphes de connaissances sont intrinsèquement incomplets et il est essentiel de les raffiner pour améliorer leur qualité. Pour compléter le graphe de connaissances, il est possible de prédire les liens manquants dans un graphe de connaissances ou d'intégrer des sources externes. En extrayant des règles du graphe de connaissances, nous pouvons les exploiter pour compléter le graphe tout en fournissant des explications. Plusieurs approches ont été proposées pour extraire efficacement des règles. Or, la littérature manque de méthodes efficaces pour incorporer des prédicats numériques dans les règles. Pour répondre à cette lacune, nous proposons REGNUM, qui permet d'extraire des règles numériques avec des contraintes d'intervalle. REGNUM s'appuie sur les règles générées par un système d'extraction de règles existant et les enrichit en incorporant des prédicats numériques guidés par des mesures de qualité. En outre, la nature interconnectée des données web offre un potentiel significatif pour compléter et raffiner les KG, par exemple, par le liage des données, qui consiste à trouver des liens d'identité entre des entités de KG différents. Nous présentons RE-miner, une approche qui extrait des expressions référentielles (RE) pour une classe dans un graphe de connaissances.Les REs sont des règles qui ne s'appliquent qu'à une seule entité. Elles facilitent la découverte de connaissances et permettent de lier les données de manière explicable. De plus, nous visons à explorer les avantages et les opportunités de l'affinage des modèles linguistiques pour combler le fossé entre les KG et les données textuelles. Nous présentons GilBERT, qui exploite le fine-tuning sur des modèles linguistiques tels que BERT en optimisant une fonction de coût par triplet pour les tâches de prédiction de relation et de classification de triple. En prenant en compte ces défis et en proposant des approches novatrices, cette thèse contribue au raffinement des KG, en mettant particulièrement l'accent sur l'explicabilité et la découverte de connaissances. Les résultats de cette recherche ouvrent la voie à de nouvelles questions de recherche qui font progresser vers des KG de meilleure qualité
Knowledge graphs (KGs) are heterogeneous graph structures representing facts in a machine-readable format. They find applications in tasks such as question answering, disambiguation, and entity linking. However, KGs are inherently incomplete, and refining them is crucial to improve their effectiveness in downstream tasks. It's possible to complete the KGs by predicting missing links within a knowledge graph or integrating external sources and KGs. By extracting rules from the KG, we can leverage them to complete the graph while providing explainability. Various approaches have been proposed to mine rules efficiently. Yet, the literature lacks effective methods for effectively incorporating numerical predicates in rules. To address this gap, we propose REGNUM, which mines numerical rules with interval constraints. REGNUM builds upon the rules generated by an existing rule mining system and enriches them by incorporating numerical predicates guided by quality measures. Additionally, the interconnected nature of web data offers significant potential for completing and refining KGs, for instance, by data linking, which is the task of finding sameAs links between entities of different KGs. We introduce RE-miner, an approach that mines referring expressions (REs) for a class in a knowledge graph and uses them for data linking. REs are rules that are only applied to one entity. They support knowledge discovery and serve as an explainable way to link data. We employ pruning strategies to explore the search space efficiently, and we define characteristics to generate REs that are more relevant for data linking. Furthermore, we aim to explore the advantages and opportunities of fine-tuning language models to bridge the gap between KGs and textual data. We propose GilBERT, which leverages fine-tuning techniques on language models like BERT using a triplet loss. GilBERT demonstrates promising results for refinement tasks of relation prediction and triple classification tasks. By considering these challenges and proposing novel approaches, this thesis contributes to KG refinement, particularly emphasizing explainability and knowledge discovery. The outcomes of this research open doors to more research questions and pave the way for advancing towards more accurate and comprehensive KGs

Thesis advisor: David Northrup
Henry Beaufoy MP (1750-1795) was one of the primary founders and first secretary of the Association for Promoting the Discovery of the Interior Parts of Africa. The Association sponsored several expeditions to the Western Sudan and North Africa during the late 1780's and 1790's including the famous Mungo Park expedition of 1795-97. Beaufoy, as a Member of Parliament, was a key figure in the nonconformist movement as well as an ardent supporter of abolition. His work in recruiting and directing the Association's explorers helped set the stage for nineteenth century British involvement in Africa. The history of the Association's early expeditions and Beaufoy's mix of humanitarian and commercial motivations in founding the Association provide revealing witness to the nature of British interest in Africa at the end of the eighteenth century
Thesis (BA) — Boston College, 2004
Submitted to: Boston College. College of Arts and Sciences
Discipline: History
Discipline: College Honors Program

Plasmodium vivax is the most geographically widespread human malaria parasite. Research on this parasite needs to be expanded in order to develop adequate tools for its control such as a highly effective vaccine. One particular feature of P. vivax is its preference to invade immature red blood cells, also known as reticulocytes. Interestingly, ultrastructural studies performed on reticulocytes enabled the discovery of exosomes, extracellular vesicles (EVs) of endocytic origin. These vesicles were initially seen as a selective cargo-disposal pathway, but later works showed the involvement of exosomes, and other extracellular vesicles, in a variety of biological processes. Importantly, exosomes derived from reticulocytes infected with P. yoelii, a murine reticulocyte-prone parasite that resembles P. vivax, contained parasite proteins. When used in CpG-adjuvanted immunizations, exosomes were able to elicit long-lasting protective responses. This thesis hypothesizes that exosomes derived from P. vivax-infected reticulocytes contain parasite antigens and stimulate immune responses. We evaluated the potential of circulating extracellular vesicles from P. vivax infections as a source of antigens and as activators of T-cell responses, and explored human reticulocyte-derived exosomes as a vaccine platform against P. vivax malaria. We isolated EVs from plasma of P. vivax-infected patients and determined their protein composition by mass spectrometry-based proteomics in order to unveil their potential use in antigen discovery. We found parasite proteins associated to these vesicles that could serve as antigens. Indeed, two of the identified vivax proteins present promising cytotoxic T-cell epitopes as evidenced by in silico analysis. Moreover, we detected HLA class I molecules and observed an altered protein cargo in vesicles from vivax patients compared to healthy donors, thus suggesting that circulating EVs might affect the course of P. vivax infection. Next, we evaluated the in vitro interaction of these vesicles with leukocyte populations from the human spleen, given the importance of this organ in the induction of adaptative immune responses. Remarkably, we observed a significant interaction of monocytes, B-cells and T-cells with vesicles from patients compared to healthy individuals. We studied the capacity of these vesicles to activate T-cells, and preliminary results indicate that circulating vesicles from infections might stimulate CD8+ T-cell responses. Recent studies highlighted the role of cytotoxic CD8+ T-cell responses against P. vivax blood-stage parasites. In parallel, we studied the proteomic composition of exosomes derived from human reticulocytes and analyzed their ability to interact with antigen-presenting cells. We identified over 300 proteins in these vesicles, including HLA class I molecules, and found that these exosomes could be taken up by antigen-presenting cells, thus suggesting their contribution to the presentation of antigens. Collectively, our results indicate that EVs from vivax infections can be used in antigen discovery and might contribute to cell-mediated immune responses that could be critical for vivax control. In particular, reticulocyte-derived exosomes represent a potential vaccine platform to be furtherly explored. We believe this work has provided novel insights for vaccine development against P. vivax malaria.
Plasmodium vivax es el parásito que causa malaria humana más extendido geográficamente. Se ha de ampliar la investigación sobre este parásito para desarrollar herramientas adecuadas para su control, entre ellas, una vacuna altamente efectiva. Una característica particular de P. vivax es su preferencia por invadir glóbulos rojos inmaduros, también conocidos como reticulocitos. Curiosamente, estudios ultraestructurales realizados en reticulocitos permitieron el descubrimiento de exosomas, vesículas extracelulares (VEs) de origen endocítico. Los exosomas y otras vesículas extracelulares, fueron vistos inicialmente como una vía selectiva de eliminación de proteínas obsoletas, pero en la actualidad, se sabe que participan en una gran variedad de procesos biológicos. Los exosomas derivados de reticulocitos infectados con P. yoelii, un parásito propenso a invadir reticulocitos murinos que se asemeja a P. vivax, contienen proteínas parasitarias. Cuando estos exosomas se usan en inmunizaciones con adyuvante de CpG son capaces de provocar respuestas protectoras duraderas. Esta tesis plantea la hipótesis de que los exosomas derivados de reticulocitos infectados con P. vivax contienen antígenos del parásito y pueden estimular respuestas inmunes. Evaluamos el potencial de las VEs circulantes en infecciones de P. vivax como fuente de antígenos y como activadoras de respuestas de células T. Además, exploramos los exosomas derivados de reticulocitos humanos como una plataforma de vacunación contra la malaria vivax. Aislamos VEs del plasma de pacientes infectados con P. vivax y determinamos su composición proteica mediante proteómica basada en espectrometría de masas para investigar su potencial uso en el descubrimiento de antígenos. Encontramos proteínas del parásito asociadas a estas vesículas, las cuales podrían actuar como antígenos. De hecho, el análisis in silico de dos de estas proteínas reveló prometedores epítopos citotóxicos de células T. Además, detectamos moléculas HLA clase I y observamos un alterado contenido de proteínas en las vesículas de pacientes con vivax en comparación con donantes sanos, lo que sugiere que los VEs circulantes podrían afectar el curso de la infección por P. vivax. A continuación, evaluamos la interacción in vitro de estas vesículas con poblaciones leucocitarias del bazo humano, dada la importancia de este órgano en la inducción de respuestas inmunes adaptativas. Observamos una interacción significativamente elevada de monocitos, células B y células T con vesículas de pacientes en comparación con VEs de individuos sanos. Estudiamos la capacidad de estas vesículas para activar las células T, y los resultados preliminares indican que las vesículas circulantes de infecciones de vivax podrían estimular las respuestas de las células T CD8+. Recientes estudios han destacado el posible papel de las respuestas citotóxicas de las células T contra los parásitos de la etapa sanguínea de P. vivax. Paralelamente, analizamos la composición proteómica de los exosomas derivados de reticulocitos humanos y determinamos su capacidad para interactuar con células presentadoras de antígenos. Identificamos más de 300 proteínas en estas vesículas, incluidas las moléculas HLA de clase I, y descubrimos que estos exosomas podían ser internalizados por células presentadoras de antígenos, lo que sugiere su contribución a la presentación antigénica. En conjunto, nuestros resultados indican que las VEs de las infecciones por vivax pueden usarse en el descubrimiento de antígenos y pueden contribuir a respuestas inmunes mediadas por células que podrían ser críticas para el control de vivax. En particular, los exosomas derivados de reticulocitos representan una potencial plataforma de vacuna. Creemos que este trabajo ha proporcionado nuevas ideas para el desarrollo de vacunas contra la malaria por P. vivax.

This thesis is an ethical and empirical exploration of the late discovery of genetic origins in two contexts, adoption and sperm donor-assisted conception. This exploration has two interlinked strands of concern. The first is the identification of ‘late discovery’ as a significant issue of concern, deserving of recognition and acknowledgment. The second concerns the ethical implications of late discovery experiences for the welfare of the child. The apparently simple act of recognition of a phenomenon is a precondition to any analysis and critique of it. This is especially important when the phenomenon arises out of social practices that arouse significant debate in ethical and legal contexts. As the new reproductive technologies and some adoption practices remain highly contested, an ethical exploration of this long neglected experience has the potential to offer new insights and perspectives in a range of contexts. It provides an opportunity to revisit developmental debate on the relative merit or otherwise of biological versus social influences, from the perspective of those who have lived this dichotomy in practise. Their experiences are the human face of the effects arising from decisions taken by others to intentionally separate their biological and social worlds, an action which has then been compounded by family and institutional secrecy from birth. This has been accompanied by a failure to ensure that normative standards and values are upheld for them. Following discovery, these factors can be exacerbated by a lack of recognition and acknowledgement of their concerns by family, friends, community and institutions. Late discovery experiences offer valuable insights to inform discussions on the ethical meanings of child welfare, best interests, parental responsibility, duty of care and child identity rights in this and other contexts. They can strengthen understandings of what factors are necessary for a child to be able to live a reasonably happy or worthwhile life.

This dissertation demonstrates an experiment in an alternative design methodology, beginning with structural and material exploration rather than conventional design processes where detailing plays less of a role in the design process. The dissertation project is driven by informants discovered through technical research in timber construction through tactile experimentation and the 'act of making'. Timber remains the material of choice for the length of the dissertation. Timber's particular inherent properties, capabilities and hindrances therefore form the parameters for creative design potential. The dissertation thus aims to demonstrate the importance of understanding materials and tests whether an alternative design process can lead to a more tectonically expressive form. The dissertation focuses on the use of standardised building components to demonstrate the way in which a timber compilation of standard components can be used to create an extremely varied building form. Additionally, it emphasises the use of localised technologies in order to show that craft still has a place within the context of contemporary South Africa where high unemployment rates and unskilled labour is experienced. The dissertation further demonstrates the way in which a designed structural timber system, designed purely through informants learnt through the 'act of making', can be applied in a contextualised setting with an appropriate site and programme in accordance with the structure's spatial potential. The final design aims to form perceptual structure through its tectonic expression in perceiving it as meaningful. Ultimately, the project strives towards depicting an architectural tectonic story where the building is contextualised, Hout Bay, South Africa, and seeks to express a narrative in which one can construe one's own tale as to the mystery of its making.

Microalgae are photosynthetic organisms considered to be one of the most promising high-value chemicals and biofuel-producing organisms. However, there are several challenges for the widespread implementation of industrial processes using microalgae. The work presented in this dissertation proposes solutions to the different challenges involving the use of microalgae as microbial cell factories. To investigate the application of anaerobic digestion as a way to generate nutrients for microbial growth, salmon offal was used as substrate for anaerobic digestion, and soil from a flooded run-off pond on the Virginia Tech campus in Blacksburg, VA. A fast reduction in volatile solids and the short-chain fatty acid production profile is favorable for the growth of microalgae. A novel algae strain Scenedesmus sp. A6 was isolated from a decorative waterfountain in a hotel in Madison, IN. Mixotrophic growth trials were conducted using wastewater from the salmon offal digestion, that demostrated the A6 isolate grows six times faster in the wastewater then autotrophically. Bioassays of ethanolic cell extracts of A6 cultures demonstrated antimicrobial activity against E. coli cells at concentrations above 50 µg/ml. Genome sequencing and assembly revealed multiple copies of genes involved with acetate and ammonia metabolism, and several genes involved with secondary metabolite synthesis. An alternative to the high capital investment of photobioreactors for the cultivation of microalgae is the use of open-source and open-hardware bioreactor controller. Here, the concept of an open-hardwate bioreactor control called ``BioBrain'' is introduced. The BioBrain device is based on the Arduino Mega micro-controller board, and is capable of monitoring and controlling culture conditions during simple strain characterization studies, with an estimated construction cost of less than $800 USD. Finally, a new primer design tool for the ligation-independant cloning technique 𝜆-PCR was developed called lambdaPrimeR. The contributions of this work are the discovery and development of different tools that can overcome the challenges of the use of microalgae as microbial cell factories in industrial processes.
Ph. D.

When Captain James Cook sailed into Botany Bay in Australia for the first time in 1770, his botanist Joseph Banks described the behaviour of the Aboriginals to be 'totally unmovd' and 'totally engagd'.During this same few days Cook named the place Stingray Bay. Within eight days the name was changed by Cook to Botany Bay. Banks' phrases generate oscillating perceptions and Cook's name change poses questions. The perceptions documented in Banks' journal, refer to an invisibility of the Aboriginals themselves. The name 'Stingray' and its change to 'Botany' raises political questions about the necessity for the change. The change also sheds light on a viewpoint at odds with its subject. The events that occurred during the eight days Cook was anchored in Botany Bay will be discussed firstly in the framework of an analysis of the implications of the terms 'totally unmovd' and 'totally engagd' in Banks' journal, and secondly in a discussion about the various historical notions concerning the name change. Did these curly histories and viewpoints render the indigenous culture invisible? Can these inscriptions made by Cook and Banks and the subsequent mythologies surrounding them, including those about the actual place, be a metaphor for 'further understanding'?
Master of Arts (Hons) (Visual Arts)

Les informations échangées dans les textes des courriels sont généralement concernées par des événements complexes ou des processus métier dans lesquels les entités qui échangent des courriels collaborent pour atteindre les objectifs finaux des processus. Ainsi, le flux d’informations dans les courriels envoyés et reçus constitue une partie essentielle, les activités métier de l’entreprise. L’extraction d’informations sur les processus métier à partir des courriels peut aider à améliorer la gestion des courriels pour les utilisateurs. Il peut également être utilisé pour trouver des réponses riches à plusieurs questions analytiques sur les employés et les organisations. Aucun des travaux précédents n’a résolu le problème de la transformation automatique des journaux de courriels en journaux d’événements pour éventuellement en déduire les processus métier non documentés. Dans ce but, nous travaillons dans cette thèse sur un framework qui induit des informations de processus métier à partir d’emails. Nous introduisons des approches qui contribuent à ce qui suit : (1) découvrir pour chaque courriel le sujet de processus qui le concerne, (2) découvrir l’instance de processus métier à laquelle appartient chaque courriel, (3) extraire les activités de processus métier des courriels et associer ces activités aux métadonnées qui les décrivent, (4) améliorer la performance de la découverte des instances de processus métier et des activités métier en utilisant la relation entre ces deux problèmes, et enfin (5) estimer au préalable la date/heure réelle d’un activité métier. En utilisant les résultats des approches mentionnées, un journal d’événements est généré qui peut être utilisé pour déduire les modèles de processus métier d’un journal de courriels. L’efficacité de toutes les approches ci-dessus est prouvée par l’application de plusieurs expériences sur l’ensemble de données de courriel ouvert d’Enron
Exchanged information in emails’ texts is usually concerned by complex events or business processes in which the entities exchanging emails are collaborating to achieve the processes’ final goals. Thus, the flow of information in the sent and received emails constitutes an essential part of such processes i.e. the tasks or the business activities. Extracting information about business processes from emails can help in enhancing the email management for users. It can be also used in finding rich answers for several analytical queries about the employees and the organizations enacting these business processes. None of the previous works have fully dealt with the problem of automatically transforming email logs into event logs to eventually deduce the undocumented business processes. Towards this aim, we work in this thesis on a framework that induces business process information from emails. We introduce approaches that contribute in the following: (1) discovering for each email the process topic it is concerned by, (2) finding out the business process instance that each email belongs to, (3) extracting business process activities from emails and associating these activities with metadata describing them, (4) improving the performance of business process instances discovery and business activities discovery from emails by making use of the relation between these two problems, and finally (5) preliminary estimating the real timestamp of a business process activity instead of using the email timestamp. Using the results of the mentioned approaches, an event log is generated which can be used for deducing the business process models of an email log. The efficiency of all of the above approaches is proven by applying several experiments on the open Enron email dataset

Les donn ́ees utilisateurs sont devenue de plus en plus disponibles dans plusieurs do- maines tels que les traces d'usage des smartphones et le Web social. Les donn ́ees util- isateurs, sont un type particulier de donn ́ees qui sont d ́ecrites par des informations socio-d ́emographiques (ex., ˆage, sexe, m ́etier, etc.) et leurs activit ́es (ex., donner un avis sur un restaurant, voter, critiquer un film, etc.). L'analyse des donn ́ees utilisa- teurs int ́eresse beaucoup les scientifiques qui travaillent sur les ́etudes de la population, le marketing en-ligne, les recommandations et l'analyse des donn ́ees `a grande ́echelle. Cependant, les outils d'analyse des donn ́ees utilisateurs sont encore tr`es limit ́es.Dans cette th`ese, nous exploitons cette opportunit ́e et proposons d'analyser les donn ́ees utilisateurs en formant des groupes d'utilisateurs. Cela diff`ere de l'analyse des util- isateurs individuels et aussi des analyses statistiques sur une population enti`ere. Un groupe utilisateur est d ́efini par un ensemble des utilisateurs dont les membres parta- gent des donn ́ees socio-d ́emographiques et ont des activit ́es en commun. L'analyse au niveau d'un groupe a pour objectif de mieux g ́erer les donn ́ees creuses et le bruit dans les donn ́ees. Dans cette th`ese, nous proposons un cadre de gestion de groupes d'utilisateurs qui contient les composantes suivantes: d ́ecouverte de groupes, analyse de groupes, et recommandation aux groupes.La premi`ere composante concerne la d ́ecouverte des groupes d'utilisateurs, c.- `a-d., compte tenu des donn ́ees utilisateurs brutes, obtenir les groupes d'utilisateurs en op- timisantuneouplusieursdimensionsdequalit ́e. Ledeuxi`emecomposant(c.-`a-d., l'analyse) est n ́ecessaire pour aborder le probl`eme de la surcharge de l'information: le r ́esultat d'une ́etape d ́ecouverte des groupes d'utilisateurs peut contenir des millions de groupes. C'est une tache fastidieuse pour un analyste `a ́ecumer tous les groupes trouv ́es. Nous proposons une approche interactive pour faciliter cette analyse. La question finale est comment utiliser les groupes trouv ́es. Dans cette th`ese, nous ́etudions une applica- tion particuli`ere qui est la recommandation aux groupes d'utilisateurs, en consid ́erant les affinit ́es entre les membres du groupe et son ́evolution dans le temps.Toutes nos contributions sont ́evalu ́ees au travers d'un grand nombre d'exp ́erimentations `a la fois pour tester la qualit ́e et la performance (le temps de r ́eponse)
User data is becoming increasingly available in multiple domains ranging from phone usage traces to data on the social Web. User data is a special type of data that is described by user demographics (e.g., age, gender, occupation, etc.) and user activities (e.g., rating, voting, watching a movie, etc.) The analysis of user data is appealing to scientists who work on population studies, online marketing, recommendations, and large-scale data analytics. However, analysis tools for user data is still lacking.In this thesis, we believe there exists a unique opportunity to analyze user data in the form of user groups. This is in contrast with individual user analysis and also statistical analysis on the whole population. A group is defined as set of users whose members have either common demographics or common activities. Group-level analysis reduces the amount of sparsity and noise in data and leads to new insights. In this thesis, we propose a user group management framework consisting of following components: user group discovery, analysis and recommendation.The very first step in our framework is group discovery, i.e., given raw user data, obtain user groups by optimizing one or more quality dimensions. The second component (i.e., analysis) is necessary to tackle the problem of information overload: the output of a user group discovery step often contains millions of user groups. It is a tedious task for an analyst to skim over all produced groups. Thus we need analysis tools to provide valuable insights in this huge space of user groups. The final question in the framework is how to use the found groups. In this thesis, we investigate one of these applications, i.e., user group recommendation, by considering affinities between group members.All our contributions of the proposed framework are evaluated using an extensive set of experiments both for quality and performance

No discreet study of the Spanish voyages of discovery and exploration to the northwest coast of North American during the 1770's has been published in English. The purpose of this thesis is to examine the Spanish expeditions of 1774, 1775, and 1779, directed by New Spain's Viceroy Antonio Maria Burareli y Ursua (1771-1779).

Lung cancer is a leading cause of cancer-related mortality irrespective of gender. The Sulfiredoxin (Srx) and Peroxiredoxin (Prx) are a group of thiol-based antioxidant proteins that plays an essential role in non-small cell lung cancer. Understanding the molecular characteristics of the Srx-Prx interaction may help design the strategies for future development of therapeutic tools. Based on existing literature and preliminary data from our lab, we hypothesized that the Srx plays a critical role in lung carcinogenesis and targeting the Srx-Prx axis or Srx alone may facilitate future development of targeted therapeutics for prevention and treatment of lung cancer. First, we demonstrated the oncogenic role of Srx in urethane-induced lung carcinogenesis in genetically modified FVB mice. The Srx-null mice showed resistance to urethane-induced lung cancer. Second, we demonstrated the Srx and Prx sites important for Srx-Prx interaction. The orientation of this arm is demonstrated to cause some steric hindrance for the Srx-Prx interaction as it substantially reduces the rate of association between Srx and Prx. Finally, we carried out virtual screening to identify molecules that can successfully target Srx-Prx interaction. Multiple in-silico filters were used to minimize the number of chemicals to be tested. We identified ISO1 as an inhibitor of the Srx-Prx interaction. KD value for Srx-ISO1 interaction is calculated to be 42 nM. Together, these data helps to identify an inhibitor (ISO1) of the Srx-Prx interaction that can be further pursued to be developed as a chemotherapeutic tool.

Technological advancements and widespread adaptation of new technology in industry have made industrial time series data more available than ever before. This trend is expected to continue, especially with the introduction of Industry 4.0, where the goal is to connect everything on the industry floor to the cloud and the Industrial Internet of Things. With this development grows the need for versatile methods for mining industrial time series data. Time series motif discovery is a sub-set of data mining and is about finding interesting patterns in time series data. The state of the art in time series motif discovery is the Matrix Profile proposed in 2016. However, there are few publications where the Matrix Profile has been applied to real-life industrial time series data despite its popularity. The goal of the thesis has been to create a tool that enables joint human-machine exploration of industrial time series data using the Matrix profile and present the challenges involved. The result is a human-machine exploration procedure called IUSE that has been applied to three data sets containing real-life industrial time series data. IUSE enables the user to extract semantic information, detect cycles, find deviating patterns and helps the user to get a deeper understanding of a time series. The description of IUSE comes alongside learned lessons, faced challenges and experience from applying the Matrix Profile to actual industrial time series data.

Comme le titre pourrait le suggérer, l’objectif principal de cette thèse est de fournir une meilleure compréhension de la tâche de la découverte de sous-groupes à travers la théorie de l’ordre. La découverte de sous-groupes (Subgroup Discovery - SD) est la tâche automatique dont le but est la découverte d’hypothèses intéressantes dans les bases de données. Autrement dit, étant donnée une base de donnée, l’espace de recherche de toutes les hypothèses que l’analyste voudra tester ainsi qu’un moyen formel pour évaluer la qualité de ces hypothèses ; la tâche automatique de la découverte de sous-groupe s’efforce de trouver les meilleurs hypothèses quant à ces trois paramètres. Afin d’élaborer des algorithmes efficaces et efficients pour cette tâche, il est important de comprendre les propriétés des espaces de recherche d’une part et les propriétés de la mesure de qualité d’autre part. Dans cette thèse, nous étendons l’état de l’art par: (i) fournir une vue unifiée sur les espaces d’hypothèses derrière la tâche de découverte de sous-groupes en utilisant la théorie de l’ordre, (ii) proposer l’espace d’hypothèses de conjonctions d’inégalités linéaires dans les bases de données numériques ainsi que différents algorithmes permettant de les énumérer et (iii) proposer un algorithme anytime - fournit progressivement des résultats - pour la tâche particulière de fouille de sous-groupe discriminants dans les bases de données numériques. Ce dernier fournit des garanties sur la qualité des sous-groupes extraits même si l’algorithme est interrompu
As the title of this dissertation may suggest, the aim of this thesis is to provide an order-theoretic point of view on the task of subgroup discovery. Subgroup discovery is the automatic task of discovering interesting hypotheses in databases. That is, given a database, the hypothesis space the analyst wants to explore and a formal way of how the analyst gauges the quality of the hypotheses (e.g. a quality measure); the automated task of subgroup discovery aims to extract the interesting hypothesis w.r.t. these parameters. In order to elaborate fast and efficient algorithms for subgroup discovery, one should understand the underlying properties of the hypothesis space on the one hand and the properties of its quality measure on the other. In this thesis, we extend the state-of-the-art by: (i) providing a unified view of the hypotheses space behind subgroup discovery using the well-founded mathematical tool of order theory, (ii) proposing the new hypothesis space of conjunction of linear inequalities in numerical databases and the algorithms enumerating its elements and (iii) proposing an anytime algorithm for discriminative subgroup discovery on numerical datasets providing guarantees upon interruption

De par leur grand nombre et leur sévérité, les maladies rares (MR) constituent un enjeu de santé majeur. Des bases de données de référence, comme Orphanet et Orphadata, répertorient les informations disponibles à propos de ces maladies. Cependant, il est difficile pour ces bases de données de proposer un contenu complet et à jour par rapport à ce qui est disponible dans la littérature. En effet, des millions de publications scientifiques sur ces maladies sont disponibles et leur nombre augmente de façon continue. Par conséquent, il serait très fastidieux d’extraire manuellement et de façon exhaustive des informations sur ces maladies. Cela motive le développement des approches semi-automatiques pour extraire l’information des textes et la représenter dans un format approprié pour son utilisation dans d’autres applications. Cette thèse s’intéresse à l’extraction de connaissances à partir de textes et propose d’utiliser les résultats de l’extraction pour enrichir une ontologie de domaine. Nous avons étudié trois directions de recherche: (1) l’extraction de connaissances à partir de textes, et en particulier l’extraction de relations maladie-phénotype (M-P); (2) l’identification d’entité nommées complexes, en particulier de phénotypes de MR; et (3) l’enrichissement d’une ontologie en considérant les connaissances extraites à partir de texte. Tout d’abord, nous avons fouillé une collection de résumés d’articles scientifiques représentés sous la forme graphes pour un extraire des connaissances sur les MR. Nous nous sommes concentrés sur la complétion de la description des MR, en extrayant les relations M-P. Cette trouve des applications dans la mise à jour des bases de données de MR telles que Orphanet. Pour cela, nous avons développé un système appelé SPARE* qui extrait les relations M-P à partir des résumés PubMed, où les phénotypes et les MR sont annotés au préalable par un système de reconnaissance des entités nommées. SPARE* suit une approche hybride qui combine une méthode basée sur des patrons syntaxique, appelée SPARE, et une méthode d’apprentissage automatique (les machines à vecteurs de support ou SVM). SPARE* bénéficié à la fois de la précision relativement bonne de SPARE et du bon rappel des SVM. Ensuite, SPARE* a été utilisé pour identifier des phénotypes candidats à partir de textes. Pour cela, nous avons sélectionné des patrons syntaxiques qui sont spécifiques aux relations M-P uniquement. Ensuite, ces patrons sont relaxés au niveau de leur contrainte sur le phénotype pour permettre l’identification de phénotypes candidats qui peuvent ne pas être références dans les bases de données ou les ontologies. Ces candidats sont vérifiés et validés par une comparaison avec les classes de phénotypes définies dans une ontologie de domaine comme HPO. Cette comparaison repose sur une modèle sémantique et un ensemble de règles de mises en correspondance définies manuellement pour cartographier un phénotype candidate extrait de texte avec une classe de l’ontologie. Nos expériences illustrent la capacité de SPARE* à des phénotypes de MR déjà répertoriés ou complètement inédits. Nous avons appliqué SPARE* à un ensemble de résumés PubMed pour extraire les phénotypes associés à des MR, puis avons mis ces phénotypes en correspondance avec ceux déjà répertoriés dans l’encyclopédie Orphanet et dans Orphadata ; ceci nous a permis d’identifier de nouveaux phénotypes associés à la maladie selon les articles, mais pas encore listés dans Orphanet ou Orphadata.Enfin, nous avons appliqué les structures de patrons pour classer les MR et enrichir une ontologie préexistante. Tout d’abord, nous avons utilisé SPARE* pour compléter les descriptions en terme de phénotypes de MR disponibles dans Orphadata. Ensuite, nous proposons de compter et grouper les MR au regard de leur description phénotypique, et ce en utilisant les structures de patron. [...]
Even if they are uncommon, Rare Diseases (RDs) are numerous and generally sever, what makes their study important from a health-care point of view. Few databases provide information about RDs, such as Orphanet and Orphadata. Despite their laudable effort, they are incomplete and usually not up-to-date in comparison with what exists in the literature. Indeed, there are millions of scientific publications about these diseases, and the number of these publications is increasing in a continuous manner. This makes the manual extraction of this information painful and time consuming and thus motivates the development of semi-automatic approaches to extract information from texts and represent it in a format suitable for further applications. This thesis aims at extracting information from texts and using the result of the extraction to enrich existing ontologies of the considered domain. We studied three research directions (1) extracting relationships from text, i.e., extracting Disease-Phenotype (D-P) relationships; (2) identifying new complex entities, i.e., identifying phenotypes of a RD and (3) enriching an existing ontology on the basis of the relationship previously extracted, i.e., enriching a RD ontology. First, we mined a collection of abstracts of scientific articles that are represented as a collection of graphs for discovering relevant pieces of biomedical knowledge. We focused on the completion of RD description, by extracting D-P relationships. This could find applications in automating the update process of RD databases such as Orphanet. Accordingly, we developed an automatic approach named SPARE*, for extracting D-P relationships from PubMed abstracts, where phenotypes and RDs are annotated by a Named Entity Recognizer. SPARE* is a hybrid approach that combines a pattern-based method, called SPARE, and a machine learning method (SVM). It benefited both from the relatively good precision of SPARE and from the good recall of the SVM. Second, SPARE* has been used for identifying phenotype candidates from texts. We selected high-quality syntactic patterns that are specific for extracting D-P relationships only. Then, these patterns are relaxed on the phenotype constraint to enable extracting phenotype candidates that are not referenced in databases or ontologies. These candidates are verified and validated by the comparison with phenotype classes in a well-known phenotypic ontology (e.g., HPO). This comparison relies on a compositional semantic model and a set of manually-defined mapping rules for mapping an extracted phenotype candidate to a phenotype term in the ontology. This shows the ability of SPARE* to identify existing and potentially new RD phenotypes. We applied SPARE* on PubMed abstracts to extract RD phenotypes that we either map to the content of Orphanet encyclopedia and Orphadata; or suggest as novel to experts for completing these two resources. Finally, we applied pattern structures for classifying RDs and enriching an existing ontology. First, we used SPARE* to compute the phenotype description of RDs available in Orphadata. We propose comparing and grouping RDs in regard to their phenotypic descriptions, and this by using pattern structures. The pattern structures enable considering both domain knowledge, consisting in a RD ontology and a phenotype ontology, and D-P relationships from various origins. The lattice generated from this pattern structures suggests a new classification of RDs, which in turn suggests new RD classes that do not exist in the original RD ontology. As their number is large, we proposed different selection methods to select a reduced set of interesting RD classes that we suggest for experts for further analysis

The Histoire de la Nouvelle-France (1609, 1611, 1612, 1617, 1618) by Marc Lescarbot (v. 1570--1641) is read as a symbolic foundation for the young colony of Port-Royal, Acadia (Annapolis, Nova Scotia), a construct which functions as a valid genesis for French America (thus, "New France" in the title refers specifically to this habitation as well as to the men who contributed to its making). Chapter I is devoted to a reading of the work's abundant paratext and identifies the topics at stake in the unfavourable rumours about the Acadian expeditions as well as about the lieutenant of Port-Royal, Jean de Biencourt, sieur de Poutrincourt. Moreover, this chapter explores the subjective marks, disseminated in the paratext, that build up the historian's ethos, which works as a proof of the validity of his object. This chapter investigates as well the metadiscursive comments on the writing of history and their incidence on the referentiality of the work. Chapter II compares the compilation of travel accounts contained in the Histoire with its sources. This comparison shows how the alteration of these accounts of travellers---who recorded themselves the result of their American expeditions---strengthens the division of the stereotyped dichotomy between the man of letters and the man of action, two functions respectively assigned to Lescarbot and Poutrincourt in the Histoire. The order of this compilation as well as the organisation of its various parts according to a diegetical logic shape specific places where a tension emerges between a reliable discourse, intended to a readership interested in the actual conditions of a colonial establishment, and the production of a textual "coating" aiming at attracting a courtly readership, to which the Jesuits, who challenged Poutrincourt's colonial project, addressed their requests. In chapter III, where are confronted the written and mapped representations of Port-Royal, this tension is even more manifest.

Open source projects do have requirements; they are, however, mostly informal, text descriptions found in requests, forums, and other correspondence. Understanding such requirements provides insight into the nature of open source projects. Unfortunately, manual analysis of natural language requirements is time-consuming, and for large projects, error-prone. Automated analysis of natural language requirements, even partial, will be of great benefit. Towards that end, I describe the design and validation of an automated natural language requirements classifier for open source software development projects. I compare two strategies for recognizing requirements in open forums of software features. The results suggest that classifying text at the forum post aggregation and sentence aggregation levels may be effective. Initial results suggest that it can reduce the effort required to analyze requirements of open source software development projects. Software development organizations and communities currently employ a large number of software development techniques and methodologies. This implied complexity is also enhanced by a wide range of software project types and development environments. The resulting lack of consistency in the software development domain leads to one important challenge that researchers encounter while exploring this area: specificity. This results in an increased difficulty of maintaining a consistent unit of measure or analysis approach while exploring a wide variety of software development projects and environments. The problem of specificity is more prominently exhibited in an area of software development characterized by a dynamic evolution, a unique development environment, and a relatively young history of research when compared to traditional software development: the open-source domain. While performing research on open source and the associated communities of developers, one can notice the same challenge of specificity being present in requirements engineering research as in the case of closed-source software development. Whether research is aimed at performing longitudinal or cross-sectional analyses, or attempts to link requirements to other aspects of software development projects and their management, specificity calls for a flexible analysis tool capable of adapting to the needs and specifics of the explored context. This dissertation covers the design, implementation, and evaluation of a model, a method, and a software tool comprising a flexible software development analysis framework. These design artifacts use a rule-based natural language processing approach and are built to meet the specifics of a requirements-based analysis of software development projects in the open-source domain. This research follows the principles of design science research as defined by Hevner et. al. and includes stages of problem awareness, suggestion, development, evaluation, and results and conclusion (Hevner et al. 2004; Vaishnavi and Kuechler 2007). The long-term goal of the research stream stemming from this dissertation is to propose a flexible, customizable, requirements-based natural language processing software analysis framework which can be adapted to meet the research needs of multiple different types of domains or different categories of analyses.

Sponge assemblages dominate several distinctive, hard-bottom environments, being one of the most important structural organisms at several locations around the world. Although the Mediterranean sponge fauna is among the world's most studied, information is minimal for sponges from Mediterranean deep-sea areas compared to shallow waters, with most of the data deriving from indirect sampling methods or from by-catch specimens collected by bottom trawlers. Taking advantage of the footage and material collected during the Life + INDEMARES, ABIDES and ABRIC projects, the present thesis aims to shed light, by means of non-invasive methods, into the sponge communities occurring in two remarkable sites of the Catalano-Balearic Sea (northwestern Mediterranean Sea): The Site of Community Interest (SCI) of the Menorca Channel (Balearic archipelago), which is to become a future Marine Protected Area (MPA), and the Cold Water-Coral (CWC) communities recently discovered in the Blanes Canyon. Regarding the Menorca Channel SCI, this thesis characterized, by means of quantitative analyses of video transects, the main sponge assemblages occurring in the area, with a special focus on the geographical, bathymetrical and size-structure distribution of its most relevant habitat-forming sponge. Quantitative analysis of 85 video-transects (a total linear distance of 75 km), together with representative collections to confirm species identifications, allowed to discriminate six major assemblages, which mainly corresponded to differences in substrate type and depth. Highest sponge densities and abundances were concentrated in areas of high hydrodynamism, namely the rocky shoals offshore Cap Formentor and the Menorca Canyon’s head. Most of the studied species were dominated by small to medium size classes, suggesting pulse recruitment events. A clear depth-zonation pattern has been observed, going from the inner continental shelf to the upper slope. At the same time, the continental shelf harbored the presence of diverse and contrasting growth morphologies, yet the biggest forms occurred at the shelf edge and the upper slope. Regarding the identified assemblages, on the inner continental shelf, a semi-sciaphilous Axinellid assemblage dominated the rocky outcrops. Maërl beds on the inner continental shelf were dominated by Haliclona (Reniera) mediterranea, whereas the horny sponge Aplysina cavernicola and several other haliclonids mostly dominated maërl beds and rocky substrates of the outer shelf. Soft sediments on the shelf break hosted a monospecific Thenea muricata assemblage, whereas rocky substrates of the shelf break were characterized by a mixture of encrusting, columnar and fan-shaped sponges. Finally, the upper slope was dominated by Hamacantha (Vomerula) falcula and the hexactinellid Tetrodictyum reiswigi. This thesis highlights the presence of dense, well-preserved sponge populations in the Menorca Channel, and provides a baseline for their future monitoring once the MPA is declared, potentially serving as reference for other areas across the Atlanto-Mediterranean region. Regarding the Blanes canyon, the present thesis provides the first insight on the associated sponge fauna of its recently discovered CWC communities, while also reviewing the current knowledge of the sponge fauna dwelling in all the Mediterranean CWC provinces. In regards to the studied area, some rare species are cited for the first time in the Mediterranean or redescribed, while two of them, Hamacantha (Hamacantha) hortae and Hamigera bibiloni are new to science. At a basin scale, Mediterranean CWC appear as poriferan biodiversity hotspots, yet current diversity values on each site rather represent a small fraction of its actual fauna. Additionally, the existence of an endemic sponge fauna exclusively dwelling on CWC is refuted. Nonetheless, the sponge fauna thriving in Mediterranean CWC appears to be unique, and different from that of other Atlantic regions.
Las comunidades de esponjas dominan multitud de entornos de fondo duros, siendo uno de los organismos estructurales dominantes en varias áreas del mundo. Aunque la fauna de esponjas mediterráneas se encuentra entre las más estudiadas del mundo, la información disponible actualmente es mínima para las esponjas que se encuentran en las zonas más profundas del mediterráneo en comparación con sus aguas más someras, y la mayoría de los datos disponibles han sido obtenidos mediante métodos de muestreo indirectos o de capturas accidentales por pesquerías de fondo. Aprovechando el metraje y material recogido durante los proyectos Life + INDEMARES, ABIDES y ABRIC, la presente tesis pretende arrojar luz, mediante métodos no invasivos, sobre las comunidades de esponjas que se dan en dos áreas destacadas del Mar Catalano-Balear (mar Mediterráneo noroccidental): el Sitio de Interés Comunitario (SCI) del Canal de Menorca (archipiélago balear), que se convertirá en un futuro Área Marina Protegida (AMP), y las comunidades de corales de agua fría recientemente descubiertas en el cañón de Blanes. En cuanto al SIC del Canal de Menorca, esta tesis caracterizó, mediante análisis cuantitativos de video-transectos, las principales comunidades de esponjas de la zona, con especial énfasis en la distribución geográfica, batimétrica y estructural de las especies formadoras de hábitat más relevantes. El análisis cuantitativo de 85 video-transectos (una distancia lineal total de 75 km), junto con el análisis de especímenes para confirmar la identificación de especies, permitió discriminar seis comunidades principales, que correspondían principalmente a diferencias en el tipo de sustrato y profundidad. Las mayores densidades y abundancias de esponjas se concentraron en áreas de alto hidrodinamismo, a saber, las zonas rocosas frente a la costa del Cabo Formentor y la cabecera del Cañón de Menorca. También se observó un patrón claro de zonificación en profundidad, que va desde la plataforma continental interior hasta el talud superior. Al mismo tiempo, la plataforma continental albergaba la presencia de diversas morfologías, pero las formas más grandes ocurrieron en el borde de la plataforma y el talud. A su vez, la mayoría de las especies estudiadas estaban dominadas por individuos de tamaño pequeño a mediano, lo que sugiere eventos de reclutamiento a pulsos. En cuanto a las comunidades de esponjas identificadas, en la plataforma continental interior dominaban axinélidos semiesciáfilos que se localizaban sobre afloramientos rocosos. A su vez, los lechos de maërl en la plataforma continental interior estaban dominados por Haliclona (Reniera) mediterranea, mientras que la esponja córnea Aplysina cavernicola y varios haliclonidos dominaban principalmente los lechos de maërl y los sustratos rocosos de la plataforma exterior. Los sedimentos blandos en el borde de la plataforma albergaban una comunidad monoespecífica de Thenea muricata, mientras que los sustratos rocosos del borde de la plataforma se caracterizaron por una mezcla de esponjas incrustantes, columnares y en forma de abanico. Finalmente, la vertiente superior del talud continental estaba dominada por Hamacantha (Vomerula) falcula y la hexactinélida Tetrodictyum reiswigi. Así pues, esta tesis pone en valor la presencia de densas poblaciones de esponjas en el Canal de Menorca y proporciona la base científica para su futuro seguimiento una vez que se declare el área como AMP, pudiendo servir a su vez los datos generados como referencia para otras comunidades de esponjas que se encuentren en la región atlántico-mediterránea. En cuanto al cañón de Blanes, la presente tesis proporciona los primeros datos sobre la fauna de esponjas asociada a las comunidades de corales de agua fría (‘CWC provinces’, del inglés cold water corals) recientemente descubiertas en el área, al tiempo que revisa el conocimiento actual de la fauna de esponjas que habita en todas las ‘CWC provinces’ del Mediterráneo. En referencia a las especies encontradas en al área de estudio, algunas se citan por vez primera en el Mediterráneo o han sido redescubiertas, siendo dos de ellas, Hamacantha (Hamacantha) hortae y Hamigera bibiloni, nuevas para la ciencia. A nivel Mediterráneo, las comunidades de corales de agua fría parecen ser puntos calientes o ‘hotspots’ de biodiversidad de poríferos. Sin embargo, los valores de diversidad actuales en cada ‘CWC province’ representan más bien una pequeña fracción de su fauna espongiológica real, que muy posiblemente este infrarrepresentada en la actualidad. Además, se refuta la existencia de una fauna de esponjas endémica que habite exclusivamente en las comunidades de corales de agua fría. No obstante, la fauna de poríferos que habita en las comunidades de corales de agua fría del Mediterráneo parece ser diferente de la de otras regiones atlánticas. Con el conocimiento actual, la fauna de esponjas de las ‘CWC provinces’ mediterráneas se agrupa en tres clusters diferenciables (Mar de Alborán, Mediterráneo Occidental y Oriental), que parecen estar determinados por la circulación de las masas de agua en la cuenca, especialmente la ‘Levantine Intermediate Water’ y la ‘Atlantic Water’, y siguiendo un patrón occidental-oriental desde el Estrecho de Gibraltar hasta el mar Adriático. Finalmente, las esponjas que viven en las ‘CWC provinces’ del Mediterráneo todavía están poco exploradas, pero parecen ser buenas candidatas para estudios biogeográficos.
Les comunitats d'esponges dominen en multitud d'entorns marins de fons durs, essent considerats com un dels organismes estructurals principals de dites comunitats en diverses àrees del món. Encara que la fauna d'esponges mediterrànies es troba entre les més ben estudiades del món, la informació disponible actualment és mínima per a les esponges que es troben en les zones més profundes del mediterrani en comparació amb les seves aigües més someres, i la majoria de les dades disponibles fins a avui en dia han estat obtingudes mitjançant mètodes de mostreig indirectes o bé de captures accidentals per pesqueres de fons. Aprofitant el metratge i material recollit durant els projectes Life + INDEMARES, ABIDES i ABRIC, la present tesi pretén aportar llum, mitjançant mètodes no invasius, sobre les comunitats d'esponges que es donen en dues àrees destacades de la Mar Catalano-Balear (mar Mediterrani nord-occidental): el Lloc d'Importància Comunitària (LIC) del Canal de Menorca (arxipèlag balear), que ha d’esdevenir en un futur pròxim una Àrea Marina Protegida (AMP), i les comunitats de coralls d'aigua freda recentment descobertes en el Rec de Blanes. En quant al LIC del Canal de Menorca, aquesta tesi va caracteritzar, mitjançant anàlisis quantitatiu de vídeo-transsectes, les principals comunitats d'esponges de la zona, amb especial èmfasi en la distribució geogràfica, batimètrica i estructural de les espècies formadores d'hàbitat més rellevants. L'anàlisi quantitatiu de 85 vídeo-transsectes (una distància lineal total de 75 km), juntament amb l'anàlisi d'espècimens per a confirmar la identificació d'espècies, va permetre discriminar sis comunitats principals, que reflectien principalment diferències en la composició del substrat i la profunditat. Les majors densitats i abundàncies d'esponges es van concentrar en àrees d'alt hidrodinamisme, a saber, les zones rocoses enfront de la costa del Cap Formentor i la capçalera del Rec de Menorca. També es va observar un patró clar de zonificació en profunditat, que va des de la plataforma continental interior fins al talús superior. Al mateix temps, la plataforma continental albergava la presència d’una major diversitat de morfologies, però les formes més grans o exuberants es concentraven en el límit de la plataforma i el talús continental. Al seu torn, l’estructura de talles de la majoria de les espècies estudiades estava dominada per individus de grandària petita i/o mitjana, la qual cosa suggereix esdeveniments de reclutament a polsos. En quant a les comunitats d'esponges identificades, en la plataforma continental interior dominaven els axinèl·lids semiesciàfils que es localitzaven sobre afloraments rocosos de la plataforma continental interior. Al seu torn, els llits de maërl de la plataforma continental interior estaven dominats per Haliclona (Reniera) mediterranea, mentre que l'esponja còrnia Aplysina cavernicola i varies ‘Haliclona’ dominaven principalment els llits de maërl i els substrats rocosos de la plataforma exterior. Alhora, els sediments tous en la vora de la plataforma albergaven una comunitat monoespecífica de Thenea muricata, mentre que els substrats rocosos de la vora de la plataforma es van caracteritzar per una mescla d'esponges incrustants, columnars i en forma de ventall. Finalment, el vessant superior del talús continental estava dominada per Hamacantha (Vomerula) falcula i la hexactinèl·lid Tetrodictyum reiswigi. Així doncs, aquesta tesi posa en valor la presència de denses poblacions d'esponges en el Canal de Menorca i proporciona la base científica per al seu futur seguiment una vegada que es declari l'àrea com AMP, podent servir al seu torn les dades generades com a referència per a altres comunitats d'esponges que es trobin a la regió atlàntomediterrània. Referent al Rec de Blanes, la present tesi proporciona les primeres dades sobre la fauna d'esponges associada a les comunitats de corals d'aigua freda (‘CWC provinces’, de l'anglès cold-water corals) recentment descobertes en l'àrea, al mateix temps que revisa el coneixement actual de la fauna d'esponges que habita en totes les ‘CWC provinces’ del Mediterrani. En referència a les espècies trobades en a l'àrea d'estudi, algunes se citen per primera vegada en el Mediterrani, sent dues d'elles, Hamacantha (Hamacantha) hortae i Hamigera bibiloni, noves per a la ciència. A nivell Mediterrani, les comunitats de corals d'aigua freda semblen ser punts calents o ‘hotspots’ de biodiversitat de porífers. No obstant això, els valors de diversitat actuals en cada ‘CWC province’ representen més aviat una petita fracció de la seva fauna espongiològica real, que molt possiblement resulta infrarepresentada en l'actualitat. A més a més, es refuta l'existència d'una fauna d'esponges endèmica que habiti exclusivament en les comunitats de corals d'aigua freda. No obstant això, la fauna de porífers que habita en les comunitats de corals d'aigua freda del Mediterrani sembla ser diferent de la d'altres regions atlàntiques. Amb el coneixement actual, la fauna d'esponges de les ‘CWC provinces’ mediterrànies s'agrupa en tres clústers diferenciables (Mar d'Alborán, Mediterrani Occidental i Mediterrani Oriental), que semblen estar determinats per la circulació de les masses d'aigua en la conca, especialment la ‘Levantine Intermediate Water’ i la ‘Atlantic Water’, i seguint un patró oest-est des de l'Estret de Gibraltar fins al Adriàtic. Finalment, les esponges que viuen en les ‘CWC provinces’ del Mediterrani encara tot i estar poc explorades, semblen ser bones candidates per a estudis biogeogràfics.
Ciències del mar

Exploiter des jeux de données labelisés est très utile, non seulement pour entrainer des modèles et mettre en place des procédures d'analyses prédictives, mais aussi pour améliorer la compréhension d'un domaine. La découverte de sous-groupes a été l'objet de recherches depuis deux décennies. Elle consiste en la découverte de règles couvrants des ensembles d'objets ayant des propriétés intéressantes, qui caractérisent une classe cible donnée. Bien que de nombreux algorithmes de découverte de sous-groupes aient été proposés à la fois dans le cas des données transactionnelles et numériques, la découverte de règles dans des données séquentielles labelisées a été bien moins étudiée. Dans ce contexte, les stratégies d'exploration exhaustives ne sont pas applicables à des cas d'application rééls, nous devons donc nous concentrer sur des approches heuristiques. Dans cette thèse, nous proposons d'appliquer des modèles de bandit manchot ainsi que la recherche arborescente de Monte Carlo à l'exploration de l'espace de recherche des règles possibles, en utilisant un compromis exploration-exploitation, sur différents types de données tels que les sequences d'ensembles d'éléments, ou les séries temporelles. Pour un budget temps donné, ces approches trouvent un ensemble des top-k règles decouvertes, vis-à-vis de la mesure de qualité choisie. De plus, elles ne nécessitent qu'une configuration légère, et sont indépendantes de la mesure de qualité utilisée. A notre connaissance, il s'agit de la première application de la recherche arborescente de Monte Carlo au cas de la fouille de données séquentielles labelisées. Nous avons conduit des études appronfondies sur différents jeux de données pour illustrer leurs plus-values, et discuté leur résultats quantitatifs et qualitatifs. Afin de valider le bon fonctionnement d'un de nos algorithmes, nous proposons un cas d'utilisation d'analyse de jeux vidéos, plus précisémment de matchs de Rocket League. La decouverte de règles intéressantes dans les séquences d'actions effectuées par les joueurs et leur exploitation dans un modèle de classification supervisée montre l'efficacité et la pertinence de notre approche dans le contexte difficile et réaliste des données séquentielles de hautes dimensions. Elle permet la découverte automatique de techniques de jeu, et peut être utilisée afin de créer de nouveaux modes de jeu, d'améliorer le système de classement, d'assister les commentateurs de "e-sport", ou de mieux analyser l'équipe adverse en amont, par exemple
It is extremely useful to exploit labeled datasets not only to learn models and perform predictive analytics but also to improve our understanding of a domain and its available targeted classes. The subgroup discovery task has been considered for more than two decades. It concerns the discovery of rules covering sets of objects having interesting properties, e.g., they characterize a given target class. Though many subgroup discovery algorithms have been proposed for both transactional and numerical data, discovering rules within labeled sequential data has been much less studied. In that context, exhaustive exploration strategies can not be used for real-life applications and we have to look for heuristic approaches. In this thesis, we propose to apply bandit models and Monte Carlo Tree Search to explore the search space of possible rules using an exploration-exploitation trade-off, on different data types such as sequences of itemset or time series. For a given budget, they find a collection of top-k best rules in the search space w.r.t chosen quality measure. They require a light configuration and are independent from the quality measure used for pattern scoring. To the best of our knowledge, this is the first time that the Monte Carlo Tree Search framework has been exploited in a sequential data mining setting. We have conducted thorough and comprehensive evaluations of our algorithms on several datasets to illustrate their added-value, and we discuss their qualitative and quantitative results. To assess the added-value of one or our algorithms, we propose a use case of game analytics, more precisely Rocket League match analysis. Discovering interesting rules in sequences of actions performed by players and using them in a supervised classification model shows the efficiency and the relevance of our approach in the difficult and realistic context of high dimensional data. It supports the automatic discovery of skills and it can be used to create new game modes, to improve the ranking system, to help e-sport commentators, or to better analyse opponent teams, for example

In 1849, President Brigham Young commissioned a fifty man company, headed by Parley P. Pratt, to explore Southern Utah for possible colonization. The four month trek spanned the coldest months of the winter, and afforded some very harrowing and hazardous experiences. These events weave a heroic story filled with excitement and adventure, while simultaneously revealing the tremendous dedication and fortitude on the part of the explorers to successfully complete their mission.Many of the Southern Utah colonies that were initiated in the subsequent years following the expedition were based on information gathered during this seven-hundred mile expedition. In addition, their findings provided a crucial link in Brigham Young's imminent decision to colonize southern Utah.

The thesis analyses the continuum of European activity that preceded establishment of an effective pastoral industry in Australia's north-west. Two strands - physical activity and evolution of legislation - are interwoven, examining growth in geographical knowledge, proposals for colonisation and the outcome of interplay between government officials and landholders over land policy. Growth in geographical knowledge gave rise to colonisation proposals from 1828. The thesis relates these proposals to events affecting northern Australia to show that promotion and occupation of north-west lands constituted an integral part of the outgrowth of colonial settlement in Australia. Europeans occupied the north-west in two waves, abortively during the 1860s and continuously from 1879. The existing literature identifies these waves but provides inadequate analysis of events to 1884. The thesis fills this gap by showing that land hunger, misinformation, land speculation, manipulation of legislation and exploitation of political power for private commercial gain determined the shape of north-west settlement. Moreover, by relating land policy to tenure and occupation, it shows that private individuals influenced land policy and impeded official plans for rapid settlement. Thus, the thesis provides a fresh perspective not only on the prelude to effective pastoral settlement in the north-west but on the management of Western Australia's outlying lands in the period before responsible government.