The main theme of this work is the detection of overlaps in NGS data. The work contains an overview of NGS sequencing technologies that are the source of NGS data. In the thesis, the problem of overlapping detection is generally defined. Next, an overview of the available algorithms and approaches for detecting overlaps in NGS data is created. Principles of these algorithms are described herein. In the second part of this work a suitable tool for detecting approximate overlaps in NGS data is designed and its implementation is described herein. In conclusion, the experiments performed with this tool and the conclusions that follow are summarized and described.

Particle Image Velocimetry (PIV) is an optical fluid measurement technique used to obtain velocity measurements. Two PIV systems were used to capture data simultaneously and measurement error for the MS PIV system is calculated. An investigation of error distribution is performed to determine when uncertainty estimations fail for the CS PIV-UQ method. Investigation of when results from multi pass PIV processing are achieve were performed so that reliable uncertainty estimations are produced with the CS method. An investigation was also performed which determined that error distributions in PIV systems are correlated with flow shear and particle seeding density. Correlation of random errors in space was also performed at the jet core and shear regions of the flow. It was found that in flow regions with large shear that error distributions were non-Gaussian. It was also found in regions of large shear that CS uncertainty results did not match the error. For multi-pass PIV processing with 50% and 75% IW overlap it was found that 4 and 6 passes should be used, respectively, in order for CS uncertainty estimations to be reliable. It was also found that the correlation of random errors in space is much larger in shear regions of the jet flow than in the jet core.

No description available.

No description available.

Intraguild competition and predation have been recognised as important ecological factors influencing the population dynamics of carnivores. The effects of these interactions are often asymmetrical due to a size-related dominancy hierarchy. However, it has been suggested that competitively subordinate carnivores can minimise the costs of predation and competition through spatial and temporal avoidance. Here I investigate the ecological and behavioural mechanisms by which cheetahs (Acinonyx jubatus) coexist with competitively stronger lions (Panthera leo) and spotted hyaenas (Crocuta crocuta). Fieldwork was carried out in the Okavango Delta, northern Botswana, between October 2008 and August 2011. A total of 20 Global Positioning System (GPS) radio-collars were fitted on all known cheetahs (n=6), lion prides (n=5) and spotted hyaena clans (n=6) in the study area (approx. 3 000 km²). Pre-programmed radio-collars recorded locations and activity continuously for each individual and these data were complemented with direct behavioural observations. Cheetah data were analysed with respect to the temporal and spatial likelihood of encountering lions and spotted hyaenas. Results suggest that the response to the risks posed by other predators is species-specific, habitat-specific and dependent on the immediacy of the risk. Resource partitioning was not the main mechanism for coexistence as cheetahs overlapped extensively with lions and spotted hyaenas in time, space and habitat use. Instead, cheetahs adjusted their spatial distribution in response to immediate risks or adapted their habitat use depending on their vulnerability (e.g. behaviours such as feeding or with differing levels of moonlight at night). In general, cheetah temporal and spatial distribution is a hierarchal process, firstly driven by resource acquisition and thereafter fine-tuned by predator avoidance. In addition, habitat heterogeneity seemed to be key in facilitating coexistence. Understanding the behavioural mechanisms that interacting apex predators adopt to regulate these negative interactions could be crucial to carnivore conservation, especially as human-related habitat loss is forcing species into ever smaller areas.

Harmonia axyridis is a ladybird native to Asia, but introduced widely as a biocontrol agent. It is invasive and detrimental to native species in North America, which meant its arrival in Britain was met with concern. Establishment was seen as an opportunity to track the spread of an invasive alien species (IAS) whilst also monitoring impacts on native species. The aims of this thesis were to examine the responses of native British ladybirds to the arrival of H. axyridis, to establish the effect of the IAS on native ladybirds when compared to other drivers, and to investigate the possible facilitation of the H. axyridis invasion by natural enemy release. Modelling ladybird distributions with life-history and resource-use traits found that species predatory on a wide range of prey families had larger range sizes than those which ate fewer prey types. This suggests that the wide diet breadth of the IAS is likely to have played a critical role in the species’ rapid spread. Dietary niche overlap between H. axyridis and native ladybirds showed positive correlation with declines of native ladybirds. This indicates that the IAS is playing an important role, but the significance of urbanisation suggests habitat destruction is also significant. Abundance of H. axyridis was influenced by habitat type and aphid abundance, but not by the native ladybird community, suggesting the spread of the IAS will not be slowed by biotic resistance. Harmonia axyridis is attacked by native parasitoids, but at a much lower rate than is the native Coccinella septempunctata, in line with natural-enemy release theory. There was no evidence of attack rate increasing with time since arrival in an area. Overall, H. axyridis is an extremely successful IAS, with detrimental effects on native ladybirds which are likely to continue.

Le présent mémoire est consacré à l'étude des chevauchements entre revendications territoriales autochtones. On s'y interroge sur l’origine et l’évolution de ces chevauchements ainsi que sur les mécanismes qui pourraient être employés pour trouver des solutions acceptables pour toutes les parties. Notre étude retrace d'abord l'évolution du critère d’exclusivité élaboré par les politiques et décisions judiciaires canadiennes relativement à l’octroi du titre autochtone, concluant que ce critère d’exclusivité est devenu un enjeu déterminant dans l’élaboration d’une solution relative aux chevauchements entre revendications territoriales. En observant la manière dont les différents paliers de gouvernement ont échoué dans leurs tentatives de solutionner les enjeux de chevauchement, nous constatons que les traditions juridiques autochtones doivent être intégrées à la résolution des conflits et à l’interprétation du critère d’exclusivité. Ceci exige de percevoir l’institution juridique de la résolution de conflits selon une certaine vision du droit. Nous utilisons ici celle de Lon Fuller, qui présente une approche permettant de réconcilier plusieurs traditions juridiques. Notre étude nous conduit à proposer le système du Indigenous Legal Lodge comme mécanisme de résolution de conflit permettant aux autochtones de faire appel à leurs traditions juridiques dans la résolution des chevauchements, permettant ainsi de réconcilier ces traditions diverses. / This thesis is dedicated to the study of overlapping aboriginal land claims. We question the origin and evolution of these overlaps and study the mechanisms which could be used in order to determine a solution acceptable to all parties. Our study first discusses the evolution of the exclusivity criterion developed in Canadian policy and case law relating to the granting of an aboriginal title, concluding that the criterion of exclusivity has become a defining issue in the development of a solution to overlaps between land claims. By observing the failures of the various levels of government in their attempts to develop solutions to overlapping claims, we find that Aboriginal legal traditions must be integrated into conflict resolution and be used when interpreting the exclusivity criterion. This requires us to perceive conflict resolution, as a legal institution, according to a certain understanding of the law. We use Lon Fuller’s vision, who presents an approach for reconciling various legal traditions. Our study brings us to propose the Indigenous Legal Lodge as a conflict resolution mechanism enabling Aboriginal groups to call upon their own legal traditions in resolving overlaps and to reconcile their differing traditions.

Maladies fréquentes, l’asthme touche 8,4% de la population canadienne âgée de 12 ans et plus et la maladie pulmonaire obstructive chronique (MPOC) touche de 5 à 15% de la population âgée entre 35 et 79 ans. L’asthme et la MPOC peuvent coexister chez un patient. Ce phénomène appelé syndrome de chevauchement de l’asthme et de la MPOC (ACOS) toucherait environ 10% à 55% des patients MPOC. Afin de mieux caractériser l’ACOS et les effets indésirables des médicaments utilisés pour traiter la MPOC, deux études ont été mises en place. Une première étude réalisée auprès de pneumologues a permis de décrire les méthodes de diagnostic, de traitement et d’évaluation de la maitrise de l’ACOS dans la pratique clinique. Les pneumologues rapportent que le diagnostic devrait être basé sur les caractéristiques cliniques, les tests de fonction pulmonaire et l'intuition clinique du médecin. De plus, un corticostéroïde inhalé en combinaison et un bronchodilatateur inhalé à longue durée d’action devraient être introduits rapidement dans le plan de traitement. La deuxième étude a permis d’évaluer la fréquence des effets indésirables chez les patients MPOC/ACOS traités avec un bronchodilatateur inhalé à longue durée d’action. Cette étude démontre que les effets indésirables sont fréquents chez les patients MPOC/ACOS et que la sécheresse buccale et la gorge sèche sont les plus rapportés. Ces résultats démontrent que la mise en place de lignes directrices pour l’ACOS ainsi qu’une meilleure connaissance du profil de tolérance des bronchodilatateurs inhalés à longue durée d’action seraient bénéfiques pour les patients / Asthma and chronic obstructive pulmonary disease (COPD) are frequent in Canada with a prevalence of 8.4% among Canadians aged 12 and over for asthma and a prevalence of 5 to 15% among Canadians aged 35 to 79 years. Asthma and COPD can coexist in a patient and this Asthma-COPD overlap syndrome (ACOS) affects about 10% to 55% of COPD patients. To better understand this syndrome, two studies were designed and conducted. First, focus groups evaluated how pulmonologists diagnose and treat ACOS, and how they assess its control in routine clinical practice. The pulmonologists reported that the diagnosis must be based on clinical characteristics, pulmonary function tests, and clinical intuition. They also agreed that the treatment should target the features of both asthma and COPD. The second study assessed the prevalence of adverse events in COPD/ACOS patients on long-acting inhaled anticholinergics (LAAC) and β2-agonists (LABA) in a real-world setting. This study demonstrates that side effects are common among COPD/ACOS patients. Dry mouth and dry throat were the most reported side effects. These results demonstrate that more explicit guidelines for ACOS and a better understanding of the safety profile of long-acting bronchodilators would be beneficial for patients.

Doctor of Philosophy(PhD) / This thesis is concerned with the theoretical and practical development of a surface-based mapping algorithm for reliable and robust localization and mapping in prior unknown and unstructured environments. A surface-based map consists of a set of compressed surfaces, processed and represented without geometrical modelling. Each surface in the surface-based map represents an object in the environment. The ability to represent the exact shapes of objects via individual surfaces during the mapping process makes the surface-based mapping algorithm valuable in a number of navigation applications, such as mapping of prior unknown indoor and outdoor unstructured environments, target tracking, path planning and collision avoidance. The ability to unify representations of the same object taken from different viewpoints into a single surface makes the algorithm capable of working in multi-robot mapping applications. A surface-based map of the environment is build incrementally by acquiring the 3D range image of the scene, extracting the objects' surfaces from the 3D range image, aligning the set of extracted surfaces relative to the map and unifying the aligned set of surfaces with surfaces in the map. In the surface unification process the surfaces representing the same object are unified to make a single surface. The thesis introduces the following new methods which are used in the surface-based mapping algorithm: the extraction of surfaces from 3D range images based on a scanned surface continuity check; homogenization of the representation of the non-homogenously sampled surfaces; the alignment of the surface set relative to a large set of surfaces based on surface-based alignment algorithm; evaluating the correspondence between two surfaces based on the overlap area between surfaces; unification of the two surfaces belonging to the same object; and surface unification for a large set of surfaces. The theoretical contributions of this thesis are demonstrated with a series of practical implementations in different outdoor environments.

自2003年布達佩斯宣言公佈起，國際間學術文獻開始開放取用的趨勢。於此背景下，本研究以諾貝爾生物醫學獎近十年23位得主為研究樣本，評比在商業資料庫(SCIE、Scopus)及開放取用系統(生物醫學類：Pubmed、Highwire；綜合類：Google Scholar)的文獻收錄狀況，除了比較其內部重複性與完整性，並交叉比對五個資料庫與系統的重複性、獨特性及完整性，同時也觀看能否取得全文的比率，來了解現今開放取用文獻的狀況，進而觀察開放取用系統和商業資料庫兩者是否可以互補，或是開放取用系統有代替商業資料庫的可能性。 研究結果顯示五個資料庫及系統的檢索形式多元。針對作者檢索而言，Scopus最完善，資料收錄也較齊全；SCIE及Pubmed兩者則是檢索結果最為相似。如果以學術出版收錄而言，則是Highwire較完整；至於Google Scholar的獨特性較高。整體而言，開放取用系統比商業資料庫的全文收錄比例高，但Scopus是收錄最多全文的資料庫。本研究同時也發現PNAS是五個資料庫與系統之重複來源及獨特來源。另外，使用PubMed及Highwire檢索生物醫學文獻會比Google Scholar來得專業。 根據研究結果建議，商業資料庫可考慮將網路開放資源納入收錄範圍，以便妥善整理及應用網路資源的書目及全文。開放取用系統則應改善索引書目之正確性及著錄完整性。另外，針對圖書館的服務宜採取以下之因應措施：(1)加強推廣商業資料庫之正確檢索方式及使用時機；(2)教導如何正確使用開放取用系統的檢索模式；(3)平衡商業資料庫和開放取用系統的使用，以達成圖書館經費的合理運用。 本研究後續可延伸至生物醫學領域的臨床及實證醫學上，以了解生物醫學中兩個最具時效性的學術文獻系統是否達到開放取用的立即性及實用性。再者，使用者對開放取用的滿意度研究是學術出版界急欲了解的課題，也是後續研究可加強努力的方向。 / The International Scholarly Communication has gradually forwarded open access system since the publication of Budapest Declaration in 2003. Under this research background, this study uses biomedical Nobel Prize winners in recent years for the study of 23 samples of appraisal in the commercial database (SCIE, Scopus) and open access systems (biomedical categories: Pubmed, Highwire ; Comprehensive: Google Scholar) literature collection status, in addition to comparing repeatability and integrity of its internal and cross-comparison of the five databases and system repeatability, uniqueness and integrity, while also viewing the ability to obtain the ratio of text to understand current status of open access literature, and then observe the open access systems and commercial databases whether the two can complement each other, or open access database system instead of commercial possibilities. The results showed that five databases have different retrieval systems in many different forms. For the purposes of retrieval, Scopus collections are more complete; SCIE and Pubmed are the most similar two databases in the search results. Inclusion academic publishing purposes, Highwire is the most complete one. For Google Scholar, the collection’s uniqueness is the highest. Overall, comparing the open access system with commercial database, open access system contains a high proportion of full text. Scopus is the most one of full text collections. The PNAS study also found that five of the duplicate database and system sources and unique source. In addition, the use of PubMed and Highwire retrieved biomedical literature is more professional than Google Scholar. According to the study results suggest that commercial databases can be considered included in the scope of network resources into the open, in order to properly organize network resources and application of bibliographic and full-text. Open access system should improve the accuracy and bibliographic indexing bibliographic completeness. In addition, for the library service should take the following measures in response to: (a) enhance the promotion of commercial database retrieval methods and the use of proper timing; (2) to teach the proper use of open access system retrieval mode; (3) Balance Business open access database and use of the system, in order to achieve rational use of library funds. The follow-up research of this study can be extended to the field of clinical and biomedical evidence-based medicine research. The follow-up research results can be used to understand the biomedical literature’ timeliness, whether the system reaches an open access immediate or practicality. Furthermore, users' satisfaction with open access scholarly publishing research is also an anxious subject to know, and the follow-up study will strengthen efforts.