Only 40 years ago, just three individuals made the journey from Finland/Russia to found the current wolf population in the southwest of Sweden. This population, that to this date descends from less than 10 founders, has a substantial increased extinction risk due to inbreeding. Several previous studies have used SNPs to monitor the level of inbreeding and homozygosity in the population, as well as measure immigration and the inflow of new genetic material. This study uses both short- and long-read data to discover structural variants (SVs) and small indels in the population, so that they may be used to extend the analyses and provide more insight into the current state of the Scandinavian wolf population. After the calling of the SVs, strict filtering and manual curation were applied to the data, thereby removing many false positive calls and increasing confidence in the remaining SVs. Short-read and long-read SV-callers found 31,800 and 57,821 SVs respectively, with relatively little overlap between the two sets. By far, the most common SV-types were deletions and insertions, at about 30,000 each with varying length ranging from a 50 base pairs to several tens of Mbp. Analyses on the data, such as PCAs and parent-offspring trio analyses, reveal high-confidence calls and consistent results between SV-types and SV-callers, as well as a low estimated genotyping error rate. PCAs performed on the SVs resembled those performed on SNPs, which strengthens the credibility of the identified variants. Finally, this study suggests several alternative steps for possible improvement to the dataset, along with some proposals for subsequent research topics that may use the variants discovered in this study.

Ziel dieser Doktorarbeit ist eine umfassende Untersuchung der Heterogenität von Mikroglia aus morphologischer, elektrophysiologischer und transkriptioneller Perspektive mit dem Schwerpunkt auf Unterschiede zwischen weißer und grauer Substanz. Im ersten Kapitel diskutiere ich die morphologische Heterogenität von Mikroglia mit dem Fokus auf Satelliten- und Parenchymale-Mikroglia. Wir führten eine eingehende Analyse mehrerer Hirnareale durch und quantifizierten die Anzahl der Satellitenmikroglia, die mit verschiedenen neuronalen Subtypen in Kontakt stehen. Wir fanden heraus, dass die Anzahl der Satellitenmikroglia stark mit der neuronalen Dichte eines bestimmten Bereichs korreliert. Im zweiten Kapitel dieser Arbeit untersuche ich die transkriptionelle Heterogenität von Mikroglia aus weißer und grauer Substanz, wobei ich die in Gliazellen neu etablierte Patch-seq-Methode anwende. Diese Methode ermöglicht es eine Kombination aus morphologischen, lektrophysiologischen und transkriptionellen Profilen einzelner Zellen zu erhalten, die es erlauben, zelluläre Unterschiede zu charakterisieren. Wir identifizieren einen zellulären Subtyp, wenn wir den Patch-seq-Datensatz mit FACS-basierter Einzelzell-RNA-seq-Datensätzen vergleichen. Dieser Subtyp gehört eindeutig zu dissoziierten Gewebeproben und ist durch die Expression von Stress-assoziierten Genen charakterisiert. Im dritten Kapitel wende ich mich der Frage zu, wie Transkripte mittels SLAM-seq nachverfolgt werden können, die während der Dissoziation des Gewebes entstehen. Das Verfahren ermöglicht es mRNA, die während der Dissoziation der Probe entsteht, metabolisch zu markieren, rechnerisch zu identifizieren und zu entfernen. Indem wir die markierten Transkripte aus dem Mikroglia “entfernen”, beobachten wir, dass ein „aktivierter Mikroglia“-Subtyp zur allgemeinen Mikroglia-Population gehört. / The aim of this doctoral work is to provide a comprehensive study and overview on the topic of the heterogeneity of microglia in the normal adult mouse brain from the morphological, electrophysiological and transcriptional perspective with the focus on differences between white and grey matters. In the first Chapter, I discuss the morphological heterogeneity of microglia in the brain with the focus on two morphologically distinct classes: satellite and parenchymal microglia. We performed an in-depth analysis of multiple brain areas and quantified the number of satellite microglia which is in contact with different neuronal subtypes. We found that satellite microglia numbers are highly correlated with neuronal densities of a certain area, while showing no preferences for any of the neuronal types. In Chapter two of this work, I study transcriptional heterogeneity of microglia from white and grey matters. For this I am employing Patch-seq, which we newly established in glial cells. This method allows a combination of morphological, electrophysiological and transcriptional profiles of single cells to assess their differences. When comparing Patch-seq dataset to the previously published FACS isolated single cell RNA-seq microglia datasets, we find a subtype of cells which uniquely belongs to FACS sample and is characterized by expression of stress-associated genes. This finding points out to the fact of dissociation-related artifacts in the single cell RNA-seq data which are not present in situ. In the third chapter, I identified transcripts which are induced during the dissociation of the tissue by employing the SLAM-seq method. This procedure allows to metabolically label newly transcribed mRNA and computationally remove transcripts from the sample. By removing the labeled transcripts from the dataset of cells isolated from the hippocampus via enzymatic dissociation, we observe that an “activated microglia” subtype merges with the general microglia population.

No description available.

Management and conservation of populations of animals requires information on where they are, why they are there, and where else they could be. These objectives are typically approached by collecting data on the animals’ use of space, relating these to prevailing environmental conditions and employing these relations to predict usage at other geographical regions. Technical advances in wildlife telemetry have accomplished manifold increases in the amount and quality of available data, creating the need for a statistical framework that can use them to make population-level inferences for habitat preference and space-use. This has been slow-in-coming because wildlife telemetry data are, by definition, spatio-temporally autocorrelated, unbalanced, presence-only observations of behaviorally complex animals, responding to a multitude of cross-correlated environmental variables. I review the evolution of techniques for the analysis of space-use and habitat preference, from simple hypothesis tests to modern modeling techniques and outline the essential features of a framework that emerges naturally from these foundations. Within this framework, I discuss eight challenges, inherent in the spatial analysis of telemetry data and, for each, I propose solutions that can work in tandem. Specifically, I propose a logistic, mixed-effects approach that uses generalized additive transformations of the environmental covariates and is fitted to a response data-set comprising the telemetry and simulated observations, under a case-control design. I apply this framework to non-trivial case-studies using data from satellite-tagged grey seals (Halichoerus grypus) foraging off the east and west coast of Scotland, and northern gannets (Morus Bassanus) from Bass Rock. I find that sea bottom depth and sediment type explain little of the variation in gannet usage, but grey seals from different regions strongly prefer coarse sediment types, the ideal burrowing habitat of sandeels, their preferred prey. The results also suggest that prey aggregation within the water column might be as important as horizontal heterogeneity. More importantly, I conclude that, despite the complex behavior of the study species, flexible empirical models can capture the environmental relationships that shape population distributions.

Cette recherche vise à résoudre un problème particulier du contrôle de vibration des structures intelligentes. Notre objectif est de réduire les vibrations dans une zone spécifique de la structure intelligente avec une perturbation qui couvre une large gamme de fréquences. De plus, dans cette zone spécifique, ni l'actionnement ni la détection ne sont possibles.Ici, nous faisons face à plusieurs défis principaux. Premièrement, nous devons contrôler les vibrations d’une zone spécifique de la structure, alors que nous n’avons accès aux mesures que dans d’autres zones. Deuxièmement, la large bande passante de la perturbation implique que nombreux modes doivent être contrôlés au même temps, ce qui nécessite l'utilisation de plusieurs actionneurs et capteurs. Cela conduit à un contrôleur MIMO difficile à obtenir avec les méthodes classiques de conception de contrôleur. Troisièmement, il faut éviter le problème de propagation, qui consiste à garantir la stabilité en boucle fermée lorsque le contrôleur basé sur un modèle est appliqué à la configuration réelle. Pour relever ces défis, nous étudions deux stratégies de contrôle: le contrôle centralisé et le contrôle distribué.Pour le contrôle centralisé, nous proposons une méthodologie qui nous permet d’obtenir un contrôleur MIMO simple permettant de relever ces défis. Tout d'abord, plusieurs techniques de modélisation et d’identification sont appliquées pour obtenir un modèle précis d'ordre faible de la structure intelligente. Ensuite, une méthode de synthèse basée sur le contrôle H_∞ avec un critère H_∞ particulièrement proposé est appliquée. Ce critère H_∞ intègre plusieurs objectifs de contrôle, y compris les défis principaux. En particulier, le problème de débordement se transforme en un problème de stabilité robuste et sera garanti en utilisant ce critère. Le contrôleur H_∞ obtenu est une solution standard du problème H_∞. Le contrôleur final est obtenu en simplifiant ce contrôleur H_∞ sans perdre la stabilité en boucle fermée ni dégrader les performances. Cette méthodologie est validée sur une structure de poutre avec des transducteurs piézoélectriques et la zone centrale est celle où les vibrations devraient être réduites. L'efficacité du contrôleur obtenu est validée par des simulations et des expériences.Pour le contrôle distribué, on considère la même structure de poutre et les mêmes objectifs de contrôle. Il existe des méthodes visant à concevoir des contrôleurs distribués pour les systèmes spatialement interconnectés. Cette recherche propose une méthode basée sur la FEM, associée à plusieurs techniques de réduction de modèle, permettant de discrétiser spatialement la structure de poutre et d'en déduire les modèles d’espace d'état des sous-systèmes interconnectés. La conception des contrôleurs distribués ne sera pas abordée dans cette recherche. / This research aims at solving a particular vibration control problem of smart structures. We aim at reducing the vibration in a specific zone of the smart structure under the disturbance that covers a wide frequency band. Moreover, at this specific zone, neither actuation nor sensing is possible.Here we face several main challenges. First, we need to control the vibration of a specific zone of the structure while we only have access to measurements at other zones. Second, the wide bandwidth of the disturbance implies that numerous modes should be controlled at the same time which requires the use of multiple actuators and sensors. This leads to a MIMO controller which is difficult to obtain using classical controller design methods. Third, the so-called spillover problem must be avoided which is to guarantee the closed-loop stability when the model-based controller is applied on the actual setup. To tackle these challenges, we investigate two control strategies: the centralized control and the distributed control.For centralized control, we propose a methodology that allows us to obtain a simple MIMO controller that accomplishes these challenges. First, several modeling and identification techniques are applied to obtain an accurate low-order model of the smart structure. Then, an H_∞ control based synthesis method with a particularly proposed H_∞ criterion is applied. This H_∞ criterion integrates multiple control objectives, including the main challenges. In particular, the spillover problem is transformed into a robust stability problem and will be guaranteed using this criterion. The obtained H_∞ controller is a standard solution of the H_∞ problem. The final controller is obtained by further simplifying this H_∞ controller without losing the closed-loop stability and degrading the performance. This methodology is validated on a beam structure with piezoelectric transducers and the central zone is where the vibration should be reduced. The effectiveness of the obtained controller is validated by simulations and experiments.For distributed control, we consider the same beam structure and the same control objectives. There exist methods aiming at designing distributed controllers of spatially interconnected system. This research proposes a FEM based method, combined with several model reduction techniques, that allows to spatially discretize the beam structure and deduce the state-space models of interconnected subsystems. The design of distributed controllers will not be tackled in this research.

La méconnaissance de l’Auvergne durant l’Antiquité tardive tient en partie à l’absence de référentiels chrono-typologiques. La découverte récente d’ensembles céramiques conséquents et la reprise de données anciennes permettent aujourd’hui de combler ce vide documentaire. Ce travail se propose ainsi de dresser un nouveau panorama du territoire arverne durant l’Antiquité tardive et le très haut Moyen Âge (fin IIIe-milieu VIIIe siècle), d’un point de vue économique et culturel par l’étude de la céramique. L’évolution des répertoires montre que les faciès antiques persistent jusqu’au VIe siècle de même que les pratiques culinaires et les manières de table. Diversifiées jusqu’au Ve siècle, les formes et les catégories céramiques s’uniformisent au VIe siècle et, à partir du VIIe siècle, les productions réductrices et les récipients fermés à usage culinaire prédominent. L’étude d’ensembles funéraires des IVe et Ve siècles montre l’insertion du territoire arverne dans l’évolution des pratiques funéraires alors en cours en Gaule. L’Auvergne se démarque néanmoins par le nombre élevé des vases céramiques déposés dans les tombes et par la préférence donnée aux récipients à solides dans la composition du repas funéraire.Les importations indiquent que le territoire arverne est bien inséré dans les circuits commerciaux à la fin de l’Antiquité. Leurs quantités parfois faibles suggèrent cependant un approvisionnement parcimonieux, qui place l’Auvergne aux confins des aires de diffusion de la plupart des productions commercialisées, comme en « bout de circuits ». Les correspondances établies avec les céramiques des IVe et Ve siècles des autres régions de Gaule du Centre montrent l’existence de traditions de fabrication communes et l’ensemble de ces territoires pourrait appartenir à une même entité économique et culturelle. Le sud du territoire arverne apparaît en revanche tourné vers les régions méridionales, comme l’a montré l’étude des céramiques des VIe et VIIe siècles du site lozérien de La Malène, influencées par les faciès de Gaule du Sud / The sparse knowledge of the late antiquity in Auvergne is partly due to the absence of chronological typology for this period. The recent uncovering of significant ceramic assemblages and the reassessment of pastdata make it possible today to fill this research gap. This thesis attempts to bring new light to the Arverne territory, its economy and culture, in the late antiquity and the early middle ages (from the late 3rd century to the mid-8th century), through the study of its pottery. The evolution observed in the repertory shows that the antique facies remained until the 6th century, as well as the culinary practices and table manners. Until the 5th century,forms and types of ceramics are very varied, becoming more standardized in the next century, and finally starting in the 7th century, closed culinary vessels are predominant.The study of funerary assemblages from the 4th and 5th centuries, demonstrates how the Arverne territory participated in the general evolution of funerary practices in Gaul. However the Auvergne region stands out by the considerable number of ceramic vases found in tombs and the clear preference for solid food vessels in funerary repasts.The presence of imported goods is evidence that the Arverne territory was part of the commercial routes by the end of Antiquity. However the small amounts of importations imply a parsimonious procurement, which would mean that the Auvergne region was actually located on the outer limits of the distribution areas of most industrial productions. The correlations established with 4th and 5th century pottery from other areas of Central Gaul could be proof of a common tradition of production, and how such territories could have possibly belonged to a same cultural and economic entity. The South of the Arverne territory seemed however more influenced by southern Gaul as shown by the study of 6th and 7th century pottery from the lozerian site of La Malène

Současné vizuální markerové systémy mají jednu zásadní nevýhodu oproti tzv. markerless přístupům - pohyb kamery je omezen na oblast pokrytou markery. V každém snímku musí být marker dostatečně velký, aby jej bylo možné identifikovat a vypočítat pozici a rotaci kamery. Zároveň musí být dostatečně malý, aby se celý (nebo alespoň jeho podstatná část) vešel do záběru kamery. Avšak tyto požadavky jsou protichůdné. Tato práce nabízí řešení tohoto problému za pomoci konceptu Marker Fields. Jde o strukturu, jejíž přítomnost je možné v obraze kamery snadno detekovat a identifikovat část, na kterou se kamera právě dívá, a to na základě jakékoli (malé) podoblasti s definovanou velikostí. Aby bylo možné podoblasti identifikovat zblízka i zdálky, nejsou od sebe odděleny, ale do velké míry se překrývají. V této práci jsou vysvětleny různé implementace konceptu marker fields, spolu s jejich zamýšleným použitím a výhodami a nevýhodami. Jako důkaz použitelnosti marker fields v reálném světě, se druhá největší část této práce věnuje popisu jejich reálných aplikací.

The aim of this diploma thesis is trying to solve difficulties connected with administrative buildings. In this thesis we are talking about possibility that administrative building can have low energy footprint. Most of energy consumption of administrative building is not created by heating but mostly by cooling and by consumption of office equipment. That is why there have been used modern equipment of the building as well as automatic control of building equipment.

Piscivorous birds are often blamed for causing significant damage to fish stocks. Various methods are used to determine the composition of their food, each of them has limits in its ability to determine the complete food spectrum. This work maps the complete food composition of 14 species of fish-eating birds with a method that is not commonly used. Method used in this work uses analysis of publicly available photos on Google.com. In addition to the complete composition of the food, the species composition of the non-fish part of the prey was also determined, and in the case of the Great Cormorant (Phalacrocorax carbo), also the length of the fishes it catches. The aim of this work is to reveal the usability of this method for these purposes. A total of 2350 retrieved photographs were analyzed. The results obtained by photo analysis are in all cases compared with data in the available literature. For representatives of heron birds (Ardeidae), the analysis of photographs provided good information on the food spectrum of individual birds and on the qualitative composition of the non-fish component. It also provided relatively good information on the diet of the White-tailed Eagle (Haliaeetus albicilla), but the bird part of the prey was slightly underestimated. In the diet of the Great Crested Grebe...

The aim of this thesis is to present, analyse, compare and evaluate the current state of digital repositories at universities in the Czech Republic that use a software application for their digital repository. A theoretical part, which introduces the reader into the issue of compilation and operating of digital repositories in the Czech academic context, precedes the practical reserach. The crucial chapter of the practical part are the results of the actual analysis. The results of a supplementary survey of universities that do not run a digital repository with usage of software application and choose a different way of storage and access to their grey literature draw on the results of this analysis. The conclusion of the entire thesis is the outline of future development of the investigated issue and the perspective of further progress of the Czech academic milieu.