In the southern Appalachians, the dominant soil order, Ultisols, is highly susceptible to erosion. If left unmanaged these soils can develop into gully systems resulting in land degradation. This study examines gully development through sidewall mass-wasting events at a high temporal resolution using 30 minute time-lapse photography. Prior research at this site found significant mass wasting events occurring between weekly monitoring periods. By shortening the interval of observation to 30-minutes, a more accurate understanding of the frequency and intensity of these mass-wasting events, and their relation to meteorological factors, can be determined. Photographs of a gully (approximately 1.5 m deep by 3 m wide at the top) were captured every 30 minutes from 11/29/17 - 2/18/2018 with a WingScape outdoor time-lapse camera mounted on a plastic stake 3.16 m from the gully facing northwest and upstream into the gully channel. A total of n=1648 images were coded using presence/absence indices for six observed geomorphic processes: creep on NE facing sidewall, creep on SW facing sidewall, slump on NE facing sidewall, slump on SW facing sidewall, channel aggradation, and channel development. Precipitation and temperature data were collected every 5 minutes using a Davis Vantage Pro 2 weather station located 240 m from the gully, and were aggregated to various time intervals. Precipitation received in previous 0.5, 1, 1.5, 2, 3, 6, 12, 24, 36, 48, and 72 hours were calculated for each image. Two binary temperature variables were generated with values of “1” if temperature dropped below 0 °C (32 °F) during the prior 30 minutes or 24 hours, respectively, and “0” otherwise. Logistic regression models (forward conditional method) for the six geomorphic index variables were generated using the precipitation and temperature data. For creep on the NE facing sidewall, the significant independent variables are 3 hour and 72 hour prior rain, and freeze conditions in the previous 0.5 and 24 hours. On the SW facing sidewall, rain and temperature variables were also important for creep; rain in the previous 12 and 24 hours, and freeze conditions within the previous 24 hours were retained in the model. For slumping on both the NE and SW facing sidewall, recent and prolonged rain were important. Specifically, 1, 6, 12, and 24 hour rainfall were retained in both models, with the addition of 3 hour rainfall in the NE facing sidewall slump model. No temperature variables were retained. For channel aggradation (deposition of material in the channel), rain in the prior 12 and 72 hours, and freezing in the prior 24 hours were important, suggesting that freeze-thaw processes loosen the soil, and subsequent rain events carry material into the channel. When rain stops, the material is then deposited in the channel. Interestingly, no viable model could be developed for channel development (erosion) using these parameters. These results will be useful to quantify meteorological controls on gully erosion at short temporal scales.

This thesis deals with the introduction into the topic of time-lapse video creation. It focuses on cases where tripod is not used and therefore it is  necessary to eliminate incurred shortcomings. The main shortcomings are different position of individual frames, different brightness and color adjustment. The next topic describes which principles should be followed during the creation process. Thesis describes and implements methods for elimination of main shortcomings during process long time-lapse videos, which are recorded by hand. Thesis also precisely describes image registration, correction of brightness and colors. Thesis is also considers histograms comparison. Result of this work is application, which eliminates problems described above.

(v anglickém jazyce) Development of tooth primordia in mice is an important model for study of odontogenesis. Several dental rudiments develop during the mouse embryogenesis. These structures develop in functional teeth in their phylogenetically older relatives. Similarly, we can initiate growth of teeth from these germs in some mutant mice. In my diploma thesis we have focused on the importance of rudimentary structures with odontogenic potential in postnatal individuals. As a model of development, we have chosen a cell population originating from rudimentary primordia MS (mesial segment) that develops in diastema of the lower jaw during the embryonic day 12.5. Using the inducible Cre-lox technology we have marked the cells which are part of the signal domain of primordia at this time. As a marker of these cells we have used gene Shh. We have found out that these cells persist prenataly and also postnatally. Further we have isolated this cell area and we have tested it using a variety of methods. We have shown that in the cells of postnatal individual are expressed markers of stem cells (Sox2, Bmi1, Gli1) and also genes for major enamel matrix structural proteins: ameloblastin and amelogenin. The same stem cell markers are also expressed in vitro culture of the isolated cells. This cell population...

The diploma thesis deals with time-lapse electrical resistivity tomography (TL-ERT) of active slope deformations. Slope deformations represent one of the important land-forming processes. Frequently, they can cause considerable property damages and can endanger health and lives of inhabitants. Therefore, we can consider them as potentially dangerous so complete understanding of their dynamics, and their mechanisms of origin, is essential. Electrical resistivity tomography (ERT) then represents an effective geophysical tool for slope deformation investigation. Within diploma thesis, the evaluation of the several different time-series of the ERT measurements was performed. Based on findings of the one- year (August 1013 to July 2014) monitoring of resistivity changes by ERT, and also, based on daily and hourly recurrences of measured resistivity data, the optimum measuring interval has been determined, namely 12 hours. The most applicable electrode arrays and their combinations were suggested based on a testing of different electrode configurations. The results of detailed measurement with 1 m electrode spacing offered the idea of shortening of the total length of the present permanent TL-ERT profile as well as shortening the electrode spacing. These conclusions and proposed adjustments then resulted in...

Sea level rise concerns millions of people in coastal areas across the globe. One of the largest uncertainties to project future sea level rise is the frontal ablation (accounting for calving and submarine melt) at marine ice margins, around the Greenland and Antarctic Ice Sheet. High rates of frontal ablation have been observed to imply, through loss of the buttressing effect but not limited to it, increased mass loss from marine terminating glaciers and hence, associated sea level rise. This study focuses on calving processes at a freshwater lake in northern Sweden, which represents a simpler environment to study calving processes than the marine one, because impacts of tides, salinity, and circulation (all known to be relevant at marine ice-ocean boundaries) can be neglected. A multi-method approach to quantify and characterize calving events is presented here, exploring and analysing the underwater acoustic soundscape at a calving glacier front, in connection with optical, image-based methods such as time- lapse photography, and photogrammetry based on footage acquired by an uncrewed aerial vehicle (UAV). An acoustic detector is developed, tested and applied to data set acquired during 2020, and results indicate that the acoustic detector can be an important complement in the range of tools used to observe, and quantify, calving. Applied in remote locations, where continuous monitoring is difficult and where optical methods are of limited use, collecting acoustic data and monitoring calving by means of its acoustic signature could render insights previously not available (because of lacking data and methodology).

This thesis analyses ice-rich mountain permafrost with regard to its genesis, distribution, deformation and interaction with other environmental factors. The processes influencing ground ice formation in ice-rich and ice-poor mountain permafrost are highlighted. Factors influencing the presence of ice-rich permafrost are identified and their individual or combined effect on frozen ground is determined. Based on these findings, a new permafrost distribution map of Switzerland was created, which specifies permafrost temperature and ice contents and considers rock glacier creep paths. The deformation of rock glaciers is investigated with newly developed monitoring systems and concepts. This enables a better understanding of the processes leading to rock glacier acceleration at different time scales.

This thesis analyses ice-rich mountain permafrost with regard to its genesis, distribution, deformation and interaction with other environmental factors. The processes influencing ground ice formation in ice-rich and ice-poor mountain permafrost are highlighted. Factors influencing the presence of ice-rich permafrost are identified and their individual or combined effect on frozen ground is determined. Based on these findings, a new permafrost distribution map of Switzerland was created, which specifies permafrost temperature and ice contents and considers rock glacier creep paths. The deformation of rock glaciers is investigated with newly developed monitoring systems and concepts. This enables a better understanding of the processes leading to rock glacier acceleration at different time scales.

Nous présentons dans la première partie du document une étude portant sur l'imagerie de temps de vie de fluorescence sur structures dynamiques dans le domaine de fréquence (FD FLIM). Une mesure en FD FLIM est définie par une série d'images présentant une variation d'intensité sinusoïdale. La variation d'un temps de vie se traduit par une variation dans la phase de la sinusoïde décrite par l'intensité. Notre étude comporte deux contributions principales: une modélisation du processus de formation de l'image et du bruit inhérent au système d'acquisition (capteur ICCD) ; une méthode robuste d'estimation du temps vie sur des structures mobiles et des vésicules intracellulaires. Nous présentons ensuite une étude en microscopie de fluorescence portant sur la quantification du transport hétérogène dans un environnement intracellulaire dense. Les transitions entre la diffusion Brownienne dans le cytoplasme et les transports actifs supportés par le cytosquelette sont en effet des scénarios très couramment observés dans des cellules vivantes. Nous montrons que les algorithmes classiques de suivi d'objets nécessaires dans ce contexte, ne sont pas conçus pour détecter les transitions entre ces deux types de mouvement. Nous proposons donc un nouvel algorithme, inspiré de l'algorithme u-track [Jaqaman et al., 2008], qui s'appuie sur plusieurs filtrages de Kalman adaptés à différents types de transport (Brownien, Dirigé ...), indépendamment pour chaque objet suivi. Nous illustrons sur séquences simulées et expérimentales (vimentine, virus) l'aptitude de notre algorithme à détecter des mouvements dirigés rares. / We propose in this manuscript a study of the instrumentation required for the quantification in frequency domain fluorescence lifetime imaging microscopy (FD FLIM). A FD FLIM measurement is defined as a series of images with sinusoidal intensity variations. The fluorescence lifetime is defined as the nanosecond-scale delay between excitation and emission of fluorescence. We propose two main contributions in the area: a modeling of the image process and noise introduced by the acquisition system (ICCD sensor); a robust statistical method for lifetime estimation on moving structures and intracellular vesicles. The second part presents a contribution to the tracking of multiple particles presenting heterogeneous transports in dense conditions. We focus here on the switching between confined diffusion in the cytosol and motor-mediated active transport in random directions. We show that current multiple model filtering and gating strategies fail at estimating unpredictable transitions between Brownian and directed displacements. We propose a new algorithm, based on the u-track algorithm [Jaqaman et al., 2008], based on a set of Kalman filters adapted to several motion types, for each tracked object. The algorithm has been evaluated on simulated and real data (vimentin, virus) data. We show that our method outperforms competing methods in the targeted scenario, but also on more homogeneous types of dynamics challenged by density.

Le cortex cérébral primate a subi des modifications majeures pendant l'évolution qui ont permis le développement de fonctions cognitives supérieures. Un accroissement massif a eu lieu avec l'extension spécifique des couches supragranulaires et une forte expansion tangentielle. Le cortex primate ne possède pas uniquement davantage de neurones, comparé au rongeur, mais aussi des différences qualitatives. Ceci suggère des différences qualitatives pendant le développement du cortex.Une zone proliférative corticale supplémentaire a été identifiée chez le singe macaque: la zone subventriculaire externe (OSVZ) supposée être impliquée dans l'expansion du cortex primate. Mais les propriétés des précurseurs de l'OSVZ restent mal connues. Des techniques de microscopie en temps réel et d'immunofluorescence ont permis de réaliser une description exhaustive des précurseurs de l'OSVZ et de leurs propriétés chez le singe macaque.Nos résultats mettent en évidence des différences primates/rongeurs majeures. Les observations en temps réel révèlent des capacités prolifératives bien plus importantes des précurseurs. Les précurseurs primates de l'OSVZ présentent des taux de prolifération variables pendant la corticogenèse liés à la cinétique du cycle cellulaire. Nos enregistrements ont permis la génération d'une grande base de données de propriétés et lignages de précurseurs et la mise en évidence d’une diversité morphologique inattendue. 5 types ont été identifiés. Impliqués dans des lignages complexes, chaque type a la capacité de s'auto-renouveler et de générer directement des neurones. Parallèlement, nous avons développé une méthode de classification non supervisée des précurseurs corticaux. Cette technique a identifié les mêmes 5 types de précurseurs.Les résultats de cette thèse apportent de nouveaux éléments dans la compréhension des spécificités de la corticogenèse primate qui contribuent à l'expansion corticale et au développement de capacités cognitives supérieures. / The primate cerebral cortex underwent major modifications during evolution that enabled the development of high cognitive functions. A massive enlargement occurred with the specific expansion of the supra granular layers and the apparition of new frontal areas. Not only quantitative differences are found compared to the rodent but also qualitative differences. This points to potential qualitative differences in primate cortical development. An extra proliferating zone had already been identified during macaque corticogenesis: the outer subventricular zone (OSVZ). This zone is assumed to play a key role in the expansion of the primate cortex but the cellular and functional properties of OSVZ precursors remain elusive. We used quantitative long-term time-lapse video-microscopy (TLV) and immunofluorescence in and ex vivo to perform a detailed and exhaustive description of OSVZ precursor types and proliferative abilities at different stages of macaque cortical development. Our results highlight major rodent/primate differences. TLV observations revealed a much higher proliferative potential of OSVZ compared to the rodent SVZ. We report variable rates of proliferation linked to cell-cycle duration in a stage-specific manner. TLV recordings allowed the formation of a large database of primate precursor properties and lineages. This dataset unravelled an unexpectedly high diversity of OSVZ precursor morphologies. Five precursor types were identified. Involved in complex lineages, each precursor type can self-renew and directly generate neurons. In a parallel approach, we developed an unbiased clustering tool to automatically classify cortical precursors. This technique returned the same five precursor types as the morphological categorization. The results of this PhD thesis provide new insights into primate specificities during corticogenesis that contribute to cortical expansion and to the development of higher cognitive abilities.

Les microfaisceaux d’ions ont, au cours de ces dernières décennies, montré leur efficacité dansl’étude des effets des rayonnements ionisants sur le vivant notamment concernant les effets des faiblesdoses ou l’étude de l’effet de proximité. Le CENBG dispose depuis 2003 d’un dispositif permettant la micro-irradiation ciblée d’échantillons biologiques vivants. Les applications des microfaisceaux dans ce domainese sont récemment diversifiées et des études plus fines sur les mécanismes de réparation desdommages ADN radio-induits aux échelles cellulaire et multicellulaire sont devenues possibles via lesévolutions en imagerie par fluorescence et en biologie cellulaire. Ces approches ont nécessité une évolutionimportante de l'instrumentation de la ligne de micro-irradiation du CENBG qui a été entièrementredessinée et reconstruite dans un souci d’optimisation d’apport de nouvelles fonctionnalités. Les objectifsde mes travaux ont été i) la mise en service du dispositif, ii) la caractérisation des performances dusystème, iii) la mise en place de protocoles pour l’irradiation ciblée à dose contrôlée aux échelles cellulaireet multicellulaire, in vitro et in vivo, et le suivi en ligne des conséquences précoces de cette irradiation,iv) la modélisation des irradiations afin d’interpréter les observables biologiques au regard des donnéesphysiques calculées.Ces travaux ont permis i) de caractériser les performances du dispositif : une taille de faisceau d’environ2 μm sur cible et une précision de tir de ± 2 μm, de développer des systèmes de détection d’ions pour uncontrôle absolu de la dose délivrée, ii) d’induire des dommages ADN fortement localisés in vitro, et devisualiser en ligne le recrutement de protéines impliquées dans la réparation de ces dommages,iii) d’appliquer ces protocoles pour générer des dommages ADN in vivo au sein d’un organisme multicellulaireau stade embryonnaire, Caenorhabditis elegans.Ces résultats ouvrent la voie vers des expériences plus fines sur la ligne de micro-irradiation ciblée duCENBG pour étudier les effets de l’interaction des rayonnements ionisants avec le vivant, aux échellescellulaire et multicellulaire, in vitro et in vivo. / The main goal of radiobiology is to understand the effects of ionizing radiations on the living.These past decades, ion microbeams have shown to be important tools to study for example the effects oflow dose exposure, or the bystander effect. Since 2003, the CENBG has been equipped with a system toperform targeted micro-irradiation of living samples. Recently, microbeams applications on this subjecthave diversified and the study of DNA repair mechanisms at the cellular and multicellular scales, in vitroand in vivo, has become possible thanks to important evolutions of fluorescence imaging techniques andcellular biology. To take into account these new approaches, the CENBG micro-irradiation beamline hasbeen entirely redesigned and rebuilt to implement new features and to improve the existing ones. My PhDobjectives were i) commissioning the facility, ii) characterizing the system on track etch detectors, and onliving samples, iii) implementing protocols to perform targeted irradiations of living samples with a controlleddelivered dose, at the cellular and multicellular scales, and to visualize the early consequencesonline, iv) modelling these irradiations to explain the biological results using the calculated physical data.The work of these past years has allowed us i) to measure the performances of our system: a beam spotsize of about 2 μm and a targeting accuracy of ± 2 μm, and to develop ion detection systems for an absolutedelivered dose control, ii) to create highly localized radiation-induced DNA damages and to see onlinethe recruitment of DNA repair proteins, iii) to apply these protocols to generate radiation-induced DNAdamages in vivo inside a multicellular organism at the embryonic stage: Caenorhabditis elegans.These results have opened up many perspectives on the study of the interaction between ionizing radiationsand the living, at the cellular and multicellular scales, in vitro and in vivo.