Time-lapse fluorescence live cell imaging has been widely used to study various dynamic processes in cell biology. As the initial step of image analysis, it is important to localize and segment cell edges with higher accuracy. However, fluorescence live-cell images usually have issues such as low contrast, noises, uneven illumination in comparison to immunofluorescence images. Deep convolutional neural networks, which learn features directly from training images, have successfully been applied in natural image analysis problems. However, the limited amount of training samples prevents their routine application in fluorescence live-cell image analysis. In this thesis, by exploiting the temporal coherence in time-lapse movies together with VGG-16 [1] pre-trained model, we demonstrate that we can train a deep neural network using a limited number of image frames to segment the entire time-lapse movies. We propose a novel framework, vU-net, which combines the advantages of VGG-16 [1] in feature extraction and U-net [2] in feature reconstruction. Moreover, we design an auxiliary convolutional block at the end of the architecture to enhance edge detection. We evaluate our framework using dice coefficient and the distance between the predicted edge and the ground truth on high-resolution image datasets of an adhesion marker, paxillin, acquired by a Total Internal Reflection Fluorescence (TIRF) microscope. Our results demonstrate that, on difficult datasets: (i) The testing dice coefficient of vU-net is 3.2% higher than U-net with the same amount of training images. (ii) vU-net can achieve the best prediction results of U-net with one third of training images needed by U-net. (iii) vU-net produces more robust prediction than U-net. Therefore, vU-net can be more practically applied to challenging live cell movies than U-net since it requires a small size of training sets and achieved accurate segmentation.

A resolução temporal é uma questão-chave em Paleontologia, uma vez que a sua magnitude define a precisão dos estudos não somente paleoecológicos como também evolutivos. A resolução temporal é estimada pela magnitude de time-averaging (mistura de gerações em uma camada, uma amostra). Tais estimativas têm sido amplamente conduzidas em ambientes marinhos recentes. A plataforma continental do sul do Brasil (PSB; 22°S – 34°S) tem sido um laboratório natural para estudos desta natureza desde o início do século XXI. Consequentemente, possui um amplo acervo de dados disponíveis para comparação. Neste contexto, esta tese visou responder (i) qual a magnitude do time-averaging em acumulações de bivalves da PSB? (ii) como este processo varia ao longo de gradientes espaciais? e (iii) como o time-averaging reflete na informação biológica preservada no registro fóssil? Para isto, mais de 140 espécimes de bivalves foram datados integrando racemização de aminoácidos e 14C AMS. Além disto, análises tafonômicas foram realizadas em todas as amostras datadas, incluindo mais sete amostras em sedimentos lamosos. A resolução temporal (time-averaging) e a variabilidade total de idades (mistura temporal) basearam-se em uma nova abordagem numérica, a estatística bayesiana, que integra os erros e as incertezas derivadas da distribuição posterior dos resíduos associados com os modelos resultantes das calibrações das idades. As tendências onshore-offshore — aumento da mediana e da uniformidade das curvas de frequência de distribuição de idades, redução da variabilidade tafonômica, ainda que a escala do time-averaging seja invariante — provavelmente refletem a interação entre as mudanças do nível relativo do mar e da bioprodutividade mais elevada em águas menos profundas. / The temporal resolution of the fossil record plays a key role in paleontology because it determines the scale and the precision of paleoecological and evolutionary studies. The temporal resolution of the fossil record is estimated by the magnitude of time-averaging (non-contemporaneous generations preserved in a single layer, a bulk-sample). Quantitative estimates of time-averaging have been conducted primarily on mollusk shells from modern shallow-water marine settings. Most of them have been addressed in the Southern Brazilian continental shelf (SBS; 22°S up to 34°S), which is considered a natural laboratory for several similar studies since the earlier of current century (XXI). Consequently, the SBS has several available datasets that allow comparisons of the new results displayed here with those previous data. Thus, this thesis aimed answer (i) what is the magnitude of time-averaging on SBS mollusk death assemblages? (ii) how does time-averaging vary across spatial gradients? and (iii) how does time-averaging can reflect on the preservation of the fossil record? Here, >140 specimens were individually dated using amino acid racemization calibrated using radiocarbon ages (14C). In addition, taphonomic analyses were conducted in all samples, including more seven muddy sites. The time-averaging and the total age variability was based on a Bayesian approach that integrates the estimation errors and uncertainties derived from the posterior distribution associated with the 14C–AAR calibration average model. The onshore-offshore trends — increased median age, decreased skewness of age distributions, decreased taphonomic variation, yet the invariant scale of time-averaging — likely reflect the interplay between sea-level changes and elevated bioproductivity in shallower water settings.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1981. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND ENGINEERING. / Includes bibliographical references. / by Arthur Douglas Fisher. / Ph.D.

The need for intergroup reconciliation programmes emerges within the prevailing narrative of cultural conflict. However, failing attempts to resolve conflict at the macro (political) level of society have called for a unique approach that seeks to address these issues creatively at the first point of contact. Therefore, the last twenty years have seen a proliferation of non-profit group workshops and interventions aimed at engaging groups in a diversity of dialogue. To date there have been very few of these interventions that have addressed conflict therapeutically at the micro level of society– at which communities interact directly with another. The aim of this research was to conduct an explorative mixed method study into how an intergroup encounter intervention between Palestinians and Israelis could encourage participants to understand each other as human beings with shared fears, hopes and rights that may surpass assumptions of the other as ‘the enemy’, thereby encouraging participants to ‘give the other a human face’. Conducted with a mixed group of twenty-eight participants, a pre-to-post survey measure analysed behavioural change, while a six-month follow-up interview with four participants explored the impact of participating in the acquaintance seminar on participants lived experiences. Final analysis indicated that while there was a trend towards behavioural change, the outcome was statistically non-significant. Meanwhile interpretive phenomenological analysis produced five key master themes that highlighted the impact of change and the contextual challenges of living with conflict. Managing new relationships and cultural barriers highlighted the key contextual challenges that participants were faced with. This highlights a need for investing resources and training into group conflict programmes that are promoted by key counselling psychology principles of practice. Overall, working with conflict is considered a relevant and unique opportunity for counselling psychologists and group facilitators, most of whom have no formal training or resources for working with conflict resolution in minority groups.

Although significant progress has been made in imaging devices during the past few decades, the photographs acquired by digital cameras are still far from perfection due to the physical limitations of hardware such as aperture, lens and sensor. This fact brings out the demand for study on image enhancement: a computational technique that aims to improve the interpretability or perception of information in photographs for human viewers. The work in this thesis mainly focuses on three tasks in image enhancement. / Finally, since the radiance of the real world spans several orders of magnitude and its dynamic range dramatically exceeds the capability of the current digital cameras, there often exist some undesirable over- or under-exposed regions in a photograph. The third part of this thesis aims at producing one great looking well-exposed image that is virtually impossible with a single exposure by compositing a stack of photos at different exposures taken with a conventional camera. Particularly, a simple but effective method is presented to describe how to take advantage of the gradient information to accomplish exposure composition in both static and dynamic scenes. Compared to conventional high dynamic range (HDR) imaging work, the proposed approach is quite appealing in practice since it is computationally efficient and easy to use, and frees users from the tedious radiometric calibration and tone mapping steps. / Firstly, since the camera sensor has limited resolution, the acquired images cannot capture the scene very detailedly. Hence, people often resort to a postprocessing technique called super-resolution (SR) to enhance the resolution of the captured images. In the first part of this thesis, two approaches are presented to address the challenging single image SR problem, which is to recover a high-resolution (HR) image from one low-resolution (LR) input. Specifically, a novel learning-based framework is designed specifically for face image SR task from the perspective of DCT domain. In addition, an efficient two-step scheme is developed to super-resolve generic image by exploiting the salient edges of the input LR image. / Secondly, due to the limitation of lens and aperture, some cameras cannot produce pleasant photographs with desired focus setting. For example, portrait photography that requires shallow depth of field (DOF) is not allowed when using the compact point-and-shoot cameras. In the second part of this thesis, a new and complete postprocessing-based focus editing system that is able to handle the tasks of focus map estimation, image refocusing and defocusing, is developed to overcome the optical limitations and create different kinds of novel photos with desired focus setting from an imperfect photo. / Throughout this work, extensive experiments on various real and synthetic image data are conducted to evaluate the performance of the proposed algorithms. / Zhang, Wei. / Adviser: Wai-Kuen Chan. / Source: Dissertation Abstracts International, Volume: 73-03, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 116-125). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Efferocytosis, the clearance of apoptotic cells including apoptotic neutrophils by macrophage phagocytosis, is a key cellular mechanism for resolution of inflammation and tissue repair. Cyclin-dependent kinases (CDKs) 7 and 9 phosphorylate RNA polymerase II that is vital for neutrophil transcriptional capacity. CDK inhibitors such as R-roscovitine, and the more selective inhibitor AT7519, induce neutrophil apoptosis and promote resolution of several mouse models of inflammation including acute lung inflammation. The hypothesis investigated here was that AT7519 would promote neutrophil apoptosis (i) in the infarcted heart, leading to macrophage polarisation, angiogenesis, reduced infarct expansion and retention of cardiac function and (ii) in the peritoneum, enhancing resolution of sterile peritonitis. AT7519 (1μM) induced apoptosis of mouse unstimulated-bone marrow derived neutrophils and thioglycollate-stimulated neutrophils in vitro in a time- and caspase-dependent manner, but did not alter activation assessed by calcium flux in response to the synthetic formyl peptide (fMLF) or platelet-activating factor (PAF). Only high concentrations of AT7519 (10 μM) induced monocyte/macrophage apoptosis and this was likely due to saturated phagocytosis of apoptotic neutrophils induced by high concentration of AT7519. Myocardial infarction (MI) was induced by coronary artery ligation in adult male mice and infarct volume was assessed 7 or 21 days later by in vitro optical projection tomography (OPT). The novel use of OPT for this purpose was validated by demonstrating correlation with infarct volume obtained by late-gadolinium enhanced magnetic resonance imaging in vivo and with infarct area assessed by histological staining (Masson’s Trichrome) in tissue sections. AT7519 (30 mg/kg i.p.) increased the number of apoptotic neutrophils (cleaved caspase-3 and Ly6G +ve) in the heart when administered after MI, but this was not associated with any subsequent alteration in macrophage polarisation, vessel density, infarct expansion or structural and functional remodelling of the left ventricle. In contrast, induction of neutrophil apoptosis by AT7519 (30mg/kg i.p.) successfully promoted macrophage polarisation and the resolution of inflammation associated with peritonitis elicited by either 10% thioglycollate or by 1mg zymosan. AT7519 treatment also reduced the number of CD19+ B cells, Foxp3+CD4+ T cells and eosinophils in peritoneal lavage, and prolonged the phase of monocyte recruitment in zymosan-induced peritonitis. In conclusion, AT7519 successfully induced mouse neutrophil apoptosis in vitro, as well as in vivo in experimental MI and peritonitis. Subsequent promotion of inflammation resolution in peritonitis was not matched by improved outcome following MI. Unexpected effects of CDK inhibition on monocytes, T cells and eosinophils that are necessary for myocardial infarct repair may have compromised any beneficial effects resulting from promotion of in situ neutrophil apoptosis. CDK inhibition may therefore have therapeutic potential for the treatment of peritonitis, but not for prevention of infarct expansion and detrimental ventricular remodelling after MI.

The settlement of petroleum expropriation disputes has been a challenging issue in the petroleum industry since the earliest cases. The issue, principally, relates to foreign investors' right to investment protection and the sovereign right of states, the clash of which causes such disputes. Striking a balance between these conflicting rights in order to save the disputants' relationship is a critical concern given the interdependent relationship of disputants which manifests itself in a cyclical manner. This in turn highlights the importance of finding a suitable dispute resolution method to reach the most appropriate and balanced resolution from both parties' viewpoint. Impartiality is, in this context, a key element when determining the most suitable method for resolving expropriation disputes. This is so considering that the reason for the abandonment of diplomatic protection and litigation as methods for resolving expropriation disputes was concerns over their partiality towards one of the disputants. Currently, with the proliferation of investment treaties, treaty-based arbitration has become the most popular method for resolving such disputes. However, the suitability of treaty-based arbitration is criticised as a process which is likely to be partial in favour of investors and their investment protection rights. Such a partiality is likely to be found in treaty-based arbitration's origin, substance and procedural aspects. Therefore, it can be argued that there is room for mediation as an alternative dispute resolution method to be adopted and supplemented arbitration for settlement of petroleum expropriation disputes. In fact, mediation enjoys various qualities which makes it especially attractive for such disputes, including its time and cost efficiency, its ability to explore win-win settlement options and to save the disputing parties' relationship, and the flexibility and collaborative nature of the process. More importantly, its self-determination principle is a feature which guarantees the impartiality of mediation. However, mediation, like other dispute resolution methods, is not without its disadvantages. It faces challenges with regard to its voluntary and non-binding nature, confidentiality, its inability to deal with the political overtones of petroleum expropriation disputes, its retarding effect on jurisprudence development and disputants' lack of familiarity with the process. Nonetheless, having proposed some solutions to these shortcomings, this thesis concludes that mediation should be used and encouraged more systematically for resolving petroleum expropriation disputes.

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Let Y be a smooth complex projective Calabi{Yau threefold. Donaldson-Thomas invariants [Tho00] are integer invariants that virtually enumerate curves on Y. They are organised in a generating series DT(Y) that is interesting from a variety of perspectives. For example, well-known series in mathematics and physics appear in explicit computations. Furthermore, closer to the topic of this thesis, the generating series of birational Calabi-Yau threefolds determine one another [Cal16a]. The crepant resolution conjecture for Donaldson-Thomas invariants [BCY12] conjectures another such comparison result. It relates the Donaldson{Thomas generating series of a certain type of three-dimensional Calabi-Yau orbifold to that of a particular resolution of singularities of its coarse moduli space. The conjectured relation is an equality of generating series. In this thesis, I first provide a counterexample showing that this conjecture cannot hold as an equality of generating series. I then verify that both generating series are the Laurent expansion about different points of the same rational function. This suggests a reinterpretation of the crepant resolution conjecture as an equality of rational functions. Second, following a strategy of Bridgeland [Bri11] and Toda [Tod10a, Tod13, Tod16a], I prove a wall-crossing formula in a motivic Hall algebra relating the Hilbert scheme of curves on the orbifold to that on the resolution. I introduce the notion of pair object associated to a torsion pair, putting ideal sheaves and stable pairs on the same footing, and generalise the wall-crossing formula to this setting, essentially breaking the former in many pieces. Pairs, and their wall-crossing formula, are fundamentally objects of the bounded derived category of the Calabi-Yau orbifold. Finally, I present joint work with J. Calabrese and J. Rennemo [BCR] in which we use the wall-crossing formula and Joyce's integration map to prove the crepant resolution conjecture for Donaldson-Thomas invariants as an equality of rational functions. A crucial ingredient is a result of J. Rennemo that detects when two generating functions related by a wall-crossing are expansions of the same rational function.

Yang, Mei. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 73-75). / Abstracts in English and Chinese. / THESIS COMMITTEE --- p.II / ABSTRACT --- p.III / 中文摘要 --- p.V / ACKNOWLEDGENTS --- p.VI / TABLE OF CONTENTS --- p.VII / LIST OF FIGURES --- p.IX / LIST OF TABLES --- p.X / Chapter CHAPTER 1 --- INTRODUCTION --- p.1 / Chapter 1.1 --- Matrix isolation spectroscopy --- p.1 / Chapter 1.2 --- Properties of Molecular Hydrogen： A Review --- p.3 / Chapter 1.3 --- Unique properties of solid hydrogen --- p.8 / Chapter CHAPTER 2 --- THEORETICAL BACKGROUND --- p.12 / Chapter 2.1 --- Multipole moments of molecules --- p.12 / Chapter 2.2 --- POLARIZABILITY --- p.14 / Chapter 2.3 --- Pair intermolecular potential --- p.15 / Chapter 2.4 --- Multipole induced transitions --- p.20 / Chapter CHAPTER 3 --- THEORY OF MATRIX ISOLATED 02 IN SOLID PARAHYDROGEN --- p.24 / Chapter 3.1 --- Structural properties of 1602 --- p.24 / Chapter 3.1.1 --- Group theoretical treatment --- p.24 / Chapter 3.1.2 --- Rovibrational wavefunctions and energies --- p.26 / Chapter 3.2 --- O2 isolated in hcp crystal field of parahydrogen --- p.31 / Chapter 3.2.1 --- Group theory --- p.31 / Chapter 3.2.2 --- Crystal field splitting --- p.37 / Chapter 3.2.3 --- Effect of quadrupolar induction --- p.42 / Chapter 3.2.4 --- Pure vibrational transitions --- p.42 / Chapter 3.2.5 --- Calculation of quadrupole matrix elements --- p.47 / Chapter CHAPTER 4 --- RESULTS AND DISCUSSION --- p.54 / Chapter 4.1 --- Results --- p.55 / Chapter 4.1.1 --- Effect of quadrupolar induction --- p.55 / Chapter 4.1.2 --- Crystal field splitting of rovibrational levels of O2 in p-H2 matrix --- p.57 / Chapter 4.1.3 --- Predicted pure vibrational spectrum --- p.64 / Chapter 4.2 --- Discussion and Conclusion --- p.67 / REFERENCE --- p.73