Crystal Structure Determination Of Two New Red Fluorescent Proteins By X-Ray Crystallography

Ph.D. Thesis. University of Hawaiʻi at Mānoa 2017

In Vitro Evolutionary Dynamics of C. albicans during Adaptation to Fluocnazole

Many drug-resistant mechanisms in Candida albicans (C. albicans), a clinical important fungal pathogen, have been well characterized. However, few studies investigated the emergence of drug resistance from the evolutionary perspective and little is known about the evolutionary trajectories during the adaptation to the drug. Here, we examined the evolutionary dynamics of C. albicans both in the presence and absence of fluconazole, a first line drug, using the visualizing evolution in real-time (VERT) method. Evolutionary dynamics of replicate C. albicans populations, either in the presence or absence of fluconazole, were determined and adaptive mutants arose in the populations were systematically isolated using the VERT method. Drug susceptibility assays were performed to measure the fluconazole minimum inhibitory concentration (MIC) for the adaptive isolates from drug-exposed populations. Analysis of the evolutionary dynamics revealed that mutations arose more frequently in the presence of the drug compared to the absence of the drug and the drug-resistant mutations occurred in independent lineages, suggesting a heterogeneous nature of the populations during the adaptation. In addition, fitness effects were evaluated for each adaptive mutant both in the presence and absence of drug and we found most of them gained significant increase in the drug resistance without a fitness cost in the absence of the drug. Interestingly, the aneuploidy and gross chromosomal rearrangements, common drug-resistant mechanisms, were not responsible for the increased resistance to fluconazole of most adaptive isolates, suggesting single-nucleotide polymorphisms (SNPs) or other stable unknown chromosomal rearrangements may contribute to the increased drug resistance

Improved Deep Forest Mode for Detection of Fraudulent Online Transaction

As the rapid development of online transactions, transaction frauds have also emerged seriously. The fraud strategies are characterized by specialization, industrialization, concealment and scenes. Anti-fraud technologies face many challenges under the trend of new situations. In this paper, aiming at sample imbalance and strong concealment of online transactions, we enhance the original deep forest framework to propose a deep forest-based online transaction fraud detection model. Based on the BaggingBalance method we propose, we establish a global sample imbalance processing mechanism to deal with the problem of sample imbalance. In addition, the autoencoder model is introduced into the detection model to enhance the representation learning ability. Via the three-month real online transactions data of a China's bank, the experimental results show that, evaluating by the metric of precision and recall rate, the proposed model has a beyond 10 % improvement compared to the random forest model, and a beyond 5 % improvement compared to the original deep forest model

1,3-Dimethyl-1H-indole-2-carbonitrile

The title compound, C11H10N2, crystallizes with two mol­ecules in the asymmetric unit, both of which are essentially planar (r.m.s. deviations = 0.014 and 0.016 Å). In the crystal, aromatic π–π stacking inter­actions occur [shortest centroid–centroid separation = 3.5569 (11) Å]

Effective skeleton stress and void ratio for constitutive modelling of fiber-reinforced sand

Inclusion of flexible fibers such as polypropylene and polyester is an effective method for soil improvement, as it significantly enhances the soil strength and ductility. A proper constitutive model is essential for assessing the stability and serviceability of fiber-reinforced slopes/foundations. A new method for constitutive modeling of fiber-reinforced sand (FRS) is proposed. It assumes that the strain of FRS is dependent on the deformation of the sand skeleton only, while the effective skeleton stress and effective skeleton void ratio, which should be used in describing the dilatancy, plastic hardening and elastic stiffness of FRS, are affected by fiber inclusion. The effective skeleton stress is dependent on the shear strain level, and the effective skeleton void ratio is affected by the fiber content and sample preparation method. A critical state FRS model in the triaxial stress space is proposed using the concept of effective skeleton stress and void ratio. Four parameters are introduced to characterize the effect of fiber inclusion on the mechanical behavior of sand, all of which can be easily determined based on triaxial test data on FRS, without measuring the stress–strain relationship of individual fibers. The model is validated by triaxial compression test results on four fiber-reinforced sands under loading conditions with various confining pressures, densities and stress paths. Potential improvement in the model for incorporating fiber orientation anisotropy is discussed

Essays on discrete choice models with fixed effects

Fixed effects in discrete choice models has been a challenge to econometricians from its existence. These unobservable heterogeneities are so important since their impacts can be seen clearly from the behavior of agents being studied. This has been consolidated by lots of studies and simulations including mine. However their existence prevent us from identifying models without restrictive assumptions about them. It is also hard to get rid of fixed effects since they enter the model not in a linear additive way and the outcomes are not continuous, therefore extant difference methods do not apply to discrete choice models with fixed effects. To have flexible specification on the fixed effects, it seems that partial identification is more practicable. There do exists some idea about set identification for discrete choice models and even some estimation methods were proposed for logistic-alike discrete choice models, whose key feature is that all model deduced conditional choice probabilities are well formulated in closed form expressions. For reasons people may want to have discrete choice models with disturbance other than extreme type I distributed one to overcome some of its implications, e.g the property of independence with irrelevant alternatives among others. The challenge to meet such requirement is that the key feature of closed form expressions does not hold anymore, and techniques like simulation should be used. My PhD thesis provides the foundation and framework on how to practice the simulation based estimation for discrete choice models with rather flexible fixed effects. This framework is both theoretical and practical, I show how to construct the simulation based estimation and study conditions about both the property of model and practice of simulation under which the estimator is consistent. This object is achieved in two steps. I first develop the theory for static discrete choice models where outcomes of behavior does not depend on previous outcomes. In this case specification of disturbance could be rather free and even serial correlation could be included. Later on, I extend the framework to dynamic discrete choice models, where current behavior depends on some state variables which depend on previous behavior in turn. In dynamic models, specification for disturbance is still free except that serial correlation could not be allowed. These two steps consist of the first and second chapters, in both chapter a numeric example is given which shows how well the simulation based estimator works. In the last chapter I turn to the real data and apply my method to the problem of career decision of young men. Essentially this is a typical application of dynamic programming discrete choice model, which means individual’s object function is the lifetime utility and it depends on both previous behavior and future states and what individual should decide is not only the current behavior but also future actions. By introducing a reduced form of the future utility I succeed in fitting this problem into the framework of dynamic discrete choice model with fixed effects.Programa Oficial de Doctorado en EconomíaPresidente: Pedro Mira Mcwilliams; Secretario: Ricardo Mora Villarrubia; Vocal: Pedro Albarrán Pére

Adaptation to Environmental Stresses in Candida glabrata

Candida glabrata (C. glabrata) is an emerging opportunistic human fungal pathogen with an increasing incidence as the cause of both mucosal and systemic infections. In addition, the fungus is the most commonly used microorganism for pyruvate production and is considered to be a potential producer of other fine chemicals and biofuels. Thus, this yeast has potential importance in both the medical and biotechnology fields. The inherent high tolerance of C. glabrata and its’ ability to readily adapt to various environmental stressors play key roles in its success as an opportunistic pathogen and potential as an industrial producer. However, the current knowledge on the underlying molecular mechanisms of C. glabtata adaptation to environmental stressors is limited. A deeper understanding of how C. glabrata adapts to environmental challenges can potentially expand our ability to combat infections involving this organism and to our toolkit for engineering better production hosts. In this dissertation, we focused on C. glabrata adaptation to two environmental stressors, hyperthermal and hydrogen peroxide. Using the strategy of adaptive laboratory evolution combined with next generation sequencing and transcriptome analyses, we begin to uncover the important genetic determinants conferring tolerance to these stressors. We showed for the first time that several genes (e.g. CAGL0B02739g and CAGL0E01243g) play important roles in cellular tolerance to selected environmental stresses (heat and H2O2) in C. glabrata; proposed potential mechanisms based on the transcriptome analyses and functions of their orthologs in the model yeast S. cerevisiae; and found that the adaptation to thermal stress in this fungus led to the acquisition of cross-tolerance to a wide range of other environmental stresses, including hydrogen peroxide, acids, and several organic solvents. Mutations in an important component of the fungal MAPK signaling cascades were shown to be responsible for the observed cross-tolerance, suggesting their critical roles in the cross-talk between different signaling pathways for cells to survive hostile environmental conditions

The Study of 3D Micro-fluid Printing in Aqueous Two-phase System

Aqueous two-phase system (ATPS) is a technology that allows phase separation in an aqueous environment. This technology can be used for the separation, extraction and purification of a variety of biomolecules and thus gained great attention in industry and academia. This thesis is a combination of ATPS, 3D printing, and microfluidics technologies and realizes the printing of biocompatible aqueous structures in another aqueous matrix. The objectives of this thesis include 1) customizing a regular thermal extrusion 3D printer for printing 3D aqueous structures, 2) printing 3D aqueous structure in an aqueous matrix, and 3) studying the stability of the printed aqueous two-phase system with a complex structure. In order to customize the thermal extrusion 3D printer into a micro-fluid printer, computer aided design (CAD) and computer aided manufacturing (CAM) was used to design and manufacture the customized parts. The CAD software “Solidworks” and Ender-5 Pro 3D printer from Creality were used to design and manufacture the customized parts. The ink phase solution and the matrix phase solution were made from PEO, dextran and water through mixing and centrifuging. The 3D micro-fluid printing system consists of a thermal extrusion 3D printer and a syringe-pump for dispensing the ink phase solution. Time-resolved imaging on the 2D pattern under UV light was used to study the stability of the structure in the matrix. The 3D printing performance of this printing system was tested based on the consistency of the printing results

Constitutive modelling of fibre-reinforced sand based on the concept of effective skeleton stress and void ratio

The inclusion of flexible fibres such as polypropylene and waste or natural fibres is an effective method for soil improvement, as it can significantly enhance soil strength. Though a lot of research has been done on fibre-reinforced sand (FRS), a simple and practical constitutive model, essential for assessing the stability and serviceability of fibre-reinforced slopes/foundations, has not yet been developed. A new method for constitutive modelling of fibre-reinforced sand (FRS) is proposed in this study. The new model has also been used to simulate the mechanical behaviour of FRS prepared by different methods. In the new modelling approach, FRS is considered as a composite material with host sand and flexible fibres. It is assumed that the strain of FRS is dependent on the deformation of the sand skeleton only. The effective skeleton stress and effective skeleton void ratio, which should be used in describing the dilatancy, plastic hardening and elastic stiffness of FRS, are affected by fibre inclusion. The effective skeleton stress is dependent on the shear strain level, and the effective skeleton void ratio is affected by the fibre content and sample preparation method. A critical state FRS model in the triaxial stress space is proposed using the effective skeleton stress and void ratio. Four parameters are introduced to characterise the effect of fibre inclusion on the mechanical behaviour of sand, all of which can be easily determined based on triaxial test data on FRS, without measuring the stress-strain relationship of individual fibres. Triaxial compression test results validate the model on fibre-reinforced sands under loading conditions with various confining pressures, densities and stress paths. Potential improvement in the model for incorporating fibre orientation anisotropy is discussed. It is well known that the mechanical behaviour of pure sand depends on the internal soil structure, which can be affected by sample preparation methods. For FRS, the sample preparation methods influence the internal structure of the sand skeleton and the distribution of fibre orientation and sand-fibre interaction. The effect of sample preparation methods on the mechanical behaviour of FRS has been investigated using comprehensive drained triaxial compression tests. The soil samples have been prepared by moist tamping (MT) and moist vibration (MV). There is a small difference in the stress-strain relationship of pure sand with different sample preparation methods. But the response of FRS is dramatically different. Under the same initial conditions of void ratio, confining pressure and fibre content, FRS prepared using the MV method shows 30–50% higher peak deviator stress and a much less dilative response. The newly developed constitutive model has been used to predict the mechanical behaviour of FRS prepared using the MT and MV methods