A Simple Model Describes Development of Early Peaks in Oomycete Zoospore Inoculum Detected in Southern UK Outdoors Horticultural Reservoirs

The numbers of water-borne oomycete propagules in outdoor reservoirs used in horticultural nurseries within the UK are investigated in this study. Water samples were recovered from 11 different horticultural nurseries in the southern UK during Jan-May in two ‘cool’ years (2010.and 2013; winter temperatures 2.0 and 0.4oC below UK Met Office 30 year winter average respectively) and two ‘warm’ years (2008 and 2012; winter temperatures 1.2 and 0.9oC above UK Met Office 30 year winter average respectively). Samples were analysed for total number of oomycete colony forming units (CFU), predominantly members of the families Saprolegniaceae and Pythiaceae, and these were combined to give monthly mean counts. The numbers of CFU were investigated with respect to prevailing climate in the region: mean monthly air temperatures calculated by using daily observations from the nearest climatological station. The investigations show that the number of CFU during spring can be explained by a linear first-order equation and a statistically significant r2 value of 0.66 with the simple relationship: [CFU] = a(T-Tb )-b, where a is the rate of inoculum development with temperature T, and b is the baseload population at temperatures below Tb. Despite the majority of oomycete CFU detected being non-phytopathogenic members of the Saprolegniaceae, total oomycete CFU counts are still of considerable value as indicators of irrigation water treatment efficacy and cleanliness of storage tanks. The presence/absence of Pythium spp. was also determined for all samples tested, and Pythium CFU were found to be present in the majority, the exceptions all being particularly cold months (January and February 2010 and January 2008). A simple scenario study (+2 deg C) suggests that abundance of water-borne oomycetes during spring could be affected by increased temperatures due to climate change.

Development of A Flow Cytometry Assay for Measurement of CD4+ T Cell Proliferation

Thesis (Master's)--University of Washington, 2016-06

Computer simulations of soft particles in flow

Understanding the dynamics of blood cells is a crucial element to discover biological mechanisms, to develop new efficient drugs, design sophisticated microfluidic devices, for diagnostics. In this work, we focus on the dynamics of red blood cells in microvascular flow. Microvascular blood flow resistance has a strong impact on cardiovascular function and tissue perfusion. The flow resistance in microcirculation is governed by flow behavior of blood through a complex network of vessels, where the distribution of red blood cells across vessel cross-sections may be significantly distorted at vessel bifurcations and junctions. We investigate the development of blood flow and its resistance starting from a dispersed configuration of red blood cells in simulations for different hematocrits, flow rates, vessel diameters, and aggregation interactions between red blood cells. Initially dispersed red blood cells migrate toward the vessel center leading to the formation of a cell-free layer near the wall and to a decrease of the flow resistance. The development of cell-free layer appears to be nearly universal when scaled with a characteristic shear rate of the flow, which allows an estimation of the length of a vessel required for full flow development, $l_c \approx 25D$, with vessel diameter $D$. Thus, the potential effect of red blood cell dispersion at vessel bifurcations and junctions on the flow resistance may be significant in vessels which are shorter or comparable to the length $l_c$. The presence of aggregation interactions between red blood cells lead in general to a reduction of blood flow resistance. The development of the cell-free layer thickness looks similar for both cases with and without aggregation interactions. Although, attractive interactions result in a larger cell-free layer plateau values. However, because the aggregation forces are short-ranged at high enough shear rates ($\bar{\dot{\gamma}} \gtrsim 50~\text{s}^{-1}$) aggregation of red blood cells does not bring a significant change to the blood flow properties. Also, we develop a simple theoretical model which is able to describe the converged cell-free-layer thickness with respect to flow rate assuming steady-state flow. The model is based on the balance between a lift force on red blood cells due to cell-wall hydrodynamic interactions and shear-induced effective pressure due to cell-cell interactions in flow. We expect that these results can also be used to better understand the flow behavior of other suspensions of deformable particles such as vesicles, capsules, and cells. Finally, we investigate segregation phenomena in blood as a two-component suspension under Poiseuille flow, consisting of red blood cells and target cells. The spatial distribution of particles in blood flow is very important. For example, in case of nanoparticle drug delivery, the particles need to come closer to microvessel walls, in order to adhere and bring the drug to a target position within the microvasculature. Here we consider that segregation can be described as a competition between shear-induced diffusion and the lift force that pushes every soft particle in a flow away from the wall. In order to investigate the segregation, on one hand, we have 2D DPD simulations of red blood cells and target cell of different sizes, on the other hand the Fokker-Planck equation for steady state. For the equation we measure force profile, particle distribution and diffusion constant across the channel. We compare simulation results with those from the Fokker-Planck equation and find a very good correspondence between the two approaches. Moreover, we investigate the diffusion behavior of target particles for different hematocrit values and shear rates. Our simulation results indicate that diffusion constant increases with increasing hematocrit and depends linearly on shear rate. The third part of the study describes development of a simulation model of complex vascular geometries. The development of the model is important to reproduce vascular systems of small pieces of tissues which might be gotten from MRI or microscope images. The simulation model of the complex vascular systems might be divided into three parts: modeling the geometry, developing in- and outflow boundary conditions, and simulation domain decomposition for an efficient computation. We have found that for the in- and outflow boundary conditions it is better to use the SDPD fluid than DPD one because of the density fluctuations along the channel of the latter. During the flow in a straight channel, it is difficult to control the density of the DPD fluid. However, the SDPD fluid has not that shortcoming even in more complex channels with many branches and in- and outflows because the force acting on particles is calculated also depending on the local density of the fluid.

Parental involvement in sport: psychometric development and empirical test of a theoretical model

The purposes of the present multistudy were to develop and provide initial construct validity for measures based on the model of parental involvement in sport (Study 1) and examine structural relationships among the constructs of the model (Study 2). In Study 1 (nparents = 342, nathletes = 223), a confirmatory factor analysis was used to verify the psychometric properties of the measures. Content and construct validity were evaluated, as well individual and composite reliability. Multi-group analysis with two independent samples provided evidence of factorial invariance. In Study 2 (nparents = 754, nathletes = 438), structural equation modeling analysis supported the hypothesised model in which athletes’ perceptions of parents’ behaviours mediated the relationship between parents’ reported behaviours and the athletes’ psychological variables conducive to their achievement in sport. The findings provide support for the parental involvement in sport model and demonstrate the role of perceptions of parents’ behaviours on young athletes’ cognitions in sport.

Investigating the role of N-WASP in the development of colorectal cancer

Colorectal cancer (CRC) is the second most common cancer in Europe, with the second highest mortality rate. Although prognosis is improving, survival rates remain poor for those presenting with the most advanced stages of the disease. There is therefore a need for improved early diagnosis and thus a greater understanding of the early stages of the development of colorectal tumours is desirable. Additionally, as most deaths in colorectal cancer are due to advanced metastatic disease, it is of great interest to explore any potential mechanisms by which metastatic disease can be inhibited. N-WASP is a ubiquitously expressed protein with multiple intracellular roles including actin regulation and maintaining stability of epithelial cell-cell junctions. Through its role as an actin regulator, it has been implicated in the processes of invasion and metastasis of multiple cancer types. Its role in the development and progression of colorectal cancer however has not been fully explored. This thesis will present a series of in vitro and in vivo studies that were carried out with the aim of answering the following questions: • Does N-Wasp have a role in normal intestinal homeostasis? • Does N-Wasp knockout affect the development of tumours in a mouse model of intestinal tumourigenesis? • Does N-Wasp knockout affect the invasive properties of intestinal cancer in vitro? • Does N-WASP correlate with prognosis or other indicators in human colorectal cancer TMAs? Findings from the in vivo experiments, using an inducible, gut-specific knockout model, have uncovered potential roles for N-Wasp in regulating differentiation and migration of intestinal epithelial cells. Although it had no effect in short term models of intestinal hyperproliferation, N-Wasp knockout increased tumour burden and decreased survival in an established in vivo model of intestinal tumourigenesis, in which there is heterozygous loss of Apc (Apcfl/+). No effect was seen on tumour development or survival when additional N-WASP knockout was introduced into a more rapid model, with heterozygous loss of Apc and mutation of Kras (Apcfl/+ KrasG12D/+). N-WASP expression in human colorectal cancer was assessed using immunohistochemical staining of two tissue microarrays. Low levels of N-WASP expression were found to be associated with presence of MMR deficiency. There was no statistically significant difference in overall or cancer specific survival based on N-WASP expression. Collectively, the data presented here suggest a previously unreported role for N-WASP in regulation of intestinal epithelial differentiation and indicate that it may act as a tumour suppressor against development of benign precursor lesions of colorectal cancer. Further research is warranted to delineate the mechanisms underlying these processes.

FLOW REGIME DRIVEN THERMAL ENHANCEMENT IN INTERNALLY-GROOVED TUBES

Internally-grooved refrigeration tubes maximize tube-side evaporative heat transfer rates and have been identified as a most promising technology for integration into compact cold plates. Unfortunately, the absence of phenomenological insights and physical models hinders the extrapolation of grooved-tube performance to new applications. The success of regime-based heat transfer correlations for smooth tubes has motivated the current effort to explore the relationship between flow regimes and enhanced heat transfer in internally-grooved tubes. In this thesis, a detailed analysis of smooth and internally-grooved tube data reveals that performance improvement in internally-grooved tubes at low-to-intermediate mass flux is a result of early flow regime transition. Based on this analysis, a new flow regime map and corresponding heat transfer coefficient correlation, which account for the increased wetted angle, turbulence, and Gregorig effects unique to internally-grooved tubes, were developed. A two-phase test facility was designed and fabricated to validate the newly-developed flow regime map and regime-based heat transfer coefficient correlation. As part of this setup, a non-intrusive optical technique was developed to study the dynamic nature of two-phase flows. It was found that different flow regimes result in unique temporally varying film thickness profiles. Using these profiles, quantitative flow regime identification measures were developed, including the ability to explain and quantify the more subtle transitions that exist between dominant flow regimes. Flow regime data, based on the newly-developed method, and heat transfer coefficient data, using infrared thermography, were collected for two-phase HFE-7100 flow in horizontal 2.62mm - 8.84mm diameter smooth and internally-grooved tubes with mass fluxes from 25-300 kg/m²s, heat fluxes from 4-56 kW/m², and vapor qualities approaching 1. In total, over 6500 combined data points for the adiabatic and diabatic smooth and internally-grooved tubes were acquired. Based on results from the experiments and a reinterpretation of data from independent researchers, it was established that heat transfer enhancement in internally-grooved tubes at low-to-intermediate mass flux is primarily due to early flow regime transition to Annular flow. The regime-based heat transfer coefficient outperformed empirical correlations from the literature, with mean and absolute deviations of 4.0% and 32% for the full range of data collected.

A Numerical study of fluid flow in peristaltic pumps and polymeric elastic pipes

This thesis work deals with a mathematical description of flow in polymeric pipe and in a specific peristaltic pump. This study involves fluid-structure interaction analysis in presence of complex-turbulent flows treated in an arbitrary Lagrangian-Eulerian (ALE) framework. The flow simulations are performed in COMSOL 4.4, as 2D axial symmetric model, and ABAQUS 6.14.1, as 3D model with symmetric boundary conditions. In COMSOL, the fluid and structure problems are coupled by monolithic algorithm, while ABAQUS code links ABAQUS CFD and ABAQUS Standard solvers with single block-iterative partitioned algorithm. For the turbulent features of the flow, the fluid model in both codes is described by RNG k-ϵ. The structural model is described, on the basis of the pipe material, by Elastic models or Hyperelastic Neo-Hookean models with Rayleigh damping properties. In order to describe the pulsatile fluid flow after the pumping process, the available data are often defective for the fluid problem. Engineering measurements are normally able to provide average pressure or velocity at a cross-section. This problem has been analyzed by McDonald's and Womersley's work for average pressure at fixed cross section by Fourier analysis since '50, while nowadays sophisticated techniques including Finite Elements and Finite Volumes exist to study the flow. Finally, we set up peristaltic pipe simulations in ABAQUS code, by using the same model previously tested for the fl uid and the structure.

The credit channel transmission of monetary policy in the European Union

This paper confirms the importance of the financial systems behaviour conditions to the credit channel of monetary policy in the entire European Union (EU). It uses panel fixed- effect estimations and quarterly data for 26 EU countries for the period from Q1 1999 to Q3 2006 in an adaptation of the Bernanke and Blinder (1988) model. The findings also reveal the high degree of foreign dependence and indebtedness of the EU banking institutions and their similar reactions to the macroeconomic and the monetary policy environments.

Introducing a pilot data collection model for real-time evaluation of data redundancy

In order to reduce serious health incidents, individuals with high risks need to be identified as early as possible so that effective intervention and preventive care can be provided. This requires regular and efficient assessments of risk within communities that are the first point of contacts for individuals. Clinical Decision Support Systems CDSSs have been developed to help with the task of risk assessment, however such systems and their underpinning classification models are tailored towards those with clinical expertise. Communities where regular risk assessments are required lack such expertise. This paper presents the continuation of GRiST research team efforts to disseminate clinical expertise to communities. Based on our earlier published findings, this paper introduces the framework and skeleton for a data collection and risk classification model that evaluates data redundancy in real-time, detects the risk-informative data and guides the risk assessors towards collecting those data. By doing so, it enables non-experts within the communities to conduct reliable Mental Health risk triage.

Development and characterisation of a neurogenic model of brain cancer

Primary glioblastoma (GB), the most common and aggressive adult brain tumour, is refractory to conventional therapies and characterised by poor prognosis. GB displays striking cellular heterogeneity, with a sub-population, called Glioblastoma Stem Cells (GSCs), intrinsically resistant to therapy, hence the high rate of recurrence. Alterations of the tumour suppressor gene PTEN are prevalent in primary GBM, resulting in the inhibition of the polarity protein Lgl1 due to aPKC hyperactivation. Dysregulation of this molecular axis is one of the mechanisms involved in GSC maintenance. After demonstrating that the PTEN/aPKC/Lgl axis is conserved in Drosophila, I deregulated it in different cells populations of the nervous system in order to individuate the cells at the root of neurogenic brain cancers. This analysis identified the type II neuroblasts (NBs) as the most sensitive to alterations of this molecular axis. Type II NBs are a sub-population of Drosophila stem cells displaying a lineage similar to that of the mammalian neural stem cells. Following aPKC activation in these stem cells, I obtained an adult brain cancer model in Drosophila that summarises many phenotypic traits of human brain tumours. Fly tumours are indeed characterised by accumulation of highly proliferative immature cells and keep growing in the adult leading the affected animals to premature death. With the aim to understand the role of cell polarity disruption in this tumorigenic process I carried out a molecular characterisation and transcriptome analysis of brain cancers from our fly model. In summary, the model I built and partially characterised in this thesis work may help deepen our knowledge on human brain cancers by investigating many different aspects of this complicate disease.

Assessing the fit of unidimensional IRT models for binary data under model misspecification

Model misspecification affects the classical test statistics used to assess the fit of the Item Response Theory (IRT) models. Robust tests have been derived under model misspecification, as the Generalized Lagrange Multiplier and Hausman tests, but their use has not been largely explored in the IRT framework. In the first part of the thesis, we introduce the Generalized Lagrange Multiplier test to detect differential item response functioning in IRT models for binary data under model misspecification. By means of a simulation study and a real data analysis, we compare its performance with the classical Lagrange Multiplier test, computed using the Hessian and the cross-product matrix, and the Generalized Jackknife Score test. The power of these tests is computed empirically and asymptotically. The misspecifications considered are local dependence among items and non-normal distribution of the latent variable. The results highlight that, under mild model misspecification, all tests have good performance while, under strong model misspecification, the performance of the tests deteriorates. None of the tests considered show an overall superior performance than the others. In the second part of the thesis, we extend the Generalized Hausman test to detect non-normality of the latent variable distribution. To build the test, we consider a seminonparametric-IRT model, that assumes a more flexible latent variable distribution. By means of a simulation study and two real applications, we compare the performance of the Generalized Hausman test with the M2 limited information goodness-of-fit test and the Likelihood-Ratio test. Additionally, the information criteria are computed. The Generalized Hausman test has a better performance than the Likelihood-Ratio test in terms of Type I error rates and the M2 test in terms of power. The performance of the Generalized Hausman test and the information criteria deteriorates when the sample size is small and with a few items.

A conceptualisation of a governance model for biobanks in the digital society

Biobanks are key infrastructures in data-driven biomedical research. The counterpoint of this optimistic vision is the reality of biobank governance, which must address various ethical, legal and social issues, especially in terms of open consent, privacy and secondary uses which, if not sufficiently resolved, may undermine participants’ and society’s trust in biobanking. The effect of the digital paradigm on biomedical research has only accentuated these issues by adding new pressure for the data protection of biobank participants against the risks of covert discrimination, abuse of power against individuals and groups, and critical commercial uses. Moreover, the traditional research-ethics framework has been unable to keep pace with the transformative developments of the digital era, and has proven inadequate in protecting biobank participants and providing guidance for ethical practices. To this must be added the challenge of an increased tendency towards exploitation and the commercialisation of personal data in the field of biomedical research, which may undermine the altruistic and solidaristic values associated with biobank participation and risk losing alignment with societal interests in biobanking. My research critically analyses, from a bioethical perspective, the challenges and the goals of biobank governance in data-driven biomedical research in order to understand the conditions for the implementation of a governance model that can foster biomedical research and innovation, while ensuring adequate protection for biobank participants and an alignment of biobank procedures and policies with society’s interests and expectations. The main outcome is a conceptualisation of a socially-oriented and participatory model of biobanks by proposing a new ethical framework that relies on the principles of transparency, data protection and participation to tackle the key challenges of biobanks in the digital age and that is well-suited to foster these goals.