Approaches and Strategy for Cancer Research and Surveillance Data: Integration, Information Pipeline, Data Models, and Informatics Opportunities

Thesis (Ph.D.)--University of Washington, 2016-04

Aspects of Markov Chains and Particle Systems

Thesis (Ph.D.)--University of Washington, 2016-06

Impaired Antigen Presentation and Effectiveness of Combined Active/Passive Immunotherapy for Epithelial Tumors

Background: Although immunization with tumor antigens can eliminate many transplantable tumors in animal models, immune effector mechanisms associated with successful immunotherapy of epithelial cancers remain undefined. Methods: Skin from transgenic mice expressing the cervical cancer-associated tumor antigen human papillornavirus type 16 (HPV16) E6 or E7 proteins from a keratin 14 promoter was grafted onto syngeneic, non-transgenic mice. Skin graft rejection was measured after active immunization with HPV16 E7 and adoptive transfer of antigen-specific T cells. Cytokine secretion of lymphocytes from mice receiving skin grafts and immunotherapy was detected by enzyme-linked immunosorbent assay, and HPV16 E7-specific memory CD8(+) T cells were detected by flow cytometry and ELISPOT. Results: Skin grafts containing HPV16 E6- or E7-expressing keratinocytes were not rejected spontaneously or following immunization with E7 protein and adjuvant. Adoptive transfer of E7-specific T-cell receptor transgenic CD8(+) T cells combined with immunization resulted in induction of antigen-specific interferon gamma-secreting CD8(+) T cells and rejection of HPV16 E7-expressing grafts. Specific memory CD8(+) T cells were generated by immunotherapy. However, a further HPV16 E7 graft was rejected from animals with memory T cells only after a second E7 immunization. Conclusions: Antigen-specific CD8(+) T cells can destroy epithelium expressing HPV16 E7 tumor antigen, but presentation of E7 antigen from skin is insufficient to reactivate memory CD8(+) T cells induced by immunotherapy. Thus, effective cancer immunotherapy in humans may need to invoke sufficient effector as well as memory T cells.

Alternatives to peace keeping in Korea: the role of non-state actors and face-to-face encounters

Korea is one of the world's most volatile areas, not least because traditional UN mediation and peacekeeping missions are impossible. Having intervened in the Korean War on behalf of the southern side, the UN is a party to the conflict, rather than a neutral arbiter. The situation is particularly problematic because political interactions are characterized by a high degree of state-control over security policy. In both parts of the peninsula the state has, at least until recently, exercised the exclusive right to deal with the opponent on the other side of the hermetically divided peninsula. Given these domestic and international constrains, alternative approaches to conflict resolution are urgently needed. The recently proliferating literature on human security offers possible solutions, for it urges policy makers to view security beyond the conventional military-based defence of the state and its territory. Using such a conceptual framework, the essay assesses the potential significance non-state interactions between North and South, particularly those that promote communication, information exchange and face-to-face encounters. Even though these interactions remain limited, they are of crucial importance, for they provide an opportunity to reduce the stereotypical threat images that continue to fuel conflict on the peninsula.

Multiple paths extraction in images using a constrained expanded trellis

Single shortest path extraction algorithms have been used in a number of areas such as network flow and image analysis. In image analysis, shortest path techniques can be used for object boundary detection, crack detection, or stereo disparity estimation. Sometimes one needs to find multiple paths as opposed to a single path in a network or an image where the paths must satisfy certain constraints. In this paper, we propose a new algorithm to extract multiple paths simultaneously within an image using a constrained expanded trellis (CET) for feature extraction and object segmentation. We also give a number of application examples for our multiple paths extraction algorithm.

Estimation of adsorption capacity for dissociating and non dissociating aromatic compounds on activated carbon with different models

The process of adsorption of two dissociating and two non-dissociating aromatic compounds from dilute aqueous solutions on an untreated commercially available activated carbon (B.D.H.) was investigated systematically. All adsorption experiments were carried out in pH controlled aqueous solutions. The experimental isotherms were fitted into four different models (Langmuir homogenous Models, Langmuir binary Model, Langmuir-Freundlich single model and Langmuir-Freundlich double model). Variation of the model parameters with the solution pH was studied and used to gain further insight into the adsorption process. The relationship between the model parameters and the solution pH and pK(a) was used to predict the adsorption capacity in molecular and ionic form of solutes in other solution. A relationship was sought to predict the effect of pH on the adsorption systems and for estimating the maximum adsorption capacity of carbon at any pH where the solute is ionized reasonably well. N-2 and CO2 adsorption were used to characterize the carbon. X-ray Photoelectron Spectroscopy (XPS) measurement was used for surface elemental analysis of the activated carbon.

A D-optimal designed population pharmacokinetic study of itraconazole capsules and solution in adults with cystic fibrosis

Background: Oral itraconazole (ITRA) is used for the treatment of allergic bronchopulmonary aspergillosis in patients with cystic fibrosis (CF) because of its antifungal activity against Aspergillus species. ITRA has an active hydroxy-metabolite (OH-ITRA) which has similar antifungal activity. ITRA is a highly lipophilic drug which is available in two different oral formulations, a capsule and an oral solution. It is reported that the oral solution has a 60% higher relative bioavailability. The influence of altered gastric physiology associated with CF on the pharmacokinetics (PK) of ITRA and its metabolite has not been previously evaluated. Objectives: 1) To estimate the population (pop) PK parameters for ITRA and its active metabolite OH-ITRA including relative bioavailability of the parent after administration of the parent by both capsule and solution and 2) to assess the performance of the optimal design. Methods: The study was a cross-over design in which 30 patients received the capsule on the first occasion and 3 days later the solution formulation. The design was constrained to have a maximum of 4 blood samples per occasion for estimation of the popPK of both ITRA and OH-ITRA. The sampling times for the population model were optimized previously using POPT v.2.0.[1] POPT is a series of applications that run under MATLAB and provide an evaluation of the information matrix for a nonlinear mixed effects model given a particular design. In addition it can be used to optimize the design based on evaluation of the determinant of the information matrix. The model details for the design were based on prior information obtained from the literature, which suggested that ITRA may have either linear or non-linear elimination. The optimal sampling times were evaluated to provide information for both competing models for the parent and metabolite and for both capsule and solution simultaneously. Blood samples were assayed by validated HPLC.[2] PopPK modelling was performed using FOCE with interaction under NONMEM, version 5 (level 1.1; GloboMax LLC, Hanover, MD, USA). The PK of ITRA and OH‑ITRA was modelled simultaneously using ADVAN 5. Subsequently three methods were assessed for modelling concentrations less than the LOD (limit of detection). These methods (corresponding to methods 5, 6 & 4 from Beal[3], respectively) were (a) where all values less than LOD were assigned to half of LOD, (b) where the closest missing value that is less than LOD was assigned to half the LOD and all previous (if during absorption) or subsequent (if during elimination) missing samples were deleted, and (c) where the contribution of the expectation of each missing concentration to the likelihood is estimated. The LOD was 0.04 mg/L. The final model evaluation was performed via bootstrap with re-sampling and a visual predictive check. The optimal design and the sampling windows of the study were evaluated for execution errors and for agreement between the observed and predicted standard errors. Dosing regimens were simulated for the capsules and the oral solution to assess their ability to achieve ITRA target trough concentration (Cmin,ss of 0.5-2 mg/L) or a combined Cmin,ss for ITRA and OH-ITRA above 1.5mg/L. Results and Discussion: A total of 241 blood samples were collected and analysed, 94% of them were taken within the defined optimal sampling windows, of which 31% where taken within 5 min of the exact optimal times. Forty six per cent of the ITRA values and 28% of the OH-ITRA values were below LOD. The entire profile after administration of the capsule for five patients was below LOD and therefore the data from this occasion was omitted from estimation. A 2-compartment model with 1st order absorption and elimination best described ITRA PK, with 1st order metabolism of the parent to OH-ITRA. For ITRA the clearance (ClItra/F) was 31.5 L/h; apparent volumes of central and peripheral compartments were 56.7 L and 2090 L, respectively. Absorption rate constants for capsule (kacap) and solution (kasol) were 0.0315 h-1 and 0.125 h-1, respectively. Comparative bioavailability of the capsule was 0.82. There was no evidence of nonlinearity in the popPK of ITRA. No screened covariate significantly improved the fit to the data. The results of the parameter estimates from the final model were comparable between the different methods for accounting for missing data, (M4,5,6)[3] and provided similar parameter estimates. The prospective application of an optimal design was found to be successful. Due to the sampling windows, most of the samples could be collected within the daily hospital routine, but still at times that were near optimal for estimating the popPK parameters. The final model was one of the potential competing models considered in the original design. The asymptotic standard errors provided by NONMEM for the final model and empirical values from bootstrap were similar in magnitude to those predicted from the Fisher Information matrix associated with the D-optimal design. Simulations from the final model showed that the current dosing regimen of 200 mg twice daily (bd) would provide a target Cmin,ss (0.5-2 mg/L) for only 35% of patients when administered as the solution and 31% when administered as capsules. The optimal dosing schedule was 500mg bd for both formulations. The target success for this dosing regimen was 87% for the solution with an NNT=4 compared to capsules. This means, for every 4 patients treated with the solution one additional patient will achieve a target success compared to capsule but at an additional cost of AUD $220 per day. The therapeutic target however is still doubtful and potential risks of these dosing schedules need to be assessed on an individual basis. Conclusion: A model was developed which described the popPK of ITRA and its main active metabolite OH-ITRA in adult CF after administration of both capsule and solution. The relative bioavailability of ITRA from the capsule was 82% that of the solution, but considerably more variable. To incorporate missing data, using the simple Beal method 5 (using half LOD for all samples below LOD) provided comparable results to the more complex but theoretically better Beal method 4 (integration method). The optimal sparse design performed well for estimation of model parameters and provided a good fit to the data.

Automatic segmentation of the knee bones using 3D active shape models

This paper presents an automated segmentation approach for MR images of the knee bones. The bones are the first stage of a segmentation system for the knee, primarily aimed at the automated segmentation of the cartilages. The segmentation is performed using 3D active shape models (ASM), which are initialized using an affine registration to an atlas. The 3D ASMs of the bones are created automatically using a point distribution model optimization scheme. The accuracy and robustness of the segmentation approach was experimentally validated using an MR database of fat suppressed spoiled gradient recall images.

Farming under constrained budgets: Practices of agricultural credit users in central Lombok, Indonesia

There has been a long dependency on credit by Indonesian farmers as a result of the lack of capital to apply proper farming practices. This paper describes the farming activities applied by agricultural credit users in Central Lombok, Indonesia. A survey was conducted during July 2001- March 2002 of 65 farmers making use of government or private credit in three villages within the Regency. Data from the farmers were collected using face-to-face, semi-structured interviews. Survey results indicated that on average, farmers had some 20 years experience of farming, were aged 40 years, but lacked of formal education. Their main asset was cropping land with average landholding of 0.69 ha. As a consequence of their capital constraints, farmers were commonly making use of credit to finance their farming activities, including both production of rice as the main crop and secondary crops. Farmers generally applied less than recommended amount of inputs in their farming practices, since the amount of credit they obtained was limited. As a result, their farms become less productive and their repayment capability of loans diminished. Of 65 farmers interviewed, 54 could earn extra income by engaging in a variety of non-farm activities, which contributed on average some 36% to family incomes of over Rp 5 million (A$ 1 thousand). The average credit repayment rate made by agricultural producers was 60%. The repayment made did not always reflect farm production capacity, being sometimes supported by other borrowings. The greater role of credit is not in increasing agricultural production or improving farmers’ income, but in helping them to sustain farm production and their living. Farmers need a bigger amount of credit to make an impact on their livelihood. This should be accompanied by extension services for farmers to enable better use of credit and to change their attitude towards it. As well, farmers require to be equipped with technical and market skills to run a business. Interdisciplinarity, holistic analysis, and an expansion of traditional ‘agricultural’ interests to embrace the span of interests included in rural livelihood, are each critical features of revision of the existing system.

Jobs, Unemployment, and Macroeconomic Transmission

Measuring Job Openings: Evidence from Swedish Plant Level Data. In modern macroeconomic models “job openings'' are a key component. Thus, when taking these models to the data we need an empirical counterpart to the theoretical concept of job openings. To achieve this, the literature relies on job vacancies measured either in survey or register data. Insofar as this concept captures the concept of job openings well we should see a tight relationship between vacancies and subsequent hires on the micro level. To investigate this, I analyze a new data set of Swedish hires and job vacancies on the plant level covering the period 2001-2012. I find that vacancies contain little power in predicting hires over and above (i) whether the number of vacancies is positive and (ii) plant size. Building on this, I propose an alternative measure of job openings in the economy. This measure (i) better predicts hiring at the plant level and (ii) provides a better fitting aggregate matching function vis-à-vis the traditional vacancy measure. Firm Level Evidence from Two Vacancy Measures. Using firm level survey and register data for both Sweden and Denmark we show systematic mis-measurement in both vacancy measures. While the register-based measure on the aggregate constitutes a quarter of the survey-based measure, the latter is not a super-set of the former. To obtain the full set of unique vacancies in these two databases, the number of survey vacancies should be multiplied by approximately 1.2. Importantly, this adjustment factor varies over time and across firm characteristics. Our findings have implications for both the search-matching literature and policy analysis based on vacancy measures: observed changes in vacancies can be an outcome of changes in mis-measurement, and are not necessarily changes in the actual number of vacancies. Swedish Unemployment Dynamics. We study the contribution of different labor market flows to business cycle variations in unemployment in the context of a dual labor market. To this end, we develop a decomposition method that allows for a distinction between permanent and temporary employment. We also allow for slow convergence to steady state which is characteristic of European labor markets. We apply the method to a new Swedish data set covering the period 1987-2012 and show that the relative contributions of inflows and outflows to/from unemployment are roughly 60/30. The remaining 10\% are due to flows not involving unemployment. Even though temporary contracts only cover 9-11\% of the working age population, variations in flows involving temporary contracts account for 44\% of the variation in unemployment. We also show that the importance of flows involving temporary contracts is likely to be understated if one does not account for non-steady state dynamics. The New Keynesian Transmission Mechanism: A Heterogeneous-Agent Perspective. We argue that a 2-agent version of the standard New Keynesian model---where a ``worker'' receives only labor income and a “capitalist'' only profit income---offers insights about how income inequality affects the monetary transmission mechanism. Under rigid prices, monetary policy affects the distribution of consumption, but it has no effect on output as workers choose not to change their hours worked in response to wage movements. In the corresponding representative-agent model, in contrast, hours do rise after a monetary policy loosening due to a wealth effect on labor supply: profits fall, thus reducing the representative worker's income. If wages are rigid too, however, the monetary transmission mechanism is active and resembles that in the corresponding representative-agent model. Here, workers are not on their labor supply curve and hence respond passively to demand, and profits are procyclical.

Adding constrained discontinuities to Gaussian process models of wind fields

Gaussian Processes provide good prior models for spatial data, but can be too smooth. In many physical situations there are discontinuities along bounding surfaces, for example fronts in near-surface wind fields. We describe a modelling method for such a constrained discontinuity and demonstrate how to infer the model parameters in wind fields with MCMC sampling.