Smooth-car mixed models for spatial count data

Penalized splines (P-splines) and individual random effects are used for the analysis of spatial count data. P-splines are represented as mixed models to give a unified approach to the model estimation procedure. First, a model where the spatial variation is modelled by a two-dimensional P-spline at the centroids of the areas or regions is considered. In addition, individual area-effects are incorporated as random effects to account for individual variation among regions. Finally, the model is extended by considering a conditional autoregressive (CAR) structure for the random effects, these are the so called “Smooth-CAR” models, with the aim of separating the large-scale geographical trend, and local spatial correlation. The methodology proposed is applied to the analysis of lip cancer incidence rates in Scotland.Mixed models, P-splines, Overdispersion, Negative Binomial, PQL, CAR models, Scottish lip cancer data

Smooth-car mixed models for spatial count data

Penalized splines (P-splines) and individual random effects are used for the analysis of spatial count data. P-splines are represented as mixed models to give a unified approach to the model estimation procedure. First, a model where the spatial variation is modelled by a two-dimensional P-spline at the centroids of the areas or regions is considered. In addition, individual area-effects are incorporated as random effects to account for individual variation among regions. Finally, the model is extended by considering a conditional autoregressive (CAR) structure for the random effects, these are the so called “Smooth-CAR” models, with the aim of separating the large-scale geographical trend, and local spatial correlation. The methodology proposed is applied to the analysis of lip cancer incidence rates in Scotland

The future of coastal and estuarine modeling: Findings from a workshop

This paper summarizes the findings of a workshop convened in the United States in 2018 to discuss methods in coastal and estuarine modeling and to propose key areas of research and development needed to improve their accuracy and reliability. The focus of this paper is on physical processes, and we provide an overview of the current state-of-the-art based on presentations and discussions at the meeting, which revolved around the four primary themes of parameterizations, numerical methods, in-situ and remote-sensing measurements,and high-performance computing. A primary outcome of the workshop was agreement on the need to reduce subjectivity and improve reproducibility in modeling of physical processes in the coastal ocean. Reduction of subjectivity can be accomplished through development of standards for benchmarks, grid generation, and validation, and reproducibility can be improved through development of standards for input/output, coupling and model nesting, and reporting. Subjectivity can also be reduced through more engagement with the applied mathematics and computer science communities to develop methods for robust parameter estimation anduncertainty quantification. Such engagement could be encouraged through more collaboration between thef orward and inverse modeling communities and integration of more applied math and computer science into oceanography curricula. Another outcome of the workshop was agreement on the need to develop high-resolution models that scale on advanced HPC systems to resolve, rather than parameterize, processes with horizontal scales that range between the depth and the internal Rossby deformation scale. Unsurprisingly,more research is needed on parameterizations of processes at scales smaller than the depth, includingparameterizations for drag (including bottom roughness, bedforms, vegetation and corals), wave breaking, and air–sea interactions under strong wind conditions. Other topics that require significantly more work to better parameterize include nearshore wave modeling, sediment transport modeling, and morphodynamics. Finally, it was agreed that coastal models should be considered as key infrastructure needed to support research, just like laboratory facilities, field instrumentation, and research vessels. This will require a shift in the way proposals related to coastal ocean modeling are reviewed and funded

Complexities in Inter-firm R&D Collaborative Partnerships in High-Tech Industries: Innovation and Financial Performances

Governments in both advanced and emerging markets invest heavily into joint R&D projects to facilitate inter-firm collaboration and scientific productivity. As a science-based cluster, nanotechnology is a highly R&D-intensive field with very complex interdisciplinary features that enables multiple interactions between scientists from diverse cultural backgrounds working for multi-faceted organizations across public and private sectors and through internationally regulated borders. In this thesis, I examine the main determinants of the dimensions of inter-firm collaboration in high-tech industries particularly among nanotechnology R&D organisations across Europe. Also, I investigate the key factors that influence the innovation, financial and exit performance of nanotech companies during the commercialisation period and across 15 developed and developing countries, taking into consideration the involvement of venture capital (VC) firms. In order to methodically integrate the qualitative and quantitative features of my research study, I employed mixed method to analyse primary and secondary data collected via survey instruments and comprehensive databases; to gain valuable insights into the complexities around nanotech R&D organisations. The regression results show that a predictable legal system; a high level of tolerance for uncertainty; the proximity to key partners; a high level of export demand for high-tech products; and expansionary economic policies, leads to highly valuable and long-term relationships which produces optimal partnership size with an effective organizational structure. I find that a high financial status of nanotech firms equips R&D project managers with sufficient tangible and intangible resources to engage into complex collaborative partnerships which yield innovative performing outcomes. Also, I find that nanotech R&D firms that exit venture capital investments via IPO are more likely to have their head offices in a big city; and access foreign capital to expand manufacturing operations. I conclude that the successful commercialisation of nanotechnology industries across the globe has been due to the substantial R&D public expenditures and private investments into the application and proliferation of nanotechnologies in key converging scientific fields which require robust inter-firm collaborative partnerships to rapidly develop and promote several portfolios of high-tech products that continually satisfy consumer needs in disruptive ways and secure long-term profitability for nanotech R&D organisations

Doctor of Philosophy

dissertationDespite the progress that has been made since the inception of the finite element method, the field of biomechanics has generally relied on software tools that were not specifically designed to target this particular area of application. Software designed specifically for the field of computational biomechanics does not appear to exist. To overcome this limitation, FEBio was developed, an acronym for “Finite Elements for Biomechanics”, which provided an open-source framework for developing finite element software that is tailored to the specific needs of the biomechanics and biophysics communities. The proposed work added an extendible framework to FEBio that greatly facilitates the implementation of novel features and provides an ideal platform for exploring novel computational approaches. This framework supports plugins, which simplify the process of adding new features even more since plugins can be developed independently from the main source code. Using this new framework, this work extended FEBio in two important areas of interest in biomechanics. First, as tetrahedral elements continue to be the preferred modeling primitive for representing complex geometries, several tetrahedral formulations were investigated in terms of their robustness and accuracy for solving problems in computational biomechanics. The focus was on the performance of quadratic tetrahedral formulations in large deformation contact analyses, as this is an important area of application in biomechanics. Second, the application of prestrain to computational models has been recognized as an important component in simulations of biological tissues in order to accurately predict the mechanical response. As this remains challenging to do in existing software packages, a general computational framework for applying prestrain was incorporated in the FEBio software. The work demonstrated via several examples how plugins greatly simplify the development of novel features. In addition, it showed that the quadratic tetrahedral formulations studied in this work are viable alternatives for contact analyses. Finally, it demonstrated the newly developed prestrain plugin and showed how it can be used in various applications of prestrain

Economic issues in resistance management

This dissertation analyzes economic issues related to the use of agricultural pesticides and antibiotics. The efficacy of both these chemical compounds depends on the existence of susceptible targets. However, through natural selection, their utilization increases the frequency of the genes resistant to the pesticide or drug in the target population, and it decreases the available biological capital of genetic susceptibility, increasing resistance;The aim of this dissertation is to analyze the characteristics of optimal resistance management strategies. An empirical analysis is offered in case of bioengineered Bt corn, which underlines the importance of pest mobility, and the externalities it causes, in the development of resistance;Chapter II consists of a general theoretical model on resistance development that incorporates a spatial dimension. This allows the analysis of the impact of pest mobility on the effectiveness of refuges, areas in which the pesticides are not used to preserve the existence of susceptible pests. A discussion of eradication policies and of the role of cross-resistance is included;Chapter III presents an empirical analysis of the role of pest mobility in the development of resistance in the case of Bt corn. The model includes the existence of mandatory (structured) refuges for farmers planting Bt crops and analyzes the impact of incomplete market penetration on resistance development and profits. If part of the crop production area is seeded with non-bioengineered seed, these fields act as an unstructured refuge. The current policy is effectively based on a 100% market penetration. This is not necessarily a realistic assumption. We explicitly evaluate the role of market penetration on resistance;Chapter IV concentrates on the optimal use of existing antibiotics and on the optimal time path of investment in the development of new technologies. The intertemporal allocation of susceptibility and the development of alternative technologies are important social issues, particularly in the case of antibiotics, because health can be considered a necessary good. The analysis focuses on the role of endogenous technological and the investment of resources in alternative technologies;Lastly, some general conclusions on the importance of externalities and technological change in the mining of susceptibility are presented