Trends in Archaeological Simulation

This paper provides an up-to-date history of archaeological computer simulation, starting with the early 1970s simulation models, but paying particular attention to those developed over the past 20-25 years. It revises earlier accounts of archaeological simulation by proposing an alternation between programmatic phases, in which published work tends to be about simulation as a method, and mature phases in which there is greater emphasis on the substantive results of simulation experiments. The paper concludes that the burgeoning interest in computer simulation since circa 2000 is largely characterized by mature application in areas where it fits naturally into existing inferential frameworks (e.g., certain strands of evolutionary archaeology) but that explicitly "sociological" simulation remains a challenge

Single cell genomics as a transformative approach for aquaculture research and innovation

Single cell genomics encompasses a suite of rapidly maturing technologies that measure the molecular profiles of individual cells within target samples. These approaches provide a large up-step in biological information compared to long-established ‘bulk’ methods that profile the average molecular profiles of all cells in a sample, and have led to transformative advances in understanding of cellular biology, particularly in humans and model organisms. The application of single cell genomics is fast expanding to non-model taxa, including aquaculture species, where numerous research applications are underway with many more envisaged. In this review, we highlight the potential transformative applications of single cell genomics in aquaculture research, considering barriers and potential solutions to the broad uptake of these technologies. Focusing on single cell transcriptomics, we outline considerations for experimental design, including the essential requirement to obtain high quality cells/nuclei for sequencing in ectothermic aquatic species. We further outline data analysis and bioinformatics considerations, tailored to studies with the under-characterized genomes of aquaculture species, where our knowledge of cellular heterogeneity and cell marker genes is immature. Overall, this review offers a useful source of knowledge for researchers aiming to apply single cell genomics to address biological challenges faced by the global aquaculture sector though an improved understanding of cell biology

User interfaces in space science instrumentation

This thesis examines user interaction with instrumentation in the specific context of space science. It gathers together existing practice in machine interfaces with a look at potential future usage and recommends a new approach to space science projects with the intention of maximising their science return. It first takes a historical perspective on user interfaces and ways of defining and measuring the science return of a space instrument. Choices of research methodology are considered. Implementation details such as the concepts of usability, mental models, affordance and presentation of information are described, and examples of existing interfaces in space science are given. A set of parameters for use in analysing and synthesizing a user interface is derived by using a set of case studies of diverse failures and from previous work. A general space science user analysis is made by looking at typical practice, and an interview plus persona technique is used to group users with interface designs. An examination is made of designs in the field of astronomical instrumentation interfaces, showing the evolution of current concepts and including ideas capable of sustaining progress in the future. The parameters developed earlier are then tested against several established interfaces in the space science context to give a degree of confidence in their use. The concept of a simulator that is used to guide the development of an instrument over the whole lifecycle is described, and the idea is proposed that better instrumentation would result from more efficient use of the resources available. The previous ideas in this thesis are then brought together to describe a proposed new approach to a typical development programme, with an emphasis on user interaction. The conclusion shows that there is significant room for improvement in the science return from space instrumentation by attention to the user interface

Modeling contaminant transport and fate and subsequent impacts on ecosystems

Assessing risks associated with the release of metals into the environment and managing remedial activities requires simulation tools that depict speciation and risk with accurate mechanistic models and well-defined transport parameters. Such tools need to address the following processes: (1) aqueous speciation, (2) distribution mechanisms, (3) transport, and (4) ecological risk. The primary objective of this research is to develop a simulation tool that accounts for these processes. Speciation in the aqueous phase can be assessed with geochemical equilibrium models, such as MINEQL+. Furthermore, metal distribution can be addressed mechanistically. Studies with Pb sorption to amorphous aluminum (HAG), iron (HFO), and manganese (HMO) oxides, as well as oxide coatings, demonstrated that intraparticle diffusion is the rate-limiting mechanism in the sorption process, where best-fit surface diffusivities ranged from 10-18 to 10-15 cm2 s-1 Intraparticle surface diffusion was incorporated into the Groundwater Modeling System (GMS) to accurately simulate metal contaminant mobility where oxides are present. In the model development, the parabolic concentration layer approximation and the operator split technique were used to solve the microscopic diffusion equation coupled with macroscopic advection and dispersion. The resulting model was employed for simulating Sr90 mobility at the U.S. Department of Energy (DOE) Hanford Site. The Sr90 plume is observed to be migrating out of the 100-N area extending into other areas of the Hanford Site and beyond. Once bioavailability is understood, static or dynamic ecological risk assessments can be conducted. Employing the ERA model, a static ecological risk assessment for exposure to depleted uranium (DU) at Aberdeen and Yuma Proving Grounds (APG and YPG) revealed that a reduction in plant root weight is considered likely to occur. For most terrestrial animals at YPG, the predicted DU dose is less than that which would result in a decrease in offspring. However, for the lesser long-nosed bat, reproductive effects are expected to occur through the reduction in size and weight of offspring. At APG, based on very limited data, it is predicted that uranium uptake will not likely affect survival of terrestrial animals and aquatic species. In model validation, sampling of pocket mice, kangaroo rat, white-throated woodrat, deer, and milfoil showed that body burden concentrations fall into the distributions simulated at both sites. This static risk assessment provides a solid background for applying the dynamic approach. Overall, this research contributes to a holistic approach in developing accurate mechanistic models for simulating metal contaminant mobility and bioavailability in subsurface environments

Large-scale inference in the focally damaged human brain

Clinical outcomes in focal brain injury reflect the interactions between two distinct anatomically distributed patterns: the functional organisation of the brain and the structural distribution of injury. The challenge of understanding the functional architecture of the brain is familiar; that of understanding the lesion architecture is barely acknowledged. Yet, models of the functional consequences of focal injury are critically dependent on our knowledge of both. The studies described in this thesis seek to show how machine learning-enabled high-dimensional multivariate analysis powered by large-scale data can enhance our ability to model the relation between focal brain injury and clinical outcomes across an array of modelling applications. All studies are conducted on internationally the largest available set of MR imaging data of focal brain injury in the context of acute stroke (N=1333) and employ kernel machines at the principal modelling architecture. First, I examine lesion-deficit prediction, quantifying the ceiling on achievable predictive fidelity for high-dimensional and low-dimensional models, demonstrating the former to be substantially higher than the latter. Second, I determine the marginal value of adding unlabelled imaging data to predictive models within a semi-supervised framework, quantifying the benefit of assembling unlabelled collections of clinical imaging. Third, I compare high- and low-dimensional approaches to modelling response to therapy in two contexts: quantifying the effect of treatment at the population level (therapeutic inference) and predicting the optimal treatment in an individual patient (prescriptive inference). I demonstrate the superiority of the high-dimensional approach in both settings

Framework for remediation of rivers impacted by legacy metal mine pollution

Seven percent of surface waters in England and Wales are impacted by pollution from abandoned non-ferrous metal mines. It is estimated that there are about five thousand five hundred of these. There is no legal liability to any party attached to abandoned metal mines in the UK if they ceased operation before 1999. Preventing pollution from entering river catchments from these sources can be expensive and public funds are limited in extent. These enduring sources of pollution are a significant impediment to compliance with the legislative requirements, such as the European Water Framework Directive. This thesis develops a framework for integrating pre-existing tools and methodologies to address this environmental problem: Environmental Impact Assessment (EIA), Life Cycle Impact Assessment (LCIA) and Payments for Ecosystem Services (PES). By fully quantifying the economic, social and environmental impacts of abandoned mine discharges and the net benefits of potential management interventions over different scales, it is proposed that the framework can provide a sustainable way forward for identifying appropriate cost-effective remedial interventions, identify sources of funding for remediation to take place through PES, while at the same time being sensitive to stakeholder concerns. To determine the effectiveness of this framework two phases of research have been undertaken. The first was a series of interviews with a range of key stakeholders with relevant knowledge and expertise, targeting key concerns and conflicts that arise in managing legacy pollution. The second was to apply the framework to a specific mine-impacted catchment to determine the effectiveness of the framework and an optimal solution for that site. Key findings of stakeholder interviews revealed the general positive attitude towards PES-schemes also discrepancies in knowledge between different sectors. Industrial representatives emphasised the likely need for regulation to initiate such processes. The potentially important role of stewardship and conservation organisations as “ethical brokers” for such schemes was highlighted, given their expertise at communicating and managing a range of stakeholder opinions. The application of the framework to the Hebden Beck catchment in North Yorkshire found that multiple small scale passive remediation at affected locations would be an optimal solution. The full costs of such systems are outweighed by the potential ecosystem service benefits of metal removal from upland streams. Fundamental to the acceptability and sustainability of the remedial solution was the requirement for habitat offsetting to be incorporated into the proposed works

Characterising the Extent of Illegal Online Trade in Wildlife Using Novel Approaches

The illegal, international trade in wildlife poses serious and pressing threats at a number of levels. Traded species are increasingly threatened with extinction and these harms extend to compromised biodiversity and ecosystem instability. Associated threats include biosecurity issues such as disease introduction (including zoonoses) and the ingress of alien species. There is acute awareness of both the critical need for enhanced understanding of the extent and nature of the illegal wildlife trade and how challenging it is to achieve this. The online trading environment presents a particular case where challenges are amplified since it is growing rapidly, diverse and complex to monitor and regulate. Mirroring patterns in conventional trade, the online environment is increasingly being used as a means to conduct legal and illegal wildlife trade. Its attractiveness for illegal trade is illustrated by recent experience where, in response to ivory trade bans, trade shifted from physical trading outlets to online media. The research focus of this thesis is to contribute towards addressing a key area of unmet need that underpins counter-illegal wildlife trade measures. Specifically, bridging an informational "gap" which the United Nations General Assembly (UNGA) has acknowledged under UN Resolution A/71/L.88 "Tackling Illicit Wildlife Trafficking" (2017). Under UN A/71/L.88 the UNGA has tasked the United Nations Office on Drugs and Crime (UNODC) with collecting information on patterns and flows of illicit wildlife trafficking as a support to addressing the trade. The UNODC describes bridging the informational gap as essential to successful counter illegal wildlife trade measures. I translate this imperative to the fast-growing online environment for illegal wildlife trade where the lack of information is a compelling unmet need. I apply two approaches to researching illegal online wildlife trade and the behaviours associated with it. These are: a) "Measurement" (modelling) of online trade postings by application of two different mark recapture (MRC) models to downloaded encounter history data for the online ivory trade (Chapters 3 and 4) and b) "Asking" people who may be involved with illegal (online) wildlife trade to share this information through an online survey incorporating sensitive question models (Chapter 5). In my initial MRC study I build on prior research into online trade in CITES-listed species to evaluate population parameters associated with (illegal) online trade in elephant ivory within the UK. Online media operate "24/7" and, currently, no suitable technology exists to monitor and interrogate this trade continuously. MRC offers a resource-efficient means to monitor trade since it can be applied to estimate trading population parameters based on incomplete observation. I assess study outcomes to identify population parameter inferences and potential actions to address trade based on these. I indicate opportunities for MRC application to enhance understanding of the illegal, online trade in ivory and, potentially, other wildlife trade commodities. I then explore application of the complex, multi-parameter multi-state open robust design (MSORD) model to time-separated sets of encounter histories of online "ivory" trade items (UK trade). My intent is to examine the suitability of MSORD for modelling data from snap-shot online wildlife trade monitoring studies to derive maximum information and resource benefit from them. In this way, to build knowledge and understanding of the illegal online trade in ivory (and potentially other wildlife trade commodities). I shift focus to engage with people more directly to understand their involvement in illegal wildlife trade, preferred transaction routes i.e. face to face or online, and how this balance may be changing. I apply sensitive question models (including a novel model) and direct questioning to investigate potentially sensitive purchasing behaviours in a reptile keeper community, principally UK-based. I discuss study outcomes in terms of comparative model performance and consider significant results in the context of the reptile trade. Aspects particular to sensitive question model application are discussed and suggestions for future research made, informed by learnings from this study. Considered as a whole, the outcomes from this thesis have potential for application to increase knowledge and understanding of the illegal online trade in wildlife and contribute towards bridging the informational gap described. The MRC approaches applied may offer resource-sparing means to monitor online trade and better understand trading population parameters. This enhanced understanding could provide a basis for informed policy development and coordinated interventions ranging from educational, to law enforcement. Behavioural elements of trading populations (such as participation in illegal wildlife trade, sensitivities to it and preferred routes for purchasing items) may be further explored using sensitive question models. This research indicates that illegal, online wildlife trade is ongoing in the (mainly) UK trading populations I have assessed, despite initiatives and enforcement actions designed to address it. This leads me to consider the effectiveness of such initiatives, and factors that may influence this. I suggest that ensuring clear understanding of the extent and nature of trade being conducted, including the behaviours that underpin it, is essential to designing suitable interventions with an increased likelihood of success. I recommend further, coordinated research as indicated in this thesis as part of a wider initiative to deepen understanding of illegal (online) wildlife trade as a support to effective counter-measures and biodiversity conservation

KINE[SIS]TEM'17 From Nature to Architectural Matter

Kine[SiS]tem – From Kinesis + System. Kinesis is a non-linear movement or activity of an organism in response to a stimulus. A system is a set of interacting and interdependent agents forming a complex whole, delineated by its spatial and temporal boundaries, influenced by its environment. How can architectural systems moderate the external environment to enhance comfort conditions in a simple, sustainable and smart way? This is the starting question for the Kine[SiS]tem’17 – From Nature to Architectural Matter International Conference. For decades, architectural design was developed despite (and not with) the climate, based on mechanical heating and cooling. Today, the argument for net zero energy buildings needs very effective strategies to reduce energy requirements. The challenge ahead requires design processes that are built upon consolidated knowledge, make use of advanced technologies and are inspired by nature. These design processes should lead to responsive smart systems that deliver the best performance in each specific design scenario. To control solar radiation is one key factor in low-energy thermal comfort. Computational-controlled sensor-based kinetic surfaces are one of the possible answers to control solar energy in an effective way, within the scope of contradictory objectives throughout the year.FC

Optical microscopy to study the role of cytoskeleton in cell locomotion and virus trafficking

3. General conclusions 150 The interest in optical microscopy is constanly growing, mainly because of its unique features in examining biological systems in four dimensions (x-y-z-t)1 . The work presented here was focused on biological applications of optical microscopy by exploring and improving the spatial and temporal resolution performances and by futher developing optical tools for manipulating biological samples. First, I studied the resolution performances of the system in the three dimensional space and I contributed in improving the experimental spatial resolution of microscope by applying deconvolution. In this respect, theoretical modelling can characterize the image formation process of the microscope, but only experimental measurement of the PSF can quantify the limitations of the real system. Indeed, experimental PSF presents shape assymetry due to spherical aberrations introduced by optical elements, while theoretical PSF is symmetric and account only for the resolution limits of an ideal imaging system. The disadvantage of experimental PSF is that could be corrupted by noise, otherwise deconvolution with the theoretical PSF offer only a qualitative improvement of the image, because the introduced artefacts cannot be quantified. Deconvolution of the acquired data with experimental PSF...3. General conclusions 150 The interest in optical microscopy is constanly growing, mainly because of its unique features in examining biological systems in four dimensions (x-y-z-t)1 . The work presented here was focused on biological applications of optical microscopy by exploring and improving the spatial and temporal resolution performances and by futher developing optical tools for manipulating biological samples. First, I studied the resolution performances of the system in the three dimensional space and I contributed in improving the experimental spatial resolution of microscope by applying deconvolution. In this respect, theoretical modelling can characterize the image formation process of the microscope, but only experimental measurement of the PSF can quantify the limitations of the real system. Indeed, experimental PSF presents shape assymetry due to spherical aberrations introduced by optical elements, while theoretical PSF is symmetric and account only for the resolution limits of an ideal imaging system. The disadvantage of experimental PSF is that could be corrupted by noise, otherwise deconvolution with the theoretical PSF offer only a qualitative improvement of the image, because the introduced artefacts cannot be quantified. Deconvolution of the acquired data with experimental PSF...Department of Genetics and MicrobiologyKatedra genetiky a mikrobiologieFaculty of SciencePřírodovědecká fakult