Mobile Augmented Reality for Flood Visualisation in Urban Riverside Landscapes

Frequency of flooding events worldwide has increased significantly over the past decades, and with it so has the need to raise citizen’s awareness of potential dangers within local flood zones. Smart phones provide a feasible means with which to educate the public in this way. We present a working smart phone app to engage the public with local flood zones by visualising potential flood levels. An interactive augmented reality (AR) tool provides in situ modeling of simple prototype 3D building models (cuboids) along a riverside, which are used to “occlude” an augmented flood plane within the scene. Flood plane height may be adjusted by the user. We discuss related AR work, tools for real-time in situ geometry modeling, app operation and present and on site demonstration

The design-by-adaptation approach to universal access: learning from videogame technology

This paper proposes an alternative approach to the design of universally accessible interfaces to that provided by formal design frameworks applied ab initio to the development of new software. This approach, design-byadaptation, involves the transfer of interface technology and/or design principles from one application domain to another, in situations where the recipient domain is similar to the host domain in terms of modelled systems, tasks and users. Using the example of interaction in 3D virtual environments, the paper explores how principles underlying the design of videogame interfaces may be applied to a broad family of visualization and analysis software which handles geographical data (virtual geographic environments, or VGEs). One of the motivations behind the current study is that VGE technology lags some way behind videogame technology in the modelling of 3D environments, and has a less-developed track record in providing the variety of interaction methods needed to undertake varied tasks in 3D virtual worlds by users with varied levels of experience. The current analysis extracted a set of interaction principles from videogames which were used to devise a set of 3D task interfaces that have been implemented in a prototype VGE for formal evaluation

Collective signalling drives rapid jumping between cell states

Development can proceed in "fits and starts", with rapid transitions between cell states involving concerted transcriptome-wide changes in gene expression. However, it is not clear how these transitions are regulated in complex cell populations, in which cells receive multiple inputs. We address this issue using Dictyostelium cells undergoing development in their physiological niche. A continuous single cell transcriptomics time series identifies a sharp "jump" in global gene expression marking functionally different cell states. By simultaneously imaging the physiological dynamics of transcription and signalling, we show the jump coincides with the onset of collective oscillations of cAMP. Optogenetic control of cAMP pulses shows that different jump genes respond to distinct dynamic features of signalling. Late jump gene expression changes are almost completely dependent on cAMP, while transcript changes at the onset of the jump require additional input. The coupling of collective signalling with gene expression is a potentially powerful strategy to drive robust cell state transitions in heterogeneous signalling environments. Based on the context of the jump, we also conclude that sharp gene expression transitions may not be sufficient for commitment

Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.

Differentiation of naïve CD4+ T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to extensive heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell transcriptomics and computational analysis using a temporal mixtures of Gaussian processes model, termed GPfates, we reconstructed the developmental trajectories of Th1 and Tfh cells during blood-stage Plasmodium infection in mice. By tracking clonality using endogenous TCR sequences, we first demonstrated that Th1/Tfh bifurcation had occurred at both population and single-clone levels. Next, we identified genes whose expression was associated with Th1 or Tfh fates, and demonstrated a T-cell intrinsic role for Galectin-1 in supporting a Th1 differentiation. We also revealed the close molecular relationship between Th1 and IL-10-producing Tr1 cells in this infection. Th1 and Tfh fates emerged from a highly proliferative precursor that upregulated aerobic glycolysis and accelerated cell cycling as cytokine expression began. Dynamic gene expression of chemokine receptors around bifurcation predicted roles for cell-cell in driving Th1/Tfh fates. In particular, we found that precursor Th cells were coached towards a Th1 but not a Tfh fate by inflammatory monocytes. Thus, by integrating genomic and computational approaches, our study has provided two unique resources, a database www.PlasmoTH.org, which facilitates discovery of novel factors controlling Th1/Tfh fate commitment, and more generally, GPfates, a modelling framework for characterizing cell differentiation towards multiple fates

Deciphering Leukaemogenic Mechanisms through System-Scale Analysis of Single-Cell RNA Sequencing Data

Haematopoietic stem cells are responsible for producing and sustaining the diverse array of cell types present in the adult blood system. This complex process requires the strict regulation of haematopoietic fate decisions and differentiation trajectories in order to maintain a healthy state. Haematological malignancies such as leukaemia are associated with various perturbations that disrupt this regulation and drive aberrant cell fate decisions, leading to disease. Much of this dysregulation is proposed to occur at the transcriptional level, and recent technological advancements in single-cell sequencing have made it possible to study the transcriptional effects of leukaemic perturbations at the scale of individual haematopoietic stem and progenitor cells. However, the mechanisms through which specific perturbations lead to dysregulation of the blood system remain poorly understood. The primary aim of this work was to build an integrative computational framework for the analysis and comparison of leukaemic perturbations of the murine blood system as measured by single-cell RNA sequencing. Presented in Chapter 3, this framework aims to dissect the perturbation response across different scales – from individual genes to specific progenitor cell types to the entire blood system – and allow informative comparisons to be made about the similarities and differences between several perturbations. In total, eight genetic perturbations known to associate with leukaemia were analysed, resulting in novel biological insights concerning the behaviour of coordinated gene modules and the cellular abundance shifts driven by them. As many leukaemic drivers act directly upon the most immature long-term haematopoietic stem cells, a highly targeted analysis of these cells was performed across the leukaemic perturbations. In Chapter 4 a novel computational pipeline was built to link FACS-sorted cell populations and single-cell transcriptional landscapes. Using this, the cellular and molecular responses of the perturbations were investigated, resulting in several novel hypotheses. For example, the data suggests that many leukaemic perturbations gain a competitive advantage against wild-type cells by pushing their MPP1 cells into more active states. Additionally the data suggests that increases in the transcriptional variability of blood stem cells is associated with pro-erythroid fate decision shifts and vice-versa. Many different types of haematopoietic perturbations exist and can drive disease progression in the blood system. Chapter 5 focuses on single-cell RNA sequencing data from three further perturbations in various settings, including an infection model of Malaria and a model susceptible to endogenous DNA damage by aldehydes. These analyses have driven and validated bodies of experimental work, and comparing them to the previously described perturbation models highlighted both conserved changes and differences in the response of the haematopoietic system across different perturbation settings. The final project aimed to improve upon current computational methods for cellular trajectory inference from single-cell data. Whilst high-throughput experiments allow for the sequencing of large cell numbers, this is balanced by the sparse and noisy nature of the returned data. Current methods perform poorly on such datasets and either cannot deal with large cell numbers or cannot extract enough relevant signal from sparse count matrices. A new computational tool was designed to work best on these large, sparse datasets, and infer the most likely cellular trajectories through snapshot sequencing data using an iterative process. In Chapter 6 this algorithm was applied to different systems including adult haematopoiesis, and was compared to state-of-the-art methods. Overall, this thesis has investigated the transcriptional consequences of numerous preleukaemic perturbations on the haematopoietic stem and progenitor cell compartment at the single-cell level. New methods have been built for integration of single-cell perturbation experiments and their analysis across different biological scales. This has revealed novel biological insights regarding the mechanisms underpinning leukaemic transformation of the blood system

Diverse perceptions of smart spaces

This is the era of smart technology and of ‘smart’ as a meme, so we have run three workshops to examine the ‘smart’ meme and the exploitation of smart environments. The literature relating to smart spaces focuses primarily on technologies and their capabilities. Our three workshops demonstrated that we require a stronger user focus if we are advantageously to exploit spaces ascribed as smart: we examined the concept of smartness from a variety of perspectives, in collaboration with a broad range of contributors. We have prepared this monograph mainly to report on the third workshop, held at Bournemouth University in April 2012, but do also consider the lessons learned from all three. We conclude with a roadmap for a fourth (and final) workshop, which is intended to emphasise the overarching importance of the humans using the spac

Elupaiga ja maastiku mõjud päevaliblikakooslustele majandatavates metsades

Väitekirja elektrooniline versioon ei sisalda publikatsiooneElurikkuse vähenemine on üleilmne probleem, mida peamiselt põhjustab looduslike ja poollooduslike elupaikade kadumine. Elupaikade liigilist mitmekesisust mõjutab ka ümbritsev maastik: mida rohkem on elupaigad üksteisest eraldatud, seda enam need liigiliselt vaesuvad. Ehkki kaitsealad on elurikkuse hoidmisel väga tähtsad, ainuüksi neist ei piisa. Järjest enam püütakse leida võimalusi liigirikkuse säilitamiseks ja suurendamiseks ka tugevate inimmõjutustega maastikes. Suurenev nõudlus puidu ja puidutoodete järele on järjest intensiivsemaks muutnud ka metsade majandamise. Metsamajanduse intensiivistumine on paljudele metsaliikidele ohuks, samas leidub ka neid, kellele majandatav metsamaastik elupaigaks sobib. Doktoritöö tulemused viitavad, et üheks selliseks liigirühmaks on metsapäevaliblikad. Paljude liikide röövikud toituvad puudel, põõsastel ja alustaimestiku taimedel, valmikud aga leiavad nektaritaimi raiesmikelt. Niisiis on metsapäevaliblikatele oluline mosaiikne metsamaastik tervikuna – doktoritöös leidsingi, et mida rohkem on ümbritsevas maastikus metsamaad, seda kõrgem on metsaliblikate liigirikkus raiesmikul. Oma töös lähen aga sammu võrra kaugemale ja näitan, et lisaks metsaliikidele pakub majandatav metsamaastik oma mitmesuguste avakooslustega elupaika ka paljudele avamaastikuliikidele. Selgus, et raiesmikud on elupaigaks enamikule regionaalsest päevaliblikafaunast, kellest suurt osa on tavapäraselt seostatud poollooduslike niitudega. Seejuures asustavad niiduliigid ka täielikult metsaga ümbritsetud raiesmikke, millest järeldub, et puistu raiesmikele jõudmisel neile oluliseks takistuseks ei ole. Nii niiduliikide kui metsaliikide koosluseid mõjutavad aga metsa lokaalsed kasvukohatingimused – teatud liigid esinevad sagedamini ja arvukamalt näiteks palumetsades, teised jällegi laane- või salumetsades. Seega on päevaliblikate liigirikkuse seisukohalt oluline elupaikade mitmekesisus, erinevad metsatüübid täiendavad teineteist.Decrease of biodiversity is a global problem mainly caused by loss of natural and semi-natural habitats. Local diversity is also affected by surrounding landscape: isolation of habitats leads to decline of species richness. Despite being important, protected areas alone may be insufficient to maintain biodiversity. The focus is shifting towards sustaining and enhancing species diversity in landscapes of significant human impact. Intensification of forest management due to increasing demand for timber, poses a threat for many forest species. However, some species may find favourable habitat in managed forests. The results of this thesis indicate that forest butterflies are among those. At caterpillar stage, forest butterflies feed on trees, bushes and understorey plants, whereas adults find nectar plants from clear-cuts. Therefore, the whole mosaic of managed forest landscape is important for forest butterflies. Indeed, I found higher species richness of forest butterflies in clear-cuts containing higher proportion of woodland in the surrounding landscape. Furthermore, my thesis shows that managed forest landscape containing various open habitats is also suitable for many open-habitat species. I found that clear-cuts serve as habitats for the majority of regional species pool of butterflies traditionally associated with semi-natural grasslands. Moreover, grassland species reach even to clear-cuts completely surrounded with forest, which implies that forest is not a significant barrier for colonisation. Assemblages of grassland species and forest species are both affected by local environmental conditions of forest: different forest types provide habitat for distinct butterfly assemblages. The diversity of forest types is therefore important for maintaining species richness of butterflies, as different forest habitat types complement each other.https://www.ester.ee/record=b524411

2011 Strategic roadmap for Australian research infrastructure

The 2011 Roadmap articulates the priority research infrastructure areas of a national scale (capability areas) to further develop Australia’s research capacity and improve innovation and research outcomes over the next five to ten years. The capability areas have been identified through considered analysis of input provided by stakeholders, in conjunction with specialist advice from Expert Working Groups   It is intended the Strategic Framework will provide a high-level policy framework, which will include principles to guide the development of policy advice and the design of programs related to the funding of research infrastructure by the Australian Government. Roadmapping has been identified in the Strategic Framework Discussion Paper as the most appropriate prioritisation mechanism for national, collaborative research infrastructure. The strategic identification of Capability areas through a consultative roadmapping process was also validated in the report of the 2010 NCRIS Evaluation. The 2011 Roadmap is primarily concerned with medium to large-scale research infrastructure. However, any landmark infrastructure (typically involving an investment in excess of $100 million over five years from the Australian Government) requirements identified in this process will be noted. NRIC has also developed a ‘Process to identify and prioritise Australian Government landmark research infrastructure investments’ which is currently under consideration by the government as part of broader deliberations relating to research infrastructure. NRIC will have strategic oversight of the development of the 2011 Roadmap as part of its overall policy view of research infrastructure

Implementation of computer visualisation in UK planning

PhD ThesisWithin the processes of public consultation and development management, planners are required to consider spatial information, appreciate spatial transformations and future scenarios. In the past, conventional media such as maps, plans, illustrations, sections, and physical models have been used. Those traditional visualisations are at a high degree of abstraction, sometimes difficult to understand for lay people and inflexible in terms of the range of scenarios which can be considered. Yet due to technical advances and falling costs, the potential for computer based visualisation has much improved and has been increasingly adopted within the planning process. Despite the growth in this field, insufficient consideration has been given to the possible weakness of computerised visualisations. Reflecting this lack of research, this study critically evaluates the use and potential of computerised visualisation within this process. The research is divided into two components: case study analysis and reflections of the author following his involvement within the design and use of visualisations in a series of planning applications; and in-depth interviews with experienced practitioners in the field. Based on a critical review of existing literature, this research explores in particular the issues of credibility, realism and costs of production. The research findings illustrate the importance of the credibility of visualisations, a topic given insufficient consideration within the academic literature. Whereas the realism of visualisations has been the focus of much previous research, the results of the case studies and interviews with practitioners undertaken in this research suggest a ‘photo’ realistic level of details may not be required as long as the observer considers the visualisations to be a credible reflection of the underlying reality. Although visualisations will always be a simplification of reality and their level of realism is subjective, there is still potential for developing guidelines or protocols for image production based on commonly agreed standards. In the absence of such guidelines there is a danger that scepticism in the credibility of computer visualisations will prevent the approach being used to its full potential. These findings suggest there needs to be a balance between scientific protocols and artistic licence in the production of computer visualisation. In order to be sufficiently credible for use in decision making within the planning processes, the production of computer visualisation needs to follow a clear methodology and scientific protocols set out in good practice guidance published by professional bodies and governmental organisations.Newcastle upon Tyne for awarding me an International Scholarship and Alumni Bursar