Winning and losing in the hall of mirrors

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Who are we? Why do we do the things we do? These questions are constantly under scrutiny, forever unable to provide us with adequate answers, it seems. Yet, with the continuing rise in popularity of digital media, we are able to situate these questions in a different sphere and see aspects of the self that we were unable to perceive before. Digital media forms have provided us with the capacity to explore whole new worlds, as well as allowing for new and innovative methods of communication. These changes make a huge impact on the daily lives of individuals. This thesis presents a theoretical contribution to both psychoanalytic thinking and to the rapidly expanding field of games studies, with especial reference to avatar-based games. It considers the status of the bond formed between the individual at play (known here as the ‘user’) and the game itself. Furthermore, it presents this as a model which identifies the user’s relation to the game dynamic through an understanding of the key components of a video game, including aspects such as the control mechanism. Elements which cross the boundary between the user/game realities are also considered with relation to hyperreality, thus forming a more complete imagining of this framework. This also allows for an application of this dynamic to what we define as violent (and associated) acts within games. In turn, this allows for a more complete understanding of the game situation, and can be applied to our understanding of the user as well. This thesis provides a standalone framework which can also be utilised in other types of investigation in future

A systematic review of speech recognition technology in health care

BACKGROUND To undertake a systematic review of existing literature relating to speech recognition technology and its application within health care. METHODS A systematic review of existing literature from 2000 was undertaken. Inclusion criteria were: all papers that referred to speech recognition (SR) in health care settings, used by health professionals (allied health, medicine, nursing, technical or support staff), with an evaluation or patient or staff outcomes. Experimental and non-experimental designs were considered. Six databases (Ebscohost including CINAHL, EMBASE, MEDLINE including the Cochrane Database of Systematic Reviews, OVID Technologies, PreMED-LINE, PsycINFO) were searched by a qualified health librarian trained in systematic review searches initially capturing 1,730 references. Fourteen studies met the inclusion criteria and were retained. RESULTS The heterogeneity of the studies made comparative analysis and synthesis of the data challenging resulting in a narrative presentation of the results. SR, although not as accurate as human transcription, does deliver reduced turnaround times for reporting and cost-effective reporting, although equivocal evidence of improved workflow processes. CONCLUSIONS SR systems have substantial benefits and should be considered in light of the cost and selection of the SR system, training requirements, length of the transcription task, potential use of macros and templates, the presence of accented voices or experienced and in-experienced typists, and workflow patterns.Funding for this study was provided by the University of Western Sydney. NICTA is funded by the Australian Government through the Department of Communications and the Australian Research Council through the ICT Centre of Excellence Program. NICTA is also funded and supported by the Australian Capital Territory, the New South Wales, Queensland and Victorian Governments, the Australian National University, the University of New South Wales, the University of Melbourne, the University of Queensland, the University of Sydney, Griffith University, Queensland University of Technology, Monash University and other university partners

Genomes, expression profiles, and diversity of mitochondria of the White-footed Deermouse Peromyscus leucopus, reservoir of Lyme disease and other zoonoses.

The cricetine rodents Peromyscus leucopus and P. maniculatus are key reservoirs for several zoonotic diseases in North America. We determined the complete circular mitochondrial genome sequences of representatives of 3 different stock colonies of P. leucopus, one stock colony of P. maniculatus and two wild populations of P. leucopus. The genomes were syntenic with that of the murids Mus musculus and Rattus norvegicus. Phylogenetic analysis confirmed that these two Peromyscus species are sister taxa in a clade with P. polionotus and also uncovered a distinction between P. leucopus populations in the eastern and the central United States. In one P. leucopus lineage four extended regions of mitochondrial pseudogenes were identified in the nuclear genome. RNA-seq analysis revealed transcription of the entire genome and differences from controls in the expression profiles of mitochondrial genes in the blood, but not in liver or brain, of animals infected with the zoonotic pathogen Borrelia hermsii. PCR and sequencing of the D-loop of the mitochondrion identified 32 different haplotypes among 118 wild P. leucopus at a Connecticut field site. These findings help to further establish P. leucopus as a model organism for studies of emerging infectious diseases, ecology, and in other disciplines

The FANTASTIC FOUR proteins influence shoot meristem size in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>Throughout their lives plants produce new organs from groups of pluripotent cells called meristems, located at the tips of the shoot and the root. The size of the shoot meristem is tightly controlled by a feedback loop, which involves the homeodomain transcription factor WUSCHEL (WUS) and the CLAVATA (CLV) proteins. This regulatory circuit is further fine-tuned by morphogenic signals such as hormones and sugars.</p> <p>Results</p> <p>Here we show that a family of four plant-specific proteins, encoded by the <it>FANTASTIC FOUR </it>(<it>FAF</it>) genes, has the potential to regulate shoot meristem size in <it>Arabidopsis thaliana</it>. <it>FAF2 </it>and <it>FAF4 </it>are expressed in the centre of the shoot meristem, overlapping with the site of <it>WUS </it>expression. Consistent with a regulatory interaction between the <it>FAF </it>gene family and <it>WUS</it>, our experiments indicate that the FAFs can repress <it>WUS</it>, which ultimately leads to an arrest of meristem activity in <it>FAF </it>overexpressing lines. The finding that meristematic expression of <it>FAF2 </it>and <it>FAF4 </it>is under negative control by CLV3 further supports the hypothesis that the FAFs are modulators of the genetic circuit that regulates the meristem.</p> <p>Conclusion</p> <p>This study reports the initial characterization of the <it>Arabidopsis thaliana FAF </it>gene family. Our data indicate that the <it>FAF </it>genes form a plant specific gene family, the members of which have the potential to regulate the size of the shoot meristem by modulating the CLV3-WUS feedback loop.</p

Context-aware movement analysis in ecology : a systematic review

This work was supported by the Coordination for the Improvement of Higher Education Personnel (BEX:13438/13-1), the Leverhulme Trust Research Project Grant (RPG-2018-258); the Discovery grant from the Natural Sciences and Engineering Research Council of Canada the Polish National Science Centre (UMO-2019/35/O/ST6/04127).Research on movement has increased over the past two decades, particularly in movement ecology, which studies animal movement. Taking context into consideration when analysing movement can contribute towards the understanding and prediction of behaviour. The only way for studying animal movement decision-making and their responses to environmental conditions is through analysis of ancillary data that represent conditions where the animal moves. In GIScience this is called Context-Aware Movement Analysis (CAMA). As ecology becomes more data-oriented, we believe that there is a need to both review what CAMA means for ecology in methodological terms and to provide reliable definitions that will bridge the divide between the content-centric and data-centric analytical frameworks. We reviewed the literature and proposed a definition for context, develop a taxonomy for contextual variables in movement ecology and discuss research gaps and open challenges in the science of movement more broadly. We found that the main research for CAMA in the coming years should focus on: 1) integration of contextual data and movement data in space and time, 2) tools that account for the temporal dynamics of contextual data, 3) ways to represent contextualized movement data, and 4) approaches to extract meaningful information from contextualized data.Publisher PDFPeer reviewe

A better sequence-read simulator program for metagenomics

BACKGROUND: There are many programs available for generating simulated whole-genome shotgun sequence reads. The data generated by many of these programs follow predefined models, which limits their use to the authors' original intentions. For example, many models assume that read lengths follow a uniform or normal distribution. Other programs generate models from actual sequencing data, but are limited to reads from single-genome studies. To our knowledge, there are no programs that allow a user to generate simulated data following non-parametric read-length distributions and quality profiles based on empirically-derived information from metagenomics sequencing data. RESULTS: We present BEAR (Better Emulation for Artificial Reads), a program that uses a machine-learning approach to generate reads with lengths and quality values that closely match empirically-derived distributions. BEAR can emulate reads from various sequencing platforms, including Illumina, 454, and Ion Torrent. BEAR requires minimal user input, as it automatically determines appropriate parameter settings from user-supplied data. BEAR also uses a unique method for deriving run-specific error rates, and extracts useful statistics from the metagenomic data itself, such as quality-error models. Many existing simulators are specific to a particular sequencing technology; however, BEAR is not restricted in this way. Because of its flexibility, BEAR is particularly useful for emulating the behaviour of technologies like Ion Torrent, for which no dedicated sequencing simulators are currently available. BEAR is also the first metagenomic sequencing simulator program that automates the process of generating abundances, which can be an arduous task. CONCLUSIONS: BEAR is useful for evaluating data processing tools in genomics. It has many advantages over existing comparable software, such as generating more realistic reads and being independent of sequencing technology, and has features particularly useful for metagenomics work

Introduction générale aux deux numéros : « Interactions tutorales et apprentissages en situation de travail »

Ce numéro double consacré à l’étude des « Interactions tutorales et apprentissages en situation de travail » tient son origine d’une rencontre de chercheurs qui a eu lieu dans le cadre du congrès de l’Actualité de la recherche en éducation et en formation (AREF) à Mons (Belgique) en juillet 2016. La rencontre coordonnée et animée par Long Pham Quang et Vanessa Rémery a permis de réunir un symposium des chercheurs sur la thématique : « Se former au travail : quelles interactions pour quels app..

Fusion of wildlife tracking and satellite geomagnetic data for the study of animal migration

This work was supported by the Leverhulme Trust [Research Project Grant RPG-2018-258].Background: Migratory animals use information from the Earth’s magnetic field on their journeys. Geomagnetic navigation has been observed across many taxa, but how animals use geomagnetic information to find their way is still relatively unknown. Most migration studies use a static representation of geomagnetic field and do not consider its temporal variation. However, short-term temporal perturbations may affect how animals respond - to understand this phenomenon, we need to obtain fine resolution accurate geomagnetic measurements at the location and time of the animal. Satellite geomagnetic measurements provide a potential to create such accurate measurements, yet have not been used yet for exploration of animal migration. Methods: We develop a new tool for data fusion of satellite geomagnetic data (from the European Space Agency’s Swarm constellation) with animal tracking data using a spatio-temporal interpolation approach. We assess accuracy of the fusion through a comparison with calibrated terrestrial measurements from the International Real-time Magnetic Observatory Network (INTERMAGNET). We fit a generalized linear model (GLM) to assess how the absolute error of annotated geomagnetic intensity varies with interpolation parameters and with the local geomagnetic disturbance. Results: We find that the average absolute error of intensity is − 21.6 nT (95% CI [− 22.26555, − 20.96664]), which is at the lower range of the intensity that animals can sense. The main predictor of error is the level of geomagnetic disturbance, given by the Kp index (indicating the presence of a geomagnetic storm). Since storm level disturbances are rare, this means that our tool is suitable for studies of animal geomagnetic navigation. Caution should be taken with data obtained during geomagnetically disturbed days due to rapid and localised changes of the field which may not be adequately captured. Conclusions: By using our new tool, ecologists will be able to, for the first time, access accurate real-time satellite geomagnetic data at the location and time of each tracked animal, without having to start new tracking studies with specialised magnetic sensors. This opens a new and exciting possibility for large multi-species studies that will search for general migratory responses to geomagnetic cues. The tool therefore has a potential to uncover new knowledge about geomagnetic navigation and help resolve long-standing debates.Publisher PDFPeer reviewe

A systematic review of speech recognition technology in health care

Background To undertake a systematic review of existing literature relating to speech recognition technology and its application within health care. Methods A systematic review of existing literature from 2000 was undertaken. Inclusion criteria were: all papers that referred to speech recognition (SR) in health care settings, used by health professionals (allied health, medicine, nursing, technical or support staff), with an evaluation or patient or staff outcomes. Experimental and non-experimental designs were considered. Six databases (Ebscohost including CINAHL, EMBASE, MEDLINE including the Cochrane Database of Systematic Reviews, OVID Technologies, PreMED-LINE, PsycINFO) were searched by a qualified health librarian trained in systematic review searches initially capturing 1,730 references. Fourteen studies met the inclusion criteria and were retained. Results The heterogeneity of the studies made comparative analysis and synthesis of the data challenging resulting in a narrative presentation of the results. SR, although not as accurate as human transcription, does deliver reduced turnaround times for reporting and cost-effective reporting, although equivocal evidence of improved workflow processes. Conclusions SR systems have substantial benefits and should be considered in light of the cost and selection of the SR system, training requirements, length of the transcription task, potential use of macros and templates, the presence of accented voices or experienced and in-experienced typists, and workflow patterns

Multi-source data fusion of optical satellite imagery to characterize habitat selection from wildlife tracking data

This work was supported by CAPES (Coordination for the Improvement of Higher Education Personnel) [BEX-13438-13-1].Wildlife tracking data allow monitoring of how organisms respond to spatio-temporal changes in resource availability. Remote sensing data can be used to quantify and qualify these variations to understand how movement is related to these changes. The use of remote sensing data with concurrent high levels of spatial and temporal detail may hold potential to improve our understanding of habitat selection. However, no current orbital sensor produces data with simultaneous high temporal and high spatial resolution, therefore alternative methods are required to generate remote sensing data that matches the high spatial-temporal resolution of modern wildlife tracking data. We present an analytical framework, not yet used in movement ecology, for data fusion of optical remote sensing data from multiple satellites and wildlife tracking data to study the impact of seasonal vegetation patterns on the movement of maned wolves (Chrysocyon brachyurus). We use multi-source data fusion to combine MODIS data with higher spatial resolution data (ASTER, Landsat 4-5-7-8, CBERS 2-2B) and create a synthetic NDVI product with a 15 m spatial detail and daily temporal resolution. We also use the higher spatial resolution data to create a multi-source NDVI product with same level of spatial detail but coarser temporal resolution and data from MODIS to create a single-source NDVI product with high temporal resolution but coarse spatial resolution. We combine the three different spatial-temporal resolution NDVI products with GPS tracking data of maned wolves to create step-selection functions (SSF), which are models used in ecology to investigate and predict habitat selection by animals. The SSF model based on multi-source NDVI had the best performance predicting the probability of use of visited locations given its NDVI value. The SSF based on the raw MODIS NDVI product, one which is commonly employed by ecologists, had the poorest performance for our study species. These findings indicate that, in contrast with current practice in movement ecology, a detailed spatial resolution of contextual environmental variable may be more important than a detailed temporal resolution, when investigating wildlife habitat selection regarding vegetation, although this result will be highly dependent on species. The choice of data set should therefore take into account not only the scale of movement but also the spatial and temporal scales at which dynamic environmental variables are changing.PostprintPostprintPeer reviewe