Waveomics: bringing experimental data to online collaboration

Systems biology offers an interdisciplinary approach to scientific research that typically involves the collaboration of teams of experimentalists and mathematical modellers. While the importance of data standards has been recognised in facilitating exchange of data between the parties, challenges still remain regarding the practicalities of disseminating experimental data.

The introduction of novel web-based tools aimed at promoting collaborative work has provided a platform upon which scientific applications can be built. The recently released Google Wave protocol provides a facility for real-time collaboration between teams of researchers.

This work introduces a customized Robot that automatically scans text in Google Waves for experimental data identifiers, extracts corresponding experimental data from remote resources associated with such identifiers, and appends charts showing this experimental data to the Wave

The SBML Level 3 Annotation package: an initial proposal

The SBML Level 3 Annotation package proposal intends to extend the current Level 3 Core annotations by increasing the range of RDF features supported.

Such an extension will support RDF Reification, annotation of SBML attributes, specification of relationships between annotations, negation of annotations and cross-references and cross-element annotations

The Effect of Pettlep Imagery in a Pre Shot Routine on Full Swing Golf Shot Accuracy: A Single Subjects Design

Context: Imagery has been shown to be an effective tool for enhancing performance in a variety of sports. Specifically, imagery has been found to be extremely effective within the sport of golf (e.g., Nicholls & Polman, 2005; Woolfork, Parish, & Murphy\u27s, 1985). For example, Ploszay, Gentner, Skinner, and Wrisberg (2006) found imagery to improve putting performance. The purpose of this study was to investigate the effect that a PETTLEP imagery intervention implemented into a pre shot routine had on a full swing golf shot. A single subjects design was used with three conditions: imagery before pre shot routine, imagery after pre shot routine and a control condition. Participants were nine undergraduate volunteers with an average age of 19.3 years and an average golf score of 82.1. Three sets of data were recorded: total score, balls in A1 (the closest area to the pin in a standardized scoring target grid), and balls in A5 (anything outside of the grid). It was found that all imagery participants improved from baseline to intervention in all three aspects, while the control group elicited consistent or decreases in performance. Imagery had the greatest impact on performance for balls hit in A5. Implications from this study may benefit golfers of any skill level and sport psychology consultants working with golfers who want to increase their full swing shot accuracy

Player experience in the academy to first team transition in professional football

The thesis explores player experience during the junior-to-senior transition. A literature review, scoping review (under review), two empirical studies (published), a general discussion, and applied applications of the research comprise the thesis. The scoping review allowed us to explore the breadth of junior-to-senior transitions research in order to identify any and all gaps in the literature. Study one explores the evolving perspectives of young players' experiences going through the junior to senior transition in professional football. Using novel methods, namely video diaries, we were able to gain a rich understanding of the experience of transition players. Unique findings included contract decisions; adaptation to senior competition; barriers to transition without early success; and social aspects of the transition. Moreover, the weekly approach to data collection and analysis allowed a clear progression of the experience to be documented. Study two explored the junior-to-senior transition from professional contract to an established first-team player in an English men’s professional football team. Using multiple interviews with each participant four unique contributions to the literature are discussed: the central role of opportunity in career progression; the presence of a “gray period”; difficulties in seeking support from coaches; and contracts’ influence across the transition. The thesis includes a discussion of the overall findings and future research directions. The final chapter provides my experiences of working with athletes in transition to professional football

Optical Relaxation of Defects in Kapton Caused by Irradiation

Radiation can create atomic-scale defect states in polymers, leading to changes in their optical, electrical and mechanical properties. Recent studies of polymers have shown that these defect states are sensitive to oxygen or air exposure. It is believed that air cause the number of defect states to decrease and the polymers to revert to their original states. However, the time scale of this regression is not known. This experiment quantified the time that it takes one polymer to recover and the extent of said recovery; polymide (PI). In order to study the regression, optical transmission data were taken using a StellarNet UV/VIS Spectrometer. Optical data were collected at different intervals of time and then compared in order to quantify the time frame of the regression. Failure to account for this time-dependent recovery in radiation studies may result in inaccurate results and has called into question previous studies involving radiation effects in polymers where exposure times were not recorded

Thermal Decomposition of Cp*Re(CO)(NO)NO2

The focus of this work is to examine the thermal reactivity of the Cp*Re(CO)(NO)NO2 complex. Upon heating with a flame, the orange crystals decompose very rapidly, with a darkening of color and gas production. To investigate this reaction, the decomposition was carefully controlled by heating with N2 gas, and in heated solution. The products obtained from the heated solution were purified using column chromatography, yielding two new interesting compounds, believed to be Cp*ReNO dimers with bridging oxygens

Laboratory Modeling of Critical Hydraulic Conditions for the Initiation of Piping

Seepage-related erosion is one of the predominant mechanisms responsible for incidents and failures of dams and levees. Current geotechnical engineering practice consists of comparing expected exit gradients with the critical gradient of the soil at the seepage exit point. The critical gradient is generally considered as the ratio of soil buoyant unit weight and the unit weight of water, suggesting that the critical gradient only depends on the void ratio and specific gravity of the solids. However, in the field and in research, it has been observed that piping can initiate at average gradients much lower than unity due to concentrations in flow and non-vertical exit faces. Therefore, there is a need for deeper understanding of the granular scale mechanisms of the piping erosion process. This thesis presents the results of a laboratory study to assess the effects that soil properties and exit face configurations have on the potential for initiation of piping and the piping mechanisms. By using a laboratory device designed and constructed specifically for this study, the critical gradients needed to initiate piping in a variety of sandy soils were measured to assess the effects that parameters such as gradation, grain size, and grain shape have on the critical gradients. The tests are also used to observe the grain scale mechanisms of piping erosion initiation. The ultimate goal of the study is to develop an empirical, but mechanism-based, grain-scale model that can take into account the effects of converging flows, non-horizontal exit faces, and soil properties while assessing the potential for piping erosion to occur

Understanding the neurocognitive mechanisms and improving cognitive and emotional health in female survivors of breast cancer

Breast cancer is the most prevalent cancer in women worldwide with incidence on the increase. Despite this, as a result of earlier detection and improvements in medical treatment outcomes, survival rates are improving. However, the longer term side effects of breast cancer can adversely affect an individual’s social, cognitive and emotional functioning, profoundly impairing quality of life. As such, the primary aim of the present PhD thesis was to better understand the mechanisms involved in cognitive and emotional vulnerability in breast cancer and to develop and assess the efficacy of interventions that could better the lives of women in survivorship post diagnosis. Findings from Experiment 1 firstly indicate that targeted neurocognitive interventions can improve cognitive control and processing efficiency in breast cancer survivors, establishing that this population is receptive to treatments that provoke brain neuroplasticity. Secondly, it demonstrates that as a result of engaging top down attentional control processes, such interventions can result in sustained reductions in emotional vulnerability. Following on, using an expressive writing intervention, Experiment 2 indicates a relationship between the use of words thought to reflect cognitive reappraisal, as well as affectively negative words, with improvements in perceived cognitive function, emotional vulnerability and quality of life. That said, refinement of expressive writing paradigms is required to optimise transfer outcomes. Experiment 3 outlines an intervention study demonstrating how both mindfulness meditation training, adaptive working memory training, and a combined course of both, can result in reductions in anxious symptomatology compared to an active control condition. As a means to further understand the neurocognitive mechanisms affected by breast cancer, Experiment 4 adopts a neural approach exploring how breast cancer survivors respond to making cognitive errors in comparison to healthy controls. Findings indicated that whilst performance effects were absent, neural differences were found between groups, indicating that compensatory processes were required in order to function efficiently. Finally, whilst a large body of research now indicates that chemotherapy affects cognitive functioning post treatment, less is known about the effects of the estrogen reducing hormone therapy Tamoxifen, which is widely administered to breast cancer survivors for five to ten years post diagnosis. Study 5 employed qualitative methods to explore the lived experience of taking Tamoxifen in the absence of chemotherapy. Findings indicate that for this subset of breast cancer survivors, cognitive deficits are also present, and can greatly diminish quality of life. Overall, findings have critical implications for informing researchers, clinicians and the breast cancer population alike on the underlying mechanisms surrounding cognitive and emotional vulnerability in breast cancer