The role of environment in infrared surveys: from supernovae to clusters

In this thesis we investigate several aspects of galaxy evolution. We begin by giving a brief introduction to the subject of galaxy evolution in the context of the Universe as we know it today. We discuss infrared surveys of galaxies as a tool for studying galaxy evolution. Initially, we are interested in the large scale environment of galaxies and identify clusters of galaxies at high redshift. We compare the mass and star-formation properties of galaxies in the cluster and field environments. To take this further we look to the AKARI all- sky survey and assess the potential of this survey for future studies. We calculate the completeness and reliability of the survey. Such wide surveys also allow for the possibility of studying rare and extreme phenomena. Such phenomena can push theories of galaxy evolution to their extremes and constrain these theories. We present the discovery of four such objects in the SWIRE survey. Finally, since environment plays a large role in the evolution of galaxies we extend this investigation to smaller scales. We investigate the progenitors of Type Ia Supernovae from a study of their host galaxies, which have implications for their use as standardisable candles

The rational parameterisation theorem for multisite post-translational modification systems

Post-translational modification of proteins plays a central role in cellular regulation but its study has been hampered by the exponential increase in substrate modification forms (“modforms”) with increasing numbers of sites. We consider here biochemical networks arising from post-translational modification under mass-action kinetics, allowing for multiple substrates, having different types of modification (phosphorylation, methylation, acetylation, etc.) on multiple sites, acted upon by multiple forward and reverse enzymes (in total number L), using general enzymatic mechanisms. These assumptions are substantially more general than in previous studies. We show that the steady-state modform concentrations constitute an algebraic variety that can be parameterised by rational functions of the L free enzyme concentrations, with coefficients which are rational functions of the rate constants. The parameterisation allows steady states to be calculated by solving L algebraic equations, a dramatic reduction compared to simulating an exponentially large number of differential equations. This complexity collapse enables analysis in contexts that were previously intractable and leads to biological predictions that we review. Our results lay a foundation for the systems biology of post-translational modification and suggest deeper connections between biochemical networks and algebraic geometry

Automated mapping of virtual environments with visual predictive coding

Humans construct internal cognitive maps of their environment directly from sensory inputs without access to a system of explicit coordinates or distance measurements. While machine learning algorithms like SLAM utilize specialized visual inference procedures to identify visual features and construct spatial maps from visual and odometry data, the general nature of cognitive maps in the brain suggests a unified mapping algorithmic strategy that can generalize to auditory, tactile, and linguistic inputs. Here, we demonstrate that predictive coding provides a natural and versatile neural network algorithm for constructing spatial maps using sensory data. We introduce a framework in which an agent navigates a virtual environment while engaging in visual predictive coding using a self-attention-equipped convolutional neural network. While learning a next image prediction task, the agent automatically constructs an internal representation of the environment that quantitatively reflects distances. The internal map enables the agent to pinpoint its location relative to landmarks using only visual information.The predictive coding network generates a vectorized encoding of the environment that supports vector navigation where individual latent space units delineate localized, overlapping neighborhoods in the environment. Broadly, our work introduces predictive coding as a unified algorithmic framework for constructing cognitive maps that can naturally extend to the mapping of auditory, sensorimotor, and linguistic inputs

Differentiated, promoter-specific response of [4Fe-4S] NsrR DNA-binding to reaction with nitric oxide

NsrR is an iron-sulfur cluster protein that regulates the nitric oxide (NO) stress response of many bacteria. NsrR from Streptomyces coelicolor regulates its own expression and that of only two other genes, hmpA1 and hmpA2, which encode HmpA enzymes predicted to detoxify NO. NsrR binds promoter DNA with high affinity only when coordinating a [4Fe-4S] cluster. Here we show that reaction of [4Fe-4S] NsrR with NO affects DNA-binding differently depending on the gene promoter. Binding to the hmpA2 promoter was abolished at ~2 NO per cluster, while for the hmpA1 and nsrR promoters, ~4 and ~8 NO molecules, respectively, were required to abolish DNA binding. Spectroscopic and kinetic studies of the NO reaction revealed a rapid, multi-phase, non-concerted process involving up to 8 – 10 NO molecules per cluster, leading to the formation of several iron-nitrosyl species. A distinct intermediate was observed at ~2 NO per cluster, along with two further intermediates at ~4 and ~6 NO. The NsrR nitrosylation reaction was not significantly affected by DNA-binding. These results show that NsrR regulates different promoters in response to different concentrations of NO. Spectroscopic evidence indicates that this is achieved by different NO-FeS complexes

Dyads, Triads and Consumer Treachery: When Interpersonal Connections Guard Against Brand Cheating

Consumers develop committed and meaningful relationships with brands, yet still sometimes buy or use options that compete directly with these ‘relationship partners’, an activity that might be understood as a form of cheating or infidelity. Using data from three studies, we assess whether so-called triadic brand relationships – those that implicate an interpersonal third party (i.e., some form of interpersonal bond) – safeguard against cheating. We find compared to dyadic brand relationships that implicate only the consumer and the brand, triadic brand relationships protect against emotional and behavioral cheating by virtue of reinforcing expectations of consumer’s exclusive behavior and monogamy within the relationship

Lifestyle Intervention in oVarian cancer Enhanced Survival (LIVES) study (NRG/GOG0225): Recruitment, retention and baseline characteristics of a randomized trial of diet and physical activity in ovarian cancer survivors

OBJECTIVE: The Lifestyle Intervention for oVarian cancer Enhanced Survival (LIVES) is a national study of a combined diet and physical activity intervention for stage II-IV ovarian cancer survival, an under-represented cancer in lifestyle behavioral intervention research. Here, we present the data on recruitment, retention, and baseline demographic, clinical and lifestyle behavior characteristics of the LIVES study participants. METHODS: The LIVES study (NRG Oncology/GOG 0225) is a Phase III diet plus physical activity intervention trial testing the hypothesis that ovarian cancer survivors in the lifestyle intervention will demonstrate better progression-free survival than those in the control condition. Study interventions were delivered via centralized telephone-based health coaching. Baseline descriptive statistics were computed for demographic, clinical, and lifestyle behavior characteristics. RESULTS: The LIVES study exceeded its recruitment goals, enrolling 1205 ovarian cancer survivors from 195 NRG/NCORP-affiliated oncology practices across 49 states from 2012 to 2018. The mean age of enrollees was 59.6 years; the majority (69.4%) with stage III disease; 89% White, 5.5% Hispanic; 64% overweight/obese. Baseline self-reported diet showed a mean daily intake of 6.6 servings of fruit and vegetables, 62.7 fat grams, and 21.7 g of fiber. Physical activity averaged 13.0 MET-hours/week of moderate to vigorous physical activity; 50.9 h/week of sedentary time. Retention rates exceeded 88%. CONCLUSION: The LIVES study demonstrates efficiency in recruiting and retaining ovarian cancer survivors in a 24-month study of diet and physical activity intervention with a primary endpoint of progression free survival that will be reported. TRIAL REGISTRATION: ClinicalTrials.govNCT00719303

Ultrasonic Non-Destructive Testing of Fibre Reinforced Composites

This thesis focuses on the application of high frequency ultrasound as a tool for performing non-destructive testing for pultruded fibre reinforced composite (FRC) rods. These composite rods are popular in the manufacturing, construction and electrical industries due to their chemical, electrical and strength properties. Such FRCs are manufactured on automated production lines that operate day and night. Non-destructive testing techniques are desired to quickly and accurately detectmanufacturing flaws such as coating thickness irregularities and surface cracks. Layers and cracks can present as large changes in acoustic impedance and will strongly reflect ultrasonic waves. Combined with their low cost, east of use and absense of potentially harmful radiation, ultrasound has proven popular worldwide for Non-Destructive Testing. Finite Element Analysis (FEA) was employed to investigate the propagation of ultrasonic waves through layers of material to simulate a thickness measurement and the ability of ultrasound to measure thicknesses was proven. Experimental work was conducted on two fibre reinforced composite samples with varying thickness coatings of plastic and paint. The thickness was measured accurately using immersion transducers at 50MHz and a resolution of 20μm was attained through the use of matched filtering techniques. Surface acoustic waves, particularly Rayleigh waves were investigated using FEA techniques so that the generation, scattering and detection of such waves was understood. This lead to the development of methods for detecting surface cracks in glass using Rayleigh waves and these methods were successfully used in experimental work. Wave propagation in fibre reinforced composites was modelled and experimentally investigated with the results confirming theoretical expectations. Finally a Rayleigh wave was launched onto a fibre reinforced composite sample however the amount of energy leakage into the water was so great, due to the acoustic impedance of water, the detection of the wave was prevented. The conclusion reached was that an immersion setup was not appropriate for launching a travelling Rayleigh wave