There are many forms of evidence that point towards an unknown form of matter, known as dark matter, making up ∼85% of the mass in the universe. Many dark matter candidates have been proposed with the Weakly Interacting Massive Particle (WIMP) being among the most favoured. There are many groups around the world actively looking for WIMPs with direct, indirect and collider searches with specific interest here in annual modulation and directional searches. The DRIFT-IId detector is the world’s largest directional dark matter detector and is operational in Boulby Mine in the UK. Members of the directional community have come together to form the CYGNUS collaboration, looking towards larger detectors with better directional sensitivity. This thesis looks towards the future scale up to larger directional detectors, specifically low-pressure gas detectors. Improvements have been made to a system used to measure the radon emanation of materials, with emanation tests taken of potential components for CYGNUS detectors. Measurements have also been taken with a small scale THGEM TPC in both CF4 and SF6 gas. The results from CF4 showed the high gas gains achievable from the THGEM detector and allowed a direct measurement of the Townsend coefficients of the gas. Gains of up to 8600 ± 150 have been achieved in low pressure SF6 with a resolution of 19%, both of these figures are the highest achieved to date. The directional sensitivity of 1D readouts has been tested with initial signals of head-tail shown in a THGEM TPC in SF6. A head-tail signature is also seen in a simplified 1D DRIFT-IId readout mode. Exclusion limits from both the full and simplified DRIFT readouts have been produced from over 100 days of background data. The result of 0.16 pb from the full analysis is the lowest limit produced by any directional detector. These results show that a one-dimensional readout may be feasible for directional WIMP detection removing the need for many hundreds or thousands of read out channels required for 3D reconstruction.

This document details the substantial individual contribution made by the author to the research & development of the ATLAS Experiment. Based at CERN, the European Organization for Nuclear Research, the Large Hadron Collider (LHC) is the world's largest and most powerful particle accelerator. ATLAS is one of two general-purpose detectors at the Large Hadron Collider; it investigates a wide range of physics, from the search for the Nobel Prize winning Higgs boson discovery to new extra dimensions and particles that could make up dark matter. At 46m long, 25m high and 25m wide, the 7000-tonne, 100m below ground ATLAS detector is the largest volume particle detector ever constructed. The author’s contribution to the construction & integration of the ATLAS Inner Detector (ID) is detailed with focus on the cooling systems. Following years of operation, the ATLAS ID requires replacement due to radiation damage to electronic components and significant major infrastructure changes are required to operate effectively at higher luminosities. Planned high-luminosity upgrades to the LHC (HL-LHC) require huge increases in power to generate higher energy particle collisions needed for new scientific discoveries. Initial research began in 2005, exploring the possible construction of an ATLAS High-Luminosity Upgrade replacement of the existing ATLAS ID. The author was heavily involved in the construction of this project from the initial conceptual ideas, to the development of radiation hard semi-conductor device qualification, irradiation facility design, construction and operation and cooling system development. Sharing a number of design philosophies with aerospace, defence and space science, particle detectors require lightweight materials with high strength. Development of modern particle physics detectors to enable new scientific discoveries requires pushing technological boundaries beyond conventional. This document and commentary demonstrate the author’s application of these technologies to the ATLAS ID and transference to the industrial domain, predominantly within aerospace and robotics.

Cataclysmic variables (CVs) are a type of close, interacting binary system containing a white dwarf primary and a low-mass, Roche lobe-filling secondary/donor. Mass is commonly transferred from the donor to an accretion disc around the white dwarf, due to the conservation of angular momentum, before eventually reaching the surface of the white dwarf. A region of increased luminosity, termed the 'bright spot', exists at the intersection of accretion disc and mass transfer stream. The transfer of mass within the system is a turbulent process, giving rise to random photometric variations commonly referred to as 'flickering'. For high inclination systems, the donor eclipses all other components within the system, resulting in complex eclipse light curves that can be fit with a parameterised model to obtain system parameters. Eclipses of the white dwarf and bright spot occur in quick succession, and therefore precise eclipse modelling requires high-time-resolution photometry. Flickering is a hindrance to eclipse modelling, however, as it can obscure ingress/egress features of the component eclipses, and therefore existing studies use eclipse averaging to minimise its effects. In this thesis, a new approach to eclipse modelling is introduced, which involves modelling flickering through the utilisation of Gaussian processes (GPs). The new modelling approach is implemented on ULTRACAM/ULTRASPEC eclipse light curves of 18 eclipsing CVs, returning 18 sets of precise system parameters. Four of these systems have been modelled previously using the existing approach, while 14 are modelled for the first time. The 18 new/revised white dwarf and donor masses from this work are used alongside other CV component masses from the literature in an attempt to secure a better understanding of CVs and their evolution. One of the outcomes is a new estimate for the CV orbital period minimum, 79.57+-0.22 min, which is over 2 min shorter than previously thought.

Chapter 1 introduces the reasons behind this study, the importance and applications of PCDTBT in organic electronic devices, thus the importance of understanding how confinement in thin films influences the crystallisation of this polymer which will have an impact on the electronic properties of the material. Chapter 2 describes the analytical techniques used (ellipsometry, atomic force microscopy and grazing incidence X-ray scattering) and their importance for this study. In chapter 3 is reported the thermal protocol that allowed the understanding of the crystallisation of PCDTBT; ellipsometry, GIWAXS and AFM results are reported in order to understand the importance of the protocol and also aid the comprehension of the rest of the thesis. Chapter 4 describes how different annealing temperatures influence the crystallisation kinetics and the amount of crystallinity in a sample. Chapter 5 looks in detail at a phenomenon occurring in the film that was quite unpredicted: the ellipsometry data are used to follow the change of the thickness of the film under the thermal treatment explained in chapter 3; an initial shrinking at the ellipsometry shows the crystallisation phenomenon, but what is causing a second expansion which is following the crystallisation. In chapter 6 is finally reported the influence of the film thickness on the crystallisation properties of the material; the influence of the two interfaces on its ordering is key in understanding how to improve the efficiency of organic electronic devices.

This thesis concerns the fabrication and study of strongly coupled organic microcavities containing a series of different boron-dipyrromethene (BODIPY) fluorescent dyes dispersed in an optically inert polystyrene matrix. The photophysics of the different BODIPY dyes are first studied and it is shown that they are promising materials for polariton condensation. DBR-DBR microcavities containing thin films of dye/polystyrene blends are then investigated under angular white-light reflectivity and CW laser excitation; measurements that show that they can enter the strong coupling regime. Polaritons in such high quality factor structures are shown to undergo a phase transition when excited with a high density pulsed excitation, forming a polariton condensate. Power dependent and interferometry measurements are used to identify the condensation threshold and the spatial coherence length of the polariton condensate. Lower Q-factor microcavities, comprised of two silver mirrors are fabricated, containing two different BODIPY dyes. Energy transfer between the molecules is engineered using two different processes; (1) direct short-range dipole-dipole coupling between the molecules, and (2) polariton-mediated energy transfer. We assess the efficiency of the energy transfer by quantifying the polariton population density along each polariton branch following laser excitation. It is concluded that short-range (< 3 nm) energy transfer induced by dipole-dipole coupling is more efficient compared to long-range (60 nm) polariton-mediated energy transfer, although the long-range process is estimated to transfer up to 87% of states to the lower-polariton branch. The generation of anti-Stokes polariton fluorescence is studied in low Q-factor metallic cavities following resonant excitation at the bottom of the lower polariton branch. Here, it is concluded that thermal energy in the system provides the excess of energy needed for emission of photons having higher energy than that of the initial laser excitation. Using temperature dependent and time resolved measurements it is concluded that polaritons return to the exciton reservoir by optically pumping a molecule in a vibrationally excited ground state. The exciton created then emits fluorescence that populates polariton states with an energy higher than the laser energy resulting in anti-Stokes polariton fluorescence. We believe such systems will be of significant interest in exploring laser-cooling phenomena in solid-state systems.

No description available.

Phospholipid oxidation generates a wide variety of products with potentially novel biological activities that may be associated with disease pathogenesis. To understand their role in disease requires precise information about their abundance in biological samples. Liquid chromatography-mass spectrometry (LCMS) is a sensitive technique that can provide detailed information about the oxidative lipidome, but challenges still remain. The work in this thesis developed improved methods for detection of OxPLs by improvement of chromatographic separation through the comparison and optimisation of several HPLC columns such as C8, C18 and C30 reverse phase, polystyrene-divinylbenzene based monolithic, and mixed-mode hydrophilic interaction (HILIC) columns & solvent systems, with use of semi-targeted mass spectrometry approaches. The results suggests that the monolithic column was the most robust method for separating short chain oxPLs from long chain oxidised and native PLs. In addition, several approaches for method validation were explored such as testing of reproducibility and repeatability of the methods, together with the reanalysis of samples on a high resolution QToF mass spectrometer with automated quantitative data analysis using the Progenesis QI software to validate the identification. The combination of the developed methods allowed the identification of several oxPLs in biological samples. These were: i) ascites fluid of lean and obese rat model of acute pancreatitis; ii) isolated components of red blood cells (RBCs) infected with the malarial parasite Plasmodium falciparum; and iii) plasma samples of healthy and diabetic patients. In addition, an evaluation of post-acquisition data handling to minimise inherent biological variation was performed. Quantitative differences in oxPLs were observed in isolated malarial components as well as other studied disease models. Overall, several protocols were developed that provide improved performance for the identification of OxPL in biological samples that can be used as a reference method by research laboratories interested in oxidative lipidomics work.

Traumatic spinal cord injury (SCI) is a devastating event. It causes severe damage to the nervous tissue which can be associated with partial or complete loss of movement and sensation. Recent studies suggested that the benefits of stem cell transplants for SCI may not be restricted to cell restoration alone, e.g. to replace damaged neurons, but also may be due to their capacity to stimulate endogenous cells at wound sites through paracrine activity. Mesenchymal stem/stromal cells (MSCs), in particular, are thought to have anti-inflammatory, neuroprotective, neurotrophic and angiogenic effects and may thus reduce secondary damage and promote neuroregeneration and wound healing after their administration. Experimental studies of small rodent SCI models are currently being used to investigate the MSCs as a promising option for treatments that repair damaged neuronal tissue. However, translation to human patients is still a challenging step. Dogs represent a good large animal model as the causes of SCI in dogs occur naturally and traumatically, and because of the similar scale and heterogeneity of the lesions formed. Therefore, this study aimed to investigate and compare the effects of canine and human MSCs, focused on the effects of MSC conditioned medium (MSC CM) on neurogenesis and angiogenesis using established responder cell lines, i.e. SH-SY5Y neuronal cells and EA.hy926 endothelial cells. All of the MSCs were derived from adipose tissue, and CD271 was used to isolate subset populations from human MSCs. The study has demonstrated for the first time the potentially beneficial effects of canine MSC CM in promoting SH-SY5Y neurite outgrowth and cell proliferation, as well as EA.hy926 endothelial cell proliferation, cell migration and the formation of endothelial tubules. Further experimentation demonstrated that canine and human adipose-derived MSCs exhibited such neurotrophic and angiogenic effects to a similar extent. This may have important implications for the pre-clinical assessment of MSC paracrine activity in the development of cell transplantation protocols both for dogs and humans. Finally, the study compared the neurotrophic and angiogenic effects of MSC CM from selected subpopulations of human MSCs, i.e. CD271+ versus CD271- and plastic adherent MSCs; this was with a view to establishing whether a more homogeneous MSC population might differ in their paracrine activity. There was no significant difference in the neurogenic effects of these various secretomes; however, MSC CM from humanCD271+MSCs was found to be significantly less pro-angiogenic than human CD271- MSCsor non-selected human MSCs. In conclusion, the study supports the use of MSCs to treat naturally occurring SCI in dogs, and suggests that there is no evidence herein to support preselecting CD271+ cells.

There is a significant loss in the efficacy of the current therapeutic regime on advanced colorectal cancer, highlighting the need to understand the tumour progression process, and to identify potential prognostic and/or therapeutic targets. This study employs well characterised human primary and metastatic colorectal cancer cell lines (CRCs); RKO, SW480 SW620, and HCT116 to investigate the involvement of pro-inflammatory protein tissue transglutaminase (TG2) in tumour progression. Cancer progression was assessed by evaluating Epithelial-Mesenchymal Transition (EMT), cancer cell invasion, drug resistance and the ability of CRCs to form spheroid containing cancer stem cells. TG2’s expression was found to correlate with the advancement of the original tumour, markers of EMT, cell invasion, drug resistance, and cancer stemness. Manipulation of TG2 expression in the different CRCs by shRNA or TG2 transduction confirmed the relationship between TG2, EMT, tumour invasion and drug resistance. TGFβ1 was shown to regulate TG2 expression and EMT in primary tumour cell lines by both canonical and non-canonical (RKO and SW480) signalling pathways. TGFβ1 also induced TG2 in the highly advanced HCT116 cells. However, the metastatic SW620 cell line was non-responsive to TGFβ1, but TG2 was associated with the increased presence of nuclear β-catenin in these cells, and TG2’s inhibition/knockdown led to an increased interaction between β-catenin and ubiquitin as determined by co-immunoprecipitation. Interestingly, β-catenin and TG2 were found to be highly expressed in spheroids containing cancer stem-like cells only formed in the aggressive SW620 and HCT116 cell lines. These cancer stem cells were associated with heightened EMT, cellular invasion and angiogenic potential, which was attenuated following TG2 inhibition. TG2 may play a role in tumour progression in human CRCs through its involvement in EMT and the acquisition of cancer stem cell-like properties and may hold both prognostic and therapeutic potentials in colorectal cancer.

Apoptotic cells (AC) are removed by macrophages (MØ) quickly to maintain healthy tissues. Apoptotic cell-derived extracellular vesicles (ACdEV) and ICAM-3 are shed during apoptosis and aid in AC removal by attracting macrophages (MØ). ICAM-3 on AC also mediates tethering to MØ. However the mechanism of ICAM-3 action is not known. This project aims to characterise the role of ICAM-3 and ACdEVs in the clearance of apoptotic cells. In agreement with previous studies, human lymphocytes were induced to apoptosis by UV irradiation and ACdEV were isolated and characterised. Using qNano, this work reveals, for the first time, release of ACdEV (~200nm) from early (6h) to late (18h) stages of apoptosis. Furthermore, the ability of ICAM-3 on ACdEV to promote phagocyte recruitment was confirmed and extended by using both vertical and horizontal migration assays. Also, ICAM-3 is confirmed as an apoptotic cell ligand that promotes interaction of AC with MØ. How ICAM-3 on ACdEV promotes MØ migration is not clear but novel data here suggests that it may be acting as an adhesion molecule to improve EV-MØ binding. Using in vitro assays of inflammation, AC and their EV were assessed for anti-inflammatory effects though any anti-inflammatory effect were unexpectedly small. In novel in vivo studies using a xenograft model, data show that anti-ICAM-3 mAb is capable of causing a significant reduction in growth of a transplanted ICAM-3+ tumour. The mAb also reduced MØ number within the tumours suggesting ICAM-3 can function in vivo for MØ recruitment to sites of cell death. Analyses of partner proteins for ICAM-3 was done in further novel studies. These were problematic as CO-IP approaches to the isolation of ICAM-3 were inefficient. However, mass spec analysis of crude membrane preparations revealed two proteins upregulated in apoptotic HeLa-ICAM-3 cells that may function to reorganize cytoskeleton. Future work is required to test if these observations are significant for the function of ICAM-3 in AC clearance.