Mesoscale particle-based modelling of active nematic liquid crystals

Active matter --- materials with energy injection at local scales --- has developed rapidly in the past few decades, with applications ranging from the macroscopic scale of crowds and animal flocks, down to the mesoscale of bacteria colonies and active gels, and finally to the microscopic scale of sub-cellular fluids. Active fluids exhibit feedback loops that can drive or mitigate activity. For example, in the quintessential experimental active-nematic system of microtubule bundles interlinked with kinesin molecular motors activity has a sigmoidal dependence on the density of ATP fuel. Likewise, bundles of contractile nematic actin-myosin systems can form into dense jammed asters, locking in myosin molecular motors and jamming the actin, and bacteria have been shown to perform quorum sensing by inhibiting their motion upon receipt of a chemical secreted by other bacteria. Despite the rapid development of active matter theory and experiment, there are still significant gaps in our understanding: Notably, there are limited simulation methods suitable for studies at the mesoscale. For instance, despite many numerical studies investigating the behaviour of colloidal particles in athermal baths, there has been little work investigating how oriented active flows, such as active-nematics, affect the dynamics of colloids. To address these gaps, this thesis presents a particle-based mesoscale simulation method known as Multi-Particle Collision Dynamics (MPCD) for simulating active fluctuating nematohydrodynamics. It extends an existing algorithm for nematic fluids in MPCD to produce an active-nematic MCPD method (AN-MPCD) through the introduction of a local force dipole. Despite its simplicity, AN-MPCD reproduces key quantities of active-nematic turbulence, such as spontaneous flows and the continuous creation/annihilation of topological defects. This simple model exhibits pronounced density fluctuations, typical of active particle models. By de-coupling the magnitude of activity from the local density, or applying a sigmoidal modulation function with respect to the local density, we show that density fluctuations are strongly mitigated while key scalings of active-nematic turbulence persist. Analysis of the density-induced pressure gradients reveal that activity modulation suppresses the effect of density fluctuations on solutes in active fluids, at the expense of fluctuations in the active force. Finally, we employ the modulated AN-MPCD method to study anchored passive colloids in active nematics. Homeotropic colloids possess non-monotonic effective diffusion, giving rise to a critical activity for enhanced diffusivity. When the colloidal radius is comparable to the active nematic length scale, active turbulence causes a colloidal companion defect to unbind from the colloid, leading to a non-zero topological charge on the colloid-companion complex. This non-zero charge encourages oppositely charged defects to approach the complex, indirectly propelling the complex through the fluid and enhancing the effective diffusion. The development of the AN-MPCD method opens up a wide range of possibilities for the study of solutes immersed in active solvents, including passive colloids, polymers, and porous media, but can be extended further to novel systems of passive clusters in active fluids. It also opens the door to future studies of how the formulation of activity and spatial modulation can affect bulk active turbulence

Addressing microarchitectural implications of serverless functions

Serverless computing has emerged as a widely-used paradigm for running services in the cloud. In this model, developers organize applications as a set of functions invoked on-demand in response to events, such as HTTP requests. Developers are charged for CPU time and memory footprint during function execution, incentivising them to reduce runtime and memory consumption. Furthermore, to avoid long start-up delays, cloud providers keep recently-triggered instances idle (or warm) for some time, anticipating future invocations. Consequently, a server may host thousands of warm instances of various functions, their executions interleaved based on incoming invocations. This thesis investigates the workload characteristics of serverless and observes that: (1) there is high interleaving among warm instances on a given server; (2) individual warm functions are invoked relatively infrequently, often at intervals of seconds or minutes; and (3) many function invocations complete within milliseconds. This interleaved execution of rarely invoked functions leads to thrashing of each function's microarchitectural state between invocations. Meanwhile, the short execution time of functions impedes the amortization of warming up on-chip microarchitectural state. As a result, when a given memory-resident function is re-invoked, it commonly finds its on-chip microarchitectural state completely cold due to thrashing by other functions---a phenomenon we term lukewarm execution. Our analysis reveals that the cold microarchitectural state severely affects CPU performance, with the main source of degradation being the core front-end, comprising instruction delivery, branch identification via the BTB, and conditional branch prediction. Based on our analysis, we propose two mechanisms to address performance degradation due to lukewarm invocations. The first technique is Jukebox, a record-and-replay instruction prefetcher specifically designed to mitigate the high cost of off-chip instruction misses. We demonstrate that Jukebox's simplistic design effectively eliminates more than 95% of long-latency off-chip instruction misses. The second technique is Ignite, which builds on Jukebox to offer a comprehensive solution for restoring front-end microarchitectural state, including instructions, BTB, and branch predictor state, via unified metadata. Ignite records an invocation's control flow graph in compressed format and uses that to restore the state of the front-end structures the next time the function is invoked. Ignite significantly reduces instruction misses, BTB misses, and branch mispredictions, resulting in an average performance improvement of 43%. In summary, this thesis demonstrates that serverless systems present distinct workload characteristics that fail to match traditional CPU designs, severely impacting performance. Two simple techniques can overcome these bottlenecks by preserving the microarchitectural state across function invocations

Parental care and cooperation in the burying beetle Nicrophorus vespilloides

In species that provide parental care, individuals must choose how to split their resources between caring for their current offspring and investing in their own reproductive potential. These decisions are made based on factors that shift the balance of costs and benefits associated with allocating resources to current or future reproduction. For parents providing uniparental care such factors relate to the value of the current brood and the likelihood of future reproduction. Females and males that cooperate to provide biparental care, must also consider factors that may influence the contribution of their partner. In this thesis, I explore what affects the level of care parents provide for their offspring and how females and males that provide biparental care balance their relative contribution in the burying beetle Nicrophorus vespilloides. I focus on four factors: previous reproductive allocation, nutritional state, social environment, and synchrony in the onset of care. First, I found that females provided the same level of care to a subsequent brood regardless of previous reproductive allocation and resource access, which suggests that neither affected future ability to provide care. Next, I found that females adjusted their level of care in response to both their own nutritional state and that of their partner and that these decisions were independent of their partner’s contribution, while males only responded to the contribution of their partner. Then, I found that parents provided a similar level of care regardless of the presence of female or male intruders. Finally, I found that males provided more care when the female and male started providing care asynchronously in comparison to when they started synchronously while females provided a similar level of care regardless

The Story of Ethiopian Governance: From a centralized public service monopoly to ‘big man’ politics

This report discusses how the EPRDF, from operating on the logic of a centralized political market, degenerated into an oligopolistic monopoly and later into a neo-patrimonial state that operates on patronage and sustaining disorder while maintaining a simulacrum of an institutionalized state. The report is divided into four parts. The first part discusses the genesis of the EPRDF and its highly centralized public service monopoly in government. The second part discusses the beginning of the end of the EPRDF’s centralized public service monopoly. The third part discusses the complete transformation of the state into what is called a typical African ‘big man’ politics. The fourth and final part is the conclusion

Reuse of excavated peat on wind farm development sites

Built development on peatlands results in the excavation and disturbance of peat. This project investigates the available evidence on the impacts and opportunities regarding the reuse of excavated peat and examines the opportunities, impacts, and challenges associated with the reuse of excavated peat from windfarm construction sites. We propose a hierarchy of peat reuse options based on environmental impact and offer recommendations for data collection and monitoring to enhance the evidence base

Development and application of cell culture and genome editing techniques in Pacific whiteleg shrimp (Litopenaeus vannamei) and Atlantic salmon (Salmo salar)

[ A B S T R A C T : R e d a c t e d

Investigating structural variants of BRCA1/2 as a novel biomarker of homologous recombination deficiency

Homologous recombination deficiency (HRD) represents a cancer vulnerability that has been successfully exploited through the use of PARP inhibitors by synthetic lethality. In high grade serous ovarian cancer (HGSOC), PARP inhibitors, such as olaparib, have revolutionised treatments outcomes for patients and are now routinely clinically used. PARP inhibitors are also approved for breast, pancreatic and prostate cancer, but their use is largely restricted to patients with a BRCA1/2 mutation. Though BRCA1/2 mutations are the archetypal event resulting in HRD, there is increasing evidence that there are patients with an HRD phenotype beyond those with a BRCA1/2 mutation. This therefore represents an opportunity to broaden the use of PARP inhibitors, including their use in other tumour types. Structural variants (SVs) are increasingly recognised as key cancer driver events. However, their importance has been underappreciated due to limited access to whole genome sequencing (WGS). Previously, SVs of BRCA1/2 were found to occur in ~15% of HGSOC cases, and were associated with reduced BRCA1/2 gene expression and higher genomic HRD scores. Furthermore, BRCA1/2 SVs have been shown to occur in a range of other tumour types, at a lower frequency. Despite the existing evidence supporting the importance of BRCA1/2 SVs in tumourigenesis, their functional impact has not been directly studied in vitro, including via functional homologous recombination (HR) assays. Moreover, the phenotype associated with this defect has not been explored in a range of different tumour types. Through in silico analysis, a provisional panel of candidate cell lines with BRCA1 or BRCA2 copy number loss were identified. These underwent detailed characterisation of existing genomic data, along with validation of copy number loss by quantitative PCR (qPCR). This resulted in a high confidence panel of candidate cell lines (n=11) from multiple tumour sites (ovary, breast, soft tissue sarcoma and bone sarcoma) with copy number loss of BRCA1 or BRCA2, which are likely to have BRCA1/2 SV deletions. These were investigated alongside known HR deficient comparator lines and an HR proficient cell line. The phenotype of these candidate cell lines was assessed, which included BRCA1/2 gene expression, BRCA1/2 protein expression and HR status by RAD51 immunofluorescence following irradiation. Drug sensitivity to chemotherapeutics and PARP inhibitors (olaparib, novel PARP1 selective PARP inhibitor AZD5305) was also performed via proliferation assay and colony formation assay. In the cell lines with BRCA1 SVs, two of the seven cell lines demonstrated a low BRCA1 gene expression (comparable to the BRCA1 mutant comparator), HR deficiency by RAD51 immunofluorescence and PARP inhibitor sensitivity. These were both Ewing’s sarcoma cell lines. There were a further two cell lines with BRCA1 SVs, originating from a breast and an ovarian tumour, that were functionally HR deficient, but did not demonstrate PARP inhibitor sensitivity. Four of the five cell lines with BRCA2 SVs had reduced BRCA2 gene expression (similar to that of a known BRCA2 mutant cell line). Furthermore, four of the five cell lines with BRCA2 SVs were functionally HR deficient and three of these cell lines were PARP inhibitor sensitive. These cell lines originated from varying tumour sites including ovary and two histological types of soft tissue sarcoma (leiomyosarcoma, rhabdomyosarcoma). These data suggest SVs, particularly in BRCA2, may represent a novel biomarker of HRD, which could be therapeutically exploitable with PARP inhibitors. Given that PARP inhibitors are not used routinely in sarcomas, this could represent a new therapeutic indication. This in vitro work therefore suggested that the accurate identification of BRCA1/2 SVs via copy number loss could have high clinical utility in identifying patients suitable for PARP inhibitors. With this in mind, the final chapter of this body of work aimed to identify a simple costeffective laboratory test to identify these defects. It was hypothesised that qPCR could be an efficient laboratory biomarker assay for detecting SVs. This work assessed the sensitivity and specificity of qPCR in detecting copy number variation of BRCA1/2, in two HGSOC clinical cohorts (cohort 1 n=355, cohort 2 n=89), in conjunction with matched next generation sequencing (cohort 1 panel sequencing, cohort 2 WGS). This work demonstrated qPCR had poor sensitivity for detecting BRCA1/2 SVs, with copy number variation at the reference probe erroneously leading to BRCA1/2 copy number loss detection. Overall, this suggests that next generation sequencing, such as WGS, remains the optimal method for accurately detecting these events

The search for valid surrogate endpoints: review of current evidence and development of practical strategies for surrogate evaluation

In light of the ongoing global pursuit of more quickly available treatments, surrogate endpoint evaluation has become a vital part of drug development. Despite the increasing uptake of surrogate endpoints and the large number of statistical methods proposed to evaluate a surrogate, there is still no consensus on how to determine when a surrogate endpoint is acceptable. Therefore, this work aimed to address three questions. PROJECT 1: How well do recently proposed statistical methods perform? PROJECT 2: What is the validation status of surrogate endpoints currently in use? PROJECT 3: Can a new framework for surrogate evaluation be developed by way of consensus? PROJECT 1. A scoping review was conducted to identify recent, novel statistical methods of surrogate evaluation. The method with the greatest research activity was the proportion of treatment effect explained (PTE). The performances of two fundamental methods based on the PTE were compared through simulations. Neither method was considered to be sufficient on its own. PROJECT 2. A systematic review was conducted to identify both validated and non-validated surrogate endpoints in use, and the statistical methods applied to evaluate the validated surrogate endpoints. Based on the combination of three surrogate evaluation frameworks, many surrogate endpoints accepted by regulatory agencies were not statistically valid. Correlation-based methods were the most frequently applied statistical approaches. PROJECT 3. A new framework was developed from a two-round Delphi survey followed by an international, multi-stakeholder consensus meeting. The survey included questions on the prioritisation of non-statistical factors in, use of numerical thresholds for and preferred statistical methods of surrogate evaluation. Four non-statistical factors reached consensus by the end of the second round. However, opinions were divided on the issues of thresholds and methods. A consensus meeting was subsequently held to ratify the factors, thresholds and methods to be included in a framework. Five non-statistical factors were deemed necessary, with two non-statistical factors for possible consideration, and correlation thresholds for possible consideration. In addition, the framework deemed trial-level analysis as necessary, and provided general guidance on the choice of statistical methods, rather than recommending specific methods. As found in all three projects, surrogate endpoint evaluation remains a challenging, multi-stakeholder task. Nonetheless, the newly-developed framework has partly resolved the longstanding lack of agreement on which factors to consider when evaluating a surrogate endpoint, and may catalyse further improvements to come in this cornerstone of drug development

Germline influences on processes that contribute to colorectal carcinogenesis

Colorectal cancer (CRC) is one of the most common causes of cancer-related death in the world with incidence rising particularly in younger individuals in the West. Understanding of the genetic causes underlying CRC has increased greatly in recent years as a result of work on familial CRC syndromes, which has identified rarer but more impactful genetic mutations, and CRC genome-wide association studies (GWAS), which have identified more common forms of DNA variation. The common variants from CRC GWAS are less impactful individually but when combined have a non-trivial effect on CRC risk. However, there are still many gaps of knowledge in terms of CRC genetics, with one notable example being the mechanisms through which variants are affecting CRC risk. This project aimed to contribute to this area by first expanding the existing GWAS meta-analysis dataset through the addition of 2,356 CRC patients and 14,162 CRC-free control patients from the 100,000 Genomes Project (100kGP). Inclusion of 100kGP data led to the identification of eight novel CRC risk loci but also called into question six previously identified loci. This modest net gain of CRC risk loci indicates that substantial expansion of GWAS cohorts (perhaps the addition of > 100,000 patients) may be needed for meaningful improvements in understanding common causes of CRC. Several risk loci identified by CRC GWAS highlight genomic regions where the target gene may not be affecting CRC predisposition through effects on the colorectal epithelium, but instead via an intermediate phenotype. The project explored two of these potential intermediate phenotypes: blood cell traits and the microbiome. For blood cell traits, genetic fine-mapping of a locus at 12q24.12 was first conducted to identify whether pan-haematopoietic regulator SH2B3 was the CRC causal risk gene, but these results were not conclusive. Work was then expanded to examine the phenotype generally, initially by using Mendelian randomisation (MR) to establish whether causal links existed between blood cell trait variation and CRC risk. A modified PCA-based GWAS and MR approach was then used to try and mitigate the high levels of horizontal pleiotropy that are apparent in haematopoietic genetics. These results showed indications of red blood cell and platelet variation affecting CRC risk but were not definitive and require further investigation. For the microbiome, fine-mapping was conducted on four risk loci, where the possible CRC causal genes (GALNT12, B3GNT8, FUT2, FUT3, and FUT6) play roles in oligosaccharide modification processes such as glycosylation and fucosylation in the colon, thereby potentially affecting susceptibility to microbial infections and subsequent CRC risk. The previous study of rare variants in GALNT12 specifically has raised the question as to whether it is a moderate CRC risk gene; this hypothesis was tested using the larger 100kGP cohort, which suggested that it is not a moderate risk gene, and then expanded to include the other four potential microbiome CRC genes. Once again, work was then extended from individual loci to the overall mechanism. First, MR was conducted using reported variants from existing microbiome association studies performed in disease-free individuals to test whether there are causal links between levels of bacterial taxa and CRC risk. This analysis suggested that variation in the Escherichia/Shigella, Fusobacterium, Streptococcus, and Bifidobacterium genera may be causal for CRC risk. A new complementary approach running GWAS in CRC patients specifically using the 100kGP cohort was performed, with relative abundance of bacterial genera and species, counts from toxin-producing bacterial strains, as well as global bacterial measures taken from the tumour directly used as phenotypes. Variants identified from these GWAS were then used in MR analyses to see whether causality between bacterial measures derived from CRC patients and CRC risk could be established. This analysis instead suggested causal associations for Oscillibacter and Blautia genera, Bacteroides fragilis and Ruminococcus faecis species, and bacterial count per human cell. In summary, this project has contributed to the understanding of the genetics of CRC carcinogenesis using methods that are, in large part, based on the intrinsic robustness of genetic data. The challenges encountered in this project are common in the field, namely (i) the weakness of most genetic associations with both CRC and its risk factors and (ii) confounding and pleiotropic effects of genes and other unobserved factors. My work provides insight into common genetic variation in CRC, as well as interesting clues for the role of blood cell levels and gut bacteria in CRC risk

​​Estimating costs and impacts of decarbonising heat in the public sector​

In this report we provide evidence on the costs, opportunities and barriers of decarbonising heat in Scotland’s public sector buildings. We use modelling to estimate the capital cost of moving to clean heating systems in all public sector buildings in. We gather evidence on the opportunities offered by decarbonising Scotland’s public sector buildings as well as the barriers to doing so by assessing wider themes including practicalities and operational considerations