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Brain morphology of the Early Triassic cynodont Thrinaxodon liorhinus and the impact of variation in digital endocranial reconstructions on understanding mammalian brain evolution
Get PDFThe mammalian brain has an evolutionary history which can be traced back to the late Permian, when basal cynodonts show the first glimmers of mammal-like characteristics. One such early cynodont, Thrinaxodon liorhinus, has been widely studied with regards to cranial and postcranial anatomy, yet the morphology of its brain has remained elusive. Given Thrinaxodon can provide insights into the baseline brain shape from which mammalian features developed, it is important to peer inside digitally-rendered (‘digitised’) skulls to reconstruct the soft tissues that may have once been present. Presented here are the first digital reconstructions of Thrinaxodon liorhinus’ endocranial anatomy for both juvenile and adult specimens, with the main mammalian brain features present (olfactory bulbs, cerebral hemispheres and cerebellum). Yet, between the growth stages there is variation in brain size and shape which has shed light on the possible ontogenetic growth trajectory the brain may have experienced. Comparisons with contemporary cynodonts and the extant opossum, Monodelphis domestica, allowed conclusions to be drawn about the cognitive, sensory and behavioural capabilities that may have been influenced by the changing size and shape of the brain. Studies have suggested that basal cynodonts may have been nocturnal, fossorial and could have cared for young. Reconstructed morphological changes to specific brain regions appear to support these statements, particularly when considering the environmental stressors persisting during cynodont diversification following the Permian-Triassic mass extinction. However, shifting endocranial morphology was also considered in the context of variation and the impact the model maker has on endocranial reconstructions. Through experiment, it was found that nineteen modellers produced noticeably different endocasts for a single skull and that neither education level nor segmentation experience significantly improved the consistency of outputs. As such, improvements to the segmentation workflow have been proposed to help minimise inter-modeller variation. Digital reconstructions of Thrinaxodon’s brain have provided a piece of the evolutionary puzzle for mammalian brain development and shown that cynodonts were important stepping stones within the advancement of the mammalian lineage
Exploring the psychological mechanisms underpinning the relationships between physical activity, perceived stress and mental health in adolescents and young adults.
Get PDFThe overarching aim of this thesis was to more comprehensively examine the relationship between physical activity (PA), stress, and mental health in adolescents and young people, by using a range of sophisticated analytical techniques to investigate factors explaining the relationship. Chapter 1 provides an overview of literature related to PA and stress. In order to examine the overarching thesis aims and to address some of the issues highlighted in Chapter 1, Chapter 2 used path analysis to examine potential factors explaining the relationship between PA and stress in adolescents. Specifically, the hypothesised model examined whether the relationship between PA and stress was indirect via self-esteem, stress appraisals, and distress tolerance. During the course of the PhD, the COVID-19 pandemic was declared, which allowed for the examination of the association between PA, stress, and mental health under these novel and unprecedented circumstances. Chapter 3 of the thesis aimed to examine the extent to which PA could protect against any negative impact of Coronavirus concerns on stress and indicators of mental health and wellbeing during lockdown. Building on the earlier cross-sectional work in the thesis demonstrating the indirect relationship between PA and stress via self-esteem, stress appraisals and distress tolerance, Chapter 4 aimed to understand the association between PA and stress further by investigating how the variables explaining the indirect relationship (identified in Chapter 2) related to PA and stress longitudinally. Over a 4-month period, data were collected at three time points (which also happened to occur during different levels of COVID-19 restrictions) and were analysed using Multilevel Modelling analysis. Finally, Chapter 5 provided a scoping review of existing literature to determine the relationship between PA, as well sedentary behaviour, and stress over a variety of differing time frames, ranging from concurrent associations to assessing PA and stress over the course of a year. The thesis concludes with a discussion of the collective findings from the body of research, along with highlighting the implications and presenting considerations and suggestions for future research. This thesis represents a novel contribution to the literature and contributes to the understanding of the association between PA and stress, presenting how additional factors can alter these associations using a range of methodological and analytical approaches
Lung clearance index in children with non-cystic fibrosis, non-primary ciliary dyskinesia bronchiectasis and in a healthy population
Get PDFIntroduction:
Non-CF, non-PCD bronchiectasis in children is a chronic, suppurative lung disease diagnosed by high resolution computed tomography (HRCT) imaging of the lungs. Spirometry can be abnormal in bronchiectasis but has been shown to be insensitive to early disease in other related conditions such as cystic fibrosis. Lung clearance index (LCI) could have a role in assessment of the disease.
Lung clearance index is calculated from multiple breath washout tests. There are limited data on the normative values expected using some devices, in a range of ages, and between ethnic groups.
The aim was to establish normative values in children aged between 6 years and 12 years, to investigate differences between ethnic groups, and to establish the relationship between lung clearance index and other measures of disease in children with bronchiectasis.
Methods:
Healthy children were recruited from a range of settings and reviewed to ensure no previous lung disease. Children with bronchiectasis diagnosed on HRCT were recruited from the outpatient service of Birmingham Children's Hospital.
All participants performed lung function tests including LCI and spirometry. Basic demographic data was collected.
Results:
72 healthy children and 13 children with bronchiectasis were recruited and performed lung function. All children with disease were able to complete testing, 70.8% of healthy children were able to perform lung clearance index.
The mean LCI of healthy children was 7.19 (0.6 SD), children with bronchiectasis had significantly higher LCI (9.51, 2.2 SD, p<0.0001). There was no difference between healthy children from White-British and Indian Subcontinent ethnicity (7.04 vs. 7.20, p=0.33). LCI in children with bronchiectasis correlated with HRCT scores, FEV1, FVC and MMEF. LCI was also more sensitive to disease than these spirometry metrics.
Conclusion:
LCI is feasible in children (both inexperienced and experienced in previous lung function testing). We have demonstrated a normative value for our cohort and have shown no difference between ethnic groups. LCI was more sensitive to disease and correlated well with other markers of disease highlighting a potential role for LCI in the monitoring of non-CF, non-PCD bronchiectasis and as a potential therapeutic outcome measure
Synergies between alternative fuels and after treatment systems for emissions control - a simulation study
Get PDFGlobal warming is a growing issue, which countries and regions are tackling by the development of policies and technologies to reduce greenhouse gas emissions. One of the key initiatives is the promotion of Net-Zero emission solutions. The use of zero carbon (e.g. hydrogen (H2), ammonia (NH3)) and carbon neutral (e.g. electrofuels) alternative fuels can contribute to reduce greenhouse gas emissions, while any unintended environmental impacts such as worsening of air quality due to local pollutants should be avoided. One of the main pollutants is nitrogen oxides (NOx), which are a major cause of air pollution and respiratory diseases. One of the most effective pathways to reduce NOx emissions is to use selective catalytic reduction (SCR) after treatment solutions. SCR commonly uses ammonia (NH3) to convert NOx into harmless nitrogen gas, while there other types of SCR which also uses H2 to reduce NOx. However, the efficiency of these after treatment systems is influenced by a number of factors, including emissions derived from different fuel types, combustion conditions and after treatment catalysts. In particular, emissions from the combustion process can affect the selectivity of SCR catalysts, leading to the generation of unwanted by-products such as nitrous oxide (N2O) and ammonia slippage. Therefore, it is crucial to study the synergy of alternative fuels and after treatment systems. Based on the AVL Cruise M software, an after-treatment system model and an alternative fuel engine model is built. Through simulation under pure gasoline exhaust conditions, the ability of after treatment components to convert pollutants was studied; and by changing the fuel in the alternative fuel engine model, the impact of zero-carbon fuels (H2 and NH3), on engine emissions is analysed
The systematic relationships, physiology and life habits of the ‘hypsilophodontid’ dinosaurs
Get PDFThe ‘hypsilophodontids’ are an informal group of ornithischian dinosaurs that share a similar bauplan: being bipedal, small to medium-bodied (~1–2 m), and relatively conservative in their morphology. These dinosaurs are known from Antarctica, Asia, Australasia, Europe, North America and South America, and have a temporal range from the Middle Jurassic to the latest Cretaceous. The phylogenetic relationships of the ‘hypsilophodontids’ remains one of the key questions in ornithischian dinosaur research, with recent phylogenetic studies recovering these taxa in one of two highly conflicting positions: (1) primarily within Cerapoda (Ornithopoda+Marginocephalia), as a paraphyletic assemblage of early ornithopods; and (2) primarily outside of Cerapoda, within the clade Thescelosauridae. This uncertainty has impeded our understanding of ornithischian evolutionary history and consequently, our interpretation of some of the major transitions in these groups, such as the acquisitions of obligate high-fibre herbivory and quadrupedality.
In this thesis, I use multiple palaeontological approaches to improve our understanding of non-cerapodan neornithischians and early-diverging ornithopods (‘hypsilophodontids’). Three recent phylogenetic studies that have recovered contrasting placements for the ‘hypsilophodontids’ were subject to in-depth character and taxon manipulation, with the aim of identifying the cause of these conflicting topologies. Results find that matrices which originally recovered the ‘hypsilophodontids’ within Cerapoda were comparably more stable in response to this manipulation, perhaps
suggesting these relationships are more robust. These three data matrices were further used to evaluate the morphological disparity within ‘hypsilophodontids’, finding that this group represents a diverse assortment of taxa. Disparity-through-time results show that the pelvic girdle and hind limb morphologies of ornithischians were comparatively diverse in the Middle Jurassic, indicating that important locomotory adaptations were evolving at this time. The long bone histology of the namesake ‘hypsilophodontid’, Hypsilophodon foxii, was examined to give insight into the growth patterns of these dinosaurs. Five histological ontogenetic stages were distinguished; however no unambiguous lines of arrested growth (LAGs) were recovered, suggesting Hypsilophodon foxii maintained uninterrupted growth even during periods of seasonal stress. The presence or absence of regular developing LAGs in other ‘hypsilophodontids’ implies that two distinct growth strategies were adopted by these taxa. Lastly, digital techniques were used to investigate the neuroanatomy and tooth replacement cycle of a new genus of ornithopod from Antarctica. Endocranial reconstructions reveal a large floccular lobe that extends considerably through the anterior canal of the endosseous labyrinth, suggesting this animal had enhanced gaze stabilisation and was capable of
rapid eye, head and neck movements. Digital segmentation of the dentary provides an in-depth assessment of an alternative ornithopod dental condition, compared to the more widely researched dental batteries of hadrosaurian ornithopods.
This thesis provides a significant contribution to our understanding of the'hypsilophodontids', showing that these dinosaurs exhibited disparate morphologies, neuroanatomies and even distinct patterns of growth. The phylogenetic affinities of the ‘hypsilophodontids’ remain contentious, but I hope the recommendations suggested in this thesis will aid future studies looking to resolve these relationships
Transport in periodic porous media: beyond homogenisation
Get PDFThe dispersion of scalars (or heat) inside a fluid flowing through a porous medium is often examined using the theory of homogenisation. Homogenisation theory provides a coarse-grained description of the scalar at large times and predicts that it diffuses with a certain effective diffusivity, so the concentration of the scalar is approximately Gaussian. This thesis improves on this by developing a large-deviation approximation which also captures the non-Gaussian tails of the scalar concentration through a rate function obtained by solving a family of eigenvalue problems. We demonstrate this on two distinct examples of idealised porous media. The first example is a medium composed of a periodic array of impermeable cylindrical obstacles. We focus on the classical problem of diffusion and examine the dilute and dense limits, when the obstacles occupy a small and large area fraction, respectively. We derive asymptotic approximations for the rate function that explain the validity of the Gaussian behaviour in the dilute limit and capture the non-Gaussian behaviour in the dense limit. We use finite-element implementations to solve the eigenvalue problems yielding the rate function for arbitrary obstacle area fractions and an elliptic boundary-value problem arising in the asymptotics calculation in the dense limit. Comparison between numerical results and asymptotic predictions confirm the validity of the latter. The second example is a periodic network composed of one-dimensional edges along which fluid flows with uniform velocity. We focus on networks generated from Bravais (triangular and square) and non-Bravais (hexagonal) lattices. We derive a set of transcendental equations from where the rate function can be extracted, yielding the effective diffusivity tensor that governs the Gaussian approximation as a byproduct. The dependence of dispersion on the underlying geometry and topology is determined by examining a set of asymptotic approximations for the effective diffusivity tensor and the rate function in a variety of physical regimes
Soteriological worship: a theological and exegetical analysis of the doctrine of worship within the reformed evangelical tradition
Get PDFThe Christian doctrine of worship has commonly been understood from ecclesiological, anthropological and soteriological perspectives. Within the Reformed evangelical tradition, each of these aspects have variously been given emphasis depending on the hermeneutical approach employed to understand scripture as a whole, or what I refer to as a ‘biblical theology.’ This thesis argues that a soteriological approach to worship makes the best sense of Christ’s abrogation and fulfilment of Old Testament worship, seen particularly in John’s Gospel and Hebrews. This is against the view of other writers within the tradition, who variously take a ‘covenantal’ view (which looks for OT patterns of corporate worship which are then retained by the church), or a Christological approach (which emphasizes all-of-life worship and edification within the gathering). Against both, I question whether there is appropriate exegetical warrant to view ‘corporate’ and ‘all-of-life’ worship as the best outcomes of biblical theology—even though these concepts are regualarly promoted within the literature. I argue, alternatively, that a better outcome is a soteriological model of worship which has elements of congruence with Paul’s doctrine of union with Christ. This doctrine better understands a life of service as the ongoing response of those who are ‘in Christ,’ as well as establishing an appropriate context for preaching, prayer, praise and thanksgiving within the gathering
Low-cost optical detection of pollen bioaerosols with machine learning for human health
Get PDFPollen and associated sub pollen particles are responsible for up to 40% of populations suffering from allergies and the situation in many countries is becoming more severe with changing lifestyles, environment, and climate. Meanwhile, pollen can interact with cloud processes, affecting cloud albedo, lifetime, and precipitation patterns. However, our means to characterise airborne pollen, and bioaerosols in general, are severely limited, making it difficult to answer many important questions and assess risk to public health. Conventional pollen monitoring instruments are generally manual samplers with crucial limitations of labour, time, and cost. There are recent advancements towards developing automated pollen monitoring instruments, however, these are expensive and not economically viable to populate large monitoring networks with high spatial resolution.
The objective of this work is to address the limitations of conventional methods by investigating alternative methods that can provide useful information on pollen bioaerosols for fundamental understanding and public health. This thesis presents and evaluates novel, low-cost methods for monitoring airborne pollen, using optical particle counters (OPCs) and machine learning, and investigating physical properties of pollen under varying atmospheric conditions, using an acoustic levitator, macroscope and computer vision techniques. The superior ability of supervised machine learning models to distinguish pollen trends from OPC data is demonstrated, as well as their potential to provide useful, high spatiotemporal resolution data in unique locations and for public health. This work provides comprehensive detail on how to train, interpret and employ such models for purpose, including scrutinising how the models learn to distinguish between different pollen types. Collectively, these studies demonstrate the potential for these low-lost techniques to provide novel information on pollen bioaerosol characteristics that was previously inaccessible. This novel information could be vital for our comprehension of the bioaerosol component of atmospheric aerosols, climate models, pollen forecasts, and public health advice and warnings
Exploring the contribution of land manager expertise when considering tree cover expansion for Natural Flood Management
Get PDFFaced with climate and biodiversity crisis, increasing tree cover has become a hot topic and a matter of significant debate. The multiple benefits of increasing tree cover have become a familiar narrative, particularly as part of Natural Flood Management (NFM). However, this increased interest is not reflected in increased tree cover in our landscapes. NFM itself is critiqued for a lack of empirical evidence, and a lack of uptake (of both NFM and tree cover) is linked to 'social barriers'.
NFM can be framed as 'wicked', a challenge in which multiple social, physical and ecological systems are entangled; water flows across socially defined boundaries. Trees are equally complex, crossing generational timescales where socio-ecological interactions may impact outcomes as readily as tree-water interactions. Understanding these interactions and entangled systems involves both interdisciplinary and participatory approaches. This has direct implications for the understanding of landscapes and decision-making at the knowledge-policy interface.
In this thesis, I demonstrate the importance of Land Managers' lived experience and expertise when exploring tree cover expansion for NFM (Trees for NFM). I explore how this impacts their decision-making and how this knowledge sits alongside the knowledge(s) that currently inform environmental decision-making, specifically hydrological modelling. This interdisciplinary, participatory study aims to inform decision-making by developing a better understanding of knowledge production for scaffolding solutions to 'wicked' problems.
In a large case study river catchment, the Trothy in South East Wales, I draw on key concepts and methods of Geography to explore landscape as both place and space. I root this disciplinary rigour and interdisciplinary perspective within a framework of participation and the co-production of knowledge. Working with Land Managers (predominantly but not exclusively farmers) through long, emplaced interviews, participatory GIS and hydrological modelling, I show the political and practical importance of lived experience. A phenomenological approach builds on current literature of agri-environment decision-making, enmeshing understandings and shedding new light on 'barriers' to uptake. Through this work, I affirm the attribution of Land Managers as relevant experts, exploring and applying their expertise. Using a hydrological model (SHETRAN) as a heuristic, I show the usefulness of modelling whilst situating the output within and recognising its entanglement with the wider relevant knowledges.
Conducting participatory reflexive work throughout, including evaluation and analysis workshops, I recognised a need for a new perspective on knowledge production and decision-making in landscapes. I introduce a concept I call 'drysi gwir', the real puzzle (work or entangled confusion!). I show that the current science-policy interface lacks key pieces of the puzzle. By recognising the importance of heterogeneity and connectivity within landscapes, I can directly reflect on 'barriers' to implementation and the impact this has on knowledge production within the context of environmental challenges. Through the analysis and work with participants, clear recommendations for alternative approaches, including the importance of relationships and the role of facilitation, are developed.
Significant landscape change is occurring, whether chosen or not. Choosing and impacting the direction of change involves a series of wicked challenges. Trees for NFM is a lens through which the decisions about this landscape change can be explored. The view through this lens shows that the current limited knowledge production at the science-policy interface is not meeting the challenge. In this thesis, I directly link landscapes, knowledge production and decision-making. In doing this, I propose ways in which knowledge production and a knowledge-policy relationship can meet the challenge and call for action to make the changes that can enable us to scaffold the solutions to the multiple wicked challenges we face
Chemical characterization and source apportionment of PM bound with primary and secondary organic compounds during haze and post-haze over the nothern Thailand
Get PDFNorthern Thailand has been facing recurrent haze events every year during the local summer season over the past few decades. Biomass burning, a well-known major source of this problem resulting from unsuitable agricultural practices, has caused several adverse impacts on human health, the environment, and socioeconomic aspects. Despite efforts, zero burning policy over northern Thailand has not been successfully implemented, as the haze persists for extended periods. In this research, daily PM was collected at a rural site in Chiang Mai, northern Thailand during haze and post-haze periods in 2019. Bulk chemical components and organic tracers were measured, including organic carbon (OC), elemental carbon (EC), water soluble inorganic ions (WSIIs), crustal and trace elements, nonpolar and polar organic compounds. Average mass of PM were 87 ± 36 and 21 ± 11 μg m-3 during haze and post-haze, respectively. Mass closure shows that during haze and post-haze, organic matter, water-soluble inorganic ions, and mineral dust were the top three contributors in PM mass. Source apportionment by positive matrix factorization (PMF) with organic tracers identified three different biomass burning sources including general biomass burning, nearby biomass burning (fresh aerosol), and softwood burning (aged aerosol) and three other sources including secondary sulfate, mixed dusts and traffic related emissions, and secondary nitrate, with contributions of 31%, 19%, 13%, 17%, 15%, and 5% during haze and 5%, 32%, 1%, 34%, 26%, and 2% during post-haze, respectively. Estimated lifetime cancer risk from exposure to PM bound PAHs ranged in moderate risk for the whole period. Biomass burning, softwood burning, and diesel combustion were the most contributor to lifetime cancer risk during haze, while diesel and gasoline combustions were the most contributors during post-haze. Several polar organic compounds display secondary organic aerosols characteristic especially dicarboxylic acids and nitrated aromatic phenols. The ratio of malic acid to succinic acid indicates stronger photooxidation during post-haze than haze period. Future study requires a longer sampling period in non-haze and different site environments for comparison and should be applied with remote sensing information. PMF model is recommended for source apportionment with comprehensive chemical species and organic tracers. Both gas and particulate phases Polycyclic Aromatic Hydrocarbons (PAHs) are recommended for lifetime cancer risk assessment
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