Spatial and Long-term Variability in Demersal Fish Species of the Western North Sea

Ph. D. ThesisThis thesis explores historical and contemporary patterns of spatial and temporal change in demersal fish species of the western North Sea. Comparing trawl data from over a century ago with those from contemporary trawl surveys are challenged by biases associated with differences in gear types and methods of operation. To compare contemporary data with rare 1892-1913 data from Northumberland Sea Fisheries Committee surveys on the Northumberland coast (UK), an attempt was made to replicate the original trawl gear and methods used by drawing on the literature, historical photographs and expertise of the trawl industry. The replica gear, comprising a 6.7 m beam connecting two Brixham-style wroughtiron trawl heads with a triangular-shaped trawl net and rounded ground-rope, was trialled in August 2018 and March 2019, and catches were compared with a modern otter trawl. In the first trial period, the otter and replica beam trawl had similar efficiencies in catching flatfish, whereas catches made by the replica gear in March were either very low or zero. As a result, the otter trawl was employed in place of the replica gear in all subsequent resurveys and catches were standardised for comparison with historical surveys. Catches revealed substantial declines in the abundance of the overall inshore fish assemblage and among individual species between 1899-1913 and 2018-2019. Elasmobranchs and historically dominant species such as grey gurnard Eutrigla gurnardus were either completely absent or rare in the 2018-2019 surveys. Abundance-size spectra also exhibited significant differences between periods, declining more steeply in contemporary trawls. Analysis of demersal fish stomach contents data revealed large shifts in diet composition over the period spanning 1896-2015. Bivalves dominated plaice Pleuronectes platessa, dab Limanda limanda and haddock Melanogrammus aeglefinus diets in the early and mid-20th century but declined ii substantially in subsequent decades. Conversely, polychaetes increased in importance by number and mass overtime and were the main prey resource for plaice in the 1970s and 2000s. These diet shifts point to likely changes in the benthic prey base of the North Sea, linked to increased beam trawling in the 1960s-1970s, eutrophication, and climatic processes. Finally, contemporary stomach contents and bulk stable isotope data were used as complementary techniques to assess temporal and spatial variation in the diet within and between two sympatric flatfishes, plaice and dab, in four coastal bays off the Northumberland coast. Stomach data indicated similar diets and significant dietary overlap at short temporal scales, yet dorsal muscle and liver tissue δ 13C, δ15N and δ 34S data revealed substantial interand intra-specific variation in resource use among sites and lower levels of niche overlap at longer time scales. Sandeels Ammodytes tobianus were highly abundant in flatfish stomachs, whereas Bayesian isotope mixing models indicated that squid were the important contributors to both predators. Dorsal and liver isotope data also indicated that bivalves and ophiuroids were major contributors to plaice and dab diet, respectively, across sites. These findings provide evidence of profound change in demersal fish species and their trophic ecology, further underpinning the value of using historical and contemporary data to elucidate broad-scale temporal and spatial patterns of changeCefas Seedcorn, The Faculty of Science, Agriculture and Engineering (SAgE) at Newcastle Universit

Reconstructing Early Cypriot Metallurgy : the Case of Pyrgos-Mavroraki

Ph. D. Thesis.Due to the extraordinary wealth of its ore deposits, Cyprus was the metal powerhouse of antiquity. The importance of Cypriot ore-mineral deposits has led to a wealth of research on prehistoric copper mining and production. However, this has overwhelmingly concentrated on provenance and exchange studies (via the isotopic fingerprinting of ores and ingots) at the expense of other research strands. In particular, important questions regarding Cypriot copper technology including the role and identity of bronzesmiths still await full investigation. Among the few cases of Early-Middle Bronze Age sites which show metallurgical evidence, Pyrgos-Mavroraki (Limassol) an early 2nd millennium BC settlement site, excavated by the Italian National Research Council (CNR) from 1998-2012, is certainly the richest known so far. The excavations unearthed a vast architectural complex, which hosted several workshops including an olive press, but most importantly, the complex yielded a great deal of metallurgical installations and residues. This research, through a combination of archaeological, analytical and experimental work, including SEM-EDX slag analysis and on-field copper smelting trials, allowed to reconstruct the smelting process used at Pyrgos. The archeological evidence shows that Pyrgos’s metallurgists used a rather primitive smelting technique, involving the use of simple bowlshaped furnaces, small crucibles and blowpipe equipped with simple clay nozzles. However, despite the high viscosity of the slags obtained did not allow a complete separation of the metallic copper, the slag-analysis proved that Pyrgos’s coppersmith were capable to smelt sulfidic ores, which are known to require a multiphase smelting process.Newcastle University, Northern Bridge Consortiu

Audience 2.0 : new dynamics of audience reception in the age of social media

PhD ThesisRecent years have seen a rise in interest in 'interactive' audiences, with the ongoing spread of digital media enabling media viewers to develop new participative and collaborative activities. As a hub of communication, the Internet has become a crucial enabling platform for these new forms of audience engagement. Audiences migrate to social media to share impressions, interpretations and issues with the content they view, an action which, it is argued, 'makes visible' the often-unseen processes that constitute audience reception. Using the microblogging site Tumblr as case study, this thesis makes a case for developing an integrative approach to media reception, by consolidating knowledge from film studies, fan studies, and participatory cultures, that these subjects might better address the mutable nature of the modern audience. This thesis commits to a radical contextualist approach which challenges the application of ‘linear’ frameworks to postmodern audiencehood, drawing specifically on the research of danah boyd, Henry Jenkins and Carolyn Michelle. This study contributes original knowledge on young adult's processes of ‘meaning-making’ when online, by examining (1) contexts of social media engagement in the audience's daily life (2) the forms of interpretative work produced online in relation to film texts (3) the social and cultural implications of this online audience activity. The research questions for this study are as follows: • How do social networking sites such as Tumblr figure in young adult’s daily media use? How do Tumblr users engage with film content when interacting online? • How are Tumblr users utilising the site in their reception of film texts? What are the forms of receptive work taking place online? • How does the audience interpret and reflect on their online activity? What do these practices reveal about the nature of online audiencehood? The study employs online ethnographic methods, including participant observation and Skype interview, to detail the processes of online audience reception. An intensive period of fieldwork was undertaken, consisting of 12 months participant observation of 150 users within the Tumblr community, followed by a series of 24 online interviews, carried out synchronously (via Skype) and asynchronously (via email). The ethnographic data collected for this study was analysed thematically in order to produce an initial conceptual guide to online audience engagement. This study identifies several key themes which typify audience work on this site, including ‘performance’, ‘anonymity’, and ‘bricolage’. The study finds that the 'exhibitive' quality of online interpretative work, being intrinsically informed by the contextual collapse between public and private in online spaces, promotes self-conscious responses whereby audiences can actively assert their sense of self and their place within a wider social and cultural sphere. This appears to have specific generational resonances, as critical discourses on the ideological basis of the film industry are increasingly propagated amongst Tumblr’s young adult userbase. The thesis concludes with an interrogation of the thresholds of participation in interactive audience engagement and the implications this has for the future of audience research. It is argued that the role of social media in audience enquiry should not be understood merely as a new source of data about audiences, but rather as a crucial enabling platform for audience participation and contribution

Learning Logical Rules from Knowledge Graphs

Ph.D. (Integrated) ThesisExpressing and extracting regularities in multi-relational data, where data points are interrelated and heterogeneous, requires well-designed knowledge representation. Knowledge Graphs (KGs), as a graph-based representation of multi-relational data, have seen a rapidly growing presence in industry and academia, where many real-world applications and academic research are either enabled or augmented through the incorporation of KGs. However, due to the way KGs are constructed, they are inherently noisy and incomplete. In this thesis, we focus on developing logic-based graph reasoning systems that utilize logical rules to infer missing facts for the completion of KGs. Unlike most rule learners that primarily mine abstract rules that contain no constants, we are particularly interested in learning instantiated rules that contain constants due to their ability to represent meaningful patterns and correlations that can not be expressed by abstract rules. The inclusion of instantiated rules often leads to exponential growth in the search space. Therefore, it is necessary to develop optimization strategies to balance between scalability and expressivity. To such an end, we propose GPFL, a probabilistic rule learning system optimized to mine instantiated rules through the implementation of a novel two-stage rule generation mechanism. Through experiments, we demonstrate that GPFL not only performs competitively on knowledge graph completion but is also much more efficient then existing methods at mining instantiated rules. With GPFL, we also reveal overfitting instantiated rules and provide detailed analyses about their impact on system performance. Then, we propose RHF, a generic framework for constructing rule hierarchies from a given set of rules. We demonstrate through experiments that with RHF and the hierarchical pruning techniques enabled by it, significant reductions in runtime and rule size are observed due to the pruning of unpromising rules. Eventually, to test the practicability of rule learning systems, we develop Ranta, a novel drug repurposing system that relies on logical rules as features to make interpretable inferences. Ranta outperforms existing methods by a large margin in predictive performance and can make reasonable repurposing suggestions with interpretable evidence

Software-in-the-Loop combined Artificial Intelligence for Optimised Design and Dynamic Performance Prediction of Floating Offshore Wind Turbines

PhD ThesisFloating Offshore Wind Turbines (FOWTs) have shown a promising future due to the goal of Net Zero emissions by 2050. However, the highly coupled nonlinear performances of FOWTs bring many challenges to the implementation of numerical and basin experimental methods in design and optimisation. This PhD project proposes an innovative method, named SADA (Software-in-the-Loop combined Artificial Intelligence Method for Dynamic Analysis of Floating Wind Turbines), to optimise the design and predict dynamic performances of FOWTs. SADA is built based on a coupled aero-hydro-servo-elastic programme DARwind and Machine Learning Algorithms. Firstly, the concept of Key Disciplinary Parameters (KDPs) is inspired by FOWT-related disciplinary theories. Secondly, DARwind will take continuous action through the Software-in-the-Loop (SIL) model to obtain more accurate prediction results. Thirdly, SADA can build data sets and analyse deep-seated physical laws of FOWTs. Then, case studies were conducted to prove the feasibility of the SADA method on the basin experiment data. The results show that the mean values of some physical quantities can be predicted by SADA with higher accuracy than the original DARwind simulation results. In addition, full-scale case studies were conducted by extending SADA to engineering applications, though some design parameters are not accessible. Furthermore, other physical quantities that cannot be obtained directly in full-scale measurement easily but are of great concern to industry can also be obtained from a more credible perspective. The proposed SADA method could benefit the wind industry by taking advantage of the numerical analysis method and AI technology. This brings a new and promising solution for overcoming the handicap impeding direct use of traditional basin experimental technology or full-scale measurement. Therefore, designers in the wind industry can optimise FOWTs designs to a higher level, thereby achieving a better method of and maintaining safe operation of FOWTs in a complex sea state

The cytoskeleton and polarity in the C. elegans embryo: Understanding microtubule dependent signalling in the generation of cellular asymmetries.

Ph. D. ThesisAsymmetry within cells relies on the uneven distribution of molecules and organelles required for cell function and viability. For example, epithelial cells form an apical-basolateral polarity which confers different protein and phospholipid compositions at the membrane of each domain. Controlled enrichment of integrins on the basolateral domain ensures that an epithelial cell remains anchored to the basement membrane, required to prevent cell plasticity and epithelial to mesenchymal transition. Migrating cells require the assembly of the cytoskeleton at their leading edge and disassembly at the rear to move with direction, whilst asymmetrically dividing cells rely on different concentrations of proteins and RNAs across the mitotic axis to program the distinct fates of each daughter cell after division. The polarity effector proteins, which control polarity establishment and maintenance in cells are broadly conserved, however respond to different cues and have variable contributions dependent on cell type, organism, and stage, be it inherited or de novo polarity. Failure to generate and maintain correct asymmetry in cells can lead to disease states including cancer. In our lab, we study the contribution of the cytoskeleton in the establishment of cell polarity. For this, we use the C. elegans zygote as a model due to the conserved molecular machinery and its well characterised embryonic development. Asymmetry first initiates in the single cell zygote, post-fertilisation, upon which the globally dynamic actomyosin network underlying the cell membrane undergoes localised relaxation at the site in closest proximity to the matured sperm-derived centrosome pair. The resultant gradient of actomyosin contraction generates a cortical cytoplasmic flow towards the future anterior pole and carries with it, the cortical anterior polarity effector PAR proteins. The newly unoccupied cortex is then inhabited by a cytoplasmic pool of posterior PAR proteins. The cue for this change in cortical dynamics is derived from a signal of sequestered AIR-1 which diffuses from the sperm donated centrosome. A second, lesser studied, pathway to establish polarity in the zygote is believed to occur due to the enhanced stabilisation of posterior PARs at the cortex, aided via centrosomal microtubules which prevent phosphorylation from anterior PARs that initially inhibit posterior PAR membrane recruitment. Through mutual antagonism the anterior and posterior PARs can define their own boundaries and maintain polarity. As both pathways rely on the centrosome, studies to characterise these processes individually have been difficult. Disrupting the centrosome compromises both pathways while interrupting downstream components of either pathway results in masked phenotypes due to effective cell polarisation via the other pathway. To overcome the functional redundancy that makes studying the microtubule-dependent pathway difficult, I have utilised a functionally null mutant of the gene, nop-1, which lacks early actomyosin flows to then screen for regulators of the microtubule-dependent pathway of polarity establishment, now required for embryo viability. Through this, and follow up immunofluorescent stains of polarity markers, I have identified novel proteins required for efficient cellular asymmetry. One such protein was the chromokinesin, KLP-19, previously known to aid chromosomal alignment and segregation during metaphase/ anaphase of IV meiosis and mitosis. I have shown that KLP-19 is required to keep the centrosome restricted to the posterior pole during polarity establishment, necessary to facilitate a robust symmetry breaking signal and ensure centrosome separation occurs in a timely manner for the setup of the mitotic spindle. It is likely that KLP-19 performs this role by localising to, and crosslinking, centrosomal and cortical microtubules that meet in an antiparallel manner

Utilization of biochar produced from agricultural residues for the removal of pesticide and pharmaceutical micropollutants in surface water biofiltration

PhD ThesisIn recent years, there has been a growing interest in exploring possible agro-based biochar for use in different remediation applications. This thesis therefore investigated the feasibility for biochar produced from rice straw (RSBC), corn cob (CCBC), coconut husk (CHBC) and coconut shell (CHBC) to immobilize micropollutants in water, with the aim of finding a better alternative to activated carbon (GAC). First, 3% (w/w) amendment applications of the selected adsorbents were set up to evaluate their influence on leachate properties. Results showed significant increase in pH (>8) in biochar leachates which decreased leachability of metals, while GAC with lower pH (<6) showed greater metal leaching. Also, all amendments increased hydraulic conductivity (K) by 11.6%, except for CHBC and CCBC that decreased K by 54.7% and 36.9%, respectively. The characteristics of the biochars in batch adsorption studies were compared to evaluate their adsorption of four pharmaceuticals and two herbicides micropollutants. Although, removal efficiencies were feedstock type dependent, RSBC exhibited significantly higher sorption capacity of 12.81±0.13 mg/g (at 0.5 g/L and 10 days contact time) for oxytetracycline (OTC), compared to that of GAC of 19.11±0.72 mg/g for the same compound. Partition coefficient (Kd) values were used to compare how effective the different adsorbents are in the reduction of micropollutants availability and transfer in aqueous solution. Comparatively, the kinetic study indicated that RSBC and CHBC showed better adsorption for most micropollutants than other biochars. CHBC amendment of sand biofilters showed a reduction in hydraulic flow from 24.48 m/day in fresh fine sand (FISA) to 1.87 m/day in CHBC amended fine sand, which facilitated the micropollutant biodegradation process. All measured compounds were attenuated by a combination of sorption and biodegradation processes, however, pharmaceuticals were removed more significantly (p<0.05) than herbicides in both amendment types. Overall, biodegradation accounted for >90% removal in CHBC and <60% for FISA columns. Microbial analysis confirmed a shift in bacterial community composition for CHBC versus FISA columns, but depth as the most critical community structuring factor. In this work, RSBC and CHBC were shown to have potential for cheap, and environmentally friendly amendments to enhance removal of micropollutants in surface water biofiltration

Voicing Contrast in Najdi Arabic Stops: Implications for Laryngeal Realism

Ph.D. (Integrated) ThesisThe present study investigates the phonetic and phonological aspects of the voicing contrast in stops in Najdi Arabic, a dialect that has been found to contrast prevoiced and aspirated stops. This study discusses the implications of the acoustic correlates of Voiceless and Voiced stops for the phonological representation of the voicing contrast in this variety and examines the connection between the acoustic signal and the distinctive features that specify the opposition by employing the types of evidence proposed in the realm of laryngeal realism. These types of evidence include the manifestation of acoustic correlates of stops in various positions, speech rate effect on aspiration and prevoicing, and the Voiceless and Voiced stops’ behaviour in stop-stop clusters across word boundary in terms of regressive voicing assimilation. The manifestation of the acoustic correlates of Voiceless and Voiced stops shows that Voiceless stops are aspirated in the examined positions whereas Voiced stops show robust prevoicing in utterance-initial and utterance-medial contexts. The acoustic correlates also show that Voiceless stops are robustly accompanied by longer closure, longer burst, higher F0 and F1 onset, and lower burst intensity. Voiced stops, on the other hand, are robustly accompanied by shorter closure (utterance-medially), shorter burst, lower F0 and F1, and higher burst intensity. Speech rate affects both aspiration and prevoicing in Voiceless and Voiced stops, respectively. Prevoicing and aspiration are lengthened in normal speech rate in comparison to fast speech rate. Stop-stop cluster results show that both Voiceless and Voiced stops trigger some (de)voicing in the preceding member of the cluster. The acoustic analysis reveals that Voiceless stops show voicing assimilation in F0/F1 and burst intensity but not in voicing in the closure. For Voiced stops, the results show a degree of devoicing in their closure but not in F0/F1 and burst intensity. The results suggest that Voiceless and Voiced stops in Najdi Arabic have features from both aspirating and voicing languages. This claim is supported by the three types of evidence implemented in this study. The assumption that both Voiceless and Voiced stops are specified implicates that the voicing contrast in Najdi Arabic is overspecified in the phonology with two features, [spread glottis] and [voice]. Applying the numeric values of phonetic distinctive features proposed by Beckman et al. (2013), on the scale of 1 to 9, the present study claims that Voiced stops in Najdi Arabic are specified with [9 voice] while Voiceless stops are specified with [8 spread glottis], mainly because of the existence of moderate aspiration in utterance-initial Voiceless stops and the robust prevoicing found in utterance-initial and utterance-medial Voiced stops (1 means inactive, 9 means highly active). The phonological repercussions for the proposed overspecification in the voicing contrast in Najdi Arabic are discussed with a specific focus on the inclusion of such a patterning in theoretical models of voicing

The regulation of feed intake in broiler chickens in sickness and in health

PhD ThesisThere is an increased interest in the use of alternative feed ingredients in broiler production systems on the grounds of food security and reduced environmental impact. Such ingredients are typically bulky in their nature and consequently lead to feeds whereby the energy and nutrient composition is diluted in comparison to more traditional feeds. Therefore, interest is growing in the ability of broiler chickens to cope with bulky ingredients. Understanding such an ability and the limiting factors of such feeds is vital for the development of accurate simulation models that predict broiler performance and the environmental impact. As broilers are challenged by ubiquitous pathogens during their growth, additional understanding of how birds deal with bulky feeds under such challenge is also relevant to such predictions. There are concerns that modern broilers have lost their ability to regulate their energy intake and that genetic selection for carcass yield has limited the size of their gastrointestinal tract (GIT), thus limiting their capacity to cope with energy dilution. The first two chapters of this thesis investigated the capacity of a modern broiler strain to deal with increasing levels of various bulky ingredients and aimed to identify a feed bulk dimension responsible for limiting feed intake. These experiments also allowed the investigation of the capacity and rate of adaptation of the gastrointestinal tract on these bulky feed ingredients. The results of these experiments showed: 1) Birds showed a remarkable ability to regulate energy intake when feed energy content was reduced up to a point, which was presumed to reflect the maximum capacity for bulk. 2) Further feed dilution with bulky ingredients limited feed intake and penalised performance. 3) The Water holding capacity of the feeds was able to predict the feed intake of birds not previously adapted to bulky feeds, i.e. in the short term. 4) Birds adapted very rapidly on the bulky feeds and the rate of adaptation depended on the bulkiness of the feed, i.e. the bulkier the feed the longer the adaptation. Infection with coccidia was used as the infectious model to investigate the interaction between feed bulkiness and infection. In the third experiment, infected birds were given access to feeds which were progressively diluted with a bulky ingredient, lignocellulose. In uninfected birds feed intake was reduced as feed dilution increased and performance decreased, whereas in infected birds feed intake increased as feed bulkiness increased, and performance was unaffected by feed bulkiness. In the final experiment, the protein content of the feed was diluted by substituting an ingredient with a high protein content for one with a low protein content, whilst maintaining the energy contents of the feeds. In both uninfected and infected birds feed intake increased as the protein level of the feed increased, and performance ii increased. The results from these experiments show that performance during infection is indeed sensitive to feed composition and it may altogether be absent when broilers are offered feeds diluted with bulky ingredients, such as lignocellulose. The findings of this thesis facilitate the development of models to predict the feed intake and performance of broiler chickens offered feeds with alternative, bulky ingredients. Unravelling how feed intake is regulated during Eimeria infection will help to understand how these birds should be fed during the critical stages of infection

The entrepreneur-financier relationship across institutional logics: A study in Thailand

Ph. D. Thesis.Entrepreneurs can draw support from various types of financiers, including crowdfunding, angel investors, venture capital funds, corporate venture capital funds, and public subsidies. However, most research focuses on a single source of finance, most often venture capital funds. Prior studies do not give a complete picture of how the relationship between entrepreneurs and investors unfolds over time. The focus is mainly on how investment decisions aremade, even though engagements after striking a deal are equally crucial to the relationship. These gaps in understanding offer an opportunity to understand entrepreneurs and their contexts, particularly when looking at the microlevel entrepreneur-financier dyad. In addition, as Welter (2011) notes, contexts matter. These contexts have a multiplicity of levels in that they both intertwine with and shape regulatory and normative contexts at wider levels (community, regional, and national). The entrepreneurfinancier dyadic relationship is arguably formed in a broader context. It is thus worth considering the potential effect of context on the relationship. This research explores the relationships between entrepreneurs and financiers in Thailand using an institutional logics perspective: a value system that prescribes behavioural templates for focal actors (Thornton et al. 2012). The focus is on the context of how a relationship is fostered during a new venture financing process. By examining fine-grain differences in practices between entrepreneurs and various financiers, the research deconstructs what comprises the emergence of their relationships and explains the distinct context within which each pathway is formed. This is a promising lens for explaining differences in entrepreneur-financier relationships. The literature has conceptually suggested that each type of financiers will possess dominant institutional logics, and such logics will shape their interactions with entrepreneurs when assessing prospective deals. The study utilises a qualitative research design involving indepth interviews with entrepreneurs and financiers – corporate venture capitalists, venture capitalists, angel investors, and government funding agencies – in Thailand. A total of 36 interviews were conducted with 20 entrepreneurs and 16 financiers. This thesis proposes a comprehensive framework that delineates the emerging relationships between entrepreneurs and various types of financiers. Each path develops under its own practices with hybrid logics that are underpinned by the broader context. However, the institutional logics shaping the relationship deviate from those previously characterised in the 3 literature. The most striking findings involve entrepreneurs’ relationships with corporate venture capital and angel investors. The former are shaped by both corporate and professional logics, whereas quasi-community logics shape the latter. A different relationship pattern is found in government funding, shaped by state logic complemented by market logic. Practices with venture capitalists coincide with those in the literature, indicating a predominance of professional logics in the relationship. Based on these findings, practical recommendations are provided for entrepreneurs planning to approach financiers in relation to what financiers look for at different phases of relationship formation and what entrepreneurs can expect from financiers. Policy recommendations are also offered for those interested in championing entrepreneurship through the design of financing tools concerning institutional logics found in entrepreneur-financier dyads in emerging economies