VictorJuiz/thesis huggingface dataset:
Mechanisms underlying the efficacy of normothermic machine perfusion in human liver transplantation
Keywords: Organ preservation
Normothermic machine perfusion
Liver transplantation

Introduction:
By perfusing a liver with oxygenated blood, medications and nutrients at 37C, normothermic machine perfusion (NMP) may improve outcomes after liver transplantation when compared with conventional static cold storage (SCS). Herein is reported the first randomised controlled trial (RCT) comparing continuous NMP with SCS in human liver transplantation. Additional work exploring the mechanisms behind the effects of NMP is also described.
Methods:
This multinational RCT was initiated by the Consortium for Organ Preservation in Europe (COPE) and involved seven European transplant centres. Adult DBD and type III DCD livers were randomly assigned (1:1) to continuous NMP or SCS. The primary end point was the difference in peak-AST, requiring 220 transplants (90% power). Secondary endpoints included: organ utilisation, preservation time, early allograft dysfunction (EAD), six month graft and patient survival and ischaemic cholangiopathy on MRCP. During NMP, perfusate and bile samples were collected and subsequently analysed to provide information regarding bile salt utilisation and identify markers that may indicate organ quality.
Results:
272 livers (135 SCS, 137 NMP) were enrolled, consisting of 194 DBD and 78 DCD organs. 48 livers were discarded (32 SCS [15 DBD, 17 DCD] vs 16 NMP [10 DBD, 6 DCD]; p=0.01). NMP livers experienced significantly longer preservation times than SCS (7hr 21min vs 11hr 39min; p&LT; 0.01). Despite this, better early graft function was observed in the NMP group with regards to peak AST (974 IU/L SCS vs 485IU/L NMP; p&LT; 0.001) and EAD (29.9% SCS vs 12.6% NMP; p=0.002) with the magnitude of these effects being greater for DCD organs (p=0.02). No measurable difference was found in radiological rates of ischaemic cholangiopathy with no demonstrable correlation between MRCP findings and clinically relevant strictures. NMP livers were found to utilise bovine bile salts effectively with bile production and several other biochemical parameters found to correlate with graft quality.
Discussion:
NMP livers show better early graft function than SCS in terms of peak-AST and EAD, both of which are surrogates for long-term graft outcomes. This is despite better organ utilisation and longer preservation times in the NMP group. NMP can be used to predict organ quality although it is not possible to draw conclusions about markers that may predict viability. If translated to clinical practice, these results would have a major impact on liver transplant outcomes and waiting list mortality. The fact that the study has definitively met its primary endpoint should now enable the exploration of the technology’s wider potential.
The politics of the English royal court, 1247-65, with special reference to the role of aliens
Keywords: English
households
court
royal
king
courtiers
aliens
politics
England

This thesis is not a straightforward account of the aliens under Henry III 1247-65 but rather an attempt to use the aliens as a pathway into the inner political life of Henry III's court. Previous generations of political historians have concentrated on the growth of the 'baronial opposition' to Henry while paying little attention to the point that the focus of political opposition for much of the reign came from the 'court', and especially members of the royal family: Richard of Cornwall, the lord Edward and Simon de Montfort. Similarly, while historians have assumed, perhaps with the exception of F.M. Powicke, that the baronage moved in 1258 against a united royal government and, foremost against the aliens in it, they have failed to observe that King Henry III's favourites took different sides over the Provisions of Oxford: the Savoyards supported it but the Poitevins were exiled from the realm. Contrary to what has become the standard interpretation, there was no united alien force at court before or after 1258 - until 1264 at the very least. The Savoyards and Poitevins at court and in the provinces had always played a distinct role in royal government and in politics; they were men of very different character, outlook and connexions. It is the purpose of this thesis to describe and explain these divergent political paths and to draw conclusions from them about the nature of government and politics in the reign of Henry III.
Continued in thesis …
Genetic susceptibility and severity factors in rheumatoid arthritis
Keywords: susceptibility
rheumatoid
severity
factors
genetic
arthritis

The aim of this D.Phil. thesis was to enrich current knowledge of genetic susceptibility and severity factors in rheumatoid arthritis (RA), a common complex disease with an estimated heritability of approximately 60% in the Northern European population. A DNA resource from 760 clinically well-characterised British Caucasian RA patients was established for use in association studies to investigate candidate genes.
The previously reported association of PTPN22 (1858C/T rs2476601) and rheumatoid factor positive disease was observed (p=0.004). Examination of PTPN22 gene for differential allelic expression (DAE) in different peripheral blood mononuclear cell populations from RA patients was undertaken. A DAE of 20% or more in 8 RA patients (p< 10-5) was observed, indicating possible existence of cis-acting genetic variation. PTPN22 DAE in a number of cell types was demonstrated in 4 RA patients and there were also different allelic ratios between these cell populations (pc < 0.05).
MHC class II expression is controlled at the transcription level by MHC class II transactivator (CIITA) and is mainly dependent on the transcription of its gene MHC2TA. The frequency of MHC2TA (-168A/G, rs3087456) polymorphism in RA cases did not differ from those in controls. Minor allele frequencies were higher in HLA-DRB1 shared epitope negative and DRB1*04 negative patients (p=0.01 and p=0.03 respectively). Further direct sequencing followed by single nucleotide polymorphism genotyping and haplotype analysis did not reveal significant skewing in the haplotype distribution.
Polymorphisms in the IL-1A and IL-1B promoter can influence gene expression and these were investigated for association. The IL-1B (-1464 C/G, rs1143623) G allele was found to be less common in the RA group (p=0.01). Meta-analysis revealed statistically significant association between IL-1B (-511 A/G, rs16944) and RA (p=0.02).
Although the importance of studied markers in predicting disease susceptibility is modest, together with future findings these results may help to provide better insight concerning the RA disease process.
From Arabidopsis model to green revolution cereal crop varieties: studies of the co-regulation of plant growth and nitrogen metabolism
Keywords: Genetics
Mutant screen
Plant nutrition

Modern semi-dwarf “Green Revolution” varieties (GRVs) of wheat and rice dramatically increased global grain yields during the mid to late 20th Century. GRVs are dwarf because they accumulate growth-repressing DELLA proteins. GRVs are thus high yielding because they apportion more resource to grain filling than to stem elongation, and are less susceptible to the yield-reducing effect of “lodging”. However, recent evidence suggests that GRVs have a low nitrogen-use efficiency (NUE) as a result of the negative pleiotropic effect of stabilised DELLAs. Therefore, the cultivation of GRVs requires environmentally unsustainable levels of inorganic fertiliser application.
The aim of this study is to uncover the underlying mechanism of DELLA-mediated inhibition of the metabolism of nitrate (the major form of nitrogen in most agricultural soils), using the Arabidopsis semi-dwarf GRV model mutant ga insensitive (gai). It was first established that gai is more resistant to chlorate, the toxic chemical analogue of nitrate, suggesting that like GRVs, Arabidopsis gai also exhibits compromised nitrate metabolism. Chimeric analyses and enzymatic assays discovered an inhibitory effect of DELLA proteins on shoot nitrate reductase activity. A similar effect of DELLAs was found to be conserved in rice, providing a potential explanation for the low NUE observed in GRV crop plants. Moreover, as DELLA-interacting proteins (DIPs), PHYTOCHROME-INTERACTING FACTOR3 (PIF3) was identified as a positive regulator of nitrate assimilation, potentially acting downstream of DELLAs.
Simultaneous forward screens for mutagenized gai isolated multiple mutants which genetically uncoupled gai-mediated inhibition of stem elongation and nitrate metabolism, with usually multiple acids move in and out transporter32 (umamit32) identified as a potential novel mutation conferring enhanced chlorate resistance. Meanwhile, several tall gai mutants were selected and initially characterised, which provided new insights into the GA-DELLA signalling pathway and how it relates to the regulation of plant growth. The ultimate goal of this research is to apply the knowledge obtained from Arabidopsis to modern crops, in the hope of improving their NUE and thereby contributing to the development of the next generation of GRVs of crops.
A muse of fire: why the U.S. Military forgets what it learns in war
Keywords: Vietnam War
Organizational Learning
Iraq War
Assessments
Intelligence
Foreign Policy
Military
Military Adaptation
U.S. Military

Wars are expensive and relatively rare, and so states have strong incentives to learn from war and improve their military performance over time. And yet, even in highly capable great power militaries, the lessons of previous wars are routinely lost. Why do militaries forget what they learn in war? Examining evidence from two cases across the American experiences in Vietnam and Iraq, I find that the strongest causal evidence for why the US military forgets what it learns in war is in organizational selection. The demobilization and post-war retooling process destroys the specific sub-organizations which learn in war, namely joint task forces and ad hoc task-built organizations. This research has the potential to make a significant and novel contribution both to our understanding of repeated American foreign policy mistakes and to the broader literature on military adaptation and effectiveness.
The Bronze-Iron Age transition in Achaea, western Greece: continuity and change from the 12th to the 8th century BC
Keywords: Western Greece
Late Bronze Age
Early Iron Age

Achaea in the Northwest Peloponnese presents unique opportunities for the study of the Late Bronze-Iron Age transition in Western Greece. During the 12th century BC, its archaeological record suggests the existence of a thriving network of sites, with a high concentration in Western Achaea, whose elites propagated their warlike ethos in the funerary record and were able to nurture and sustain interregional and overseas contacts long after the demise of the palatial economies.
The beginning of the Iron Age saw the disappearance of the conditions that prompted these developments, and brought drastic changes to burial customs and settlement patterns, with the shift of the regional centre of gravity towards Northeast Achaea. By the 8th century new political economies and social dynamics are manifested in the growth of local cult-sites.
The present study explores these issues through the examination of the published settlement, funerary, and ceramic evidence. It also considers Achaea’s position in the wider context of Western Greece, through the lasting interactions visible in the ceramic production. Moreover, it addresses the character of the Achaean engagement in the communication networks towards the West, and peninsular Italy in particular, as these contacts were manipulated by the post-palatial elites and re-surfaced in a completely different framework in the late 8th century, with the Achaean involvement in the colonisation movement.
The study of Achaea thus offers a regional perspective into the diverse socio-political and cultural transformations that occurred in the Aegean between the 12th and the 8th centuries BC. By elucidating aspects of continuity and change across this crucial transitional period it is possible to observe a regional shift from local chiefdoms with warlike ruling ideology communicated in the mortuary record, to communities structuring their identities in the sphere of communal cults.
How did mammals evolve into their ecological niches through time? Quantitative tests for classic macroevolutionary questions
Keywords: Mammalogy
Palaeontology
Evolution
Palaeobiology
Macroevolution

Observations that the taxonomic and ecomorphological diversity of mammals increased across the Cretaceous/Paleocene (K/Pg) boundary led to the model of adaptive radiation. These rapid and large-scale increases in diversity and disparity are thought to have resulted from unprecedented ecological opportunity for mammals in the wake of the K/Pg event, during which numerous niches previously occupied by the non-avian dinosaurs and other components of the Mesozoic fauna were cleared. Although patterns of increased body size and body size disparity have been thoroughly explored, fundamental questions remain regarding both the magnitude and exact nature of mammalian ecomorphological change across the K/Pg boundary. It has long been established that Cenozoic mammals appear to exhibit a wider range of ecomorphotypes associated with feeding ecology in comparison to the Mesozoic. Here I use a dataset of six functionally-relevant traits made up of ten continuous character measurements across 276 fossil and 730 modern (including 23 recently extinct Pleistocene megafauna) mammal jaws to quantify and explore patterns of jaw ecomorphological disparity from the Late Triassic– end-Eocene and Pleistocene–Recent. I further explore the evolutionary rate across the K/Pg boundary by analysing six functional jaw traits for 69 Jurassic- Eocene mammals in a phylogenetic framework. The results presented herein demonstrate that, despite an immediate increase in therian mammal jaw ecomorphological disparity across the K/Pg boundary, mammals as a whole did not show an increase until the Paleocene/Eocene boundary. This lag of ~10 My is interpreted as an interval of ecological recovery, during which high rates of mandibular ecomorphological trait evolution are detected. Much of the Paleocene/Eocene increase in disparity can be attributed to mammals with larger body sizes. My results are indicative of an adaptive radiation of placental mammals in the early Paleogene, in response to large-scale niche clearing.
Targeting the chemokine signalling pathway using tick saliva peptides
Keywords: Inflammation
Ticks
Chemokine
Evasin

Chemokines are signalling proteins that function to recruit immune cells from the innate and adaptive immune response. Chemokines are classified based on the position of their cysteine residues at the N-terminus as CC, CXC, CX3C or XC (C-cysteine, X-amino acid). Increased expression of chemokines is one of the key findings in a range of inflammatory diseases. Chemokines operate in a network, where multiple chemokines bind a single receptor, and vice versa, and multiple chemokine receptors are expressed on immune and inflammatory cells. While chemokines are validated therapeutic targets, targeting a single chemokine or receptor has failed as a therapeutic approach in inflammatory disease.
Ticks, blood-feeding parasites, feed on their hosts for several days to weeks without eliciting their hosts immune response. Ticks achieve this through secreting numerous anti-inflammatory peptides into their hosts, during feeding. Evasins are proteins identified from tick saliva that bind and neutralize multiple chemokines and are thought to reduce inflammation at the site of the tick bite. Systemic administration of evasins effectively reduce inflammation in a range of preclinical models of inflammatory disease, suggesting that they could be used as therapeutics for such diseases. Limitations of published evasins include lack of binding to important chemokines (e.g. CCL2, CCL13, CXCL10), and inability of a single evasin to target both CC and CXC chemokines. Therefore, this thesis aimed to expand the chemokine-binding repertoire of identified evasins and hypothesised that other tick species would have novel evasins that are also capable of modulating chemokine activity.
Using bioinformatic analysis of eight tick species from the Amblyomma, Rhipicephalus and Ixodes genera, 352 evasin-like sequences were identified, and constructed into a yeast surface display library. This library was screened using fluorescently labelled CC and CXC chemokines to identify individual clones that bound. 16 novel evasins were identified, including P1156 and P1243. P1156 binds six ELR+ CXC chemokines with high affinity and neutralises CXC chemokine function. P1243 evasin binds 21 CC chemokines with high affinity and neutralises CC chemokine function.
Typically, both CC and CXC chemokines are expressed in inflammatory disease. To develop agents that can target both chemokine classes, genetically engineered ‘two-warhead’ evasins were created and were shown to be capable of simultaneously binding CC and CXC chemokines and neutralising their function, in vitro. Thus, the two-warhead evasin provides a concept of achieving precision targeting of disease-relevant CC and CXC chemokine subsets, as a single agent.
Development of lung and muscle factories to deliver therapeutic monoclonal antibodies
Keywords: Antibodies
AAV
Rheumatoid arthritis
Lentiviral vectors
RSV

Monoclonal antibodies (mAbs), which represent the largest market of any protein therapeutic, are used in the treatment of conditions such as cancer and autoimmune diseases, and prophylaxis of infections. The complexity of manufacture of mAbs translates to a high cost compared with small-molecule drugs, and their use may be restricted as a result. Gene transfer for direct production of mAbs in vivo could offer an alternative to parenteral administration, with the added benefit of easing patient burden caused by repeated injections or infusions. Studies presented in this thesis investigated the possibility of using gene transfer agents for expression of mAbs in the lung lumen and circulation. Using the secreted reporter protein Gaussia luciferase, delivery of the lentiviral vector recombinant simian immunodeficiency virus, pseudotyped with F and HN proteins from Sendai virus (rSIV.F/HN) for targeting of pulmonary epithelium, was identified as an efficient means of gene transfer to the murine lung, with transgene expression in the lung lumen lasting for at least 12 months in BALB/c mice. The recombinant adeno-associated viral vector serotype 8 (rAAV2/8) injected into the muscle directed robust expression of the reporter protein into the circulation and lung lumen of mice for at least 12 months. Two model applications were used to assess the effectiveness of these vectors for mAb gene transfer: respiratory syncytial virus (RSV) infection and rheumatoid arthritis. Both rSIV.F/HN and rAAV2/8 vectors expressing the anti-RSV mAb palivizumab protected mice from weight loss upon RSV infection. Recombinant AAV2/8 delivered intramuscularly was also used to express the anti-tumour necrosis factor alpha (TNFa) biologics infliximab and etanercept for at least 6 months and 56 days, respectively. Due to the immunosuppressive nature of TNFα antagonists, constitutive expression is undesirable and small molecule-assisted shutoff (SMASh) was investigated as a possible method of regulation of etanercept production. In conclusion, viral vectormediated mAb gene transfer to the muscle and lung could be a feasible alternative to parenteral administration provided that an effective method of regulation of expression following vector delivery can be developed.
Genome-scale characterisation of symbiotic fitness determinants of Rhizobium leguminosarum using INSeq
Keywords: Symbiosis
Rhizobium leguminosarum
Insertion Sequencing

Mariner-based insertion sequencing (INSeq) has been used to characterise symbiotic fitness determinants in Rhizobium leguminosarum bv. viciae 3841 (Rlv3841) on a whole genome-scale. An INSeq database has been constructed that defines the mutational phenotypes for 7316 genes (99.7% of the genome) in Rlv3841 across nine in vitro and in planta INSeq conditions, including growth on glucose or succinate at both 21% and 1% O2, growth in the pea rhizosphere, attachment to pea roots and pea nodulation (collaboration). A total of 463 genes were identified to be required for the successful nodulation of pea, and a genetic map was generated identifying the specific stages of symbiosis these genes are required in. There was identification of 55 genes required specifically for growth in the rhizosphere and 101 genes required specifically for root attachment. Analysis of the central carbon metabolism pathways indicated presence of a methylglyoxal pathway in Rlv3841 and suggested that in planta bacteroids might synthesise glycogen for carbon storage via gluconeogenesis of the plant-provided TCA- cycle intermediates. Only one gene, RL2393 (glnB), was found to be uniquely essential for growth under 1% O2 with succinate. RL2393 (glnB) encodes the nitrogen regulatory protein (PII). Mutation of glnB effectively generates a constitutively activated glutamine synthesis response that increases the removal of 2-ketoglutarate from the TCA-cycle to combine with ammonium to form glutamine. This removal of 2-ketoglutarate from the TCA-cycle becomes problematic under low O2, replenishing 2-ketoglutarate requires an additional turn of the TCA-cycle and the generation of NADH, NADPH and FADH2 reductant molecules whose reoxidation is limited by O2-availability. Ammonium assimilation similarly relies on the removal of 2-ketoglutarate. A reoxidation block model was proposed, in which the provision of dicarboxylates under low O2 prevents removal of 2-ketoglutarate from the TCA-cycle and the assimilation of ammonium. This reoxidation block model provides a novel driving force behind ammonium export in symbioses, alongside explaining why legumes always provide TCA-cycle dicarboxylates to fuel N2-fixation in the low O2 environment of the nodules.