VictorJuiz/thesis huggingface dataset:
Non-invasive vital-sign monitoring and data fusion in acute care

Post-operative patients can deteriorate physiologically, leading to adverse events such as cardiac arrest, unexpected intensive care unit (ICU) admission or death. Clinical staff monitor patients by observation of the vital signs. Early warning scores (EWS) are computed from vital-sign values to indicate when a patient requires an escalation in care. The investigations in this thesis assess the use of machine learning and continuous vital-sign monitoring to improve detection of physiological deterioration.
Two post-operative datasets are introduced; vital-sign data collected from 407 patients using manual and continuous methods, and vital-sign data collected from 447 patients using manual methods. A machine learning model is trained on the first manual dataset using vital sign and diurnal vital-sign variability values, and is tested on the second dataset. The model achieves an Area Under the Receiver-Operator Characteristic curve (AUROC) of 0.886 for predicting adverse events within 24 hours, with the National Early Warning Score achieving an AUROC of 0.848. Respiratory rate variability, blood oxygen saturation variability and systolic blood pressure variability are more predictive of adverse events than the corresponding vital signs.
A method comparison study is conducted for manual and continuous vital-sign measurements. There is no evidence of a bias towards normal readings in manual observations, or an arousal effect due to the vital-sign taker. However, differences between manual and continuous data are shown to be frequently large. EWS models should be designed specifically for continuous vital-sign data. Methods for estimating diurnal vital-sign variability from continuous data are described, and are shown to discriminate between physiological stability and deterioration.
A clinical study of video camera-based non-contact monitoring of 15 post-operative patients is described. Heart rate and respiratory rate estimation methods are developed with mean average errors of 0.8 to 2.8 heart-beats/minute and 0.6 to 2.0 breaths/minute during 5 periods of physiological deterioration. Spatial maps of respiratory signal amplitude are shown for a patient with abnormal respiratory physiology.
In summary, EWSs should incorporate features of vital-sign variability, with future work on continuous monitoring implementations. Camera-based methods may provide continuous vital-sign monitoring and spatial physiological maps in post-operative care.

Advisor: Tarassenko, L
Pimentel, M
An investigation of the utility of remote sensing imagery for predicting the distribution and abundance of the tsetse fly (Diptera: Glossinidae)

This thesis investigates the potential contribution of data from the Advance Very High Resolution Radiometer (A VHRR) on-board the National Oceanic and Atmospheric Administrations (NOAA) polar-orbiting meteorological satellites and data from the High Resolution Radiometer (HRR) on-board the Meteosat geostationary meteorological satellites for predicting the distribution and abundance of the tsetse fly (Diptera: Glossinidae) in Africa. The images were processed to produce a range of monthly land surface temperature, atmospheric moisture and rainfall indices for the period 1988 to 1990. The performance of these indices, derived from several different methods, was tested using meteorological records collected during these years at stations across continental Africa and the most accurate used to form a refined dataset for subsequent analysis. The time-series of these land surface temperature, atmospheric moisture and rainfall indices and a range of Spectral Vegetation Indices (SVI) were subject to temporal Fourier analysis to parameterise the seasonal variation in these variables. These data, in combination with elevation information from a digital elevation model (DEM) were used to predict the land-cover of Nigeria determined independently by an aerial survey in 1990. The Normalised Difference Vegetation Index (NDVI) performed best and so was used in combination with the satellite proxy meteorological and D EM data to predict the distribution and abundance of eight tsetse fly species in Cote d'Ivoire and Burkina Faso, West Africa. The results are discussed in relation to the ecology of the different tsetse species. Conclusions are then drawn on the potential of such meteorological satellite data for remote tsetse fly population surveillance and, in the wider context, to the study and control of arthropod vectors of disease.
Targeting the chemokine signalling pathway using tick saliva peptides

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.

Keywords: Inflammation
Ticks
Chemokine
Evasin
Advisor: Bhattacharya, S
Kawamura, A
Noise and prediction in molecular systems

Living systems are inherently stochastic and operate in a noisy environment: in single cells, reactions that involve low numbers of molecules generate stochastic fluctuations that propagate to all dependent processes. Such a noise can be a disturbance, for example by disrupting cell cycle control, or could be advantageous by enabling probabilistic strategies when favourable. Unfortunately, the underlying principles behind these probabilistic phenomena are still not well understood. This also limits our capacity to engineer reliable synthetic biological circuits.
In this thesis we study Chemical Reaction Networks (CRNs) with a stochastic semantics as a probabilistic model for biochemical systems. In the first part of the thesis we consider probabilistic model checking of CRNs, which enables rigorous quantitative analysis of stochastic CRNs against a fragment of Continuous Stochastic Logic (CSL) with reward operators. Classical numerical algorithms for CSL model checking are hindered by the state space explosion problem. Here, we employ a continuous-space approximation of the stochastic model of a CRN in terms of a Gaussian process through the Central Limit Approximation (CLA). We then develop efficient and scalable approximate model checking algorithms on the resulting Gaussian process, where we restrict the probabilistic reachability problem to convex target regions. This allows us to derive an abstraction in terms of a time-inhomogeneous discrete-time Markov chain (DTMC), whose dimension is independent of the number of species on which model checking is performed, thus alleviating the state space explosion problem. We prove the correctness of our approach by demonstrating the convergence in distribution of our algorithms.
In the second part of the thesis we employ mathematical analysis and the previously developed model checking techniques to reverse engineer molecular systems. We investigate how CRNs propagate and reduce the noise. Inspired by the concept of low-pass filters in electronics, we introduce the concept of molecular filter, which is a CRN that can reduce the noise of an input signal while still maintaining certain features of its time evolution. We investigate three different molecular noise filtering mechanisms, study their noise reduction capabilities and limitations, and show that non-linear dynamics, such as complex formation, are necessary for efficientcient noise reduction. We further suggest that the derived molecular filters are widespread in gene expression and regulation and, particularly, that microRNAs can serve as such noise filters.

Advisor: Cardelli, L
Kwiatkowska, M
Investigation of CD27-CD70 co-stimulation in human regulatory T cells for enhanced cellular therapy in transplantation

CD4+FOXP3+ regulatory T cells (Tregs) are essential for maintaining immune homeostasis and are a focus of investigation in the treatment of transplant rejection and autoimmune diseases. Current clinical protocols for Treg cellular therapy production are heavily reliant on in vitro expansion techniques. However, post-expansion Tregs demonstrate heterogeneity with some subpopulations displaying unstable regulatory phenotype and function. The aim of this study was to investigate this phenomenon in depth, in order to improve the efficacy and safety of Treg cellular therapy.
Cell surface CD27 is a useful marker for the identification of Tregs with potent suppressive capacity after expansion. Signalling via the CD27-CD70 co-stimulatory receptor-ligand interaction is important for T cell function but its role in Tregs is not known. In this study, the CD27+ Treg population is characterised in depth. The differential expression of CD27 and CD70 is shown to identify distinct human Treg populations. Stable and potent suppressive function after in vitro expansion is confined principally to cells with a CD27+CD70- phenotype. However, this suppressive function is not reliant on CD27 expression. Prolonged in vitro expansion of Tregs results in stable CD70 expression with concomitant CD27 downregulation in a subset of Tregs, and these CD27-CD70+ Tregs provide pro-inflammatory co-stimulation to conventional T cells via CD70. Genetic deletion (using CRISPR/Cas9) or monoclonal antibody-based blockade of CD70 rescues Tregs from hypofunctionality, highlighting a potential therapeutic intervention.
Taken together, our data identify CD70 as a molecular target via which in vitro-expanded human Tregs exert detrimental pro-inflammatory effects. For clinical application, the availability and ongoing development of antibodies that target the CD27/CD70 pathway provides an opportunity for the therapeutic manipulation of Tregs. Furthermore, relatively straightforward genetic engineering techniques could be exploited to disrupt CD70 expression and improve the efficacy of Treg cellular therapy.

Advisor: Hester, J
Issa, F
Wood, K
Genetic and molecular genetic studies of sporophytic self- incompatibility in senecio squalidus

Angiosperms are the most successful group of land plants in terms of their diversity, abundance and distribution. In order to ensure obligate outcrossing, hermaphrodite flowers have evolved elaborate systems of pollen-pistil recognition, including self-incompatibility (SI). Research on SI systems in many families such as Brassicaceae, Papaveraceae, and Solanaceae has shown that a range of divergent molecular mechanisms is involved in different families even when they share the same genetic basis. Therefore, to better understand the evolution of these processes in angiosperms and the molecular diversity of SI, one UK species, Senecio squalidus (Oxford Ragwort) is taken as an Asteraceae model species to investigate pollen-pistil recognition and SI. This project characterized further the genetics of sporophytic SI (SSI) in S. squalidus, in particular the dominance interactions between S haplotypes. Among its low number of S haplotypes, novel dominance interactions were observed in pollen (male gametophyte). Then to identify the S locus, genomic maps of model plants in the Asteraceae family (sunflower, lettuce, chicory and Tolpis coronopifolia) that are reported to contain molecular markers or quantitative trait loci (QTL) associated with SI or self-fertility, were analyczed to identify any shared region. Pairwise comparisons between these genome sequences were conducted and aslo their synteny pattern with the draft genome sequence for S. squalidus were searched. Some synteny was revealed between lettuce and Tolpis. At the same time, a few linkage groups of S. squalidus are highlighted to contain the S locus potentially. Finally, the expression pattern and polymorphism between S genotypes were investigated for a candidate S gene belonging to the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family. All the available LRR-RLK homolog sequences of S. squalidus were analyzed. Through molecular experiments, they shown to lack the tissue-specific expression pattern and polymorphism characteristics predicted for an S gene. So they are considered not to be the S determinant of S. squalidus. Together, these three lines of researches provide new insights into the genetic and molecular genetic basis of SSI in S. squalidus, and establish a better foundation for further research on SI in S. squalidus and Asteraceae generally.

Advisor: Hiscock, S
Filatov, D
The microRNA FEW RHIZOIDS1 controls rhizoid patterning in the liverwort Marchantia polymorpha

MicroRNAs (miRNAs) control gene expression and consequently play regulatory roles in the development of plants and animals. The FEW RHIZODS 1 (MpFRH1) miRNA of the liverwort Marchantia polymorpha was identified as a negative regulator of rhizoid development. ROOT HAIR DEFECTIVE 6-LIKE (RSL) class I basic Helix-Loop-Helix transcription factors (TFs) positively regulate rhizoid development in bryophytes and root hair development in angiosperms, thus being conserved positive regulators of tip-growing cells with a rooting function in land plants. Here, I demonstrate that MpFRH1 directly targets the MpRSL1 mRNA, the only RSL class I TF in M. polymorpha. While GLABRA2 (AtGL2) negatively regulates RSL class I TF expression in the angiosperm Arabidopsis thaliana, the function of MpFRH1 as a negative regulator of RSL class I TFs in liverworts demonstrates that independent mechanisms evolved to repress RSL class I TF expression in different land plant lineages.
To determine how MpFRH1 represses rhizoid development I generated loss of function (LOF) mutations in the MpFRH1 gene. I showed that rhizoid initials develop larger clusters in Mpfrh1LOF plants than in wildtype. Furthermore, the lack of MpFRH1 activity causes the development of supernumerary mucilage papillae cells and meristematic notches. These findings indicate that MpFRH1 suppresses the development of ectopic epidermal structures such as rhizoid cells and mucilage papillae cells as well as apical cells in meristems.
By combining functional and spatiotemporal expression data of both MpFRH1 and MpRSL1, using promoter reporter constructs, an MpFRH1 activity biosensor and in situ hybridizations, I suggest that MpFRH1 may act as a mobile miRNA required for lateral inhibition during epidermal patterning formation.

Advisor: Dolan, L
Poole, P
Development of lung and muscle factories to deliver therapeutic monoclonal antibodies

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.

Keywords: Antibodies
AAV
Rheumatoid arthritis
Lentiviral vectors
RSV
Advisor: Gill, D
Hyde, S
Genome-scale characterisation of symbiotic fitness determinants of Rhizobium leguminosarum using INSeq

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.

Keywords: Symbiosis
Rhizobium leguminosarum
Insertion Sequencing
Advisor: Poole, P
Imaging molecular processes of neural plasticity

Memories are believed to be encoded by changes in the efficacy of synaptic connections between neurons in the brain. Neurons are highly specialised cells which receive input and send outputs through morphologically and functionally distinct cellular compartments known as axons and dendrites. This polarised morphology requires that neurons asymmetrically distribute cellular components between compartments. To achieve this, neurons regulate the asymmetric distribution of specific mRNA transcripts as a means of spatially and temporally regulating gene expression within functional compartments. In recent years, the development of single-molecule mRNA imaging techniques has revolutionised the study of mRNA biology. Such techniques include single molecule fluorescent in situ hybridisation (smFISH) and MS2 labelling. smFISH involves labelling an mRNA of interest with a set of fluorescently-labelled oligonucleotide probes. While the MS2 system involves the binding of fluorescent coat proteins to RNA hairpin structures engineered into an mRNA of interest, enabling mRNA to be visualised live. In this thesis, both techniques were applied to visualise mRNA in the brain of the fruit fly Drosophila melanogaster. mRNA localised within axonal and dendritic compartments of memory-relevant neurons in the whole Drosophila brain were visualised at single-neuron resolution. Specific mRNAs were found to localise within neuronal compartments in a manner that recapitulated the localisation of the encoded protein product. Moreover, dynamic behaviours were visualised in real-time. These developments enable the molecular correlates of plasticity to be visualised within the well described memory circuitry of the Drosophila mushroom body.

Advisor: Waddell, S