Outcomes from elective colorectal cancer surgery during the SARS-CoV-2 pandemic

This study aimed to describe the change in surgical practice and the impact of SARS-CoV-2 on mortality after surgical resection of colorectal cancer during the initial phases of the SARS-CoV-2 pandemic

Investigating the utility of multi-parametric magnetic resonance imaging, biomarkers, active surveillance and robotic surgery in the contemporary diagnosis and management of localised prostate cancer

Current strategies for the diagnosis and management of prostate cancer have been criticised due to four major problems:1) the majority of biopsies are negative and thus potentially avoidable, which is important because they are associated with major anxiety, costs and complications;2) current biopsy techniques miss the cancer in a quarter of cases and where cancer is diagnosed it is mis-classified in one third of cases;3) current diagnostic tools are inaccurate at determining which men require treatment, therefore most men undergo unnecessary over-treatment and a small minority undergo inappropriate under-treatment;4) current open surgical techniques are associated with peri-operative complications, long-term urinary and sexual dysfunction.This thesis aimed to evaluate strategies to improve prostate cancer management in each of these 4 areas.We evaluated multi-parametric MRI prior to biopsy, finding that MRI reduced unnecessary biopsies by half and over-detection of insignificant cancer by one third, was able to localise 97% of significant cancers, missed a grade 2/5 cancer in 1% of cases and missed no grade 3-5 cases.We compared MRI to PCA3 and PHI in men undergoing repeat biopsy, and whilst we were unable to draw definitive conclusions due to small sample size, MRI appeared to have the highest overall utility.We performed the first analysis of medium- to long-term outcomes for surveillance of low risk cancer, finding oncologic safety for both eligible and ineligible low-risk men and no difference between standard versus saturation biopsy or trans-perineal versus trans-rectal biopsy. We did, however, find that trans-perineal biopsy had lower rates of adverse pathology than trans-rectal biopsy, suggesting earlier detection of significant tumours with trans-perineal saturation biopsy.We compared outcomes for robotic versus open prostatectomy across the robotic learning curve of a high-volume, highly-experienced open surgeon. We found outcomes were inferior for robotic surgery for the initial ~100 cases, then became superior after ~300 cases, then plateaued after ~500 cases. Roboticprostatectomy achieved superior sexual, early urinary and oncologic outcomes after a long learning curve, suggesting value over open prostatectomy but optimal community benefits may be achieved by high-volume surgeons and centres.Further imaging and genomic studies are underway

Reperfusion injury and cardiac magnetic resonance imaging in acute myocardial infarction

The process of restoring coronary flow during STEMI is associated with an increase in myocardial damage due to reperfusion injury. Previous studies have suggested that adenosine is effective at reducing reperfusion injury and infarct size. A limitation of these trials has been the lack of accurate endpoints. The ability of cardiac magnetic resonance (CMR) imaging to quantify infarct characteristics provides a potent tool for assessing the effectiveness of adenosine in this setting. The aim of this thesis was to examine whether an intracoronary bolus of adenosine would improve CMR defined myocardial salvage, infarct size and microvascular injury. Additional sub-studies were designed to compare these CMR characteristics with existing methods of assessing microvascular perfusion. Finally the monitoring of platelet activation was undertaken to ensure its exclusion as a confounding variable. Patients undergoing primary percutaneous coronary intervention were randomised to adenosine 4mg or placebo. There was collection of serial electrocardiograms, biomarkers, platelet function and angiographic makers of microvascular perfusion. CMR and echocardiography studies were done early and late, with more frequent CMR scans in a subset to explore the dynamic nature of microvascular obstruction. It was demonstrated that adenosine does not improve myocardial salvage on CMR. The sub-studies confirmed a relationship between adverse prognostic features on CMR and both ST segment resolution and electrocardiography defined ischaemia severity. Assessment of biomarkers levels revealed that microvascular injury does affect the rate of troponin release but alternate variables influence NT pro-BNP levels. The process of infarct healing is a gradual process in most patients; however, in some it is dynamic with transient increases in microvascular injury and tissue oedema. Maladaptive healing processes, such as adverse remodelling, segmental dyskinesis and restrictive filling are more common in those with microvascular injury and less myocardial salvage. Finally an insight into the complexity of platelet function analysis during STEMI is discussed. In conclusion this thesis suggests that a bolus dose of adenosine does not improve myocardial salvage during STEMI. Whilst evaluating this hypothesis a better understanding of microvascular injury on CMR and its relationship with infarct healing and alternate modalities of perfusion was obtained

Improving Cardiovascular Risk Assessment with CT Coronary Angiography and Myocardial CT Perfusion

Accurate assessments of coronary atherosclerosis, calcification and myocardial perfusion are necessary to determine future cardiovascular risk in various clinical settings. CT coronary angiography (CTCA) and myocardial CT perfusion (CTP) are promising techniques for the assessment of these factors. This thesis is comprised of several projects which explore refinements and new techniques aimed at improving diagnosis and risk stratification by CTCA.In order to improve CT methodology, coronary motion in mid-diastole was examined utilizing both high temporal-resolution tissue Doppler imaging and CT. The period of mid-diastole was found to occur relatively later in the cardiac cycle with increasing heart rate. The study demonstrated the importance of heart rate control and precise timing in cardiac imaging.The coronary calcium score allows quantification of cardiovascular risk in asymptomatic patients. A new method of calculating the coronary calcium score from contrast-enhanced CTCA was developed and assessed. Within the validation cohort, the calculated calcium score was highly correlated with the measured calcium score with minimal bias. Coronary calcium may also affect accurate assessment of the degree and extent of coronary disease at CTCA. We examined CTCA findings in patients with a calcium score of >600. Downstream investigations, cardiovascular events, revascularization and mortality were recorded. It was shown that while CT in this setting has reduced specificity, the sensitivity to clinically significant disease appears to be preserved.CTP may be used to assess the functional significance of coronary disease. Utilizing a validated CT and MRI compatible perfusion phantom, the sensitivity of CTP and magnetic resonance perfusion were directly compared under various conditions. Despite the distinct physical basis of each technique, the sensitivity and signal-to-noise ratios were similar, supporting the further development of CTP techniques.Image noise is a major limitation of current CTP methods. A novel four-dimensional median value filter was developed which selects the most stable voxels over both time and surrounding image space. The technique reduced transient image artifact and improved contrast to noise ratios.As a whole, the thesis provides the basis for ongoing improvements in coronary CT and CT myocardial perfusion and supports an increasing role for these techniques in cardiovascular risk assessment

Studies of neurotransmitter release mechanisms in dopamine neurons

Medications that treat diseases such as Parkinson’s disease work by regulating dopamine transmission at synapses. Surprisingly, little is known about the mechanisms regulating dopamine release at synapses. In this thesis, we study mechanisms that regulate vesicle recycling in axons and dendrites of dopamine neurons. Key questions we addressed were: (1) Are vesicles in axons and dendrites associated with the sameregulatory proteins, and thus by implication the same regulatory mechanisms, as in excitatory neurons; (2) Do vesicles undergo recycling, and (3) if so, are they characterised by a distinct pool size and rate of recycling. To study this, we cultured dopamine neurons and used immunocytochemistry to detect vesicular monoaminetransporter 2 (VMAT2) and identify axons, dendrites and synaptic proteins, combined with labelling of recycling vesicles using FM 1-43. Vesicles in axons, but not in dendrites, were associated with presynaptic proteins such as Synaptophysin and Bassoon. We identified two kinds of presynaptic sites in axons: ‘synaptic’ (locatedclose to soma and dendrites’ and ‘orphan’. The recycling vesicle pool size was smaller at orphan sites than at synaptic sites, and the initial rate of vesicle pool release was also lower at orphan sites. Both synaptic and orphan sites exhibited lower rates of vesicle pool release compared to hippocampal synapses, suggesting functionaldifferences in presynaptic physiology between dopamine neurons and hippocampal neurons. In somatodendritic regions, VMAT2 was localised to the endoplasmic reticulum, Golgi, endosome, and large dense-core vesicles, suggesting that thesevesicles might function as a part of the regulated secretory pathway in mediating dopamine release. None of the synaptic vesicle proteins we studied were detected in these regions, although some preliminary evidence of vesicle turnover was detected using FM 1-43 labelling. This thesis provides a detailed analysis of neurotransmitterrelease mechanisms in dopamine neurons. Our data suggests that presynaptic release of dopamine is mediated by mechanisms similar to those observed in excitatory neurons. In somatodendritic regions, our data suggests that VMAT2 is localised toorganelles in secretory pathways, and that distinct mechanisms of release might be present at somatodendritic sites to those present in presynaptic sites. This thesis provides novel methods for analysing vesicle recycling in dopamine neurons, which provides the basis for further studies examining presynaptic function of dopamine neurons in normal brain function, disease, and therapeutic approaches

Notch4 is an inhibitor of canonical Notch signalling.

Notch signal transduction is evolutionarily conserved with essential functions identified in numerous species from C.elegans to H.Sapiens. Notch is critical during embryonic development, in the adult, and in cancer. In mammals there are four Notch receptors; much of our understanding of Notch signalling comes from the study of NOTCH1. During embryogenesis, Notch1 is widely expressed and is required in numerous processes including blood vessel formation and remodelling (angiogenesis). The view of Notch signal transduction, achieved primarily through studying NOTCH1, is that Notch receptors undergo processing and are transported to the cell surface as a heterodimer. Ligand binding triggers a series of proteolytic cleavages leading to the release of the Notch intracellular domain, which translocates to the nucleus to activate transcription. In contrast to NOTCH1, little is known about NOTCH4; Notch4 is expressed in endothelial cells of the circulatory system, trans-activation by ligand is difficult to detect, and a phenotype in mice, reported to be null for Notch4 (Notch4d1 allele), has not been identified. Here, further analysis of NOTCH4 has revealed many features that are in contrast to NOTCH1: (i) unprocessed NOTCH4 was present on the cell surface, (ii) ligand did not trans-activate NOTCH4 signalling, (iii) NOTCH4 inhibited NOTCH1 signal transduction in a dose dependent manner, (iv) NOTCH4 induced the differentiation of myoblasts, and (v) subcellular localisation of NOTCH4 was different to NOTCH1, and coexpression resulted in NOTCH1 adopting the NOTCH4 pattern of localisation. In addition, postnatal retinal angiogenesis was examined in mice carrying the Notch4d1 allele. A delay in the expansion of the retinal vasculature was equally observed in both Notch4d1+/- and Notch4d1-/- mice. This suggested that Notch4d1 was not a null allele. Fittingly, the Notch4d1 allele produced transcripts that encode for much of the extracellular domain of NOTCH4. The expression pattern of this transcript was equivalent to Notch4 in mouse embryos. Like full length NOTCH4, expression of a cDNA based on this transcript also inhibited NOTCH1 signal transduction. These studies reveal for the first time a function for NOTCH4 that is, as an inhibitor of NOTCH1. Accordingly it is postulated that Notch4 will have a crucial function in angiogenesis, since Notch1 is required for angiogenesis and Notch4 is expressed in endothelial cells of the circulatory system

The Insulin-regulated Phosphoproteome

A major challenge of the post-genomics era is to define the connectivity of protein phosphorylation networks. In this thesis, I describe and quantitatively delineate the insulin signalling network in adipocytes by high-resolution mass spectrometry-based proteomics. These data reveal the complexity of intracellular protein phosphorylation. In these studies I identified over 30,000 phosphorylation sites on around 5,000 proteins in this single-cell type, making this amongst the largest phosphoproteomes reported to date. I integrated these large-scale phosphoproteomics data using a machine learning approach to predict physiological substrates of several diverse insulin regulated kinases. This led to the identification of a novel Akt substrate, SIN1, a core component of the mTORC2 complex. I found thatSIN1 is phosphorylated by Akt on threonine 86 (Thr86). I found that phosphorylation of SIN1 Thr86 enhancedmTORC2 activity in response to growth factors, revealing topological insights into the AkUmTOR signalling network. The dynamic phosphoproteome I describe here contains numerous phosphorylation sites on proteins involved in diverse molecular functions and should serve as a useful functional resource for cell biologists

peterjc/thapbi-pict: THAPBI PICT (all versions)

Released on PyPI on 2022-09-14: https://pypi.org/project/thapbi-pict/0.13.0/ The main change is faster distance based classifiers by efficient use of the RapidFuzz library. This requires at least RapidFuzz version 2.4.0 to work. This release drops the human readable plain text sample report which was not useful with large datasets, and now always includes the threshold columns (previously hidden when their values were the same for all samples). Finally importing sequences into a database is now faster, and the NCBI taxonomy used in the default DB has been updated adding taxids to recently added species