VictorJuiz/thesis huggingface dataset:
Statistical models for single-cell data
Keywords: dimensionality reduction
statistics
cancer
single-cell data

The growing use of single-cell gene expression data (scRNA-seq data) has made it possible to more precisely identify cellular subpopulations with distinct characteristics. This offers insight both into normal cellular function and into diseases such as cancer. However, single-cell data presents new challenges which standard clustering and dimensionality reduction methods are not designed to confront. Rather than being drawn from Gaussians as assumed by most models, single-cell datasets contain an overabundance of zeros. We use several scRNA-seq datasets to investigate how zeros are distributed in real biological data. Based on our findings, we perform a series of simulations to examine how standard clustering and dimensionality reduction methods perform on high-dimensional, zero-inflated data. We show that performance suffers as the fraction of zeros increases and that more complex non-linear models fail to alleviate this problem. Based on this, we then present two new models that account for zeros: one to perform dimensionality reduction, and one to perform clustering. For dimensionality reduction, we present an extension of the factor analysis model which accounts for zero-inflation by adding a single parameter which describes how the probability of technical zeros decreases with the expression level of a gene. We show that our model, ZIFA, outperforms factor analysis and probabilistic principal components analysis on simulated data. For clustering, we present a extension of the Gaussian mixture model which accounts for zero-inflation. We show that our model, ZIMM, outperforms k-means and Gaussian mixture models on simulated data. We also show that both ZIFA and ZIMM better fit real data from several scRNA-seq experiments, and provide fast software implementations of both models. Lastly, we explore applications of our models to several other classes of non-biological datasets.
Investigation of binding preferences and identification of novel binding partners for the SH3 domains of the multifunctional adaptor protein CD2AP
Keywords: isothermal titration calorimetry
SH3 domain
cell culture
podocyte
peptide array
protein crystallography
CD2AP
ARAP1
RIN3

CD2AP is a member of the CD2AP/CIN85 family of adaptors and involved in several cellular processes, such as kidney podocyte development, actin mediated membrane trafficking and T cell activation. It contains three SH3 domains whose binding properties and interaction partners remain largely unexplored.
The CD2AP SH3 interaction with the novel partner Rab5-activating GEF RIN3 was studied extensively by isothermal titration calorimetry (ITC), peptide scanning arrays, mutagenesis and X-ray crystallography. Mapping of the interaction regions showed that human RIN3 contains two binding sites for the CD2AP SH3 domains. From these studies, the CD2AP SH3 recognition motif P-x-P/A-x-x-R emerged. Two crystal structures (1.65 Å and 1.2 Å) of the SH3 1 and SH3-2 domains in complex with RIN3 epitopes 1 and 2 respectively revealed that these residues serve as anchoring points. With the aid of bioinformatics tools, this motif was used to conduct a peptide array-based screen for additional signalling partner candidates. One of the hits was the Arf-GAP ARAP1. ITC data indicate that the three SH3 domains differentially recognise three ARAP1 epitopes, with the first ARAP1 epitope binding to SH3-2 in the nanomolar range. A crystal structure (1.6 Å) of the SH3-2 domain in complex with the first ARAP1 epitope implicates two additional anchoring residues that extend beyond the PPII helical region of the canonical motif. The CD2AP/ARAP1 interaction was confirmed in podocytes and cancer cells at the endogenous protein level. Even though RIN3 and ARAP1 are involved in membrane trafficking, a direct link to CD2AP had not been reported before. Other candidates from the peptide array analyses were also investigated by ITC.
In conclusion, this study led to the elucidation of the CD2AP SH3-1 and SH3-2 domain binding signatures and the identification of putative novel binding partners for all three SH3 domains. Lastly, insight was gained into the binding preferences of CD2AP SH3-3.
Development of clinical biomarkers of DNA double strand breaks for cancer care
Keywords: functional imaging
DNA damage
biomarker

Many anticancer therapies, including radiotherapy, act by damaging the deoxyribosenucleic acid (DNA) that is fundamental to cell function and proliferation. H2AX is a histone protein associated with DNA that is phosphorylated to produce γH2AX in response to DNA double strand breaks (DSBs), the most lethal lesions caused in cancer cells. This thesis examines the translation of γH2AX detection assays to clinical situations in order to provide biomarkers of response that might help to guide the treatment of cancer patients.
γH2AX immunohistochemistry was developed in preclinical xenograft models, and validated over a range of radiation doses and over time after irradiation. The method was prepared for translation to archived clinical biopsy and surgical specimens.
The DSB Biomarkers Pilot Study was established in order to develop a method for γH2AX quantification in direct tumour cell specimens obtained using the clinical technique of fine needle aspiration (FNA) cytology. Eleven patients undergoing anticancer therapy were recruited to the study, and the method evaluated. The coefficient of variation of the measure was 49%.
Non-invasive imaging for γH2AX would allow DNA damage to be quantified in all tumour sites, and on multiple occasions. An antibody-based nuclear medicine imaging agent was re-engineered using Fab fragments of the antibody. The novel agent demonstrated improved pharmacokinetics when compared to the whole antibody agent, but reduced target specificity.
The findings further develop the potential to exploit DNA damage biomarker measurements in clinical oncology.
Autophagy in hematopoiesis and acute myeloid leukemia
Keywords: Metabolism
Autophagy
Acute Myeloid Leukemia (AML)
Hematopoietic Stem Cell
Glycolysis
Cancer
Hematopoiesis
Myeloid cells

Acute myeloid leukemia (AML) develops following oncogenic alterations to hematopoietic stem (HSC) and progenitor cells (HSPCs) in the bone marrow, resulting in dysregulated proliferation of immature myeloid progenitors that interferes with normal hematopoiesis. Understanding the mechanisms of HSPC protection against damage and excessive division, and how these pathways are altered during leukemic progression, is vital for establishing effective therapies. Here, we show that autophagy, a lysosomal degradation pathway, is increased in HSPCs using a novel imaging flow cytometry autophagy assay. Loss of hematopoietic autophagy following deletion of key gene Atg5 resulted in increased HSC proliferation, leading to HSC exhaustion and bone marrow failure. Although erythrocyte and lymphocyte populations were negatively impacted by autophagy loss, myeloid cells showing immature characteristics were expanded. Deletion of Atg5 in an AML model resulted in increased proliferation under metabolic stress, dependent on the glycolytic pathway, and aberrant upstream mTOR signaling. Moreover, modulation of Atg5 altered leukemic response to culture with stromal cells. Finally, primary AML cells displayed multiple markers of decreased autophagy. These data suggest a role for autophagy in preserving HSC function, partially through suppression of HSPC proliferation, and indicate that decreased autophagy may benefit AML cells. We postulate that modulation of autophagy could help maintain stem cell function, for example during transplantation, and aid AML therapy in a setting-specific manner.
Selective routes to substituted dihydropyridones
Keywords: dihydropyridones
reduction
asymmetric synthesis
pyridines

Introduction: The introduction provides a survey of the natural product and pharmaceutical targets accessible from dihydropyridines and dihydropyridones as well as an overview of previous work carried out towards the synthesis of these valuable intermediates. The mechanism, scope and limitations of the various approaches are covered, along with the goals of this project.
Results and Discussion: A Regioselective Route to Dihydropyridones. The regioselective addition of nucleophiles to a range of disubstituted pyridinium salts has been achieved, with selectivity determined by hard/soft factors. Certain nucleophiles can be added with complete regioselectivity to either C-2 or C-6 of these salts, depending on the conditions employed. Addition at C-2 allows the generation of a quaternary centre in high yield. The conditions discovered can be applied to pyridinium salts with different substitution patterns and an effective procedure has been developed for the removal of the nitrogen protecting group post reduction.
The Preparation of Enantiopure Dihydropyridones.After unsuccessful attempts to find a reagent-controlled asymmetric synthesis of dihydropyridones, a highly diastereoselective and non-chiral auxiliary based substrate-controlled procedure has been developed. By prompting an intramolecular hydride migration from a secondary silyl ether onto the pyridinium core, the corresponding dihydropyridones are available in high yield, with the diastereoselectivity being controlled by the minimization of 1,3-allylic strain between the N-allyl group and the hydride-bearing side chain. Thus, an enantiopure pyridyl alcohol may be converted to the corresponding dihydropyridone without loss of enantiomeric purity. Furthermore, the dihydropyridones can be easily converted to complex bicyclic systems via a ring closing metathesis reaction.
Experimental: Full experimental procedures and spectroscopic characterization of compounds are provided.
Nonstandard inner products and preconditioned iterative methods
Keywords: preconditioning
nonstandard inner products
linear systems
Krylov subspace methods

By considering Krylov subspace methods in nonstandard inner products, we develop in this thesis new methods for solving large sparse linear systems and examine the effectiveness of existing preconditioners. We focus on saddle point systems and systems with a nonsymmetric, diagonalizable coefficient matrix.
For symmetric saddle point systems, we present a preconditioner that renders the preconditioned saddle point matrix nonsymmetric but self-adjoint with respect to an inner product and for which scaling is not required to apply a short-term recurrence method. The robustness and effectiveness of this preconditioner, when applied to a number of test problems, is demonstrated. We additionally utilize combination preconditioning (Stoll and Wathen. SIAM J. Matrix Anal. Appl. 2008; 30:582-608) to develop three new combination preconditioners. One of these is formed from two preconditioners for which only a MINRES-type method can be applied, and yet a conjugate-gradient type method can be applied to the combination preconditioned system. Numerical experiments show that application of these preconditioners can result in faster convergence.
When the coefficient matrix is diagonalizable, but potentially nonsymmetric, we present conditions under which the pseudospectra of a preconditioner and coefficient matrix are identical and characterize the pseudospectra when this condition is not exactly fulfilled. We show that when the preconditioner and coefficient matrix are self-adjoint with respect to nearby symmetric bilinear forms the convergence of a particular minimum residual method is bounded by a term that depends on the spectrum of the preconditioned coefficient matrix and a constant that is small when the symmetric bilinear forms are close. An iteration-dependent bound for GMRES in the Euclidean inner product is presented that shows precisely why a standard bound can be pessimistic. We observe that for certain problems known, effective preconditioners are either self-adjoint with respect to the same symmetric bilinear form as the coefficient matrix or one that is nearby.
The evaluation and expansion of methodologies relating to the reporting and analyses of intermediate test results: improving the clinical utility of diagnostic research
Keywords: diagnosis; inconclusive; accuracy

Background and objectives:
It has been argued that the binary framework frequently adopted to analyse test accuracy does not represent the clinical reality of diagnostic practice, and the recognition of an intermediate category of test result could make the utility of diagnostic tests more transparent. The objective of this thesis is to explore the value of moving away from the binary framework when evaluating and interpreting quantitative diagnostic tests.
Methods:
This thesis starts with an overview of the key arguments against dichotomising quantitative test results and a summary of some of the alternative methods proposed. Four distinct studies are then reported: 1) a systematic review of the methods currently used to evaluate the accuracy of quantitative cancer biomarkers, 2) a survey of GPs exploring preferences for threshold guidance 3) an evaluation of existing methods for identifying an intermediate range of test values, and 4) an assessment of the feasibility of applying these methods to the results of a meta-analysis.
Results:
The binary framework remains the most common method for evaluating the accuracy of quantitative tests, despite the survey of GPs indicating that a single threshold interpretation is less helpful than identifying rule-in and rule-out thresholds. Existing methods for identifying an intermediate range of values require some adaptation to incorporate the cost trade-offs relating to different outcomes but, given complete reporting at the primary research, could be applied to the results of a meta-analysis.
Conclusion:
The 2 x 2 diagnostic framework frequently fails to capture many of the realities and complexities of clinical research questions. Standardised methods that facilitate complete reporting of test accuracy in primary diagnostic accuracy studies are required to allow for greater flexibility when producing threshold recommendations further down the evidence pathway.
Challenging the boundaries of criminal justice and social policy: responses to priority offenders
Keywords: persistent offenders
criminal justice policy
criminalisation of social policy
rehabilitation
drugs and crime
prolific offenders
information sharing
multi-agency working
policing
intelligence
probation

This thesis examines the interaction of criminal justice policy and social policy within the Prolific and Priority Offenders Scheme (PPOS), a government initiative which aims to reduce offending by persistent offenders. The research on which this thesis is based takes an interpretative approach to social inquiry and employs a qualitative methodology. It examines the operation of four PPO Schemes in the Thames Valley through semi-structured interviews with 22 practitioners and 16 offenders, and participant observation of over 45 multi-agency meetings. The interaction between crime and social policy is explored through examination of three aspects of the PPOS: the coercion of offenders within the Schemes; the working practices and roles of the police and probation officers seconded to the Schemes; and the way in which information and intelligence is used and generated within the Schemes. The central argument of this thesis is that the widely-accepted idea that social policy is being ‘criminalised’ provides an inadequate account of the relationship between criminal justice and social policy in the PPOS. Rather, this Scheme evidences a merger of criminal justice and social welfare agendas, which includes elements of the ‘socialisation’ of crime policy in addition to elements of ‘criminalisation’ of social policy. Whilst the ultimate aim of the PPOS is to reduce crime, and whilst social welfare services such as health, housing and benefits are provided in pursuance of this aim, the ways in which these services are provided accords with the ethos and values of social policy. The idea of a merger of criminal justice and social policy has relevance beyond the PPOS, providing a framework for analysis of other contemporary criminal justice policies, and contributing to broader debates in criminology which have for so long been dominated by the ‘criminalisation’ thesis.
Justice, governance and climate change: designing fair and effective climate institutions
Keywords: Climate Change
Procedural Justice
Governance
Democracy

Multilateral efforts are yet to produce meaningful action on climate change. Part of the problem with these approaches is a perceived lack of fairness among state actors. Whilst academic discussion has traditionally focused on the issue of distributive fairness, very little has been said about procedural fairness in this respect. To this end, this thesis analyses principles of procedural justice in order to develop practical policy measures for institutional design. It does so in four steps. First, it argues that procedural justice is important for reaching a mutually acceptable agreement when there is reasonable disagreement about the substantive ends that collective action should achieve. Second, it develops several principles of procedural justice that should govern the decision-making processes of climate institutions. This includes principles that govern who should participate in decisions, how these decisions should take place, and how transparent they should be. Third, it considers the relative value that procedural justice should be given against other important ends. In doing so, it proposes that procedural justice is a fundamental feature of fair and effective climate institutions. Finally, it considers what this means for climate institutions in practice by determining a set of pragmatic policy prescriptions that can guide the design of climate governance institutions.
Underpowered: electricity policy and the state in India, 1991-2014
Keywords: India
economic reform
policy
energy
electricity
government

How has the Indian state changed with economic liberalization? While many scholars have explored the altered party politics and class basis of the liberalization-era state, few have studied its transforming internal organizational forms and functioning. This thesis aims to provide an empirically grounded answer to this question. To do this it uses the lens of electricity: the sector lies at the heart of contemporary capital accumulation, state power, and distributive politics, and has witnessed almost a quarter-century of institutional reforms since 1991.
In the sector, new or reworked organizational forms—such as imported regulatory agencies, corporatized state-owned enterprises, and public-private partnerships—have been grafted onto the older statist system in a process of institutional layering. Favouring state-business collaboration and prioritizing rapid economic growth, this mode of state operation is distinct both from a liberal, market-oriented state and from India’s older state-led mode. It combines state intervention and selective adoption of parts of the Washington Consensus template to produce a reinvented mode of power governance that I term state capitalism 2.0.
India’s new state-market hybrid is not a functional alternative to the older models, however. The layered process through which it has emerged means that it is distinctively dysfunctional. Organizations have emerged in an ad hoc fashion, each shaped and reshaped by multiple collective interests, while existing organizations are rarely destroyed. The resulting layered amalgam institutionalizes contradictory state strategies, co-optation by competing interest groups, and a dualistic system of services and subsidies. Consequently the sector’s performance remains poor.
As a result, developments in the Indian power sector suggest that the state's 'pro-business' transition has been painful and incomplete. At least in this sector, the Indian state remains simultaneously more indispensable, more ambivalently pro-business, and more chaotic than much theory might suggest.
Correction of miscarriages of justice in New Zealand and England
Keywords: Royal prerogative of mercy
New Zealand
CCRC
miscarriages of justice
wrongful convictions
criminal cases review commission
England
criminal procedure
criminal appeals

This thesis sets out to provide a deep analysis of the mechanisms for review of convictions in New Zealand and England after initial appeal rights are exhausted, and to identify the key areas of similarity and difference between these systems, the reasons for these differences, and their implications.
The appeal systems in each jurisdiction are briefly examined, alongside the pressures and restrictions on their functioning. Particular attention is paid to the options for appeal out of time, and for revisiting appeal decisions if new material comes to light.
The main discussion is of the specialist procedures for review of suspect convictions in each jurisdiction: the Royal Prerogative of Mercy process carried out by the New Zealand Ministry of Justice and the work of the English Criminal Cases Review Commission. This discussion presents the results of empirical research carried out by the author utilising the files of each of these bodies. It investigates the legal context in which each body functions, and provides an account of how each body functions in practice, by examining the circumstances in which each body will contemplate referring a matter back to an appeal court and the means by which a determination is made as to whether to do so in an individual case. In addition it examines the various factors (legal and non-legal) which impact on their work.
Finally, the key features of the two systems are contrasted, with a discussion of the areas of similarity and difference, as well as the possible implications of these, in particular for reform of the New Zealand processes.