VictorJuiz/thesis huggingface dataset:
A perinatal monitoring system for low-resource settings
Keywords: Low-cost fetal monitoring
Fetal risk assessment in low-resource settings
Global Health
Automated IUGR risk detection
Decision support for traditional birth attendants
mHealth

The reduction of maternal and child morality has been central to international development efforts over the past twenty years, spurred on by global initiatives such as the Millennium Development Goals. Whereas a significant decrease in mortality rates has been achieved in mothers and the under-five, the fetal and early neonatal period has received less attention resulting in slower progress. Resource-poor settings suffer from the highest stillbirth, maternal and early neonatal death rates, with 99% occurring in low- and middle income countries.
Causes of fetal and maternal compromise can be manifold, both infrastructural and pathophysiological. Common problems remain a scarcity of skilled healthcare personnel leading to low health risk detection, referral and ultimately intervention rates. In the absence of sophisticated equipment fetal compromise may go unnoticed, such as fetal growth restriction, one of the primary causes of poor health outcome.
To work towards improved fetal and maternal risk assessment enabling timely and appropriate referral, this thesis proposes a low-cost mHealth monitoring platform for use in low-resource settings. The analysis of the fetal cardiac activity, prerequisite in hospitals in developed nations, may provide important insights on fetal stress levels and more specifically growth retardation. The fetal cardiac signal is accessible and obtained at low-cost with the help of a Doppler transducer. This thesis in healthcare innovation investigates the feasibility of introducing such technology in communities not familiar with their application, proposes a novel signal quality algorithm suitable for implementation on the phone, develops a classifier based on fetal heart rate variability to distinguish growth restricted from normal babies, and introduces the design of the mHealth platform, results of a pilot deployment in rural Guatemala and the design and implementation of a full randomised control trial.
Recursive construction of continuum random trees and some contributions to the theory of tree-valued stochastic processes
Keywords: regenerative interval partition
line-breaking construction
string of beads
Brownian CRT
marked metric space
recursive distribution equation
tree-valued Markov process
Chinese restaurant process
stable tree
Poisson-Dirichlet
branch merging
continuum random tree
Ford CRT

We introduce a general recursive method to construct continuum random trees (CRTs) from i.i.d. copies of a string of beads, that is, any random interval equipped with a random discrete measure. We prove the existence of these CRTs as a new application of the fixpoint method formalised in high generality by Aldous and Bandyopadhyay. We further apply this recursive construction to "embed" Duquesne and Le Gall's stable tree into a binary compact CRT in a way that solves an open problem posed by Goldschmidt and Haas. Some of these developments are carried out in a space of ∞-marked metric spaces generalising Miermont’s notion of a k-marked metric space.
Furthermore, we introduce a family of branch merging operations on continuum trees and show that Ford CRTs are distributionally invariant. This operation is new even in the special case of the Brownian CRT, which we explore in more detail. The operations are based on spinal decompositions and a regenerativity preserving merging procedure of (α, θ)-strings of beads, that is, regenerative strings of beads arising in the limit of ordered (α, θ)-Chinese restaurant processes as introduced by Pitman and Winkel. Indeed, we iterate the branch merging operation recursively and give a new approach to the leaf embedding problem on Ford CRTs related to (α, 2−α)-tree growth processes.
Algorithmic verification problems in automata-theoretic settings
Keywords: temporal logic
parametric timed automata
automata theory
formal verification
bounded model checking

Problems in formal verification are often stated in terms of finite automata and extensions thereof. In this thesis we investigate several such algorithmic problems.
In the first part of the thesis we develop a theory of completeness thresholds in Bounded Model Checking. A completeness threshold for a given model M and a specification φ is a bound k such that, if no counterexample to φ of length k or less can be found in M, then M in fact satisfies φ. We settle a problem of Kroening et al. [KOS+11] in the affirmative, by showing that the linearity problem for both regular and ω-regular specifications (provided as finite automata and Buchi automata respectively) is PSPACE-complete. Moreover, we establish the following dichotomies: for regular specifications, completeness thresholds are either linear or exponential, whereas for ω-regular specifications, completeness thresholds are either linear or at least quadratic in the recurrence diameter of the model under consideration.
Given a formula in a temporal logic such as LTL or MTL, a fundamental problem underpinning automata-based model checking is the complexity of evaluating the formula on a given finite word. For LTL, the complexity of this task was recently shown to be in NC [KF09]. In the second part of the thesis we present an NC algorithm for MTL, a quantitative (or metric) extension of LTL, and give an AC1 algorithm for UTL, the unary fragment of LTL. We then establish a connection between LTL path checking and planar circuits which, among others, implies that the complexity of LTL path checking depends on the Boolean connectives allowed: adding Boolean exclusive or yields a temporal logic with P-complete path-checking problem.
In the third part of the thesis we study the decidability of the reachability problem for parametric timed automata. The problem was introduced over 20 years ago by Alur, Henzinger, and Vardi [AHV93]. It is known that for three or more parametric clocks the problem is undecidable. We translate the problem to reachability questions in certain extensions of parametric one-counter machines. By further reducing to satisfiability in Presburger arithmetic with divisibility, we obtain decidability results for several classes of parametric one-counter machines. As a corollary, we show that, in the case of a single parametric clock (with arbitrarily many nonparametric clocks) the reachability problem is NEXP-complete, improving the nonelementary decision procedure of Alur et al.. The case of two parametric clocks is open. Here, we show that the reachability is decidable in this case of automata with a single parameter.
A multi-paradigm modelling framework for simulating biocomplexity
Keywords: bioreactors
dynamic assimilation
computational fluid dynamics
Agent-based modelling
design
biocomplexity
dynamic reciprocity
osteocytes
stem cells
osteblasts
osteogenesis,

The following thesis presents a computational framework that can capture inherently non-linear and emergent biocomplex phenomena. The main motivation behind the investigations undertaken was the absence of a suitable platform that can simulate, both the continuous features as well as the discrete, interaction-based dynamics of a given biological system, or in short, dynamic reciprocity. In order to determine the most powerful approach to achieve this, the efficacy of two modelling paradigms, transport phenomena as well as agent-based, was evaluated and eventually combined. Computational Fluid Dynamics (CFD) was utilised to investigate optimal boundary conditions, in terms of meeting cellular glucose consumption requirements and exposure to physiologically relevant shear fields, that would support mesenchymal stem cell growth in a 3-dimensional culture maintained in a commercially available bioreactor. In addition to validating the default bioreactor configuration and operational parameter ranges as suitable towards sustaining stem cell growth, the investigation underscored the effectiveness of CFD as a design tool. However, due to the homogeneity assumption, an untenable assumption for most biological systems, CFD often encounters difficulties in simulating the interaction-reliant evolution of cellular systems. Therefore, the efficacy of the agent-based approach was evaluated by simulating a morphogenetic event: development of in vitro osteogenic nodule. The novel model replicated most aspects observed in vitro, which included: spatial arrangement of relevant players inside the nodule, interaction-based development of the osteogenic nodules, and the dependence of nodule growth on its size. The model was subsequently applied to interrogate the various competing hypotheses on this process and identify the one that best captures transformation of osteoblasts into osteocytes, a subject of great conjecture. The results from this investigation annulled one of the competing hypotheses, which purported the slow-down in the rate of matrix deposition by certain osteoblasts, and also suggested the acquisition of polarity to be a non-random event. The agent-based model, however, due to being inherently computationally expensive, cannot be recommended to model bulk phenomena. Therefore, the two approaches were integrated to create a modelling platform that was utilised to capture dynamic reciprocity in a bioreactor. As a part of this investigation, an amended definition of dynamic reciprocity and its computational analogue, dynamic assimilation, were proposed. The multi-paradigm platform was validated by conducting melanoma chemotaxis under foetal bovine serum gradient. Due to its CFD and agent-based modalities, the platform can be employed as both a design optimisation as well as hypothesis testing tool.
Social policy, protest participation and violent crime in Latin America
Keywords: Latin America
violence
social protest

This thesis consists of four self-contained articles which focus on different aspects of citizens' demand for and governments' supply of social policy in Latin American democracies. The underlying questions that link the four papers are a) do social and economic grievances affect citizens' propensity to protest? and, b) do democratic governments in the region use social policy as an instrument to mitigate social discontent and violent crime? In the first two papers, I use public opinion data in order to examine the determinants of citizens' participation in protest with a special focus on dissatisfaction with the quality of public services, demands for inequality-reduction policies and economic deprivation. The results show that among other factors, protest participation is motivated by citizens' discontent over the quality of basic social services, support for redistributive policies, and relative economic deprivation. The third and fourth papers analyze the "supply side" of social spending in the region focusing on collective protest and violent crime, respectively. The third article argues that under democracy, organized labor is in a better position relative to other groups in society to obtain social policy concessions as a consequence of their collective action efforts. The results show that whereas social security spending increases as a consequence of labor militancy, cutbacks in human capital spending are less likely as peaceful large-scale demonstrations increase. The fourth paper argues that political leaders use education spending as an instrument to mitigate violent crime. It also argues that the effect of violent crime on education spending is larger when leftist governments are in power. The empirical analysis provides support for these arguments.
Democracy and the disengaged: a multi-dimensional study of voter mobilization in Alabama
Keywords: Health politics
Voter turnout
Political participation
Policy design

This thesis investigates if and how poor, mostly minority citizens can be mobilized by a campaign whose principal policy objective would materially enhance their lives by including them in a major public program. The question is put to the test through a multi-dimensional study of voter mobilization in Alabama during the 2014 election for Governor. At stake in the election was whether Alabama would expand Medicaid through the Affordable Care Act in Alabama, an issue emblematic of "submergedness" (Mettler, 2011). In order to understand the extent to which the policy was submerged—measured by knowledge and awareness of the policy, along with its key provisions—I distributed a survey to 868 Alabamians weeks before the election. The survey used the experimental design of conjoint analysis to test which aspects of the policy were most persuasive among the target population. Additionally, I performed a randomized field experiment across the four major metropolitan areas of Alabama, micro-targeting 6,021 registered voters living in the "Coverage Gap," citizens who could gain health insurance if Medicaid were expanded. The campaign yielded negligible effects on voter turnout among subjects in the Coverage Gap, even though the interventions shifted voter knowledge, “surfacing” the policy. In addition to the survey and field experiments, this research benefits from qualitative insights gathered in 22 semi-structured interviews conducted among poor Alabamians, many of whom were uninsured. From these interviews, it became clear that the political disengagement of the poor is deeply entrenched, prohibitive of policy-based mobilization. Disengagement is driven by a complex mix of barriers to registration and perceptions of political inefficacy based on interpretations of extant policy designs. These results have important implications for our understanding of the limitations of policy-based mobilization, suggesting that more attention must be paid to how current policies shape predispositions for mobilization.
Community structure in temporal multilayer networks, and its application to financial correlation networks
Keywords: Multilayer Networks
Clustering
Temporal Networks
Network Science

Many real-world applications in the social, biological, and physical sciences involve large systems of entities that interact together in some way. The number of components in these systems can be extremely large, so some simplification is typically needed for tractable analysis. A common representation of interacting entities is a network. In its simplest form, a network consists of a set of nodes that represent entities and a set of edges between pairs of nodes that represent interactions between those entities. In this thesis, we investigate clustering techniques for time-dependent networks.
An important mesoscale feature in networks is communities. Most community-detection methods are designed for time-independent networks. A recent framework for representing temporal networks is multilayer networks. In this thesis, we focus primarily on community detection in temporal networks represented as multilayer networks. We investigate three main topics: a community-detection method known as multilayer modularity maximization, the development of a benchmark for community detection in temporal networks, and the application of multilayer modularity maximization to temporal financial asset-correlation networks. We first investigate theoretical and computational issues in multilayer modularity maximization. We introduce a diagnostic to measure persistence of community structure in a multilayer network partition and we show how communities one obtains with multilayer modularity maximization reflect a trade-off between time-independent community structure within layers and temporal persistence between layers. We discuss computational issues that can arise when solving this method in practice and we suggest ways to mitigate them. We then propose a benchmark for community detection in temporal networks and carry out various numerical experiments to compare the performance of different methods and computational heuristics on our benchmark. We end with an application of multilayer modularity maximization to temporal financial correlation networks.
Verifying information flow and metaprogramming in dynamically typed languages
Keywords: metaprogramming
dynamically typed languages
static analysis
information flow

The ubiquity of JavaScript in Web applications means that its analysis has become an important security problem. This thesis develops techniques for analysing information flow in JavaScript programs and verifying the absence of undesirable flows (for example, of sensitive data to untrusted third parties).
JavaScript presents a unique combination of challenges not usually addressed by information flow analyses: its semantics are quaint and poorly specified, making formal reasoning largely infeasible; it is dynamically typed, which precludes the use of the most advanced existing analyses; and its eval construct, which executes a string as program code, allows arbitrary behaviour to result from data manipulated within the program.
The thesis focuses on the last of these problems. It considers an idealised subset of JavaScript and augments it with staged metaprogramming, a formalism that captures the construction, execution and manipulation of code templates. The resulting language is called SLamJS. An information flow analysis for SLamJS is developed and its correctness is proved. This builds on the existing analysis 0CFA, but adds support for metaprogramming (paying particular attention to the difficult behaviour of variable capture) and information flow.
In order to demonstrate the applicability of this analysis to JavaScript, where eval-using programs operate on code strings formed through concatenation, rather than splicing of templates, an algorithm to transform an eval-using program into one that uses staged metaprogramming is also developed. The transformation repurposes an existing lexer/parser (for example, one produced by the popular tools lex and yacc) to parse fragments of program code out-of-order.
The transformed program is then a suitable target for the analysis. This multi-step approach is vital to allow subdivision of the complex overall problem into smaller, more manageable parts.
Effect of shear patterns and EPS on fouling in microfiltration
Keywords: membrane
extracellular polysaccharides
fouling
transmission
microfiltration
shear

Concentration polarisation and fouling reduce performance as well as increase costs. In order to mitigate these effects, understanding the cause and effects of these phenomena is crucial. It has been hypothesized, and to a certain extent shown, that amelioration of fouling can be achieved through the use of time varying shear for example use of air-sparging or sharp changes in crossflow velocity. Nevertheless the effect of shear on membrane fouling, in particular its effect on the foulant deposition and the transmission of small molecules in microfiltration, is not well understood.
The goal of this project was to achieve an understanding of various foulant behaviour. The work was divided into two parts. Firstly, the observations of fouling by freshwater algae, Chlorella Sorokiniana, were carried out at Nanyang Technological University, Singapore. Observations using macroscopic parameters were examined with an optical non-invasive observation technique called Direct Observation Through Membrane (DOTM). The result yielded a novel relationship between operating flux, crossflow velocity and transmission of extracellular polysaccharide. Interestingly shear was shown to have positive as well as negative effects on fouling of microfiltration membrane. The analysis of permeate has clearly shown that a maximisation of shear rate was not ideal.
The second part was concerned with observations of the effect of shear patterns on membrane fouling using newly fabricated special membrane filtration cell, Direct Shear Stress Test Cell (DSSTC), designed to fit an Anton Paar rheometer and operate at constant flux. Unlike the constant-shear-filtration cells, one could impose a very wide variety of shear regimes including intermittent sharp changes of direction and sinusoidal oscillations in the DSSTC. The effect of shear patterns on transmission and fouling of a model polysaccharide (Dextran Blue) through microfiltration membranes was carried out at various conditions. Again, the results showed that the maximisation of shear rate was not ideal. The effect of shear patterns and EPS on fouling by yeast suspension was also studied using the DSSTC. The benefit of oscillatory shear is foulant dependent. For example, square wave oscillatory shear led to lower relative fouling for yeast EPS, but it resulted in higher relative fouling for unwashed yeast.
Organomediated approaches to 18F-radiochemistry for PET
Keywords: radiochemistry
organomediated
fluorination
18F
asymmetric

This thesis has focussed on 18F-fluorination reactions activated by an organomediator, with the aim of broadening the scope of metal-free reactions in 18F-radiosynthesis.
Chapter 1 provides an introduction to positron emission tomography (PET) and 18Fradiochemistry, including radioisotope production and modes of activation in 18Fradiosynthesis.
In Chapter 2, the concept of chirality and its relevance in the context of radiotracer design is introduced. The previously disconnected fields of organomediated asymmetric fluorination and 18F-radiosynthesis are merged for the first time via investigation of three distinct activation modes: chiral non-racemic secondary amine-mediated asymmetric α-18F-fluorination of aldehydes employing [18F]N-fluorobenzenesulfonimide; use of a phase transfer reagent for asymmetric 18F-fluorocyclisation and application of a chiral nonracemic 18F-fluorinating agent, chiral [18F]Selectfluor bis-triflate. Application of the first of these approaches to the radiosynthesis of the PET tracer (2S,4S)-4-[18F]fluoroglutamic acid with high d.r. is described.
Chapter 3 explores the use of hypervalent iodine reagents to mediate the oxidative fluorination of N-arylsulfonamides with nucleophilic fluoride via an umpolung approach. Preliminary studies on translation to radiosynthesis with [18F]fluoride are also disclosed.
In Chapter 4, experimental data is provided for all compounds, as well as analytical and chiral HPLC traces for 18F-reactions.