VictorJuiz/thesis huggingface dataset:
Microfluidic Point-of-care Diagnostics for Global Health

In this thesis, microfluidic diagnostic technologies are developed for sample collection, sample processing, and detection and analysis for disease diagnosis, from initial conception to field validation in Vietnam. The most impactful contributions of this thesis consist of a total analysis system called the lab-in-a-pen for hepatitis B screening (Chapter 3), and strategies for advancing the diagnostic capabilities of paper-based assays (Chapters 4 and 5). The lab-in-a-pen offers comparable diagnostic performance as conventional testing in an easy-to-use format, with potential to transform the current rapid test market. An electrokinetic phenomenon, called ion concentration polarization (ICP), is leveraged to improve the detection sensitivity of paper-based assays, up to 40-fold improvement in signal intensity of a fluorescent tracer and 5-fold improvement in the detection limit for a model protein. The ICP approach is further developed for direct DNA analysis in paper, to detect hepatitis B virus DNA without prior viral load amplification and to clinically assess human sperm DNA integrity for informing male fertility potential. Clinical outcome using the ICP approach was 100% in agreement with that of the conventional method. Chapters 6 and 7 summarize my earlier work on developing modular units for sample collection and processing, as envisioned by Grand Challenges Canada. These units provide capabilities to transport and process milliliter sample volumes, enabling downstream multiplexed analysis. Microfluidic diagnostic technologies show promise for enabling low cost and scalable point-of-care diagnostics.

Keywords: diagnostics
global health
microfluidic
paper-based
point-of-care
Advisor: Sinton, David
Simple Distributed Programming for Scalable Software-defined Networks

Software Defined Networking (SDN) aims at simplifying the process of network programming, by decoupling the control and data planes. This is often exemplified by implementing a complicated control logic as a simple control application deployed on a centralized controller. In practice, for scalability and resilience, such simple control applications are implemented as complex distributed applications, that demand significant efforts to develop, measure, and optimize. Such complexities obviate the benefits of SDN. In this thesis, we present two distributed control platforms, Kandoo and Beehive, that are straightforward to program. Kandoo is a two-layer control plane: (i) the bottom layer is a colony of controllers with only local state, and (ii) the top layer is a logically centralized controller that maintains the network-wide state. Controllers at the bottom layer run only local control applications (i.e., applications that can function using the state of a single switch) near datapath. These controllers handle frequent events and shield the top layer. Using Kandoo, programmers flag their applications as either local or non-local, and the offloading process is seamlessly handled by the platform. Our evaluations show that a network controlled by Kandoo has an order of magnitude lower control channel consumption compared to centralized controllers. We demonstrate that Kandoo can be used to adapt and optimize Transform Control Protocol (TCP) in a large-scale High-Performance Computing (HPC) datacenter with a low network overhead. Beehive is a more generic proposal built around a programming model that is similar to centralized controllers, yet enables the platform to automatically infer how applications maintain their state and depend on one another. Using this programming model, the platform automatically generates the distributed version of each control application. With runtime instrumentation, the platform dynamically and seamlessly migrates applications among controllers aiming to optimize the control plane. Beehive also provides feedback to identify design bottlenecks in control applications, helping developers enhance the performance of the control plane. Implementing a distributed controller and a simple routing algorithm using Beehive, we demonstrate that Beehive is as simple to use as centralized controllers and can scale on par with existing distributed controllers. Moreover, we demonstrate that Beehive automatically improves control plane’s latency by optimizing the placement of control applications without any intervention by network operators.

Keywords: Computer Networks
Control Plane
Distributed Controllers
Distributed Systems
Scalability
Software-Defined Networking
Advisor: Ganjali, Yashar
High Resolution Hydro-climatological Projections for Western Canada

Accurate identification of the impact of global warming on water resources and hydro-climatic extremes represents a significant challenge to the understanding of climate change on the regional scale. Here an analysis of hydro-climatic changes in western Canada is presented, with specific focus on the Fraser and Athabasca River basins and on changes in hydro-climatic extremes. The analysis is based on a suite of simulations designed to characterize internal variability, as well as model uncertainty. A small ensemble of Community Earth System Model version 1 (CESM1) simulations was employed to generate global climate projections, which were downscaled to 10 km resolution using the Weather Research and Forecasting model (WRF V3.4.1) with several sets of physical parameterizations. Downscaling was performed for a historical validation period and a mid- and end-21st-century projection period, using the RCP8.5 greenhouse gas trajectory. Daily station observations and monthly gridded datasets were used for validation. Changes in hydro-climatic extremes are characterized using Extreme Value Analysis. A novel method of aggregating data from climatologically similar stations was employed to increase the statistical power of the analysis. Changes in mean and extreme precipitation are found to differ strongly between seasons and regions, but (relative) changes in extremes generally follow changes in the (seasonal) mean. At the end of the 21st century, precipitation and precipitation extremes are projected to increase by 30% at the coast in fall and land-inwards in winter, while the projected increase in summer precipitation is smaller and changes in extremes are often not statistically significant. Reasons for the differences between seasons, the role of precipitation recycling in atmospheric water transport, and the sensitivity to physics parameterizations are discussed. Major changes are projected for the Fraser River basin, including earlier snowmelt and a 50% reduction in peak runoff. Combined with higher evapotranspiration, a significant increase in late summer drought risk is likely, but increasing fall precipitation might also increase the risk of moderate flooding. In the Athabasca River basin, increasing winter precipitation and snowmelt is balanced by increasing evapotranspiration in summer and no significant change in flood or drought risk is projected.

Keywords: Dynamical Downscaling
Extreme Value Analysis
Hydro-climatology
Precipitation
Regional Climate
Western Canada
Advisor: Peltier, William R
Utilizing Biomarkers to Assess Prevalence and Trends of Substance Use During Pregnancy in Canada

Substance use during pregnancy is associated with numerous risks to both mother and fetus. Studies of the prevalence and trends of substance use during pregnancy have predominantly relied on maternal self-report, which is known to be unreliable and inaccurate. The emerging use of biomarkers has presented researchers and clinicians with the opportunity to assess this complex matter in a more objective and reliable manner. The overall objective of the research described in this thesis is to utilize biomarkers to assess prevalence rates and trends of substance use during pregnancy in Canada. This objective was addressed through three studies focusing on distinct populations. The first study focuses on a highly specific population of methadone-using pregnant women involved in social services, and found that rates of polydrug use (specifically opioid use) were similar to a negative control group, with approximately half of individuals continuing to use additional opioids during pregnancy. The second study highlights a routine urine drug screen program within the obstetric unit of a regional hospital; we conclude that the prevalence of substance use in this population is close to three times the national average, and that drug use during pregnancy is associated with more maternal and neonatal complications. Lastly, the third study aims to estimate the prevalence of heavy fetal alcohol exposure through the analysis of fatty acid ethyl esters in meconium samples collected nationwide, and reveals that the prevalence ranges between 1.16 and 2.40%, the equivalent of at least 1,800 new cases of Fetal Alcohol Spectrum Disorder in Canada each year. Overall, this research provides new insights into the prevalence and trends of substance use during pregnancy, and aims to guide future public education initiatives and highlight the continuing need for more effective, accessible treatment options for pregnant women who struggle with substance use.

Keywords: Alcohol
Biomarkers
Epidemiology
Illicit Drugs
Pregnancy
Substance Use
Advisor: Ito, Shinya
In School but not of the School: Teaching Aboriginal Students, Inferiorizing Subjectivities, and Schooling Exclusions

Education for Aboriginal peoples is championed as a great equalizer and antithetical to a future of incarceration. Even though Aboriginal peoples are experiencing upward trends in education, they continue to be incarcerated at ten times the rate of their non-Aboriginal counterparts in the Canadian prairies. This study explores the discursive connections between education and incarceration for Aboriginal students. Specifically, the researcher sought to understand how educators’ normative discourses about learning and school legitimize and make possible the criminalization of Aboriginal students, and how educators work to disrupt normative discourses and open up possibilities for who can be a learner. This study is informed by multiple race frameworks, and poststructural theorizing about knowledge, power and subjectivities, and offers a discourse analysis of interviews with Aboriginal and non-Aboriginal educators working across one prairie province. The central finding of this thesis is that normative discourses about Aboriginal students are exclusionary discourses that position Aboriginal students outside of acceptable learner status, and effectively, outside of settler society. This argument is constructed over three interrelated chapters: Chapter Five demonstrates how cultural discourses are often racializing discourses that allow educators to evade considerations of racism and claim commitment to Aboriginal students, Chapter Six explores how inferiorizing discourses produce Aboriginal students as impossible learners and naturalize schooling exclusions, and Chapter Seven presents the discourse of the taken-for-granted-as-troublesome Aboriginal male student and the normalization of a police presence in schools. Throughout each chapter, the author demonstrates how subjectivities imposed upon Aboriginal students are not only incommensurable with normative expectations of student behaviour, but also at odds with the imagined qualities of citizens of the nation state. Counter-narratives of participants who disrupt normative discourses and produce Aboriginal students as belonging in school are also included. Emphasizing the school as a powerful identity-making space where students learn who they are and where they belong in a settler society, the author suggests race power deployed through normative educational discourses naturalizes spaces of abjection as rightful spaces of belonging for Aboriginal peoples.

Keywords: Aboriginal education
discourse analysis
racism
school-to-prison pipeline
settler colonialism
teachers
Advisor: Sykes, Heather
Examining Marginalizing Acts of Social Positioning in Mathematical Group Work: Towards a Better Understanding of how Microaggressions and Stereotype Threat Unfold in Intergroup Interactions

Mathematics learning is documented as being racialized and gendered. Power dynamics between students from various social groups can become particularly problematic during collaborative group work when students from dominant social groups position group members from stereotyped social groups in ways that hinder their opportunities to learn. The present study seeks to investigate how marginalization unfolds during everyday interpersonal interactions within mathematical group work and how students from stereotyped social groups talk about these experiences. Employing an interdisciplinary theoretical framework that cuts across the fields of the learning sciences and social psychology, this qualitative study aims to further understand not only the sociohistorical stereotypes and systems of power that are entrenched within mathematics classrooms, but also how power is constructed through the ways students position one another in their moment-to-moment interactions. Drawing from six episodes of videotaped collaborative group work wherein students from stereotyped social groups are working with students from dominant social groups, the study examines the microdynamics of marginalizing acts of social positioning. Using a stimulated recall interview technique, the study also explores how six focal students from stereotyped social groups, identify, interpret, and discuss their experiences with marginalization. The findings demonstrate the verbal and non-verbal dimensions of marginalization; highlight the intersectionality of race and gender and pinpoint racialized and/or gendered patterns in social positioning; and acknowledge the different interpretations and observations of the researcher versus the focal students. The findings also demonstrate how the focal students responded to potential threats to their identity and pushed back against marginalization: While two of the focal students appeared to adopt silence as a means of resistance to marginalization; two of the other focal students verbally contested marginalizing acts of positioning; and the remaining two focal students pretended to agree and get along with group members in an attempt to maintain group cohesion. The study’s theoretical contributions include a synthesis of sociocultural theories of learning with social psychological theories that foreground race and gender. Implications for mathematics education are also raised, including suggestions for the design and implementation of collaborative group work as well as incorporating video methods into professional development initiatives.

Keywords: collagorative group work
identity
mathematics education
social positioning theory
sociocultural theory
video research methods
Advisor: Esmonde, Indigo
Education in and by rhythm: Exploring holistic experiences in Dalcroze pedagogy

Holistic education seeks to engage students intellectually, physically, spiritually, and emotionally, and to build connections between the student’s inner and outer worlds. Dalcroze Eurhythmics is an approach to music education that uses movement to teach musical concepts in a socially interactive setting. Jaques-Dalcroze developed a system of rhythmic training to provide a foundation for later musical studies; his méthode also provides students with increased awareness of self and of social and spatial relationships and interactions. This dissertation investigates holistic education as it occurs in Dalcroze pedagogy. Five Dalcroze teachers and students with varying levels of experience were asked to consider and express holistic learning experiences they encountered when participating in Dalcroze classes. The data is developed and portrayed as narratives, guided by the qualitative research philosophies of Beattie, Eisner, and Clandinin and Connelly. The ensuing discussion explores emergent themes that illustrate holistic aspects of the participants’ lived experiences. Dominant themes include: community, global education, mindfulness, transformational learning, creativity, personal connections, and emotional involvement.

Keywords: Dalcroze pedagogy
eurhythmics
holistic education
music education
spirituality in education
Advisor: Miller, John P
Analyzing the Role of Users' Interactions in Information Spread

The emergence of social platforms has provided us with a vast amount of raw data on people's daily activities, their social connections, interactions, interests, influence, etc. This creates an opportunity to extract valuable insights, helpful in various applications including but not limited to the identification of the trending topics, community detection, health purposes, and marketing. This thesis designs a platform that analyzes users' interactions (e.g., posts, likes, and shares) and connections (e.g., friendship and followership), and maximizes information spread in the network accordingly. There are numerous applications to this such as advertising, knowledge dissemination, encouraging the adoption of productive behavior in a society, etc. I present a 3-part platform that utilizes users' activities to maximize information spread. It starts by analyzing users' posts (Step 1), and proceeds with users' interactions (Step 2), and connections (Step 3). This information is utilized to locate user communities formed based on topical cascades. Targeting these communities helps to increase the spread of information. In the first step, posts (e.g., tweets) are categorized into partitions representing topics of discussion. Part 2 identifies bursty user groups for each topic of interest. A bursty user group includes a collection of socially connected users who are active and influential with regard to a specific topic. Bursty user groups for a topic are the sources of previous activities on that topic and are of high importance in marketing campaigns. Finally having a limited budget for advertising (i.e., a fixed seed set size), Part 3 determines the best groups among all to target to maximize the spread of information in the network. The analysis is based on the state-of-the-art viral marketing models. All of the proposed algorithms have been extensively evaluated on real-world datasets including Twitter fire-hose, co-authorship, and telecommunication datasets. We present quantitative and qualitative experimental results in each chapter attesting to the practicality of our algorithms.

Keywords: Bursty Subgraphs
Data Mining
Information Cascade
Social Advertising
Social Media Analysis
Trending Topics
Advisor: Ganjali, Yashar
Koudas, Nick
Subconvexity for a Twisted Double Dirichlet Series and Non-vanishing of L-functions

We study a double Dirichlet series of the form P d L(s, χdχ)χ 0 (d)d −w, where χ and χ 0 are quadratic Dirichlet characters with prime conductors N and M respectively. A functional equation group isomorphic to the dihedral group of order 6 continues the function meromorphically to C 2 . A convexity bound at the central point is established to be (MN) 3/8+ε and a subconvexity bound of (MN(M +N))1/6+ε is proven. This bound is used to prove an upper bound for the smallest positive integer d such that L(1/2, χdN ) does not vanish.

Keywords: analytic number theory
double Dirichlet series
L-functions
non-vanishing
subconvexity
Advisor: Blomer, Valentin
Whole Body Synthesis of Docosahexaenoic Acid from Alpha-Linolenic Acid in Rodents

Docosahexaenoic acid (DHA) is an omega 3 polyunsaturated fatty acid (n-3 PUFA) that is thought to be important for neurological function partly through its role in the regulation of cell survival and neuroinflammation. The main dietary source of DHA is fish. Therefore, recommendations to increase DHA consumption may not be sustainable. Alternatively, DHA can be synthesized from precursor n-3 PUFA found in plants, primarily α-linolenic acid (ALA). DHA synthesis is generally accepted to be low, however, the requirement for DHA in the brain is not agreed upon and recent estimates for the brain DHA requirement range from 2.4-3.8 mg/day (

Advisor: Bazinet, Richard P
Population Stress, Growth Deficit and Degenerative Joint Disease in Foragers from South Africa's Later Stone Age

Harsh conditions during development may alter the human adult phenotype in ways that affect vulnerability to disease and death. This study’s objectives are A) to explore the utility of neural canal size and appendicular osteoarthritis as prospective indicators of developmental stress; B) to test for developmental stress effects in a foraging population with no significant socioeconomic stratification; and C) to explore temporal variation in neuroskeletal size and joint degeneration. The study sample consists of 143 Later Stone Age foragers (M=75, F=64, I=4) from the Cape Floristic Region of southern Africa. 135 cases have radiocarbon dates between 9100 and 560 uncalibrated years BP. Osteoarthritis was quantified with an ordinal scoring procedure. Relationships among radiocarbon date, measures of body and neural canal size, OA, and age at death were explored using logistic and ordinary least squares regression, independence tests, and means contrasts. Age, sex, and body size were controlled where appropriate. A positive relationship is observed between age at death and both body size and ML NC diameter, but reaches statistical significance only in the latter case (OR=1.74, 95% CI=1.08–2.82). The effect is detected in both sexes but odds ratios are greater and p values smaller in females (Male OR=1.50, 95% CI=0.82–2.73; Female OR=2.14, 95% CI=1.02–4.50). Age at death is the only significant predictor for both presence and severity of osteoarthritis. No significant relationship is observed between age and anteroposterior diameter. Average mediolateral diameter of the neural canal declines between 3000–2000BP and increases slightly afterwards (β 1 = −0.83, β 2 = 0.68, adjusted R 2 = 0.06, SEE=0.99). This quadratic curve is consistent with published accounts of temporal change in average body size. No temporal pattern is identified in osteoarthritis.

Keywords: bioarchaeology
developmental origins of health and disease
human biology
KhoeSan
Khoisan
Bushmen
prehistory
palaeopathology
Southern African Later Stone Age
Advisor: Pfeiffer, Susan K
The Development of Receptors and Chemosensors for the Recognition of Proximally Phosphorylated Motifs

Protein phosphorylation is an important post-translational modification central to controlling protein activity and function. While single residue phosphorylation is common, di- or poly- phosphorylation on proximal residues has emerged as a functionally significant motif often implicated in certain diseased states. Despite the relevance of these motifs, there has been limited effort towards the development of tools to target this type of phosphosite. To advance the understanding of this field, a metal-based triethylbenzene receptor was developed with the goal of selectively targeting proximally phosphorylated motifs over mono-phosphorylated motifs on peptides. While this receptor scaffold was not sufficiently suitable for this aim, it was successfully applied towards the recognition of small molecule phosphoanions ATP and PPi and was used for their selective sequestration in a phosphopeptide detection assay. The conclusion of these findings prompted a change in the initial receptor-based recognition strategy of di-phosphorylated motifs, which resulted in the development of a lanthanide-based chemosensing approach. Tb3+ luminescence was used for the selective detection of a specific subset of proximally phosphorylated peptide motifs over mono-phosphorylated peptides and off-target phosphoanions. This chemosensing strategy has the potential to be applied as a high-throughput screening tool for different subsets of the phosphoproteome and could be of significant value in elucidating diseased states.

Keywords: chemosensor
lanthanide
metal
phosphorylation
receptor
Advisor: Gunning, Patrick