VictorJuiz/thesis huggingface dataset:
Relationships between Missing Response and Skill Mastery Profiles of Cognitive Diagnostic Assessment
Keywords: missing response, large-scale assessment, psychometrics, Cognitive Diagnostics Assessment/ Models, Skill Mastery Profiles, and Item Response Theory

This study explores the relationship between students’ missing responses on a large-scale assessment and their cognitive skill profiles and characteristics. Data from the 48 multiple-choice items on the 2006 Ontario Secondary School Literacy Test (OSSLT), a high school graduation requirement, were analyzed using the item response theory (IRT) three-parameter logistic model and the Reduced Reparameterized Unified Model, a Cognitive Diagnostic Model. Missing responses were analyzed by item and by student. Item-level analyses examined the relationships among item difficulty, item order, literacy skills targeted by the item, the cognitive skills required by the item, the percent of students not answering the item, and other features of the item. Student-level analyses examined the relationships among students’ missing responses, overall performance, cognitive skill mastery profiles, and characteristics such as gender and home language. Most students answered most items: no item was answered by fewer than 98.8% of the students and 95.5% of students had 0 missing responses, 3.2% had 1 missing response, and only 1.3% had more than 1 missing responses). However, whether students responded to items was related to the student’s characteristics, including gender, whether the student had an individual education plan and language spoken at home, and to the item’s characteristics such as item difficulty and the cognitive skills required to answer the item. Unlike in previous studies of large-scale assessments, the missing response rates were not higher for multiple-choice items appearing later in the timed sections. Instead, the first two items in some sections had higher missing response rates. Examination of the student-level missing response rates, however, showed that when students had high numbers of missing responses, these often represented failures to complete a section of the test. Also, if nonresponse was concentrated in items that required particular skills, the accuracy of the estimates for those skills was lower than for other skills. The results of this study have implications for test designers who seek to improve provincial large-scale assessments, and for teachers who seek to help students improve their cognitive skills and develop test taking strategies.
Does Duration of Nicotine Replacement Therapy Use Matter in Quitting Smoking? A Longitudinal Study of Smokers in the General Population
Keywords: Nicotine replacement therapy (NRT)
Population-based prospective cohort study
Smoking cessation

Background and Objectives: Little is known about the impact of nicotine replacement therapy (NRT) use duration on smoking cessation in the general population. This study determines whether duration of NRT use is associated with smoking cessation. Methods: Data were from the Ontario Tobacco Survey longitudinal study of a population-based cohort of baseline smokers who made serious quit attempts during 18 months of follow-up. The association between NRT (any NRT, patches, or gum) use duration and smoking cessation outcomes (short-term abstinence ≥1 month and long-term abstinence ≥12 months) was estimated by Poisson regression, adjusting for all confounding variables. Results: Among the 1,590 eligible smokers, 933 (59%) did not use any NRT, 535 (34%) used NRT <8 weeks, and 112 (8%) used NRT ≥8 weeks at follow-up. The median duration of NRT use was 14 days. A consistent “J” shape of associations between quit aid use duration and smoking cessation outcomes (quit rates) was found. Using any NRT, patches, or gum <8 weeks was generally associated with a lower likelihood of quitting, but using them ≥8 weeks was generally associated with a higher likelihood of quitting, compared to not using them. Only using patches for the recommended duration (≥8 weeks) was associated with a higher likelihood of short-term (relative risk, RR 1.74, 95% confidence interval, CI 1.21-2.50) and long-term (RR 2.62, 95% CI 1.25-5.50) abstinence at the end of 18 months of follow-up, compared to not using patches. Using gum ≥8 weeks was not associated with short- or long-term abstinence at the end of 18 months of follow-up. Conclusions: Using nicotine patches for the recommended duration is associated with successful short- and long-term abstinence in the general population. More efforts are needed to encourage smokers to use nicotine patches for eight or more weeks when attempting to quit.
Investigation of ClpXP Protease Mechanism of Function and its Interaction with the Folding Chaperone Trigger Factor
Keywords: chaperones
proteases
cotranslational
ClpP dynamics

The major chaperones identified in Escherichia coli that assist in protein folding include trigger factor (TF), DnaK/DnaJ/GrpE and GroEL/GroES systems. The main ATP-dependent proteases are ClpXP, ClpAP, HslUV, Lon, and FtsH. From detailed sequence analysis, we found that tig (gene for TF), clpX, and clpP genes co-localize next to each other in most examined bacteria. We hypothesized that TF and ClpXP are functionally associated. TF is a ribosome-associated folding chaperone whereas ClpXP is a degradation complex. ClpX serves as the regulatory ATPase that recognizes substrates, unfolds and translocates polypeptides into ClpP for degradation. I found that TF physically interacts with ClpX, and that they collaborate to enhance degradation of certain ClpXP substrates. It is estimated that TF enhances the degradation of about 2% of newly synthesized E. coli proteins. One of the ClpXP substrates with degradation enhanced by TF was λO, the λ phage replication protein. Furthermore, TF also enhanced the degradation of ribosome-stalled λO nascent chains. Experiments suggest that TF transfers ribosome-stalled λO to ClpX for degradation by ClpP, demonstrating the existence of co-translational protein degradation in E. coli. To understand ClpXP mechanism, we had previously proposed that the degraded peptides are released from ClpP through transient equatorial side pores. To further understand ClpP dynamics, we determined the structure of ClpP(Ala153Cys) in its oxidized state. The structure shows that each opposing pair of protomers is linked by a disulfide bond. Unexpectedly, this structure resembles the compact structures of Streptococcus pneumoniae, Mycobacterium tuberculosis, and Plasmodium falciparum ClpPs, rather than the extended states seen in previous E. coli ClpP structures. Normal mode analysis of ClpP structures suggested that the iii compact structure is a naturally sampled conformation of WT ClpP. My findings provide insights for understanding ClpP dynamics as well as reveal a novel association between ClpXP protease and TF folding chaperone.
Adaptation Techniques for Publish/Subscribe Overlays
Keywords: Publish/subscribe
Overlay networks
Distributed systems
Adaptive systems

Publish/Subscribe (in short pub/sub) allows clients that share common interest communicate in an asynchronous and loosely-coupled fashion. This paradigm is adopted by many distributed event-driven applications such as social networking services, distributed business processes and cyber-physical systems. These applications cannot afford to have the underlying pub/sub substrate perform unreliably, permanently fail or behave arbitrarily as it will cause significant disturbance to stably serving many end-users. Therefore, a research effort on making pub/sub systems resilient against various failures to sustain high quality of service to the clients is imperative. In this thesis, we focus on the overlay of pub/sub brokers that are widely adopted as a popular architecture for large-scale pub/sub systems. Broker overlays can suffer from various issues such as degradation of topology quality, brokers causing transient or permanent benign failures and Byzantine brokers behaving arbitrarily. We aim to make novel research contributions by exploring fundamental techniques that can help the broker overlays maintain functional and non-functional requirements even under the presence of the aforementioned failures and necessary administrative updates. We first build a set of overlay adaptation primitives that re-configure topologies such as shifting links and replicating brokers. These primitives are designed to involve a small local group of brokers in the pub/sub overlays so that the disruption during the execution of large-scale and dynamic changes can be controlled in a fined-grained manner. For the problem of degrading topology quality, automated planning systems are developed to find a sequence of adaptations that would cause minimal disruption to running services. Also, our primitives can be executed on demand to quickly fail-over a crashed broker or off-load congested brokers. In addition, these on-demand primitives can be used to form a group of dynamically replicated brokers that enforce a novel safety measure to prevent Byzantine brokers from sabotaging the pub/sub overlays. Our contributions are evaluated with systematic consideration of various trade-offs between functional and non-functional properties.
Determination of the Sub-cellular Mechanisms Underlying Neurodegeneration in Parkinson's Disease
Keywords: Parkinson's disease
mitochondria

Parkinson’s disease (PD) is the second most common neurodegenerative disease affecting approximately 1.8% of the population over 65 years of age. It is characterized by three cardinal symptoms: bradykinesia, muscle rigidity and resting tremor. Symptoms are presented following 50% loss of dopaminergic neurons within the substantia nigra pars compacta (SNc). Neurodegeneration is associated with reactive oxygen species (ROS) production, protein aggregation, mitochondrial dysfunction, ubiquitin-proteasome system (UPS) inhibition and lysosomal malfunction; however it is unclear if a single mechanism or multiple mechanisms lead to disease onset. The primary aim of the studies described in this thesis was to elucidate the interactions between various pathological mechanisms underlying PD pathology. An examination of organelle function during exposure of SH-SY5Y neuroblastoma to a variety of toxins which mimic purported pathological processes in PD reveal mitochondrial membrane potential becomes depolarized, not only following mitochondrial impairment, but also after the UPS and lysosome are inhibited. Given that mitochondrial dysfunction appeared to be central to PD pathology, mitochondrial dysfunction was studied in more detail. Mitochondrial fission and fusion maintains mitochondrial integrity, which is critical to neuronal health. Thus, we examined mitochondrial dynamics in a common genetic variant linked with familial PD, known as leucine-rich repeat kinase 2 (LRRK2). Upon the expression of wild-type and mutant LRRK2, mitochondrial fusion was inhibited causing fragmentation of mitochondria. This inhibition of fusion may be the initial step leading to mitochondrial dysfunction, since inhibition of fusion occurs prior to the induction of cell stress. The findings that mitochondrial dysfunction appears to be central to PD pathology, suggest that mitochondria may be an excellent therapeutic target for PD. Thus, the potential neuroprotective function of a regulator of mitochondrial function, known as SIRT3 was examined. In SH-SY5Y cells, over-expression of SIRT3 protected neurons from degeneration associated with LRRK2 over-expression. The studies described in this thesis provide evidence that multiple sub-cellular mechanisms converge to inhibit mitochondrial function. Furthermore, mitochondrial dynamics which regulate mitochondrial function could be a key mediator in the pathology associated with PD. The work herein suggests therapies which target the mitochondria are likely to be successful in the treatment of PD.
Generalizing Contexts Amenable to Greedy and Greedy-like Algorithms
Keywords: Computer Science
Algorithms
Greedy
Approximation

One central question in theoretical computer science is how to solve problems accurately and quickly. Despite the encouraging development of various algorithmic techniques in the past, we are still at the very beginning of the understanding of these techniques. One particularly interesting paradigm is the greedy algorithm paradigm. Informally, a greedy algorithm builds a solution to a problem incrementally by making locally optimal decisions at each step. Greedy algorithms are important in algorithm design as they are natural, conceptually simple to state and usually efficient. Despite wide applications of greedy algorithms in practice, their behaviour is not well understood. However, we do know that in several specific settings, greedy algorithms can achieve good results. This thesis focuses on examining contexts in which greedy and greedy-like algorithms are successful, and extending them to more general settings. In particular, we investigate structural properties of graphs and set systems, families of special functions, and greedy approximation algorithms for several classic NP-hard problems in those contexts. A natural phenomenon we observe is a trade-off between the approximation ratio and the generality of those contexts.
Economic Spillovers and Learning from Others
Keywords: Empirical industrial organization
Urban economics

In chapter 1, I study how spillover effects from competitors' choices affect a firm's decision to open a store. Using panel data from the United Kingdom's fast food industry, I propose and estimate a game of entry under incomplete information that incorporates spillover effects between firms' entry decisions. A positive spillover is identified for Burger King - increasing the stock of existing McDonald's by 1 outlet increases Burger King's estimated equilibrium probability of opening a new store by approximately 18 percentage points. Chapter 2 advances our collective knowledge about the impact of learning from others in industry dynamics, and whether it can generate the clustering of rival retailers. Uncertainty about new markets provides an opportunity for learning from others, where one firm's past entry decisions signal to others the potential profitability of risky markets. The setting is Canada's hamburger fast food industry from its inception in 1970 to 2005, where I introduce a new estimable dynamic oligopoly model of entry/exit with unobserved heterogeneity, common uncertainty about demand, learning through entry, and learning from others. I find that the presence of uncertainty induces retailers to herd into markets that others have previously done well in. Finally, chapter 3 (joint with Feng Chi) studies the early adoption of Twitter in the 111th House of Representatives. Our main objective is to determine whether successes of past adopters have the tendency to speed up Twitter adoption, where past success is defined as the average followers per Tweet - a common measure of "Twitter success" - among all prior adopters. The data suggests that accelerated adoption can be associated with favorable past outcomes: increasing the average number of followers per Tweet among past adopters by a standard deviation (of 8 followers per Tweet) accelerates the adoption time by about 112 days.
Efficient Workload and Resource Management in Datacenters
Keywords: Data centers
Cloud computing
Request mapping
Optimization
VM placement
ADMM
Cooling efficiency
Stable matching

This dissertation focuses on developing algorithms and systems to improve the efficiency of operating mega datacenters with hundreds of thousands of servers. In particular, it seeks to address two challenges: First, how to distribute the workload among the set of datacenters geographically deployed across the wide area? Second, how to manage the server resources of datacenters using virtualization technology? In the first part, we consider the workload management problem in geo-distributed datacenters. We first present a novel distributed workload management algorithm that jointly considers request mapping, which determines how to direct user requests to an appropriate datacenter for processing, and response routing, which decides how to select a path among the set of ISP links of a datacenter to route the response packets back to a user. In the next chapter, we study some key aspects of cost and workload in geo-distributed datacenters that have not been fully understood before. Through extensive empirical studies of climate data and cooling systems, we make a case for temperature aware workload management, where the geographical diversity of temperature and its impact on cooling energy efficiency can be used to reduce the overall cooling energy. Moreover, we advocate for holistic workload management for both interactive and batch jobs, where the delay-tolerant elastic nature of batch jobs can be exploited to further reduce the energy cost. A consistent 15% to 20% cooling energy reduction, and a 5% to 20% overall cost reduction are observed from extensive trace-driven simulations. In the second part of the thesis, we consider the resource management problem in virtualized datacenters. We design Anchor, a scalable and flexible architecture that efficiently supports a variety of resource management policies. We implement a prototype of Anchor on a small-scale in-house datacenter with 20 servers. Experimental results and trace-driven simulations show that Anchor is effective in realizing various resource management policies, and its simple algorithms are practical to solve virtual machine allocation with thousands of VMs and servers in just ten seconds.
A Quantum Light Source for Light-matter Interaction
Keywords: quantum information
quantum optics
narrowband
light source
light-matter interaction
multidimensional
quantum computation

I present in this thesis the design, implementation and measurement results of a narrowband quantum light source based on cavity-enhanced Parametric Down-Conversion (PDC). Spontaneous Parametric Down-Conversion (SPDC) is the workhorse in the field of optical quantum information and quantum computation, yet it is not suitable for applications where deterministic nonlinearities are required due to its low spectral brightness. By placing the nonlinear crystal inside a cavity, the spectrum of down-conversion is actively modified, such that all the non-resonant modes of down-conversion experience destructive interference, while the resonant mode sees constructive interference, resulting in great enhancement in spectral brightness. I design and construct such a cavity-enhanced down-conversion source with record high spectral brightness, making it possible to use cold atoms as the interaction medium to achieve large nonlinearity between photons. The frequency of the photons is tunable and their coherence time is measured to be on the order of 10 nanoseconds, matching the lifetime of the excited state of typical alkali atoms. I characterize extensively the output of the source by measuring the second-order correlation function, quantifying two-photon indistinguishability, performing quantum state tomography of entangled states, and showing different statistics of the source. The unprecedented long coherence time of the photon pairs has also made possible the encoding of quantum information in the time domain of the photons. I present a theoretical proposal of multi-dimensional quantum information with such long-coherence-time photons and analyze its performance with realistic parameter settings. I implement this proposal with the quantum light source I have built, and show for the first time that a qutrit can be encoded in the time domain of the single photons. I demonstrate the coherence is preserved for the qutrit state, thus ruling out any classical probabilistic explanation of the experimental data. Such an encoding scheme provides an easy access to multi-dimensional systems and can be used as a versatile platform for many quantum information and quantum computation tasks.
Expanding the uses of Split-inteins through Protein Engineering
Keywords: Intein
Protein Engineering

Split-protein systems are invaluable tools used for the discovery and investigations of the complexities of protein functions and interactions. Split-protein systems rely on the non-covalent interactions of two fragments of a split protein to restore protein function. Because of this, they have the ability to restore protein functions post-translationally, thus allowing for quick and efficient responses to a milieu of cellular mechanisms. Despite this, split-protein systems have been largely limited as a reporting tool for protein-protein interactions. The recent discovery of inteins has the potential of broadening the scope of split-protein systems. Inteins are protein elements that possess the unique ability of post-translationally ligating protein fragments together with a native peptide bond, a process termed protein splicing. This allows split-proteins to reassemble in a more natural state. Exploiting this property and utilizing protein engineering techniques and methodologies, several approaches are described here for restoring and controlling split-protein functions using inteins. First, the protein splicing behaviour was demonstrated with the development of a simple in vitro visual fluorescence assay that relies on examining the subcellular localization of different fluorescent proteins. Inteins were then used to reassemble and restore function to artificially split genetically encoded Ca2+ indicators. Second, inteins were shown to be able to simultaneously restore protein function to two target proteins. The first target protein was restored through the normal protein splicing pathway while the second was restored through non-covalent interactions of the split-protein fragments. This is a previous unknown property of inteins. Lastly, an intein was engineered to respond to an external light-stimulus that triggered protein splicing to restore split-protein function. The photoactivatable intein, coupled with the versatility of light, allows exquisite control in both space and time for the restoration of protein function within cells. The modularity of the photoactivatable intein can be simply attached to a variety of split-proteins. This was demonstrated with the restoration of various split-protein functions.