VictorJuiz/thesis huggingface dataset:
Resource Allocation and Risk Analysis of Dialysis Centres
Keywords: Heuristic
Mixed Integer Programming
Optimization
Risk Analysis
Scheduling
Tabu Search

The number of hemodialysis patients is growing every year. The majority of these patients visit centres at least three times a week for their treatment. Two types of nurses perform general dialysis procedures on the patients. These are registered nurses (RNs) and registered practical nurses (RPNs). Hemodialysis patients may experience complications during their treatment. When complications occur, patients need the assistance of RNs. The time RNs spend with patients increases the duration of their treatment. It is essential for all centres to hire enough nurses to maintain the quality of service for the growing number of patients while minimizing nursing cost. However, facilities have different nurse-to-patient ratio because they are unique in terms of the combination of patients and the workload policies regulating their nurses. Moreover, since there are no generally accepted guidelines, the staffing decisions at each centre are highly subjective. As a result, it is very difficult for the decision makers to create consistent guidelines to determine the number of nurses required in each centre. In this research, we assume that the centre has a given list of specific patients, each of which is defined by patient type. Two approaches are used to help dialysis units schedule their patients and minimize nursing cost while having enough nurses to maintain quality of service. In the first approach, an MIP model and a heuristic algorithm are developed separately to minimize the number of nurses (RPNs or RNs) to set up, monitor, and disconnect patients from dialysis machines. The methods find the start time of the dialysis session for each patient. An M/M/s queuing equation is then used to find the number of RNs needed to attend to any potential complications of scheduled patients. In the second approach, the methodologies are merged into a non-linear model to find patient schedules that minimize the number of RNs and RPNs. Tabu Search is used to solve the non-linear model. Further, the models and results presented in this study can be treated as benchmarks for decision makers to find the approximate number of nurses needed for each unit as well as a forecasting tool to estimate the average number of nurses needed for any patient size population based on their historical data.
Scaling Macro- and microevolutionary Dynamics in the Caesar’s Mushrooms (Amanita sect. Caesareae)
Keywords: Biogeorgaphy
Diversification
Ectomycorrhizal fungi
Genomics
Population genetics
Speciation

Biological diversity is the product of evolutionary and ecological factors that operate at different spatial, temporal, and genomic scales. Phylogenies and genomes have the potential to uncover the mechanisms leading to such diversity, with clues imprinted throughout the evolution of DNA sequences. There are several challenges to study fungal evolution, some of which include inaccurate species delimitations, unknown distributions, sampling biases, and a poor fossil record. However, most fungi have small genomes, making them practical for studying evolutionary genomics. This thesis includes four Chapters that use phylogenetic and genomic approaches to answer questions related to the ecology and evolution of the Caesar’s mushrooms (Amanita sect. Caesareae). Chapters 2 and 3 show how diversification and historical biogeogaphical models explain the distribution, geographic disjunctions, and diversity of temperate and tropical taxa worldwide. Results indicate that land-mediated dispersal and high diversification rates in the New World and in the temperate region have played important roles, which explain, in part, “shifted” latitudinal diversity gradients within the group. Chapter 4 describes new genomic data from A. jacksonii, and comparing it with that of other species. Chapters 5 and 6 deal with the interrelationships between past climate change, regional geography, species richness, genomic variation, selection, and historical demography. Gene genealogies and coalescent-based multi-locus species delimitations reveal high levels of cryptic diversity in North America (NA). Higher speciation rate in climatically stable areas and recent population expansions highlight the importance of Pleistocene glacial dynamics in shaping diversity patterns within NA Caesar’s mushrooms. Finally, both natural selection on coding DNA and demography explain genome-wide diversity across 500 single-copy genes within eight species from a recently diverged species complex. This work evidences the spatial dynamics of populations and species of a gastronomically and culturally important group of mushrooms over millions of years, adding significant insights onto the evolution of symbiotic fungi.
Chronicling the Relationships, Attitudes, and Sexual Encounters of Men who have Sex with Men in Shanghai, China: A Web-administered Sexual Events Diary
Keywords: Men who have sex with men
Sexual Behavior
Sexual events
Sexual Partners
Socio-cultural
Unsafe Sex

Background: Unprotected anal intercourse (UAI) remains the primary mode of HIV infection among MSM in China. As no sexual events studies have been conducted to date, little is known about how characteristics of a sexual event influence sexual behaviour. Objectives: Utilizing a conceptual framework to situate the quantitative analyses within the community, cultural, and social structures that affect the lives of MSM, this dissertation describes attitudes towards homophobia and masculinity; characterizes community involvement and social support; describes egocentric sexual networks; and investigates individual- and event level variables associated with UAI during sexual events (UAIevents). Methods: Data were collected using a cross-sectional questionnaire and a 28-day event-based, web-administered diary. Bivariable and multivariable logistic regression models with GEE were used to investigate associations between individual- and event- level variables and UAIevents. Results: During 4,172 days of follow-up, 149 diary participants reported 854 sexual events with 389 unique partners. Individual-level variables associated with UAIevents included the end of a close relationship; number of social contacts; uncertain filial intentions; masculinity (selfreliance); internalized homophobia (failings and heteronormativity); perceived community homophobia (acceptance), sexual history; and attachment to the Tongzhi circle. Event-level variables associated with UAIevents included: the discussion of personal matters during the sexual event; partner dynamics (confidence), partnership duration; and participant intoxication. Conclusions: The novel diary method allowed an in-depth exploration of partners and partnerships which revealed that the duration of the partnership and the discussion of personal matters (but not partner type) were associated with UAIevents. This suggests that the former two should be considered as alternatives to the traditional measure of partner type. Childrearing is important to many Shanghainese MSM. Uncertainty about one’s filial intentions increases the odds of UAIevents. Failure to acknowledge the socio-cultural and political context in which men live can affect the collection, interpretation and utility of epidemiologic findings.
The Creators of Information in Eighteenth-century Britain
Keywords: Authorship
Book History
Dictionaries
Eighteenth-Century British
Information
Reading

In twenty-first-century accounts of how knowledge was transmitted at second hand in the early modern period and the eighteenth century, the idea of information has played a crucial role. “Information” refers to the content that was compiled and stored on paper and shared in reference books and periodical sheets. My thesis argues that eighteenth-century Britons understood printed information through the lens of cultural discourses that privileged engagements with books that we would now call “literary.” By re-thinking the transmission of information as a textual object in eighteenth-century Britain, I argue, we can better understand the complex ways in which information was credited, acquired, and shared. I show how the author-function played a role in the public sharing of information in Samuel Johnson’s Dictionary of the English Language (1755). Johnson’s rhetoric of personal sacrifice in the “Preface” and Plan of an English Dictionary (1747), I argue, should be contrasted with the methods of Johnson’s rival, Nathan Bailey. Bailey’s Universal Etymological English Dictionary (1721-1802) offers an example of the failure of compiled information to gain cultural authority without authorial control. I argue that Jonathan Swift’s satires on textual criticism, cryptanalysis, and scientific languages can be seen as critiques of mechanical reading “devices” that extracted information from texts. A direct challenge to informational uses of language was offered at the end of the eighteenth century in the work of Johnson’s friend, Hester Lynch Piozzi. Piozzi’s English-language reference work, British Synonymy (1794), showed how direct engagement with the “redundant” material of language provided a knowledge of texts that was difficult to communicate but necessary to observe. I suggest that the mediation of public information in eighteenth-century Britain was balanced in important ways by literary discourses that argued for the importance of the specific ways in which knowledge was credited, acquired, and shared through language.
Using Esterase and Laccase Enzymes to Derivatize Bioactive Plant Phenolics for Altered Chemistry
Keywords: antioxidant
esterase
flavonoids
laccase
phytochemicals
transesterification

Plant phenolics have notable antioxidant activity and there is potential to improve their action by chemical modification. Two enzyme classes carry out reactions that can act on the hydroxyl moiety of phenolics. Esterase enzymes can be used in non-aqueous solvents to esterify a long chain acyl group onto the phenolic compound. Laccase enzymes can be used to form phenoxy radicals that can then couple to form larger molecular weight oligomers. Both enzymatic modifications may produce a new antioxidant with altered chemistry. One archaeal esterase (AF1753) from Archaeoglobus fulgidus and one bacterial esterase (PP3645) from Pseudomonas putida were assayed for activity in organic solvents. Both enzymes catalyzed hydrolysis of phenyl acetate and vinyl acetate in 98:2 (v/v) (t-amyl alcohol):buffer; with continued activity up to 96 h of reaction. However, the enzymes were not able to catalyze transesterification of 4’-hydroxyacetophenone with vinyl acetate in 9:1 (v/v) cyclohexane:(t-amyl alcohol), which was not explained by enzyme inactivation during lyophilization. Still, alanine scanning mutagenesis revealed that R37A substitution improved activity of AF1753 on long-chain p-nitrophenyl (pNP) esters. A multicopper oxidase (SCO6712) from Streptomyces coelicolor displayed activity on a variety of phenolics including caffeic acid, ferulic acid, resveratrol, quercetin, morin, kaempferol and myricetin. Among the products formed by action on flavonols were dimers of quercetin, morin, and myricetin. Quercetin and myricetin dimers showed longer retention time on reversed phase chromatography. All three dimers could be detected by 5 min of reaction but depleted by 3 h and 24 h. The TRAP and FRAP antioxidant activity of the whole reaction mixture of modified quercetin, morin, and myricetin decreased, as starting phenolic was depleted over 24 h. Accordingly, mass spectrometry was used to shed light on the molecular structure of the dimers produced from quercetin and myricetin. In both cases, mass spectrometric analyses ruled out dimer formation through the A ring of each monomer. For myricetin, the most likely linkage structure was determined to be between either two B rings or a B ring with a C ring. These predicted linkage positions are in agreement to those observed for quercetin dimers previously extracted from natural plant sources.
The Neural and Behavioral Profile of Older Adults at Risk for Developing Mild Cognitive Impairment
Keywords: Aging
Dementia
Memory

Improving the ability to detect Alzheimer’s disease (AD) at the earliest stages is essential to effectively treat afflicted individuals. Mild cognitive impairment (MCI) is thought to be an intermediary state between healthy aging and AD. The goal of the present dissertation was to examine older adults who are at heightened risk of developing AD – both patients with diagnosed MCI and a preclinical group of older adults at-risk for developing MCI. Our preclinical participants were undiagnosed and supposedly healthy members of the community, but were defined to be at-risk for MCI based on performance from a brief, standardized neuropsychological test. We administered a full neuropsychological battery after our screening and found that the preclinical group performed in the lowest quartile on measures that are conventionally impaired in MCI (Chapter 2). To establish a neural profile of this population, we investigated an ERP component associated with visual short-term memory (VSTM) capacity, the CDA (Chapter 2). We found that older adults at-risk for MCI had reduced VSTM and reduced differentiation of the CDA (Chapter 2). Additionally, we found that the P300, a well-characterized ERP component shown to be useful in determining conversion from MCI to AD, showed reduced amplitude in our at-risk group (Chapter 2). Electrophysiological signatures may be especially sensitive markers of the very earliest stages of AD. To further characterize the preclinical group, we administered an object discrimination task to older adults at-risk for developing MCI and diagnosed MCI patients (Chapter 3). We based the task design on previous research showing that the medial temporal lobe (MTL), a region damaged early in MCI, is necessary to resolve visual interference in this object discrimination task. Critically, we manipulated the level of visual interference across conditions, and found that both memory-impaired groups, but not controls, benefited from reduced interference on the perceptual task. Indeed, by reducing the requirement to bind features of an object together, performance in the memory-impaired group rose to the level of healthy controls. In Chapter 4, we sought to extend these findings by investigating the role of interference in a task assessing VSTM. We reduced interference by presenting a retroactive spatial cue (retrocue, providing a cue for binding object to location), which again elevated performance in patients with MCI and MTL amnesia to the level of their age-matched controls. The results of these experiments suggest that one of the most critical determinants of behavior is interference in the environment, and that increased vulnerability to interference may be one of the first symptoms of pathological aging.
Study of Natural Fiber Breakage during Composite Processing
Keywords: Biofiber-polymer composites
Composites
Discontinuous reinforcement
Natural fibers
Thermoplastic resin
Wood

Biofiber-thermoplastic composites have gained considerable importance in the last century. To provide mechanical reinforcement to the polymer, fibers must be larger than a critical aspect ratio (length-to-width ratio). However, biofibers undergo breakage in length or width during processing, affecting their final aspect ratio in the composites. In this study, influence on biofiber breakage by factors related to processing conditions, fiber morphology and the flow type was investigated through: a) experiments using an internal mixer, a twin-screw extruder (TSE) or a capillary rheometer; and b) a Monte Carlo computer simulation. Composites of thermomechanical fibers of aspen or wheat straw mixed with polypropylene were studied. Internal mixer experiments analyzed wheat straw and two batches of aspen fibers, named AL and AS. AL fibers had longer average length. Processing variables included the temperature, rotors speed and fiber concentration. TSE experiments studied AL and AS fiber composites under various screws speeds, temperatures and feeding rates of the polymer and fibers. Capillary rheometers experiments determined AL fiber breakage in shear and elongational flows for composites processed at different concentrations, temperatures, and strain rates. Finally, the internal mixer experimental results where compared to Monte Carlo simulation predictions. The simulation focused on fiber length breakage due to fiber–polymer interactions. Internal mixer results showed that final fiber average length depended almost solely on processing conditions while final fiber average width depended on both processing conditions and initial fiber morphology. In the TSE, processing conditions as well as initial fiber length influenced final average length. TSE results showed that the fiber concentration regime seems to influence the effect of processing variables on fiber breakage. Capillary rheometer experiments demonstrated that biofiber breakage happens in both elongational and shear flows. In some cases, percentage of biofiber breakage in elongational flow is higher. In general, simulation predictions of final average lengths were in good agreement with experiments, indicating the importance of fiber–polymer interactions on fiber breakage. The largest discrepancies were obtained at higher fiber concentration composites; these differences might be resolved, in future simulations, by including the effect of fiber–fiber interactions.
Device Transparent RSS-based Indoor Localization
Keywords: Cooperation
Device Diversity
Indoor Localization
Linear Transformation
RSS-based Localization

Signal strength variation across diverse devices is a major problem with RSS-based indoor localization. This thesis aims to solve this problem by considering two factors: the instability of collected RSS samples and linear shift of RSS patterns collected by different devices. We propose different techniques to handle the uncertainty of samples. Furthermore, we propose four different algorithms that make the localization system device-transparent. All solutions rely on the linear relationship across diverse devices. The first algorithm is the independent linear transformation algorithm. It starts by finding a set of candidate nearest neighbour fingerprints for an online point through correlation coefficient. Then, a series of linear transformations is applied to find nearest neighbours with high accuracy. The algorithm is justified through an analytical study of probability of error. The second algorithm is the cooperative linear transformation algorithm. This algorithm considers the case where multiple online points are available. The algorithm uses independent linear transformation algorithm to find the set of nearest neighbour fingerprints for each online point independently. Next, the online points and their detected nearest neighbours are used cooperatively to enhance the transformation model. The probability of error is also analyzed. The third algorithm utilizes label propagation algorithm for localization. Label propagation is a graph-based semi-supervised algorithm that requires the collection of some labeled points by the localization device. We propose to use label propagation in an un-supervised way. The algorithm transforms all fingerprints to the signal space of the localization device. All available online points are used cooperatively to find the transformation parameters. Next, it finds the weights of all edges connecting RSS points through Euclidean distances. Finally, label propagation is applied for localization. Those three algorithms utilize ordinary least squares as the linear regressor. The fourth algorithm is the robust linear transformation algorithm that utilizes robust linear regression for localization. Robust regression minimizes the effect of outliers by giving less weights to potential outliers. KNN is used as the localization engine. All proposed systems are automatic and do not require any training period. Experimental results indicate the proposed systems are reliable with very high positional accuracy.
The Experiences of Postsecondary Students with Learning Disabilities in Summer Transition Programs: A Multi-case Study of Six Programs in Ontario
Keywords: First Year Experience
Learning Disabilities
Ontario
Transition Programs

Students with Learning Disabilities (LD) are the largest and fastest growing sub group of students with disabilities in postsecondary education. Despite their increasing enrollment, students with learning disabilities remain an under-represented group, and are categorized at risk due to the low graduation rates compared to their peers, specifically at the university level. The first year is a critical year for all students entering postsecondary education as it is this year where students are most likely to drop-out. For students with learning disabilities, the first year is particularly important as they must adjust to a new academic environment and accommodations from what they are accustomed to in high school. Understanding what supports and influences improve these experiences for students with learning disabilities at the onset of their postsecondary education is a crucial step in augmenting their persistence and graduation prospects. Using a multi-case study design, I examine the experiences of students with learning disabilities in six summer transition programs in public universities in Ontario, Canada and how these programs prepared students in making the transition from high school to university. The summer transition programs under investigation resulted from the recommendations made by Ontario’s Learning Opportunity Task Force to the Ministry of Training Colleges and Universities to fund transition programs to increase the retention and graduation of students with learning disabilities. Findings from this study show that students with learning disabilities who participate in transition programs gain academic tools and strategies that help them transition into their first year of university (and beyond) such as time-management, note taking, and seeking disability related support services and accommodations; learn about the importance of self-advocacy and communicating with faculty, staff, and peers regarding their disability; and learn how to navigate the university and the services available to help them succeed. In addition, participants noted that attending the transition program helped them find new confidence in themselves and find a sense of community amongst other participants in the program.