VictorJuiz/thesis huggingface dataset:
Change point models for discontinuation rates of Pneumocystis carinii pneumonia prophylaxis in an Ontario HIV patient population

Background. In an article published in the Lancet (Schneider et al., 1999), a prospective observational study's preliminary results indicated that the prophylactic treatment to eliminate the Pneumocystis carinii Pneumonia (PCP) fungi could safely be discontinued if a patient's CD4 cell count had increased above 200 cells/mm3 and later guidelines indicated the increase should be sustained for at least three months. Conclusions. The analysis of time to discontinuation of PCP prophylaxis in a cohort of HIV patients provides evidence that there was a significant change in the discontinuation rate in late January, 1999 for most sites with one site having a separate change point in early November, 1999. The adjusted rate of discontinuation rate doubles after clinical evidence was published that it was safe to discontinue PCP prophylaxis under certain conditions. Results. The adjusted discontinuation rate doubles after the change point at January 25, 1999 for all sites except site X1 where the change point is November 1, 1999 (relative rate=2.01, 95% confidence interval 1.25,3.21)). Being a patient at site X2, or having a high CD4 count, and 'after change point' are factors associated with higher discontinuation rates. Lower discontinuation rates are associated with HIV Risk (sex with men) or patients at site X1. Interpretation of the significant interaction, indicates that undetectable viral load values are related to higher discontinuation rates after the change point. Methods. An extract from the HIV Ontario Observational Database included patients who were HIV positive and had a record of initiating PCP prophylaxis before January 1, 1998. Bootstrap methods were developed to estimate the change points in the underlying discontinuation rates of PCP prophylaxis and corresponding confidence intervals for an exponential survival model with one or two change points.
Exploring the protective effects of positive sibling relationships on child adjustment in stressed families: a longitudinal assessment

A two-wave longitudinal design was used to examine the protective effects of positive sibling and peer relationships on child adjustment for children whose families experienced negative life events. At Time 1, mothers provided information about negative life events experienced in the previous twelve months, closeness of the target child to their peers, and the target child's emotional and behavioural adjustment. Older siblings assessed the quality of relationship between themselves and target children. Two years later, mothers provided information about the target child's current emotional and behavioural adjustment. Results revealed that sibling affection moderated the relationship between exposure to negative life events and internalizing outcomes but closeness to peers did not. Notably, the protective effect of sibling affection was evident regardless of the relationship quality between mother and the target child. Neither sibling affection nor closeness to peers moderated the relationship between exposure to negative life events and externalizing outcomes.

Keywords: Brothers and sisters
Families
Dysfunctional families
Life change events
Stress in children
Friendship in children
Modelling and diagnostics of atmospheric argon radio frequency inductively coupled plasma

This dissertation describes the work on the modelling and diagnostics of atmospheric argon radio frequency (RF) inductively coupled plasma (ICP).A fully computer-controlled optical emission spectroscopy (OES) experimental system was established during this project, and it was used to measure the plasma temperature and electron densities of a 40 MHz argon RF ICP. The excitation temperature measured from the Boltzmann plot, and electron density from the continuum emission are proved to be reliable estimations. The temperature measurement showed agreement with the prediction of the model, whereas the estimation of the electron density needed improvement. Emission asymmetry was found to exist within the coil zone of the RF plasma. The tomography technique was applied to obtain the two-dimensional local emission profile of a 40 MHz argon RF ICP. This technique provides the basis for further investigation of the effect of the emission asymmetry on the plasma field measurement, and development of the current model. We developed a new integrated model by applying the EEDF obtained using the Boltzmann equation solver ELENDIF. The two-temperature model and ELENDIF program were combined and numerically solved together. The Maxwellian EEDF assumption was then relaxed in the new model. The model was applied to calculate the plasma fields for argon RF ICP at frequencies 13.56 and 40 MHz. The results show that the Maxwellian EEDF is still a good assumption for a 40 MHz argon RF ICP, whereas it will cause errors for the predictions of the plasma fields of the 13.56 MHz plasma. The new model can treat more complicated cases of argon RF ICP. The assumption of the Maxwellian electron energy density function (EEDF) in the two-temperature model was examined by applying the Boltzmann equation solver ELEN-DIF program. The Maxwellian EEDFs of 13.56 and 40 MHz argon RF ICP, under non-equilibrium conditions, are proved to give inaccurate estimations of the high energy electron population and the energy transfer from the electrons to atoms/ions, which will consequently affect prediction of the plasma fields.
Facing the legacy of the 'Dirty War': A truth commission for Mexico

In this thesis I analyse Mexican transitional justice policies adopted in 2001 by the Fox administration. After facing a legacy of human rights abuses perpetrated by public authorities, the new democratically elected government undertook an ambitious plan to deal with the past. The main objectives of this endeavour were delivering justice, uncovering the truth and providing reparations. To accomplish these goals, a Special Prosecutor Office was created and conceived as the key actor. After assessing the strengths and flaws of the transitional justice policies implemented, particularly in light of their ineffective results, I propose the creation of a truth commission as an instrument to promote democratic values, such as accountability and rule of law. I examine some of the possible contributions of a truth commission in the Mexican context. Finally, I suggest a holistic approach, in which a truth commission co-exists with criminal prosecution and other transitional justice mechanisms.

Keywords: Criminal justice, Administration of, Mexico
Rule of law, Mexico
Truth commissions, Mexico
Development of coupled mercury fate-TRANsport, SPECiation and BIOaccumulation (BIOTRANSPEC) model: Application to Lahontan Reservoir, Nevada

The steady-state version of mathematically linked multispecies fugacity/aquivalence based fate-TRANsport, equilibrium SPECiation-complexation, kinetics, and simple BIOtic uptake (BIOTRANSPEC) model has been developed to estimate fate and biotic uptake of inorganic (HgII and Hg 0) and organic mercury (MeHg) species in dissolved, colloidal and particulate phases in surface aquatic systems. The model considered pseudo-steady-state conditions to describe mercury dynamics in the Lahontan Reservoir, Nevada, wherein the historically deposited mercury is remobilized, and maintains elevated sediment concentrations. The model results for four seasonal snapshots indicate that over 90% of mercury input is retained in sediments as most mercury is in particulate form but movement within the sediments and between sediments and water prolongs its residence time. Aqueous species are dominated by Hg(OH) 2, HgOHCl and MeHgOH in dissolved and Hg(OH)L− in colloidal forms. Reservoir sediments support mercury methylation, whereas MeHg is lost via water-column demethylation and subject to fish uptake.
Practical considerations for the surveillance of multidrug-resistant organisms in the hospital setting

Surveillance for multidrug resistant bacteria is an important strategy to control the spread of infection in hospitals. This thesis is composed of three studies. The first study compared three laboratory protocols for the detection of methicillin-resistant Staphylococcus aureus (MRSA) from surveillance specimens. The broth-containing protocol detected 13.3% to 23.3% more MRSA-positive patients per surveillance event than the 2 solid agar protocols, but was more expensive. The second study examined the natural history of Multi-drug resistant Enterobacteriaceae (MDRE) colonization and infection for an 18 month period in solid organ transplant recipients. We found that 24% of patients were colonized with MDRE and 6 (9%) developed clinical infections. Most colonizing isolates were unique (66/69). No clinical infections resulted from patient to patient transmission. The annual cost of a surveillance program was calculated at $CDN 1,130,184.44. We suggest that MDRE surveillance and isolation precautions are not warranted in the absence of a clonal outbreak.
Structural analysis of three proteins affecting global transcription levels: Using X-ray crystallography to elucidate functions of non-enzymatic proteins

Classically, only such proteins that had been well characterized using biochemical techniques were selected for structural studies. This allowed researchers to utilize known protein properties in determining conditions optimal for structural investigation. However, as structural biology has matured, at the same time generating structural characteristics about functionally less well characterized proteins, structural studies can now also offer insight into protein function when sequence and biochemical data offer only limited clues. In this thesis, three proteins were chosen for such an approach, KaiA and KaiB from cyanobacterium Anabaena sp. PCC 7120 and Rcd-1 from Homo Sapiens. As a common theme, they are involved directly or indirectly in the regulation of global cellular transcription complexes. The structures determined account for various aspects of their known biological effects as well as offering intriguing insights and allowing more educated exploring of probable functions on a molecular level. Structure-guided site-specific mutation experiments accompanied the analysis of aspects of the proteins' functions. This combined approach allows one to suggest specific functions and to propose mechanistic details of the regulatory actions of the proteins under study.
Spatiotemporal relation between the primary cilium and Sonic Hedgehog signaling effectors during renal development

Sonic Hedgehog (SHH) - GLI signaling is essential for murine renal development. In the gastrulating embryo primary cilia are required for the transduction of SHH-dependent signals. Yet, the role of primary cilia in epithelial-mesenchymal signaling during kidney development is undefined. Using immunofluorescence microscopy we identified primary cilia in both epithelial and mesenchymal cell lineages in the embryonic mouse kidney. Scanning electron microscopy identified cilia of varying morphology on the apical surface of tubular epithelia. Transmission electron microscopy revealed ciliary axonemes with 9+0 arrangements. GLI2 and GLI3, SHH-dependent transcriptional effectors, localized to cilia in wild-type embryonic mouse kidneys. These results suggest an intersection between cilia and SHH signaling during kidney development and serve as a basis for continuing studies aimed at determining SHH pathway activity and function in mice deficient in primary cilia in specific kidney cell lineages.
Copyright law, digital technology and the future of entertainment

Evolutions in file sharing technologies and the Internet are transforming the way that entertainment content is delivered and used by consumers. The traditional control that the entertainment industry was able to exert over content is being usurped as music and movies become increasingly digitized and freely and instantaneously accessible around the globe. Once content is made available in this way, it can be reproduced with perfect fidelity, thereby undermining the exclusive rights to which creators and owners of such content are entitled pursuant to copyright laws. This thesis will critically examine the legality of downloading unauthorized entertainment content over the Internet. This thesis concludes by recommending a compulsory licensing scheme with a "sunset" provision that not only compensates rights holders, but also encourages the use and further development of various technologies, including Digital Rights Management and Peer-to-Peer file sharing systems.

Keywords: Downloading of data
Copyright infringement, Prevention
Copyright, Performing arts
Copyright, Music
Copyright, Motion pictures
Peer-to-peer architecture (Computer networks)
What's in, what's out Stakeholders': views on the boundaries of Medicare

Although there was consensus that the system should continue to be needs based but needed reform, the concept of path dependency explains why reform remains stalled. It was found that the ideas of the policy elites are "stuck" in what has been created. The ideas and interests supported the existing institutional framework that privileges the public funding of medically necessary hospital services and physician services. Policy decisions that have been made at an earlier time have limited the choices and influenced the ideas of the policy elites on what should be funded under Medicare. The sustainability of the Canadian model of health care known as Medicare is the subject of intense public debate and has focused on updating the determination of what services should be publicly funded. Provincial/territorial health insurance plans must fully cover all medically necessary hospital and/or physician services. Even though there have been numerous reports over the last few decades identifying similar themes, reform has been stalled. The objective of this thesis was to assist in the policy process by ascertaining the views of policy elites from key stakeholder groups across Canada on what should be "in" and "out" of the publicly funded system. Using a non-experimental, cross-sectional design, a self-administered questionnaire (available in both French and English) was distributed between January and April, 2002, to policy elites involved in health policy discussions, either as health providers (doctors, nurses, pharmacists, home care providers, hospital/health authorities) or as business. The results are based on 2,523 responses. The ability of government to "buy real change" will largely depend upon its ability to mediate the scope of conflict within the existing institutional framework. Even incremental changes could prove contentious, as evidenced by the views on funding insured hospital services regardless of the site of delivery. A shift to a more holistic approach that would include an expanded funding role for government could be even more contentious, as the path of the medical model is so solidly established in governmental regulations and funding frameworks. Successful reform will need to address, rather than assume, a broader view of health.
Equity-linked annuities and insurances

In this thesis, we will introduce a consistent pricing method for Equity-Linked products and Equity-Indexed Annuities in particular. Due to their unique design, these products involve mortality and financial risks, and hence have to be valuated in an "incomplete market" framework. The no-arbitrage argument of Harrison and Pliska (1981) leads to the derivation of martingale probability measures for the valuation of these products. By assuming the separation of the insurance and annuity markets, we derive an age-dependent, mortality risk-adjusted martingale probability measure for term life insurance and pure endowment insurance. This method is similar to that of Jarrow and Turnbull (1995) and Ho and Lee (1986) in the sense that we derive martingale probability measures using the price information of standard insurance and annuity products exogenously. We then extend these martingale structures to include the financial market information. As a result, we are able to valuate an Equity-Linked product by pricing its death benefits and survival benefits separately. We also provide an alternative approach by considering the endowment insurance market and derive an associated age-dependent, mortality risk-adjusted martingale probability measure. In this case, an Equity-Linked product is valuated in a unified manner. Recursive pricing algorithms for equity-linked contracts that include surrender options are also introduced. The additional structure used to describe the dependence relationship defining the martingale measures are obtained using copulas. Numerical examples on EIAs are provided to illustrate the implementation of these methods. The aforementioned framework is developed under deterministic interest rates as well as under stochastic interest rates. The latter approach leads to martingale probabilities that evolve with the stochastic interest rates. Similar to Black, Derman and Toy, we assume that the volatilities for standard insurance and annuity prices are given exogenously. We then derive martingale probability measures allowing to value equity-linked products.
Fibre bonding and mass decay near a fracture line in paper

Fracture in paper is generally “hairy”, with fibres protruding from the fracture line. Hairy fractures are characterized by a gradual decay of mass near the fracture line. The abruptness of the mass decay depends on the ratio between the number of fibres that break and the number that are pulled from the network. This ratio depends on a number of structural parameters, including fibre length, strength and bond strength. If the first two are known, the bond strength can be deduced by comparing the measured mass decay near the fracture line to the results of a micro mechanical model. In this study, fracture in paper is characterized theoretically using both analytical and Monte Carlo methods. A comparison between the experimental results and theoretical results led to a measurement of effective bond strength in paper. This method incorporates a factor accounting for the inactivation of bonds far from the crack line.
A G-theory based adjustment process for calibrating marker scores

Many large-scale educational assessments require examinees to construct a response for one or more tasks. The responses are then scored by markers who have been trained to adhere to certain scoring criteria and standards. When a marker does not adhere exactly to the criteria and standards, systematic error—or bias—may be evident in the marker's scores. In this thesis, bias is defined as the systematic difference between scores assigned by a novice marker and scores assigned by an expert marker (or panel of expert markers). A model is proposed for use in calibrating scores from biased markers. The model is based in generalizability theory and defines a separate universe of generalization for each marker. The universe scores in the universe of generalization for the expert marker are the scores to which biased scores must be calibrated. The calibration procedure involves adjusting scores by a weighted average of the task difficulties for the various tasks and scoring components. The effectiveness of the proposed calibration procedure was compared to the effectiveness of two other calibration procedures: (1) least squares estimation of true scores using a linear model; (2) adjustment of scores for mean differences between markers. Improvement in score accuracy was measured using the kappa and weighted kappa coefficients. Written responses for three writing tasks were collected from 28 grade 2 students. The responses were scored by one expert marker and four novice markers on three components: Artistry, Content, and Conventions. The proposed calibration procedure was not effective. It usually resulted in no improvement in agreement between novice and expert scores, and sometimes it resulted in worse agreement. The calibration of scores by adjusting for differences between means was also usually ineffective. The least squares procedure, however, was very effective for calibrating scores. This procedure always improved agreement between novice and expert scores. The proposed calibration procedure may have been ineffective because of the small proportion of variance due to tasks, as the calibration procedure adjusts scores by weighting the tasks difficulties. Further research could reveal the conditions under which the proposed model might be more effective.
Recent trends and scenarios of climate change in Hudson Bay and surrounding seas

This study compares the response of Hudson Bay to a transient warming scenario provided by six coupled atmosphere-ocean general circulation models. The analysis focused on surface temperature, precipitation, sea-ice coverage, and permafrost distribution. The response of the sea-ice cover and permafrost to climate change was found to vary considerably among the models and thus large differences were observed in the projected regional increase in temperature and precipitation. In addition, the climate and hydrology of the Hudson Bay region were analysed for trends in order to provide early evidence of climate change in the region. The Theil-Sen slope approach was used to identify the magnitude of the trends and the Mann-Kendall test assessed their statistical significance. The results showed that warming over Hudson Bay has not occurred in a unidirectional way and, consequently, the trends are sensitive to the time periods chosen for analysis. The warming trends of the last few decades are reflected in the timing of sea-ice formation and break-up, but the strong dependence of ice thickness on snow depth suggests that it is more challenging to identify an early climate change signal using ice thickness data than it is using freeze-up/break-up dates. An asymmetry was observed in the trends of maximum ice thickness, as the ice cover has become thicker over time on the western side of Hudson Bay, while slightly thinning trends and statistically significant trends towards an earlier occurrence of the peak ice thickness were detected on the eastern side. It is inevitable that increasing temperatures in the Hudson Bay region will result in a thinning of the ice cover in the long run, but changes in snow depth will tend to offset the ice thickness trends in the short run. If this trend towards a longer ice-free season continues, as the models suggest, it will have disastrous consequences for the polar bear populations that inhabit the region.