VictorJuiz/thesis huggingface dataset:
Balance dynamics and gravity waves in four-dimensional data assimilation

This thesis examines the application of three methods of so-called four-dimensional data assimilation to dynamical models where there exists a timescale separation between vortical motion and (relatively fast) inertia-gravity waves. Using a highly simplified dynamical model which admits one nonlinear vortical mode and one inertia-gravity wave, we evaluate the relative strengths and weaknesses of linearization-based and ensemble-based sequential assimilation (i.e. two varieties of the Kalman filter), and four-dimensional variational assimilation (4DVAR). The first part of this study is concerned with balanced flow, or flow where vortical motion dominates and inertial/gravitational motion is "slaved" to the dominant flow. The goal of assimilation in this context is to recover the true balanced state, without the excitation of spurious inertia-gravity waves. It is shown that the excitation of spurious waves becomes more difficult to control as the nonlinearity of the assimilation system is increased, for example by decreasing observation frequency. If not enough components of the true state are observed or observations are infrequent relative to the nonlinearity of the model, the explicit evolution of error covariances using a tangent-linear model can easily become quite inaccurate, which results in a highly unstable assimilation cycle wherein spurious waves are excited and not controlled. Both ensemble-based and implicit variational covariance models offer improvements, but these are themselves limited by error due to sampling and non-Gaussianity of the ensemble and by the tendency to settle into local minima of a non-quadratic cost function. The analysis is then extended to dynamical regimes where the inertia-gravity wave becomes more important to the evolution of the system as a whole, either by increasing its magnitude, decreasing the timescale separation, or increasing the coupling between fast and slow modes. It is found that recovery of either mode from observations that contain both timescales benefits from the four-dimensional estimation of error statistics. The ability to extract both modes from observations which contain both timescales of motion depends both on the estimated fast-slow covariances, as well as the estimated error variance ascribed to the gravity wave. Recovery of a non-negligible inertia-gravity wave is found to be possible with the Kalman filter, and more so if an ensemble is used to estimate covariances, but extremely difficult for variational assimilation. It is also found that accuracy of the assimilation for the different regimes of balance/imbalance can be weakened considerably as systematic model error is added and increased. Some typical modifications designed to counter systematic error are shown to alleviate some of these problems, but also increase the excitation of spurious imbalance.
Quantitative descriptions of the temporal dynamics of physiological time series: Towards a method for detecting dynamical change

Physiological rhythms, such as stride intervals, the beating of our hearts, arterial blood pressure and subtle rhythms underlying the release of hormones regulating growth and metabolism, the digestion of food and many other bodily processes are central to life. A defining but elusive feature of physiological systems is their daunting complexity that arises from the interaction of myriad of structural units over a wide range of temporal and spatial scales. Quantifying and modelling this remarkable and often bewildering repertoire of behaviours exhibited by living organisms is one of the major challenges of contemporary science. Thus, in this thesis we have thoroughly examined the suitability of three methods, capable of capturing intricate scaling properties of physiological time series. The examined methods were estimators of a multifractal spectrum, the Poincare plot analysis and statistical analysis of the wavelet modulus maxima. Their competence was primarily gauged in terms of estimation precision and resolution.
Molecular characteristics associated with the elm response in the Dutch elm disease complex

In vitro and in vivo investigations were carried out to improve the understanding of the elm (Ulmus sp.) response to Ophiostoma ulmi (sensu lato), the fungal causal agent of Dutch elm disease (DED).A C-TAB based DNA/RNA extraction method, including LiCl2 and PVP, assisted in the isolation of pure, high molecular weight nucleic acid from all elm tissues studied. RT-PCR and sequence analysis of U. americana and U. pumila phenylalanine ammonia lyase (PAL), chitinase (CHT) and polygalacturonase inhibiting protein (PGIP) transcripts revealed variation between elm species. Steady state northern analysis of U. americana and U. pumila PAL, CHT, and PGIP transcripts, showed differences between elm tissue sources. A novel RNA dot blot study of PAL, CHT and PGIP expression during in vivo DED infection was performed employing leaf midrib analyses. All genes displayed differential expression compared to water controls. Both PAL and PGIP were systemically induced prior to isolating the fungus in expressed leaf midribs. These studies identify exciting new opportunities for directly assessing DED in vivo. In vitro protein isolation, sequence and PCR analysis of a 22 kDa mansonone inducing glycoprotein gene, from O. ulmi (sensu lato) strains, revealed no amino acid differences. Sequence analysis of DED fungal polygalacturonase (PG) genes indicated three nucleotide changes, causing three amino acid changes between O. ulmi and O. novo-ulmi strains. Inoculation tests in the field confirmed that U. pumila is resistant to the DED aggressive strain O. novo-ulmi (H175), displaying no field symptomatic variation compared to controls. During routine field sampling of U. pumila, natural branch infections of early vessels were identified. One isolate designated as FI, was confirmed as an O. novo-ulmi strain following morphological and molecular (RAPD, CU, and ITS-rDNA gene) analyses. Elm tissues were investigated for their sensitivity to elicitors that induce mansonone F phytoalexin accumulation, on DED susceptible U. americana and DED resistant U. pumila. Elm inner bark was particularly sensitive to elicitors. O. ulmi, O. novo-ulmi, O. ulmi (Q412) derived culture filtrate elicitor (QCFE), and a polygalacturonase preparation all induced high amounts of mansonone F. Elm inner bark sensitivity to elicitor induction varied during the growing season.
Learning to write in English: A comparative study of first and second language learners with and without reading disabilities

The present study examined writing ability in English as L1 (EL1) and English as L2 (ESL) children in Grade 5. The performance of children with reading disabilities (RD), as identified by having below average scores on tests of phonological processing and word recognition skills, was also examined. It was hypothesized that being ESL and having poorer English language proficiency skills would exacerbate difficulties that RD children experienced in the area of written expression. The children with RD did perform significantly more poorly than children without RD on various components of the measures of writing ability. However, there were no significant differences between EL1-RD and ESL-RD children on any writing components. It was also hypothesized that in the normally developing group, ESL children would have more difficulty with the writing tasks than EL1 children. However, ESL children performed as well as their EL1 peers on all aspects of the writing tasks.

Keywords: English language, Written English
English language, Written English
Learning disabled children, Education (Elementary)
Reading disability
Reading (Elementary)
Water quality transformations in pipelines: A two-dimensional multi-component simulation model

This thesis studies the critical problem of water quality in a pipeline system considering the fate of disinfectant, the corrosion of the system, and the change in turbidity of water. The dissertation investigates a two-dimensional unsteady, multi-component, water quality model by coupling a mass transport equation including all transport mechanisms (namely advection, diffusion, and reaction) for the chemical constituents with a water hammer model. The decay/growth of the constituent is investigated with (but not limited to) a first-order reaction term. A suitable turbulence model is used to determine the velocity fluctuations and therefore the turbulence shear stresses and the corresponding diffusivity terms. The hydraulic and the mass transport equations are, then, coupled by two different numerical schemes; a finite difference method for the mass transport and the method of characteristics for the hydraulic part. Finally, the numerical results of the proposed model are compared with the results of available models in the literature.
Constructing the world: Russell and the Edwardian philosophers

This thesis attempts to place Bertrand Russell's work on the problem of the external world into a particular philosophical and historical context. This context is provided by considering a Controversy that raged among philosophers of various stripes in England between 1904 through to 1916. Central to this Controversy is G.F. Stout's "Proto-Realism," which was informed by the Brentaman realist tradition. From this dialectic, which pivoted around Stout's doctrine, there developed and emerged the nascent British New Realism of Samuel Alexander and T.P. Nunn. I trace the development of various philosophical arguments that took place in this Controversy, especially those centered on the nature of sensible objects, and how they are connected to physical things in the world. Another important aspect of the Controversy is the explicit and conscious desire to avoid merely postulating the elements of the world in need of explanation. Certain significant aspects appear in relation to our understanding of Russell's work dealing with similar issues from this period. For one, I show that one gains a better understanding of the nature of Russell's "sense-data," as "real," "physical" and "ultimate constituents" of the world. I will also examine the significance and distinguishing features of Russell's method of logical construction, especially in contrast to Stout's "ideal constructions," and other psychological constructions advanced in this Controversy. Finally, I believe a better appreciation and understanding of Russell's insistence that philosophers examining such issues ought to be familiar with the developments of mathematics and mathematical logic, can be provided by highlighting certain analogies between the way issues were construed in the Controversy and the way specific problems were addressed in the nineteenth century developments of mathematics.
Comparing the behavioural profiles of children with Fetal Alcohol Spectrum Disorders (FASDs), Attention Deficit Hyperactivity Disorder (ADHD), and Oppositional Defiant/Conduct Disorder (ODD/CD): Working towards differential diagnosis

Fetal Alcohol Spectrum Disorders (FASDs) is a complex disorder characterized by a pervasive pattern of cognitive and behavioural impairments. Children with FASDs have behavioural profiles that are strikingly similar to children with ADHD and ODD/CD; however no study to date has compared children with FASDs to these two groups. It was hypothesized that children with FASDs would present with a unique behavioural profile compared to typically developing children and children with ADHD and ODD/CD. Furthermore, we expected that individual items from a standardized questionnaire could be used to produce an FASD screening tool. An exploratory hypothesis investigated whether the severity of socioemotional disturbance seen in children with FASDs would be reflective of environmental risk factors. Results revealed that children with FASDs had a unique behavioural profile. Additionally, an FASD screening tool is proposed. Background factors were not found to influence the problem behaviours seen in children with FASD.
Biochemical and molecular characterization of anaerobic benzene-degrading, nitrate-reducing cultures

The second objective of this research was to determine which species of bacteria are present in the cultures, and which are active in the benzene degradation process. Direct correlation of an active species to benzene degradation rates was not possible using these methods; and molecular investigations revealed the presence of numerous organisms thought to be carrying out side-reactions in the cultures. Stoichiometry and molecular evidence also pointed towards the involvement of anammox in benzene degradation under nitrate-reducing conditions. Characterization of benzene-degrading nitrate-reducing enrichment cultures was carried out using both biochemical and molecular methods. The first objective of this research was to gain a better understanding of conditions under which benzene degradation is promoted or inhibited in order to improve consistent benzene degradation in the nitrate-reducing cultures. Fe(II), H2, resazurin, and nitrite were observed to inhibit benzene degradation, while acetate addition was shown to promote faster benzene degradation.
Consequences of reduced carbonic anhydrase activity on the gas exchange physiology of Arabidopsis Thaliana

Carbonic anhydrase (CA) (EC 4.2.1.1) catalyzes the reaction CO2 + H2O ↔ HCO3− + H +. Two isoforms of the β-CA type have been characterized in C 3 plants: the chloroplast isoform CA1, and the cytosol isoform CA2. To determine the roles of CA1 and CA2 in photosynthesis, the gas exchange physiology of transgenic lines of Arabidopsis thaliana was examined in air- and low-CO2-grown (200 μmol mol−1 CO2) plants. Wild-type and air-grown CA1 anti-sense displayed similar net CO2 assimilation rates and stomatal conductance. Low-CO 2-grown CA1 anti-sense had enhanced stomatal conductance, but not higher Ci/Ca. Modeled assessments of the results indicate that CA1 activity promotes mesophyll conductance. Low-CO2-grown CA2 anti-sense plants exhibited high stomatal conductance, and both air- and low-CO 2-grown plants displayed reduced net CO2 assimilation rates and increased Ci/Ca. In addition to facilitating CO 2 diffusion across the cytosol, the results indicate that CA2 activity might be critical to CO2 sensing.
A 4-bit analog-to-digital converter for high-speed serial links

The data-processing speed of digital systems has drastically increased with scaling of VLSI technology. Their performance, however, has become severely limited by interconnection bandwidth between chips. This is mainly because interconnect links filter high-speed signals causing severe signal degradation and intersymbol-interference. To improve the performance of links, digital communication techniques are required to compensate for ISI and transmission loss. These techniques imply increased complexity and extra resolution in transmitters/receivers. Thus, their effectiveness strongly depends on the performance of high-speed ADCs and DACs that need to realize high sample rates and achieve multiple bits of resolution. To understand applicability of digital communication techniques to high-speed links, a 4-bit 2-way time-interleaved ADC is fabricated in a 0.18-μm standard CMOS technology. This ADC consumes about 131mW from 1.8-V at 3.2 GSamples/s and occupies an active area of 0.27-mm2, which is small enough to allow integration of the converter in a complete transceiver chip.
The expression patterns of the Arabidopsis perk receptor kinases 1-7

The purpose of this project was to study the expression patterns of the Arabidopsis PERK family members (AtPERKs), 1-7, using RNA blot analysis and promoter-GUS studies. RNA blot analysis was performed on RNA samples extracted from Arabidopsis thaliana ecotype Columbia seedlings, roots, leaves, bolts, buds and siliques. Generally, the AtPERKs showed little or no RNA transcripts in leaves, and high levels of steady-state RNA in buds (except AtPERK4). Some AtPERKs were found to be broadly expressed, while others showed a tissue-specific pattern of expression. For example, AtPERK1, 2 and 3 are expressed in most tissues, while AtPERK4 is bolt-specific, and AtPERK6 and 7 are bud-specific. To study the expression patterns of AtPERK3 more closely, the promoter region of AtPERK3 was fused to the GUS reporter gene and transformed into Arabidopsis thaliana ecotype Columbia. Preliminary results on transformed 6-day seedlings showed GUS staining specifically in the basal region of the hypocotyls.
The direct medical costs associated with suspected (confirmed and negative) heparin-induced thrombocytopenia

Purpose. The objective of this study was to identify and quantify the direct medical costs associated with suspected (confirmed and negative) heparin-induced thrombocytopenia (HIT) from a Canadian hospital perspective. Conclusions. This is the first study to quantify the costs associated with suspected HIT cases. These cases increase the costs of hospital care. Results. Confirmed HITT cases incurred substantially greater average costs ($34,155, range $358-$202,069, n=12) than confirmed HIT cases without thrombosis ($4,575, range $39-$16,373, n=8). The average cost of a negative HIT case was $119 (range $39-$4,181, n=88). Methods. A cost of illness analysis was conducted in patients with suspected HIT during 2005. Resource utilization variables included: (1) laboratory tests to investigate HIT, (2) HIT-safe anticoagulant use, (3) diagnostic imaging for HIT with thrombosis (HITT), and (4) additional hospital days attributed to HIT. The average cost per case of confirmed HIT, confirmed HITT, and negative HIT was calculated.
The pharmacokinetic analysis of a therapeutic drug interaction between a type-1 multidrug resistance modulator, valspodar (PSC 833), and an anticancer agent, doxorubicin, in patients

It is believed that the inhibition of multidrug resistance type 1 with valspodar (PSC 833, [PSC]) would enhance chemotherapeutic effectiveness of doxorubicin (Dox). The co-administration of Dox with PSC, however, did not improve patient anti-tumor response. We therefore, hypothesized that the pharmacokinetic analysis of Dox and PSC interaction will uncover a mechanistic basis for their chemotherapeutic failure. An in-depth pharmacokinetic analysis was conducted on Dox, doxorubicinol (Doxol), a metabolite of Dox, and PSC plasma concentrations, in the absence and presence of Dox and PSC, within a patient population having a solid-tumor diagnosis. Both non-parametric and compartmental modeling pharmacokinetic analyses were applied. Dox and PSC appeared to affect each other's clearance and apparent distribution. Unexpectedly, both Dox and PSC distribution and efflux rate constants decreased. PSC anticipated effect on Dox distribution is an expansion not a contraction. Our findings furnish evidence that there is a need for a PSC clinical paradigm shift.
Finding a way, finding the self: the journeys of nine physical education students pursuing 'non-traditional' paths

This study first explores the ways in which nine men and women of South, Southeast and East Asian backgrounds came to be enrolled in a post-secondary physical education program, and secondly asks how these journeys influenced their sense of identity. Multiple, semi-structured, one-on-one interviews were conducted, asking about physical activity and physical education experiences, and how students came to study physical education. Most individuals negotiated with their parents in order to pursue their physical activity interests. Many participants also stated that they were one of few people of their background who showed an interest in sport. Thus, questions about identity and belonging resulted in answers ranging from feeling different and distinct, to feeling a stronger sense of ethnic identity and connection to one's community. Moreover, some participants' comments pointed to the contested nature of 'authentic' ethnic identity and how it is negotiated among members of a particular group.
Uncertainty management method for a terrain scanning robot

Remote sensing of buried explosives has continuously been a great concern, especially for detecting landmines jeopardizing the human lives and economic development of the war-torn countries. This dissertation describes the software development for a mobile terrain scanning robot capable of autonomously manipulating a typical handheld detector for remote sensing of buried landmines in a manner similar to a human operator. The autonomous manipulation of the detector on unknown terrain requires acquiring sensor data for developing an online terrain map and generating an obstacle free path for the end effector of the robot. Thus, the software includes a twofold process of map building and path planning that are specifically designed for a real-time platform to be orchestrated with the other functions of the robot. Map building features a distributed sensor fusion system to tackle the uncertainties associated with the sensor data. It provides local terrain maps by fusing the redundant measurements and the complementary data obtained from competitive rangefinders and joint position sensors, respectively. The fusion takes place in a compound data processing module that includes a batch processing filter, a static filter, and a fuzzy adaptive Kalman filter. The Kalman filter requires a dynamic model of the process so that a novel stochastic model is introduced for the terrain undulations. An important parameter of the model that significantly influences the output of the filter is the standard deviation of the probability distribution of the process disturbances modeled by white noise. A systematic fuzzy modeling technique is used to determine the standard deviation based on the terrain type and adapt the filter, accordingly. The outlier rejection is carried out using the Mahalanobis distance between the estimates and the new measurements. Path planning determines the desired joint coordinates of the robot to move the detector at a constant distance from the ground when the normal to the detector plate is maintained parallel to the local normal of terrain. Unlike the traditional methods, the path is generated in the non-Cartesian coordinate frame of the sensors to avoid a great deal of transformations involved in reproducing the terrain map in the Cartesian coordinate frame. The software has been successfully implemented into the Mine Detection Robot (MR-2) manufactured by Engineering Services Inc. (ESI) to synthesize the autonomous manipulation of a metal detector.