VictorJuiz/thesis huggingface dataset:
The influence of spatial scale and land-use on macroinvertebrate community organization in four neotropical streams

I characterized the structure (taxonomic composition) and function (functional feeding group (FFG) composition) of macroinvertebrate communities, along an altitudinal and stream-size gradient of four neotropical streams. In addition, I quantified both inter-stream and inter-habitat variation benthic community composition, with a view to discovering the influence of spatial scale upon the structure and function of macroinvertebrate communities in a tropical locality. In addition, these measures were compared with changes in organic matter standing stock and algal biomass both among stream reaches and among habitat-types within a given stream. Finally, I assessed the degree to which energy sources and the benthic communities that are associated with them are altered by agricultural activity and the input of treated domestic waste, by comparing the longitudinal patterns in these variables between the north-flowing (pristine) and south-flowing (impacted) streams. Only the Guanapo River demonstrated any significant functional differences from the other streams, although this was not reflected in an overall effect for stream system on benthic community composition. Both univariate and multivariate analyses indicated significant changes in macroinvertebrate community function, with smaller changes in taxonomic composition, from headwaters through to low-reach sites. Conversely, inter-habitat variation in assemblage structure was generally less than that seen between sites. However, the mid-reaches and low-reaches of the south-flowing streams demonstrated greater degrees of inter-habitat variation than those of the north-flowing streams. In both the south-flowing streams, algal biomass was strongly correlated with scraper importance, this being the FFG that processes algae, and filterer importance was correlated with moss biomass, this being reflected in the decline of filterers in the low-reaches of the south-flowing streams. The results of this study indicate that in these tropical streams, variation in macroinvertebrate community structure and function alter with spatial scale, and that there is an overall hierarchical influence of reach-scale variables over habitat-scale variables, although the degree of this influence varies across stream reaches. Also, this study shows that land-use can have more of an influence on the macroinvertebrate community than the natural longitudinal gradient, resulting in benthic communities that are tolerant of non-point source pollution and that are influenced by largely autotrophic processes.
Helping hand: an anatomically accurate inverse dynamics solution for unconstrained hand motion

The human hand is a marvelously useful biomechanical device that has inspired numerous depictions and models, however its complexity, makes the construction of accurate visual and physical models an extremely challenging goal. We present, Helping Hand, a realistic skeletal musculo-tendon model of the human hand and forearm. The model permits direct forward dynamics simulation, which accurately predicts hand joint orientation given a set of muscle activations. We also present a solution to the inverse problem of determining an optimal set of muscle activations to achieve a given pose or motion; muscle fatigue, injury can also be specified, yielding different control solutions that favor healthy muscle. The model can take kinematic pose data and predict animation sequences of the hand to fit or indeed physically improve upon kinematic data. Lastly, we demonstrate ways to isolate and visualize muscle groups as their effect on hand motion is animated.
Thermo-oxidation as a means of tritium recovery from DIII-D and JET carbon codeposits

This thesis continues studies on thermo-oxidation as a method for the removal of tokamak codeposits. Oxidation conditions were extended to pressures 79kPa and temperatures 673 K. Codeposit specimens with a variety of compositions, densities and thicknesses were taken from DIII-D and JET. It was confirmed that increasing the temperature and pressure improves the effectiveness of codeposit removal as measured by the initial D removal rate and by the final D content after prolonged oxidation. The removal effectiveness is much more sensitive to changes in temperature than to changes in pressure. Of particular importance, the initial D removal rates were found to increase linearly with increasing inherent D content independent of Be content, ranging from 0-60% Be/(Be+C), and thickness, ranging from 10-270 mum. The total amount of D removed does not appear to be affected by thickness or beryllium content of the JET codeposits. In contrast, the DIII-D codeposits show the D removal efficiency decreasing with increasing inherent boron content.

Keywords: Aerospace engineering
Quantitative trait loci mapping of elevated carbon dioxide induced anthocyanin in Arabidopsis accessions

We investigated natural variation among 121 accessions of Arabidopsis thaliana, for anthocyanin accumulation as a stress response to continuous elevated CO2 exposure. The greatest range of anthocyanin accumulation was observed between the accessions Columbia (Col) and Landsberg erecta (Ler). The F2 progeny of a Col x Ler and Ler x Col cross demonstrated variation in anthocyanin accumulation, suggesting that CO2-induced anthocyanin accumulation was a quantitative trait. A major QTL, CIAA1, was identified using a RIL population. Genetic analysis linked the CIAA1 trait to a small region on chromosome 2; while the nearby erecta locus was excluded as a contributor to the trait. Using NILs, we confirmed CIAA1 as an individual QTL. In addition, beta-amylase expression and activity remained low in Ler, while Col showed a significant increase under continuous high CO2 levels. Correlation between anthocyanin accumulation with beta-amylase expression and activity was established.
Parallel implicit Newton-Krylov-Schwarz method for predicting compressible turbomachinery flows

A parallel Newton-Krylov-Schwarz (NKS) algorithm is presented for solving two-dimensional steady compressible flows in turbomachinery. The spatial discretization of the governing equations is carried out on multiblock quadrilateral mesh using an upwind finite-volume formulation with limited linear reconstruction and Riemann-solver-based flux functions. A matrix-free inexact Newton method is used to solve the system of nonlinear equations arising from the finite-volume discretization procedure and a preconditioned GMRES method is used to solve the resulting linear system of equations. A Schwarz global preconditioner is used in conjunction with block incomplete LU (BILU) preconditioners based on the Jacobian of the first-order scheme for the mesh sub-domains. The preconditioning and multiblock mesh structure allow efficient and scalable parallel implementation of the implicit algorithm. Numerical results are described for several flow cases, demonstrating both the effectiveness of the algorithm and parallel implementation. Influences of the global and local preconditioning are also investigated and discussed.

Keywords: Fluid dynamics, Mathematical models
Compressibility, Mathematical models
Turbomachines, Fluid dynamics
The impact of accessibility on business location and performance

This study analyzes the impact of accessibility on business location and business performance in Toronto. A multinomial logit model of intra-metropolitan business location is used to assess the relative importance of accessibility variables, such as proximity to infrastructure, customers, competitors and complimentary businesses on firm location. Key accessibility variables are plotted against business performance indicators (sales and productivity) for analysis of their relationship. This study uses a detail classification of industry (4 digit SIC) so that close attention can be given to the idiosyncrasies among different industries. Specific types of business studied are: law firms, pharmacy stores and car dealerships. Results show that proximity to infrastructure is not a signification factor affecting business locations. Rather, it is the relative locations of all other socio-economic activities that matters. Further, analysis of relationship between accessibility and productivity indicates that accessibility is a necessary condition but not sufficient condition for business success.
The shape of things to come: The roles of linguistic and perceptual information during online processing

Some researchers have suggested that anticipatory processes in language processing are restricted to "grammatically-legitimate" combinatorial possibilities (e.g., Dahan et al., 2000), while other discuss combinatorial relationships as being influenced by the "real world" compatibility of objects properties (e.g., Kaschak Glenberg, 2000). The present experiment examines Cantonese Chinese classifiers (grammatical articles that correspond to real-world physical properties of the nouns they classify) to study anticipatory effects when grammatical and perceptual constraints diverge. When asked to make explicit judgments about how well classifiers "fit" with certain objects, participants ignored the objects' shape properties and made ratings based on linguistic rules. During an online sentence processing task, however, participants showed sensitivity to both linguistic and perceptually-based combinatorial constraints. Results from this study indicate that online sentence processing incorporates both linguistic and perceptual information, and reveals that perceptual and semantic information can drive anticipatory processes even when grammatical information provides incompatible cues.
Interfacial electronic structure of an organic-inorganic hybrid optical upconverter device

Recent technological advancement in near-infrared (NIR) optical upconverter has integrated an organic light emitting diode (OLED) with an inorganic infrared photodetector, which allows upconversion from NIR to any visible light wavelength. The structure has incorporated C60 as an interlayer between the OLED and the InGaAs/InP PIN photodiode, resulting in superior device performance. In this work, the interfacial electronic structures of three different device structures are elucidated and compared: InP-S/C 60/CuPc, InP-S/CuPc, and InP-S/NPB. Contrary to traditional views on inorganic/organic heterojunctions interface where the charge injections are thought to be from the VBM to the HOMO levels of the organics, the actual charge injections occur from the surface states near the Fermi level to the HOMO levels. Therefore, the Fermi level serves as a good reference level for hole injection barrier at such heterojunctions interfaces, regardless of the hole's energy level, i.e. the valence band maximum. It is found that the C 60 interlayer acts as a surface modifier and increases the work function of InP, which effectively reduces the hole injection barrier for the device.
Multidisciplinary studies of Ca2+-mediated cellular processes: sequence to structure to cellular dynamics

Through the highly regulated events of intracellular Ca2+ homeostasis, often seen as a Ca2+, wave or spike, intracellular Ca2+ acts as a second messenger that regulates numerous physiological cellular phenomena including fertilization, development and apoptosis. To study these Ca2+-mediated cellular processes, multidisciplinary approaches were employed combining information ranging from sequence to structure to cellular dynamics. First, the impressive growth of sequence databases inspired a bioinformatics approach to studying the function of large Ca2+-mediated protein superfamilies. To improve function prediction, a bioinformatics algorithm was developed for classifying subfamilies of large protein superfamilies and was demonstrated on the EF-hand superfamily. Using this algorithm combined with an understanding of the domain architecture of subfamilies, a classification tool and web-accessible database was created for the cadherin superfamily of Ca2+-dependent adhesion molecules (http://calcium.uhnres.utoronto.ca/cadherin). Though rapid, these sequence-based approaches can only vaguely predict Ca2+-mediated functions, while a higher resolution understanding would require spatio-temporal imaging of Ca2+, signals in living cells. Thus, the second part of this thesis is focused on imaging Ca2+-related signaling events using FP (fluorescent protein)-based ratiometric FRET (fluorescence resonance energy transfer) probes (hereafter, FP-based probes). Using the atomic structure of the CaM (calmodulin) in complex with CKKp (CaM kinase kinase peptide), a new FP-based probe was modeled and created with improved characteristics for imaging of Ca 2+ signaling. In in vivo imaging, this new design resulted in a two-fold enhancement in the FRET efficiency, thereby expanding the ability of Ca2+ FP-based probe to visualize Ca2+ mobilization in living cells where a higher sensitivity is required for detection. Similarly, probes were created for detecting caspase proteolytic cleavage and using a co-culture of cells expressing different FP-based probes, simultaneous Ca2+ signaling and caspase cleavage events were imaged in cell death induced by an oxidative burst modeled by a bolus addition of [H2O2]f = 10 mM. When COS-7 cells were induced by an oxidative burst, caspase activation was observed within 2 minutes. This is faster than previously thought and could not been observed using standard in vitro caspase cleavage kits.
MO-PECVD (metal-organic plasma enhanced chemical vapour deposition) of erbium-doped hydrogenated and deuterated amorphous carbon

Erbium-doped hydrogenated and deuterated amorphous carbon (a-C:H(Er) and a-C:D(Er)) is fabricated through controlled thermal evaporation of metal-organic compounds in a hydrocarbon discharge generated by the DC saddle-field plasma enhanced chemical vapour deposition system. Er photoluminescence (PL) is successfully demonstrated for the first time in Er-doped deuterated amorphous carbon (a-C:D(Er)). Uniform distribution of optically active Er 3+ ions is attained by using tris(2,2,6,6-tetramethyl-3-5-heptanedionato) Erbium(III) (Er(tmhd)3) compound as revealed by XPS analysis. Er(tmhd) 3 is observed to be a preferred dopant over Erbium(III) 2,4-pentanedionate (Er(acac)3). Deuteration of amorphous carbon has effectively removed the PL quenching effect caused by non-radiative C-H and O-H vibrational transitions. An improvement factor of ∼4.4 is observed in the minimum doping level of Er required to attain PL in a-C:D(Er), compared to a-C:H(Er). The results of this thesis suggest that a-C:D(Er) material can potentially be used for silicon-compatible opto-electronics applications in 1.5 μm region.
Elucidating the neuroprotective role of teneurin C-terminal associated peptide (TCAP)-1

The physiology of neuroprotection includes the mechanisms and strategies utilized to guard against neuronal injury or degeneration in the central nervous system (CNS). Degenerative disorders may be generally classified as either acute, such as stroke or nervous system injury/trauma or chronic such as Parkinson's (PD) or Alzheimer's (AD) The goal of neuroprotection is to limit neuronal dysfunction and death after such injury and attempt to maintain the highest possible integrity of cellular interactions in the brain resulting in undisturbed neural function. There is a wide range of agents currently under investigation and some can potentially be used in more than one disorder, as many of the underlying mechanisms of damage to neural tissues, in both acute disorders and in chronic neurodegenerative diseases, are similar. These agents include: free radical trappers/scavengers, anti-excitotoxic agents, apoptosis/programmed cell death (PCD) inhibitors, anti-inflammatory agents, and neurotrophic factors. The objective of this research is to characterize a novel family of neuroprotective peptides, teneurin C-terminal associated peptide (TCAP), and to elucidate their protective mechanism.

Keywords: Neurosciences
Statistical learning of gene annotations in Saccharomyces cerevisiae

We present machine learning algorithms for predicting the biological functions of genes. Determining function is simplified to a series of binary classifications. The main challenge of this learning task lies in the extremely small number of positives, compared with large amounts of negatives. We develop a method based on hierarchical clustering with labeled data to search for regions of high positive concentrations. We investigate logistic regression as a baseline for comparing to our technique. These methods are based on different views of the data and depending on the biological processes, one or the other of these approaches performs better, although our method makes more confident predictions for more biological processes. We also investigate data-preprocessing methods, and develop two algorithms for filling missing values in the datasets, which is necessary before some statistical methods can be used.
Reading and rhetoric in Teresa of Avila's Libro de la Vida

This dissertation examines Teresa of Avila's Libro de la vida to show that her discourse contains rhetorical elements that contribute toward the construction of a style that deliberately draws the reader into the text. This leads to the creation of a rhetoric of obedience and implication which helps to defend Teresa's spiritual life and her texts. Teresa did not receive a formal education, but her extensive reading familiarized her with systems of rhetoric inherited from antiquity through the Middle Ages. Teresa did not need a schoolroom to learn about modesty formulas, metaphors or the inexpressibility topoi; her search for a rich spiritual life through her love of books exposed her to the persuasive nature of rhetoric. Medieval and Renaissance attitudes toward women and the absence of parameters that governed women's writing made female texts not only curious things, but dangerous ones, in Counter-Reformation Spain. The added inconvenience of banned or suspect books, which reached its climax with the Valdes Index of 1559, also motivated Teresa to provide her nuns with spiritual readings to guide their progress toward God. But while the Index spurred her writing, it also dealt Teresa with the problems of censorship. Her texts would be scrutinized by her confessors for their orthodoxy. Her awareness of the reading process as a consequence of her own reading experience, consciously or intuitively, led her to incorporate him—the masculine reader who will first read the Vida—into the text. Reader-response theory is applied allowing us to study the reader included in the text—Iser's intended and ideal reader—in order to understand the rhetorical mechanisms at work that collaborated toward the survival of Teresa's manuscripts. Teresa's rhetorical strategies of obedience and implication, developed to counteract the difficulties and challenges she faced, helped to present her as conforming to the social and spiritual context in which she wrote, and implicate her first male readers by questioning their spirituality.
Evaluating the life-cycle of biodiesel in North America

Concerns about climate change and domestic energy security have resurged interest in biodiesel. A number of LCAs of biofuels have been published over the last decade, however none have focused on biodiesel fuel production pathways. In this thesis, biodiesel pathways are compared with respect to life cycle energy use, GHG emissions and land use. Jatropha curcas is a promising feedstock that could be commercially cultivated on non-arable lands in Mexico and perhaps in parts of the southern U.S. Despite such promise, the life cycle environmental performance of Jatropha biodiesel (JBD) have not been assessed for North America. This thesis models the cultivation of J. curcas in Mexico and the conversion into biodiesel for use in the light-duty vehicle fleet in the U.S. When compared to low sulphur diesel and soybean biodiesel, the LCA of JBD shows 54% and 24% lower GHG emissions, respectively, when utilized in a light-duty vehicle.
A pilot study examining acute occupational fatalities involving traumatic brain injury in Ontario between 1996 and 2000 using the files from the Coroner's Office of Ontario

Traumatic brain injury (TBI) at the workplace is a significant contributor to the number of work-related deaths that occur per year. This research aimed to quantify and characterize these deaths in Ontario between 1996 and 2000 using the Coroner's Office data. The research methodology was a comprehensive case series with both analytic and surveillance components. There were a total of 488 work-related deaths identified through the Coroner's files, 98% of which were experienced by men. There was evidence of TBI in 45% of these cases (n = 211). Industries with the highest rate of work-related TBI mortality included other primary (59.1 per 100,000 working population, WP), agriculture (24.5 per 100,000 WP), construction (20.0 per 100,000 WP), and the transportation/communications/utilities industries (13.9 per 100,000 WP). Deaths involving TBI were more likely to be due to falls than non-TBI-related deaths among workers. Implications for injury prevention programs and future research are addressed.
Nearshore small fishes of Lake Huron: Maximizing the detection of species in sampling surveys, demography of an invasive species, round goby, and nest defense of native smallmouth bass against round gobies

This research is part of the Lake Huron Nearshore Small Fish Community and Exotic Species Assessment. Chapter 1: For twenty fish species of interest, I determined the probabilities of detection (p) and the proportions of sites occupied (psi) by a binomial-with-added-zeros mixture model and maximum likelihood estimation. Perca flavescens, Notropis hudsonius, Micropterus dolomieu, Sander vitreus, and Catostomus commersoni had the highest p values. Chanter 2: In the demographic and life history study of round gobies (Apollonia melanostomus), population densities were 0.88 +/- SE 0.19 m-2. Annual survival rate was between 0.012 and 0.036 for young-of the-year, and 0.0239 for one-year-olds, 0.200 for two-year-olds, and 0 for three-year-olds. Chapter 3: My observations of nest-guarding Micropterus dolomieu support previous findings that round gobies increase the frequency of defensive behaviours. Furthermore, as the round goby population density increased from 0 to 3.96 m-2, the probability of a nest success decreased by 65%.
Integrated power-supplies for portable applications

The quest to integrate an increasing number of advanced features into battery-powered mobile devices is driving the need for high-performance power-conversion techniques to extend battery life, while minimizing volume, weight and cost. The focus of this thesis is the power-delivery path from the battery to the load, which typically consists of a combination of analog and digital ICs. The main objective is to develop micro-power fully-digital and mixed-signal control schemes, as well as efficiency improvement techniques that demonstrate the advantages and future potential of digital control. The first part of the thesis deals with implementation challenges for high-performance control-loops, where both digital voltage-mode and mixed-signal current-mode dc-dc converter designs are presented. The second part of the thesis is dedicated to efficiency improvement/optimization in low-power integrated dc-dc converters. The main contributions of this thesis include a self-calibrated digital pulse-width modulator architecture with a current consumption of only 2.56 muA/MHz, as well as a compatible spread spectrum technique for reducing electromagnetic interference by up to 23 dB. A mixed-signal peak current-mode control scheme is presented, with three new low-power architectures, each having distinct advantages. One of these architectures is demonstrated on a custom CMOS IC, which achieves a transient-response time of only 4 mus for V out = 1 V. Two automatic power-stage optimization schemes are demonstrated using two power-stage ICs, where a peak efficiency of 91.4% is achieved at 4 MHz.