VictorJuiz/thesis huggingface dataset:
Evolutionary relationships among members of the fungal form-genus Stachybotrys, with emphasis on indoor-occurring taxa and the phylogenetic distribution and evolution of the trichothecene biosynthetic gene, tri5

Members of the genus Stachybotrys are haploid mitosporic fungi capable of dense colonization of water-damaged building materials such as drywall and ceiling tiles. Current interest in Stachybotrys however, is due to their ability to produce protein-synthesis inhibiting, trichothecene mycotoxins, which have been suggested as linked to a variety of putatively indoor-environment related illness. I used five sequence-based markers and a geographically and otherwise broad set of isolates to investigate the degree of divergence among a set of indoor isolates consistent with the traditional S. chartarum morphotype. Phylogenetic analyses supported the recognition of two distinct phylogenetic lineages within the morphotype. For the lineage most commonly found in Ontario indoor environments, I then used AFLP-based markers to investigate the degree of genetic diversity and pattern of haplotype distribution. Results of cluster and linkage analyses suggested both a strong clonal component and some level of recombination in the evolutionary history of this set of isolates. With respect to distribution, I found no correlation between geographic and genetic distances and the distribution of isolates within a single multi-floor institutional building suggested that indoor isolates had been largely drawn from some, as yet unidentified, external reservoir. Lastly, I explored the broader evolutionary relationships of indoor-occurring and other species of Stachybotrys using both nrDNA and protein-encoding genes and found that species of Stachybotrys partitioned into three strongly supported intrageneric lineages. Two of these clades included common indoor-occurring species. Bayesian analysis suggested that the trichothecene biosynthetic gene, tri5, might be incongruent with the combined phylogeny for this group. Maximum likelihood bootstrap analyses and SH-test results however, did not support this interpretation. Moreover, PAML sites rates analysis indicated that the sampled portion of tri5 was highly conserved suggesting that, for many homoplasic sites, identity between divergent taxa at the amino acid level might be the result of stochastic processes. Results of Southern analyses supported one intrageneric clade, including isolates representing morpho-species S. albipes, S. bisbyi and S. parvispora, as lacking the tri5 gene. The latter results have broad implications in terms of the phylogenetic distribution of trichothecene biosynthetic pathway genes among ascomycetous fungi.**This dissertation is a compound document (contains both a paper copy and a CD as part of the dissertation). The CD requires the following system requirements: Microsoft Office.
Systemic and tissue level stress responses in the rat: Effects of chronic sleep restriction

Sleep restriction is becoming commonplace in today's society and is linked to cardiovascular disease. The present study was designed to determine whether chronic sleep restriction (CSR) and/or extended wakefulness affect growth, and activate the adrenocortical and tissue stress responses. Wistar rats (n = 6-8 per group) accumulated a sleep debt of 250 hours over 31 days using three different sleep-wake schedules (varying in both sleep and wake duration). HSP25 concentrations were measured in the heart, cerebral cortex and plantaris muscle, and cardiac weight and whole body growth rate were investigated. The present study found that: (1) CSR stunted growth rate as a function of extension of wakefulness, (2) CSR did not elicit changes in baseline corticosterone concentrations, (3) chronic 20 hour extension of wakefulness induced a 53% increase in whole heart and ventricular weight (P
Proof-of-concept model of a tethered, high-altitude, rigid-wing platform

This paper covers the construction and testing of a proof-of-concept model of a high altitude, rigid-winged, tethered aircraft. The aircraft is designed as a replacement for aerostats, to act as a payload positioning platform for communication and surveillance equipment. The initial design was found to be unstable through testing, and a series of 60 cm wingspan, small-scale models were constructed to experimentally modify the design into a stable aircraft. Once a suitable design was obtained, a 1.2 m scale model was constructed with a horizon sensing, closed-loop proportional feedback control system for lateral stability augmentation. The stability-augmented model flew stably, for extended periods. Lift and drag measurements were obtained from the flight tests and compared to theoretical calculations. A wind tunnel test was also conducted on the small-scale model to verify the flight test results. Finally, improvements to the stability control system design were suggested, and recommendations were made for larger-scale model construction.

Keywords: Aerodynamics
Kites
The hazards of helping: Mission, work and risk in nonprofit social service organizations

Governments, aiming to contain spending and reduce deficits, have transferred the delivery of many social and health services to the nonprofit sector (NPS). Since services are typically offered at no cost, nonprofit organizations (NPOs) often provide these services to marginalized populations---the homeless, those struggling with poverty, addiction and mental illness. Although most NPOs employ paid staff and volunteers they are rarely viewed as workplaces by researchers and policy makers. Little is known about the nature of work or working conditions in these organizations. A particularly glaring gap is the lack of research on occupational health and safety (OHS) issues affecting NPOs and how well current policy and practice is suited to the challenges and needs of these workplaces. This study examined the nature of work and working conditions in three NPOs providing social and health services to marginalized clients. I took an interactionist approach that recognizes meanings as context dependent and produced via social interaction. By interviewing managers and workers, and through the process of direct observation, I characterized the nature of work in these NPOs. I examined how organizational missions and the process of providing "help" shaped how risks were understood and managed by workers. Missions shaped how workers conceptualized risk by "making visible" some risks while obscuring others. Missions also seemed to have an impact on risk taking and acceptance. Sometimes workers accepted less-than-ideal working conditions or engaged in activities that could hurt them, if doing so allowed them to fulfill the mission of helping marginalized clients. In many instances workers resisted and rejected changes imposed on them that challenged the mission that was so central to their work. The function of missions in these workplaces underscores the importance of understanding the context and social production of risks in workplaces. This study also speaks to how working conditions can be improved in social service NPOs and to some of the shortcomings of mainstream OHS systems of policy and practice.
Rho G proteins and filamin c in insulin action in muscle cells

Insulin-induced GLUT4 translocation in muscle cells involves the activation of Akt and Rac1-mediated actin remodelling, both downstream of PI3K. Our study was aimed at establishing the nature of the relationship between these two signalling arms. The first aim was to test the existence of crosstalk between Akt and Rac1, in an acute fashion. Our results confirm that Akt does not regulate Rac1 activation or actin remodelling. Interestingly, we observed an Akt-dependent activation of Cdc42 in response to insulin. The second aim was to analyze the function of a cytoskeletal protein, FLNc, as a "molecular bridge" between the Akt and Rac1 signalling cascades. The results of this thesis establish that FLNc is an in vivo substrate of Akt. However, we failed to see any functional significance of FLNc in insulin action. Our present study offers further support to the theory of bifurcation of PI3K signals into Akt and Rac1-dependent actin remodelling.
Prefrontal cortical dopamine depletion in neonatal and adult rats: Neurochemical and behavioural consequences

The mesolimbic and mesocortical dopamine systems share a complex and interactive relationship. It is widely held that mesocortical DA serves an inhibitory function over mesolimbic DA activity; impairment of this function is believed to contribute to disordered states including schizophrenia and substance abuse, via permission of mesolimbic sensitisation, a maladaptive form of neuroplasticity that leaves the mesolimbic dopamine system overactive. Previous experiments examining the effects of neurotoxin-induced depletion of prefrontal dopamine (PFC-DA) have only partially supported these hypotheses, as results have been mixed. Moreover, these experiments did not take into account the preponderance of evidence suggesting that the pathogenesis of both schizophrenia and substance abuse is, in part, congenital. As well, a group of rats lesioned on PND11 were tested for behavioural sensitisation to amphetamine both pre- and post-adolescence. These rats were no different from controls during the pre-adolescent tests, but were found post-adolescence to be more susceptible to amphetamine sensitisation than sham-lesioned rats, implying that this deficit does not manifest until adulthood. Two groups of rats were given the PFC-DA-depleting lesion in adulthood (PND60); these rats did not display increased response to or sensitisation by amphetamine, or greater responding for conditioned reinforcers. Together these data indicate that the effects of early depletion of PFC-DA include behavioural symptoms consistent with excess mesolimbic dopamine activity, and that these effects do not emerge until post-adolescence, while adult PFC-DA depletion has no such effects. This research has implications for the study of schizophrenia and substance abuse, both of which are often modeled using lesions of adult rats, and both of which have suspected neurodevelopmental underpinnings. The experiments presented here tested the hypothesis that neonatal insult to PFC-DA-neurons leads to a state of mesolimbic dopaminergic overactivity in adulthood. Rats were given 6-OHDA to deplete PFC-DA on PND11 and were tested for locomotor response and behavioural sensitisation to amphetamine, and responding for conditioned reinforcement after amphetamine challenge in adulthood. Dopamine release in the nucleus accumbens (NAcc) after two doses of amphetamine was also measured. These rats demonstrated hypersensitivity to systemic amphetamine, increased responding for conditioned reward, and elevated dopamine release in the NAcc, all of which suggest excess mesolimbic dopamine activity.
Acid tolerance and the involvement of secondary metabolism in Streptococcus mutans

Dental caries is the dissolution of tooth enamel caused by the acidic end-products produced from bacterial metabolism of dietary carbohydrates. Streptococcus mutans, a ubiquitous constituent of human dental plaque, is an etiological agent of dental caries. Two of S. mutans' cariogenic attributes are acidogenicity and aciduricity. Acidogenicity is the ability to produce acids from carbohydrate catabolism. Furthermore, S. mutans has developed a complex response network allowing it the ability to survive in this acidic environment, termed aciduricity. Studies have shown regulation at the genomic and proteomic levels is paramount in aciduricity for S. mutans (29, 91, 92, 153, 168, 170). Among the pathways showing up-regulation to acid were the citrate metabolism pathway (29), the glyoxalase pathway (91, 170), and the pyruvate dehydrogenase pathway (168). The goal of this work was to investigate the mode of acid tolerance for three secondary metabolic pathways; citrate transport and metabolism, the glyoxalase pathway (focused on LGL) and pyruvate dehydrogenase (focused on PdhA) in S. mutans. S. mutans is capable of citrate transport, via the CitM transporter. Transport is most efficient when coupled with Fe 3+. The end-product of citrate metabolism is aspartate. The citrate metabolic pathway includes citrate lyase as citrate accumulates in a citrate lyase knockout mutant. Citrate was found to be toxic to S. mutans, however, pre-exposure to citrate resulted in increased acid tolerance. LGL is involved in the detoxification of methylglyoxal, illustrated by the absence of enzyme activity in an lgl mutant (LGLKO), hypersensitivity of LGLKO to methylglyoxal, and increased transcription of lgl in the presence of exogenous methylglyoxal. Transcriptional analysis revealed pdhA responded to conditions favouring heterofermentation; decreased expression in response to excess glucose, and increased expression during stationary growth phase compared with mid-logarithmic phase growth. The isogenic mutants, LGLKO and PDHAKO, were acid-sensitive. Both mutants had reduced growth capacity at pH 5.0, decreased survival at pH 3.2, and decreased survival in an acidic bio-fermenter compared with wild-type. Both genes were up-regulated during growth at pH 5.0 compared with growth at pH 7.5 and during the process of acid adaptation. This work highlighted the importance of these three secondary metabolic pathways in the aciduricity of S. mutans.
The question of punishment and the contemporary relevance of Thomas Aquinas

Justifying the human institution of punishment has been a central theme in the history of moral and political philosophy. At no time has this been more apparent than at the present, where this question has evoked a great debate between two schools of thought, namely, utilitarianism and retributivism. This thesis firstly attempts to articulate the central questions underlying this debate and to articulate the powerful criticisms each side renders against one another. It is our thesis that, whereas each side seems to be successful in pointing out the defects of their opponent, neither has been able to answer the most powerful criticisms rendered against them. The result of this, we argue, is that one must look beyond the contemporary debate to see the true meaning and justification of punishment within political life. This is possible either by construing a theory of punishment not yet considered by the tradition of political philosophy, or by rediscovering a theory of punishment articulated by one of that tradition's non-contemporary members. This thesis opts for the latter, and considers the contribution Thomas Aquinas can make to this great question.
From humanism to the Reformation: Letters of recommendation in early modern Germany (1490--1560)

This study offers a cultural and intellectual history of letters by humanists and reformers written to recommend candidates for positions in the schools, the clergy, or government service in early modern Germany. These letters were shaped by the educational, cultural, professional or doctrinal agendas of humanism and Protestantism. The thesis illuminates the triangular relationship among authors, those recommended, and the recipients of the letters. Particular emphasis is placed on the role friendship and kinship played in letters of recommendation, for the letters show that a deliberate and continuous attention to the fashioning and advertising of one's album amicorum, one's list of friends, was necessary in order to win powerful patrons among established intellectuals. In the first half of the sixteenth century, the reformation perturbed humanist patterns of personal and professional friendship, as creed and confession came to displace the bonae literae as the common ground amongst friends. This study also explores the rhetorical strategies by which humanists and reformers recommended neophyte scholars for positions in education, church or state. The words and phrases used in letter of recommendation not only provide a graphic depiction of the person of the recommended, but also reveal what their authors identified as the qualities of the ideal job candidate. The rhetoric of the letters changed over the period, as previous concerns for a proper humanist style became subsumed in more immediate concerns of confession, orthodoxy and public concord. The letters enhance our understanding of the job market for people with advanced education, of how people obtained positions, and of the grounds on which hiring decisions were made. Humanists and reformers wrote informal, personal recommendations that were intended just for their friends, but formal recommendations to a university senate, a nobleman or town council. Moreover, they promoted the scholarship of other scholars by writing prefaces to their proteges' publications, using strategies developed for letters of recommendation to recommend the works as well as the men.

Keywords: Employment references
Interpersonal relations, History
Interpersonal relations, Germany
Social interaction, History
Social interaction, Germany
Letters, History and criticism
Humanism
Reformation
Environmental parasitology of trematodes, snails and larval amphibians

Environmental influences on trematode parasite infection in larval frogs may be mediated through effects on the frog hosts, other hosts in the parasite life cycle, or on the various life history stages of the parasites. Herein, I investigated effects of corn agriculture and landscape characteristics on trematode infection in both snails and tadpoles, and report that both affect infection patterns seen in these first and second intermediate hosts. Tadpoles from ponds adjacent to corn fields exhibit a higher prevalence of infection, whereas snails from such ponds show the opposite pattern. Landscape features likely exert an influence via habitat suitability for the definitive hosts. I also examined the impact of the herbicide atrazine (commonly used on corn crops) on the free-living cercarial infective stage of trematodes. Mortality, activity and infectivity are reduced in some species; however, when tadpoles and cercariae are exposed to the same concentration of atrazine, increased host susceptibility can be countered by detrimental effects on cercariae. This demonstrates the importance of examining the effects of an environmental factor on all aspects of a parasite life cycle. In addition to physiological or immunological effects, environmental perturbations may affect host susceptibility to trematode infection through behavioural alterations. I demonstrate that tadpoles exhibit an effective anti-parasite behaviour and that suppression of this activity results in an increase in trematode parasitism. The impact of trematode parasitism for natural frog populations was examined by investigating the interaction of infection with competition with conspecifics, a common stressor for tadpoles. Trematode infection and high rearing density had an additive negative effect on tadpole growth and development; effects were likely mediated by parasite-induced changes in resource allocation. The pattern of trematode infection observed in natural tadpole populations is thus the result of many factors, including those affecting host susceptibility (behavioural and immunological), cercarial infectivity, and abundance of definite hosts.
An inductively tuned silicon germanide BiCMOS quadrature VCO for clock and data recovery applications

An inductively tuned quadrature oscillator for clock and data recovery applications which use a half rate architecture is described in this thesis. The oscillator is based on a delay line architecture with tunable LC delay lines inserted between 2 gain stages to set the operating frequency. The oscillator incorporates a novel inductive tuning scheme by electronically varying magnetic coupling in the LC delay lines. With this method, a large tuning range is achieved which amply covers typical process, temperature and supply voltage spreads. The inductive tuning concept is demonstrated with a test chip fabricated in a 0.5mum SiGe BiCMOS technology. The fabricated oscillator is tunable from 3.75--4.48 GHz giving a tuning range of over 700 MHz or 18% of the center frequency. The measured phase noise is -92.4 dBc/Hz at a 1 MHz offset. The oscillator core dissipates 26.4 mW from a 3.3V supply.
An in vitro analysis of the relationship between human B cell development and Epstein-Barr virus (EBV) life cycle

EBV persists for the life of the host by accessing the long-lived memory B cell pool. It has been proposed that EBV uses different combinations of viral proteins, known as latency types, to drive infected B cells to make the transition from resting B cells to memory cells. This process is normally antigen-driven. A major unresolved question is what factors coordinate expression of EBV latency and lytic proteins in context of late B cell development. In vitro assays with EBV-transformed B cell lines have provided invaluable insights into the biology of EBV. This thesis describes establishment of novel synovial tissue-derived human B cell lines (OCI-BCLs) infected with naturally occurring strains of EBV. Phenotypic and molecular profiling of these cell lines place them at the post-germinal centre stage of B cell development. The process of B cell development is controlled by multiple factors from the surrounding microenvironment including cytokines. IL-21 is a recently identified member of the common cytokine receptor gamma-chain (gammac)-dependent family, and is exclusively produced by activated CD4+ T cells. In the following section of this thesis we used OCI-BCLs as a model system to describe cellular intermediates that exist during the IL-21-induced transition from an activated, post-GC B cell to an Ig-secreting cell and to identify molecular mechanisms involved in this process. Our results reveal the link between IL-21-induced JAK/STAT signalling, proliferation, and subsequent differentiation of OCI-BCLs into late plasmablasts/early plasma cells. Finally, our data shows that this window of development is associated with regulation of expression of key EBV-oncoproteins, including growth-transforming EBV nuclear antigen 2 (EBNA2), and CD40-like, latent membrane protein 1 (LMP1), as well as with regulation of expression of the immediate-early and early lytic cycle proteins.
Solution-processed infrared light emitting diodes: Origins and optimization of quantum efficiency

This thesis reports on a systematic investigation of the factors that affect the electroluminescence quantum efficiency of solution-processed polymer-nanocrystal light emitting diodes. The overall efficiency is the product of the nanocrystal internal efficiency, the energy/charge capture efficiency and the carrier injection efficiency. Polymer nanocomposites are used as the active layer of the device and concentration regimes are determined, where the internal efficiency and energy transfer efficiency are both maximized. Maximization of bipolar carrier injection efficiency is also sought through variation of the active layer thickness and contact technology. Maximum external electroluminescence quantum efficiency of 0.22% is achieved---25 times higher than previously reported results in PbS systems. Discoveries on the physical excitation mechanism of the nanocrystals are also reported.