VictorJuiz/thesis huggingface dataset:
Mechanistic Investigation of Penicillamine-induced Autoimmunity: Covalent Binding of Penicillamine to Macrophages, Involvement of Th17 cells, and Its Relation to Idiosyncratic Drug-induced Liver Injury

The mechanisms of idiosyncratic drug reactions (IDRs) are unknown; however, most appear to be immune-mediated. Their idiosyncratic nature and the paucity of animal models make mechanistic studies very difficult. One of the few animal models is penicillamine-induced autoimmunity in Brown Norway rats. The major focus of this thesis was the use of this model to study the interaction between penicillamine and macrophages, the involvement of Th17 cells, and extension of this model to idiosyncratic drug-induced liver injury. One of the costimulatory signals leading to T cell activation appears to be reversible Schiff-base formation between an amine on T cells and an aldehyde on macrophages. We hypothesized that penicillamine binds to these aldehydes leading to macrophage activation and autoimmunity. By using biotinylated aldehyde-reactive agents such as ARP, we demonstrated the existence of aldehydes on the surface of macrophages. We synthesized biotinylated-penicillamine and it also binds to macrophages. Several proteins to which ARP binds were identified providing clues to the signal transduction pathways leading to macrophage activation. Biological consequences of this binding were investigated with a microarray study. ARP binding was also observed in the macrophage cell line, RAW264.7, and incubation with penicillamine stimulated the production of TNF-α, IL-6, and IL-23. Hydralazine and isoniazid, which are known to cause a lupus-like syndrome in humans and irreversibly bind to aldehyde groups, were also found to activate RAW264.7 cells. Th17 cells are prominent in autoimmune syndromes and Th17-associated cytokines such as IL-17 were elevated in the penicillamine-treated animals that developed autoimmunity. We have hypothesized that some drug-induced liver injury has an autoimmune component. A pilot study quantified serum concentrations of 26 cytokines/chemokines in patients with various forms of acute liver failure (ALF): idiosyncratic drug-induced ALF, acetaminophen-induced ALF, and viral hepatitis. IL-17 was elevated in 60% of patients with idiosyncratic drug-induced ALF, which supports an autoimmune component in these patients; however, it was also elevated in many cases of acetaminophen-induced ALF, presumably released by the innate immune system. These studies provide important insights into the mechanism of penicillamine-, hydralazine-, and isoniazid-induced autoimmunity and also provide clues to other IDRs that may have an autoimmune component.

Keywords: idiosyncratic
macrophages
aldehyde
penicillamine
liver injury
Th17
Advisor: Uetrecht, Jack
Astrometry.net: Automatic Recognition and Calibration of Astronomical Images

We present Astrometry.net, a system for automatically recognizing and astrometrically calibrating astronomical images, using the information in the image pixels alone. The system is based on the geometric hashing approach in computer vision: We use the geometric relationships between low-level features (stars and galaxies), which are relatively indistinctive, to create geometric features that are distinctive enough that we can recognize images that cover less than one-millionth of the area of the sky. The geometric features are used to generate rapidly hypotheses about the location---the pointing, scale, and rotation---of an image on the sky. Each hypothesis is then evaluated in a Bayesian decision theory framework in order to ensure that most correct hypotheses are accepted while false hypotheses are almost never accepted. The feature-matching process is accelerated by using a new fast and space-efficient kd-tree implementation. The Astrometry.net system is available via a web interface, and the software is released under an open-source license. It is being used by hundreds of individual astronomers and several large-scale projects, so we have at least partially achieved our goal of helping ``to organize, annotate and make searchable all the world's astronomical information.''

Keywords: Astrometry
Computer vision
Astronomy
Advisor: Roweis, Sam
Hogg, David W.
Plasticity and Gene by Environment Interactions in Complex Phenotypes of Adult Drosophila melanogaster

Behaviour genetics deals with complex phenotypes which respond flexibly to environments animals experience. Change of phenotype in response to environment is phenotypic plasticity. A central question is how genes influence plasticity. I study plasticity and gene by environment interactions (GEI) relating to behaviours, metabolic, and genomic phenotypes of adults of the fruit fly Drosophila melanogaster. Chapters 1-3 study cuticular hydrocarbon (CH) levels of male flies. Chapter 1 shows male CH levels respond to time of day and light. Methods are developed to reduce high variability of CH. I show variation in CH parallels activity of two classes of CH synthesis hormones. Analysis of rate of variation gives estimates of turnover rates of CH and the metabolic cost of signaling. Chapter 2 studies mixed groups of genetically different flies, “hosts” and “visitors”. GEI of CH are found with both abiotic factors and with social mix. Social mix results in GEI as strong as abiotic factors. Indirect Genetic Effects (IGE) theory is used to show frequency-dependent IGE interactions. Chapter 3 shows that males in mixed social environments reduce expression of clock and CH synthesis genes, resulting in different signals. Females mate more often with males in a mixed group than with single-genotype males. Plasticity in male gene expression in response to social environment leads to different signals, mating levels, and potentially different fitness. Chapter 4 deals with behaviour, metabolite, and genomic phenotypes in flies differing in foraging gene alleles, as the food environment is changed. Strong GEI is found, structured by food type, chemical class of metabolite, and gene metabolic roles. A concept called “relative nutrient sensitivity” suggests an interaction between foraging and the insulin signaling pathway. I demonstrate epistasis between for and insulin with quantitative genetic methods and bioinformatics. These results lead to the conclusion that GEI are common in many fly phenotypes in response to well studied environments such as food and less studied ones such as social group. Some implications of this for maintenance of genetic variance are discussed.

Keywords: behaviour genetics
systems biology
Advisor: Levine, Joel
Sokolowski, Marla B.
Interacting Disturbances in the Boreal Forest and the Importance of Spatial Legacies at Multiple Scales

Forest disturbances and the spatial patterns they create affect ecosystem processes through their influence on forest vegetation from individual trees to landscapes. In the boreal and mixed-wood forests of eastern Canada the main agents of disturbance are logging, fire, and defoliation by the spruce budworm (SBW, Choristoneura fumiferana). These disturbances are similar in that they remove forest biomass and influence forest succession but also distinct in that logging creates patterns that are different than those created by natural disturbances. All disturbances are indirectly linked to each other through their mutual effects on forest spatial structure and succession. Through such feedbacks, spatial disturbance legacies can facilitate or constrain further disturbances, including forest management. Surprisingly, the long term spatial consequences of interactions among multiple natural and anthropogenic disturbances remain largely unexplored. This thesis investigates how, and at what spatial scale, legacies in forest composition and age structure influence natural disturbance dynamics, and how natural disturbances constrain forest management. I address four specific questions: (i) For how long do spatial legacies of different forest management strategies persist on the landscape? (ii) How do interactions among logging, fire, SBW, and succession affect timber availability and long term forest patterns in age and composition? (iii) How do these patterns differ from those created by each disturbance individually? And, (iv) How can management be used to reduce the extent and severity of fires and SBW defoliation through the manipulation of forest structure? The key scientific innovations of this thesis are: (i) Characterization of the duration and influence of spatial legacies on forest disturbances and sustainability; (ii) Development of a dynamic spatial forest simulation model that includes distinct successional rules that respond to different types of disturbance and shifts in disturbance regimes; and, (iii) Development and application of a wavelet-based significance testing framework to identify key scales of expression in forest spatial patterns. These innovations provide a scientific basis for landscape level forest management strategies designed to reduce the long term impacts of defoliating insects and to meet multiple objectives.

Keywords: landscape ecology
wavelet analysis
forest disturbance
spruce budworm
Advisor: Fortin, Marie-Josee
Phagosome Maturation: Aging with pH, Lysosome-associated membrane proteins, and Cholesterol; while staying young with Burkholderia cenocepacia

Phagocytosis is an innate immune response that is paramount in the clearance of pathogenic particles. Recognition of target particles by phagocytic receptors expressed on phagocytes induces modifications in the underlying actin cytoskeleton to form pseudopods that encircle and internalize the target particle into a membrane bound organelle called the phagosome. The nascent phagosome undergoes a maturation sequence that is characterized by substantial remodeling of the membrane and its luminal contents through interactions with components of the endocytic pathway, culminating in an acidic and hydrolytic organelle capable of digesting and elminating pathogens. Phagosome maturation is a complicated pathway that involves many protein and lipid signaling molecules. Several factors that influence phagosome maturation particularly the participation of pH, lysosome-associated membrane proteins-1 and –2, cholesterol, in addition to the survival and escape mechanisms used by, Burkholderica cenocepacia were explored. All three tenets are essential for phagosome maturation, although each factor has different mechanistic consequences. Acidification alters Rab5 activation, while ablation of LAMPs and accumulation of cholesterol interferes with various aspects of Rab 7 turnover in phagosomes and/or endosome membranes. Moreover, Burkholderia cenocepacia, an intracellular pathogen, inactivates Rab7 on phagosome membranes from within the vacuole lumen. Herein, mechanisms that govern phagosome maturation are explored and several molecules are added to the long list of essential players in this complicated pathway.

Keywords: phagocytosis
phagosome maturation
lysosome
cholesterol
acidification
Advisor: Grinstein, Sergio
Approximation Techniques for Large Finite Quantum Many-body Systems

In this thesis, we will show how certain classes of quantum many-body Hamiltonians with [special characters omitted](2)1 ⊕ [special characters omitted](2)2 ⊕...⊕ [special characters omitted](2)k spectrum generating algebras can be approximated by multidimensional shifted harmonic oscillator Hamiltonians. The dimensions of the Hilbert spaces of such Hamiltonians usually depend exponentially on k. This can make obtaining eigenvalues by diagonalization computationally challenging. The Shifted Harmonic Approximation (SHA) developed here gives good predictions of properties such as ground state energies, excitation energies and the most probable states in the lowest eigenstates. This is achieved by solving only a system of k equations and diagonalizing k × k matrices. The SHA gives accurate approximations over wide domains of parameters and in many cases even across phase transitions. The SHA is first illustrated using the Lipkin-Meshkov-Glick (LMG) model and the Canonical Josephson Hamiltonian (CJH) which have [special characters omitted](2) spectrum generating algebras. Next, we extend the technique to the non-compact [special characters omitted](1, 1) algebra, using the five-dimensional quartic oscillator (5DQO) as an example. Finally, the SHA is applied to a k-level Bardeen-Cooper-Shrieffer (BCS) pairing Hamiltonian with fixed particle number. The BCS model has a [special characters omitted](2)1 ⊕ [special characters omitted](2)2 ⊕...⊕ [special characters omitted](2)k spectrum generating algebra. An attractive feature of the SHA is that it also provides information to construct basis states which yield very accurate eigenvalues for low-lying states by diagonalizing Hamiltonians in small subspaces of huge Hilbert spaces. For Hamiltonians that involve a smaller number of operators, accurate eigenvalues can be obtained using another technique developed in this thesis: the generalized Rowe-Rosensteel-Kerman-Klein equations-of-motion method (RRKK). The RRKK is illustrated using the LMG and the 5DQO. In RRKK, solving unknowns in a set of 10 × 10 matrices typically gives estimates of the lowest few eigenvalues to an accuracy of at least eight significant figures. The RRKK involves optimization routines which require initial guesses of the matrix representations of the operators. In many cases, very good initial guesses can be obtained using the SHA. The thesis concludes by exploring possible future developments of the SHA.

Keywords: Quantum Many-body systems
Approximation Techniques
Algebraic Hamiltonian
Eigenvector
Advisor: Rowe, David J.
Biotic Resistance to Non-indigenous Plants: Are Phylogenetically Novel Invaders More Likely to Escape Enemies?

The degree to which biotic interactions influence invasion success may partly depend on the evolutionary relationship between invaders and native species. In particular, since host-use by enemies such as invertebrate herbivores and fungal pathogens tends to be phylogenetically conserved, exotic plants that have close native relatives in the invaded range should be more likely to interact with enemies. In this thesis, I explore this idea using a series of experiments and field surveys at nested taxonomic levels. My results indicate that exotics from multiple plant families experience lower damage if their average phylogenetic distance from locally co-occurring native family members is higher. I then demonstrate that within the Asteraceae, foliar and capitular damage are lower on exotic compared to native species. Both damage types had a relatively large phylogenetic component, but did not decline with phylogenetic distance to native or exotic confamilials. Finally, I show that communities with versus without close relatives are unlikely to differ in resistance to the novel invader, Solidago virgaurea: biotic resistance imposed by competitors, generalist vertebrates, and specialist invertebrates resulted in similar patterns of damage and mortality regardless of the presence of congeneric natives. In some cases, effects of biota were positive: growth of S. virgaurea seedlings in soils collected near congeneric natives was enhanced more than in soils from communities where congenerics were absent. Overall, these results suggest that biotic interactions between exotic and native species can be phylogenetically structured, although trends based on distance measures tend to be weak. In some cases, damage does decline with phylogenetic distance to native species; however this trend is unlikely to be a strong force limiting invasion or structuring plant communities. These results have significant implications for current theories of invasion biology including the "Enemy Release Hypothesis" and "Darwin's Naturalization Hypothesis", as well as for community phylogenetics.

Keywords: invasion biology
enemy release hypothesis
community phylogenetics
Darwin's naturalization hypothesis
community ecology
plant ecology
Advisor: Kotanen, Peter M.
Cis-elements Affecting Disease-associated Repeat Sequences

The expansion of repetitive sequences leads to more than 40 neurological, neurodegenerative and neuromuscular diseases. These diseases are frequently characterized by ongoing DNA repeat instability upon transmission, worsening of disease severity and decreasing age of onset with each successive generation. The mechanism of repeat instability and contribution of repeat instability to disease pathogenesis are unknown. My thesis examines the contribution of cis-elements – sequences around and within repeats as well as surrounding epigenetic environments – to repeat instability, and discusses their possible contribution to repeat diseases. Here I identify the first cis-element regulating repeat instability, a DNA binding site for a trans factor protein, CTCF. Loss of CTCF binding at the spinocerebellar ataxia type 7 disease locus induces somatic and germline instability in an age- and tissue-specific manner in mice. CTCF protects against instability in an epigenetic manner, and may function at other disease loci also possessing CTCF binding sites near the repeat. Given that CTCF flanks many repeat loci and is often situated between a replication origin and disease-associated repeat, I assess the role of CTCF on replication and instability at the myotonic dystrophy repeat locus. Templates with CTCF binding sites reduce overall replication efficiency in primate cells that may be partly due to replication fork stalling. Mutating CTCF binding sites can alter the stability of the repeat depending on the distance from the origin of replication to the repeat. Finally I examine chromatinization of (ATTCT)n repeats from the spinocerebellar ataxia type 10 locus. These repeats induce very strong nucleosome formation, and at physiological conditions form even more strongly on (ATTCT)n repeats with interruptions that are also found in some patients. These data contribute to the understanding of repeat instability in the causation of many diseases, and suggest that the presence of cis-elements at repeat-associated disease loci alter the behaviour of repeats.

Keywords: trinucleotide
myotonic dystrophy
CTCF
Spinocerebellar ataxia
cis-element
Advisor: Pearson, Christopher E.
Is Evidence-based Psychiatric Practice, Ethical Practice?: A Conceptual and Qualitative Study

Since its addition to the medical lexicon in 1992, the concept of ‘evidence-based medicine’ (EBM) has captured the imagination of the medical world, attracting both passionate advocates and ardent opponents. EBM is defined clinically as “the conscientious, explicit, and judicious use of current best evidence in making decisions about the care of individual patients.” Yet, its boldest claim is an ethical one: that EBM, rather than any other method, is the most effective way to fulfill our moral duty to help patients achieve better health. Academic debate on this point has been deeply polarized, from those who assert that ethical practice is evidence-based practice to those who argue that evidence-based practice impoverishes practice and robs it of ethical substance. Mainstream psychiatrists have endorsed EBM which holds out the promise of greater ethical legitimacy for psychiatric disorders and treatments through improved scientific substantiation. Evidence-based psychiatry arises through the straightforward application of EBM to the practice of psychiatry and thus shares the same ethical goal of EBM, to improve patients’ health. Given the ethical debates that have framed psychiatry since its inception as a medical specialty, and the particular nature of mental disorders and their treatments, it is unclear if EBM can be applied to psychiatry, and therefore, whether it can deliver on its ethical promises. This thesis project involved two phases. The first, a conceptual phase, included an analysis of EBM’s ethical commitments as they are represented in its two authoritative textbooks (‘literal’ EBM). This provisional analysis was then extended by a qualitative analysis of the views of three groups of participants concerning the ethics of EBM: 1) EBM developers; 2) mental health practitioners; and 3) philosophers or bioethicists. Combining the analyses from both phases, a more complete depiction of the ethics of EBM was developed in order to address the main thesis question. Evidence-based psychiatric practice cannot be ethical practice by itself. Instead, it can play a small ethical role in clinical practice, only if it is situated within the larger value structure of contemporary medicine and psychiatry.

Keywords: evidence-based medicine
psychiatry
ethics
Advisor: Upshur, Ross
The Functional Characterization of Two Regulators of G-protein Signaling Proteins Abundantly Expressed in Vascular Smooth Muscle Cells

Precise regulation of heterotrimeric G-protein signaling is important for maintaining proper cardiovascular system function. Indeed, G-protein signaling is frequently upregulated during cardiovascular disease suggesting that identifying mechanisms for inhibiting G-protein signaling may be an effective therapeutic strategy for the treatment and prevention of disease. The work presented in this thesis is directed at two RGS proteins, RGS2 and RGS5, the two highest expressing RGS proteins in VSMCs. Despite the large number of studies published on them, there is still much to be learned about the specific G-protein pathways that each RGS protein controls. Using genetic and molecular models, we set out to identify novel regulatory pathways controlling RGS2 and RGS5 function. We hypothesize that characterizing the determinants and regulation of RGS protein function will provide a better understanding of the signaling that occurs within VSMCs under both physiologic and pathophysiologic conditions. Our work presented in the first three studies of this thesis, describes novel regulatory pathways that are involved in regulating RGS2 protein function. We describe the production of RGS2 protein isoforms that are the result of alternative translational start site usage. Interestingly, the expression pattern of these proteins is controlled by the signaling status of the cell. In the second two studies, we identify a functional consequence of RGS2-interaction with the plasma membrane. We show that this is dependent on the interaction between the amphipathic α-helix and anionic phospholipids present in the plasma membrane. We further show that disruptions in this interaction, as occurs in the human population, can lead to reduced RGS2 function and thus potentially hypertension. Finally, our last study focuses on the function and regulation of RGS5, the single highest expressing RGS protein in VSMCs. We show that the regulation of RGS5 is dependent, similar to other VSMC-specific genes, on the activity of SRF and myocardin. However, interestingly, RGS5 expression is further controlled by the extent of DNA methylation that occurs in its proximal promoter. We show that this is an important regulator of RGS5 expression both in development as well as during disease, specifically in-stent restenosis.

Keywords: Regulators of G-protein Signaling
Cell physiology
Advisor: Heximer, Scott P.