VictorJuiz/thesis huggingface dataset:
Robustness and Vulnerability Design for Autonomic Management

This thesis presents network design and operations algorithms suitable for use in an autonomic management system for communication networks with emphasis on network robustness. We model a communication network as a weighted graph and we use graph-theoretical metrics such as network criticality and algebraic connectivity to quantify robustness. The management system under consideration is composed of slow and fast control loops, where slow loops manage slow-changing issues of the network and fast loops react to the events or demands that need quick response. Both of control loops drive the process of network management towards the most robust state. We fist examine the topology design of networks. We compare designs obtained using different graph metrics. We consider well-known topology classes including structured and complex networks, and we provide guidelines on the design and simplification of network structures. We also compare robustness properties of several data center topologies. Next, the Robust Survivable Routing (RSR) algorithm is presented to assign working and backup paths to online demands. RSR guarantees 100% single-link-failure recovery as a path-based survivable routing method. RSR quanti es each path with a value that represents its sensitivity to incremental changes in external traffic and topology by evaluating the variations in network criticality of the network. The path with best robustness (path that causes minimum change in total network criticality) is chosen as primary (secondary) path. In the last part of this thesis, we consider the design of robust networks with emphasis on minimizing vulnerability to single node and link failures. Our focus in this part is to study the behavior of a communication network in the presence of node/link failures, and to optimize the network to maximize performance in the presence of failures. For this purpose, we propose new vulnerability metrics based on the worst case or the expected value of network criticality or algebraic connectivity when a single node/link failure happens. We show that these vulnerability metrics are convex (or concave) functions of link weights and we propose convex optimization problems to optimize each vulnerability metric. In particular, we convert the optimization problems to SDP formulation which leads to a faster implementation for large networks.

Keywords: Vulnerability
Robustness
Advisor: Leon-Garcia, Alberto
Signal Processing Techniques for High-speed Chip-to-chip Links

This thesis tackles the problem of high-speed data communication over wireline channels. Particular attention is paid to backplane channels which have impedance discontinuities and high-frequency loss. These channels require extra equalization effort in order to produce an open eye diagram at the receiver. Three signal processing techniques were investigated in the pursuit of higher data rates over backplane channels: transmit-side FIR filter equalization with variable tap spacing, bidirectional communication using frequency-division multiplexing, and an ADC-based receiver to provide a capability for non-linear equalization. The ADC presented here is a 5-bit flash ADC intended to be time-interleaved to attain a sufficient data rate. This ADC uses redundant comparators to obtain sufficient resolution without an explicit threshold tuning circuit. A resonant clocking line is used to reduce power and increase the maximum clock frequency.

Keywords: analog electronics
Advisor: Carusone, Anthony Chan
Characterization of Azobenzene-based Photo-switches and their Evaluation for In Vivo Applications

Photoisomerization of azobenzene can be used to reversibly photo-control peptide and protein structure, thereby offering the potential to probe peptide and protein function directly in living systems. Most azobenzene photo-switches to date however require the use of UV light, which suffers from poor tissue penetration and can lead to cell damage. In addition, the unknown stability of azobenzene photo-switches within the reducing intracellular environment has limited these switches to extracellular applications. The ability to red-shift the photo-switching wavelength and tune the thermal cis-to-trans rate independently from one another has been a central challenge. Incorporating a piperazine-like moiety at the 4,4′-para positions red-shifts the π-π* band of an azobenzene-based cross-linker such that trans-to-cis photoisomerization can be triggered with blue light. Accompanying this red-shift was a faster cis-to-trans thermal rate, which allowed for fast secondary structural changes of the attached peptides (τ½ ~2s). Piperazine-like moieties at the 2,2′-ortho positions of an azobenzene-based cross-linker resulted in a similar red-shift in the π-π* band but a longer-lived cis isomer relative to its para-counterpart (τ½ ~minutes). These results suggest that the thermal rate could be tuned independently from the photo-switching wavelength by appropriate para or ortho substitution. The effect of 2,2′,6,6′-ortho-tetramethoxysubstitution provided an alternative approach to red-shifting the photo-switching wavelength. These groups caused an unconventional red-shift in the n-π* band of the trans isomer allowing for trans-to-cis and cis-to-trans photoisomerization to occur with green and blue light, respectively. In this case, the half-life of the cis isomer was not shortened, but rather extended relative to its parent compound (τ½ ~days versus minutes). These results provide progress in tuning the photo-switching wavelength independently from the thermal rate. A fluorescent reporter was developed to determine the stability of a commonly employed 4,4′-diamido derivative in vivo. Photoisomerization was found to cause time-dependent changes in fluorescein emission intensity. The reporter was microinjected in zebrafish embryos and photo-switching could be imaged for at least two days. This work provides the first direct evidence of azobenzene photo-switching in vivo, and indicates that it will be possible, in general, to photo-control peptide and protein function in living systems.

Keywords: Biological Chemistry
Advisor: Woolley, Andrew
Canadian Campaign Finance in Comparative Perspective 2000-2011: A Failed Paradigm or Just a Cautionary Tale?

This thesis compares the public policies of campaign finance in Canada with those in the U.S. and the U.K. in the period 2000-2011. The majority of the Canadian literature on party finance demonstrates a belief in the efficacy and necessity of the enterprise. This dissertation suspends this disposition and offers a critical approach to the regulation of money in Canadian elections. This thesis situates the discussion of party finance regulation in the context of contending models of democracy. Campaign finance rule changes are conceptualized within a new institutionalist framework. Changes in campaign finance rules are seen as changes in incentives and are seen to work in configurations, that is, interacting with existing formal and informal constraints. New institutionalism provides the avenue of inquiry into the position of political parties on the boundary of the public and private spheres and how campaign finance regulation may shift that boundary. This thesis adopts a mixed-method approach, incorporating the results of 65 semi-structured interviews with academics and political practitioners with primary document research. This thesis demonstrates that campaign finance rule changes interact with other electoral rules, types of parties and the nation’s historic institutions. The need to meld Quebec’s statist and civil-code traditions with Westminster democratic traditions, the introduction of the Charter of Rights and Freedoms and the role of subsequent court decisions, and the role of Elections Canada in its political finance oversight capacity, constitute major catalysts for Canadian party finance rule changes and for understanding the impact of rule changes. Contrary to the majority of literature on campaign finance reform, this thesis demonstrates that there may be diminishing marginal returns to additional campaign finance regulations, at least in a mature democracy such as Canada. Campaign finance rules reveal preferences for different models of democracy. As such, they must be carefully monitored.

Keywords: Campaign finance reform 2000-2011
Political party finance
Canada/U.S./U.K.
Public administration of political finance
Canada political parties
Political finance Anglo-American democracies
Public policy of campaign finance
Advisor: White, Graham
They Don't Stand for Me: Generational Difference in Voter Motivation and the Importance of Symbolic Representation in Youth Voter Turnout

Building from Hannah Pitkin’s work on forms of representative democracy, this thesis demonstrates how differing generational expectations of political representation affect participation in electoral politics. Consistent with earlier work, it confirms that youth voting decreases when young people are less educated, less interested, or when they lack a sense of responsibility. However these factors only explain part—and not necessarily the most important part—of the younger generation’s motivations for voting. The analysis also shows that youth are markedly less likely to vote when young people feel that their values are not aligned with those of political leaders. The relationship between values—or symbolic representation—and voting remains significant and strong for young people even when the classic predictors of voting are included in the model. In fact, symbolic representation is a stronger predictor of voting than such factors as education, political interest, or the sense of responsibility to vote. This new variable is therefore important in understanding why the most recent decline in voting occurs predominantly among youth. Issue campaigns are less likely to move young people one way or another with respect to voting, as the majority of issues do not affect young people directly, if at all. As a consequence youth are left to rely on their own understanding of what political leaders actually stand for to pull them in or entice them to vote. But if the values that young people care about are not symbolically represented by political leaders and their electoral platforms, then youth will have less to vote for, and will likely just stay home and ignore elections altogether. Conversely, if political leaders make modest changes to their campaign strategies that also appeal to values—rather than strictly to interests—we could also see an increase in turnout among youth, and therefore an increase in democratic legitimacy.

Keywords: Youth Voter Turnout
Political Engagement
Advisor: Fletcher, Joseph F.
CDK-independent Initiation of the S. cerevisiae Cell Cycle -- Analysis of BCK2

Much of the work on how the cell cycle is regulated has focused on Cyclin-Dependent Kinase (CDK)-mediated regulation of factors that control the coordinate expression of genes required for entry into the cell cycle. In Saccharomyces cerevisiae, SBF and MBF are related transcription factors that co-ordinately activate a large group of genes at the G1/S transition, and their activation depends on the Cln3-Cdk1 form of the cyclin-dependent kinase. However, cells are viable in the absence of Cln3, or SBF and MBF, indicating that other regulatory pathways must exist that activate the budding yeast cell cycle. The known CDK-independent pathways are made up of various phosphatases and plasma membrane transporters that control ion homeostasis in early G1 phase, a time when cells assess environmental growth conditions in order to commit to cell cycle entry. The enigmatic Bck2 protein is thought to act within these CDK-independent pathways, but the means by which it activates G1/S-regulated genes is not known. Bck2 contains little sequence homology to any known protein. In order to understand how CDK-independent pathways operate, I have studied the Bck2 protein using multiple approaches. In one approach, I have screened for novel SBF/MBF-binding proteins in order to determine if other non-CDK proteins, such as Bck2, might activate SBF and MBF. I have also investigated which region of Bck2 is required for its activity in order to determine if Bck2’s transcriptional activation region is essential. Using one of the iii truncation derivatives from this analysis, I have screened for proteins that interact with Bck2. One of these novel proteins is Mcm1, a global transcriptional activator of genes involved in cell cycle progression, mating gene transcription and metabolism. My studies suggest that Bck2 regulates the activity of Mcm1 in early G1 phase to activate the expression of SWI4, CLN3, and others. My evidence suggests that Bck2 competes for binding to a specific pocket on Mcm1 that is also bound by an Mcm1 repressor called Yox1. My findings suggest that CDK-independent pathways function through Bck2, in order to induce the initial suite of genes required for entry into the cell cycle.

Keywords: yeast cell cycle
G1 transcription Bck2
Advisor: Andrews, Brenda
Accommodative Capacity of Multinational States

This dissertation explains the extent and durability of the institutions of territorial autonomy in multinational states. Its main argument is that the viability of territorial autonomy hinges on the relative economic importance of the minority-inhabited region for the central government. If the fiscal resources of the minority-inhabited region are critical for the funding of the central government’s policy objectives, autonomy is likely to be limited and short lived. If those resources are not as crucial for the governability of the entire state, autonomy is likely to be more extensive and durable. The importance of the minority-inhabited region depends on two sets of factors. The first is the relative level of economic development of majority and minority-inhabited areas. The second is the strategy of governance adopted by the central state elites. Strategies of governance determine the extent of the fiscal burden that the central government will place on the population of the state, thereby exerting significant influence on accommodative outcomes. The theoretical framework developed in this dissertation refers to statist (high spending) and laissez-faire (low spending) strategies of governance. The framework is tested in four multinational states: the former Yugoslavia, the former Czechoslovakia, Canada and Spain. The empirical chapters combine structured-focused comparison with longitudinal case study analysis. The cases largely bear out the hypotheses presented in the dissertation. However, analysis of the cases also demonstrates the importance of minority-group influence at the central state level in accounting for accommodative outcomes. In cases where minority elites have extensive influence at the centre, attempts at limiting the autonomy of minority-inhabited regions tend to be unsuccessful. This thesis contributes to a greater understanding of the design and durability of the institutions of territorial autonomy, which have important consequences for the stability and viability of multinational states.

Keywords: federalism
multinational federalism
nationalism
accommodation
ethnic conflict
state
decentralization
centralization
political institutions
comparative institutional dynamics
Advisor: Kopstein, Jeffrey
Structural Investigation of Processing α-Glucosidase I from Saccharomyces cerevisiae

N-glycosylation is the most common eukaryotic post-translational modification, impacting on protein stability, folding, and protein-protein interactions. More broadly, N-glycans play biological roles in reaction kinetics modulation, intracellular protein trafficking, and cell-cell communications. The machinery responsible for the initial stages of N-glycan assembly and processing is found on the membrane of the endoplasmic reticulum. Following N-glycan transfer to a nascent glycoprotein, the enzyme Processing α-Glucosidase I (GluI) catalyzes the selective removal of the terminal glucose residue. GluI is a highly substrate-specific enzyme, requiring a minimum glucotriose for catalysis; this glycan is uniquely found in biology in this pathway. The structural basis of the high substrate selectivity and the details of the mechanism of hydrolysis of this reaction have not been characterized. Understanding the structural foundation of this unique relationship forms the major aim of this work. To approach this goal, the S. cerevisiae homolog soluble protein, Cwht1p, was investigated. Cwht1p was expressed and purified in the methyltrophic yeast P. pastoris, improving protein yield to be sufficient for crystallization screens. From Cwht1p crystals, the structure was solved using mercury SAD phasing at a resolution of 2 Å, and two catalytic residues were proposed based upon structural similarity with characterized enzymes. Subsequently, computational methods using a glucotriose ligand were applied to predict the mode of substrate binding. From these results, a proposed model of substrate binding has been formulated, which may be conserved in eukaryotic GluI homologs.

Keywords: Biomolecular structure
Eukaryotic glycosylation
glycosylation
N-glycan
N-linked glycosylation
Carbohydrate
biochemistry
Inhibitor
antiviral therapeutic
Structure-based drug design
glucosidase
glycosidase
glycoside hydrolase
post-translational modification
enzyme
enzyme mechanism
inverting mechanism
structural biology
protein structure
6xHis tag
Crystal packing
sugar
substrate
X-ray crystallography
single anomalous dispersion
PHENIX
heavy-atom phasing
docking
autodock
autodock vina
biophysical methods
tryptophan fluorescence
glucose oxidase
activity assay
enzyme inhibition
Protein expression
Protein purification
Pichia pastoris
Saccharomyces cerevisiae
fondue
AOX1 promoter
glycoside hydrolysis
substrate binding model
molecular dynamics
molecular dynamics
Binding site
Active site cleft
Endoplasmic reticulum
Glycan processing
Glycan trimming
protein-protein interactions
cell-cell communication
X-ray diffraction
crystallization
secreted protein
substrate selectivity
kojibiose
glucotriose
miglitol
deoxynojirimycin
Glc3Man9GlcNAc2
free oligosaccharide species
GluI
Cwh41
Cwh41p
Cwht1p
Advisor: Rose, David
How Much or How Many? Partial Ostracism and its Consequences

Ostracism, the process of socially ignoring and excluding certain people, has attracted attention in recent years. Most studies have looked at full ostracism, in other words, when everyone in a group ignores a person. However, in real life, people are usually only partially ostracized – excluded by some members of a group and not by others. The present study is one of the first to provide an in-depth examination of reactions when different forms of partial ostracism occur in a group. It looks at partial ostracism in a field study and an experimental study. In the field study I proposed that because targets of partial ostracism receive mixed signals from their group, it is easier for them to interpret ostracism as an external event rather than internal; whereas in full ostracism because all the signs received by the target are the same, the target cannot interpret the act of ostracism in different ways. The results of the field study indicate that partial ostracism is not only more common than full ostracism at work, but targets of partial ostracism also make fewer internal attributions than do targets of full ostracism. The experimental study examined two dimensions of partial ostracism: activity exclusion (AE) and people exclusion (PE). Results indicate that as AE increases, i.e. targets are excluded from more activities, targets make fewer internal attributions, feel more threats to their basic needs (mediated by internal attributions), and have more desire to help others. As PE increases, targets feel more threats to their needs and put less effort into group tasks. Comparing AE and PE simultaneously, AE makes a difference in targets’ well-being while PE affects targets’ efforts in group tasks

Keywords: Ostracism
Exclusion
Group
Advisor: Berdahl, Jennifer
The Structure of Bovine Mitochondrial ATP Synthase by Single Particle Electron Cryomicroscopy

Single particle electron cryomicroscopy (cryo-EM) is a method of structure determination that uses many randomly oriented images of the specimen to construct a three-dimensional density map. In this thesis, single particle cryo-EM has been used to determine the structure of intact adenosine triphosphate (ATP) synthase from bovine heart mitochondria, an approximately 550 kDa membrane protein complex. In respiring organisms, ATP synthase is responsible for synthesizing the majority of ATP, a molecule that serves as an energy source for many cellular reactions. In order to understand the mechanism of ATP synthase, knowledge of the arrangement of subunits in the intact complex is necessary. To obtain maps of intact ATP synthase showing internal density distributions by single particle cryo-EM, methodological improvements to image acquisition, map reﬁnement, and data selection were developed. Further, a novel segmentation algorithm was developed to aid in interpretation of maps. The use of these tools allowed for construction and interpretation of two maps of ATP synthase, solubilized in diﬀerent membrane mimetics, in which the arrangement of subunits could be identiﬁed. These maps revealed interactions within the complex important for its function. In addition, evidence was obtained for curvature of membrane mimetics around ATP synthase, suggesting a role for the complex in maintenance of mitochondrial membrane morphology.

Keywords: electron cryomicroscopy
ATP synthase
mitochondria
membrane protein
radiation damage
map segmentation
single particle EM
map refinement
tilt pairs
Advisor: Rubinstein, John
On the Local and Global Classification of Generalized Complex Structures

We study a number of local and global classiﬁcation problems in generalized complex geometry. Generalized complex geometry is a relatively new type of geometry which has applications to string theory and mirror symmetry. Symplectic and complex geometry are special cases. In the ﬁrst topic, we characterize the local structure of generalized complex manifolds by proving that a generalized complex structure near a complex point arises from a holomorphic Poisson structure. In the proof we use a smoothed Newton’s method along the lines of Nash, Moser and Conn. In the second topic, we consider whether a given regular Poisson structure and transverse complex structure come from a generalized complex structure. We give cohomological criteria, and we ﬁnd some counterexamples and some unexpected examples, including a compact, regular generalized complex manifold for which nearby symplectic leaves are not symplectomorphic. In the third topic, we consider generalized complex structures with nondegenerate type change; we describe a generalized Calabi-Yau structure induced on the type change locus, and prove a local normal form theorem near this locus. Finally, in the fourth topic, we give a classiﬁcation of generalized complex principal bundles satisfying a certain transversality condition; in this case, there is a generalized ﬂat connection, and the classiﬁcation involves a monodromy map to the Courant automorphism group.

Keywords: Mathematics
Geometry
Differential geometry
Geometric analysis
Symplectic geometry
Poisson geometry
Complex geometry
Mathematical physics
Advisor: Gualtieri, Marco
Karshon, Yael