VictorJuiz/thesis huggingface dataset:
Photon Echoes from Retinal Proteins

This thesis focuses on the ultrafast isomerization reaction of retinal in both rhodopsin and bacteriorhodopsin, examples of sensory and energy transduction proteins that exploit the same photoactive chromophore for two very different functions. In bacteriorhodopsin, retinal isomerizes from an all-trans to 13-cis conformation as the primary event in light- driven proton pumping. In the visual pigment rhodopsin, the retinal chromophore isomerizes from an 11-cis to all-trans geometry as the primary step leading to our sense of vision. This diversity of function for nominally identical systems raises the question as to just how optimized are these proteins to arrive at such drastically different functions? Previous work has employed transient absorption spectroscopy to probe retinal protein photochemistry, but many of the relevant electronic and nuclear dynamics of isomerization are masked by inhomogeneous broadening effects and strong spectral overlap between reactant and photoproduct states. This work exploits the unique properties of two-dimensional photon echo spectroscopy to deconvolve inhomogeneous broadening and spectral overlap effects and fully reveal the dynamics that direct retinal isomerization in proteins. In bacteriorhodopsin, vibrational coupling to the reaction coordinate results in a surface crossing event prior to the conventional conical intersection associated with isomerization to the J intermediate. In rhodopsin, however, a similarly early vibrationally-mediated barrier crossing event is observed, resulting in spectral signals consistent with the known photoproduct state appearing an order of magnitude faster than determined from conventional transient absorption measurements. The competing overlapping spectral signals that obscured the initial dynamics when probed with transient absorption spectroscopy are now clearly resolved with two-dimensional photon echo spectroscopy. These experiments illustrate the critical role of the protein in directing the outcome of retinal photochemistry. The protein controls the reaction pathway through steric interactions between the binding pocket and the retinal chromophore, the result of which directly sets the isomerization coordinate and indirectly controls the vibrational coupling to the reaction coordinate based on the local retinal structure. The new insight from this work is the extraordinary degree of selective vibrational coupling involved in directing the isomerization reaction in retinal proteins.

Keywords: vision
rhodopsin
spectroscopy
photon echoes
Advisor: Miller, R. J. Dwayne
Variability of Handwriting Biomechanics: A Focus on Grip Kinetics during Signature Writing

Grip kinetics are emerging as an important measure in clinical assessments of handwriting pathologies and fine motor rehabilitation as well as in biometric and forensic applications. The signature verification literature in particular has extensively examined the spatiotemporal, kinematic, and axial pressure characteristics of handwriting, but has minimally considered grip kinetics. Therefore, the focus of this thesis was to investigate the variability of grip kinetics in adults during signature writing. To address this goal, a database of authentic and well-practiced bogus signatures were collected with an instrumented pen that recorded the forces applied to its barrel. Four different analytical studies were conceived. The first study investigated the intra- and inter-participant variability of grip kinetic topography on the pen barrel based on authentic signatures written over 10 days. The main findings were that participants possessed unique grip force topographies even when the same grasp pattern was employed and that participants could be discriminated from each other with an average error rate of 1.2% on the basis of their grip force topographies. The second study examined the stability of different grip kinetic features over an extended period of a few months. The analyses revealed that intra-participant variation was generally much smaller than inter-participant variations even in the long term. In the third study, grip kinetics associated with authentic and well-practiced bogus signatures were compared. Differences in grip kinetic features between authentic and bogus signatures were only observed in a few participants. The kinetics of bogus signatures were not necessarily more variable. The variation of grip kinetic profiles between participants writing the same bogus signature was evaluated in the fourth study and an average error rate of 5.8% was achieved when verifying signatures with kinetic profile-based features. Collectively, the findings of this thesis serve to inform future applications of grip kinetic measures in biometric, clinical and industrial applications.

Keywords: Handwriting biomechanics
Grip kinetics
Biometrics
Variability
Advisor: Chau, Tom
A Detailed Examination of the Phosphorylation of APLF Residue Serine-116 in the Context of DNA Damage

APLF is a forkhead associated (FHA) domain-containing protein with unique poly(ADP)-ribose (PAR)-binding zinc finger (PBZ) domains that are involved in the DNA damage response. The interaction of the APLF PBZ domains with PAR is essential for the rapid recruitment of APLF to sites of DNA double strand breaks (DSBs), while the FHA domain facilitates non-homologous end-joining. In response to ionizing radiation (IR), APLF is phosphorylated at Serine-116 (APLFS116), although the function of this post-translational modification has yet to be defined. Here we provide a detailed characterization of the IR-induced and ATM- dependent phosphorylation of endogenous APLF at Serine-116 in the context of DNA damage. We additionally examine a novel APLF FHA-dependent interaction with 53BP1 (p53 Binding protein 1). Together, we illustrate that APLFS116 phosphorylation is dependent upon both the tandem PBZ domains, as well as the FHA-domain, and that the depletion of either PARP3 or 53BP1, similarly affected APLFS116 phosphorylation. Furthermore, we show that DSB-repair was compromised in cells expressing the APLFS116A mutation. Collectively, our findings provide a detailed understanding of the molecular pathway that leads to the phosphorylation of APLF following DNA damage and suggest that APLFS116 phosphorylation facilitates APLF-dependent DSB repair.

Keywords: DNA Damage
Cancer
Advisor: Koch, C. Anne
Search for Heavy Resonances Decaying to Top Quark Pairs in the Boosted All-Hadronic Decay Channel

Many theories of physics beyond the Standard Model predict the existence of TeV-scale resonances that decay to top quark pairs. This thesis presents a search for such resonances produced in proton-proton collisions at a centre-of-mass energy of 7 TeV at the CERN Large Hadron Collider with 4.7 fb−1 of data collected by the ATLAS detector in 2011. The search is performed in the channel where both top quarks decay hadronically and emerge in highly boosted states, and the collimated decay products of each boosted top quark are reconstructed as a single large jet (a “top quark jet”). A tagging technique based on the distinctive masses and substructures of these top quark jets is used to distinguish them from light quark and gluon jets. The data are found to be consistent with Standard Model predictions, and 95% credibility level upper limits are set on the cross section times branching ratio for leptophobic Z' bosons in a Topcolour model and Kaluza-Klein gluons as predicted by the bulk Randall-Sundrum model. These limits exclude Kaluza-Klein gluons with masses between 1.02 TeV and 1.62 TeV. The substructure of light quark and gluon jets, which form the dominant background to hadronically decaying boosted top quarks, is studied in an auxiliary measurement using 35 pb−1 of data collected by ATLAS during the 2010 run period. The observed substructure of these jets are found to be in good agreement with theoretical predictions.

Keywords: particle physics
experimental
high energy
top quark
BSM physics
resonance search
jet substructure
Advisor: Sinervo, Pekka
Advanced Three-dimensional Nonlinear Analysis of Reinforced Concrete Structures Subjected to Fire and Extreme Loads

With the rise in hazards that structures are potentially subjected to these days, ranging from pre-contemplated terror attacks to accidental and natural disasters, safeguarding structures against such hazards has increasingly become a common design requirement. The extreme loading conditions associated with these hazards renders the concept of imposing generalized codes and standards guidelines for structural design unfeasible. Therefore, a general shift towards performance-based design is starting to dominate the structural design field. This study introduces a powerful structural analysis tool for reinforced concrete structures, possessing a high level of reliability in handling a wide range of typical and extreme loading conditions in a sophisticated structural framework. VecTor3, a finite element computer program previously developed at the University of Toronto for nonlinear analysis of three-dimensional reinforced concrete structures employing the well-established Modified Compression Field Theory (MCFT), has been further developed to serve as the desired tool. VecTor3 is extended to include analysis capabilities for extreme loading conditions, advanced reinforced concrete mechanisms, and new material types. For extreme loading conditions, an advanced coupled heat and moisture transfer algorithm is implemented in VecTor3 for the analysis of reinforced concrete structures subjected to fire. This algorithm not only calculates the transient temperature through the depth of concrete members, but also calculates the elevated pore pressure in concrete, which enables the prediction of the occurrence of localized thermally-induced spalling. Dynamic loading conditions are also extended to include seismic loading, in addition to blast and impact loading. Advancing the mechanisms considered, VecTor3 is developed to include the Disturbed Stress Field Model (DSFM), dowel action and buckling of steel reinforcement bars, geometric nonlinearity effects, strain rate effects for dynamic loading conditions, and the deterioration of mechanical properties at elevated temperatures for fire loading conditions. Finally, the newly-developed Simplified Diverse Embedment Model (SDEM) is implemented in VecTor3 to add analysis capability for steel fibre-reinforced concrete (SFRC). Various analyses covering a wide range of different structural members and loading conditions are carried out using VecTor3, showing good agreement with experimental results available in the literature. These analyses verify the reliability of the models, mechanisms, and algorithms incorporated in VecTor3.

Keywords: Reinforced Concrete
Fire
Extreme Loads
Three-Dimensional Finite Element Analysis
Heat and Moisture Transfer
Fibre-Reinforced Concrete
Seismic Loads
Blast Loads
Impact Loads
Advisor: Vecchio, Frank J.
Economics of Influenza Vaccine Development

In this thesis we are particularly concerned about the development of new and improved influenza vaccines with in the changing external economic environment. The thesis covers two major objectives: 1) Developing methods to estimate the costs of influenza vaccine development The ability to calculate the development costs for specific medicines and vaccines are important to inform investments in innovation. Unfortunately, the literature is predominated by non-reproducible studies only measuring aggregate level drug research and development (R&amp;D) costs. Further, the literature appears very scant on the development costs of new vaccines. In the first objective we therefore describe methodology that improves the transparency and reproducibility of primary indication expected R&amp;D expenditures of influenza vaccines. 2) Developing methods to focus influenza vaccine R&amp;D towards meeting cost-effectiveness targets The second objective is focused on how to forecast evidence requirements for cost effectiveness analysis (CEA) of influenza vaccines. The guidance to manufacturers on what evidence would optimally support acceptable CEA is scant. The absence of such guidance and the increased emphasis on CEA can add significant risk to the vaccine development process. Thus we perform a Value of Information (VOI) analysis on the parameters of a cost effectiveness model designed to evaluate new influenza vaccines designed for use in elderly adults. The results of this study highlight what type of endpoints that should be studied in influenza vaccine R&amp;D programs. From our work on these objectives we are able to shed light on economics that should be considered while developing a new influenza vaccine. Though our contribution is mainly methodological, we conclude the thesis suggesting changes in the way the vaccine industry and HTA agencies work. These changes are in our view necessary to meet society&rsquo;s demand for new vaccines that deliver high value for money.

Keywords: Economics
Vaccines
Advisor: Grootendorst, Paul
Nanoscale Manipulation under Scanning Electron Microscopy

A nanomanipulation system operating inside a scanning electron microscope (SEM) enables visual observation and physical interactions with objects at the nanometer scale. Compared to SEM that is a powerful imaging platform (&lsquo;eyes&rsquo;), the development of nanomanipulation systems (&lsquo;hands) and techniques for transporting, modifying, and interacting with micro/nanoscaled objects is lagging behind. Two generations of nanomanipulation systems were developed with high SEM compatibility. The vacuum load-lock feature allows setup/sample/end-tools changes to be made within minutes instead of hours as with existing nanomanipulation systems. The integrated high resolution encoders and automation features significantly ease the skill dependency in nanomanipulation. Its small shape factor minimizes effects on SEM imaging performance, and does not restrict the use of the many detectors inside a SEM. The new nanomanipulation systems were applied to the manipulation of sub-cellular structures and the characterization of nano-structures. The first application involves the development of a technique to surgically extract sub-micrometer-sized subnuclear structures within a single cell&rsquo;s nucleus, followed by biochemical analysis to amplify and sequence the genes contained within. Enabled by the technique, four novel genomic loci associations with promyelocytic leukemia nuclear bodies (PML NB) were discovered in Jurkat cells. The second application targets automated probing of nanostructures under poor imaging conditions. Through real-time image drift compensation and visual servoing of the nano probes, automated probing of nanostructures was achieved with a high success rate and a speed at least three times higher than skilled operator. To enhance the functions of the nanomanipulation system, new types of end-effectors were also developed. A MEMS tool with changeable tool tips was design and prototyped. In-situ (i.e., inside SEM) tool tip change was demonstrated for gripping objects that vary in size by two orders of magnitude (15 um to 100 nm) with a single microgripper body. Furthermore, a microfabrication process was developed to produce changeable nano-spatulas with tip size less than 10 nm, intended for use in the subnuclear structure extraction work. Finally, a local precursor sublimation technique compatible with the nanomanipulation system was developed for enhancing electron beam induced deposition (EBID) inside the SEM.

Keywords: Nanomanipulation
scanning electron microscopy
Advisor: Sun, Yu
The Effect of Physicochemical Properties of Secondary Treated Wastewater Flocs on UV Disinfection

The microbial aggregates (flocs) formed during secondary biological treatment of wastewater shield microbes from exposure to ultraviolet (UV) light, and decrease the efficiency of disinfection, causing the tailing phenomena. This thesis investigates whether the formation of compact cores within flocs induces higher levels of UV resistance. Moreover, it investigates the effect of secondary treatment conditions on the physicochemical properties of flocs’, effluent quality, and UV disinfection performance. Compact cores were isolated from the flocs using hydrodynamic shearing. The UV dose response curves (DRC) were constructed for flocs and cores, and the 53-63 μm cores showed 0.5 log less disinfectability, compared to flocs of similar size. Based on a structural model developed for the UV disinfection of flocs, floc disinfection kinetics was sensitive to the core’s relative volume, their density, and viability. The UV disinfection and floc properties of a conventional activated sludge (CAS) system, and a biological nutrient removal (BNR-UCT) system, including both biological nitrogen and phosphorus removal, was compared. The 32-53 μm flocs and the final effluent from the BNR-UCT reactor showed 0.5 log and 1 log improvement in UV disinfectability, respectively, compared to those from the CAS reactor. The BNR-UCT flocs were more irregular in structure, and accumulated polyphosphates through enhanced biological phosphorus removal. Polyphosphates were found to be capable of producing hydroxyl radicals under UV irradiation, causing the photoreactive disinfection of microorganisms embedded within the BNR-UCT flocs, accelerating their UV disinfection. Comparing the UV disinfection performance and floc properties at various operating conditions showed that increasing the operating temperature from 12 ºC to 22 ºC, improved the UV disinfection of effluent by 0.5 log. P-Starved condition, i.e. COD:N:P of 100:10:0.03, decreased the average floc size and sphericity, both by 50%. Despite the higher effluent turbidity of the P-Starved reactor, the final effluent’s UV disinfection improved by at least 1 log compared to the P-Normal and P-Limited conditions. The improvement in the floc and effluent disinfectability were accompanied by a decrease in floc sphericity and a decrease in the number of larger flocs in the effluent, respectively.

Keywords: Wastewater Treatment
UV Disifnection
Microbial Flocs
Modeling
Phosphorus
Biological Nutrient Removal
Advanced Oxidation
Phosphate Accumulating Organisms
Activated Sludge Process
Temperature
Sludge Retention Time
Floc Structure and Composition
Floc UV Resistance
Photooxidation
Advisor: Farnood, Ramin
Allen, Grant
The Molecular Characterization and Role of Teneurin C-terminal Associated Peptide (TCAP)-1 in the Regulation of Neuronal Cytoskeletal Dynamics and Male Reproduction

eneurin C-terminal associated peptides (TCAPs) are a novel family of peptides encoded on the last exon of the teneurin genes. The predicted peptide sequences are highly conserved across metazoans and possess the structural hallmarks of a cleavable bioactive peptide that are 40 or 41 amino acid residues. One of the peptides in the family, TCAP-1, is a potent regulator of neurite outgrowth and dendritic spine density in the hippocampus and inhibits corticotropin-releasing factor (CRF)-associated stress-induced and cocaine-seeking behaviours. The effects of TCAP-1 are long lasting, suggesting that TCAP-1 plays a significant role in the regulation of cell-to-cell communication and cellular plasticity. Moreover, TCAP-1 regulates cellular energy, metabolism and cell survival and may, therefore, possess functional attributes outside of the CNS. However, the molecular mechanisms associated with TCAP-1-mediated trophic effects are not known. My research was aimed to 1) determine whether TCAP-1 exerts its effects as part of a direct teneurin-1 function, whereby TCAP-1 represents a functional region of the large teneurin-1 protein, or if it has an independent role, either as a splice variant or post-translational proteolytic cleavage product of teneurin-1; 2) map the distribution of TCAP-1-immunoreactivity and TCAP-1 binding sites in mouse; 3) elucidate the molecular mechanism by which TCAP-1 regulates cytoskeletal dynamics; and 4) investigate a role for TCAP-1 in male reproduction. My research establishes that the C-terminal region of teneurin-1, corresponding to TCAP-1, can be both structurally and functionally independent from teneurin-1 in both the brain and testis of the adult mouse. Furthermore, I provide novel evidence that functionally links the teneurin-TCAP-1 system with the dystroglycan complex and provide new insight into the molecular and signaling mechanisms by which TCAP-1 regulates cytoskeletal dynamics. These studies implicate the teneurins in a broader range of neuroendocrine and trophic functions than previously thought and furthers our understanding of the mechanisms associated with TCAP-1-mediated function in the body.

Keywords: Teneurin
Cytoskeleton
Reproduction
Peptide processing
Signal transduction
Advisor: Lovejoy, David
Invasive Species Distribution Models: An Analysis of Scale, Sample Selection Bias, Transferability and Prediction

Species distribution models must balance the need for model generality with that for precision and accuracy. This is critical when modelling range-expanding species such as invasive species. Given the increased use of species distribution models to study invasive species-landscape relationships, a better understanding of the effect of spatial scales, sampling biases, model transferability and discrepancies between different models’ future predictions is necessary. This dissertation addresses these knowledge gaps using mute swans (Cygnus olor) as a case study species. I specifically examine mute swan’s distributions in parts of their native range of Britain and their non-native range of Ontario, Canada. I first investigate which environmental variables at which spatial scales best explain mute swan’s distribution in its non-native range. Second, I perform a sample selection bias study to examine predictive accuracy when species distribution models are built using varying ranges of environmental variables and applied to broader spatial extents. Third, I examine the potential for, and limitations of model transferability between native and non-native regions. Finally, I use two different modelling approaches and three different climate change and land use change scenarios to predict future mute swan habitat suitability. The results indicate that (1) models with better predictive accuracy include environmental variables from multiple ecologically-meaningful scales and measured at spatial extents that include a broad range of environmental variable values; (2) models can exhibit asymmetrical transferability; (3) climate change will facilitate mute swan range expansion in the future more than land use change; and (4) mute swans are often found near urban waterbodies. When modelling invasive species distributions, I suggest that ecologists consider: (I) spatial scale of the underlying landscape processes and species’ use of the landscape; (II) variability and range of each environmental variable used for building models; and (III) stage of establishment of the invasive species.

Keywords: landscape ecology
biogeography
species distribution models
invasive species
climate change
land use change
Advisor: Conway, Tenley
Fortin, Marie-Josee