VictorJuiz/thesis huggingface dataset:
The development of executive functions and working memory in children and adolescents with Autism Spectrum Disorder: A longitudinal study of brain and behaviour
Keywords: Autism Spectrum Disorder
DTI
executive function
fMRI
working memory

Children with Autism Spectrum Disorder (ASD) exhibit social and communicative problems, repetitive and restrictive patterns of behaviour, and a range of cognitive deficits, including executive functioning (EF) impairments. Literature in ASD has focused mostly on the behavioural phentotype of the disorder and less research has investigated the cognitive and EF profiles in this population. The objective of this thesis was to gain a greater understanding of EF deficits, their longitudinal development, their underlying neural correlates using neuroimaging techniques, and their impact on critical outcomes in children with ASD compared to typical developing (TD) individuals. Structural and functional brain disturbances were evident in children and adolescents with ASD, relative to controls. In a diffusion tensor imaging (DTI) study, significant white matter differences were found in tracts essential for higher order cognitive processing, such as EF, and general information processing in children with ASD (ages 7-15 years). White matter developmental trajectories did not appear to differ between groups. Functional neural systems associated with EF, specifically working memory, were also impaired in youth ASD (ages 7-13 years) relative to controls, particularly in parietal and temporal regions. In this functional magnetic resonance imaging (fMRI) study, children with ASD showed inadequate modulation of neural activity in response to increasing cognitive demands, which did not improve over two years. Last, children with ASD (ages 7-14 years) showed marked EF impairments in everyday settings as observed by parents, which persisted over time compared to TD children. Early EF deficits predicted later symptoms of co-morbid psychopathology and social difficulties in ASD. Findings suggest that children with ASD exhibit structural and functional neural deficits associated with EF across childhood that make them vulnerable to the increasing complexity of environmental demands as they mature. Results support EF as potential target in autism interventions for improving executive development, and also for preventing co-morbid psychopathology and promoting social competence in ASD.
Balance of Forces in Bitumen-particle-water Systems
Keywords: bitumen
capillary number
emuslion
oil-particle cluster
oil sands
separation

The oil sands in Canada are an abundant source of energy, but must be utilized in a way that bitumen can be extracted economically while it is environmentally responsible. This thesis focuses on three distinct studies on the interaction of bitumen-particle-water systems from a fluid dynamic perspective. The goal of this work is to understand the role of viscosity, interfacial tension, shear rate, shearing time, bitumen chemistry, and other process variables on separation processes related to bitumen production. These processes include the separation of oil from particles, the separation of particles from oil-particle clusters, and the separation of water from a water-in-bitumen emulsion. Results are quantified using different image analysis techniques, and characterized using dimensionless numbers, including capillary and Reynolds numbers, to understand the fundamentals of the governing forces and their mutual interactions. The first part of this thesis describes the separation of oil from an oil-coated sphere falling through an aqueous solution. Results reveal that maximum separation takes place when the capillary number is close to unity. The experiments are then extended to a more complicated geometry, where we examined the breakup and separation of oil-particle clusters in a simple shear flow. At high solid volume fraction, the oil that binds the particles together governs the dynamics of the cluster deformation, and therefore the critical capillary number for cluster breakup is the same as those already published in the literature for oil droplet breakup. Also, at capillary numbers above unity, clean particles separate from the cluster. Results from both studies show that maximum separation takes place when the oil-to-water viscosity ratio is between 0.1 and 1. An analytical solution shows that at those viscosity ratios, both normal and tangential stresses at the oil-water interface contribute to greater separation. In the final study, the formation of water in diluted bitumen emulsions was evaluated as a function of hydrodynamic conditions, pH, dilution ratio, and bitumen composition. A bimodal population of drop sizes was identified. The viscosity ratio was found to be a determining factor in the fraction of sub-micron droplets. A process of dilution and shear was introduced to mitigate this sub-micron fraction.
Formulation and Evaluation of Multi-particulate Antibiotic Alternatives for Oral Delivery to Livestock Animals to Target Gut Pathogens
Keywords: animal science
antibiotic resistance
bacteriophage
coating
essential oil
formulation

This thesis explored strategies for enhanced oral delivery of antibiotic alternatives to the livestock intestinal tract to target enteric pathogens. The first part dealt with formulating a liquid essential oil (EO) into solidified granules and subsequently enteric coated for intestinal release. Trans-cinnamaldehyde (CIN), a model EO compound with strong antibacterial activity was formulated into granules using a three-component phase-diagram, yielding granules with high loading and stability, and enteric coated by fluid-bed processing. Antibacterial activity of CIN remained intact throughout manufacturing, after addition of 1% eugenol to prevent autoxidation of CIN which lasted for at least 1 year under ambient storage. In animal trials, coated granules delivered CIN in higher concentrations than free oil to the lower intestinal regions where pathogens colonize. The second part explored bacteriophage microencapsulation for oral, bio-control of intestinal Salmonella in chickens. Preliminary studies revealed the phage intestinal distribution and fecal excretion pattern following a single oral dose, and optimized the Ca-alginate-whey protein formulation of microbeads for quicker phage release. Phage lytic activity studies against a target pathogen showed single phages were insufficient at maintaining reduction of STT104NalR, rather phage cocktails were required to maintain reduction in vitro and in animal digesta, which achieved reductions of several log10CFU/g digesta. Two trials were carried out, testing the effectiveness of pathogen reduction by phage cocktails administered to chicks experimentally infected with STDT104NalR. Trial #1 showed that cocktail 1 did not significantly affect the colonization levels even though in vitro activity was good. Trial 2 re-tested CT1 along with an expanded cocktail 2, with larger animal groups. CT1 yielded a similar lack of efficacy, while CT2 achieved significant reductions of STDT104NalR in ileum, ceca, and colon after 7 days, twice-daily administration with feed. This study suggests that phage cocktails microencapsulated for continuous oral administration with feed could reduce intestinal pathogens.
Historical Contingencies in the Ecology and Evolution of Species Diversity
Keywords: Biodiversity
Community ecology
Competition
Maternal effects
Metacommunities
Plant ecology

Ecologists have long-sought to explain the high diversity of species in biological communities, given that classic theory predicts that diversity is limited by available niche space. In recent years, ecologists have looked towards â historical contingenciesâ , the persistent effects of past ecological and evolutionary processes, as possible mechanisms that maintain diverse communities, either by relaxing the constraints of niche availability or by adding temporal dimensions to speciesâ niches. In this thesis, I use field and greenhouse experiments to explore three ways in which historical contingencies manifest in annual plant communities. First, my work on maternal effects shows that abiotic (ch. 2) and biotic (ch.3) conditions in the maternal generation have diverse effects on offspring phenotypes across an assemblage of species. Because species differences in environmental responses can facilitate coexistence, these studies suggest that maternal effects could act as a form of niche differentiation, and motivate future research to clarify their influences on coexistence outcomes. Second, I performed, to my knowledge, the first experimental decoupling of dispersal limitation and environmental sorting in a natural landscape by manipulating entire seed pools of annual plants (ch. 4). In doing so, I was able to identify the pervasive and scale-specific influences of dispersal limitation that constrain species distributions in plant communities. Lastly, I used competitive trials to identify macroevolutionary divergence in competitive interactions among species (ch. 5), and found evidence that divergence is contingent on historical competitive interactions in ways that are consistent with character displacement. In sum, my dissertation work has expanded our understanding of (i) the number of potential niche dimensions that might allow species to differentiate, (ii) how this differentiation can arise over evolutionary time, and (iii) the interplay of current and historical conditions in the maintenance of species diversity, and the timescales over which they play out.
Polymer Hydrogels, Aerogels, and Foams as Biomimetics of the Extracellular Matrix
Keywords: Aerogel
Extracellular Matrix
Foam
Hydrogel
Microgel
Polyurethane

Three-dimensional (3D) scaffolds that recapitulate the mammalian extracellular matrix (ECM) have potential applications as tissue engineering scaffolds and as in vitro cell culture material. This thesis describes the fabrication and characterization of microgels, aerogels, hydrogels, and foams that are biomimetics of the natural ECM. The ability to tune the mechanical property and structure of the resulting scaffolds is of particular importance. In Chapter 3, we explore a microfluidic platform for making biopolymer composite microgels in which the rigidity and structure can be tuned in high-throughput manner. Chapter 4 describes how cellulose nanocrystals can be used to make nanofibrillar hydrogels, in which the rheological properties and pore sizes can be controlled by the addition of inorganic salts. These properties are highly dependent on the size, charge, and concentration of the cations added. Chapter 5 describes the freeze-casting of aldehyde-functionalized cellulose nanocrystals and hydrazide-functionalized poly(oligoethylene glycol methacrylate) into anisotropic composite aerogels and their corresponding hydrogels. The aerogel structure could be tuned from fibrillar to columnar and lamellar by varying the freeze-cast composition. The Youngâ s modulus and swelling of the hydrogels differed parallel and perpendicular to the freeze-cast direction. Chapter 6 describes the freeze-casting of polyurethanes into anisotropic open-cell foams, which have anisotropic mechanical and thermal properties. The thermal conductivity of these foams could also be switched between anisotropic and isotropic modes.
Prevalence, Diversity, Impact, and Applications of CRISPR-Cas Inhibitors
Keywords: anti-CRISPR
bacteriophage
CRISPR
horizontal gene transfer
mobile genetic elements
phage-host coevolution

One of the most important modes of bacterial evolution is horizontal gene transfer (HGT), a process by which bacteria acquire foreign DNA, often encoding antibiotic resistance or virulence genes, from other strains or species. CRISPR-Cas systems are one of several mechanisms bacteria employ for protection from potentially harmful foreign nucleic acids, including mobile genetic elements (MGEs) like bacteriophages. CRISPR-Cas systems use an RNA-guided nuclease to locate and destroy foreign DNA, and are expected to constitute a major barrier to HGT. However, studies have shown that the presence of a CRISPR-Cas system does not correlate with lower rates of HGT. An explanation for this paradox could lie in widespread MGE-encoded inhibitors of CRISPR-Cas systems. In support of this idea, the Davidson lab previously discovered the first examples of anti-CRISPRs in bacteriophages infecting Pseudomonas aeruginosa. We hypothesized that anti-CRISPRs were likely to exist for each of the sixteen subtypes of CRISPR-Cas systems present in diverse bacterial species. Since the known anti- CRISPR proteins did not share any common features, I used a bioinformatics â guilt by associationâ method to identify new candidate anti-CRISPRs and to predict their likely CRISPR-Cas target types. Here, I present my discovery of twelve novel anti-CRISPR protein families that are widespread in MGEs of Proteobacteria. Each of these families inhibits type I-E, I-F, or II-C CRISPR-Cas systems. I provide structural and mechanistic data supporting the independent evolution of protein families that inhibit CRISPR-Cas function in distinct ways. Anti-CRISPR genes themselves are transferred among MGEs, and many anti-CRISPRs can inhibit a wide range of homologous CRISPR-Cas systems in different species. Anti-CRISPRs likely have a broad ecological impact on CRISPR-Cas systems, not only by inhibiting but also by modulating their function. Overall, anti-CRISPRs not only impact CRISPR-Cas function and HGT among diverse bacterial species, but they also provide important tools for the study and modulation of CRISPR- Cas activity.
Virtual Endocasts for Ischyromyidae and Sciuridae: Brain Evolution in Rodentia and a Deeper Understanding of the Ancestral Condition for the Brain of Euarchontoglires
Keywords: Endocast
Euarchontoglires
Paleogene
Rodentia
X-Ray computed tomography

The brain of rodents has rarely been studied from the perspective of the fossil record, and little is known of the process of brain evolution in this group. Whatâ s more, rodents are members of Euarchontoglires and could help form a better understanding of the ancestral condition for this group, augmenting what has been learned from primates. This thesis describes the first fossil and extant virtual endocasts for Rodentia. The study of primitive members of Ischyromyidae, Ischyromys typus (Oligocene), Paramys copei and P. delicatus (Eocene), show that exposure of the midbrain is likely to be primitive for rodents, as observed for Primates. Decrease in the proportion of the olfactory bulbs and increase in neocortical surface area may have occurred through time in rodent evolution similar to Primates, but with less intensity in Rodentia. Ischyromyids exhibit variation in EQ through time, with Eocene taxa displaying a higher EQ compared to Oligocene species, demonstrating that the group did not show a simple increase in EQ through time, although an increase in EQ may have occurred in sciurid evolution specifically. Study of the early squirrel Cedromus wilsoni and extant members of Sciuridae reveal that fundamental changes in the organization of the brain occurred in the transition from more primitive ischyromyids to early squirrels, with an increase in neocortex size, the appearance of a sylvian fossa, and a more complex cerebellar structure including an increase in the relative size of the paraflocculi. These changes could potentially be related to the process of becoming arboreal in rodents. Rather than locomotion, diet may have played a more critical role in Primates, since key changes in that Order postdated the origin of arboreality. Ultimately, this thesis provides a better understanding of the process of brain evolution for Euarchontoglires by studying another Order in this group aside from Primates.
Unique Lemur Traits: Proximate and Ultimate Perspectives
Keywords: Behaviour
Dominance
Evolution
Growth
Hormone
Primate

Members of the lemur clade are known to exhibit a number of traits that are unusual in the context of living primates. Here, I investigate the basis of three of these traits: sexual size monomorphism, female dominance over males, and rapid rates of growth and attainment of adult body mass. My research focuses on multiple lemur species from the current and historic colony residing at the Duke Lemur Center in Durham, NC. Using long-term morphological data on 18 lemur species, I determine that rapid growth and early attainment of adult body mass do not constrain the development of sexual size dimorphism in lemurs. Next, I conduct behavioural observations and hair hormone analysis on ring-tailed lemurs (Lemur catta), revealing that receiving aggression leads to chronic stress in males and females and that female dominance and high rates female of aggression in females are potentially mediated by sex steroid hormone concentrations. Finally, using growth records and hair hormone analysis in Coquerelâ s sifakas (Propithecus coquereli), I identify a negative relationship between chronic stress and relative body mass in early life, and demonstrate a potential carryover effect of low body mass in early life on relative body mass in adulthood. Uncovering the proximate and ultimate causes of these unique lemur traits can advance our understanding of the factors underlying trait variation in primates and other mammals.
Early Volume Change of High Performance Concrete
Keywords: Autogenous strain
Concrete
Heat of hydration
High Performance Concrete
Shrinkage
Thermal strain

In severe chloride/sulfate exposure conditions, there is need to provide more durable concrete, but this usually requires use of concretes with high cementitious binder contents that increase the risk of cracking due to thermal, autogenous, and drying shrinkage. Cracking is counter-productive to obtaining durability in the field. High performance concrete (HPC) can be durable in aggressive environments due to its superior mechanical, resistance to fluid transport, and durability characteristics. However, HPC mixtures typically have high binder contents (cement, pozzolanic minerals), and low w/cm, and therefore undergo high heat of hydration as well as autogenous shrinkage, resulting in rapid volume changes. The increased risk of autogenous deformation in high performance concrete can increase the risk of the cracking and durability of reinforced concrete structures such as bridge decks. For example, in Ontario the MTO had issues with in-creased incidence of transverse cracking in bridge decks when 50 MPa HPC was used relative to traditional 35 MPa concretes. A review of their construction records indicated that this problem was often related to concretes that set quickly and rapidly developed high temperature rise due to heat of hydration. The effects of ground granulated blast-furnace slag (GGBFS) and silica fume (SF) on the durability of HPC were investigated. In this study, HPC mixtures at 0.33 w/c were made with three sources of blended cements containing 8% SF mixed with 25, 35 and 50% GGBFS replacements by mass of cement. The compressive strength, drying shrinkage, and transport properties were measured. The test results have shown that increased fineness of the silica fume blended cement enhances the resistance to fluid transport and mechanical properties, but results in increased drying shrinkage, leading to increased cracking potential. A comprehensive study was conducted to understand (a) the interrelation between different mechanisms of volume change (thermal deformation, autogenous shrinkage, drying shrinkage) under different standard and non-standard conditions and (b) the role of different shrinkage mitigation methods (e.g. by either increasing GGBFS content to overcome early-age free and re-strained thermal deformation as well as autogenous shrinkage, or by reducing the cement binder content).
Social Interaction in Zebrafish: Effects of Social Isolation on Behaviour, Neurochemistry, and Stress
Keywords: Anxiety
Isolation
Monoamine
Social Behaviour
Stress
Zebrafish

Characterization and detailed analysis of social behaviour are necessary to further establish zebrafish as a model for developmental disorders such as Autism Spectrum Disorders and Fetal Alcohol Syndrome Disorder. Social isolation has been used as a tool to study regulation of social behaviour in various species before. The purpose of this thesis was to investigate how social isolation (during development or in adulthood) affects subsequent social and non-social behaviours. I also examined neurotransmitter systems associated with social interaction, namely dopamine and serotonin, and stress hormone cortisol, as isolated fish responded to novelty or to social stimuli. I found that life-long developmental isolation increased locomotor activity, and altered responses to social stimuli and dopaminergic metabolite levels. On the other hand, locomotor activity and social responses of socially raised zebrafish remained unchanged after chronic isolation in adulthood, but a reduction in serotonin metabolite levels was found in response to novelty and social interaction. Behavioural and physiological responses of fish isolated in adulthood were also affected by social stimulus type and prior social hierarchy status. Both developmental and chronic adult isolation reduced anxiety-related behaviour, and cortisol levels indicated that long-term social isolation is not stressful in zebrafish. Findings from zebrafish experiments are discussed in light of isolation literature in other social animals. These analyses help establish translationally relevant zebrafish research as a tool to simplify, explore, and understand behaviour and disorders involving social abnormalities in social vertebrates.