VictorJuiz/thesis huggingface dataset:
Development of Indium Arsenide Nanowire Field-Effect Transistors as Chemical Sensors
Keywords: chemical sensor
field-effect transistor
indium arsenide
ion-sensitive
nanowire

Chemical sensors based on field-effect transistors were fabricated from hundreds of aligned indium arsenide nanowires which show promise for high performance based on their high electron mobility and charge sensitivity. Sensing responses to analytes in vapour and solution phases were collected from these multi-wire devices via real-time current measurements and parameters extracted from electrical transport characterization. In the vapour phase, a linear response to acetic acid was observed in surface charge densities determined from a model for the sub-threshold behaviour. These responses distinguished between strongly chemisorptive bonding of acetic acid versus weaker bonding of methanol and 2-butanone. In the solution phase, near-Nernstian sensitivity to sodium ions of a crown ether functionalized, fluorosilicone membrane was determined from the threshold voltage and hysteresis in transport characteristics. A Nernst-Planck-Poisson model was investigated to interpret the electro-diffusive processes but did not accurately capture the electric field dependence. Suggestions to address the shortcomings are given.
Testing for Convergent Evolution in Semi-aquatic Anolis Lizards
Keywords: Anolis lizards
Convergent evolution
Macroevolution
Morphology
Swimming performance

Twelve species from six different clades of Anolis lizard exhibit a semi-aquatic lifestyle. These unusual species are found only along neotropical streams, and are known to swim, capture aquatic prey, and dive to escape predators. Based on ecomorphology theory, and anoles’ famed predisposition for convergence, we would predict that these anole lineages should have undergone convergent evolution. However, previous morphometric research suggested that semi-aquatic anoles are not convergent. This thesis reinvestigates whether semi-aquatic anoles have convergently evolved using novel morphometric and experimental approaches. I assessed the morphology, swimming speed, and diving performance of semi-aquatic and non-aquatic anole species from throughout the neotropics. My results suggest that semi-aquatic anoles have converged upon similar morphologies, superior swimming performance, and a previously undiscovered potential adaptation for diving: underwater rebreathing. Semi-aquatic anoles show evidence of repeated multidimensional convergence, and, somewhat uniquely for Anolis, provide strong evidence for convergence between mainland and island forms.
Microfluidics for Measuring Mutual Properties of the CO2–Crude Oil System
Keywords: CO2-oil
Contact angle
Diffusivity
Microfluidics
solubility
swelling

Successful implementation of CO2 enhanced oil recovery critically relies on detailed measurements of CO2–oil properties at relevant reservoir conditions. In this work, a microfluidic platform was developed to quantify the comprehensive suite of mutual properties of a CO2 and crude oil mixture. The time-lapse oil swelling/extraction in response to CO2 exposure under step-wise increasing pressure was quantified via fluorescence microscopy, leveraging the inherent fluorescence property of the oil. The solubility and diffusion coefficient of CO2 in the crude oil as well as CO2–oil MMP were determined from the oil swelling/extraction data with measurements in strong agreement with previous results. In addition, the oil–CO2–silicon contact angle was measured, with contact angle increasing with pressure. In contrast with conventional methods which require days and ~500 mL fluid sample, this approach provides a comprehensive suite of measurements, 100-fold faster with less than 1 μL of sample.
FuNTAP: A Fusarium graminearum Protein-Protein Interaction Network to Study Deoxynivalenol Biosynthesis Pathways
Keywords: Deoxynivalenol
Fusarium graminearum
Protein-protein interaction network
Tricothecene
Yeast-Two-Hybrid

Protein interaction networks provide invaluable information on the complexity of biological pathways within organisms. These networks help identify proteins of interest along with groups of closely associated proteins with common functions. The fungus Fusarium graminearum is a pathogen of agriculturally significant crops such as wheat. The infection process includes production of harmful mycotoxins such as deoxynivalenol (DON). To study the signalling pathways leading to biosynthesis of DON in F. graminearum, we constructed the Fusarium Network of Trichothecene Associated Proteins (FuNTAP) based on yeast two-hybrid interactions of proteins differentially expressed under DON inducing conditions. The FuNTAP network categorizes the metabolic pathway which produces this important mycotoxin without the drawbacks of previous predicted-based model interactomes. As such, we present the FuNTAP network as a tool to identify proteins regulating the biosynthesis of DON. This network may also integrate other sources of data including gene expression profiles and biological function through sequence similarity.
High-Speed Baud-Rate Clock and Data Recovery
Keywords: Baud-rate
Circuits
Clock and Data Recovery
High-speed Signalling
Receiver
Wireline

This thesis presents an adaptive baud-rate CDR with CTLE and 1-tap DFE. The novelty in this design is the adaptation engine tailored for baud-rate clock and data recovery where the comparators for the DFE and the PD are shared to save power. A testchip was fabricated in TSMC 28nm CMOS. The adaptation engine is demonstrated for 34-36Gb/s operation with a Tyco 5" channel resulting in 15.05-18.25dB channel losses. At 35Gb/s, the total power consumption is measured to be 106.3mW or a FOM of 3.04pJ/bit. This thesis also presents a 2x half-baud-rate clock and data recovery technique with 2x oversampling at half-baud-rate (every other UI). A testchip was also fabricated in TSMC 28nm CMOS. A 30Gb/s 2x half-baud-rate CDR was tested with a Tyco 5" channel with 13.06dB of loss. The total power consumption is measured to be 79.2mW or a FOM of 2.64pJ/bit.
Widening the Gap Between Egoists and Altruists: A Computational Study of Altruistic Choice under Time Pressure.
Keywords: Altruism
Computational Modelling
Eye-Tracking
Social-Decision Making
Time Pressure

Popular models of altruistic choice typically assume some universal disposition that is curbed by the employment of control. The “self-control model” assumes humans are fundamentally self-interested and require self-control to overcome their egoistic impulses. Meanwhile, the “social-intuitionist model” posits that humans are intuitively prosocial and self-interests require controlled deliberation. Many studies investigating these theories measure changes in altruistic choice under time pressure, assuming that time pressure reveals our most automatic preferences. However, these studies yield mixed support for both theories and report overwhelming interindividual variability in the effects of time pressure: selfish individuals may become more selfish while generous individuals become more generous. Using novel computational modelling and eye-tracking, we propose a resolution to these conflicting findings. We show that individuals vary widely in their social preferences and that time pressure multiply disrupts choice processes, simultaneously increasing choice errors and interacting with existing preferences and biases to extremify choice behavior.
The Role Of Oxidative Stress Following Antenatal Synthetic Glucocorticoid Therapy
Keywords: Antenatal
Glucocorticoid
Oxidative stress

We investigated the role of oxidative stress following sGC treatment in a guinea pig model of gestation through measures including: expression of antioxidant enzyme genes, protein carbonylation, and the glutathione ratio in the hippocampus, placenta, and liver of female and male fetuses treated with two courses of betamethasone in utero. Results indicated no significant differences in hippocampal or placental gene expression. Peroxiredoxin-6 expression was significantly downregulated in the male liver following sGC, but there were no differences in the female liver. There were no differences in protein carbonylation or glutathione ratio in the fetal placenta or liver. To investigate long-term outcomes of sGC exposure in utero, we used gene set enrichment analysis of post-natal day 40 female hippocampi, and found significant downregulation of a gene set for oxidative phosphorylation. These finding suggest that while the fetus is acutely protected from oxidative stress following sGC, there might be long-term programming of mitochondrial functions.
Direct Sensing of Hydrocarbon Pollutants via Soluble Polymeric Sensors
Keywords: Composites
Environment
Hydrocarbons
Pollutants
Polymers
Sensors

Hydrocarbon leakages are a prominent environmental and economic issue in today’s oil and gas transportation infrastructure. In the US alone, over 100 hydrocarbon spills occur yearly, resulting in billions of dollars of civil and environmental damage. To mitigate the impacts of this issue, development and implementation of leak detection systems are prominently applied in industry. However, current state-of-the-art sensor systems utilize indirect methods of sensing that feature poor hydrocarbon selectivity and low detection accuracies of 16-17%. Herein we employ hydrocarbon-soluble polymers in fabrication of sensor designs for direct and selective crude oil sensing. Composite EVA/carbon fiber sensors are fabricated and show 421% sensor responses after 6 hours of oil exposure, while reflectometry sensing via EVA and silicone coaxial cables show sensor responses of 9.71% to 115% after 24 hours of oil exposure. Overall, high efficacy in hydrocarbon leak detection is achieved, validating the sensing effectiveness of hydrocarbon-soluble polymers.
Assessing the immunomodulatory effects of Ganoderma lucidum and Coriolus versicolor on the cancer killing capacity of natural killer cells
Keywords: antibody dependent cytotoxicity
cell therapy
Coriolus versicolor
Ganoderma lucidum
immunotherapy
natural killer cells

Ganoderma lucidum and Coriolus versicolor are medicinal mushrooms with diverse immunomodulatory properties. This work demonstrates the effects of mushroom extracts on the survival of different cancer and natural killer (NK) cell lines (NK-92, CD16+IL-2+NK-92, KHYG-1) and NK cytotoxicity against different cancers. G. lucidum ethyl acetate and C. Versicolor aqueous extracts completely inhibited the growth of all tested cancer targets at 100 ug/mL, whereas G. lucidum aqueous extract enhanced NK-92 cell survival. At a 5:1 effector to target ratio, aqueous G. lucidum and C. Versicolor extract significantly enhanced the cytotoxicity of NK-92 and KHYG-1 against leukemia, multiple myeloma (2.2x fold increase), and breast cancer. G. lucidum aqueous extract pretreated CD16+IL-2+NK-92 cells in combination with Herceptin demonstrated 2x higher killing against ovarian cancer compared to untreated CD16+IL-2+NK-92. Five distinct fractions from the crude aqueous extract were isolated and shown to have promising NK immunostimulatory activity that merits further investigation into their bioactive components.
Coronavirus Evolution and Immune Evasion
Keywords: Adaptation
Coronavirus
Crystallography
Evolution
Immune
Phylogeny

Coronaviruses are emerging pathogens that threaten human health and prosperity. Each year, hundreds of millions of people are infected with continually circulating coronaviruses that cause the common cold in healthy individuals and kill the most vulnerable of us. Coronaviruses adapt to environmental change at a remarkable rate. The HCoV-229E coronavirus has adapted and evolved over the last 50 years by mutating residues in the receptor-binding loops of the receptor binding domain (RBD) of its spike (S) protein. These sequences phylogenetically segregate into Classes whose viruses have successively replaced one another in the human population. These Classes possess different receptor (hAPN) and antibody binding characteristics and the crystal structures of RBD-hAPN complexes have been solved. Structural insights into the ever-changing RBD and its interaction with hAPN show the use of secondary structure-less loops facilitate tremendous structural variability, a trait that likely enables changes in viral fitness and immune evasion.
Alcohol Use and Emerging Adult Development: A Latent Profile Analysis of Community Drinkers
Keywords: alcohol problems
alcohol use
binge drinking
drinking motives
emerging adult development
latent profile analysis

Latent profile analysis was used to establish profiles of emerging adult development and then test associations with drinking behaviors both concurrently and prospectively. To differentiate between different patterns of emerging adult drinking, 153 regular drinkers from the community (ages 18-24 years; M = 20.9, SD = 1.9) completed the Inventory of Dimensions of Emerging Adulthood (IDEA) and measures of alcohol use, motives and consequences. The EA-Consistent (90%) profile had elevated scores on the five typical IDEA subscales; the Non-Exploring EA profile (10%) had low scores on four dimensions. The Non-Exploring EA profile consumed significantly less alcohol, experienced fewer alcohol consequences, and had lower social and enhancement motives at baseline and lower scores on drinking volume, alcohol consequences, and social motives at the one-year follow-up. The findings provide support that emerging adult development profiles reflect different patterns of alcohol use and differentiate between those with lower- vs. higher-risk alcohol use.
Novel Mechanism of Thrombosis: Role of β3 Integrin PSI Domain in Blood Coagulation
Keywords: cell-based blood coagulation
integrin αIIbβ3
PSI domain
thiol isomerase
thromboelastography
thrombosis

Integrin αIIbβ3 is a key receptor in platelet adhesion/aggregation. We recently showed the plexin-semaphorin-integrin (PSI) domain of β3 has thiol isomerase activity. We developed four monocloncal antibodies (mAbs) that bind PSI and inhibit thiol isomerase activity, platelet adhesion/aggregation and thrombosis. The inhibitory effect of the mAbs was much stronger in vivo than in vitro (anticoagulated), suggesting that anti-PSI mAbs decrease blood coagulation. The anti-PSI mAbs were shown to inhibit blood clot retraction. Anti-PSI mAb-treated platelet-rich plasma decreased fibrin network formation in laser scanning and spinning disk confocal microscopy. In thromboelastography, anti- PSI mAbs inhibited blood coagulation. Furthermore, anti-PSI B1 significantly inhibited blood coagulation more than other anti-β3 mAbs (JAN D1, M1 and Abciximab precursor 7E3). This supports a novel role of PSI in enhancing blood coagulation, particularly through intrinsic pathway factors. For the first time, αIIbβ3 has been targeted at an allosteric region (PSI). This novel anti-thrombotic inhibits platelet aggregation and blood coagulation without increasing bleeding or requiring combinatorial therapy.
Socio-Structural inference in Stereotype and Impression Formation
Keywords: Archetype
Impression-Formation
Social Psychology
Stereotype
Stereotype Formation
Traits

Recent advances in stereotyping and prejudice literature, such as the Stereotype Content Model, explain the content of stereotypes in terms of common aspects of social structure. Yet despite this, the question of how these common aspects of social structure may direct stereotype formation remains unaddressed. In this article, we outline a theory for how common social contexts predict common behavioral tendencies and traits in the individuals and groups within these common social contexts. These common traits could then be represented in a prototype, and used to draw inferences about the traits of novel groups and individuals, directing stereotype and impression formation. Across 3 studies, we show support for 2 key assumptions of this model: that these prototypes should significantly explain stereotypic trait content, and that using these prototypes to infer stereotypes is more explanatory of the correlation between these prototypes and stereotypes than the reverse.
Regeneration of Neurons in the Inner Ear by Reprogramming Spiral Ganglion Glial Cells
Keywords: adult
glia
hearing
in vitro
regeneration
spiral ganglion

Disabling hearing loss affects over 5% of the world’s population and impacts the lives of individuals from all age groups. A leading cause of hearing loss is the degeneration of primary auditory neurons through exposure to noise, infection, ototoxic drugs and/or aging. Primary auditory neurons are the sensory neurons of the auditory system that receive input from mechanosensory hair cells in the cochlea. Hence, it may be possible to restore hearing by regenerating these primary auditory neurons. A direct reprogramming approach can be used to convert the resident spiral ganglion glial cells into induced neurons to restore hearing. This thesis lays the groundwork for future steps in regenerating the peripheral auditory system by demonstrating the reprogramming of both neonatal and adult glia. In the coming years, reprogramming of spiral ganglion cells has the potential to become one of the leading biological strategies to treat hearing impairment.
Rescuing TTC7A mutant phenotypes associated with Very Early Onset Inflammatory Bowel Disease via high throughput drug screening
Keywords: Drug screen
IBD
phenotypic drug screen
TTC7A
VEOIBD
zebrafish

Mutations in tetratricopeptide repeat domain 7A (TTC7A) cause a severe form of Very Early Onset Inflammatory Bowel Disease (VEOIBD). Since 2013, >52 patients were reported with TTC7A-deficiency, having poor survival outcomes with combined primary immunodeficiency and severe intestinal phenotypes, including apoptotic enterocolitis and multiple intestinal atresia. Human TTC7A-knockout cells demonstrated abnormal phenotypes related to morphology and apoptosis. ttc7a-mutant zebrafish displayed abberant intestinal features, recapitulating patient disease features and establishing a novel model system for TTC7A and VEOIBD. A high-throughput drug screen identified FDA-approved drugs that rescued the apoptotic phenotype in the knockout cells. Hits of interest were further validated with orthogonal cell and zebrafish phenotypes. Our lead compound, a drug used to treat inflammatory diseases, was identified as a novel therapy to rescue TTC7A-deficiency phenotypes. Since there is no treatment option for TTC7A-deficiency and the pathobiology remains unclear, target-agnostic phenotypic drug discovery was an efficient strategy to identify novel therapeutics.
The Role of Diacylglycerol Kinase Epsilon (DGKE) in Regulating Cellular Phosphoinositide Levels in Endothelial Cells
Keywords: Atypical Hemolytic Uremic Syndrome (aHUS)
Diacylglycerol Kinase Epsilon (DGKE)
Endothelial Cells
Phosphoinositides
Phospholipids
Thrombotic Microangiopathy

Atypical hemolytic uremic syndrome (aHUS) is a rare kidney disease that leads to thrombosis of the kidney microvasculature. A majority of aHUS patients with some genetic diagnosis display complement abnormalities. However, mutations in complement-independent genes, such as diacylglycerol kinase epsilon (DGKE) have also been shown to lead to aHUS. DGKE is a lipid kinase that is involved in the phosphatidylinositol-cycle (PI-cycle) that regenerates and breaks down various phospholipids. Unfortunately, DGKE-aHUS patients do not benefit from current therapy options and the pathophysiology of DGKE deficiency is not well understood. We aimed to study the role of DGKE in regulating PI-cycle phospholipids in endothelial cells. Using orthogonal approaches, we found that DGKE deficiency in endothelial cells leads to reductions in various PI-cycle phosphoinositides. In addition, DGKE-null mice did not develop TMA or renal impairments as a function of age, and likely require an immunological challenge to recapitulate aHUS pathology.
Role of Acid Sphingomyelinase in Murine Placentation
Keywords: Acid Sphingomyelinase
Murine Placenta
Placentation
Sphingolipids

Growing evidence has implicated bioactive sphingolipids and their associated enzymes in proper placentation. Previous experiments done in our lab have showed compromised placental development and function in mice deficient for aSMase (aSMase-KO). We hypothesized that aSMase is involved in trophoblast lineage differentiation either through its product CER or derivatives of it. Here we show an altered sphingolipid profile in aSMase-KO placentas with increased levels of SM16:0 and decreased levels of S1P, results in line with human studies on abnormal placentation. During normal placentation, we found Smpd1 mRNA expression to be significantly increased around d13.5 while protein expression was localized to the SpT and labyrinth layers of the murine placenta with staining present in several S-TGCs. Analysis of potential trophoblastic differentiation defects in aSMase-KO placentas revealed decreased mRNA expression of Prl7c1, a marker of glycogen and SpA-TGCs.
Risk factors for low physical activity levels in preschool-aged children in urban Bangladesh
Keywords: Accelerometry
Anemia
Bangladesh
Built environment
Physical activity

Physical activity (PA) is a known determinant of health and is important in the development of young children. Risk factors for PA may be different in low- and middle-income countries, such as urban Bangladesh, where the environment is densely populated and nutritional deficits are common. We aimed to describe the PA levels of preschoolers in Dhaka, Bangladesh, as well as estimate the associations between preschooler PA levels and household and nutritional factors. We conducted a cross-sectional, observational study, collecting accelerometry, hemoglobin concentration, socioeconomic status, anthropometry, and data on the home built environment. Linear mixed-effects models were used to assess the associations between PA and the exposures of interest. The entire sample were found to meet Canadian preschooler PA guidelines for daily activity. There were no associations between PA and characteristics of the built environment of the home, nor hemoglobin concentration, suggesting a need for further exploration of potential influential factors.
EFFECTS OF FLAXSEED AND ITS COMPONENTS ON THE INTESTINAL MICROBIOTA AND MAMMARY GLAND MICRORNA SIGNATURE IN FEMALE C57BL/6 MICE
Keywords: flaxseed
gut microbiota
mammary gland
microRNA

Flaxseed (FS) is an oilseed rich in α-linolenic acid, lignans, and dietary fiber. Due to this unique composition, FS has potential to affect the health of the gut and breast. This study determined the effect of FS and its components, FS oil (FSO) and secoisolariciresinol diglucoside (SDG), on the gut microbiota, serum concentration of microbial-derived SDG metabolites, and mammary gland microRNA signature. It was found that animals maintained on 10% FS experienced the most prominent changes in gut microbiota composition and diversity compared to other groups. Higher concentrations of SDG metabolites were detected in the 10% FS and SDG diet groups, while not detectable in FSO or control. Lastly, four microRNAs in the mammary gland were downregulated in the experimental diet groups indicating that the mammary gland microRNA signature responded to FS and its components.