VictorJuiz/thesis huggingface dataset:
Supporting Biomimetic Design by Categorizing Search Results and Sense Disambiguation, with Case Studies on Fuel Cell Water Management Designs
Keywords: Biomimetic
Fuel Cell

Biology is a good source of analogies for engineering design. One approach of retrieving biological analogies is to perform keyword searches on natural-language sources such as books, journals, etc. A challenge in retrieving information from natural-language sources is the potential requirement to process a large number of search results. This thesis describes two methods on improving the relevancy of the search results. The first method is inserting metadata such as part- of-speech, word sense and lexicographical data for each word in a natural-language. The second method is categorizing the search results, using WordNet relationships and Wikipedia structures as ontologies. Although this research is still exploratory, initial qualitative observations demonstrate successful identification and separation of biological phenomena relevant to either desired functions or desired qualities. The benefits of embedding metadata are demonstrated through a case study on the redesign of a fuel cell bipolar plate. A prototype was constructed with ability to passively prevent prolonged catastrophic flooding.
Correlating Neuropsychiatric Symptoms with Regional Beta-Amyloid Load in the Alzheimer’s Disease Brain Using [11C]SB-13 Positron Emission Tomography
Keywords: Alzheimer's Disease
beta-amyloid
behaviour
neuropsychiatric symptoms
neuroimaging
positron emission tomography
PET
SB-13

Correlations between neuropsychiatric symptoms and beta-amyloid (Aβ) burden in specific brain regions in living Alzheimer’s disease (AD) patients remain to be elucidated. Ten mild AD patients underwent MR and [11C]SB-13 PET imaging. Neuropsychiatric symptoms were quantified with the Neuropsychiatric Inventory (NPI). NPI-depression/dysphoria, -apathy, -agitation/aggression, -anxiety, and -appetite/eating disorders scores were hypothesized to correlate with Aβ burden in particular brain regions. Pearson’s correlation coefficient revealed that depression/dysphoria scores positively correlated (p<0.05) with standardized uptake values (SUVs) from left medial temporal lobe (r=0.67), and agitation/aggression correlated with SUVs from bilateral anterior cingulate (right, r=0.71; left, r=0.78), temporal (right, r=0.71; left, r=0.75), parietal (right, r=0.77; left, r=0.81), and dorsolateral prefrontal cortex (right, r=0.74; left, r=0.73). However, NPI scores did not significantly correlate with better estimates of Aβ burden that use the cerebellum as reference region. Overall, our results confirm the lack of association between Aβ burden and neuropsychiatric symptoms reported in autopsy studies.
Technology Transfer Agreements Containing Tacit Knowledge
Keywords: know-how
tacit knowledge
technology transfer
codified knowledge
know how
tacit

In the world we live in transfer of technology is of a great importance. The primary means of technology transfer is by imitating and making copies. However, there are cases where copying is impossible or prohibited. In those cases, technology transfer involves contracting. Those agreements may contain both transfer of codified and tacit knowledge. Technology transfer agreements, containing tacit knowledge, have special characteristics due to the presence of the know-how, and to the need to transfer it. In this paper, I explore the special measures of technology transfer agreements containing tacit knowledge. I explain why general contract law does not address properly those challenges. I elaborate on the current solutions to these problems, adopted both by the parties and by legislatures, as well as their difficulties. Eventually, I propose possible solutions, either to the legislature or to the judiciary, in order to address those issues in a better way.
Evaluating the Relative Effectiveness of Two Supplemental Foods for the Treatment of Moderate Acute Malnutrition in Children 6 to 60 Months of Age in Southern Ethiopia
Keywords: malnutrition
treatment food
ethiopia
united nations
RUSF
CSB

The purpose of this cluster-randomized equivalence trial was to investigate the effectiveness of two supplemental foods in children with moderate malnutrition by comparing: (i) time to recovery by survival analysis, and (ii) recovery rates (after 16 weeks of treatment). A total of 2,600 children 6-60 months of age were randomized by cluster (district) to receive 16 weeks of conventional (Corn-Soya Blended flour, CSB) or intervention (Ready-to-Use Supplemental Food, RUSF) foods. Overall, time to recovery from malnutrition (mean 74 days) and recovery rates (mean 76%) were equivalent with both foods. The time to recovery outcomes were equivalent, independent of location, whereas the recovery rate in children receiving CSB was significantly higher in the more food insecure southern region. Intra-household food sharing was significantly higher in the CSB group compared to RUSF. Overall, the response to the two different supplemental foods was equivalent for the treatment of moderately malnourished children in Ethiopia.
Paraesthesia Following Dental Local Anaesthetic Administration in the United States
Keywords: Paraesthesia
Articaine
Prilocaine
Inferior alveolar nerve
Lingual nerve
Local Anaesthetics
Dentistry

Background: Several studies have suggested that the likelihood of paraesthesia may depend on the local anaesthetic (LA) used. The purpose of this study was to analyze reports of paraesthesia among dental LAs used in the U.S. Methods: Reports of paraesthesia involving LAs between November 1997 through August 2008 were obtained from the U.S. Food and Drug Administration Adverse Event Reporting System. Chi-Square analysis compared expected frequencies, based on U.S. LA sales data, to observed reports of oral paraesthesia. Results: During the study period 248 cases of paraesthesia following dental procedures were reported. Most (94.5%) cases involved mandibular nerve block. The lingual nerve was affected in 89.0% of cases. Reports involving 4%-prilocaine and 4%-articaine were 7.3-times and 3.6-times, respectively, greater than expected (χ2, p<0.0001) based on LA usage by U.S. dentists. Conclusions: Consistent with previous reports, these data suggest that paraesthesia is more common following use of 4% LA formulations.
Neural Correlates of Driving in a Virtual Reality Environment
Keywords: driving
fMRI
virtual reality

Driving is a cognitively complex task, yet the areas of the brain involved in driving are not well understood. This thesis investigates the neural correlates of driving using functional magnetic resonance imaging and driving simulations with custom built driving hardware (steering wheel and foot pedals). The feasibility of driving in fMRI is first investigated, and a methodology is described to minimize head motions. Next, the functional neuroanatomical correlates of driving tasks of varying complexity are explored. Simple tasks such as straight driving activate areas of the brain related to motion, spatial navigation and coordination. Complex tasks are found to recruit additional areas of the brain, including areas of higher cognitive function such as the prefrontal cortex. Developing a better understanding of the areas involved in different driving tasks is an important first step in understanding the neural basis of driving skill and safe driving.
Quality of Life in Pediatric Patients with Intestinal Failure on Home Parenteral Nutrition
Keywords: Quality of Life
Pediatrics
Intestinal Failure
Parenteral Nutrition
Functional Status
Home Parenteral Nutrition
Child Health Questionnaire
PedsQL
Focus Group
Mixed Methods
Nutrition
Battery Assessment
CHQ
Pediatric Quality of Life Questionnaire

Introduction: Medical advances have resulted in reduced mortality of pediatric patients with Intestinal Failure. Consequently, more patients go home on parenteral nutrition (PN) for extended durations. This time-consuming and complicated therapy necessitates persistent vigilance in monitoring and response to potential life-threatening side effects. These issues may impact quality of life (QOL) for patients, caregivers and families. Methods: This observational, cross-sectional, mixed-methods analysis of multidimensional QOL used a quantitative battery assessment and a qualitative focus group. Questionnaire results were compared to published norms, published small bowel transplant (SBTx), and institutional SBTx patients. Results: Home PN proxy assessments scored children lower than published norms but similar to SBTx. The child self-reports were similar to both normative and SBTx populations, except lower general and overall health. Generic questionnaires did not capture disease-specific issues. Conclusion: QOL is compromised in children on home PN and caregivers compared to norms but is similar to SBTx.
Nonlinear Parametric Generation in Birefringent Poled Fibers
Keywords: Nonlinear Optics
Optical Fibers
Second-Harmonic Generation

Conventional step-index silica fibers do not possess a second-order optical nonlinearity due to symmetry concerns. However, through the process of poling, the generation of a frozen-in DC field EDC, and in turn, a non-zero second-order nonlinearity ?(2) =3?(3)EDC, can be created in optical fibers. In this thesis, I measure the individual ?(2) tensor elements of birefringent periodically poled fiber via second-harmonic generation and sum-frequency generation experiments. The symmetry of the ? (2) tensor is consistent with that of the ?(3) for isotropic media. This is the first study that characterizes all the ? (2) tensor elements in birefringent poled fiber. Furthermore, I investigate the intermix of the ?(2) tensor elements by twisting the fiber, which results in the generation of new second-harmonic signals not observed in untwisted fiber. The conversion efficiencies and spectral positions of these new signals can be varied by twisting the fiber.
Silicon Refining Through Chemical Vapor Deposition
Keywords: Solar Silicon
Chemical Vapor Deposition
Silicon Refining

Currently the cost of solar grade silicon accounts for approximately one third of the total solar cell cost, therefore a new silicon refining process is being proposed with the goal of lowering the cost of producing solar grade silicon. In this new process, Si-Cu alloys were used as the silicon source. One to one molar ratio H2-HCl gas mixtures were used as transport agents to extract Si out from the Si-Cu alloy at about 300-700oC, with following reaction taking place: Si+3HCl(g)=HSiCl3(g)+H2(g) While at about 1000-1300oC, pure Si deposits onto a hot silicon rod according to: Si+3HCl(g)=HSiCl3(g)+H2(g) The role of the copper in the alloy was to trap impurities in the Si and catalyze the gas solid reaction. A study on determining the rate limiting step and impurity behavior was done. A possible silicon extraction reaction mechanism was also addressed.
Hydraulophones: Acoustic Musical Instruments and Expressive User Interfaces
Keywords: hydraulophone
acoustics
liquid
state of matter
water
oscillation
hydraulophonic
sound production
karmanizer
turbulence
Von Karman
vortex
Poiseuille
Embouchure
user interface
expressivity
suite for hydraulophone
composition
absement
presement
musical instruments
underwater
hydrophone
jet
Particle Rejection Theory
0986
0413

Fluid flow creates an expansive range of acoustic possibilities, particularly in the case of water, which has unique turbulence and vortex shedding properties as compared with the air of ordinary wind instruments. Sound from water flow is explained with reference to a new class of musical instruments, hydraulophones, in which oscillation originates directly from matter in its liquid state. Several hydraulophones which were realized in practical form are described. A unique user-interface consisting of a row of water jets is presented, in terms of its expressiveness, tactility, responsiveness to derivatives and integrals of displacement, and in terms of the direct physical interaction between a user and the physical process of sound production. Signal processing algorithms are introduced, which extract further information from turbulent water flow, for industrial applications as well as musical applications.
Structural Effects of Photodynamic Therapy and Bisphosphonates on Healthy and Metastatically Involved Vertebral Bone
Keywords: photodynamic therapy
spinal metastasis

The vertebral column is the most common site of skeletal metastatic development secondary to breast cancer. Multiple clinical treatments are available for spinal metastasis, including systemic bisphosphonates and radiation therapy, however the success of current treatment approaches varies considerably. Alternative treatment strategies for spinal metastatic destruction must be aimed at both reducing tumor burden and restoring mechanical stability. Photodynamic therapy (PDT) has been shown to be successful at destroying osteolytic lesions in preclinical models of breast cancer spinal metastasis. However, the clinical feasibility of PDT for spinal metastasis is dependent on its potential effects on the structural integrity of vertebral bone. This thesis aims to determine the effects of PDT alone and in combination with bisphosphonate therapy on the structural architecture and mechanical properties of healthy and metastatically involved vertebrae. PDT was shown to have a positive effect on vertebral bone structure, alone and in combination with previous bisphosphonate therapy.
Molecular Identification and Physiological Characterization of Alternative Oxidase Gene Family Members in Nicotiana tabacum
Keywords: Plant physiology
Molecular biology
Alternative oxidase
Reactive oxygen species

Two projects were undertaken to study the non-energy conserving alternative pathway present in the plant mitochondrial ETC. In the first project, a tobacco AOX2 gene was cloned and characterized. AOX2 showed tissue specificity in expression and could not be induced by common stresses. In the second project I carried out a physiological characterization of transgenic tobacco plants with increased or decreased expression of AOX1 subjected to cold stress. Under non-stress condition, a strong inverse relationship between levels of AOX1 and levels of oxidative damage was observed, while after cold treatment AOX1 transgenic lines and WT showed more complicated and differential responses in aspects of oxidative damage and the capacity of antioxidant system. I also discovered that the pool sizes of monosaccharides after temperature shift were proportional to AOX1 levels. These results indicated that AOX1 might have crucial but complex impacts on ROS balance and carbon metabolism during cold stress.
Discovery and Characterization of Microbial Esterases for Fiber Modification
Keywords: microbial esterases
enzymatic assays

Carboxyl esterases, particularly arylesterases, were predicted from 16 microbial genomes, and then expressed in E. coli. Of the more than 175 cloned genes, 86 were expressed in soluble form. These were screened for activity using a range of both commercial and natural substrates. Forty-eight proteins were active on pNP-acetate at pH 8 whereas 38 proteins did not exhibit any activity towards any substrates. Among the 48 active proteins, 20 proteins showed arylesterase activity. To date, 8 bacterial esterases and 2 archaeal arylesterases were characterized in terms of pH stability and optima, thermal inactivation, solvent stability, and kinetics. To our knowledge there is only one other published report of arylesterases from archaea. The synthetic capability of arylesterases can transform phenolic acids to value-added chemicals. Accordingly, this project provides an arsenal of industrially significant activities that can extend the antioxidant properties of lignin-derived molecules in a broader range of renewable products.
Upregulation of VEGF-A using Engineered Zinc Finger Protein Gene Therapy Increases Cell Survival After Lateral Fluid Percussion Injury in Rats
Keywords: Traumatic Brain Injury
VEGF

Vascular endothelial growth factor (VEGF) may play a role in neuroprotection after traumatic brain injury (TBI) in addition to being a regulator of angiogenesis. Gene therapy using an adenovirus carrying an engineered zinc-finger protein (Adv-ZFP) and transcription factor construct targeted to the VEGF gene, has been shown to upregulate genomic expression of VEGF-A isoforms in skeletal muscle. Our objective was to use this gene therapy to explore cell survival in TBI. Rats were subjected to a unilateral fluid percussion injury (FPI) in the cortex. Groups consisted of control, injured and injured-treated animals. Adv-ZFP-VEGF was injected into the cortex and hippocampus. Engineered ZFP-VEGF increases VEGF-A protein levels and correlates with increased CA2 hippocampal cell survival and reduction in apoptotic cell death following TBI. NF200 expression in TBI+VEGF animals was comparable to levels in naive animals. This study suggests a therapeutic strategy to treat delayed cell death in a model of TBI.
Initial Flare Symptoms Resulting from Use of LHRH Agonist in Metastatic Prostate Cancer: Systematic Review and Economic Evaluation
Keywords: prostate cancer
LHRH agonist

Background LHRH agonists decrease tumour size/activity by suppressing testosterone in prostate cancer; however, initial injection causes testosterone surge that triggers flare symptoms. Anti-androgen given with agonist may reduce/avoid flare symptoms. When LHRH antagonist/blocker is introduced, testosterone suppression is immediate, but there is uncertainty about significance of flare symptoms without anti-androgen. Objective Systematic review compared significance of flare symptoms avoided and cost utility analysis using modelling comparing incremental value of blocker (degarelix) OR agonist (goserelin)+anti-androgen (bicalutamide) VERSUS agonist alone in prostate cancer patients. Outcome Incremental cost/QALY of bone pain as flare symptom between treatments Results Thirteen studies were reviewed. There was no standard definition for flare symptoms or data on LHRH antagonist versus other treatments on flare. From societal perspective, goserelin+bicalutamide was dominated over goserelin alone and similarly, from public perspective, goserelin+bicalutamide had favourable cost effectiveness profile against goserelin. Conclusion With bone pain as clinical endpoint, LHRH agonist+anti-androgen had favourable cost-effectiveness profile compared to goserelin.
A Series-parallel Resonant Converter for Electrochemical Wastewater Treatment
Keywords: resonant converter
modeling and control
electrochemical cell model
power supply
pulsed power converter

Advantages of electrochemical wastewater treatment over conventional wastewater treatment include its smaller footprint, modularity, and ability to meet increasingly stringent government regulations. A power supply that can be packaged with an electrochemical stack could make electrochemical wastewater treatment more cost-effective and scalable. For this application, the series and series-parallel resonant converters are suitable power converter candidates. With an output current specification of 100A, the series-parallel resonant converter (SPRC) is superior due to its simpler output stage. The thesis presents the design of a 500W SPRC for a wastewater treatment cell stack. A rudimentary cell model is derived experimentally. The closed loop analysis, controller design and simulation results are presented. The output voltage and current are estimated using sensed quantities extracted from the high voltage, low current primary side. Low voltage experimental results verify the operation of the power stage and voltage estimation circuitry in open loop pulsed operation.
Roles of Sec5 in the Regulation of Dense-Core Vesicle Secretion in PC12 Cells
Keywords: dense-core vesicle
exocytosis
docking
tethering
exocyst
Sec5

The exocyst is thought to tether secretory vesicles to specific sites on the plasma membrane. As a member of the exocyst, Sec5 is implicated in cell survival and membrane growth in Drosophila. Little is known of the exocyst function in mammals, with previous work suggesting involvement of exocyst in GTP-dependent exocytosis. Using RNA interference, we stably down-regulated Sec5 in PC12 cells. We found that these knockdown cells exhibit decreased GTP- and Ca2+-dependent exocytosis of dense-core vesicles (DCVs), and contain less proportion of docked vesicles. Expression of Sec6/8 is also slightly reduced in Sec5 knockdown cells. Our results suggest that Sec5 is involved in both GTP- and Ca2+-dependent exocytosis, possibly through the regulation of DCV docking. We also established doxycycline-inducible knockdown system for Sec5 in PC12 cells which may be more appropriate to study development-related proteins. Efforts were also made to re-introduce Sec5 into the Sec5 knockdown cells for rescue purposes.
The Small Ubiquitin-related Mmodifier in the Stress Response and the Use of Mass Spectrometry/SUMmOn for Identification of Ubiquitin and Ubiquitin-like Protein Conjugation Sites
Keywords: SUMO
mass spectrometry
ubiquitin
alcohol stress
NEDD8
SUMmOn

Ubiquitin (Ub) and the ubiquitin-like proteins (Ubls) are polypeptides that can be covalently conjugated to a variety of “target” molecules to modulate their turnover rate, localization and/or function. The full range of Ubl functions is only beginning to be understood. The Raught lab is using mass spectrometry and high throughput screening methods, along with standard cell biology and biochemistry approaches, to better understand Ubl function. Here, I describe the role of a Ubl called small ubiquitin-related modifier (SUMO) in the budding yeast alcohol stress response. We identified a regulatory mechanism of the SUMO system, involving modulation of the localization of a SUMO protease. Secondly, using mass spectrometry (MS), I assisted in identifying several yeast and mammalian Ubl “chain” linkages. Finally, I propose an integrated MS methodology designed to complement standard database software for the confident identification of Ub/Ubl conjugation sites.
Comparing the Use of Abundance and Consistent Occupancy Measures to Predict Local Species Persistence
Keywords: persistence
point-count
presence-absence
abundance
permanence
Breeding Bird Survey
area selection
reserve design

I compared the utility of two continuous time-series data measures for applied conservation biology by investigating how well each could predict future local persistence of a diverse set of bird species. I used 37 years of data from the North American Breeding Bird Survey to calculate abundance from yearly point-counts and permanence (i.e., consistent occupancy over time) from yearly presence-absence data in the early portion of the study period, then used the later portion of data to empirically evaluate how well each measure predicted persistence two decades into the future. I found that permanence could only match the ability of abundance to accurately predict local species persistence if multiple within-year repeated observations contributed to its calculation. Neither measure was effective at predicting persistence for regionally rarer species. I suggest the yearly and within-year repeated collection of abundance estimating data for use in applied conservation biology to best ensure biodiversity persistence.