Texas A&M University at College Station

Permanent URI for this collectionhttps://hdl.handle.net/2249.1/23606

Texas A&M University is a land-grant, sea-grant and space-grant institution located in College Station, Texas. The university’s enrollment includes approximately 44,000 students studying for degrees in 10 academic colleges. This collection contains the theses and dissertations produced at A&M since 2002.


Recent Submissions

Now showing 1 - 20 of 13127
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    Dietary Cholesterol and Resistance Training as Countermeasures to Accelerated Muscle Loss
    (2015-12-09) Lee, Teak Veng
    Cholesterol plays an important role in physiology, serving as a membrane constituent and steroid hormone precursor. Recently, cholesterol has also been associated with skeletal muscle homeostasis, leading to the purpose of this research, which was to examine the role of cholesterol metabolism during perturbations of skeletal muscle homeostasis. We evaluated skeletal muscle responses and proteins involved in cholesterol metabolism [sterol regulatory element-binding protein-2 (SREBP-2) and low-density lipoprotein-receptor (LDL-R)] under conditions of unloading, exercise and dietary cholesterol (D-CL) administration. We hypothesized that skeletal muscle mass, fractional synthesis rates (FSR), SREBP-2, and LDL-R would be lower in unloaded muscle while exercise and D-CL would have a positive effect. The first study examined the effect of hindlimb unloading (HU) on muscle mass, SREBP-2, and LDL-R. HU animals showed lower muscle mass and a trend towards lower gastrocnemius SREBP-2 than cage controls (CC). The second study examined the effect of D-CL and resistance training (RT) on lean mass, FSR, SREBP-2, and LDL-R in ambulatory rats. Unexpectedly, rats performing exercise without added resistance [(RT-Control (RTC)] had greater lean mass responses than the RT groups. However, RT groups had higher plantaris to body mass ratio and FSR than RTC (plantaris FSR only) and CC (both variables) animals. RT plus high D-CL administration resulted in greater plantaris FSR than the RT group consuming normal D-CL. Quadriceps SREBP-2 trended towards an increase in response to RT. The third study investigated the effect of D-CL and RT on muscle mass, FSR, SREBP-2, and LDL-R in the context of HU. HU and HU rats performing RT had lower muscle mass than CC. HU rats showed higher liver mature LDL-R than CC but showed a trend towards lower gastrocnemius SREBP-2 than CC. There was no difference in FSR among activity or D-CL groups. These studies show evidence of shifts in content of proteins related to cholesterol metabolism and muscle FSR when muscle activity is manipulated from RT to complete unloading. However, effects such as elevated FSR with RT and high D-CL were not consistent throughout the studies, leaving doubt of the effect of activity on cholesterol metabolism.
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    Observed Characteristics of Clouds and Precipitating Systems Associated with the Tropical Circulation in Global Models and Reanalyses
    (2013-03-25) Stachnik, Justin Paul
    This dissertation presents a series of work related to the representation of the Hadley circulation (HC) in atmospheric reanalyses and general circulation models (GCMs), with connections to the underlying tropical and subtropical cloud systems that comprise the mean meridional circulation. An intercomparison of eight atmospheric reanalyses showed that significant variability exists in the mean state for HC intensity, with less variability in HC width. Ensemble trends were broadly consistent with previous work and suggest a strengthening and widening of the tropical circulation over the last 30 years. Composite profiles of the apparent heat source and moisture sink were calculated for the International Satellite Cloud Climatology Project (ISCCP) cloud regimes using sounding observations from 10 field campaigns. Distinct heating profiles were determined for each ISCCP cloud regime, ranging from strong, upper-tropospheric heating for mesoscale convective systems to integrated cooling for populations associated with marine stratus and stratocumulus clouds. The derived profiles were generally similar over land and ocean with the notable exception of the fair-weather cumulus regime, which leads to some uncertainty in the mid- and upper-level reconstruction of subtropical heating. An instrument simulator indicated that low-latitude cloud properties from the NASA MERRA reanalysis qualitatively matched the distributions of cloud-top pressure and optical thickness in the ISCCP data, though the tallest and thickest clouds were missing from the reanalysis. Simulator results were sensitive to the choice of cloud overlap parameterization and the reanalysis consistently underpredicted the observed cloud fractions for all regimes. The vertical velocity, temperature, and moisture for each regime in MERRA largely matched observations from previous studies, suggesting that the dynamic and thermodynamic properties of the cloud regimes are well captured by the reanalysis. Finally, HC interannual variability was examined as a function of the observed frequency of the ISCCP cloud regimes. The strongest HC overturning events were attributed to an El Ni?o response in the central Pacific Ocean in addition to links between the intensity and position of the Pacific ITCZ. The ISCCP regime describing the most vigorous and organized convection contributed the most towards the total anomalous heating during HC extremes, despite an overall low frequency of occurrence. Idealized GCM simulations forced with the observed three-dimensional diabatic heating from ISCCP data produced too strong a HC with some improvement in other fields. Overall, much progress has been made regarding the links between low-latitude cloud systems and the HC, though future work will continue to address the upscale feedbacks of regional cloud variations upon the tropical circulation.
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    Experimental Study on the Subcooled Boiling Flow via Optical Measurement Techniques
    (2015-04-16) Yoo, Jun Soo
    A series of experimental work to investigate the subcooled boiling flow in a vertical square upward flow channel is described. As experimental methods, high-speed photography and infrared (IR) thermometry were employed simultaneously. The research scope explored includes (i) measurement issues of fundamental bubble parameters through visualization, (ii) experimental methodology to achieve both enhanced two-phase flow visualization and accurate wall temperature measurement, and (iii) measurement of diverse aspects of bubble dynamics as well as wall heat transfer by applying the verified experimental approach. Before producing the actual data, substantial effort was first made to identify the critical measurement issues of fundamental bubble parameters in a forced convective boiling system. Those issues have never been explicitly addressed in previous studies despite the possibly critical impacts on the experimental results. Thus, a series of systematic experimental investigations was performed to uncover those issues and to verify the errors created by not addressing them, based on which more suitable ways of observing and characterizing such parameters through experiments were discussed. Then, an experimental strategy to achieve high-fidelity optical measurements using both high-speed photography and IR thermometry was established. To attain the goal, the important issues such as test section design, IR thermal imaging issues, visualization strategy, wall temperature tracking method, and experimental validations were extensively addressed. Also, the feasibility of current experimental approach was demonstrated through the subcooled flow boiling experiment. Finally, by employing the experimental strategy established, an experimental investigation of the subcooled boiling flow was conducted. The experiment was performed in a vertical square upward flow channel using refrigerant NovecTM 7000, in which a single nucleation site was purposely activated for a fundamental study of subcooled flow boiling process. The various aspects of bubble behavior under different subcooled flow boiling conditions were examined using both micro- and macroscopic views of high-speed cameras while measuring the wall temperature/heat flux with IR thermometry. Additionally, based on the measurements of various bubble parameters as well as wall heat transfer, relevant relations among those parameters and the underlying mechanisms were intensively discussed.
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    Developing Emission Factors of Fugitive Particulate Matter Emissions for Construction Sites in the Middle East
    (2015-04-20) Hassan, Hala Abdelrahman Medani
    A major source of airborne pollution in the arid Middle East countries is the fugitive particulate matter (PM), a frequent product of wind erosion. The meteorological conditions and topography of this region makes it highly susceptible to wind-blown particles which raise many air quality concerns. Important tools for estimating the dispersion and deposition of dust particles, which also help in designing dust control procedures, are Air Quality Models (AQM). The cornerstone of every AQM system is an emission inventory, but these are only available currently for the European and North American domains, calling for an immediate need to develop similar knowledge for MEA. The increasing level of urbanization in Middle East countries has thrown the light on the airborne pollution caused by construction and earth work activities. The main scope of the present study is to develop fugitive particulate matter emission factors for construction sites in MEA and to evaluate the accuracy of the existing emission factors to apply for Middle Eastern hot and arid conditions. An experimental campaign along with dispersion modeling using the Fugitive Dust Model (FDM) were implemented in a construction site to examine the relation between the meteorological variables, concentrations and emission rates to understand the behavior of the fugitive dust emissions for MEA. The time period of this work was chosen while the construction site was at rest, where the only particles source was wind erosion of the loose soil. A data analysis was done, using the modeling results, to identify the effect of each meteorological variable (i.e. wind direction, wind speed, stability, .etc.) and its relation to emissions concentrations and rates. Considering the wind-speed dependence of the source emission rate, a power law function was obtained for the calculation of the emission rates. This function was used to re-run the FDM model and the results were evaluated compared to the on-site measured concentrations and to the emission factors reported in USEPA?s AP-42 (the related emission rates in this emission inventory have been developed mainly for open coal-mines). Surprisingly, our study showed that a very good agreement between the AP-42 emission factors and our calculations can be obtained if the former are slightly modified. The emission factors developed in this study have been confirmed and can be applied for the impact assessment of similar sources in Middle East and other dry-arid locations.
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    Analysis of Genomic Imprinting of UBE3A in Neurons
    (2015-05-05) Hillman, Paul Randolph
    Angelman syndrome (AS), chromosome 15q11-q13 duplication syndrome (Dup15q), and Prader-Willi syndrome (PWS) are neurodevelopmental disorders associated with dysregulated expression of imprinted genes located within the human 15q11-13 imprinted region. Angelman syndrome is caused by loss-of-function or loss-of-expression of the maternally inherited UBE3A allele; Dup15q syndrome is attributed to maternally inherited copy number gains of UBE3A; and, paternally inherited deletions of the SNORD116 cluster cause PWS. The UBE3A gene is imprinted in the brain with maternal-specific expression and biallelically expressed in all other cell types. The imprint is regulated by expression of the UBE3A antisense transcript (UBE3A-AS), which is expressed only in neurons and imprinted with paternal-specific expression. The UBE3A-AS represents the 3` end of a long polycistronic transcript that includes the SNORD116 and SNORD115 gene clusters. Thus, the genes causing AS, Dup15q, and PWS are transcriptionally linked; however, the functional significance of the neuron specific imprint is largely unknown. In this dissertation, it was hypothesized that imprinting of UBE3A evolved as a mechanism to negatively regulate UBE3A protein levels in neurons. This hypothesis was tested by examining allelic expression patterns and associated protein levels of the mouse 7c imprinted region, the orthologous region of human 15q11-q13. Analyses revealed that imprinted expression of Ube3a in the brain resulted in elevated RNA and protein levels compared to tissues where Ube3a was biallelically expressed. Likewise, Snord116, Snord115, and Ube3a-AS transcripts were highly expressed in the brain. The elevated Ube3a protein levels in the brain were due to increased maternal-allelic expression during neurogenesis concurrent with paternal-allelic suppression. Analysis of UBE3A expression in the opossum, a metatherian mammal lacking an orthologous imprinted region, showed that the UBE3A imprint did not evolve to negatively regulate UBE3A protein levels in the brain. Extensive alternative splicing of Ube3a-AS was detected in the brain, which generated at least two transcripts containing novel open reading frames. Novel Ube3a alternatively spliced transcripts were also identified in the brain. Collectively, these data reject the hypothesis that the UBE3A imprint evolved to negatively regulate UBE3A protein levels in the brain; instead, they suggest that the UBE3A imprint may allow co-expression of the UBE3A and SNORD gene cluster in neurons, which may also facilitate or regulate the expression of novel brain-specific UBE3A transcripts.
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    Process Improvements for Gas Barrier Thin Films Deposited Via Layer-By-Layer Assembly
    (2015-05-04) Hagen, David Austin
    Thin layers of aluminum have provided good oxygen barrier for food packaging for many years, but aluminum coatings can easily crack, are completely opaque, and are not environmentally friendly. One gas barrier solution for food, to flexible electronics, and pressurized bladders is to create polymer nanocomposite thin-films using layer-by-layer (LbL) assembly. These non-metal, water-based thin films contain a tortuous path through which a gas molecule must navigate. The work in this dissertation focuses on improving the process of creating these thin films to optimize their performance and achieve lower transmission rates with fewer layers. Excellent gas barrier was achieved in a layer-by-layer thin film with fewer layers by optimizing deposition time of cationic polyethylenimine (PEI) and anionic poly(acrylic acid) [PAA]. Substantial deposition occurs with short deposition times for the first four PEI/PAA bilayers, while thicker deposition occurs with longer deposition times beyond 4 bilayers. Eight bilayers (650 nm) were required to achieve an undetectable oxygen transmission rate (<0.005 cm^3/(m^2?day)) using 1 min deposition steps, but this barrier was obtained with only 6 BL (552 nm) using 1s deposition of the first four bilayers, reducing total deposition time by 73%. Polymer?clay bilayer films show good oxygen barrier properties due to a nanobrick wall structure consisting of clay nanoplatelets within polymeric mortar. Super oxygen barrier trilayer thin films have been deposited using two successive anionic layers of montmorillonite (MMT) clay and polymer (PAA) following every cationic polymer (PEI) layer during layer-by-layer assembly. It is shown here that adding an anionic polymer layer reduces free volume of the film by filling in gaps of the similarly charged clay layer, which increases the barrier performance by at least one order of magnitude. Barrier improvement can also be achieved by reducing the pH of the clay suspension in the PEI/MMT system. The charge of the deposited PEI layer increases in the clay suspension environment as the pH decreases, attracting more clay. This enables a 5? improvement in the gas barrier for a 10 PEI/MMT bilayer thin film (85 nm) made with pH 4 MMT, relative to the same film made with pH 10 MMT (57 nm).
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    A New Application of Potassium Nitrate as an Environmentally Friendly Clay Stabilizer in Water-Based Drilling Fluid
    (2015-04-15) Zhou, Jing
    The application of potassium chloride (KCl) as a temporary clay stabilizing additive in water-based drilling fluids is problematic in chloride-sensitive formations. However, failure to utilize clay stabilization leads to additional costs to drilling operations due to wellbore stability and drilling fluid residual problems. In addition, the chloride ions can be defined as a contaminant in land operations, with the potential to inhibit the growth of vegetation and the potential to pollute aquifers. The purpose of this study is to propose a new, high performance water-based fluid system using potassium nitrate instead of potassium chloride as the clay stabilizing additive for drilling applications. Water-based drilling fluids using potassium nitrate and potassium chloride, respectively, were prepared with a density of 1.3 S.G. using various weighting materials. Capillary suction time (CST) test was used to optimize the potassium salt concentration in drilling fluids for effective clay swelling inhibition. HPHT filtration tests under static and dynamic conditions were conducted at 250?F and 300 psi. Berea sandstone cores with an average porosity of 23 vol% and an average permeability of 50 md were used in the filtration tests. The rheological properties, the volume of filtrate, and the filter cake thickness of the water-based drilling fluids were determined and compared. The CST tests show that potassium nitrate performs comparably to potassium chloride as a clay stabilizer. However, the water-based drilling fluid containing potassium nitrate has better rheological properties than that containing potassium chloride. The HPHT filtration press tests show that water-based drilling fluid with potassium nitrate has a low filtration volume, less than 1 mL out of a total solution of 200 - 250 mL, when using barite as the weighting material. This paper not only highlights the successful replacement of KCl by KNO3 to achieve good rheological properties in water-based drilling fluids, but also shows that KNO3-based drilling fluids are more economical as well as environmentally friendly than KCl-based drilling fluids in drilling waste management.
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    The Effect of Digital Die Spacer on the Marginal Fit of Cad Pressed Lithium Disilicate Complete Coverage Copings: An SEM Assessment
    (2015-04-24) Fischer, James
    The purpose of this in vitro study was to evaluate the marginal fit of pressed IPS e.max copings fabricated from a computer-aided designed and milled PMMA acrylic resin burnout coping of various cement spacer thicknesses. Three groups of ten PMMA acrylic burnout copings were designed and milled utilizing computer-aided software for a total sample size of thirty copings. Each group differed only by the die-spacer parameters indicated within the design software. Group 1, Group 2, and Group 3 were digitally designed with 25, 40, and 60 ?m of die-spacer respectively. All acrylic resin copings were pressed with IPS e.max lithium disilicate and adhesively bonded to thirty identical epoxy resin dies. Cross-sections of each specimen were obtained and viewed with a scanning electron microscope. Direct measurements were obtained at five pre-determined locations and data analyzed using statistical analysis software. An analysis of variance (ANOVA) followed by a Mann-Whitney test was used to indicate significant differences between groups (p ? 0.017). A statistically significant difference was found between groups for each measured location: buccal margin (p=0.005), buccal-axial (p=0.013), mid-occlusal (p=0.030), lingual-axial (p=0.022), lingual margin (p=0.005). When 60 ?m of die spacer was utilized in the fabrication of the milled acrylic resin coping, the definitive bonded ceramic coping yielded the best marginal fit. Cement thickness was greatest, and marginal fit was poorest when 25 ?m of die spacer was utilized. Observed differences between groups can be attributed to the utilization of acrylic resin patterns in the fabrication of pressed IPS e.max copings. The obtained results suggest that appropriate die spacer parameters indicated within computer-aided design software are critical in the fabrication of clinically acceptable indirect restorations.
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    PerCon: A Personal Digital Library for Heterogeneous Data Management and Analysis
    (2015-03-31) Park, Su Inn
    Systems are needed to support access to and analysis of larger and more heterogeneous scientific datasets. Users need support in the location, organization, analysis, and interpretation of data to support their current activities with appropriate services and tools. We developed PerCon, a data management and analysis environment, to support such use. PerCon processes and integrates data gathered via queries to existing data providers to create a personal or a small group digital library of data. Users may then search, browse, visualize, annotate, and organize the data as they proceed with analysis and interpretation. Analysis and interpretation in PerCon takes place in a visual workspace in which multiple data visualizations and annotations are placed into spatial arrangements based on the current task. The system watches for patterns in the user?s data selection, exploration, and organization, then through mixed-initiative interaction assists users by suggesting potentially relevant data from unexplored data sources. In order to identify relevant data, PerCon builds up various precomputed feature tables of data objects including their metadata (e.g. similarities, distances) and a user interest model to infer the user interest or specific information need. In particular, probabilistic networks in PerCon model user interactions (i.e. event features) and predict the data type of greatest interest through network training. In turn, the most relevant data objects of interest in the inferred data type are identified through a weighted feature computation then recommended to the user. PerCon?s data location and analysis capabilities were evaluated in a controlled study with 24 users. The study participants were asked to locate and analyze heterogeneous weather and river data with and without the visual workspace and mixed-initiative interaction, respectively. Results indicate that the visual workspace facilitated information representation and aided in the identification of relationships between datasets. The system?s suggestions encouraged data exploration, leading participants to identify more evidences of correlation among data streams and more potential interactions among weather and river data.
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    Invisible Minority: Experience of Middle Eastern American Women in Using Health Care Services
    (2015-04-02) Kalbasi-Ashtari, Shaida
    Issues related to the experiences of minority populations have received increasing attention during the last few decades. The research has been mostly focused on minority populations that are known to the U.S. general population including Hispanics, Asians, Native Americans, and African Americans. However, the Middle Eastern American population has received little attention. As the research on health disparities advances, there has been a growing attempt to reduce disparities that cause Middle Eastern populations to have chronic or life-threatening diseases. Some of these research studies have looked at the experiences of discrimination as a factor that would make a difference in the health of this population. While these studies are important, they usually engage a quantitative research method that is not fully equipped to evaluate the experiences of discrimination in a fuller sense. Addressing this gap in the literature, I conducted 30 in-depth interviews with Middle Eastern American women about their experiences with the U.S. health care system. Based on these interviews, there seem to be signs of anti-Middle Eastern racial framing among health care professionals that often caused significant problems for these respondents in their attempts to access the U.S. health care system.
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    The Network Influences of Innovation and Lifetime Career Success in Jazz Musicians between 1945 and 1958
    (2015-02-18) Hannibal, Bryce
    In this project I explore how career success and historical importance is an outcome of social network characteristics. Specifically, I look at jazz collaboration networks at the height of small-group jazz popularity (1945-1958) to determine if one?s structural location within the larger network influences career success. Using a network dataset collected from the Tom Lord Discography I use social network analysis techniques and longitudinal logistic regression to examine a statistical relationship between network characteristics and success. I test several existing hypotheses in network literature, e.g., centrality, brokerage, and closure, as well as newer assertions that are gaining widespread use. Because jazz is based on improvisation there are incentives to creating a well-functioning closed group that remains cohesive so that musicians can become familiar with and attuned to one another?s musical styles. However, while this logic is sound the results of this project do not follow the closure tradition and are instead consistent with the sparse networks or brokerage hypotheses. Empirically, individuals within jazz networks who form a closed group are less likely to have a successful career. More broadly, significant conclusions of this project suggest that individuals within a rapidly changing network of innovators should maintain open networks with connections to diverse areas of the larger network.
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    Ethanol Targeting nELAVs: Implications for Neural Stem Cell Maturation
    (2015-04-29) Holgate, Rhonda Renay
    Neurological deficits caused by fetal exposure to ethanol remains prevalent and are recognized as a serious public health issue. The effects of fetal alcohol exposure are multifaceted and is characterized by multiple structural malformations and cognitive deficiencies, however the basic molecular mechanisms central to these defects are not thoroughly understood. A central factor in embryonic development is posttranscriptional gene regulation. Post-transcriptional regulation governs all aspects of development and is an area of vulnerability that is targeted by ethanol. nELAVs RNA binding proteins are important post transcriptional regulators involved in RNA translocation and stability. Elucidating ethanol's effects as a teratogen on these regulators their target transcripts and binding partners will enable us to implement strategies to diminish several long-term effects of fetal ethanol exposure.
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    Carriage of Virulence Factors and Antimicrobial Resistance Genes in Staphylococcus pseudintermedius from Dogs
    (2015-02-12) Gold, Randi
    Staphylococcus pseudintermedius is the most common microorganism isolated from canine pyoderma and opportunistic infections. Prevalence of methicillin-resistant S. pseudintermedius (MRSP) has increased and multi-drug resistance has become common. A total of 734 S. pseudintermedius isolates collected from dogs presented to the Veterinary Medical Teaching Hospital from 2007 to 2012 were studied. Isolates were analyzed for antimicrobial resistance and virulence gene carriage. With the emergence of methicillin resistance, veterinarians have begun to use antimicrobials such as amikacin, to treat life-threatening MRSP infections. The most widespread mechanism of amikacin resistance is drug inactivation by aminoglycoside modifying enzymes (AMEs). The most prevalent gene detected here was aph(3?)- IIIa found in 75% (24/32) of isolates followed by aac(6?)/aph(2??) and ant(4?)-Ia in 12% (4/32) and 3% (1/32), respectively. There was a significant association between amikacin and methicillin resistance. Since AMEs can be transferred from one bacteria to another, amikacin resistance may represent a new nosocomial and zoonotic threat. Clindamycin is an alternative to ?-lactam antimicrobial therapy for canine pyoderma. Inducible and constitutive resistance to clindamycin can occur. Approximately forty erm genes encoding methylases involved in clindamycin resistance have been reported, with ermB most commonly found among S. pseudintermedius. We found eight of 608 isolates tested, positive for inducible clindamycin resistance by D-test and PCR detection of ermB. A vaccine against staphylococcal pyoderma would reduce the reliance on antimicrobial drugs. Staphylococcal cell-wall associated proteins (CWAPs) involved in colonization of the host are attractive potential vaccine targets. Eighteen CWAPs encoded by sps genes have been described in S. pseudintermedius; however, four vary in occurrence. Isolates were analyzed by polymerase chain reaction (PCR) for the presence of mecA, SCCmec type I-VI, and spsF, spsO, spsP, and spsQ. There was a significant association between methicillin resistance and carriage of spsP and spsQ. spsP and spsQ may be viable vaccine targets.
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    Transcriptional Profiling of Polarized Macrophages using RNA-Sequencing
    (2015-04-17) Kanameni, Srikanth
    Adipose tissue macrophages (ATMs) are pivotal regulators for adipose tissue function, specifically contributing to the homeostasis of the adipose niche. Significantly increased ATMs and their altered activation patterns are causal factors to the pathogenesis of adipose tissue inflammation, and subsequently, obesity associated cardiovascular risks, type II diabetes and other metabolic syndromes. Macrophages primarily display an anti-inflammatory M2 status in lean adipose tissues whereas a pro-inflammatory M1 state in adipose tissues of obese individuals. Modulatory networks governing ATMs polarized activation have been investigated but the full picture remains vague. To understand the genome wide signaling networks in controlling ATM polarization, we generated transcriptome profiles from macrophages with various activation statuses- M0, M1 and M2. Among 23400 aligned unique loci from the RNA-sequencing results, around 3500 displayed differential expression pattern during macrophage polarization. The most enriched Gene Ontology terms in the category of KEGG pathways are allograft rejection and Type I diabetes mellitus pathways in M1 macrophages. IFNg was found to be one of the top upstream regulator in M1 playing pivotal role in different functional pathways. In addition, the anti-inflammatory regulator miR-223 was found to be one of top upstream regulator in M2 datasets and playing role in important functional pathways. Understanding of the complex network of interactions among different factors involved in state of polarization of macrophages would be of great advantage in finding solutions to major health issues.
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    A Content Analysis of the Coverage of Gun Trafficking Along the U.S.-MEXICO Border
    (2015-02-18) Camarillo, Omar
    This dissertation analyzed how the media on both sides of the U.S.-Mexico border portrayed the issue of gun trafficking?s into Mexico and its impact on Mexico?s border violence. National newspapers from both sides of the U.S.-Mexico border were analyzed from January 2009 through January 2012, The New York Times for the U.S. and El Universal for Mexico, which resulted in a sample of 602 newspaper articles. Qualitative research methods were utilized to collect and analyze the data, specifically content analysis. Drawing on a theoretical framework of social problems and framing this study addressed how gun trafficking along the U.S.-Mexico border impacted the drug related violence that is ongoing in Mexico, how gun trafficking was portrayed as a social problem by the media, and how the media depicted the victims of drug related violence. This study revealed six framing devices, ?the blame game,? ?worthy and unworthy victims,? ?positive aspects of gun trafficking,? ?negative aspects of gun trafficking,? ?indirect mention of gun trafficking,? and ?direct mention of gun trafficking? that were utilized by The New York Times and El Universal to discuss and frame the issue gun trafficking into Mexico and its impact on Mexico?s border violence. Gun trafficking into Mexico was found to have met all three of Jamrozik and Nocella?s criteria for a social problem. It had a societal origin in the media of 2008, constituted a threat toward the freedoms and values of the citizens of Mexico, and was found to be amendable to solution through cooperation between the U.S-Mexican governments. In the end, this dissertation understands that gun trafficking into Mexico along with the supply and demand of drugs are social problems that needs to be addressed by both the American and Mexican governments in order to prevent further drug related violence.
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    Enzymes in COG2159 of the Amidohydrolase Superfamily: Structure and Mechanism of 5-Carboxyvanillate Decarboxylase (LIGW)
    (2015-04-06) Vladimirova, Anna V
    COG2159 of the Amidohydrolase Superfamily (AHS) is composed of a wide range of enzymes, which catalyze hydration, hydrolysis, and decarboxylation reactions. 5-Carboxyvanillate decarboxylase (LigW) belongs to COG2159 and catalyzes the conversion of 5-carboxyvanillate (5-CV) to vanillate (VAN) in the pathway for the degradation of lignin. The recombinant genes from Sphingominas paucimobilis SYK-6 (LigW) and Novosphingobium aromaticivorans DSM 12444 (LigW2) were expressed in E. coli in the presence of Mn^2+ and the purified enzymes contained 1 equivalent of Mn^2+. The kinetic constants for the decarboxylation of 5-CV are as follows: kcat = 2.0 s^-1 and kcat/Km = 4.4 x 10^4 M^-1 s^-1 for the SYK-6 LigW and kcat = 27 ? 1.0 s^-1 and kcat/Km = 1.1 x 10^4 M^-1 s^-1 for the DSM 12444 LigW2. The pH-rate profiles are bell-shaped, these results are consistent with the required deprotonation of the invariant Asp-296 and protonation of His-226 for catalysis and/or substrate binding to occur. Alterations of LigW metal ligands significantly decrease the catalytic activity with kcat/Km values at least three orders of magnitude lower than that of the wild-type enzyme. Site-directed mutagenesis of substrate binding resides substantially lower or abolish the activity in LigW. The enzyme is also inhibited by the product vanillate, 3-methoxy-5-carboxybenzoate, and 4-hydroxy-3-methoxy-5-nitrobenzoate. The latter proved to be a tight binding inhibitor of LigW and LigW2 with a Ki^app = 17 nM for each of the enzymes. LigW catalyzes the exchange of the hydrogen at C-5 of VAN with deuterium over time and the product isotope effect (PIE) in a 50:50 mixture of D2O:H2O at pD 9.0 is 4.3. The crystal structures of LigW from SYK-6 and DSM 12444 with Mn^2+ in the active site were determined to a resolution of 1.8 A (PDB id: 4ICM) and 1.5 A (PDB id: 4INF). The structure of LigW was also determined complexed with the inhibitors 5-NV, MCB, and VAN. A chemical mechanism for the decarboxylation of 5-CV to VAN by LigW has been proposed. LigW requires Mn2+ for catalysis, proton transfer to C-5 is likely rate limiting for the overall reaction and precedes the decarboxylation step. The protonation of the si-face of C5 is performed from either the hydroxyl group at C4 or the carboxylate group of Asp-296. In addition, COG2159 ?-resorcylate decarboxylase (?-RSD) from Polaromonas sp. JS666 catalyzes the conversion of ?-resorcylate to resorcinol this enzyme also catalyzes the decarboxylation of 2, 4, 6- trihydroxybenzoate, 2, 3- dihydroxybenzoate, and 2, 6-dihydroxy-4-methylbenzoate.
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    Stratification Prediction and Bottom Boundary Layer Dynamics over the Texas-Louisiana Continental Shelf
    (2015-03-02) Zhang, Wenxia
    The bottom boundary layer is an unstratified thin layer above the sea floor, separated from the more strongly stratified interior. Formation of a thin bottom boundary layer in the presence of stratification and a sloping bottom is common, and well characterized by theory. This thin layer is an important source of mixing over the continental shelf, and it plays a fundamental role in several continental shelf physical and biogeochemical processes, such as buoyancy advection, bottom material transport and hypoxia formation. In this research, Both observations and numerical models are used to study models' ability of reproducing observed stratification and bottom boundary layer dynamics over the Texas-Louisiana shelf. Simulated vertical stratification, which is also representing the vertical density structure, was first evaluated since it directly controls the bottom boundary layer structure itself and is important for other bottom boundary layer dynamics. A new metric, the histogram of vertical stratification, is introduced in this research to evaluate the models' ability of reproducing observed stratification in a bulk sense. The improvement in model performance is attributed to the finer horizontal and temporal resolutions of a model, while factors like open boundary conditions and vertical resolutions are modified without any improvement in the ability of the model to simulate observed stratification. Towed, undulating CTD profiles collected during Mechanisms Controlling Hypoxia (MCH) program also detected mid-water oxygen minima in many transects. These intrusions are connected with the bottom boundary layer and follows the pycnocline seaward as a mid-water column tongue of low oxygen. We calculate convergence within the bottom boundary layer relative to density surfaces using the simulated results; there is a convergence in the bottom boundary layer at the location where the pycnocline intercepts the bottom, creating an injection of bottom boundary layer water into the pycnocline. Convergent flow at the bottom, relative to isopycnal surfaces, is strongest in the density classes associated with the oxygen minimum layer. We believe these mid-water oxygen minima are actually intrusions of low oxygen protruding from the bottom boundary layer via buoyancy advection driven convergence, following the main pycnocline.
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    Acidizing High-Temperature Carbonate Formations Using Methanesulfonic Acid
    (2015-03-25) Ortega, Alexis
    Hydrochloric acid (HCl) is the most commonly used stimulation fluid for high-temperature wells drilled in carbonate reservoirs due to its high dissolving power and low cost. However, the high corrosion rate of HCl on well tubulars could make its use in deep wells non-viable. The current study introduces the novel application of methanesulfonic acid (MSA), a strong organic acid, to increase the permeability of carbonate formations, specifically at temperatures above 200?F. The objective of the experimental study is to evaluate the performance of MSA as stand-alone stimulation fluid for high-temperature limestone and dolomite formations. Coreflood studies were conducted at temperature up to 320?F using limestone and dolomite cores and diluted MSA aqueous solutions. A constant injection rate, ranging from 1 to 25 cm3/min, was maintained during the coreflood tests and the differential pressure through the core was measured until acid breakthrough. Samples of the effluent fluids were collected and analyzed using Inductively Coupled Plasma (ICP) to measure the calcium and magnesium concentrations, and a computed tomography (CT) scan of each core was performed after the acid injection to study the characteristics of the generated wormholes. MSA was found effective in creating wormholes in carbonate cores at the temperatures tested. At low injection rates, face dissolution and conical channels were observed in the cores. At intermediate injection rates, the tendency was to create a few dominant wormholes. At high injection rates, ramified wormhole structures were found, with increased branching for increased flow rates. For each condition tested, an optimum flow rate was identified. Additionally, analysis of the coreflood effluent samples showed no sign of methanesulfonate salts precipitation. Demonstration of the effectiveness of MSA in propagating wormholes in carbonate cores will offer the petroleum industry with another alternative strong acid to HCl for stimulating high-temperature carbonate formations. MSA?s high acidity, solubility of its salts, and thermal stability, along with its readily biodegradable composition provide a beneficial use for MSA as a stimulation fluid in carbonate acidizing techniques. MSA also has a more favorable corrosion profile on metals, such as high chromium alloys, than usual mineral acids employed in well stimulation.
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    Occlusal Harmony of Hand Articulated Digitally Mastered Definitive Casts Mounted in Maximal Intercuspal Position
    (2015-04-24) Bone, Sven Erik
    Digital acquisition of a patient?s oral anatomy has the potential to improve the accuracy of dental restorations. The iTero intraoral scanner is emerging as a popular system in clinical practice, however the accuracy of the digitally mastered (DM) casts acquired with this system has not been evaluated. In this study, 20 scans were acquired of a simulated patient producing 10 pairs digitally mastered (DM) definitive casts. The occlusal differences between DM casts and SP were evaluated by comparing the differences in areas of actual contact and near contact. The DM casts were significantly different in both areas of actual contact and near contact compared to the simulated patient (p < 0.001). The null hypothesis of no detectable occlusal differences was rejected. It is postulated final restorations fabricated on these DM casts may require adjustments upon delivery to attain occlusal harmony.
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