Digital Commons Network^™

Fluvial-Lacustrine Processes Shaping The Landforms Of The Distal Paraguay Fluvial Megafan, Edward Limin Lo

Theses and Dissertations--Earth and Environmental Sciences

Tropical wetlands such as the Pantanal help regulate global biogeochemical cycles, but climate change is modifying these environments. Controls on environmental changes can potentially be assessed from ancient, well-dated lacustrine sedimentary records. An integrated field and laboratory approach was undertaken to study the limnogeology of Lake Uberaba in the northern Pantanal, and test whether the lake has preserved a reliable record of environmental change in its strata. This study was designed to understand how the basin accumulates sediment and to assess its sensitivity to hydroclimatic variability. The data showed that modern Lake Uberaba is a highly dynamic, freshwater fluvial-lacustrine basin. …

An Exploratory Statistical Method For Finding Interactions In A Large Dataset With An Application Toward Periodontal Diseases, Joshua Lambert

Theses and Dissertations--Epidemiology and Biostatistics

It is estimated that Periodontal Diseases effects up to 90% of the adult population. Given the complexity of the host environment, many factors contribute to expression of the disease. Age, Gender, Socioeconomic Status, Smoking Status, and Race/Ethnicity are all known risk factors, as well as a handful of known comorbidities. Certain vitamins and minerals have been shown to be protective for the disease, while some toxins and chemicals have been associated with an increased prevalence. The role of toxins, chemicals, vitamins, and minerals in relation to disease is believed to be complex and potentially modified by known risk factors. A …

Expression Of Fam171b Protein In Mouse Brain Tissue, Quan Tran

All Graduate Theses, Dissertations, and Other Capstone Projects

Polyglutamine (polyQ) diseases are inherited fatal neurodegenerative disorders caused by expansion of trinucleotide cytosine-adenine-guanine (CAG) repeats, encoding abnormally long glutamine tracts in respective disease proteins. Currently, there are nine polyQ diseases- including Huntington’s disease and a number of Spinocerebellar ataxias. Interestingly, expanded polyQ proteins are prone to aggregate, and this aggregation may underlie neurodegeneration. In this study, we investigate the expression and localization of FAM171B (a novel polyQ protein) in the brain. Western blotting reveals that FAM171B protein is indeed expressed in the developing and adult mouse brain. Furthermore, immunohistochemical analyses suggests widespread localization of FAM171B to many brain regions …

Prediction Of Local Quality Of Protein Structure Models Considering Spatial Neighbors In Graphical Models., Woong Hee Shin, Xuejiao Kang, Jian Zhang, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Protein tertiary structure prediction methods have matured in recent years. However, some proteins defy accurate prediction due to factors such as inadequate template structures. While existing model quality assessment methods predict global model quality relatively well, there is substantial room for improvement in local quality assessment, i.e. assessment of the error at each residue position in a model. Local quality is a very important information for practical applications of structure models such as interpreting/designing site-directed mutagenesis of proteins. We have developed a novel local quality assessment method for protein tertiary structure models. The method, named Graph-based Model Quality assessment method …

Identification Of Cdks As Novel Targets Of Aspirin And Its Metabolites: A Potential Role In Cancer Prevention, Rakesh Dachineni

Electronic Theses and Dissertations

Background:
The pursuit of drugs that inhibit cyclin-dependent kinases (CDKs) has been an intense area of research for more than 15 years. Till date, although multiple CDK inhibitors have been identified and few are undergoing clinical trials, only two synthetic drugs have been approved by Food and Drug Administration (FDA) for use in the treatment of cancer. These two drugs are mainly used for the treatment of metastatic breast cancer in combination with other drugs; however they have toxicity associated with their use and extends patients life not more than 24 months. Therefore, there is an urgent need for …

Tracing Ainu And Pre-Ainu Cultural Continuity Through Cladistic Analysis Of Faunal Assemblages, Christopher Lowry

All Master's Theses

Cladistics (Hennig 1950, 1965, 1966), a method for establishing evolutionary relationships, is used to compare faunal assemblages from Jōmon (14,000-500 BC; 14,000–2700 cal. BP), Epi-Jōmon (3rd – 7th century; 2700-1500 cal. BP), Satsumon (7th century - 13th century AD; ca. 1500-800 cal. BP), and Ainu (13th century AD – present) period components (Habu et al. 2011; Matsumura 2006; Ōnishi 2014; Weber et al. 2013) from sites in Central Hokkaido, Japan using Generalized Frequency Coding methods (Smith & Gutberlet 2001). Associations of site components follow geographic rather than temporal trends, showing similarities in animal use across these time periods but differentiated …

Copper And Zinc Speciation In The Tamar Estuary, Holly Beverley Clare Pearson

School of Geography, Earth and Environmental Sciences Theses

The chemical speciation of trace metals controls their potential bioavailability and therefore toxicity to exposed organisms. Despite previous studies demonstrating the ameliorative effects of dissolved organic carbon (DOC) on metal toxicity, the effectiveness of ligands from varying sources and of potentially variable composition in controlling speciation has not been studied in detail in estuarine waters. In addition, the effect of DOC on radionuclide contaminants in combination with trace metals has not been investigated in any waters. This is of particular interest in the estuarine environment, where both anthropogenic and natural ligands, and contaminants that pose a potential threat to ecosystem …

Ultrafast Comparison Of Personal Genomes Via Precomputed Genome Fingerprints., Gustavo Glusman, Denise E Mauldin, Leroy E Hood, Max Robinson

Articles, Abstracts, and Reports

We present an ultrafast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into "genome fingerprints" via locality sensitive hashing. The resulting genome fingerprints can be meaningfully compared even when the input data were obtained using different sequencing technologies, processed using different pipelines, represented in different data formats and relative to different reference versions. Furthermore, genome fingerprints are robust to up to 30% missing data. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. For example, we could compute all-against-all pairwise comparisons among the …

Population Genetics Of The Giant Red Centipede Along The Appalachian Mountains, Kayla Elayne Ladner

Honors Theses

This study focused on population genetics of the giant red centipede, Scolopocryptops sexpinousus, in the Southern Appalachian Mountains. Two genetic markers were used—the mitochondrial COI gene, and the nuclear RNA Polymerase II gene. The goal of this study was to determine how many genetically distinct populations of this invertebrate species exist within the study area, and to understand the spatial distribution of genetic diversity within and among populations. I hypothesized several genetically distinct populations of S. sexpinosus would be detected because the complex topographic characteristics and historical climate cycles of the region are thought to limit movement of many forest …

Occurrence And Phenology Of Polistine Wasps (Hymenoptera: Vespidae) In Southern Louisiana, Scott Nacko

LSU Master's Theses

Phylogenetic studies suggest that historically all paper wasps (Vespidae: Polistinae) in North America have tropical origins. However, paper wasps have adapted to thrive in temperate conditions. Subtropical and temperate climates allow for a study of adaptive traits which can be retained or lost within populations, and ultimately help elucidate the process of social wasp evolution. Additionally, species occurrence patterns can help us to understand partitioning and resource use within populations. We investigated the occurrence and phenology of each Polistine species found at four sites in southern Louisiana around Baton Rouge, and also examined the occurrence and behavior of a closely …

Ebola Virus Vp30 And Nucleoprotein Interactions Modulate Viral Rna Synthesis, Wei Xu, Priya Luthra, Chao Wu, Jyoti Batra, Daisy W. Leung, Christopher F. Basler, Gaya K. Amarasinghe

Open Access Publications

No abstract provided.

Multimodal Fluorescence Molecular Imaging For In Vivo Characterization Of Skin Cancer Using Endogenous And Exogenous Fluorophores, Jessica P. Miller, Lemoyne Habimana-Griffin, Tracy S. Edwards, Samuel Achilefu

Open Access Publications

No abstract provided.

Facile Purification Of Milligram To Gram Quantities Of Condensed Tannins According To Mean Degree Of Polymerization And Flavan-3-Ol Subunit Composition, Ron H. Brown, Irene Murray-Harvey, Wayne E. Zeller, Laurie Reinhardt, Elisabetta Stringano, An Gea, Christopher Drake, Honorata M. Ropiak, Christos Fryganas, Aina Ramsay, Emily E. Hardcastle

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Unambiguous investigation of condensed tannin (CT) structure−activity relationships in biological systems requires well-characterized, high-purity CTs. Sephadex LH-20 and Toyopearl HW-50F resins were compared for separating CTs from acetone/water extracts, and column fractions analyzed for flavan-3-ol subunits, mean degree of polymerization (mDP), and purity. Toyopearl HW-50F generated fractions with higher mDP values and better separation of procyanidins (PC) and prodelphinidins (PD) but required a prepurification step, needed more time for large scale purifications, and gave poorer recoveries. Therefore, two gradient elution schemes were developed for CT purification on Sephadex LH-20 providing 146−2000 mg/fraction. Fractions were analyzed by thiolysis and NMR spectroscopy. …

Racial Disparities In Renal Cell Carcinoma: A Single Payer Healthcare Experience, Abiodun Mafolasire

Yale Medicine Thesis Digital Library

Introduction: Significant racial disparities in survival for renal cell carcinoma (RCC) exist between whites and blacks. Differences in access to care and comorbidities are possible contributors. To investigate if racial disparities persist when controlling for access to care, we analyzed data from a single payer healthcare system.

Methods: As part of a case-control study within the Kaiser Permanente Northern California system, pathologic and clinical records were obtained for RCC cases (2,152 white, 293 black) diagnosed from 1998 to 2008. Patient demographics, comorbidities, tumor characteristics, and treatment status were compared between whites and blacks. Overall survival and disease specific survival (DSS) …

Are Mussel Shells Environmental Dna Time Capsules? A Comparison Of Extraction Methods For Obtaining Dna From Shell Material., Kelsey Elizabeth Rogers

Online Theses and Dissertations

Freshwater mussels have become some of the most imperiled species in North America and widespread populations have succumbed to pollution and many other anthropogenic-related factors. With molecular techniques evolving, a recent interest in ancient DNA and museum specimens has emerged and prompted a study to test the ability of several extraction methods to isolate DNA from museum mussel specimens. The purpose of this study was to determine if four DNA extraction methods had influence on total DNA yield (ng/mg) from mussel tissue. The hinge ligaments of freshwater mussels ranging in collection date (1984-2015) were used as the source of genetic …

Pollen Viability And Meiotic Abnormalities In Brome Grasses(Bromus L., Section Ceratochloa) From Argentina, Gabriela Leofanti, Elsa Lucila Camadro

Turkish Journal of Botany

Bromus Section Ceratochloa includes temperate forage species. South American species form a morphologically very variable hexaploid complex (2n = 6x = 42), with a controversial taxonomic classification. Reproductive biology has been studied in several of them, but the number of analyzed plants has seldom been reported. Further investigations might clarify breeding relations and the adequacy of current classifications. Pollen viability and size, which can provide evidence of spontaneous hybridization, were studied in seven accessions (six plants/accession) classified as B. catharticus var. catharticus, var. elata, and var. rupestris; B. parodii; B. bonariensis; B. lithobius; and B. coloratus. Variability was detected among …

Hydrogen Sulfide Regulation Of Kir Channels, Junghoon Ha

Theses and Dissertations

Inwardly rectifying potassium (Kir) channels establish and regulate the resting membrane potential of excitable cells in the heart, brain and other peripheral tissues. Phosphatidylinositol- 4,5-bisphosphate (PIP2) is a key direct activator of ion channels, including Kir channels. Gasotransmitters, such as carbon monoxide (CO), have been reported to regulate the activity of Kir channels by altering channel-PIP2 interactions. We tested, in a model system, the effects and mechanism of action of another important gasotransmitter, hydrogen sulfide (H2S) thought to play a key role in cellular responses under ischemic conditions. Direct administration of sodium hydrogen sulfide (NaHS), as an exogenous H2S source, …

A Roadmap For Development Of Novel Antipsychotic Agents Based On A Risperidone Scaffold, Urjita H. Shah

Theses and Dissertations

Schizophrenia is a chronic psychotic illness affecting ~21 million people globally. Currently available antipsychotic agents act through a dopamine D₂ receptor mechanism, and produce extrapyramidal or metabolic side effects. Hence, there is a need for novel targets and agents. The mGlu₂/5-HT_2A receptor heteromer has been implicated in the action of antipsychotic agents, and represents a novel and attractive therapeutic target for the treatment of schizophrenia. A long-term goal of this project is to synthesize bivalent ligands where a 5-HT_2A receptor antagonist is tethered to an mGlu₂ PAM via a linker.

The goals of the …

Improving Peptide Identification By Considering Ordered Amino Acid Usage, Ahmed Al-Qurri

Theses and Dissertations

Proteomics has made major progress in recent years after the sequencing of the genomes of a substantial number of organisms. A typical method for identifying peptides uses a database of peptides identified using tandem mass spectrometry (MS/MS). The profile of accurate mass and elution time (AMT) for peptides that need to be identified will be compared with this database. Restricting the search to those peptides detectable by MS will reduce processing time and more importantly increase accuracy. In addition, there are significant impacts for clinical studies. Proteotypic peptides are those peptides in a protein sequence that are most likely to …

Induction Of Haploid Plants In Citrus Through Gamma-Irradiated Pollen And Ascertainment Of Ovule Age For Maximum Recovery Of Haploid Plantlets, Manoj Kundu, Anil Dubey, Manish Srivastav, Surendra Kumar Malik

Turkish Journal of Biology

The present investigation was carried out for the induction of haploid plants in Citrus grandis through in situ parthenogenesis by pollination with gamma-irradiated pollen of C. limetta and C. sinensis, treated with 50, 100, 200, 300, and 400 Gy gamma ray doses followed by in vitro ovule culture. Ovule culture at 50 days after pollination (DAP) was found optimum for the maximum recovery of in vitro-raised plantlets as compared to 35 and 20 DAP. At 50 DAP, irrespective of the pollen parent, plantlet regeneration capacity decreased at 300 and 400 Gy irradiation treatment (0.62% and 0.60%, respectively) with maximum recovery …

Investigate Genomic 3d Structure Using Deep Neural Network, Yan Zhang

Theses and Dissertations

The 3D structures of the chromosomes play fundamental roles in essential cellular functions, e.g., gene regulation, gene expression, evolution and Hi-C technique provides the interaction density between loci on chromosomes. In this dissertation, we developed multiple algorithms, focusing the deep learning approach, to study the Hi-C datasets and the genomic 3D structures.

Building 3D structure of the genome one of the most critical purpose of the Hi-C technique. Recently, several approaches have been developed to reconstruct the 3D model of the chromosomes from HiC data. However, all of the methods are based on a particular mathematical model and lack of …

Frequency Of Colistin And Fosfomycin Resistance In Carbapenem-Resistant Enterobacteriaceae From A Tertiary Care Hospital In Karachi, Salima Qamar, Najma Shaheen, Sadia Shakoor, Joveria Farooqi, Kauser Jabeen, Rumina Hasan

Department of Pathology and Laboratory Medicine

Introduction:
Management of infections with carbapenem-resistant Enterobacteriaceae (CRE) is challenging. In recent times, agents such as colistin and fosfomycin have been used in combination with other antibiotics to treat such infections. In this study, we aim to seek frequency of colistin and fosfomycin resistance in CRE from Pakistan.
Methods:
This study was conducted at clinical laboratories, Aga Khan University Hospital. In total, 251 CRE were included in the study. Colistin minimum inhibitory concentrations (MICs) were performed using broth microdilution (BMD) method and VITEK 2 system, whereas fosfomycin susceptibility was performed using Kirby-Bauer method. MIC50 and MIC90 were calculated for colistin …

Ammonium Removal And Biomass Production By Unicellular Cyanobacterium Synechococcus Sp., Piroonporn Srimongkol

Chulalongkorn University Theses and Dissertations (Chula ETD)

Using microalgae as a biofuel feedstock has played more attention over a decade. The cultivation of microalgae requires high water use and high initial investment that can make the process still not economically appealing. This study attempted to examine the potential for using brackish shrimp aquaculture effluents as culture medium for algal biomass production. To investigate whether algae could be used to remove ammonium from brackish shrimp aquaculture wastewater, marine cyanobacterium, Synechococcus sp. was cultured in BG-11 medium supplemented with Turks Island salt solution and different concentrations of NH4Cl (10-40 mg N L-1) for 18 days. The results showed that, …

Bodipy-Based Red Sensitizers For Near-Infrared Emission Of Lanthanide Complexes, Priyangika Prasadini Senevirathne

Masters Theses

During the past 20 years there has been a remarkable growth in the use of the fluorescence technique in biological studies. Fluorescence and time-resolved fluorescence spectroscopy are considered primary research tools in the field of biochemistry. Currently, fluorescence spectroscopy is a dominant methodology and used widely in biotechnology and medical diagnosis process. One impediment in using fluorescent probes is the fluorescence of biological substrates and fluorescence of diagnostic probes are significantly overlapped, and it decreases the detection sensitivity. Also, commercially available probes require UV or near-UV light excitation, causing severe degradation of biological substrates. Near-infrared emitting lanthanide complexes can overcome …

A Computational Study Of Vegf Production By Patterned Retinal Epithelial Cell Colonies As A Model For Neovascular Macular Degeneration, Qanita Bani Baker, Gregory J. Podgorski, Elizabeth Vargis, Nicholas Flann

Biology Faculty Publications

Background: The configuration of necrotic areas within the retinal pigmented epithelium is an important element in the progression of age-related macular degeneration (AMD). In the exudative (wet) and non-exudative (dry) forms of the disease, retinal pigment epithelial (RPE) cells respond to adjacent atrophied regions by secreting vascular endothelial growth factor (VEGF) that in turn recruits new blood vessels which lead to a further reduction in retinal function and vision. In vitro models exist for studying VEGF expression in wet AMD (Vargis et al., Biomaterials 35(13):3999–4004, 2014), but are limited in the patterns of necrotic and intact RPE epithelium they can …

Design And Synthesis Of Selenium Nanoparticles To Overcome Multiple Drug Resistance Of Cancer Cells, Urarika Luesakul

Chulalongkorn University Theses and Dissertations (Chula ETD)

The objective of this research is to synthesize selenium nanoparticles (SeNPs) stabilized by chitosan as a drug carrier for delivery doxorubicin to overcome drug-resistant in cancer cells. One important mechanism of multidrug resistance (MDR) includes decreased drug influx and increased drug efflux, leading to insufficient drug concentration to kill cancer cells. Therefore, to overcome MDR by increasing cellular uptake, the surface of SeNP was functionalized to provide 3 structural features: (i) a positive charge to improve their solubility, (ii) gallic acid, a hydrophobic molecule to enhance biocompatibility and (iii) folic acid, a targeting molecule to target cancer cells and enhance …

Synthesis Of Cationic Cdse/Zns Quantum Dots And Applications In Dna Detection, Jamornpan Yangcharoenyuenyong

Chulalongkorn University Theses and Dissertations (Chula ETD)

Semiconductor nanoparticles or quantum dots (QDs), especially CdSe/ZnS QDs, are of great interest in bioapplications due to their unique size-dependent optical properties and photo-stability. One of the plausible applications of QDs is DNA detection using QDs as a novel fluorescence tool for sensing of DNA using the electrostatic interaction between negative charge of DNA and positive charge on QDs surface. In this work, CdSe/ZnS QDs were synthesized using a hot-solution decomposition process resulting in hydrophobic CdSe/ZnS QDs. To obtain water-soluble and cationic QDs, the surface of QDs were modified with poly(ethylene)imine (PEI) via micelle formation. Because of hydrophilicity of PEI …

Density-Based Spatial Clustering Of Applications With Noises For Dna Methylation Data, Mohammed Atef Alghzzy

Graduate Research Theses & Dissertations

Density-based spatial clustering of applications with noise (DBSCAN) is one of the most popular clustering methods to classify nonlinearly grouped data. In particular, DNA methylations are considered to be differently skewed by CpG sites and to be nonlinearly grouped by cancer statuses. Under this circumstance, DBSCAN is expected to have a desirable clustering feature. This thesis reviews the DBSCAN algorithm and compares its performance to the other traditional clustering algorithm, K-means method. Simulation studies show the misclassification ratios of DBSCAN with the comparison of K-means method to evaluate their performance, and the classification of DNA methylations from patients with lung …

Process-Structure-Property Relationship In Magnesium-Based Biodegradable Alloy For Biomedical Applications, Pramanshu Trivedi

Open Access Theses & Dissertations

Magnesium alloys are considered to be the next generation of biomaterials because of their ability to degrade in the physiological environment. We elucidate here the impact of multiaxial forging of Mg-2Zn-2Gd alloy on grain refinement to sub-micron regime and relate the structure to mechanical properties and biological functionality. As-cast and annealed samples were multiaxial forged (MAF) for a total number of two passes with a true strain of ~2/pass. Considering that the microstructure governs the biological response of materials, we studied the constituents of the microstructure in conjunction with the mechanical behavior. The antimicrobial behavior in a Mg-2Zn-2Gd alloy with …

Contextual Representation Of Documents, Entities, And Faces Of People Using A News Corpus, Md Abdul Kader

Open Access Theses & Dissertations

A massive amount of unstructured data, in this information age, is composed of document collections. Examples include news articles, blog posts, scholarly publications, and reports generated by organizations as well as people. Many data mining and machine learning algorithms have been developed in the past decade to support text mining in many applications. Text mining applications cover a wide range of tasks spanning from personal information management --- to organizational decision making, to disease control through epidemic prediction, and to intelligence analysis for national security. One bottleneck has been dominating data mining and machine learning theories for all these text …