Matching Items (75)
Description
Immunosignaturing is a technology that allows the humoral immune response to be observed through the binding of antibodies to random sequence peptides. The immunosignaturing microarray is based on complex mixtures of antibodies binding to arrays of random sequence peptides in a multiplexed fashion. There are computational and statistical challenges to the analysis of immunosignaturing data. The overall aim of my dissertation is to develop novel computational and statistical methods for immunosignaturing data to access its potential for diagnostics and drug discovery. Firstly, I discovered that a classification algorithm Naive Bayes which leverages the biological independence of the probes on our array in such a way as to gather more information outperforms other classification algorithms due to speed and accuracy. Secondly, using this classifier, I then tested the specificity and sensitivity of immunosignaturing platform for its ability to resolve four different diseases (pancreatic cancer, pancreatitis, type 2 diabetes and panIN) that target the same organ (pancreas). These diseases were separated with >90% specificity from controls and from each other. Thirdly, I observed that the immunosignature of type 2 diabetes and cardiovascular complications are unique, consistent, and reproducible and can be separated by 100% accuracy from controls. But when these two complications arise in the same person, the resultant immunosignature is quite different in that of individuals with only one disease. I developed a method to trace back from informative random peptides in disease signatures to the potential antigen(s). Hence, I built a decipher system to trace random peptides in type 1 diabetes immunosignature to known antigens. Immunosignaturing, unlike the ELISA, has the ability to not only detect the presence of response but also absence of response during a disease. I observed, not only higher but also lower peptides intensities can be mapped to antigens in type 1 diabetes. To study immunosignaturing potential for population diagnostics, I studied effect of age, gender and geographical location on immunosignaturing data. For its potential to be a health monitoring technology, I proposed a single metric Coefficient of Variation that has shown potential to change significantly when a person enters a disease state.
ContributorsKukreja, Muskan (Author) / Johnston, Stephen Albert (Thesis advisor) / Stafford, Phillip (Committee member) / Dinu, Valentin (Committee member) / Arizona State University (Publisher)
Created2012
Description
When examining the medical doctrines of previous empires, they reveal the influence of religion, societal attitudes, and the historical context that influenced the scholars that penned them. The advancements during the Islamic Golden age can be seen in the field of medicine, which had the Greco-Roman medical corpus as their foundation and the source of the theory of the four humors and anatomical beliefs. This paper will analyze the effect of cultural, societal, and historical influences on the medical doctrines of Muslim medieval physicians in the Golden Age and the works of the Roman physician Galen, and demonstrate how these effects result in similarities and differences in medical practice and the understanding of disease and anatomy. Due to translation efforts that were supported by religious views on the accumulation of knowledge and the efforts of the Abbasid empire, resultant acceptance of the theory of the four humors and anatomical doctrines is observed in the treatment and perception of disease, which would consist of this paper's focus on surgery, diet therapy and associations with nature. However, with further analysis of the extent of this acceptance and the findings in the Islamic medical doctrines, the differences in experimental methods, religious interpretations, and cultural attitudes shows a deviation from the Galenic tradition, with the second set of the paper's focus being human dissection, cause of disease, and experimentation. The purpose of this research is to demonstrate the impact of religion, societal attitudes, culture and the accepted paradigm on the practice of medicine and the study of anatomy, and what would cause a challenge against the legacy of Galen.
ContributorsAlzuhairi, Fatemah Saad (Author) / Vélez-Ibáñez, Carlos (Thesis director) / Smith, Brian (Committee member) / Historical, Philosophical & Religious Studies (Contributor) / Historical, Philosophical & Religious Studies, Sch (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Honey bee (Apis mellifera) colonies have experienced substantial losses due to colony collapse disorder (CCD) since the first officially reported cases in 2006. Many factors have been implicated in CCD, including pests, pathogens, malnutrition, and pesticide use, but no correlation has been found between a single factor and the occurrence of CCD. Fungicides have received less research attention compared to insecticides, despite the fact that fungicide application coincides with bloom and the presence of bees. Pristine fungicide is widely used in agriculture and is commonly found as a residue in hives. Several studies have concluded that Pristine can be used without harming bees, but reports of brood loss following Pristine application continue to surface across the country. The primary objectives of this study were to determine whether Pristine causes an aversive gustatory response in bees and whether consumption of an acute dose affects responsiveness to sucrose. An awareness of how foragers interact with contaminated food is useful to understand the likelihood that Pristine is ingested and how that may affect bees' ability to evaluate floral resources. Our results indicated that Pristine has no significant effect on gustatory response or sucrose responsiveness. There was no significant difference between bee responses to Pristine contaminated sucrose and sucrose alone, and no significant effect of Pristine on sucrose responsiveness. These results indicate that honey bees do not have a gustatory aversion to Pristine. A lack of aversion means that honey bees will continue collecting contaminated resources and dispersing them throughout the colony where it can affect brood and clean food stores.
ContributorsMcHugh, Cora Elizabeth (Co-author) / Jernigan, Christopher (Co-author, Committee member) / Burden, Christina (Co-author) / DeGrandi-Hoffman, Gloria (Co-author) / Smith, Brian (Thesis director) / Fewell, Jennifer (Committee member) / Barrett, The Honors College (Contributor) / School of Geographical Sciences and Urban Planning (Contributor) / School of Life Sciences (Contributor) / School of Art (Contributor)
Created2015-05
Description
This study illustrates the abilities of the honeybee, Apis mellifera, to learn and differentiate between patterns solely off their spatial frequencies. Patterns were chosen based off of calculations derived from the measurements of the physical construction of the apposition compound eye, which led to predictions of what the bees could theoretically see. The hypothesis was then that bees would have a visual threshold where patterns with spatial frequencies that fall below this line should be easily distinguishable, and patterns above the threshold would have scores that mimic if the bees made choices randomly. There were 9 patterns tested, all with different spatial frequencies and in the colors of black, white, and gray. The bees were tested on their learning and pattern differentiation abilities with 10 pattern comparisons, with the lower frequency of the two being associated with an unscented sucrose solution reward. The results were surprising in that the previous studies pointing towards this visual threshold were inaccurate because of some of the patterns being learning in an intermediate ability. These intermediate scores suggest that the calculations predicting what the bees could see clearly were slightly wrong because it was more likely that the bees saw those images in more of a blur, which resulted in their intermediate score. Honeybees have served as a useful model organisms over the decades with studying learning involving visual information. This study lacked in its total numbers of trials and bees tested, which could have led to incomplete results, and this showing of an intermediate score and ability. Future studies should continue in order to advance this understanding of a perceptually and cognitively advance processing animal.
ContributorsBalsino, Brandon Bartholomew (Author) / Harrison, Jon (Thesis director) / Smith, Brian (Committee member) / Duell, Meghan (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12
Description
Selenium, a group 16 metalloid on the periodic table, is a necessary mineral for many organisms. Trace amounts of selenium are essential for normal development, antioxidant protein function, enzyme function, and hormone regulation (Burden et al., 2016). However, when selenium is found in toxic amounts in organisms, it has been found to substitute for sulfur in proteins, which can be toxic to these animals, and cause oxidative stress (Quinn et al., 2007). Using the previous research done with acute exposure to organic and inorganic selenium compounds, we hypothesized that the inorganic sodium selenate would significantly decrease learning and memory recall for both chronic and acute exposure. We also hypothesized that the consumption of organic methylseleno-L-cysteine by honey bees would decrease learning and memory recall for both the chronic and acute exposure. We further hypothesized that protein carbonyl content would be increased due to oxidative damage caused by selenium in both the sodium selenate and the methylseleno-L-cysteine treatment groups, but that the inorganic selenium compound would increase the carbonyl content more than the methylseleno-L-cysteine. To run the experiments, three tents outside had two colonies in each tent. One tent contained the sodium selenate group, another had the sucrose control, and one contained the methylseleno-L-cysteine group. The treatment groups were fed selenium in their sucrose feeders. The first part of the experiment was training the bees by using proboscis extension response (PER) to teach them to extend their proboscis to the rewarded odor and not to the unrewarded odor. This was done by pairing the rewarded odor with a sucrose reward and not pairing it with the unrewarded odor. Then their short-term and long-term memory recall was tested. The second part of the experiment was checking for oxidative damage by measuring the protein carbonyl content in the bees. Three boxes were set up with the same three treatment groups as used in the tents. The treatment group bees were exposed to selenium in the sucrose feeders and in the pollen patties. After one week, the living bees were removed and frozen. They were then homogenized to extract protein. The first assay run was the protein content assay to establish a standard protein concentration for samples. Then a protein carbonyl assay was run, to determine the protein carbonyl content. Overall, the experiment found that exposure to selenium negatively impacted honey bees learning and memory recall significantly. Chronic exposure to the inorganic selenate reduced the bees' long-term memory abilities to differentiate between odors. With methylseleno-L-cysteine, it had no significant effect for the chronic exposure, but for the acute exposure, it had a significant impairment on their abilities to distinguish between the rewarded and unrewarded odors during conditioning. Our results showed that from our experiment there appeared to be no significant effect of selenium exposure on the increase of carbonylation content in the different treatment groups. This is most likely due to the fact the carbonyl content was not detectable because the protein concentration was low in the samples (approximately 3.5 mg/mL).
ContributorsWinski, Alexandra (Co-author) / Winski, Brandon (Co-author) / Smith, Brian (Thesis director) / Harrison, Jon (Committee member) / Burden, Christina (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
DNA methylation, a subset of epigenetics, has been found to be a significant marker associated with variations in gene expression and activity across the entire human genome. As of now, however, there is little to no information about how DNA methylation varies between different tissues inside a singular person's body. By using research data from a preliminary study of lean and obese clinical subjects, this study attempts to put together a profile of the differences in DNA methylation that can be observed between two particular body tissues from this subject group: blood and skeletal muscle. This study allows us to start describing the changes that occur at the epigenetic level that influence how differently these two tissues operate, along with seeing how these tissues change between individuals of different weight classes, especially in the context of the development of symptoms of Type 2 Diabetes.
ContributorsRappazzo, Micah Gabriel (Author) / Coletta, Dawn (Thesis director) / Katsanos, Christos (Committee member) / Dinu, Valentin (Committee member) / Barrett, The Honors College (Contributor) / Harrington Bioengineering Program (Contributor) / Department of Psychology (Contributor)
Created2013-12
Description
Continuous advancements in biomedical research have resulted in the production of vast amounts of scientific data and literature discussing them. The ultimate goal of computational biology is to translate these large amounts of data into actual knowledge of the complex biological processes and accurate life science models. The ability to rapidly and effectively survey the literature is necessary for the creation of large scale models of the relationships among biomedical entities as well as hypothesis generation to guide biomedical research. To reduce the effort and time spent in performing these activities, an intelligent search system is required. Even though many systems aid in navigating through this wide collection of documents, the vastness and depth of this information overload can be overwhelming. An automated extraction system coupled with a cognitive search and navigation service over these document collections would not only save time and effort, but also facilitate discovery of the unknown information implicitly conveyed in the texts. This thesis presents the different approaches used for large scale biomedical named entity recognition, and the challenges faced in each. It also proposes BioEve: an integrative framework to fuse a faceted search with information extraction to provide a search service that addresses the user's desire for "completeness" of the query results, not just the top-ranked ones. This information extraction system enables discovery of important semantic relationships between entities such as genes, diseases, drugs, and cell lines and events from biomedical text on MEDLINE, which is the largest publicly available database of the world's biomedical journal literature. It is an innovative search and discovery service that makes it easier to search
avigate and discover knowledge hidden in life sciences literature. To demonstrate the utility of this system, this thesis also details a prototype enterprise quality search and discovery service that helps researchers with a guided step-by-step query refinement, by suggesting concepts enriched in intermediate results, and thereby facilitating the "discover more as you search" paradigm.
avigate and discover knowledge hidden in life sciences literature. To demonstrate the utility of this system, this thesis also details a prototype enterprise quality search and discovery service that helps researchers with a guided step-by-step query refinement, by suggesting concepts enriched in intermediate results, and thereby facilitating the "discover more as you search" paradigm.
ContributorsKanwar, Pradeep (Author) / Davulcu, Hasan (Thesis advisor) / Dinu, Valentin (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2010
Description
Fruit flies show a strong attraction to fruit odors. Most fruit odors, including strawberry scent, are complex multimolecular mixtures comprised of many chemically distinct constituents. How animals are able to process these mixtures and derive behaviorally relevant information is largely unknown. A new procedure was created to test odor preference for Heisenberg canton-s strain of Drosophila melanogaster. 30 flies were cold anesthetized at 4.2°C for 30 minutes and then placed in a testing arena. After acclimating for 45 minutes, the flies were exposed to two sources of air, one with ripe strawberry odor and one with only humidified air. Images were captured every minute for an hour and a preference index was calculated for every 10th image. The Drosophila had a positive average preference for the strawberry odor. Five out of six trials showed a general increase in odor preference over the course of the trial. While there was a generally positive trend for average preference over time, there was not a significant increase in average odor preference from time 1 to time 60. The data indicates that Drosophila show a preference for strawberry odor over humidified air, and we propose to extend this test to investigate how Drosophila process and react to complex odors and their chemical constituents.
ContributorsSteinmetz, Kyle J (Author) / Smith, Brian (Thesis director) / Jernigan, Chris (Committee member) / School of Life Sciences (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Recent data suggests that olfactory input is important for antennal lobe development in honey bees. Chronic association of a single odor to food resources during crucial stages of development results in delayed antennal lobe development for mature foraging bees. The antennal lobes of these bees instead closely resemble an immature network observed in young, newly emerged bees. Using an odor stimuli variance assay, learning and memory tests can be used to explore how well honey bees discriminate single odors within complex odor mixtures. Here we are validating two different odor mixtures, a Brassica rapa floral blend and a second replicate mixture composed of common molecularly dissimilar odors. Odors in each mixture are either held constant or varied in concentration over 16 conditioning trials. Subsequent memory tests are performed two hours later to observe the ability of bees to distinguish and recognize specific odor components in each mixture. So far in our assay we find high rates of generalization for both odor mixtures. In general, more bees responded to all odors in the replicate treatment group over the Brassica treatment group. Additionally, bees in the Brassica treatment group did not respond to the target odor. More data is being collected to validate this assay. In future studies, I propose to apply this behavioral assay to bees with an altered olfactory developmental in order to see the functional impacts of this chronic odor association treatment.
ContributorsHalby, Rachael (Author) / Smith, Brian (Thesis director) / Jernigan, Christopher (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Asperger's syndrome is a high-functioning subset of Autism Spectrum Disorders (ASD). Diagnosed patients often lack refined social skills but possess a normal level of cognitive skills without delay in language development. These deficient social skills can impact the ability to find and maintain a job, which can be burdensome for all individuals involved in the patient's life. Although the causes of this condition are largely unknown, a wide variety of social and cognitive therapies have been used to reduce symptom severity, one of which is Mindfulness-Based Stress Reduction (MBSR). Mindfulness is the act of being aware on purpose to whatever is being experienced in the present moment with non-judgment and receptivity. MBSR has been used to bring greater awareness to sensations, thoughts and emotions with the result being reduced reactivity and increased purposeful responsiveness. It is therefore the aim of this study to address the use of an 8-week Mindfulness-Based Stress Reduction in adolescents with clinical Asperger's Syndrome to reduce reactive tendencies. This study will utilize a randomized control group of waitlisted participants given MBSR informational material and a practicing MBSR group. Post-MBSR Parent Global Impressions-III (PGI-III) and Social Responsiveness Scale scores are hypothesized to be improved in MBSR group and unaffected in the control for behavioral markers with no change in core autistic symptoms. Daily average cortisol response is also expected to decrease in the experimental group with unaffected levels in the control.
ContributorsBrzezinski, Molly Alexandra (Author) / Smith, Brian (Thesis director) / Sebren, Ann (Committee member) / School of Music (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05