Matching Items (140)
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
When viewing vitamins and minerals, it is seen that they are essential for human life and vital for pregnancy. When paired with a healthy diet, prenatal supplements can allow for a healthy pregnancy and reduced maternal and infant health problems. Within this thesis, I was able to break down each vitamin and mineral necessary for a healthy pregnancy and birth. Further, I had the opportunity to dive into the addition of Omega-3 Fatty Acid during pregnancy to add more evidence to the study.
ContributorsSaad, Sophia Saad (Author) / Adams, James (Thesis director) / Haiwei, Gu (Committee member) / Coleman, Devon (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
Description
Introduction: The Eye to Eye mentorship program is a national program in which college or high school students with learning differences mentor middle school students with learning differences. There are 68 Eye to Eye programs around the country, but little research has been done on their effectiveness and how to improve it. We conducted and evaluated one program site at Arizona State University and implemented this mentorship program for the first time during 2019. We hypothesized the Eye to Eye mentorship program that paired college students who have learning differences with middle school students who have similar learning differences would improve the outcomes and socio-behavior skills of both mentors and mentees.
Methods: The Eye to Eye mentorship program assessed involved mentors and mentees who completed 12 in-person art sessions out of the normal 20 in-person sessions. The first main assessment was the BLD (Breger Learning Difference) Feedback Survey addressing one’s experience in the Eye to Eye program and which were completed at the end of the mentorship program and filled out by mentors, mentees, and mentees parents (one parent for each mentee). A total of 12 mentors, 6 mentees, and 6 mentee parents were included in the feedback survey final analysis. The second main assessments were the pre and post Behavior Assessment System for Child, Third Edition (BASC-3) provided to mentors, mentees, and mentees parents (one parent for each mentee). A total of 10 mentors, 5 mentees, and 5 mentee parents were included in pre and post BASC-3 final analysis. Fall 2019 (pre) and Spring 2020 (post) optional interviews involved 5 mentors and 3 mentees who showed interest and were comfortable participating with additional release forms.
Results: The program was generally positively rated in the feedback survey by mentors, mentees, and mentee parents. The highest responses for mentors, mentees, and mentee parents all incorporated average ratings of 4.0 or higher (out of 5.0) for perceived understanding of socio-emotional skills after Eye to Eye, experience in Eye to Eye, how having a mentor or mentee made them feel, and perceived change in self-awareness. All three groups reported fairly high ratings of improved self-awareness of 4.0/5.0 or above. No negative ratings were provided by any participants and the lowest response was no change. The BASC-3 evaluation found statistically significant improvement in mentors’ anxiety and atypicality and mentees’ sense of inadequacy.
Discussion: The Eye to Eye program was popular and well-rated despite only involving 12 in- person one-hour art sessions. The mentors, mentees, and mentee parents felt positive about the Eye to Eye program when answering the feedback survey. Some suggestions are made on how to improve this program to better enhance someone with learning differences future ability to succeed. Future research is needed to assess the true impact due to the COVID-19 epidemic and other limitations.
Methods: The Eye to Eye mentorship program assessed involved mentors and mentees who completed 12 in-person art sessions out of the normal 20 in-person sessions. The first main assessment was the BLD (Breger Learning Difference) Feedback Survey addressing one’s experience in the Eye to Eye program and which were completed at the end of the mentorship program and filled out by mentors, mentees, and mentees parents (one parent for each mentee). A total of 12 mentors, 6 mentees, and 6 mentee parents were included in the feedback survey final analysis. The second main assessments were the pre and post Behavior Assessment System for Child, Third Edition (BASC-3) provided to mentors, mentees, and mentees parents (one parent for each mentee). A total of 10 mentors, 5 mentees, and 5 mentee parents were included in pre and post BASC-3 final analysis. Fall 2019 (pre) and Spring 2020 (post) optional interviews involved 5 mentors and 3 mentees who showed interest and were comfortable participating with additional release forms.
Results: The program was generally positively rated in the feedback survey by mentors, mentees, and mentee parents. The highest responses for mentors, mentees, and mentee parents all incorporated average ratings of 4.0 or higher (out of 5.0) for perceived understanding of socio-emotional skills after Eye to Eye, experience in Eye to Eye, how having a mentor or mentee made them feel, and perceived change in self-awareness. All three groups reported fairly high ratings of improved self-awareness of 4.0/5.0 or above. No negative ratings were provided by any participants and the lowest response was no change. The BASC-3 evaluation found statistically significant improvement in mentors’ anxiety and atypicality and mentees’ sense of inadequacy.
Discussion: The Eye to Eye program was popular and well-rated despite only involving 12 in- person one-hour art sessions. The mentors, mentees, and mentee parents felt positive about the Eye to Eye program when answering the feedback survey. Some suggestions are made on how to improve this program to better enhance someone with learning differences future ability to succeed. Future research is needed to assess the true impact due to the COVID-19 epidemic and other limitations.
ContributorsBreger, Chloe Levana (Author) / Adams, James (Thesis director) / Harris, Pamela (Committee member) / School of Criminology and Criminal Justice (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Spaceflight and spaceflight analogue culture enhance the virulence and pathogenesis-related stress resistance of the foodborne pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium). This is an alarming finding as it suggests that astronauts may have an increased risk of infection during spaceflight. This risk is further exacerbated as multiple studies indicate that spaceflight negatively impacts aspects of the immune system. In order to ensure astronaut safety during long term missions, it is important to study the phenotypic effects of the microgravity environment on a range of medically important microbial pathogens that might be encountered by the crew. This ground-based study uses the NASA-engineered Rotating Wall Vessel (RWV) bioreactor as a spaceflight analogue culture system to grow bacteria under low fluid shear forces relative to those encountered in microgravity, and interestingly, in the intestinal tract during infection. The culture environment in the RWV is commonly referred to as low shear modeled microgravity (LSMMG). In this study, we characterized the stationary phase stress response of the enteric pathogen, Salmonella enterica serovar Enteritidis (S. Enteritidis), to LSMMG culture. We showed that LSMMG enhanced the resistance of stationary phase cultures of S. Enteritidis to acid and thermal stressors, which differed from the LSSMG stationary phase response of the closely related pathovar, S. Typhimurium. Interestingly, LSMMG increased the ability of both S. Enteritidis and S. Typhimurium to adhere to, invade into, and survive within an in vitro 3-D intestinal co-culture model containing immune cells. Our results indicate that LSMMG regulates pathogenesis-related characteristics of S. Enteritidis in ways that may present an increased health risk to astronauts during spaceflight missions.
ContributorsKoroli, Sara (Author) / Nickerson, Cheryl (Thesis director) / Barrila, Jennifer (Committee member) / Ott, C. Mark (Committee member) / School of Life Sciences (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
The International Space Station (ISS) utilizes recycled water for consumption, cleaning and air humidity control. The Environmental Control and Life Support Systems (ECLSS) have been rigorously tested at the NASA Johnson Space Center. Despite the advanced engineering of the water recovery system, bacterial biofilms have been recovered from this potable water source. Microbial contamination of potable water poses a potential threat to crew members onboard the ISS. Because astronauts have been found to have compromised immune systems, bacterial strains that would not typically be considered a danger must be carefully studied to better understand the mechanisms enabling their survival, including polymicrobial interactions. The need for a more thorough understanding of the effect of spaceflight environment on polymicrobial interactions and potential impact on crew health and vehicle integrity is heightened since 1) several potential pathogens have been isolated from the ISS potable water system, 2) spaceflight has been shown to induce unexpected alterations in microbial responses, and 3) emergent phenotypes are often observed when multiple bacterial species are co- cultured together, as compared to pure cultures of single species. In order to address these concerns, suitable growth media are required that will not only support the isolation of these microbes but also the ability to distinguish between them when grown as mixed cultures. In this study, selective and/or differential media were developed for bacterial isolates collected from the ISS potable water supply. In addition to facilitating discrimination between bacteria, the ideal media for each strain was intended to have a 100% recovery rate compared to traditional R2A media. Antibiotic and reagent susceptibility and resistance tests were conducted for the purpose of developing each individual medium. To study a wide range of targets, 12 antibiotics were selected from seven major classes, including penicillin, cephalosporins, fluoroquinolones, aminoglycosides, glycopeptides/lipoglycopeptides, macrolides/lincosamides/streptogramins, tetracyclines, in addition to seven unclassified antibiotics and three reagents. Once developed, medium efficacy was determined by means of growth curve experiments. The development of these media is a critical step for further research into the mechanisms utilized by these strains to survive the harsh conditions of the ISS water system. Furthermore, with an understanding of the complex nature of these polymicrobial communities, specific contamination targeting and control can be conducted to reduce the risk to crew members. Understanding these microbial species and their susceptibilities has potential application for future NASA human explorations, including those to Mars.
ContributorsKing, Olivia Grace (Author) / Nickerson, Cheryl (Thesis director) / Barrila, Jennifer (Committee member) / Ott, Mark (Committee member) / School of Sustainability (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
Graphene has the ability to advance many common fields, including: membranes, composites and coatings, energy, and electronics. For membranes, graphene will be used as a filter for desalination plants which will reduce the cost of desalination and greatly increase water security in developing countries. For composites and coatings, graphene's strength, flexibility, and lightweight will be instrumental in producing the next generation of athletic wear and sports equipment. Graphene's use in energy comes from its theorized ability to charge a phone battery in seconds or an electric car in minutes. Finally, for electronics, graphene will be used to create faster transistors, flexible electronics, and fully integrated wearable technology.
ContributorsSiegel, Adam (Author) / Adams, James (Thesis director) / Krause, Stephen (Committee member) / Materials Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
This is a two-part thesis, completed in conjunction with my Materials Science and Engineering Capstone Project. The first part involves the design and testing of cold-extruded high-density polyethylene for student oboe reeds. The goal of this section was to create a longer-lasting reed that produces a similar sound to a cane reed, has less variation in quality, and costs less per year than cane reeds. For low-income students in particular, the cost of purchasing cane oboe reeds ($500-$2,000 per year) is simply not feasible. This project was designed to allow oboe to be a more affordable option for all students. Money should not be a factor that limits whether or a not a child is able to explore their interests. The process used to create the synthetic reed prototype involves cold-extrusion of high-density polyethylene in order to induce orientation in the polymer to replicate the uniaxial orientation of fibrous cane. After successful cold-extrusion of a high-density polyethylene (HDPE) cylinder, the sample was made into a reed by following standard reedmaking procedures. Then, the HDPE reed and a cane reed were quantitatively tested for various qualities, including flexural modulus, hardness, and free vibration frequency. The results from the design project are promising and show a successful proof of concept. The first prototype of an oriented HDPE reed demonstrates characteristics of a cane reed. The areas that need the most improvement are the flexural modulus and the stability of the higher overtones, but these areas can be improved with further development of the cold-extrusion process. The second part of this thesis is a survey and analysis focusing on the qualitative comparison of synthetic and cane oboe reeds. The study can be used in the future to refine the design of synthetic reeds, more specifically the cold-extruded high-density polyethylene student oboe reed I designed, to best replicate a cane reed. Rather than approaching this study from a purely engineering mindset, I brought in my own experience as an oboist. Therefore, the opinions of oboists who have a wide range of experience are considered in the survey. A panel of five oboists participated in the survey. They provided their opinion on various aspects of the five reeds, including vibrancy, response, stability, resistance, tone, and overall quality. Each of these metrics are rated on a scale from one to five, from unacceptable to performance quality. According to the survey, a participant's personal, hand-made cane reed is overall the most preferred option. My prototype HDPE student reed must be improved in many areas in order to rank near the other four reeds. However, its vibrancy and resistance already rival that of a Jones student reed. As this is just the first prototype, that is a significant accomplishment. With further refinement of the cold-extrusion and reedmaking method, the other areas of the HDPE reed may be improved, and the reed may eventually compete with the existing synthetic and cane reeds on the market.
ContributorsMitchell, Alexis Jacqueline (Author) / Adams, James (Thesis director) / Schuring, Martin (Committee member) / School of Music (Contributor) / Materials Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The gastrointestinal (GI) tract is home to a complex and diverse microbial ecosystem that contributes to health or disease in many aspects. While bacterial species are the majority in the GI tract, their cohabitants, fungal species, should not be forgotten. Children with autism spectrum disorder (ASD) often suffer from GI disorders and associated symptoms, implying a role the bacterial and fungal gut microbiota play in maintaining human health. The irregularities in GI symptoms can negatively affect the overall quality of life or even worsen behavioral symptoms the children present. Even with the increase in the availability of next-generation sequencing technologies, the composition and diversities of fungal microbiotas are understudied, especially in the context of ASD. We therefore aimed to investigate the gut mycobiota of 36 neurotypical children and 38 children with ASD. We obtained stool samples from all participants, as well as autism severity and GI symptom scores to help us understand the effect the mycobiome has on these symptoms. By targeting the fungal internal transcribed spacer (ITS) and bacterial 16S rRNA V4 regions, we obtained fungal and bacterial amplicon sequences, from which we investigated the diversities, composition, and potential link between two different ecological clades. From fungal amplicon sequencing results, we observed a significant decrease in the observed fungal OTUs in children with ASD, implying a lack of potentially beneficial fungi in ASD subjects. We performed Bray-Curtis principal coordinates analysis and observed significant differences in fungal microbiota composition between the two groups. Taxonomic analysis showed higher relative abundances of Candida , Pichia, Penicillium , and Exophiala in ASD subjects, yet due to a large dispersion of data, the differences were not statistically significant. Interestingly, we observed a bimodal distribution of Candida abundances within children with ASD. Candida's relative abundance was not significantly correlated with GI scores, but children with high Candida relative abundances presented significantly higher Autism Treatment Evaluation Checklist (ATEC) scores, suggesting a role of Candida on ASD behavioral symptoms. Regarding the bacterial gut microbiota, we found marginally lower observed OTUs and significantly lower relative abundance of Prevotella in the ASD group, which was consistent with previous studies. Taken together, we demonstrated that autism is closely linked with a distinct gut mycobiota, characterized by a loss of fungal and bacterial diversity and an altered fungal and bacterial composition.
ContributorsPatel, Jigar (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Kang, Dae Wook (Committee member) / Adams, James (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
As the prevalence and awareness of Autism Spectrum Disorder (ASD) increases, so does the variety of treatment options for primary symptoms (social interaction, communication, behavior) and secondary symptoms (anxiety, hyperactivity, GI problems, and insomnia). Various treatments, from Adderall to Citalopram to Flax Seed Oil promise relief for these symptoms. However, very little research has actually been done on some of these treatments. Additionally, the research that has been done fails to compare these treatments against one another in terms of symptom relief. The Autism Treatment Effectiveness Survey, written by Dr. James Adams, director of the Autism/Asperger's Research Program at ASU, and graduate student/program coordinator Devon Coleman, aims to fill this gap. The survey numerically rates medications based on benefit and adverse effects, in addition to naming specific symptoms that are impacted by the treatments. However, the survey itself was retrospective in nature and requires further evidence to support its claims. Therefore, the purpose of this research paper is to evaluate evidence related to the results of the survey. After the performing an extensive literature review of over 70 different treatments, it appears that the findings of the Autism Treatment Effectiveness Survey are generally well supported. There were a few minor discrepancies regarding the primary benefitted symptom, but there was not enough of a conflict to discount the information from the survey. As research is still ongoing, conclusions cannot yet be drawn for Nutritional Supplements, although the current data looks promising.
ContributorsAnderson, Amy Lynn (Author) / Adams, James (Thesis director) / Coleman, Devon (Committee member) / School of Nutrition and Health Promotion (Contributor) / W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Vitamins and minerals are, by definition, essential substances that are necessary for good health, and needed by every cell and organ to function appropriately. A deficiency of any one vitamin or mineral can be very serious. Although a very healthy diet rich in vegetables, fruits, and protein can provide sufficient amounts of most vitamins and minerals, many people do not consume an adequate diet. During pregnancy, there is an increased need for vitamins and minerals to promote a healthy pregnancy and a healthy baby. Prenatal supplements are intended to supplement a normal diet to ensure that adequate amounts of vitamins and minerals are consumed. The US Food and Drug Administration (FDA) has established Recommended Dietary Allowances for total vitamin/mineral intake from food and supplements, but they have not established recommendations for prenatal supplements. Therefore, there is a very wide variation in the content and quality of prenatal supplements. Many prenatal supplements contain only minimal levels of some vitamins and few or no minerals, in order to minimize cost and the number of pills. This results in insufficient vitamin/mineral supplementation for many women, and hence does not fully protect them or their children from pregnancy complications and health problems. Therefore, we have created our own set of recommendations for prenatal supplements. Our recommendations are based primarily on four sources: 1) FDA's Recommended Daily Allowances for pregnant women, which are estimated to meet the needs of 97.5% of healthy pregnant women. 2) FDA's Tolerable Upper Limit, which is the maximum amount of vitamins/minerals that can be safely consumed without any risk of health problems. 3) National Health and Nutrition Examination Survey (NHANES), which evaluates the average intake of vitamins and minerals by women ages 20-40 years in the US 4) Research studies on vitamin/mineral deficiencies or vitamin/mineral supplementation during pregnancy, and the effect on pregnancy, birth, and child health problems. In summary, the RDA establishes minimum recommended levels of vitamin/mineral intake from all sources, and the NHANES establishes the average intake from foods. The difference is what needs to be consumed in a supplement, on average. However, since people vary greatly in the quality of their diet, and since most vitamins and minerals have a high Tolerable Upper Limit, we generally recommend more than the difference between the RDA and the average NHANES. Vitamins generally have a larger Tolerable Upper Limit than do minerals. So, we recommend that prenatal vitamin/mineral supplements contain 100% of the RDA for most vitamins, and about 50% of the RDA for most minerals. However, based on additional research studies described below, in some cases we vary our recommendations from those averages.
ContributorsSorenson, Jacob (Author) / Adams, James (Thesis director) / Pollard, Elena (Committee member) / College of Integrative Sciences and Arts (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05