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As much as SARS-CoV-2 has altered the way humans live since the beginning of 2020,<br/>this virus's deadly nature has required clinical testing to meet 2020's demands of higher<br/>throughput, higher accuracy and higher efficiency. Information technology has allowed<br/>institutions, like Arizona State University (ASU), to make strategic and operational changes to<br/>combat the

As much as SARS-CoV-2 has altered the way humans live since the beginning of 2020,<br/>this virus's deadly nature has required clinical testing to meet 2020's demands of higher<br/>throughput, higher accuracy and higher efficiency. Information technology has allowed<br/>institutions, like Arizona State University (ASU), to make strategic and operational changes to<br/>combat the SARS-CoV-2 pandemic. At ASU, information technology was one of the six facets<br/>identified in the ongoing review of the ASU Biodesign Clinical Testing Laboratory (ABCTL)<br/>among business, communications, management/training, law, and clinical analysis. The first<br/>chapter of this manuscript covers the background of clinical laboratory automation and details<br/>the automated laboratory workflow to perform ABCTL’s COVID-19 diagnostic testing. The<br/>second chapter discusses the usability and efficiency of key information technology systems of<br/>the ABCTL. The third chapter explains the role of quality control and data management within<br/>ABCTL’s use of information technology. The fourth chapter highlights the importance of data<br/>modeling and 10 best practices when responding to future public health emergencies.

ContributorsKandan, Mani (Co-author) / Leung, Michael (Co-author) / Woo, Sabrina (Co-author) / Knox, Garrett (Co-author) / Compton, Carolyn (Thesis director) / Dudley, Sean (Committee member) / Computer Science and Engineering Program (Contributor) / Department of Information Systems (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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The purpose of this thesis study was to examine whether the "war on cancer" metaphor influences cancer perception and treatment decision. A total of 249 undergraduates (152 females) from a large southwestern university participated in an online survey experiment and were either randomly assigned to the control condition (N=123) or

The purpose of this thesis study was to examine whether the "war on cancer" metaphor influences cancer perception and treatment decision. A total of 249 undergraduates (152 females) from a large southwestern university participated in an online survey experiment and were either randomly assigned to the control condition (N=123) or to the war prime condition (N=126). Participants in the control condition did not receive the metaphor manipulation while participants in the war prime condition received the subtle "war on cancer" metaphor prime. After the prime was given, participants read a scenario, answered questions related to the situation, and responded to demographic questions. The results suggested that, compared to participants in the no-prime condition, participants exposed to the war metaphor were more likely to (a) view melanoma as an acute disease, (b) choose chemotherapy over molecular tests, and (c) prefer more aggressive treatment. These findings illustrated the unintended consequences of the "war on cancer" slogan. The results were encouraging and in the predicted direction, but the effect size was small. The discussion section described possible future directions for research.
ContributorsShangraw, Ann Mariah (Author) / Kwan, Virginia (Thesis director) / Neuberg, Steven (Committee member) / Cavanaugh Toft, Carolyn (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor)
Created2015-05
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In the past year, considerable misinformation about the COVID-19 pandemic has circulated on social media platforms. Faced with this pervasive issue, it is important to identify the extent to which people are able to spot misinformation on social media and ways to improve people’s accuracy in spotting misinformation. Therefore, the

In the past year, considerable misinformation about the COVID-19 pandemic has circulated on social media platforms. Faced with this pervasive issue, it is important to identify the extent to which people are able to spot misinformation on social media and ways to improve people’s accuracy in spotting misinformation. Therefore, the current study aims to investigate people’s accuracy in spotting misinformation, the effectiveness of a game-based intervention, and the role of political affiliation in spotting misinformation. In this study, 235 participants played a misinformation game in which they evaluated COVID-19-related tweets and indicated whether or not they thought each of the tweets contained misinformation. Misinformation accuracy was measured using game scores, which were based on the correct identification of misinformation. Findings revealed that participants’ beliefs about how accurate they are at spotting misinformation about COVID-19 did not predict their actual accuracy. Participants’ accuracy improved after playing the game, but democrats were more likely to improve than republicans.

ContributorsKang, Rachael (Author) / Kwan, Virginia (Thesis director) / Corbin, William (Committee member) / Cohen, Adam (Committee member) / Bunker, Cameron (Committee member) / Department of Psychology (Contributor) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description
Immunotherapy is an effective treatment for cancer which enables the patient's immune system to recognize tumor cells as pathogens. In order to design an individualized treatment, the t cell receptors (TCR) which bind to a tumor's unique antigens need to be determined. We created a convolutional neural network to predict

Immunotherapy is an effective treatment for cancer which enables the patient's immune system to recognize tumor cells as pathogens. In order to design an individualized treatment, the t cell receptors (TCR) which bind to a tumor's unique antigens need to be determined. We created a convolutional neural network to predict the binding affinity between a given TCR and antigen to enable this.
ContributorsCai, Michael Ray (Author) / Lee, Heewook (Thesis director) / Meuth, Ryan (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
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Cancer is the second leading cause of death in the United States. Cancer is a serious, complex disease which causes cells to grow uncontrollably, causing millions of deaths per year [1]. Cancer is usually caused by a combination of environmental variables and biological pathways. The pathways have a very robust

Cancer is the second leading cause of death in the United States. Cancer is a serious, complex disease which causes cells to grow uncontrollably, causing millions of deaths per year [1]. Cancer is usually caused by a combination of environmental variables and biological pathways. The pathways have a very robust structure normally, but are altered because of cancer, resulting in a loss of connectivity between pathways. In order detect these pathways, a PageRank-based method called Pathways of Topological Rank Analysis (PoTRA) was created, which measures the relative rankings of the genes in each pathway. Applying this algorithm will allow us to figure out what pathways differed significantly in areas with cancer and areas without cancer. This would allow scientists to focus on specific pathways in order to learn more about the cancer and find more effective ways to treat it. So far, analysis using PoTRA has been successfully conducted on hepatocellular carcinoma (HCC) and its subtypes, resulting in all significant pathways found being cancer-associated. Now, using the TCGA data stored in Google Cloud's BigQuery, we created a pipeline to apply PoTRA to other cancer data sets and see how well it cross-applies to other cancers. The results show that even though some modification may need to be made to adapt to other datasets, many significant pathways were found for both HCC and breast cancer.
ContributorsMahesh, Sunny Nishant (Author) / Valentin, Dinu (Thesis director) / Liu, Li (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Prostate cancer is the second most common kind of cancer in men. Fortunately, it has a 99% survival rate. To achieve such a survival rate, a variety of aggressive therapies are used to treat prostate cancers that are caught early. Androgen deprivation therapy (ADT) is a therapy that is given

Prostate cancer is the second most common kind of cancer in men. Fortunately, it has a 99% survival rate. To achieve such a survival rate, a variety of aggressive therapies are used to treat prostate cancers that are caught early. Androgen deprivation therapy (ADT) is a therapy that is given in cycles to patients. This study attempted to analyze what factors in a group of 79 patients caused them to stick with or discontinue the treatment. This was done using naïve Bayes classification, a machine-learning algorithm. The usage of this algorithm identified high testosterone as an indicator of a patient persevering with the treatment, but failed to produce statistically significant high rates of prediction.
ContributorsMillea, Timothy Michael (Author) / Kostelich, Eric (Thesis director) / Kuang, Yang (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
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The advent of big data analytics tools and frameworks has allowed for a plethora of new approaches to research and analysis, making data sets that were previously too large or complex more accessible and providing methods to collect, store, and investigate non-traditional data. These tools are starting to be applied

The advent of big data analytics tools and frameworks has allowed for a plethora of new approaches to research and analysis, making data sets that were previously too large or complex more accessible and providing methods to collect, store, and investigate non-traditional data. These tools are starting to be applied in more creative ways, and are being used to improve upon traditional computation methods through distributed computing. Statistical analysis of expression quantitative trait loci (eQTL) data has classically been performed using the open source tool PLINK - which runs on high performance computing (HPC) systems. However, progress has been made in running the statistical analysis in the ecosystem of the big data framework Hadoop, resulting in decreased run time, reduced storage footprint, reduced job micromanagement and increased data accessibility. Now that the data can be more readily manipulated, analyzed and accessed, there are opportunities to use the modularity and power of Hadoop to further process the data. This project focuses on adding a component to the data pipeline that will perform graph analysis on the data. This will provide more insight into the relation between various genetic differences in individuals with breast cancer, and the resulting variation - if any - in gene expression. Further, the investigation will look to see if there is anything to be garnered from a perspective shift; applying tools used in classical networking contexts (such as the Internet) to genetically derived networks.
ContributorsRandall, Jacob Christopher (Author) / Buetow, Kenneth (Thesis director) / Meuth, Ryan (Committee member) / Almalih, Sara (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description

Early stages of the COVID-19 pandemic introduced a change in communication norms in regard to well-being. People traversed through different forms of communication to adapt to policies and regulations that limited in-person interactions to prevent the spread of the COVID-19 virus. Social interactions have been found to be an innate

Early stages of the COVID-19 pandemic introduced a change in communication norms in regard to well-being. People traversed through different forms of communication to adapt to policies and regulations that limited in-person interactions to prevent the spread of the COVID-19 virus. Social interactions have been found to be an innate human need, important to one’s health and well-being. The study looked at the relationship between socializing and well-being during the state of the COVID-19 pandemic. Socializing variables consisted of remote and in-person socializing which in-person socializing was divided into two distinct categories. In-person socializing was divided into in-person safe socializing, indicating socializing that was safe from the risk of contracting the virus, and in-person unsafe socializing which indicates that socializing was at risk of contracting the virus. Additionally, the current study also investigated how age moderates this relationship between socializing and well-being. SEM analyses reported that in-person unsafe socializing has a significant positive association with well-being outcomes: anxiety and depression which indicate high levels of anxiety and depression with increased in-person unsafe socializing. The study also found remote socializing to have a significant positive association with the well-being outcome: positive affect, indicating increased levels of positive affect with increased remote socializing. Regression analyses looked at moderation by age, finding no significant interactions of age between socializing and well-being. Findings suggest the beneficial role of remote socializing and although remote socializing cannot replace in-person interactions, it serves as a supplemental resource during unpredictable events such as the COVID-19 pandemic.

ContributorsDecena, Sommer (Author) / Shiota, Michelle (Thesis director) / Doane, Leah (Committee member) / Kwan, Virginia (Committee member) / Barrett, The Honors College (Contributor) / Department of Psychology (Contributor)
Created2023-05
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Description
Increasing misinformation in social media channels has become more prevalent since the beginning of the COVID-19 pandemic as countless myths and rumors have circulated over the internet. This misinformation has potentially lethal consequences as many people make important health decisions based on what they read online, thus creating an urgent

Increasing misinformation in social media channels has become more prevalent since the beginning of the COVID-19 pandemic as countless myths and rumors have circulated over the internet. This misinformation has potentially lethal consequences as many people make important health decisions based on what they read online, thus creating an urgent need to combat it. Although many Natural Language Processing (NLP) techniques have been used to identify misinformation in text, prompt-based methods are under-studied for this task. This work explores prompt learning to classify COVID-19 related misinformation. To this extent, I analyze the effectiveness of this proposed approach on four datasets. Experimental results show that prompt-based classification achieves on average ~13% and ~6% improvement compared to a single-task and multi-task model, respectively. Moreover, analysis shows that prompt-based models can achieve competitive results compared to baselines in a few-shot learning scenario.
ContributorsBrown, Clinton (Author) / Baral, Chitta (Thesis director) / Walker, Shawn (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / Computer Science and Engineering Program (Contributor)
Created2022-05
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Description

Molecular pathology makes use of estimates of tumor content (tumor percentage) for pre-analytic and analytic purposes, such as molecular oncology testing, massive parallel sequencing, or next-generation sequencing (NGS), assessment of sample acceptability, accurate quantitation of variants, assessment of copy number changes (among other applications), determination of specimen viability for testing

Molecular pathology makes use of estimates of tumor content (tumor percentage) for pre-analytic and analytic purposes, such as molecular oncology testing, massive parallel sequencing, or next-generation sequencing (NGS), assessment of sample acceptability, accurate quantitation of variants, assessment of copy number changes (among other applications), determination of specimen viability for testing (since many assays require a minimum tumor content to report variants at the limit of detection) may all be improved with more accurate and reproducible estimates of tumor content. Currently, tumor percentages of samples submitted for molecular testing are estimated by visual examination of Hematoxylin and Eosin (H&E) stained tissue slides under the microscope by pathologists. These estimations can be automated, expedited, and rendered more accurate by applying machine learning methods on digital whole slide images (WSI).

ContributorsCirelli, Claire (Author) / Yang, Yezhou (Thesis director) / Yalim, Jason (Committee member) / Velu, Priya (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2022-05