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Systematic Reviews (SRs) aim to synthesize the totality of evidence for clinical practice and are important in making clinical practice guidelines and health policy decisions. However, conducting SRs manually is a laborious and time-consuming process. This challenge is growing due to the increase in the number of databases to search

Systematic Reviews (SRs) aim to synthesize the totality of evidence for clinical practice and are important in making clinical practice guidelines and health policy decisions. However, conducting SRs manually is a laborious and time-consuming process. This challenge is growing due to the increase in the number of databases to search and the papers being published. Hence, the automation of SRs is an essential task. The goal of this thesis work is to develop Natural Language Processing (NLP)-based classifiers to automate the title and abstract-based screening for clinical SRs based on inclusion/exclusion criteria. In clinical SRs, a high-sensitivity system is a key requirement. Most existing methods for SRs use binary classification systems trained on labeled data to predict inclusion/exclusion. While previous studies have shown that NLP-based classification methods can automate title and abstract-based screening for SRs, methods for achieving high-sensitivity have not been empirically studied. In addition, the training strategy for binary classification has several limitations: (1) it ignores the inclusion/exclusion criteria, (2) lacks generalization ability, (3) suffers from low resource data, and (4) fails to achieve reasonable precision at high-sensitivity levels. This thesis work presents contributions to several aspects of the clinical systematic review domain. First, it presents an empirical study of NLP-based supervised text classification and high-sensitivity methods on datasets developed from six different SRs in the clinical domain. Second, this thesis work provides a novel approach to view SR as a Question Answering (QA) problem in order to overcome the limitations of the binary classification training strategy; and propose a more general abstract screening model for different SRs. Finally, this work provides a new QA-based dataset for six different SRs which is made available to the community.
ContributorsParmar, Mihir Prafullsinh (Author) / Baral, Chitta (Thesis advisor) / Devarakonda, Murthy (Thesis advisor) / Riaz, Irbaz B (Committee member) / Arizona State University (Publisher)
Created2021
Description

This study highlights the significance of zoonotic diseases, which make up almost 60% of infectious diseases in humans, and their origin from animals. Among mammalian viruses, primates, bats, and rodents have been identified as high-risk carriers. Within the rodent family Cricetidae, the species complex of Peromyscus eremicus, Peromyscus californicus, Peromyscus

This study highlights the significance of zoonotic diseases, which make up almost 60% of infectious diseases in humans, and their origin from animals. Among mammalian viruses, primates, bats, and rodents have been identified as high-risk carriers. Within the rodent family Cricetidae, the species complex of Peromyscus eremicus, Peromyscus californicus, Peromyscus fraterculus, and Osgoodomys banderanus have been found to play a crucial role in disease transmission. These four species are phylogenetically related and share similar physical appearances and ecological niches. They have been identified as carriers of several zoonotic diseases, including Hantavirus, Arenavirus, Yersinia pestis, and Flavivirus, with a history of spread to humans. Despite their implications for public health, many of these species remain understudied. Thus, this study aims to provide a systematic review of the existing literature on these four species to summarize the findings on virus prevalence and distribution. The review shows that sampling efforts have been uneven and recent efforts have been lacking, with potential undiscovered zoonotic diseases. The concentration of sampling efforts in California and gaps in the literature are concerning, especially with changing agriculture and climate change potentially affecting rodent communities.

ContributorsTariq, Muhamamad (Author) / Sterner, Beckett (Thesis director) / Upham, Nate (Committee member) / Barrett, The Honors College (Contributor) / Dean, W.P. Carey School of Business (Contributor) / School of Life Sciences (Contributor)
Created2023-05
Description

This thesis presents a systematic review of viruses found in the Peromyscus leucopus rodent species in North America. Various viruses cause serious illness in humans through contact with infected rodent urine, droppings, or saliva, or inhalation of dust contaminated with the virus, with Hantavirus pulmonary syndrome (HPS) being the most

This thesis presents a systematic review of viruses found in the Peromyscus leucopus rodent species in North America. Various viruses cause serious illness in humans through contact with infected rodent urine, droppings, or saliva, or inhalation of dust contaminated with the virus, with Hantavirus pulmonary syndrome (HPS) being the most severe manifestation. Therefore, studying their distribution in rodent populations can inform public health interventions to reduce the risk of transmission. Through a literature review and data analysis, this study found that studying the distribution of viruses in rodents can help identify areas where humans may be at higher risk of contracting the virus, inform public health interventions to reduce the risk of HPS transmissions, and better understand the ecology of the virus and its host species, which can, in turn, inform conservation efforts. Furthermore, monitoring the spread of viruses over time and across regions can help us better understand their epidemiology and potential for future outbreaks, which can inform surveillance and response efforts to mitigate the impact of the virus on human and animal health. Overall, this study highlights the importance of interdisciplinary approaches in addressing complex public health and conservation issues and underscores the need for continued research in this area.

ContributorsJain, Tanishq (Author) / Sterner, Beckett (Thesis director) / Upham, Nathan (Committee member) / Barrett, The Honors College (Contributor) / School of Sustainability (Contributor) / School of Life Sciences (Contributor)
Created2023-05