Matching Items (17)
Description
Translating research has been a goal of the Department of Health and Human Services since 1999. Through two years of iteration and interview with our community members, we have collected insights into the barriers to accomplishing this goal. Liberating Science is a think-tank of researchers and scientists who seek to create a more transparent process to accelerate innovation starting with behavioral health research.
ContributorsRaghani, Pooja Sioux (Author) / Hekler, Eric (Thesis director) / Buman, Matthew (Committee member) / Pruthi, Virgilia Kaur (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Biomedical Informatics Program (Contributor)
Created2014-05
Description
Methane (CH4) is very important in the environment as it is a greenhouse gas and important for the degradation of organic matter. During the last 200 years the atmospheric concentration of CH4 has tripled. Methanogens are methane-producing microbes from the Archaea domain that complete the final step in breaking down organic matter to generate methane through a process called methanogenesis. They contribute to about 74% of the CH4 present on the Earth's atmosphere, producing 1 billion tons of methane annually. The purpose of this work is to generate a preliminary metabolic reconstruction model of two methanogens: Methanoregula boonei 6A8 and Methanosphaerula palustris E1-9c. M. boonei and M. palustris are part of the Methanomicrobiales order and perform hydrogenotrophic methanogenesis, which means that they reduce CO2 to CH4 by using H2 as their major electron donor. Metabolic models are frameworks for understanding a cell as a system and they provide the means to assess the changes in gene regulation in response in various environmental and physiological constraints. The Pathway-Tools software v16 was used to generate these draft models. The models were manually curated using literature searches, the KEGG database and homology methods with the Methanosarcina acetivorans strain, the closest methanogen strain with a nearly complete metabolic reconstruction. These preliminary models attempt to complete the pathways required for amino acid biosynthesis, methanogenesis, and major cofactors related to methanogenesis. The M. boonei reconstruction currently includes 99 pathways and has 82% of its reactions completed, while the M. palustris reconstruction includes 102 pathways and has 89% of its reactions completed.
ContributorsMahendra, Divya (Author) / Cadillo-Quiroz, Hinsby (Thesis director) / Wang, Xuan (Committee member) / Stout, Valerie (Committee member) / Barrett, The Honors College (Contributor) / Computing and Informatics Program (Contributor) / School of Life Sciences (Contributor) / Biomedical Informatics Program (Contributor)
Created2014-05
Description
This study focused on the connection between the EnvZ/OmpR two-component regulatory system and the iron homeostasis system in Escherichia coli, specifically how a mutant form of EnvZ11/OmpR is able to reduce the expression of fepA::lacZ, a reporter gene fusion in E. coli. FepA is one of several outer membrane siderophore receptors that allow extracellular siderophores bound to iron to enter the cells to power various biological processes. Previous studies have shown that in E. coli cells that expressed a mutant allele of envZ, called envZ11, which led to altered expression of various iron genes including down regulation of fepA::lacZ. The wild type EnvZ/OmpR system is not considered to regulate iron genes, but because these envz11 strains had downregulated fepA::lacZ, this study was undertaken to understand the connection and mechanisms of this downregulation. A large number of Lac+ revertants were obtained from the B32-2483 strain (envz11 and fepA::lacZ) and 7 Lac+ revertants that had reversion mutations not directly correcting the envZ11 allele were further characterized. With P1 phage transduction genetic mapping that involved moving a kanamycin resistance marker linked to fepA::lacZ, two Lac+ revertants were found to have their reversion mutations in the fepA promoter region, while the other five revertants had their mutations mapping outside the fepA region. These two revertants underwent DNA sequencing and found to carry two different single base pair mutations in two different locations of the fepA promoter region. Each one is in the Fur repressor binding region, but one also may have affected the Shine-Dalgarno region involved in translation initiation. All 7 reveratants underwent beta-galactosidase assays to measure fepA::lacZ expression. The two revertants that had mutations in the fepA promoter region had significantly increased fepA activity, with the revertant with the Shine-Dalgarno mutation having the most elevated fepA expression. The other 5 revertants that did not map in the fepA region had fepA expression elevated to the same level as that found in the wild type EnvZ/OmpR background. The data suggest that the negative effect of envZ11 can be overcome by multiple mechanisms, including directly correcting the envZ11 allele or changing the fepA promoter region.
ContributorsKalinkin, Victor Arkady (Co-author) / Misra, Rajeev (Co-author, Thesis director) / Mason, Hugh (Committee member) / Foy, Joseph (Committee member) / Biomedical Informatics Program (Contributor) / School of Life Sciences (Contributor) / W. P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Medical students acquire and enhance their clinical skills using various available techniques and resources. As the health care profession has move towards team-based practice, students and trainees need to practice team-based procedures that involve timely management of clinical tasks and adequate communication with other members of the team. Such team-based procedures include surgical and clinical procedures, some of which are protocol-driven. Cost and time required for individual team-based training sessions, along with other factors, contribute to making the training complex and challenging. A great deal of research has been done on medically-focused collaborative virtual reality (VR)-based training for protocol-driven procedures as a cost-effective as well as time-efficient solution. Most VR-based simulators focus on training of individual personnel. The ones which focus on providing team training provide an interactive simulation for only a few scenarios in a collaborative virtual environment (CVE). These simulators are suited for didactic training for cognitive skills development. The training sessions in the simulators require the physical presence of mentors. The problem with this kind of system is that the mentor must be present at the training location (either physically or virtually) to evaluate the performance of the team (or an individual). Another issue is that there is no efficient methodology that exists to provide feedback to the trainees during the training session itself (formative feedback). Furthermore, they lack the ability to provide training in acquisition or improvement of psychomotor skills for the tasks that require force or touch feedback such as cardiopulmonary resuscitation (CPR). To find a potential solution to overcome some of these concerns, a novel training system was designed and developed that utilizes the integration of sensors into a CVE for time-critical medical procedures. The system allows the participants to simultaneously access the CVE and receive training from geographically diverse locations. The system is also able to provide real-time feedback and is also able to store important data during each training/testing session. Finally, this study also presents a generalizable collaborative team-training system that can be used across various team-based procedures in medical as well as non-medical domains.
ContributorsKhanal, Prabal (Author) / Greenes, Robert (Thesis advisor) / Patel, Vimla (Thesis advisor) / Smith, Marshall (Committee member) / Gupta, Ashish (Committee member) / Kaufman, David (Committee member) / Arizona State University (Publisher)
Created2014
Description
Glioblastoma (GBM) is an extremely malignant form of brain cancer characterized by rapid progression and poor patient survival. Even after standard of care treatments, less than ten percent of patients with this disease survive five years. More effective therapeutic options are urgently needed to improve outcomes for patients with GBM. Adequate drug delivery is a critical challenge in GBM treatment, as drugs delivered systemically must be able to penetrate the blood brain barrier (BBB) and reach the tumor at therapeutic levels. To address this, we developed a resource to catalog BBB penetration information for investigational agents currently in clinical trials in cancer. Using an in silico prediction model and manual annotation to capture existing knowledge from the published literature, BBB content for ~500 investigational drugs was added to the investigational database tool. In addition to BBB content, the database also includes information on the gene targets of the included therapies. The investigational database tool was used to identify investigational agents that (1) may have increased activity against GBM based on the presence of a specific mutation in the tumor sample and (2) have evidence suggesting the compounds may penetrate the BBB. By prioritizing investigational agents for further study based on evidence for BBB penetration, this resource can help the GBM research community pursue more effective treatments for GBM.
ContributorsHerring, Emily Lora (Author) / Coursen, Jerry (Thesis director) / Byron, Sara (Committee member) / Biomedical Informatics Program (Contributor) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Concept maps are teaching tools used to encourage students to utilize active learning strategies and to take responsibility for their own learning. The purpose of this two-semester study is to evaluate the use of concept maps in a junior-level Biomaterials classroom. The maps are assessed based on students' attitude, achievement, and persistence. No significant correlation was determined between concept map score and achievement (correlation coefficient = 0.1739 in the first semester, 0.2208 in the first set of the second semester, and 0.0829 in the second set of the second semester), though further studies should be completed to support the effects of concept mapping. Statistically significant increases in student attitude regarding concept mapping cost, interest, and utility between the two semesters were found (p = 0.013, p = 0.105, p = 0.002, p = 0.083 overall). Persistence was moderately high throughout the entire study (98% in the first semester and 100% in the second semester).
ContributorsHolm, Mikayle Ashlyn (Author) / Ankeny, Casey (Thesis director) / Graham, Kaely (Committee member) / Harrington Bioengineering Program (Contributor) / Biomedical Informatics Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Usability problems associated with electronic health records can adversely impact clinical workflow, leading to inefficiencies, error, and even clinician burnout. The work presented in this dissertation is concerned with understanding and improving clinical workflow. Towards that end, it is necessary to model physical and cognitive aspects of task performance in clinical settings. Task completion can be significantly impacted by the navigational efficiency of the electronic health record (EHR) interface. Workflow modeling of the EHR-mediated workflow could help identify, diagnose and eliminate problems to reduce navigational complexity. The research goal is to introduce and validate a new biomedical informatics methodological workflow analysis framework that combines expert-based and user-based techniques to guide effective EHR design and reduce navigational complexity. These techniques are combined into a modified walkthrough that aligns user goals and subgoals with estimated task completion time and characterization of cognitive demands. A two-phased validation of the framework is utilized. The first is applied to single EHR-mediated workflow tasks, medication reconciliation (MedRec), and medication administration records (MAR) to refine individual aspects of the framework. The second phase applied the framework to a pre/post EHR implementation comparative analysis of multiple workflows tasks. This validation provides evidence of the framework's applicability and feasibility across several sites, systems, and settings. Analysis of the steps executed within the interfaces involved to complete the medication administration and medication reconciliation and patient order management tasks have provided a basis for characterizing the complexities in EHR navigation. An implication of the work presented here is that small tractable changes in interface design may substantially improve EHR navigation, overall usability, and workflow. The navigational complexity framework enables scrutinizing the impact of different EHR interfaces on task performance and usability barriers across different sites, systems, and settings.
ContributorsDuncan, Benjamin (Author) / Grando, Adela (Thesis advisor) / Doebbeling, Bradley (Thesis advisor) / Kaufman, David (Committee member) / Greenes, Robert (Committee member) / Arizona State University (Publisher)
Created2021
Description
Perioperative care has a direct and crucial impact on patient safety and patient outcomes, as well as the financial viability of the healthcare facility. The time pressure and workload of caring patients facing surgery are heavier than caring inpatients of other departments. This workload raises requirements for PreOp nurses, the primary PreOp caregiver, to complete information gathering, screening, and verification tasks accurately and efficiently. EHRs (Electronic Health Record System) have evolved continuously with increasing features to meet newly raised needs and expectations. Many healthcare institutions have undergone EHR conversion since the introduction of first-generation EHRs. Thus, the need for a systematic evaluation of changed information system workflow following conversion is becoming more and more manifest. There are a growing number of methods for analyzing health information technology use. However, few studies provide and apply a standard method to understand the impact of EHR transition and inspire opportunities for improvement.
This dissertation focuses on PreOp nurse’s EHR use in PreOp settings. The goals of this dissertation are to: (a) introduce a systematic framework to evaluate EHR-mediated workflow and the impact of the EHR transition; (b) understand the impact of different EHR systems on PreOp nurse’s workflow and preoperative care efficiency; (c) transform the evaluation results into practical user-centered EHR designs. This research draws on computational ethnography, cognitive engineering process and user-centered design concepts to build a practical approach for EHR transition-related workflow evaluation and optimization.
Observational data were collected before and after a large-scale EHR conversion throughout Mayo Clinic’s different regional health systems. For a structured computational evaluation framework, the time-efficiency of PreOp nurses’ work were compared quantitatively by means of coding and segmenting nurses’ tasks. Interview data provided contextual information, reflecting practical challenges and opportunities before and after the EHR transition.
The total case time, the time spent on EHR, and the task fragmentation were improved after converting to the new EHR system. A trend of standardization of information-related workflow and EHR transition was observed. Notably, the approach helped to identify current new system challenges and pointed out potential optimization solutions.
ContributorsZheng, Lu (Author) / Doebbeling, Bradley (Thesis advisor) / Kaufman, David (Committee member) / Wang, Dongwen (Committee member) / Patel, Vimla (Committee member) / Chiou, Erin (Committee member) / Arizona State University (Publisher)
Created2021
Description
The rate of progress in improving survival of patients with solid tumors is slow due to late stage diagnosis and poor tumor characterization processes that fail to effectively reflect the nature of tumor before treatment or the subsequent change in its dynamics because of treatment. Further advancement of targeted therapies relies on advancements in biomarker research. In the context of solid tumors, bio-specimen samples such as biopsies serve as the main source of biomarkers used in the treatment and monitoring of cancer, even though biopsy samples are susceptible to sampling error and more importantly, are local and offer a narrow temporal scope.
Because of its established role in cancer care and its non-invasive nature imaging offers the potential to complement the findings of cancer biology. Over the past decade, a compelling body of literature has emerged suggesting a more pivotal role for imaging in the diagnosis, prognosis, and monitoring of diseases. These advances have facilitated the rise of an emerging practice known as Radiomics: the extraction and analysis of large numbers of quantitative features from medical images to improve disease characterization and prediction of outcome. It has been suggested that radiomics can contribute to biomarker discovery by detecting imaging traits that are complementary or interchangeable with other markers.
This thesis seeks further advancement of imaging biomarker discovery. This research unfolds over two aims: I) developing a comprehensive methodological pipeline for converting diagnostic imaging data into mineable sources of information, and II) investigating the utility of imaging data in clinical diagnostic applications. Four validation studies were conducted using the radiomics pipeline developed in aim I. These studies had the following goals: (1 distinguishing between benign and malignant head and neck lesions (2) differentiating benign and malignant breast cancers, (3) predicting the status of Human Papillomavirus in head and neck cancers, and (4) predicting neuropsychological performances as they relate to Alzheimer’s disease progression. The long-term objective of this thesis is to improve patient outcome and survival by facilitating incorporation of routine care imaging data into decision making processes.
Because of its established role in cancer care and its non-invasive nature imaging offers the potential to complement the findings of cancer biology. Over the past decade, a compelling body of literature has emerged suggesting a more pivotal role for imaging in the diagnosis, prognosis, and monitoring of diseases. These advances have facilitated the rise of an emerging practice known as Radiomics: the extraction and analysis of large numbers of quantitative features from medical images to improve disease characterization and prediction of outcome. It has been suggested that radiomics can contribute to biomarker discovery by detecting imaging traits that are complementary or interchangeable with other markers.
This thesis seeks further advancement of imaging biomarker discovery. This research unfolds over two aims: I) developing a comprehensive methodological pipeline for converting diagnostic imaging data into mineable sources of information, and II) investigating the utility of imaging data in clinical diagnostic applications. Four validation studies were conducted using the radiomics pipeline developed in aim I. These studies had the following goals: (1 distinguishing between benign and malignant head and neck lesions (2) differentiating benign and malignant breast cancers, (3) predicting the status of Human Papillomavirus in head and neck cancers, and (4) predicting neuropsychological performances as they relate to Alzheimer’s disease progression. The long-term objective of this thesis is to improve patient outcome and survival by facilitating incorporation of routine care imaging data into decision making processes.
ContributorsRanjbar, Sara (Author) / Kaufman, David (Thesis advisor) / Mitchell, Joseph R. (Thesis advisor) / Runger, George C. (Committee member) / Arizona State University (Publisher)
Created2017
Description
Type 1 diabetes (T1D) is a chronic disease that affects 1.25 million people in the United States. There is no known cure and patients must self-manage the disease to avoid complications resulting from blood glucose (BG) excursions. Patients are more likely to adhere to treatments when they incorporate lifestyle preferences. Current technologies that assist patients fail to consider two factors that are known to affect BG: exercise and alcohol. The hypothesis is postprandial blood glucose levels of adult patients with T1D can be improved by providing insulin bolus or carbohydrate recommendations that account for meal and alcohol carbohydrates, glycemic excursion, and planned exercise. I propose an evidence-based decision support tool, iDECIDE, to make recommendations to improve glucose control by taking into account meal and alcohol carbohydrates, glycemic excursion and planned exercise. iDECIDE is deployed as a low-cost and easy to disseminate smartphone application.
A literature review was conducted on T1D and the state-of-the-art in diabetes technology. To better understand self-management behaviors and guide the development of iDECIDE, several data sources were collected and analyzed: surveys, insulin pump paired with glucose monitoring, and self-tracking of exercise and alcohol. The analysis showed variability in compensation techniques for exercise and alcohol and that patients made unaided decisions, suggesting a need for better decision support.
The iDECIDE algorithm can make insulin and carbohydrate recommendations. Since there were no existing in-silico methods for assessing bolus calculators, like iDECIDE, I proposed a novel methodology to retrospectively compare insulin pump bolus calculators. Application of the methodology shows that iDECIDE outperformed the Medtronic insulin pump bolus calculator and could have improved glucose control.
This work makes contributions to diabetes technology researchers, clinicians and patients. The iDECIDE app provides patients easy access to a decision support tool that can improve glucose control. The study of behaviors from diabetes technology and self-report patient data can inform clinicians and the design of future technologies and bedside tools that integrate patient’s behaviors and perceptions. The comparison methodology provides a means for clinical informatics researchers to identify and retrospectively test promising insulin blousing algorithms using real-life data.
A literature review was conducted on T1D and the state-of-the-art in diabetes technology. To better understand self-management behaviors and guide the development of iDECIDE, several data sources were collected and analyzed: surveys, insulin pump paired with glucose monitoring, and self-tracking of exercise and alcohol. The analysis showed variability in compensation techniques for exercise and alcohol and that patients made unaided decisions, suggesting a need for better decision support.
The iDECIDE algorithm can make insulin and carbohydrate recommendations. Since there were no existing in-silico methods for assessing bolus calculators, like iDECIDE, I proposed a novel methodology to retrospectively compare insulin pump bolus calculators. Application of the methodology shows that iDECIDE outperformed the Medtronic insulin pump bolus calculator and could have improved glucose control.
This work makes contributions to diabetes technology researchers, clinicians and patients. The iDECIDE app provides patients easy access to a decision support tool that can improve glucose control. The study of behaviors from diabetes technology and self-report patient data can inform clinicians and the design of future technologies and bedside tools that integrate patient’s behaviors and perceptions. The comparison methodology provides a means for clinical informatics researchers to identify and retrospectively test promising insulin blousing algorithms using real-life data.
ContributorsGroat, Danielle (Author) / Grando, Maria Adela (Thesis advisor) / Kaufman, David (Committee member) / Thompson, Bithika (Committee member) / Arizona State University (Publisher)
Created2017