Matching Items (40)
Description
Laboratory automation systems have seen a lot of technological advances in recent times. As a result, the software that is written for them are becoming increasingly sophisticated. Existing software architectures and standards are targeted to a wider domain of software development and need to be customized in order to use them for developing software for laboratory automation systems. This thesis proposes an architecture that is based on existing software architectural paradigms and is specifically tailored to developing software for a laboratory automation system. The architecture is based on fairly autonomous software components that can be distributed across multiple computers. The components in the architecture make use of asynchronous communication methodologies that are facilitated by passing messages between one another. The architecture can be used to develop software that is distributed, responsive and thread-safe. The thesis also proposes a framework that has been developed to implement the ideas proposed by the architecture. The framework is used to develop software that is scalable, distributed, responsive and thread-safe. The framework currently has components to control very commonly used laboratory automation devices such as mechanical stages, cameras, and also to do common laboratory automation functionalities such as imaging.
ContributorsKuppuswamy, Venkataramanan (Author) / Meldrum, Deirdre (Thesis advisor) / Collofello, James (Thesis advisor) / Sarjoughian, Hessam S. (Committee member) / Johnson, Roger (Committee member) / Arizona State University (Publisher)
Created2012
Description
Single cell analysis has become increasingly important in understanding disease onset, progression, treatment and prognosis, especially when applied to cancer where cellular responses are highly heterogeneous. Through the advent of single cell computerized tomography (Cell-CT), researchers and clinicians now have the ability to obtain high resolution three-dimensional (3D) reconstructions of single cells. Yet to date, no live-cell compatible version of the technology exists. In this thesis, a microfluidic chip with the ability to rotate live single cells in hydrodynamic microvortices about an axis parallel to the optical focal plane has been demonstrated. The chip utilizes a novel 3D microchamber design arranged beneath a main channel creating flow detachment into the chamber, producing recirculating flow conditions. Single cells are flowed through the main channel, held in the center of the microvortex by an optical trap, and rotated by the forces induced by the recirculating fluid flow. Computational fluid dynamics (CFD) was employed to optimize the geometry of the microchamber. Two methods for the fabrication of the 3D microchamber were devised: anisotropic etching of silicon and backside diffuser photolithography (BDPL). First, the optimization of the silicon etching conditions was demonstrated through design of experiment (DOE). In addition, a non-conventional method of soft-lithography was demonstrated which incorporates the use of two positive molds, one of the main channel and the other of the microchambers, compressed together during replication to produce a single ultra-thin (<200 µm) negative used for device assembly. Second, methods for using thick negative photoresists such as SU-8 with BDPL have been developed which include a new simple and effective method for promoting the adhesion of SU-8 to glass. An assembly method that bonds two individual ultra-thin (<100 µm) replications of the channel and the microfeatures has also been demonstrated. Finally, a pressure driven pumping system with nanoliter per minute flow rate regulation, sub-second response times, and < 3% flow variability has been designed and characterized. The fabrication and assembly of this device is inexpensive and utilizes simple variants of conventional microfluidic fabrication techniques, making it easily accessible to the single cell analysis community.
ContributorsMyers, Jakrey R (Author) / Meldrum, Deirdre (Thesis advisor) / Johnson, Roger (Committee member) / Frakes, David (Committee member) / Arizona State University (Publisher)
Created2012
Description
Inflammation is part of the body’s response to invading pathogens, injury, and a wide range of diseases. Although inflammation is paramount to maintain a healthy immune system, unregulated inflammation can aggravate chronic conditions or cause severe, acute pathologies. Pyroptosis, a caspase-1-dependent, pro-inflammatory cell death that results in the release of IL-1β and IL-18, has been implicated in propagating an inflammatory response in the body. Pyroptosis has been shown to result from the activation of the NLRP3 inflammasome. Furthermore, multiple reports have demonstrated that intracellular potassium efflux and spleen tyrosine kinase (Syk) activity are both essential for facilitating the assembly of the NLRP3 inflammasome and proper processing and release of IL-1β and IL-18. The focus of this thesis was to determine the relationship between intracellular potassium efflux and Syk during key regulatory events in the activation of the NLRP3 inflammasome by identifying their effect on pro-inflammatory cytokine release, inflammasome assembly, mitochondrial reactive oxygen species (mROS) generation, and cell death. Both inhibiting potassium efflux from occurring and deactivating Syk significantly reduced the amount of pro-inflammatory cytokine released (70-100% reduction), the number of inflammasomes assembled (60-80% reduction), the amount of mROS generation, and the quantity of cell death (50-90% reduction). Moreover, it was discovered that potassium efflux was required for Syk activation, but Syk activation had no effect on potassium efflux. Their relationship proved to be unidirectional. This study provides the first demonstration of ion flux-dependent regulation of kinase activation in the NLRP3 inflammasome pathway and provides support for targeting ion regulation mechanisms and Syk kinase activity to manipulate macrophage-mediate inflammatory processes.
ContributorsRao, Mounica Yarlagadda (Author) / Meldrum, Deirdre R. (Thesis director) / Ankeny, Casey (Committee member) / Glenn, Honor (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2015-05
Description
Background
Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D) objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading criteria.
Methodology
We applied micro-optical computed tomographic imaging and automated 3D nuclear morphometry to quantify and compare morphological variations between human cell lines derived from normal, benign fibrocystic or malignant breast epithelium. To reproduce the appearance and contrast in clinical cytopathology images, we stained cells with hematoxylin and eosin and obtained 3D images of 150 individual stained cells of each cell type at sub-micron, isotropic resolution. Applying volumetric image analyses, we computed 42 3D morphological and textural descriptors of cellular and nuclear structure.
Principal Findings
We observed four distinct nuclear shape categories, the predominant being a mushroom cap shape. Cell and nuclear volumes increased from normal to fibrocystic to metastatic type, but there was little difference in the volume ratio of nucleus to cytoplasm (N/C ratio) between the lines. Abnormal cell nuclei had more nucleoli, markedly higher density and clumpier chromatin organization compared to normal. Nuclei of non-tumorigenic, fibrocystic cells exhibited larger textural variations than metastatic cell nuclei. At p<0.0025 by ANOVA and Kruskal-Wallis tests, 90% of our computed descriptors statistically differentiated control from abnormal cell populations, but only 69% of these features statistically differentiated the fibrocystic from the metastatic cell populations.
Conclusions
Our results provide a new perspective on nuclear structure variations associated with malignancy and point to the value of automated quantitative 3D nuclear morphometry as an objective tool to enable development of sensitive and specific nuclear grade classification in breast cancer diagnosis.
Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D) objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading criteria.
Methodology
We applied micro-optical computed tomographic imaging and automated 3D nuclear morphometry to quantify and compare morphological variations between human cell lines derived from normal, benign fibrocystic or malignant breast epithelium. To reproduce the appearance and contrast in clinical cytopathology images, we stained cells with hematoxylin and eosin and obtained 3D images of 150 individual stained cells of each cell type at sub-micron, isotropic resolution. Applying volumetric image analyses, we computed 42 3D morphological and textural descriptors of cellular and nuclear structure.
Principal Findings
We observed four distinct nuclear shape categories, the predominant being a mushroom cap shape. Cell and nuclear volumes increased from normal to fibrocystic to metastatic type, but there was little difference in the volume ratio of nucleus to cytoplasm (N/C ratio) between the lines. Abnormal cell nuclei had more nucleoli, markedly higher density and clumpier chromatin organization compared to normal. Nuclei of non-tumorigenic, fibrocystic cells exhibited larger textural variations than metastatic cell nuclei. At p<0.0025 by ANOVA and Kruskal-Wallis tests, 90% of our computed descriptors statistically differentiated control from abnormal cell populations, but only 69% of these features statistically differentiated the fibrocystic from the metastatic cell populations.
Conclusions
Our results provide a new perspective on nuclear structure variations associated with malignancy and point to the value of automated quantitative 3D nuclear morphometry as an objective tool to enable development of sensitive and specific nuclear grade classification in breast cancer diagnosis.
ContributorsNandakumar, Vivek (Author) / Kelbauskas, Laimonas (Author) / Hernandez, Kathryn (Author) / Lintecum, Kelly (Author) / Senechal, Patti (Author) / Bussey, Kimberly (Author) / Davies, Paul (Author) / Johnson, Roger (Author) / Meldrum, Deirdre (Author) / Ira A. Fulton Schools of Engineering (Contributor) / School of Electrical, Computer and Energy Engineering (Contributor) / Biodesign Institute (Contributor) / Center for Biosignatures Discovery Automation (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / Department of Physics (Contributor)
Created2012-01-05
Description
An aim of fundamental immunology is quantifying the diversity of the T cell receptor (TCR) repertoire to elucidate the vast recognition by T cells for protection against pathogen and cancer. The utilization of DNA origami nanostructures engineered to capture single cell paired TCR mRNA sequences has transformed the financial and time requirements of repertoire establishment. To further support this protocol, confocal laser scanning microscopy was implemented following transfection to visualize the stability of the DNA origami within primary immune lymphocytes.
ContributorsReed, Abigail Elizabeth (Author) / Blattman, Joseph (Thesis director) / Glenn, Honor (Committee member) / Schoettle, Louis (Committee member) / School of Life Sciences (Contributor) / W.P. Carey School of Business (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Breast cancer is one of the leading causes of cancer-related deaths among women in the United States. Uninsured women are less likely to receive breast cancer screenings, more likely to be diagnosed at an advanced stage, and more likely to have poorer outcomes following a breast cancer diagnosis (Abdelsattar et al., 2016; Akinlotan et al., 2021; Ko et al., 2020; & Ntiri et al., 2018). Women in underserved communities often experience socioeconomic barriers which impact obtaining preventative screenings, such as mammograms. Lack of patient navigation, transportation, and financial concerns interfere with obtaining breast cancer screening (Akinlotan et al., 2021 & Miller et al., 2019). Through the intervention of mobile mammography, uninsured women in underserved communities can be reached and access to screening mammograms can be achieved (Stanley et al., 2017 & Vang et al., 2018). Two mobile mammography events were hosted at the project site which provided 35 women with screening mammograms. All scheduled mammogram time slots at the events were filled and completed. Offering mobile mammography to this population has the potential to increase breast cancer surveillance.
ContributorsGlessner-Vallee, Paula (Author) / Santerre, Jennifer (Thesis advisor) / College of Nursing and Health Innovation (Contributor)
Created2023-04-26
Description
Introduction: The objective of this study is to emphasize the significance of exclusive breastfeeding (EB) and investigate methods to encourage and sustain it within a hospital environment. Using the self-efficacy theory, the study seeks to improve the current support system for breastfeeding mothers and their families. Methods: The project was approved by the university IRB and facility IRB; guidelines were maintained. The project takes place in a non-profit organization in the southwestern United States. Education was conducted at a required staff meeting for Women and Infant Services (WIS) floor about supporting breastfeeding mothers. A pre- and post-education Breastfeeding Knowledge Scale (BKS) survey was performed, effectiveness was measured using a two-tailed t-test. The reliability of the BKS scale is 0.83 and the validity of the scale is reported to be strong. The hospital measures the EB rates of patients that are greater than 37 weeks gestation without need for neonatal intensive unit care and the mom requests to breastfeed. Results: The goal was 42% rate of EB in the first 48 hours after birth. After education the average rate of EB was 39.6%, lower than the goal but higher than the 33.7% rate before education. A two-tailed paired sample t-test (n=27) was used for BKS and the results were significant based on an alpha value; thus, showing significant knowledge gain. Conclusion: Consistent staff education improves breastfeeding support for moms in the hospital, leading to successful exclusive breastfeeding. This project benefits various settings, such as pediatric, postpartum, labor and delivery, and pediatric offices.
ContributorsHudson, Jennifer (Author) / Esperas, Amanda (Thesis advisor) / College of Nursing and Health Innovation (Contributor)
Created2023-04-26
Description
Introduction: Depression screening in the pediatric setting is a crucial part of the adolescent's examination. A standardized screening tool and protocol streamlines the process of assessing adolescents and minimizes the chances of serious mental health disorders going undetected and untreated. Evaluation of current evidence demonstrates the use of a standardized tool improves detection, diagnosis, and management of depression and other mental health illnesses.
Method: The Patient Health Questionnaire—modified for adolescents (PHQ9-A) was administered to all eligible adolescents, ages 12-18, during an annual well visit for a period of 6 weeks. Lewin's Change Theory guided a system change in the electronic health record, and the questionnaire results were documented and provided to the pediatric provider at the time of the appointment. A chart review was conducted to determine whether all eligible patients were administered the questionnaire and if a depression diagnosis or mental health referral had been made.
Results: Out of 76 eligible well visits, 65 (86%) patients completed the PHQ9-A. The average score was 5.29 (SD = 6.49) with a maximum score of 25. Out of those that completed screening, 11 (17%) had a positive PHQ9-A score resulting in 8 referrals to mental health services and 2 mental health diagnoses in the clinic.
ContributorsCoomer, Meagan (Author) / Rauton, Monica (Thesis advisor) / College of Nursing and Health Innovation (Contributor)
Created2023-04-27
Description
Background: There is growing evidence that persistent exposure to the adverse effects of stressful work conditions, abuse, and re-traumatization without proper intervention leads to compassion fatigue (CF) and reduced compassion satisfaction (CS). Without appropriate intervention, the outcome of CF affects the patient, staff, and the organization. Despite proposed self-care measures, mental health (MH) workers continue to struggle with CF and lack the resources to combat the issue.
Objectives: Ongoing awareness on the implications of trauma and its impact on one's behavior, supports the use of Trauma-informed care (TIC) skills in creating a conducive work environment. This quality improvement project examines the efficacy of TIC education as an intervention for CF pre/post-one-hour education session among MH workers.
Methods: MH nurses (n=8) from diverse backgrounds in a Phoenix inpatient psychiatric hospital gave consent for the study. Participation was sought via flyers and entailed attending the one-hour education session, filling out a demographic, and pre/post-professional quality of life (ProQol) surveys. The ProQol standardized tool measures CF, CS, and burnout with reliability >0.70. Expected outcomes include a reduction in CF and an improvement in CS. Data analysis using intellectus software involved descriptive analysis and paired t-tests to compare outcomes.
Results: Pre/post data analysis was statistically significant, P = 0.003, which shows a reduction in CF and an improvement in CS.
Conclusion: TIC as an intervention for CF looks promising. MH nurses can manage their stress symptoms and that of their patients using TIC skills.
ContributorsOnyia, Nneka (Author) / Guthery, Ann (Thesis advisor) / College of Nursing and Health Innovation (Contributor)
Created2023-04-29
Description
Substance use disorder has been increasing in the United States year after year. Modern treatments fail as often as they succeed. The current standards of practice fail to provide patients with the ability to harness thoughts and control anxiety. Mindfulness practices are currently being adapted as a therapeutic technique to address some of these concerns. An exhaustive literature review was conducted to investigate how various mindfulness techniques impact substance use disorder. Ten high-quality studies were retained and synthesized to show current understandings of the effectiveness of a mindfulness therapeutic technique. An evidence-based intervention is suggested for implementing mindfulness-based relapse prevention into a residential treatment facility. The intervention created incorporates the self-efficacy theory and an adapted health-belief model. Adults in a residential treatment facility for substance use disorder were given eight mindfulness sessions over the course of four weeks. Participants were given pre- and post-intervention screenings for mindful attention and anxiety. The data analysis after two-tailed paired T-tests showed that anxiety significantly decreased (α=.05, p<.001) and mindful attention increased significantly (α=.05, p=.015). Overall, mindfulness shows promise in its potential to reduce substance abuse.
ContributorsWandler, Ryan (Author) / Nunez, Diane (Thesis advisor) / College of Nursing and Health Innovation (Contributor)
Created2023-04-27