Matching Items (72)
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
In the frenzy of next generation genetic sequencing and proteomics, single-cell level analysis has begun to find its place in the crux of personalized medicine and cancer research. Single live cell 3D imaging technology is one of the most useful ways of providing spatial and morphological details inside living single cells. It provides a window to uncover the mysteries of protein structure and folding, as well as genetic expression over time, which will tremendously improve the state of the fields of biophysics and biomedical research. This thesis project specifically demonstrates a method for live single cell rotation required to image them in the single live cell CT imaging platform. The method of rotation proposed in this thesis uses dynamic optical traps generated by a phase-only spatial light modulator (SLM) to exert torque on a single mammalian cell. Laser patterns carrying the holographic information of the traps are delivered from the SLM through a transformation telescope into the objective lens and onto its focal plane to produce the desired optical trap "image". The phase information in the laser patterns being delivered are continuously altered by the SLM such that the structure of the wavefront produces two foci at opposite edges of the cell of interest that each moves along the circumference of the cell in opposite axial directions. Momentum generated by the motion of the foci exerts a torque on the cell, causing it to rotate. The viability of this method was demonstrated experimentally. Software was written using LabVIEW to control the display panel of the SLM.
ContributorsChan, Samantha W (Author) / Meldrum, Deridre R (Thesis advisor) / Kleim, Jeffrey A (Committee member) / Johnson, Roger H (Committee member) / Kelbauskas, Laimonas (Committee member) / Arizona State University (Publisher)
Created2013
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
In vitro measurements of cellular respiration have proven to be key biomarkers for the early onset of tumor formation in certain pathological mechanisms.1 The examination of isolated single cells has shown promise in predicting the onset of cancerous growth much earlier than current methods allow.2 Specifically, measurements of the oxygen consumption rates of precancerous cells have elucidated outliers which predict the early onset of esophageal cancer.2 Single cell profiling can fit in to current pathology studies and can serve as a step along the way, much like PCR or gel assays, in detecting biomarkers earlier than current clinical methods.3 Measurement of these single cell metabolic rates is currently limited to 25 cells per experiment. It is the aim of this project to increase throughput from 25 cells to 225 cells per experiment via the implementation of new hardware and software which fit with current methods to allow the same experimental structure. Successful implementation of such methods will allow for more rapid and efficient data collection, facilitating quantitative results and nine times the yield from the same experimental manpower and funding. This document focuses on the implementation ultra high density (UHD) hardware consisting of a pneumatic molar design, angular adjustment features and a mechanical Z-stage. These components have produced the most encouraging results thus far and are the key changes in transitioning to higher throughput experiments.
ContributorsUeberroth, Benjamin Edward (Author) / Kelbauskas, Laimonas (Thesis director) / Ashili, Shashanka (Committee member) / Myers, Jakrey (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2013-05
Description
Esophageal adenocarcinoma (EAC) is one of the most lethal and fastest growing cancers in the United States. Its onset is commonly triggered by metaplastic transformation of normal squamous esophageal epithelial cells to Barrett's esophagus (BE) cells in response to acid reflux. BE patients are believed to progress through non-dysplastic metaplasia and increasing grades of dysplasia prior to EAC. Conventional cancer diagnostic tools rely on bulk-cell analyses that are incapable of identifying intratumoral heterogeneity or rare driver cells that play important roles in cancer progression. An improved single-cell method of cancer diagnosis would overcome this challenge by detecting cancer initiating cells before they progress into untreatable stages. In this study, using EAC as a model, we attempted to identify a more effective method of cancer diagnosis. We quantified the single- and bulk-cell mRNA expression of genes that have been proposed to be instrumental in the progression of EAC through BE. Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) analysis was performed on human primary cells to measure the mRNA expression levels of BE- and EAC-associated genes. Our results showed high levels of heterogeneity of CDX2 and TFF3 at the single-cell resolution in human BE and EAC samples. Additionally, while expression of VEGF is generally low at the bulk-cell level, our results showed that a few, rare cells had significantly higher VEGF expression levels than the majority of cells in the EAC sample. In conclusion, we have affirmed that EAC cancer cells, as well as BE cells, show high levels of heterogeneity. Based on the VEGF gene expression pattern, single-cell analysis could potentially be more effective for identifying rare, but essential cells for cancer progression, which could then be targeted for treatment. Future studies will focus on analyzing human samples from thousands of normal and cancer subjects to validate the use of single-cell profiling in cancer.
ContributorsHaeuser, Kelsey Lynn (Author) / Tran, Thai (Thesis director) / Kelbauskas, Laimonas (Committee member) / Gao, Weimin (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2013-12
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
The development of stab-resistant Kevlar armor has been an ongoing field of research
since the late 1990s, with the ultimate goal of improving the multi-threat capabilities of
traditional soft-body armor while significantly improving its protective efficiency - the amount
of layers of armor material required to defeat threats. To create a novel, superior materials
system to reinforce Kevlar armor for the Norica Capstone project, this thesis set out to
synthesize, recover, and characterize zinc oxide nanowire colloids.
The materials synthesized were successfully utilized in the wider Capstone effort to
dramatically enhance the protective abilities of Kevlar, while the data obtained on the 14
hydrothermal synthesis attempts and numerous challenges at recovery provided critical
information on the synthesis parameters involved in the reliable, scalable mass production of the
nanomaterial additive. Additionally, recovery was unconventionally facilitated in the absence of
a vacuum filtration apparatus with nanoscale filters by intentionally inducing electrostatic
agglomeration of the nanowires during standard gravity filtration. The subsequent application of
these nanowires constituted a pioneering use in the production of nanowire-reinforced
STF-based Kevlar coatings, and support the future development and, ultimately, the
commercialization of lighter and more-protective soft armor systems.
since the late 1990s, with the ultimate goal of improving the multi-threat capabilities of
traditional soft-body armor while significantly improving its protective efficiency - the amount
of layers of armor material required to defeat threats. To create a novel, superior materials
system to reinforce Kevlar armor for the Norica Capstone project, this thesis set out to
synthesize, recover, and characterize zinc oxide nanowire colloids.
The materials synthesized were successfully utilized in the wider Capstone effort to
dramatically enhance the protective abilities of Kevlar, while the data obtained on the 14
hydrothermal synthesis attempts and numerous challenges at recovery provided critical
information on the synthesis parameters involved in the reliable, scalable mass production of the
nanomaterial additive. Additionally, recovery was unconventionally facilitated in the absence of
a vacuum filtration apparatus with nanoscale filters by intentionally inducing electrostatic
agglomeration of the nanowires during standard gravity filtration. The subsequent application of
these nanowires constituted a pioneering use in the production of nanowire-reinforced
STF-based Kevlar coatings, and support the future development and, ultimately, the
commercialization of lighter and more-protective soft armor systems.
ContributorsDurso, Michael Nathan (Author) / Tongay, Sefaattin (Thesis director) / Zhuang, Houlong (Committee member) / Materials Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
With renewable energy on the rise, researchers have turned their funding and their focus towards new solar cell technologies, and perovskites are a major source of interest. This class of materials is particularly interesting due to their quick, simple synthesis as well as their physical and electrical superiority when compared to current silicon-based solar cells. Through this thesis, we will explore the synthesis of various types of perovskites and their subsequent characterization, which includes optical microscopy, photoluminescence spectroscopy, Raman microscopy, and X-ray diffraction. Analyzing two different perovskites both before and after a two-week period of storage revealed that while synthesis is indeed experiment-friendly, these materials have a concerning lack of stability even in ideal conditions.
ContributorsBuzas, Benjamin Joseph (Author) / Tongay, Sefaattin (Thesis director) / Muhich, Christopher (Committee member) / Materials Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Graphene is a very strong two-dimensional material with a lot of potential applications in microelectromechanical systems (MEMS). In this research, graphene is being optimized for use in a 5 m x 5 m graphene resonator. To work properly, this graphene resonator must have a uniform strain across all manufactured devices. To reduce strain induced in graphene sheets grown for use in these resonators, evaporated platinum has been used in this investigation due to its relatively lower surface roughness compared to copper films. The final goal is to have the layer of ultrathin platinum (<=200 nm) deposited on the MEMS graphene resonator and used to grow graphene directly onto the devices to remove the manual transfer step due to its inscalability. After growth, graphene is coated with polymer and the platinum is then etched. This investigation concentrated on the transfer process of graphene onto Si/SiO2 substrate from the platinum films. It was determined that the ideal platinum etchant was aqua regia at a volumetric ratio of 6:3:1 (H2O:HCl:HNO3). This concentration was dilute enough to preserve the polymer and graphene layer, but strong enough to etch within a day. Type and thickness of polymer support layers were also investigated. PMMA at a thickness of 200 nm was ideal because it was easy to remove with acetone and strong enough to support the graphene during the etch process. A reference growth recipe was used in this investigation, but now that the transfer has been demonstrated, growth can be optimized for even thinner films.
ContributorsCayll, David Richard (Author) / Tongay, Sefaattin (Thesis director) / Lee, Hyunglae (Committee member) / Mechanical and Aerospace Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Solid-state lithium-ion batteries are a major area of research due to their increased safety characteristics over conventional liquid electrolyte batteries. Lithium lanthanum zirconate (LLZO) is a promising garnet-type ceramic for use as a solid-state electrolyte due to its high ionic conductivity. The material exists in two dierent phases, one that is cubic in structure and one that is tetragonal. One potential synthesis method that results in LLZO in the more useful, cubic phase, is electrospinning, where a mat of nanowires is spun and then calcined into LLZO. A phase containing lanthanum zirconate (LZO) and amorphous lithium occursas an intermediate during the calcination process. LZO has been shown to be a sintering aid for LLZO, allowing for lower sintering temperatures. Here it is shown the eects of internal LZO on the sintered pellets. This is done by varying the 700C calcination time to transform diering amounts of LZO and LLZO in electrospun nanowires, and then using the same sintering parameters for each sample. X-ray diraction was used to get structural and compositional analysis of both the calcined powders and sintered pellets. Pellets formed from wires calcined at 1 hour or longer contained only LLZO even if the calcined powder had only undergone the rst phase transformation. The relative density of the pellet with no initial LLZO of 61.0% was higher than that of the pellet with no LZO, which had a relative density of 57.7%. This allows for the same, or slightly higher, quality material to be synthesized with a shorter amount of processing time.
ContributorsLondon, Nathan Harry (Author) / Chan, Candace (Thesis director) / Tongay, Sefaattin (Committee member) / Department of Physics (Contributor) / Materials Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05