Matching Items (56)
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

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
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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 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
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Description

Critical flicker fusion thresholds (CFFTs) describe when quick amplitude modulations of a light source become undetectable as the frequency of the modulation increases and are thought to underlie a number of visual processing skills, including reading. Here, we compare the impact of two vision-training approaches, one involving contrast sensitivity training

Critical flicker fusion thresholds (CFFTs) describe when quick amplitude modulations of a light source become undetectable as the frequency of the modulation increases and are thought to underlie a number of visual processing skills, including reading. Here, we compare the impact of two vision-training approaches, one involving contrast sensitivity training and the other directional dot-motion training, compared to an active control group trained on Sudoku. The three training paradigms were compared on their effectiveness for altering CFFT. Directional dot-motion and contrast sensitivity training resulted in significant improvement in CFFT, while the Sudoku group did not yield significant improvement. This finding indicates that dot-motion and contrast sensitivity training similarly transfer to effect changes in CFFT. The results, combined with prior research linking CFFT to high-order cognitive processes such as reading ability, and studies showing positive impact of both dot-motion and contrast sensitivity training in reading, provide a possible mechanistic link of how these different training approaches impact reading abilities.

ContributorsZhou, Tianyou (Author) / Nanez, Jose (Author) / Zimmerman, Daniel (Author) / Holloway, Steven (Author) / Seitz, Aaron (Author) / New College of Interdisciplinary Arts and Sciences (Contributor)
Created2016-10-26
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Description

Although autism spectrum disorder (ASD) is a serious lifelong condition, its underlying neural mechanism remains unclear. Recently, neuroimaging-based classifiers for ASD and typically developed (TD) individuals were developed to identify the abnormality of functional connections (FCs). Due to over-fitting and interferential effects of varying measurement conditions and demographic distributions, no

Although autism spectrum disorder (ASD) is a serious lifelong condition, its underlying neural mechanism remains unclear. Recently, neuroimaging-based classifiers for ASD and typically developed (TD) individuals were developed to identify the abnormality of functional connections (FCs). Due to over-fitting and interferential effects of varying measurement conditions and demographic distributions, no classifiers have been strictly validated for independent cohorts. Here we overcome these difficulties by developing a novel machine-learning algorithm that identifies a small number of FCs that separates ASD versus TD. The classifier achieves high accuracy for a Japanese discovery cohort and demonstrates a remarkable degree of generalization for two independent validation cohorts in the USA and Japan. The developed ASD classifier does not distinguish individuals with major depressive disorder and attention-deficit hyperactivity disorder from their controls but moderately distinguishes patients with schizophrenia from their controls. The results leave open the viable possibility of exploring neuroimaging-based dimensions quantifying the multiple-disorder spectrum.

ContributorsYahata, Noriaki (Author) / Morimoto, Jun (Author) / Hashimoto, Ryuichiro (Author) / Lisi, Giuseppe (Author) / Shibata, Kazuhisa (Author) / Kawakubo, Yuki (Author) / Kuwabara, Hitoshi (Author) / Kuroda, Miho (Author) / Yamada, Takashi (Author) / Megumi, Fukuda (Author) / Imamizu, Hiroshi (Author) / Nanez, Jose (Author) / Takahashi, Hidehiko (Author) / Okamoto, Yasumasa (Author) / Kasai, Kiyoto (Author) / Kato, Nobumasa (Author) / Sasaki, Yuka (Author) / Watanabe, Takeo (Author) / Kawato, Mitsuo (Author) / New College of Interdisciplinary Arts and Sciences (Contributor)
Created2016-04-14
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Description

Fetal androgen exposure and childhood experiences are believed to contribute to the development and organization of the hypothalamic-pituitary-adrenal (HPA) and hypothalamic-pituitary-gonadal (HPG) axes, which are responsible for the regulation and release of stress and sex hormones, respectively. Evidence suggests the HPA and HPG axes can couple in response to childhood

Fetal androgen exposure and childhood experiences are believed to contribute to the development and organization of the hypothalamic-pituitary-adrenal (HPA) and hypothalamic-pituitary-gonadal (HPG) axes, which are responsible for the regulation and release of stress and sex hormones, respectively. Evidence suggests the HPA and HPG axes can couple in response to childhood adversity, and that hormonal dysregulation contributes to psychopathological disorders such as anxiety and depression. Recent research also suggests self-compassion interventions could reduce PTSD symptoms, and that the experience of childhood trauma is related to increased empathy. Still, little is known regarding the impact of fetal androgen exposure on PTSD susceptibility and the relationships between self-compassion, compassion for others, and empathy. The current study aims to determine whether fetal androgen exposure mitigates PTSD susceptibility, and to clarify the relationships between empathy, compassion for others, self-compassion, and PTSD symptoms. A sample of 208 adults completed an online survey designed to measure fetal androgen exposure, childhood maltreatment, self-compassion, compassion for others, empathy, and PTSD symptoms. Findings show a significant difference in PTSD symptoms between individuals in high and low fetal androgen exposure groups, and significant correlations were discovered between empathy and compassion for others, empathy and self-compassion, but not compassion for others and self-compassion. Future studies could explore the extent to which fetal androgen exposure influences PTSD symptom susceptibility and the clinical implications therein.

ContributorsMoore, Robin Ann (Author) / Holloway, Steven (Thesis director) / Lewis, Stephen (Committee member) / Nanez, Jose (Committee member) / School of Public Affairs (Contributor) / School of Social and Behavioral Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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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,

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.
Created2012-01-05
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Description
Androgen has been shown to affect functioning of the central nervous system by modulating neural circuitry during in-utero development subsequently affecting parts of the brain implicated in the evaluation of socially relevant stimuli. This can suggest an examination of underlying neurobiological mechanisms that may influence androgen in the brain and

Androgen has been shown to affect functioning of the central nervous system by modulating neural circuitry during in-utero development subsequently affecting parts of the brain implicated in the evaluation of socially relevant stimuli. This can suggest an examination of underlying neurobiological mechanisms that may influence androgen in the brain and likewise human cognition and behavior. Since the index and ring finger ratio is associated with androgen related outcomes, this study sought to identify a relationship between a participant's implicit race association test score and left-handed ring (4D) and index (2D) finger ratio. Specifically, we found that higher androgen exposure in our female subjects equated to a stronger bias for European American faces over African American faces.
ContributorsSaari, Sydney (Author) / Holloway, Steven (Thesis director) / Kim, Linda (Committee member) / Nanez, Jose (Committee member) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The importance of mobility and psychological attitude during hospitalization and how they correlate with recovery is highlighted in this paper through a review of the research literature on both topics. The literature review revealed that increased mobility and positive psychological cognitive state are correlated positively with increased recovery among hospitalized

The importance of mobility and psychological attitude during hospitalization and how they correlate with recovery is highlighted in this paper through a review of the research literature on both topics. The literature review revealed that increased mobility and positive psychological cognitive state are correlated positively with increased recovery among hospitalized individuals. The research findings have led to the development of child mobility apparatuses called "Lily Pads" being constructed and donated to pediatric hospitals with the intention of helping increase patient mobility and positivity in pediatric wards of hospitals. A history of the lily pads and their potentially positive impact is presented as well as a brief description of the construction process, should readers like to build and donate these apparatuses to their local hospital. It is concluded that further empirical research on the use and effects of lily pads in pediatric wards and the possible correlation with pediatric recovery is needed in order to qualitatively and quantitatively assess the apparatuses' effectiveness.
ContributorsPologa, Chase Thomas (Author) / Sweat, Ken (Thesis director) / Nanez, Jose (Committee member) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
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Description
Historically, Supreme Court interpretations of the Constitution of the United States have been significantly important, impacting the lives of every American. This honors thesis seeks to understand the ways in which the Constitution has been interpreted through the lens of political ideology. Using constitutional theory, I explain how the political

Historically, Supreme Court interpretations of the Constitution of the United States have been significantly important, impacting the lives of every American. This honors thesis seeks to understand the ways in which the Constitution has been interpreted through the lens of political ideology. Using constitutional theory, I explain how the political ideologies of classical liberalism, conservatism, libertarianism, and progressive liberalism have played a role in the interpretations of the First, Second, and Fourth Amendments. I also examine how these ideological interpretations have changed from 1776 to 2017, dividing the history of the United States into four eras: the Founding Era, the Civil War Era, the New Deal Era, and the Modern Era. First, the First Amendment's clauses on religion are examined, where I focus on the separation between church and state as well as the concepts of "establishment" and "free exercise." The First Amendment transitions from classically liberal, to conservative, to progressively liberal and classically liberal, to progressively liberal and libertarian. Next, we look at the Second Amendment's notions of a "militia" and the "right to keep and bear arms." The Second Amendment's interpretations begin classically liberal, then change to classically liberal and progressively liberal, to progressively liberal, to conservative. Finally, the analysis on the Fourth Amendment's "unreasonable searches and seizures" as well as "warrants" lends evidence to ideological interpretations. The Fourth Amendment, like the other two, starts classically liberal for two eras, then becomes libertarian, and finally ends libertarian and conservative. The implications of each of these conclusions are then discussed, with emphasis on public opinion in society during the era in question, the ways in which the ideologies in each era seem to build upon one another, the ideologies of the justices who wrote the opinions, and the ideology of the court.
Created2017-12
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Description
Anecdotally, native Mandarin speakers have difficulty distinguishing between the “s” (as in sink) and the “th” (as in think) sounds as well as between the “a” (as in dad) and “ea” (as in dead) sounds. Here, 29 native English speakers, 52 native Mandarin speakers who live in China, and 34

Anecdotally, native Mandarin speakers have difficulty distinguishing between the “s” (as in sink) and the “th” (as in think) sounds as well as between the “a” (as in dad) and “ea” (as in dead) sounds. Here, 29 native English speakers, 52 native Mandarin speakers who live in China, and 34 native Mandarin speakers who have been living in an English language dominant environment were recruited to serve as participants. To assess the phoneme contrasts that may occur in native Mandarin speakers in China, and possible improvement in native Mandarin speakers living in an English environment, relative to Native English speakers living in America, a phoneme discrimination test was administered, three paired phonemes were used in the current study: /b/ paired with /p/ as a control pair, /æ/ paired with /ɛ/, and /θ/ paired with /s/. The results showed that native English speakers have significantly higher accuracy rates for the three paired phoneme discrimination tasks than the native Mandarin speakers who live in China. But there was no significant difference between the native English speakers and native Mandarin speakers who have lived in an English environment on the phonemes or words discriminations tasks.
ContributorsChen, Hao (Author) / Nanez, Jose (Thesis advisor) / Horne, Zachary (Thesis advisor) / Holloway, Steven (Committee member) / Arizona State University (Publisher)
Created2021