Matching Items (107)
Description
Climate change presents the urgent need for effective sustainable water management that is capable of preserving natural resources while maintaining economical stability. States like California rely heavily on groundwater pumping for agricultural use, contributing to land subsidence and insufficient returns to water resources. The recent California drought has impacted agricultural production of certain crops. In this thesis, we present an agent-based model of farmers adapting to drought conditions by making crop choice decisions, much like the decisions Californian farmers have made. We use the Netlogo platform to capture the 2D spatial view of an agricultural system with changes in annual rainfall due to drought conditions. The goal of this model is to understand some of the simple rules farmers may follow to self-govern their consumption of a water resource. Farmer agents make their crop decisions based on deficit irrigation crop production function and a net present value discount rate. The farmers choose between a thirsty crop with a high production cost and a dry crop with a low production cost. Simulations results show that farmers switch crops in accordance with limited water and land resources. Farmers can maintain profit and yield by following simple rules of crop switching based on future yields and optimal irrigation. In drought conditions, individual agents expecting lower annual rainfall were able to increase their total profits. The maintenance of crop yield and profit is evidence of successful adaptation when farmers switch to crops that require less water.
ContributorsGokool, Rachael Shanta (Author) / Janssen, Marco (Thesis director) / Eakin, Hallie (Committee member) / School of Human Evolution and Social Change (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Major Depressive Disorder (MDD) affects over 300 million people worldwide, with the hippocampus showing decreased volume and activity in patients with MDD. The current study investigated whether a novel preclinical model of depression, unpredictable intermittent restraint (UIR), would decrease hippocampal neuronal dendritic complexity. Adult Sprague Dawley rats (24 male, 24 female) were equally divided into 4 groups: control males (CON-M), UIR males (UIR-M), control females (CON-F) and UIR females (UIR-F). UIR groups received restraint and shaking on an orbital shaker on a randomized schedule for 30 or 60 minutes/day for two to six days in a row for 26 days (21 total UIR days) before behavioral testing commenced. UIR continued and was interspersed between behavioral test days. At the end of behavioral testing, brains were processed. The behavior is published and not part of my honor’s thesis; my contribution involved quantifying and analyzing neurons in the hippocampus. Several neuronal types are found in the CA3 subregion of the hippocampus and I focused on short shaft (SS) neurons, which show different sensitivities to stress than the more common long shaft (LS) variety. Brains sections were mounted to slides and Golgi stained. SS neurons were drawn using a microscope with camera lucida attachment and quantified using the number of bifurcations and dendritic intersections as metrics for dendritic complexity in the apical and basal areas separately. The hypothesis that SS neurons in the CA3 region of the hippocampus would exhibit apical dendritic simplification in both sexes after UIR was not supported by our findings. In contrast, following UIR, SS apical dendrites were more complex in both sexes compared to controls. Although unexpected, we believe that the UIR paradigm was an effective stressor, robust enough to illicit neuronal adaptations. It appears that the time from the end of UIR to when the brain tissue was collected, or the post-stress recovery period, and/or repeated behavioral testing may have played a role in the observed increased neuronal complexity. Future studies are needed to parse out these potential effects.
ContributorsAcuna, Amanda Marie (Author) / Conrad, Cheryl (Thesis director) / Corbin, William (Committee member) / Olive, M. Foster (Committee member) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
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
Major Depressive Disorder (MDD) is a widespread mood disorder that affects more than 300 million people worldwide and yet, high relapse rates persist. This current study aimed to use an animal model for depression, unpredictable intermittent restraint (UIR), to investigate changes in a subset of neurons within the hippocampus, a region of high susceptibility in MDD. Adult male and female Sprague-Dawley rats were randomly assigned to four treatment groups based on sex (n = 48, n = 12/group). Half of the rats underwent UIR that involved restraint with orbital shaking (30 min or 1 h) for 2-6 consecutive days, followed by one or two days of no stressors; the other half of the rats were undisturbed (CON). UIR rats were stressed for 28 days (21 days of actual stressors) before behavioral testing began with UIR continuing between testing days for nearly 70 days. Rats were then euthanized between 9 and 11 days after the last UIR session. Brains were processed for Golgi stain and long-shaft (LS) neurons within the hippocampal CA3a and CA3b regions were quantified for dendritic complexity using a Camera Lucida attachment. Our findings failed to support our hypothesis that UIR would produce apical dendritic retraction in CA3 hippocampal LS neurons in both males and females. Given that UIR failed to produce CA3 apical dendritic retraction in males, which is commonly observed in the literature, we discuss several reasons for these findings including, time from the end of UIR to when brains were sampled, and the effects of repeated cognitive testing. Given our published findings that UIR impaired spatial ability in males, but not females, we believe that UIR holds validity as a chronic stress paradigm, as UIR attenuated body weight gain in both males and females and produced reductions in thymus gland weight in UIR males. These findings corroborate UIR as an effective stressor in males and warrant further research into the timing of UIR-induced changes in hippocampal CA3 apical dendritic morphology.
ContributorsReynolds, Cindy Marie (Author) / Conrad, Cheryl D. (Thesis director) / Olive, M. Foster (Committee member) / School of Molecular Sciences (Contributor) / Department of English (Contributor) / Barrett, The Honors College (Contributor)
Created2020-12
Description
Coffee is an important link between the United States and Latin America and an important part of Latin America’s culture and economy. This paper looks at the similarities and differences between coffee organizations in Colombia, Ecuador, Peru, and Guatemala. Colombia has the strongest coffee organizations with the most political power. Guatemala and Peru, to a lesser extent, have well organized and powerful organizations that make up their industry. However, Ecuador has a significantly less organized organization. At their core, each country has a similar structure. There is one organization on the national level that watches out for the industry as a whole. Underneath that, there are smaller, often regional organizations made up of cooperatives pooling their resources for export. They function in similar ways as the national organizations, but have less reach. At the bottom, there are individual cooperatives and independent farmers. These cooperatives do not have much reach or connection to international markets.
ContributorsChabin, James Edward (Author) / Janssen, Marco (Thesis director) / Taylor, Keith (Committee member) / School of Sustainability (Contributor) / School of International Letters and Cultures (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
The first numerical predictions of the dynamical diquark model of multiquark exotic hadrons are presented. Using Born-Oppenheimer potentials calculated from lattice QCD and phenomenological diquark(triquark) masses, mass eigenvalues that are degenerate in spin and isospin are computed from numerical solutions to both coupled and uncoupled Schroedinger equations. Assuming reasonable estimates of the fine-structure splittings, we find that the band structure of our mass spectra agrees well with the experimentally observed spectrum of charmonium-like states. Using our best fits, we predict a number of unobserved states, such as pentaquark states that lie below the charmonium-plus-nucleon threshold.
ContributorsPeterson, Curtis Taylor Taylor (Author) / Lebed, Richard (Thesis director) / Belitsky, Andrei (Committee member) / Department of Physics (Contributor, Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
With opioid use disorder (OUD) being an epidemic, it is important to investigate the mechanisms as to why this is so. This study established a self-administration paradigm to model and investigate the mechanisms of polysubstance, sequential use in conjunction with the analysis of withdrawal symptomatology driven by opioid withdrawal. The independent variables were dichotomized into the control group (food/cocaine) and the experimental group (oxycodone/cocaine). We hypothesized that more cocaine would be self-administered on the first day of oxycodone withdrawal. In addition, we hypothesized that somatic signs of withdrawal would increase at 16 hours post-oxycodone self-administration. Finally, we hypothesized that cocaine intake during oxycodone withdrawal would potentiate subsequent oxycodone self-administration. Our findings revealed that animals readily discriminated between the active (food or oxycodone) and inactive levers - but will however require more animals to achieve the appropriate power. Further, the average cocaine infusions across phases exhibited significance between the oxycodone/cocaine and food/cocaine group, with the average cocaine infusions being lower in food than in oxycodone-experienced animals. This implies that the exacerbation of the sequential co-use pattern in this case yields an increase in cocaine infusions that may be driven by oxycodone withdrawal. Further, to characterize withdrawal from oxycodone self-administration, somatic signs were examined at either 0 or 16 hrs following completion of oxycodone self-administration. The oxycodone/cocaine group exhibited significantly lower body temperature at 16 hrs of oxycodone withdrawal compared to 0 hrs. No differences in somatic signs of withdrawal in the food/cocaine group was found between the two timepoints. Oxycodone withdrawal was not found to potentiate any subsequent self-administration of oxycodone. Future research is needed to uncover neurobiological underpinnings of motivated polysubstance use in order to discover novel pharmacotherapeutic treatments to decrease co-use of drugs of abuse. Overall, this study is of importance as it is the first to establish a working preclinical model of a clinically-relevant pattern of polysubstance use. By doing so, it enables an exceptional opportunity to examine co-use in a highly-controlled setting.
ContributorsUlangkaya, Hanaa Corsino (Author) / Gipson-Reichardt, Cassandra (Thesis director) / Olive, M. Foster (Committee member) / Department of Psychology (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Alzheimer’s disease (AD) is a progressive cognitive and behavior disorder that is characterized by the deposition of extracellular Aβ plaques, intracellular neurofibrillary tangles, and neuroinflammation. Aβ is generated by cleavage of the amyloid precursor protein (APP) by β-secretase (BACE1) and, subsequently, y- secretase. In recent years, there has been an increasing interest in studying and understanding inflammation as a therapeutic target for AD. Inflammation manifests in the brain in the form of activated microglia and astrocytes. These cells are able to release high levels of inflammatory cytokines such as Tumor Necrosis Factor-α (TNF-α). TNF-α is a major cytokine, which is involved in early inflammatory events and plays a role in the progression of AD pathology. There are currently no treatments that target chronic neuroinflammation. However, previous work in our laboratory with transgenic mice modeling AD suggested that the anti-cancer drug lenalidomide could lower neuroinflammation and slow AD progression, though the cellular and molecular mechanisms are yet to be elucidated. Here we hypothesized that lenalidomide can modulate TNF-α production in microglia and decrease amyloidogenesis. Using immortal cell lines mimicking several brain cell types, we discovered that lenalidomide is likely to decrease inflammation by modulating microglia cells rather than neurons or astrocytes. In addition, the drug may prevent the overexpression of BACE1 upon inflammation, thus blocking the overproduction of Aβ. If confirmed, these results could lead to a better understanding of how inflammation regulates Aβ synthesis and provide novel cellular and molecular therapeutic targets to control the progression AD.
ContributorsGujju, Manasa (Author) / DeCourt, Boris (Thesis director) / Olive, M. Foster (Committee member) / Department of Psychology (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Nicotine addiction remains a prevalent public health issue, and the FDA has released a statement outlining the systematic reduction of nicotine to non-zero levels in the coming years. Current research has not yet established the effects of abrupt nicotine dose reduction on vulnerability to relapse, nor has abrupt nicotine dose reduction been evaluated in terms of behavioral economic characteristics of demand and elasticity been evaluated for reduced doses of nicotine. Using a rat model, we first evaluated the comparability of between- and within-session protocols for establishing characteristics of demand and elasticity for nicotine to shorten experimental timelines for this study and future studies. We then tested environmental enrichment and sex as factors of elasticity of demand for nicotine. Using a rat model of relapse to cues, we also examined the effects of nicotine dose-reduction on vulnerability to relapse. We found differences in maximum consumption and demand between the between- and within-session protocols, as well as sex differences in elasticity of demand on the within-session protocol where male demand was more elastic than female demand. Additionally, we found that enrichment significantly increased elasticity of demand for nicotine for both males and females. Finally, preliminary analyses revealed that nicotine dose reduction yields more inelastic demand and higher maximum consumption, and these outcomes predict increased time to extinction of the association between nicotine and contingent cues, and increased rates of relapse. These studies highlight the usefulness and validity of within-session protocols, and also illustrate the necessity for rigorous testing of forced dose reduction on nicotine vulnerability.
ContributorsCabrera-Brown, Gabriella Paula (Author) / Gipson-Reichardt, Cassandra (Thesis director) / Olive, M. Foster (Committee member) / Davis, Mary (Committee member) / Sanford School of Social and Family Dynamics (Contributor) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12
Description
Cases of heroin use and overdose are on the rise in the United States which has created what some call a public health crisis. Previous studies have investigated the beneficial effect of social interaction recovering addicts, and in animal models of addiction, social interaction can prevent or reverse the conditioned rewarding effects of cocaine. This study sought to determine if social interaction would prevent or diminish a conditioned preference for a heroin-paired context. Following establishment of baseline place preference, adult male Sprague-Dawley rats underwent once daily conditioning with either saline, heroin (1 mg/kg), or the animal's cage-mate for a total of 8 conditioning sessions. Assessment of post-conditioning place preference revealed that both the heroin injections and the presence of the cage-mate produced a place preference . In contrast to the findings of previous studies using cocaine as the conditioning drug, it was determined that rats preferred the heroin-paired context over that paired with the cage-mate.. These findings suggest that the protective effects of social interaction found in prior studies using cocaine as the conditioning drug may not extend to opiates, perhaps a result of stronger contextual conditioning and/or rewarding effects of this class of abused drugs.
ContributorsMarble, Krista Lillian (Author) / Olive, M. Foster (Thesis director) / Tomek, Seven (Committee member) / Department of Psychology (Contributor) / Barrett, The Honors College (Contributor)
Created2017-12