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Title: Multi-Modal Interfaces for Sensemaking of Graph-Connected Datasets.
Creator: Wehrer, Anthony, Hughes, Charles, Wisniewski, Pamela, Pattanaik, Sumanta, Specht, Chelsea, Lisle, Curtis, University of Central Florida
Abstract / Description: The visualization of hypothesized evolutionary processes is often shown through phylogenetic trees. Given evolutionary data presented in one of several widely accepted formats, software exists to render these data into a tree diagram. However, software packages commonly in use by biologists today often do not provide means to dynamically adjust and customize these diagrams for studying new hypothetical relationships, and for illustration and publication purposes. Even where these options are...
Show moreThe visualization of hypothesized evolutionary processes is often shown through phylogenetic trees. Given evolutionary data presented in one of several widely accepted formats, software exists to render these data into a tree diagram. However, software packages commonly in use by biologists today often do not provide means to dynamically adjust and customize these diagrams for studying new hypothetical relationships, and for illustration and publication purposes. Even where these options are available, there can be a lack of intuitiveness and ease-of-use. The goal of our research is, thus, to investigate more natural and effective means of sensemaking of the data with different user input modalities. To this end, we experimented with different input modalities, designing and running a series of prototype studies, ultimately focusing our attention on pen-and-touch. Through several iterations of feedback and revision provided with the help of biology experts and students, we developed a pen-and-touch phylogenetic tree browsing and editing application called PhyloPen. This application expands on the capabilities of existing software with visualization techniques such as overview+detail, linked data views, and new interaction and manipulation techniques using pen-and-touch. To determine its impact on phylogenetic tree sensemaking, we conducted a within-subject comparative summative study against the most comparable and commonly used state-of-the-art mouse-based software system, Mesquite. Conducted with biology majors at the University of Central Florida, each used both software systems on a set number of exercise tasks of the same type. Determining effectiveness by several dependent measures, the results show PhyloPen was significantly better in terms of usefulness, satisfaction, ease-of-learning, ease-of-use, and cognitive load and relatively the same in variation of completion time. These results support an interaction paradigm that is superior to classic mouse-based interaction, which could have the potential to be applied to other communities that employ graph-based representations of their problem domains.
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Date Issued: 2019
Identifier: CFE0007872, ucf:52788
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0007872

Title: NEW COMPUTATIONAL APPROACHES FOR MULTIPLE RNA ALIGNMENT AND RNA SEARCH.
Creator: DeBlasio, Daniel, Zhang, Shaojie, University of Central Florida
Abstract / Description: In this thesis we explore the the theory and history behind RNA alignment. Normal sequence alignments as studied by computer scientists can be completed in $O(n^2)$ time in the naive case. The process involves taking two input sequences and finding the list of edits that can transform one sequence into the other. This process is applied to biology in many forms, such as the creation of multiple alignments and the search of genomic sequences. When you take into account the RNA sequence...
Show moreIn this thesis we explore the the theory and history behind RNA alignment. Normal sequence alignments as studied by computer scientists can be completed in $O(n^2)$ time in the naive case. The process involves taking two input sequences and finding the list of edits that can transform one sequence into the other. This process is applied to biology in many forms, such as the creation of multiple alignments and the search of genomic sequences. When you take into account the RNA sequence structure the problem becomes even harder. Multiple RNA structure alignment is particularly challenging because covarying mutations make sequence information alone insufficient. Existing tools for multiple RNA alignments first generate pair-wise RNA structure alignments and then build the multiple alignment using only the sequence information. Here we present PMFastR, an algorithm which iteratively uses a sequence-structure alignment procedure to build a multiple RNA structure alignment. PMFastR also has low memory consumption allowing for the alignment of large sequences such as 16S and 23S rRNA. Specifically, we reduce the memory consumption to $\sim O(band^2*m)$ where $band$ is the banding size. Other solutions are $\sim O(n^2*m)$ where $n$ and $m$ are the lengths of the target and query respectively. The algorithm also provides a method to utilize a multi-core environment. We present results on benchmark data sets from BRAliBase, which shows PMFastR outperforms other state-of-the-art programs. Furthermore, we regenerate 607 Rfam seed alignments and show that our automated process creates similar multiple alignments to the manually-curated Rfam seed alignments. While these methods can also be applied directly to genome sequence search, the abundance of new multiple species genome alignments presents a new area for exploration. Many multiple alignments of whole genomes are available and these alignments keep growing in size. These alignments can provide more information to the searcher than just a single sequence. Using the methodology from sequence-structure alignment we developed AlnAlign, which searches an entire genome alignment using RNA sequence structure. While programs have been readily available to align alignments, this is the first to our knowledge that is specifically designed for RNA sequences. This algorithm is presented only in theory and is yet to be tested.
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Date Issued: 2009
Identifier: CFE0002736, ucf:48166
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0002736

Title: CLONALITY AND GENETIC DIVERSITY IN POLYGONELLA MYRIOPHYLLA, A LAKE WALES RIDGE ENDEMIC PLANT.
Creator: Metzger, Genevieve, Parkinson, Christopher, University of Central Florida
Abstract / Description: Although capable of sexual reproduction, many plants also rely heavily on clonal reproduction. The formation of multiple, physiologically-independent units with the same genotype has important implications for spatial genetic structure and genetic diversity in these plants. The endangered scrub-dwelling perennial, Polygonella myriophylla is known to reproduce both sexually and clonally but no study to date has been able to investigate the spatial genetic patterns that occur in this species. I...
Show moreAlthough capable of sexual reproduction, many plants also rely heavily on clonal reproduction. The formation of multiple, physiologically-independent units with the same genotype has important implications for spatial genetic structure and genetic diversity in these plants. The endangered scrub-dwelling perennial, Polygonella myriophylla is known to reproduce both sexually and clonally but no study to date has been able to investigate the spatial genetic patterns that occur in this species. I use microsatellite markers to investigate questions about clonal structure and genetic diversity in five populations of P. myriophylla and address some of the implications of my findings for conservation of this species: Overall, I find that 57% of sampled clusters of P. myriophylla are composed of a single genet (genetic individual) with multiple physiological units (ramets) while the remainder are made up of two or more genets. I found differences in both clonal reproduction and genetic diversity among populations. I also found evidence of limited gene flow even over small spatial scales (less than 10 km) and for at least 4 genetic clusters occurring within the species range. Despite high levels of genetic diversity overall, there is evidence of reduced genetic diversity in two populations My results suggest that high levels of clonality may be important in maintaining genetic diversity in P. myriophylla. I also provide evidence that dirt roadsides may not represent a refuge for this species.
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Date Issued: 2010
Identifier: CFE0003264, ucf:48516
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0003264

Title: AN INVESTIGATION OF THE EFFECTS OF USING DIGITAL FLASH CARDS TO INCREASE BIOLOGY VOCABULARY KNOWLEDGE IN HIGH SCHOOL STUDENTS WITH LEARNING DISABILITIES.
Creator: Grillo, Kelly, Dieker, Lisa, University of Central Florida
Abstract / Description: The field of science education, specifically biology, is becoming more challenging due to richer and more rigorous content demands. Along with new demands is the emergence of National Common Core Standards and End of Course Exams. Despite these changes, one factor remains consistent: As content knowledge increases, language demands also increase. For students with learning disabilities (LD), specifically those with language-based disabilities, the increasing vocabulary demand can lead to...
Show moreThe field of science education, specifically biology, is becoming more challenging due to richer and more rigorous content demands. Along with new demands is the emergence of National Common Core Standards and End of Course Exams. Despite these changes, one factor remains consistent: As content knowledge increases, language demands also increase. For students with learning disabilities (LD), specifically those with language-based disabilities, the increasing vocabulary demand can lead to failure due not to a lack of understanding biology but the vocabulary associated with the content. In an attempt to impact high school students with learning disabilities'success in biology, a vocabulary intervention was investigated. Research suggests as more and more content is compressed into science courses, teachers are looking toward technology to assist with vocabulary mastery. The current research study examined the effects of a digital flash card intervention, Study Stack, versus a paper flash card intervention in biology for students with LD by measuring students'word knowledge and overall biology course achievement. Findings from repeated measures ANOVA showed a statistically significant increase on both the vocabulary assessment as well as the course grades in biology over time. However, the test of between effects considering card type yielded no differential change on vocabulary assessment and course grades in biology. Based on qualitative data, students interviewed liked the tool and found it to be helpful in learning biology terminology.
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Date Issued: 2011
Identifier: CFE0003972, ucf:48662
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0003972

Title: The effect of glycerol on readily biodegradable chemical oxygen demand (RBCOD) in a wastewater stream.
Creator: Rawut, Rojina, Sadmani, A H M Anwar, Lee, Woo Hyoung, Duranceau, Steven, University of Central Florida
Abstract / Description: This study evaluated the short-term effects of glycerol addition on readily biodegradable (RB) chemical oxygen demand (COD) in a carbon limited wastewater influent. The presence of an RB fraction provides with a suitable substrate for microorganisms to produce volatile fatty acids (VFA). The oxygen utilization rate (OUR) has been used to evaluate the oxygen consumption for RB substrate in wastewater. Wastewater with low organic content contains limited RB substrate, and thus, additional...
Show moreThis study evaluated the short-term effects of glycerol addition on readily biodegradable (RB) chemical oxygen demand (COD) in a carbon limited wastewater influent. The presence of an RB fraction provides with a suitable substrate for microorganisms to produce volatile fatty acids (VFA). The oxygen utilization rate (OUR) has been used to evaluate the oxygen consumption for RB substrate in wastewater. Wastewater with low organic content contains limited RB substrate, and thus, additional carbon source is required to improve biological treatment capability. Acetate, propionate, methanol, and glycerol are the commonly available carbon sources for biological treatment process. However, the cost of acetate and propionate are relatively high, and it is not economical to use these carbon sources in the wastewater plant. The use of methanol as a carbon source inherently poses safety issues in field applications due to its toxic and flammable properties. On the other hand, crude glycerol is the byproduct of biodiesel, which is an excellent carbon source alternative. However, crude glycerol contains impurities and requires a certain degree of purification to enhance the performance. The samples for the study were collected from the Iron Bridge Wastewater Reclamation Facility (Oviedo, FL) designed for treating municipal wastewater. The total COD (TCOD) of the sample influent was in the range of 237 to 408 mg COD/L, and RBCOD value was between 38 and 80.5 mg COD/L, containing up to 10 mg COD/L of VFA. This study also demonstrates the relationship between the glycerol concentration and OURs during the diauxic growth phase from the addition of glycerol. The growth was due to the existence of RB substrate and availability of glycerol for the microorganisms. TCOD increased from 284 to 378 mg COD/L and from 284 mg COD/L to 323 mg COD/L by spiking approximately 30 and 15 mL of glycerol stock solution (6.67 g/L), respectively. RBCOD increased from 45 to 89 mg COD/L and 55 mg COD/ L by spiking 30 mL and 15 ml glycerol stock solution, respectively. The initial influent heterotrophic active biomass (ZBH) increased from 5.4 to 15.8 mg VSS/L (8 to 23.4 mg COD/L) due to the addition of glycerol, indicating that the glycerol may be an adequate carbon source. The COD of wastewater with limited VFA (e.g., 10 mg COD/L) increased up to 2,502 mg COD/L where propionic acid (2,468 mg COD/L) exists as the primary end product with a small quantity of acetic acid (34 mg COD/L). Propionic acid was the main VFA component fermented from the glycerol addition. Glycerol addition led to increased RBCOD accompanied by high VFA production. This research investigated the short-term effect of glycerol addition on existing RBCOD in wastewater. It is recommended to explore the effect of increased RBCOD by the addition of glycerol to the effluent N and P for future study.
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Date Issued: 2016
Identifier: CFE0006543, ucf:51324
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006543

Title: Imperial Japan's Human Experiments Before and During World War Two.
Creator: Vanderbrook, Alan, Zhang, Hong, Larson, Peter, Lester, Connie, University of Central Florida
Abstract / Description: After Japan occupied Manchuria in 1931, Ishii Shiro created Unit 731 and began testing biological weapons on unwilling human test subjects. The history of Imperial Japan's human experiments was one in which Ishii and Unit 731 was the principal actor, but Unit 731 operated in a much larger context. The network in which 731 operated consisted of Unit 731 and all its sub-units, nearly every major Japanese university, as well as many people in Japan's scientific and medical community, military...
Show moreAfter Japan occupied Manchuria in 1931, Ishii Shiro created Unit 731 and began testing biological weapons on unwilling human test subjects. The history of Imperial Japan's human experiments was one in which Ishii and Unit 731 was the principal actor, but Unit 731 operated in a much larger context. The network in which 731 operated consisted of Unit 731 and all its sub-units, nearly every major Japanese university, as well as many people in Japan's scientific and medical community, military hospitals, military and civilian laboratories, and the Japanese military as a whole. Japan's racist ultra-nationalist movement heavily influenced these institutions and people; previous historians have failed to view Japan's human experiments in this context. This thesis makes use of a combination of declassified United States government and military documents, including court documents and the interviews conducted during the Unit 731 Exhibition that traveled Japan in 1993 and 1994, and then recorded by Hal Gold in his book, Unit 731 Testimony, along with a number of secondary sources as supporting material. Each of these sources has informed this work and helped clarify that Unit 731 acted within a broader network of human experimentation and exploitation in a racist system, which normalized human atrocities. Attitudes of racism and superiority do not necessarily explain every action taken by Japanese military personnel and scientists, nor did every individual view their actions or the actions of their countrymen as morally correct, but it does help explain why these acts occurred. What enabled many Japanese scientists was the racist ideology of the ultra-nationalist movement in Japan.
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Date Issued: 2013
Identifier: CFE0004767, ucf:49769
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0004767

Title: Evaluation of the three-dimensional patterns and ecological impacts of the invasive Old World climbing fern (Lygodium microphyllum).
Creator: Maldonado, Alexis, Weishampel, John, VonHolle, Mary, Hinkle, Charles, University of Central Florida
Abstract / Description: Invasion by non-native species has had significant ecological and economic impacts on a global scale. In the state of Florida, Old World climbing fern (Lygodium microphyllum) is an invasive plant listed by FLEPPC as a category one invader with significant ecological impacts that threaten native plant diversity. This species relies on existing vegetative structures for support to climb into the forest canopy and forms dense mats that cover tree crowns. This subsequently affects the resources...
Show moreInvasion by non-native species has had significant ecological and economic impacts on a global scale. In the state of Florida, Old World climbing fern (Lygodium microphyllum) is an invasive plant listed by FLEPPC as a category one invader with significant ecological impacts that threaten native plant diversity. This species relies on existing vegetative structures for support to climb into the forest canopy and forms dense mats that cover tree crowns. This subsequently affects the resources available to other species present. Quantifying the structural changes due to the presence of this species has proved logistically difficult, especially on a large spatial scale.Airborne LiDAR (Light Detection And Ranging) technology is a form of remote sensing that measures the elevation of surfaces over a site. In this study I utilized LiDAR to calculate various forest structure metrics at Jonathan Dickinson State Park (JDSP) in Hobe Sound, Florida across various management frequencies and densities of Old World climbing fern. These data were used to quantify the degree to which this invasive species alters forest structure across these two gradients. I also recorded species composition in the field to relate how Old World climbing fern impacts native plant diversity. Structural measurements including average canopy height, height of median energy (HOME), rugosity, canopy openness, and vertical structural diversity (LHDI) were calculated for a total of three hundred 0.25ha sites stratified by invasion density and management frequency.Using a combination of univariate and multivariate statistical analyses I found that the presence of Old World Climbing fern altered the physical structure of the forest communities itivinvades. Higher percent cover of Old World climbing fern decreased structural diversity while increased management effort was found to mitigate those impacts. The management for Old World Climbing fern was also found to impact both species richness and diversity at JDSP. I also demonstrated that there were several species that were not found and others that were more common in the presence of Old World climbing fern and that there was a relationship between management and what species were present. The results show that both Old World climbing fern and the management practices used to control it have had significant ecological impacts on the natural communities in South Florida.
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Date Issued: 2014
Identifier: CFE0005206, ucf:50651
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005206

Title: Variation in Prospecting Behavior and Drivers of Post-Fire Habitat Preference Among Juvenile Florida Scrub-Jays.
Creator: Sherer, David, Bohlen, Patrick, Bowman, Reed, Jenkins, David, University of Central Florida
Abstract / Description: Florida Scrub-Jays (Aphelocoma coerulescens, FLSJ; federally Threatened) are cooperatively breeding birds endemic to Florida and dependent on fire-maintained xeric oak scrub. FLSJs are year-round residents, highly territorial, and rarely disperse far from their natal territory. Lifetime reproductive success is highest among individuals breeding in early-successional habitat, usually less than 9 to 10 years post-fire. However, because scrub burns infrequently such early-successional, high...
Show moreFlorida Scrub-Jays (Aphelocoma coerulescens, FLSJ; federally Threatened) are cooperatively breeding birds endemic to Florida and dependent on fire-maintained xeric oak scrub. FLSJs are year-round residents, highly territorial, and rarely disperse far from their natal territory. Lifetime reproductive success is highest among individuals breeding in early-successional habitat, usually less than 9 to 10 years post-fire. However, because scrub burns infrequently such early-successional, high-quality habitat is extremely limited and competition for it as breeding space is likely intense. Because some birds live long enough to experience habitat succession, FLSJs also occupy later-successional overgrown scrub, even though both survival and fecundity decline. Although immigration rates into later-successional habitat decline, some birds settle there, perhaps to avoid competition. Prior to dispersal into new breeding territories, most non-breeders engage in pre-dispersal forays, which occur before and immediately after the breeding season. Because FLSJ territories occur across a gradient of post-fire succession, and young birds make frequent forays beyond their natal territories, and are highly visible while doing so, they are ideal models to test how individual and environmental factors drive habitat preference when exploring a post-fire mosaic. I investigated how individual behavioral phenotype, natal territory condition, and body condition relative to conspecifics influence extra-territorial foray behavior across a habitat mosaic that includes various time-since-fire (TSF) intervals. My study system was a population of individually marked FLSJs on 1,214-ha of managed scrub at Archbold Biological Station (Highlands County, Florida). I measured off-territory movements of 114 yearling birds in three annual cohorts and quantified habitat preference using fine-scale fire history records. These data, paired with behavioral assays and morphometric records for each individual FLSJ, allowed me to create and compare models of exploratory behavior underlying searching patterns during pre-breeding forays. My results indicate significant variation in habitat preference by individual FLSJs during forays, driven by an individual's behavioral phenotype and the TSF of its natal territory.
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Date Issued: 2019
Identifier: CFE0007864, ucf:52790
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0007864

Title: PHYSICAL CHARACTERISTICS OF AN INDIVIDUAL: THE IDENTIFICATION OF BIOMARKERS FOR BIOLOGICAL AGE DETERMINATION.
Creator: Alvarez, Michelle, Ballantyne, Jack, University of Central Florida
Abstract / Description: It is now a matter of routine for the forensic scientist to obtain the genetic profile of an individual from DNA recovered from a biological stain deposited at a crime scene. Potential contributors of the stain must either be known to investigators (i.e. a developed suspect) or the questioned profile must be searched against a database of DNA profiles such as those maintained in the CODIS National DNA database. However, in those instances where there is no developed suspect and no match is...
Show moreIt is now a matter of routine for the forensic scientist to obtain the genetic profile of an individual from DNA recovered from a biological stain deposited at a crime scene. Potential contributors of the stain must either be known to investigators (i.e. a developed suspect) or the questioned profile must be searched against a database of DNA profiles such as those maintained in the CODIS National DNA database. However, in those instances where there is no developed suspect and no match is obtained after interrogation of appropriate DNA databases, the DNA profile per se presently provides no meaningful information to investigators, with the notable exception of gender determination. In these situations it would be advantageous to the investigation, if additional probative information could be obtained from the biological stain. A useful biometric that could provide important probative information, and one that may be amenable to molecular genetic analysis, is the biological age of an individual. The ability to provide investigators with information as to whether a DNA donor is a newborn, infant, toddler, child, adolescent, adult, middle-aged or elderly individual could be useful in certain cases, particularly those involving young children such as kidnappings or in providing additional intelligence during terrorist investigations. Currently no validated molecular assays exist for age determination. Biological human ageing can be defined by two distinct processes, degenerative and developmental ageing. The degenerative process of ageing is based on theories which identify an increase or decrease in physiological conditions with increasing age. In contrast, the developmental process of ageing is based on the theory that as individuals increase in chronological age, there will be subtle corresponding molecular based biological changes, each requiring genes to be expressed or silenced, indicative of that particular stage of life. We investigated the degenerative process of chromosomal telomere shortening, as well as the developmental process of gene expression profiling analysis, in an attempt to identify biomarkers of biological age in a self-renewing tissue such as blood. While telomere length analysis was an ineffective method for age determination; gene expression analysis revealed three gene transcripts expressed in an age-dependent physiological manner. These species namely- COL1A2, HBE1 and IGFBP3, were found to be expressed at elevated levels in younger individuals, newborns, or post-pubertal individuals, respectively. The biological process of hemoglobin switching was also investigated for the possibility of determining human age. While experimenting with the potential of using the gamma-hemoglobin chains, as newborn specific gene candidates, we serendipitously discovered four novel truncated transcripts, which we have termed HBG1n1, HBG1n2, HBG2n2 and HBG2n3; whose expression was restricted to whole-blood newborn samples and specific fetal tissues. The molecular origin of these transcripts appears to be at the RNA level, being produced by specific rearrangement events occurring in the standard gamma hemoglobin transcripts (HBG1 and HBG2), which yield these new isoforms that are expressed in a highly regulated tissue specific manner.
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Date Issued: 2007
Identifier: CFE0001737, ucf:47297
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0001737

Title: Cost and Environmental Impacts of Leachate Nitrogen/Phosphorus Management Approaches.
Creator: Alanezi, Alaa, Reinhart, Debra, Randall, Andrew, Sadmani, A H M Anwar, University of Central Florida
Abstract / Description: Landfill leachate is a challenging wastewater to discharge into municipal wastewater treatment plants (WWTPs), the most common approach for leachate management, due to the presence of contaminants that may affect the performance of the treatment plant. Treatment, disposal, and transportation of leachate are expensive and therefore a concern. Currently, sidestream treatment is becoming increasingly common in WWTPs prior to returning the liquid to the plant influent. For this research, a new...
Show moreLandfill leachate is a challenging wastewater to discharge into municipal wastewater treatment plants (WWTPs), the most common approach for leachate management, due to the presence of contaminants that may affect the performance of the treatment plant. Treatment, disposal, and transportation of leachate are expensive and therefore a concern. Currently, sidestream treatment is becoming increasingly common in WWTPs prior to returning the liquid to the plant influent. For this research, a new treatment scheme is introduced combining centrate and leachate to reduce contaminants, recover phosphorous and nitrogen through struvite precipitation, and reduce energy requirements through anaerobic ammonium oxidation (Anammox). By combining the two waste streams, the respective limited nutrients (nitrogen in centrate and nitrogen in leachate) can be removed in a low cost chemical treatment resources can be recovered. Carbon contaminants and remaining nutrients can be removed in subsequent innovative biological treatment units. The objective of this thesis is to conduct a cost analysis and environmental assessment of the proposed novel treatment approach and to compare it to more traditional landfill on-site leachate treatment approaches (e.g., membrane bioreactors (MBR) and sequencing batch reactors (SBR)). The study was completed with the use of spreadsheet-based models. Spreadsheets have been developed to evaluate treatment costs (Capital + O(&)M) for both the proposed nutrient recovery/biological and traditional on-site leachate treatments. Transportation costs of leachate to the WWTP have been studied and analyzed by the use of a spreadsheet model as a function of distance. Results suggest that treatment using Struvite (-) Aerobic Granular Sludge (-) Anammox (SGA) was higher in cost compared to traditional approaches. However, positive outcomes from this process include: lower N_2 O emissions, lower power consumption, struvite fertilizer, and overall recovery of nitrogen and phosphorus with the combination of centrate and leachate.
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Date Issued: 2018
Identifier: CFE0007147, ucf:52310
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0007147

Title: Biogeochemical Cycling and Nutrient Control Strategies for Groundwater at Stormwater Infiltration Basins.
Creator: O'Reilly, Andrew, Chang, Ni-bin, Wanielista, Martin, Chopra, Manoj, Wang, Dingbao, Katz, Brian, University of Central Florida
Abstract / Description: Elevated concentrations of nutrients, particularly nitrate, in groundwater and springs in Florida are a growing resource management concern. Stormwater infiltration basins, which are a common stormwater management practice in the well-drained karst terrain areas of Florida, are a potentially important source of nutrients to the groundwater system because stormwater exits the basin by only evaporation or infiltration. To better understand the biogeochemical processes integrating stormwater...
Show moreElevated concentrations of nutrients, particularly nitrate, in groundwater and springs in Florida are a growing resource management concern. Stormwater infiltration basins, which are a common stormwater management practice in the well-drained karst terrain areas of Florida, are a potentially important source of nutrients to the groundwater system because stormwater exits the basin by only evaporation or infiltration. To better understand the biogeochemical processes integrating stormwater infiltration impacts on groundwater resources in a field-scale setting, a combination of hydrologic, soil chemistry, water chemistry, dissolved and soil gas, isotope, and microbiological data was collected from 2007 through 2010 at two stormwater infiltration basins receiving runoff from predominantly residential watersheds in north-central Florida. Substantially different biogeochemical processes affecting nitrogen fate and transport were observed beneath the two stormwater infiltration basins. Differences are related to soil textural properties that deeply link hydroclimatic conditions with soil moisture variations in a humid, subtropical climate. During 2008, shallow groundwater beneath the basin with predominantly clayey soils (median 41% silt+clay content) exhibited decreases in dissolved oxygen from 3.8 to 0.1 mg/L and decreases in nitrate-nitrogen from 2.7 mg/L to less than 0.016 mg/L, followed by manganese and iron reduction, sulfate reduction, and methanogenesis. In contrast, beneath the basin with predominantly sandy soils (median 2% silt+clay content), aerobic conditions persisted from 2007 through 2009 (dissolved oxygen of 5.0(-)7.8 mg/L), resulting in nitrate-nitrogen of 1.3(-)3.3 mg/L in shallow groundwater. Soil extractable nitrate-nitrogen was significantly lower and the copper-containing nitrite reductase gene density was significantly higher beneath the clayey basin. Differences in moisture retention capacity between fine- and coarse-textured soils resulted in median volumetric gas-phase contents of 0.04 beneath the clayey basin and 0.19 beneath the sandy basin, inhibiting surface/subsurface oxygen exchange beneath the clayey basin. Subsurface biogeochemical processes at the clayey stormwater infiltration basin were further analyzed to better understand the effects of the highly variable hydrologic conditions common in humid, subtropical climates. Cyclic variations in biogeochemical processes generally coincided with wet and dry hydroclimatic conditions. Oxidizing conditions in the subsurface persisted for about one month or less at the beginning of wet periods with dissolved oxygen and nitrate showing similar temporal patterns. Reducing conditions in the subsurface evolved during prolonged flooding of the basin. At about the same time oxygen and nitrate reduction concluded, manganese, iron, and sulfate reduction began, with the onset of methanogenesis one month later. Reducing conditions persisted up to six months, continuing into subsequent dry periods until the next major oxidizing infiltration event. Evidence of denitrification in shallow groundwater at the site is supported by median nitrate-nitrogen less than 0.016 mg/L, excess nitrogen gas up to 3 mg/L progressively enriched in delta-15N during prolonged basin flooding, and isotopically heavy delta-15N and delta-18O of nitrate (up to 25 and 15 per mil, respectively). Isotopic enrichment of newly infiltrated stormwater suggests denitrification was partially completed within two days. Soil and water chemistry data suggest a biogeochemically active zone exists in the upper 1.4 m of soil, where organic carbon was the likely electron donor supplied by organic matter in soil solids or dissolved in infiltrating stormwater. The cyclic nature of reducing conditions effectively controlled the nitrogen cycle, switching nitrogen fate beneath the basin from nitrate leaching to reduction in the shallow saturated zone. Soil beneath the sandy stormwater infiltration basin was amended using biosorption activated media (BAM) to study the effectiveness of this technology in reducing inputs of nitrogen and phosphorus to groundwater. The functionalized soil amendment BAM consists of a 1.0:1.9:4.1 mixture (by volume) of tire crumb (to increase sorption capacity), silt and clay (to increase soil moisture retention), and sand (to promote sufficient infiltration), which was applied to develop an innovative best management practice (BMP) utilizing nutrient reduction and flood control sub-basins. Construction and materials costs, excluding profit and permit fees, for the innovative BMP were about $US 65 per square meter of basin bottom. Comparison of nitrate/chloride ratios for the shallow groundwater indicate that prior to using BAM, nitrate concentrations were substantially influenced by nitrification or variations in nitrate input. In contrast, for the new basin utilizing BAM, nitrate/chloride ratios indicate minor nitrification and nitrate losses with the exception of one summer sample that indicated a 45% loss. Biogeochemical indicators (denitrifier activity derived from real-time polymerase chain reaction and variations in major ions, nutrients, dissolved and soil gases, and stable isotopes) suggest nitrate losses are primarily attributable to denitrification, whereas dissimilatory nitrate reduction to ammonium and plant uptake are minor processes. Denitrification was likely occurring intermittently in anoxic microsites in the unsaturated zone, which was enhanced by increased soil moisture within the BAM layer and resultant reductions in surface/subsurface oxygen exchange that produced conditions conducive to increased denitrifier activity. Concentrations of total dissolved phosphorus and orthophosphate were reduced by more than 70% in unsaturated zone soil water, with the largest decreases in the BAM layer where sorption was the most likely mechanism for removal. Post-BAM orthophosphate/chloride ratios for shallow groundwater indicate predominantly minor increases and decreases in orthophosphate with the exception of one summer sample that indicated a 50% loss. Differences in nutrient variations between the unsaturated zone and shallow groundwater may be the result of the intensity and duration of nutrient removal processes and mixing ratios with water that had undergone little biogeochemical transformation. In order to quantify potential processes leading to observed nitrogen losses beneath the innovative BMP, an integrated infiltration basin(-)nitrogen reduction (IBNR) system dynamics model was developed. Based on two simulation periods, the IBNR model indicated denitrification accounted for a loss of about one-third of the total dissolved nitrogen mass inflow and was occurring predominantly in the BAM layer. The IBNR model results in combination with the field-based biogeochemical assessment demonstrated that the innovative BMP using the functionalized soil amendment BAM is a promising passive, economical, stormwater nutrient-treatment technology. Further field- and laboratory-scale research on the long-term sustainability of nutrient losses and further elucidation of causative physicochemical and biogeochemical mechanisms would contribute to improved BAM performance and green infrastructure development in the future.
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Date Issued: 2012
Identifier: CFE0004419, ucf:49391
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0004419

Title: Genetically-programmed suicide of adrenergic cells in the mouse leads to severe left ventricular dysfunction, impaired weight gain, and symptoms of neurological dysfunction.
Creator: Owji, Aaron, Ebert, Steven, King, Stephen, Sugaya, Kiminobu, University of Central Florida
Abstract / Description: Phenylethanolamine-N-methyltransferase (Pnmt) catalyzes the conversion of noradrenaline to adrenaline and is the last enzyme in the catecholamine biosynthetic pathway. Pnmt serves as a marker for adrenergic cells, and lineage-tracing experiments have identified the embryonic heart and hindbrain region as the first sites of Pnmt expression in the mouse. Pnmt expression in the heart occurs before the adrenal glands have formed and prior to sympathetic innervation, suggesting that the heart is...
Show morePhenylethanolamine-N-methyltransferase (Pnmt) catalyzes the conversion of noradrenaline to adrenaline and is the last enzyme in the catecholamine biosynthetic pathway. Pnmt serves as a marker for adrenergic cells, and lineage-tracing experiments have identified the embryonic heart and hindbrain region as the first sites of Pnmt expression in the mouse. Pnmt expression in the heart occurs before the adrenal glands have formed and prior to sympathetic innervation, suggesting that the heart is the first site of catecholamine production in the mouse. The function of these Pnmt+ cells in heart development remains unclear. In the present study, we test the hypothesis that (i) a genetic ablation technique utilizing a suicide reporter gene selectively destroys Pnmt cells in the mouse, and (ii) Pnmt cells are required for normal cardiovascular and neurological function.To genetically ablate adrenergic cells, we mated Pnmt-Cre mice, in which Cre-recombinase is under the transcriptional regulation of the Pnmt promoter, and a Cre -activated diphtheria toxin A (DTA) mouse strain (ROSA26-eGFP-DTA), thereby causing activation of the toxic allele (DTA) in Pnmt-expressing (adrenergic) cells resulting in selective (")suicide(") of these cells in approximately half of the offspring. The other half serve as controls because they do not have the ROSA26-eGFP-DTA construct. In the Pnmt+/Cre; R26+/DTA offspring, we achieve a dramatic reduction in Pnmt transcript and Pnmt immunoreactive area in the adrenal glands. Furthermore, we show that loss of Pnmt cells results in severe left ventricular dysfunction that progressively worsens with age. These mice exhibit severely reduced cardiac output and ejection fraction due to decreased LV contractility and bradycardia at rest. Surprisingly, these mice appear to have a normal stress response, as heart rate and ejection fraction increased to a similarextent compared to controls. In addition to baseline cardiac dysfunction, these mice fail to gain body weight in a normal manner and display gross neurological dysfunction, including muscular weakness, abnormal gaiting, and altered tail suspension reflex, an indicator of neurological function.This work demonstrates that selective Pnmt cell destruction leads to severe left ventricular dysfunction, lack of weight gain, and neurological dysfunction. This novel mouse is expected to shed insight into the role of Pnmt cells in the heart, and suggests a role for Pnmt cells in neurological regulation of feeding behavior, metabolism, and motor control.
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Date Issued: 2015
Identifier: CFE0006048, ucf:50984
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006048

Title: A Study of Central Florida College Students' Acceptance of the Theory of Evolution, Microevolution, Macroevolution, and Human Evolution.
Creator: Schleith, David, Murray, Kenneth, Baldwin, Lee, Doherty, Walter, Everett, Robert, University of Central Florida
Abstract / Description: In order to study the teaching and learning of the theory of evolution and determine levels of acceptance of the theory of evolution among college students studying biology in Central Florida, the Inventory of Student Evolution Acceptance, I-SEA, was administered to over 500 university students enrolled in a biology course during the Fall 2016 term. An analysis of 489 completed surveys demonstrated strong overall acceptance of the theory of evolution (average score = 103 out of 120 total...
Show moreIn order to study the teaching and learning of the theory of evolution and determine levels of acceptance of the theory of evolution among college students studying biology in Central Florida, the Inventory of Student Evolution Acceptance, I-SEA, was administered to over 500 university students enrolled in a biology course during the Fall 2016 term. An analysis of 489 completed surveys demonstrated strong overall acceptance of the theory of evolution (average score = 103 out of 120 total possible). Of all students, 78% fell into the category of very high acceptance of the theory of evolution. Students who reported attending worship services weekly or more scored statistically significantly lower on the I-SEA than students who reported attending worship services less than weekly. The level of previous high school coursework in biology(-)whether honors, or advanced biology courses were taken-- did not translate into statistically significant differences in acceptance of evolution as measured by the I-SEA. Three subscales contained within the Inventory of Student Evolution Acceptance are designed to measure student acceptance of microevolution, macroevolution, and human evolution. Students demonstrate higher levels of acceptance of microevolution than macroevolution or human evolution. These findings serve to inform educational leaders and science educators regarding students' worldview and how worldview may inform what students accept as true and valid. The I-SEA serves as a useful educational tool to inform instructional decisions in the biology classroom.
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Date Issued: 2017
Identifier: CFE0006792, ucf:51818
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006792

Title: INTELLIGENT DESIGN.
Creator: Dudziak, Jillian, Poindexter, Carla, University of Central Florida
Abstract / Description: As human beings we are designed and created in a fabric that is profound and complex. We are built with a framework where mind and body work in a concerted effort to maintain our lives automatically. A deep and defining part of our existence as humans is not just the innate desire to live but to live in consistent well-beingemotionally, physically, and mentally. I believe when we incorporate our knowledge of human physiology into our creative process then we allow ourselves a greater...
Show moreAs human beings we are designed and created in a fabric that is profound and complex. We are built with a framework where mind and body work in a concerted effort to maintain our lives automatically. A deep and defining part of our existence as humans is not just the innate desire to live but to live in consistent well-beingemotionally, physically, and mentally. I believe when we incorporate our knowledge of human physiology into our creative process then we allow ourselves a greater opportunity to create an authentic connection with our intended audience. My work during the past three years has been rooted in the study of these philosophical and scientific principles. I created a series of visual experimentations that aim to assist in my understanding of human beings at an emotional and biological level. Armed with a deep desire to understand humanity, my goal is to create work that fosters positive change and has significant impact in the world. My past and present research has been focused on human emotions, the intuitive creative process and the relationship between technology and establishing social identity.
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Date Issued: 2011
Identifier: CFE0003693, ucf:48844
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0003693

Title: Ozone and GAC Treatment of a Central Florida Groundwater for Sulfide and Disinfectant By-Product Control.
Creator: Lamoureux, Tara, Duranceau, Steven, Randall, Andrew, Wang, Dingbao, University of Central Florida
Abstract / Description: This study evaluated the combination of ozone and granular activated carbon (GAC) treatment for the removal of sulfide and disinfection byproduct (DBP) precursors in drinking water at the pilot-scale. The research conducted was performed at the Auxiliary (Aux) and Main Water Treatment Plants (WTPs) in Sanford, Florida. Both WTPs rely upon groundwater sources that contain total sulfide ranging from 0.02 to 2.35 mg/L and total organic carbon (TOC) ranging from 0.61 to 2.20 mg/L. The Aux WTP's...
Show moreThis study evaluated the combination of ozone and granular activated carbon (GAC) treatment for the removal of sulfide and disinfection byproduct (DBP) precursors in drinking water at the pilot-scale. The research conducted was performed at the Auxiliary (Aux) and Main Water Treatment Plants (WTPs) in Sanford, Florida. Both WTPs rely upon groundwater sources that contain total sulfide ranging from 0.02 to 2.35 mg/L and total organic carbon (TOC) ranging from 0.61 to 2.20 mg/L. The Aux WTP's raw water contains, on average, 88% more sulfide and 24% more TOC than the Main WTP. Haloacetic acids (HAA5) and total trihalomethanes (TTHMs) comprise the regulated forms of DBPs. HAA5 are consistently below the maximum contaminant level (MCL) of 60 ?g/L, while TTHM ranges from 70 to 110 ?g/L, at times exceeding the MCL of 80 ?g/L in the distribution system. Ozone alone removed total sulfide and reduced UV-254 by about 60% at the Aux Plant and 35% at the Main Plant. Producing an ozone residual of 0.50 mg/L prevented the formation of bromate while removing approximately 35 to 60% concentration of DBP precursors as measured by UV-254. Operating the GAC unit at an empty bed contact time (EBCT) of 10 minutes for the Aux Plant and 5.5 minutes for the Main Plant resulted in 75% and 53% of UV-254 reduction, respectively. The average 120 hour TTHM formation potential for the Aux and Main Plants were 66 ?g/L and 52 ?g/L, respectively, after treatment by ozone and GAC. GAC exhaustion was deemed to have occurred after seven weeks for the Aux Plant and eleven weeks for the Main Plant. The GAC columns operated in three phases: an adsorption phase, a transitional phase, and a biologically activated carbon (BAC) phase. The GAC adsorption phase was found to produce the lowest TTHMs; however, TTHMs remained less than 80 ?g/L during the BAC stage at each plant. BAC exhaustion did not occur during the course of this study. Ozone-GAC reduced chlorine demand by 73% for the Aux Plant and 10% for the Main Plant.
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Date Issued: 2013
Identifier: CFE0004708, ucf:49824
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0004708

biology (5)	+ -
biological nutrient removal (3)	+ -
biological treatment (3)	+ -
denitrification (3)	+ -
ecology (3)	+ -

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RNA (2)	+ -
conservation biology (2)	+ -
dispersal (2)	+ -
science education (2)	+ -
Ablation (1)	+ -
Adrenaline (1)	+ -
Adrenergic Cells (1)	+ -
Age Determination (1)	+ -
Alignment (1)	+ -
Aphelocoma coerulescens (1)	+ -
Behavioral ecology (1)	+ -
Bioinformatics (1)	+ -
Biological (1)	+ -
Biological Age (1)	+ -
Biological Filtration (1)	+ -
Biological Treatment (1)	+ -
Biological Warfare (1)	+ -
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Body Fluid (1)	+ -
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Cardiovascular Biology (1)	+ -
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Christianity (1)	+ -
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ETD Collection (33)	+ -
Honors Collection (1)	+ -
PRISM: Political & Rights Issues & Social Movements (1)	+ -

University of Central Florida (33)	+ -
Randall, Andrew (5)	+ -
Duranceau, Steven (4)	+ -
Sadmani, A H M Anwar (3)	+ -
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