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(1 - 9 of 9)
- Title
- Prediction of survival of early stages lung cancer patients based on ER beta cellular expressions and epidemiological data.
- Creator
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Martinenko, Evgeny, Shivamoggi, Bhimsen, Chow, Lee, Peale, Robert, Brandenburg, John, University of Central Florida
- Abstract / Description
-
We attempted a mathematical model for expected prognosis of lung cancer patients based ona multivariate analysis of the values of ER-interacting proteins (ERbeta) and a membranebound, glycosylated phosphoprotein MUC1), and patients clinical data recorded at the timeof initial surgery. We demonstrate that, even with the limited sample size available to use,combination of clinical and biochemical data (in particular, associated with ERbeta andMUC1) allows to predict survival of lung cancer...
Show moreWe attempted a mathematical model for expected prognosis of lung cancer patients based ona multivariate analysis of the values of ER-interacting proteins (ERbeta) and a membranebound, glycosylated phosphoprotein MUC1), and patients clinical data recorded at the timeof initial surgery. We demonstrate that, even with the limited sample size available to use,combination of clinical and biochemical data (in particular, associated with ERbeta andMUC1) allows to predict survival of lung cancer patients with about 80% accuracy whileprediction on the basis of clinical data only gives about 70% accuracy. The present work canbe viewed as a pilot study on the subject: since results conrm that ER-interacting proteinsindeed inuence lung cancer patients' survival, more data is currently being collected.
Show less - Date Issued
- 2011
- Identifier
- CFE0004134, ucf:49120
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004134
- Title
- Functional Data Analysis and its application to cancer data.
- Creator
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Martinenko, Evgeny, Pensky, Marianna, Tamasan, Alexandru, Swanson, Jason, Richardson, Gary, University of Central Florida
- Abstract / Description
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The objective of the current work is to develop novel procedures for the analysis of functional dataand apply them for investigation of gender disparity in survival of lung cancer patients. In particular,we use the time-dependent Cox proportional hazards model where the clinical information isincorporated via time-independent covariates, and the current age is modeled using its expansionover wavelet basis functions. We developed computer algorithms and applied them to the dataset which is...
Show moreThe objective of the current work is to develop novel procedures for the analysis of functional dataand apply them for investigation of gender disparity in survival of lung cancer patients. In particular,we use the time-dependent Cox proportional hazards model where the clinical information isincorporated via time-independent covariates, and the current age is modeled using its expansionover wavelet basis functions. We developed computer algorithms and applied them to the dataset which is derived from Florida Cancer Data depository data set (all personal information whichallows to identify patients was eliminated). We also studied the problem of estimation of a continuousmatrix-variate function of low rank. We have constructed an estimator of such functionusing its basis expansion and subsequent solution of an optimization problem with the Schattennormpenalty. We derive an oracle inequality for the constructed estimator, study its properties viasimulations and apply the procedure to analysis of Dynamic Contrast medical imaging data.
Show less - Date Issued
- 2014
- Identifier
- CFE0005377, ucf:50447
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0005377
- Title
- Accelerated Life Model with Various Types of Censored Data.
- Creator
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Pridemore, Kathryn, Pensky, Marianna, Mikusinski, Piotr, Swanson, Jason, Nickerson, David, University of Central Florida
- Abstract / Description
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The Accelerated Life Model is one of the most commonly used tools in the analysis of survival data which are frequently encountered in medical research and reliability studies. In these types of studies we often deal with complicated data sets for which we cannot observe the complete data set in practical situations due to censoring. Such difficulties are particularly apparent by the fact that there is little work in statistical literature on the Accelerated Life Model for complicated types...
Show moreThe Accelerated Life Model is one of the most commonly used tools in the analysis of survival data which are frequently encountered in medical research and reliability studies. In these types of studies we often deal with complicated data sets for which we cannot observe the complete data set in practical situations due to censoring. Such difficulties are particularly apparent by the fact that there is little work in statistical literature on the Accelerated Life Model for complicated types of censored data sets, such as doubly censored data, interval censored data, and partly interval censored data.In this work, we use the Weighted Empirical Likelihood approach (Ren, 2001) to construct tests, confidence intervals, and goodness-of-fit tests for the Accelerated Life Model in a unified way for various types of censored data. We also provide algorithms for implementation and present relevant simulation results.I began working on this problem with Dr. Jian-Jian Ren. Upon Dr. Ren's departure from the University of Central Florida I completed this dissertation under the supervision of Dr. Marianna Pensky.
Show less - Date Issued
- 2013
- Identifier
- CFE0004913, ucf:49613
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004913
- Title
- Effect of predation risk and food availability on parental care and nest survival in suburban and wildland Florida Scrub-Jays.
- Creator
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Niederhauser, Joseph, Jenkins, David, Fedorka, Kenneth, Bowman, Reed, University of Central Florida
- Abstract / Description
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Individual organisms often use cues from their natural environments to determine many behavioral and life-history (")decisions.(") These (")decisions(") are usually adaptive, i.e. a response to selection, because the environmental cues on which they are based reliably correlate with increased fitness over time. When the selected behavioral response to a natural cue no longer provides a fitness benefit, then selection for a new response may occur but individuals maintaining the previously...
Show moreIndividual organisms often use cues from their natural environments to determine many behavioral and life-history (")decisions.(") These (")decisions(") are usually adaptive, i.e. a response to selection, because the environmental cues on which they are based reliably correlate with increased fitness over time. When the selected behavioral response to a natural cue no longer provides a fitness benefit, then selection for a new response may occur but individuals maintaining the previously selected response may suffer reduced survival and reproduction. Especially in human-modified landscapes individuals making a maladaptive behavioral or life-history choice based on those formerly reliable environmental cues may be faced with an (")evolutionary trap("). In urban, or suburban, environments many factors have been altered in ways that could lead to evolutionary traps. Inappropriate behavioral responses by many individuals could lead to reduced demographic performance of urban populations relative to their wildland counterparts and to the decline of entire urban populations. In birds, maladaptive patterns of nest provisioning or vigilance may occur (a) when human-provided adult foods are easier to feed young because they are more abundant and predictable than foods appropriate for nestlings, or (b) when birds' perception of predation risk, which can be influenced by human disturbance, is greater than the real risk. By provisioning or attending their nests more or less than what is appropriate given the environmental level of resources and risks, the behavior of suburban parents may be contributing to high levels of nest failure during the nesting stage. To determine whether maladaptive parental care influences nest survival during the nestling stage, I conducted an experiment using Florida Scrub-Jays (Aphelocoma coerluscens). Suburban scrub-jays have lower nest survival during the nestling stage but higher survival during the incubation stage relative to wildland jays. Both predators and food abundance vary greatly between suburban and wildland scrub. The suburbs have a greater abundance of predators that may prey on both adult scrub-jays and their nests and more foods appropriate for adults but less nestling-appropriate food. This variation in risks and resources should affect the parental care behavior of suburban scrub-jays, which in turn may affect patterns of nest survival. In pre-treatment observations, I found that suburban females spent more time brooding than wildland birds but suburban males did not provision any more than wildland males. Experimentally increasing the perception of adult predation risk reduced parental care in both suburban and wildland females. Increasing the availability of nestling food reduced parental care in suburban females but had no effect in wildland females. Increasing food availability, but not predation risk, decreased call rates but increased call frequency in nestling scrub-jays from both habitats. However, neither parental care nor food availability had much influence on nest survival during the nestling stage. Instead, side nest concealment and the presence of helpers were the most important variables in nest survival analyses prompting other explanations besides maladaptive parental behavior or lack of nestling food resources for the habitat-specific difference in nest survival during the nestling stage.
Show less - Date Issued
- 2012
- Identifier
- CFE0004219, ucf:49015
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004219
- Title
- LANDCOVER CHANGE AND POPULATION DYNAMICS OF FLORIDA SCRUB-JAYS AND FLORIDA GRASSHOPPER SPARROWS.
- Creator
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Breininger, David, Noss, Reed, University of Central Florida
- Abstract / Description
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I confronted empirical habitat data (1994-2004) and population data (1988-2005) with ecological theory on habitat dynamics, recruitment, survival, and dispersal to develop predictive relationships between landcover variation and population dynamics. I focus on Florida Scrub-Jays, although one chapter presents a model for the potential influence of habitat restoration on viability of the Florida Grasshopper Sparrow. Both species are unique to Florida landscapes that are dominated by shrubs and...
Show moreI confronted empirical habitat data (1994-2004) and population data (1988-2005) with ecological theory on habitat dynamics, recruitment, survival, and dispersal to develop predictive relationships between landcover variation and population dynamics. I focus on Florida Scrub-Jays, although one chapter presents a model for the potential influence of habitat restoration on viability of the Florida Grasshopper Sparrow. Both species are unique to Florida landscapes that are dominated by shrubs and grasses and maintained by frequent fires. Both species are declining, even in protected areas, despite their protected status. I mapped habitat for both species using grid polygon cells to quantify population potential and habitat quality. A grid cell was the average territory size and the landcover unit in which habitat-specific recruitment and survival occurred. I measured habitat-specific recruitment and survival of Florida Scrub-Jays from 1988-2008. Data analyses included multistate analysis, which was developed for capture-recapture data but is useful for analyzing many ecological processes, such as habitat change. I relied on publications by other investigators for empirical Florida Grasshopper Sparrow data. The amount of potential habitat was greatly underestimated by landcover mapping not specific to Florida Scrub-Jays. Overlaying east central Florida with grid polygons was an efficient method to map potential habitat and monitor habitat quality directly related to recruitment, survival, and management needs. Most habitats for both species were degraded by anthropogenic reductions in fire frequency. Degradation occurred across large areas. Florida Scrub-Jay recruitment and survival were most influenced by shrub height states. Multistate modeling of shrub heights showed that state transitions were influenced by vegetation composition, edges, and habitat management. Measured population declines of 4% per year corroborated habitat-specific modeling predictions. Habitat quality improved over the study period but not enough to recover precariously small populations. The degree of landcover fragmentation influenced mean Florida Scrub-Jay dispersal distances but not the number of occupied territories between natal and breeding territories. There was little exchange between populations, which were usually further apart than mean dispersal distances. Florida Scrub-Jays bred or delayed breeding depending on age, sex, and breeding opportunities. I show an urgent need also for Florida Grasshopper Sparrow habitat restoration given that the endangered bird has declined to only two sizeable populations and there is a high likelihood for continued large decline. A major effect of habitat fragmentation identified in this dissertation that should apply to many organisms in disturbance prone systems is that fragmentation disrupts natural processes, reducing habitat quality across large areas. Humans have managed wildland fire for > 40,000 years, so it should be possible to manage habitat for many endangered species that make Florida's biodiversity unique. This dissertation provides methods to quantify landscape units into potential source and sink territories and provides a basis for applying adaptive management to reach population and conservation goals.
Show less - Date Issued
- 2009
- Identifier
- CFE0002537, ucf:47638
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0002537
- Title
- TREEFROG (HYLA SQUIRELLA) RESPONSES TO RANGELAND MANAGEMENT IN SEMI-TROPICAL FLORIDA, USA.
- Creator
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Windes, Kathryn, Fauth, John, University of Central Florida
- Abstract / Description
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As urban areas expand, agricultural lands become increasingly important habitat for many species. Compared to some types of agricultural land-use, ranchlands provide vast expanses of minimally modified habitat that support many threatened and endangered species. Conservation biologists can promote ecologically sound management approaches by quantifying the effects of agricultural practices on resident species. I examined the effects of pasture management, cattle grazing, and landscape...
Show moreAs urban areas expand, agricultural lands become increasingly important habitat for many species. Compared to some types of agricultural land-use, ranchlands provide vast expanses of minimally modified habitat that support many threatened and endangered species. Conservation biologists can promote ecologically sound management approaches by quantifying the effects of agricultural practices on resident species. I examined the effects of pasture management, cattle grazing, and landscape characteristics on both adult and larval treefrogs in a ranchland in south-central Florida. I experimentally determined optimal deployment of artificial treefrog shelters constructed of polyvinylchloride (PVC) pipe to efficiently sample adult treefrogs (Chapter 1). Seventy-two shelters were hung on oak trees (Quercus virginiana) and cabbage palm trees (Sabal palmetto) with smooth trunks or boots (residual palm fronds), at all possible combinations of three heights (2, 3, and 4 m), four compass directions (N, S, E, and W) and two water levels (with or without 10 cm). Shelter residence was completely dominated by the Squirrel Treefrog, Hyla squirella (N = 65). Significantly fewer H. squirella were found in shelters on palms with boots than on smooth palms or oak trees (0.29 ± 0.21 [mean ± 1 SE hereinafter] versus 1.3 ± 0.21 and 1.1 ± 0.21, respectively), and shelters with water had slightly more H. squirella than those without (1.5 ± 0.19 versus 0.88 ± 0.19, respectively). Orientation and height did not affect the number of treefrogs encountered; thus, the optimal protocol is to deploy shelters on either smooth palms or oak trees, with water, at 2 m height for easy sampling, and in random compass orientations. I used this protocol to sample H. squirella in woodlots surrounding twelve wetlands and examined how time, frog stage and sex, and landscape features influenced treefrog survival, recapture and site fidelity (Chapter 2). I deployed 15 shelters/ha of woodlot within a 100 m buffer around each wetland. I sampled shelters three times during the fall breeding season, removed all shelters to force frogs to overwinter in natural refugia, and replaced shelters for the final spring sampling. During sampling periods, I sexed, measured, and individually marked each frog using visual implant elastomer (VIE) tags. I used Program MARK to build linear models that included either gender group (female, male or juvenile) or life history stage (adult, juvenile) and either time (sampling interval 1, 2, or 3) or season (fall, spring). I used the most informative model as a null model to assess effects of landscape covariates on survival and recapture. Females had higher survival than either males or juveniles, for which estimates were similar (0.867 vs 0.741 and 0.783, respectively). Survival did not vary over time, although there was some support for an effect of season, with lower survival during the final over-wintering period than in the fall intervals (relative variable importance: group = 0.730; stage = 0.134; time = 0.200; season = 0.310). Adults had higher recapture rates than juveniles (average recapture 0.214 vs 0.102), and recapture for both stages varied over time, with highest recapture in sampling interval two (relative variable importance: group = 0.262; stage = 0.514; time = 0.513; season = 0.229). Hyla squirella was extremely site loyal; no individuals moved between sampling sites, and 95% of recaptured individuals were in their original shelter. Strong terrestrial site fidelity calls into question the traditional ÂÂ"ponds as patchesÂÂ" metapopulation view of treefrog population dynamics. Area of woodlot within 250 m was the most important landscape variable in explaining additional variation in both survival and recapture. Frogs had higher survival and lower recapture in larger woodlots, indicating that intact, contiguous woodlots are higher quality habitat than more fragmented woodlots. Neither survival nor recapture varied with wetland grazing treatments or between pasture types. Finally, I experimentally assessed the effects of cattle grazing and pasture management on larval H. squirella. I selected four wetlands: two in semi-natural pastures (SN) and two in intensively managed pastures (IM). One wetland in each pasture type was fenced so that it was released from cattle grazing (R). I collected three clutches of H. squirella eggs (Clutches A, B, and C) and reared tadpoles in the laboratory until Gosner stage 25. In each wetland, I deployed a total of 50 tadpoles from each clutch into 105 L pens constructed of plastic laundry baskets and mesh window screening. Clutch significantly affected tadpole survival, with Clutch A having the highest percent survival, followed by Clutch B and finally Clutch C (41.66, 32.11 – 53.95 [mean, 95% confidence limits hereinafter]; 9.00, 6.76 – 11.88; 2.89, 2.02 – 4.01, respectively). Wetland type also affected survival, with SN wetlands supporting significantly higher survival than IM wetlands (SN-R: 53.95, 32.88 – 88.13; SN-G: 18.95, 11.30 – 31.36 vs IM-R: 7.32, 4.13 – 12.49; IM-G: 1.09, 0.29 – 2.39). Genetic variation in survival confirms the potential for H. squirella to adapt to rangeland management, but extremely low survival of some clutches indicates that few clutches may be able to survive in low quality wetlands, such as IM-G wetlands. Higher survival in SN pasture wetlands suggest this is a superior habitat and future management objectives should conserve semi-natural pastures and limit further modification of intensively managed pastures, including removing woodlots near wetlands.
Show less - Date Issued
- 2010
- Identifier
- CFE0003178, ucf:48592
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0003178
- Title
- Autonomous Recovery of Reconfigurable Logic Devices using Priority Escalation of Slack.
- Creator
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Imran, Syednaveed, DeMara, Ronald, Mikhael, Wasfy, Lin, Mingjie, Yuan, Jiann-Shiun, Geiger, Christopher, University of Central Florida
- Abstract / Description
-
Field Programmable Gate Array (FPGA) devices offer a suitable platform for survivable hardware architectures in mission-critical systems. In this dissertation, active dynamic redundancy-based fault-handling techniques are proposed which exploit the dynamic partial reconfiguration capability of SRAM-based FPGAs. Self-adaptation is realized by employing reconfiguration in detection, diagnosis, and recovery phases.To extend these concepts to semiconductor aging and process variation in the deep...
Show moreField Programmable Gate Array (FPGA) devices offer a suitable platform for survivable hardware architectures in mission-critical systems. In this dissertation, active dynamic redundancy-based fault-handling techniques are proposed which exploit the dynamic partial reconfiguration capability of SRAM-based FPGAs. Self-adaptation is realized by employing reconfiguration in detection, diagnosis, and recovery phases.To extend these concepts to semiconductor aging and process variation in the deep submicron era, resilient adaptable processing systems are sought to maintain quality and throughput requirements despite the vulnerabilities of the underlying computational devices. A new approach to autonomous fault-handling which addresses these goals is developed using only a uniplex hardware arrangement. It operates by observing a health metric to achieve Fault Demotion using Reconfigurable Slack (FaDReS). Here an autonomous fault isolation scheme is employed which neither requires test vectors nor suspends the computational throughput, but instead observes the value of a health metric based on runtime input. The deterministic flow of the fault isolation scheme guarantees success in a bounded number of reconfigurations of the FPGA fabric.FaDReS is then extended to the Priority Using Resource Escalation (PURE) online redundancy scheme which considers fault-isolation latency and throughput trade-offs under a dynamic spare arrangement. While deep-submicron designs introduce new challenges, use of adaptive techniques are seen to provide several promising avenues for improving resilience. The scheme developed is demonstrated by hardware design of various signal processing circuits and their implementation on a Xilinx Virtex-4 FPGA device. These include a Discrete Cosine Transform (DCT) core, Motion Estimation (ME) engine, Finite Impulse Response (FIR) Filter, Support Vector Machine (SVM), and Advanced Encryption Standard (AES) blocks in addition to MCNC benchmark circuits. A significant reduction in power consumption is achieved ranging from 83% for low motion-activity scenes to 12.5% for high motion activity video scenes in a novel ME engine configuration. For a typical benchmark video sequence, PURE is shown to maintain a PSNR baseline near 32dB. The diagnosability, reconfiguration latency, and resource overhead of each approach is analyzed. Compared to previous alternatives, PURE maintains a PSNR within a difference of 4.02dB to 6.67dB from the fault-free baseline by escalating healthy resources to higher-priority signal processing functions. The results indicate the benefits of priority-aware resiliency over conventional redundancy approaches in terms of fault-recovery, power consumption, and resource-area requirements. Together, these provide a broad range of strategies to achieve autonomous recovery of reconfigurable logic devices under a variety of constraints, operating conditions, and optimization criteria.
Show less - Date Issued
- 2013
- Identifier
- CFE0005006, ucf:50005
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0005006
- Title
- APPLICATION OF THE EMPIRICAL LIKELIHOOD METHOD IN PROPORTIONAL HAZARDS MODEL.
- Creator
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HE, BIN, Ren, Jian-Jian, University of Central Florida
- Abstract / Description
-
In survival analysis, proportional hazards model is the most commonly used and the Cox model is the most popular. These models are developed to facilitate statistical analysis frequently encountered in medical research or reliability studies. In analyzing real data sets, checking the validity of the model assumptions is a key component. However, the presence of complicated types of censoring such as double censoring and partly interval-censoring in survival data makes model assessment...
Show moreIn survival analysis, proportional hazards model is the most commonly used and the Cox model is the most popular. These models are developed to facilitate statistical analysis frequently encountered in medical research or reliability studies. In analyzing real data sets, checking the validity of the model assumptions is a key component. However, the presence of complicated types of censoring such as double censoring and partly interval-censoring in survival data makes model assessment difficult, and the existing tests for goodness-of-fit do not have direct extension to these complicated types of censored data. In this work, we use empirical likelihood (Owen, 1988) approach to construct goodness-of-fit test and provide estimates for the Cox model with various types of censored data.Specifically, the problems under consideration are the two-sample Cox model and stratified Cox model with right censored data, doubly censored data and partly interval-censored data. Related computational issues are discussed, and some simulation results are presented. The procedures developed in the work are applied to several real data sets with some discussion.
Show less - Date Issued
- 2006
- Identifier
- CFE0001099, ucf:46780
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0001099
- Title
- Estimation for the Cox Model with Various Types of Censored Data.
- Creator
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Riddlesworth, Tonya, Ren, Joan, Mohapatra, Ram, Richardson, Gary, Ni, Liqiang, Schott, James, University of Central Florida
- Abstract / Description
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In survival analysis, the Cox model is one of the most widely used tools. However, up to now there has not been any published work on the Cox model with complicated types of censored data, such as doubly censored data, partly-interval censored data, etc., while these types of censored data have been encountered in important medical studies, such as cancer, heart disease, diabetes, etc. In this dissertation, we first derive the bivariate nonparametric maximum likelihood estimator (BNPMLE) Fn(t...
Show moreIn survival analysis, the Cox model is one of the most widely used tools. However, up to now there has not been any published work on the Cox model with complicated types of censored data, such as doubly censored data, partly-interval censored data, etc., while these types of censored data have been encountered in important medical studies, such as cancer, heart disease, diabetes, etc. In this dissertation, we first derive the bivariate nonparametric maximum likelihood estimator (BNPMLE) Fn(t,z) for joint distribution function Fo(t,z) of survival time T and covariate Z, where T is subject to right censoring, noting that such BNPMLE Fn has not been studied in statistical literature. Then, based on this BNPMLE Fn we derive empirical likelihood-based (Owen, 1988) confidence interval for the conditional survival probabilities, which is an important and difficult problem in statistical analysis, and also has not been studied in literature. Finally, with this BNPMLE Fn as a starting point, we extend the weighted empirical likelihood method (Ren, 2001 and 2008a) to the multivariate case, and obtain a weighted empirical likelihood-based estimation method for the Cox model. Such estimation method is given in a unified form, and is applicable to various types of censored data aforementioned.
Show less - Date Issued
- 2011
- Identifier
- CFE0004158, ucf:49051
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0004158
