Search results

Title: An Efficient And Long-time Accurate Third-order Algorithm For The Stokes-darcy System.
Creator: Chen, Wenbin, Gunzburger, Max, Sun, Dong, Wang, Xiaoming
Abstract/Description: A third-order in time numerical IMEX-type algorithm for the Stokes-Darcy system for flows in fluid saturated karst aquifers is proposed and analyzed. A novel third-order Adams-Moulton scheme is used for the discretization of the dissipative term whereas a third-order explicit Adams-Bashforth scheme is used for the time discretization of the interface term that couples the Stokes and Darcy components. The scheme is efficient in the sense that one needs to solve, at each time step, decoupled...
Show moreA third-order in time numerical IMEX-type algorithm for the Stokes-Darcy system for flows in fluid saturated karst aquifers is proposed and analyzed. A novel third-order Adams-Moulton scheme is used for the discretization of the dissipative term whereas a third-order explicit Adams-Bashforth scheme is used for the time discretization of the interface term that couples the Stokes and Darcy components. The scheme is efficient in the sense that one needs to solve, at each time step, decoupled Stokes and Darcy problems. Therefore, legacy Stokes and Darcy solvers can be applied in parallel. The scheme is also unconditionally stable and, with a mild time-step restriction, long-time accurate in the sense that the error is bounded uniformly in time. Numerical experiments are used to illustrate the theoretical results. To the authors' knowledge, the novel algorithm is the first third-order accurate numerical scheme for the Stokes-Darcy system possessing its favorable efficiency, stability, and accuracy properties.
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Date Issued: 2016-12
Identifier: FSU_libsubv1_wos_000386770800006, 10.1007/s00211-015-0789-3
Format: Citation

Title: Analytical Results on the Role of Flexibility in Flapping Propulsion.
Creator: Moore, Nicholas
Abstract/Description: Wing or fin flexibility can dramatically affect the performance of flying and swimming animals. Both laboratory experiments and numerical simulations have been used to study these effects, but analytical results are notably lacking. Here, we develop small-amplitude theory to model a flapping wing that pitches passively due to a combination of wing compliance, inertia and fluid forces. Remarkably, we obtain a class of exact solutions describing the wing's emergent pitching motions, along with...
Show moreWing or fin flexibility can dramatically affect the performance of flying and swimming animals. Both laboratory experiments and numerical simulations have been used to study these effects, but analytical results are notably lacking. Here, we develop small-amplitude theory to model a flapping wing that pitches passively due to a combination of wing compliance, inertia and fluid forces. Remarkably, we obtain a class of exact solutions describing the wing's emergent pitching motions, along with expressions for how thrust and efficiency are modified by compliance. The solutions recover a range of realistic behaviours and shed new light on how flexibility can aid performance, the importance of resonance, and the separate roles played by wing and fluid inertia. The simple robust estimates afforded by our theory may prove valuable even in situations where details of the flapping motion and wing geometry differ.
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Date Issued: 2014
Identifier: FSU_migr_math_faculty_publications-0002, 10.1017/jfm.2014.533
Format: Citation

Title: Automatic stage identification of Drosophila egg chamber based on DAPI images.
Creator: Jia, Dongyu, Xu, Qiuping, Xie, Qian, Mio, Washington, Deng, Wu-Min
Abstract/Description: The Drosophila egg chamber, whose development is divided into 14 stages, is a well-established model for developmental biology. However, visual stage determination can be a tedious, subjective and time-consuming task prone to errors. Our study presents an objective, reliable and repeatable automated method for quantifying cell features and classifying egg chamber stages based on DAPI images. The proposed approach is composed of two steps: 1) a feature extraction step and 2) a statistical...
Show moreThe Drosophila egg chamber, whose development is divided into 14 stages, is a well-established model for developmental biology. However, visual stage determination can be a tedious, subjective and time-consuming task prone to errors. Our study presents an objective, reliable and repeatable automated method for quantifying cell features and classifying egg chamber stages based on DAPI images. The proposed approach is composed of two steps: 1) a feature extraction step and 2) a statistical modeling step. The egg chamber features used are egg chamber size, oocyte size, egg chamber ratio and distribution of follicle cells. Methods for determining the on-site of the polytene stage and centripetal migration are also discussed. The statistical model uses linear and ordinal regression to explore the stage-feature relationships and classify egg chamber stages. Combined with machine learning, our method has great potential to enable discovery of hidden developmental mechanisms.
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Date Issued: 2016-01-06
Identifier: FSU_libsubv1_wos_000368658200001, 10.1038/srep18850
Format: Citation

Title: Automatic stage identification of Drosophila egg chamber based on DAPI images.
Creator: Jia, Dongyu, Xu, Qiuping, Xie, Qian, Mio, Washington, Deng, Wu-Min
Abstract/Description: The Drosophila egg chamber, whose development is divided into 14 stages, is a well-established model for developmental biology. However, visual stage determination can be a tedious, subjective and time-consuming task prone to errors. Our study presents an objective, reliable and repeatable automated method for quantifying cell features and classifying egg chamber stages based on DAPI images. The proposed approach is composed of two steps: 1) a feature extraction step and 2) a statistical...
Show moreThe Drosophila egg chamber, whose development is divided into 14 stages, is a well-established model for developmental biology. However, visual stage determination can be a tedious, subjective and time-consuming task prone to errors. Our study presents an objective, reliable and repeatable automated method for quantifying cell features and classifying egg chamber stages based on DAPI images. The proposed approach is composed of two steps: 1) a feature extraction step and 2) a statistical modeling step. The egg chamber features used are egg chamber size, oocyte size, egg chamber ratio and distribution of follicle cells. Methods for determining the on-site of the polytene stage and centripetal migration are also discussed. The statistical model uses linear and ordinal regression to explore the stage-feature relationships and classify egg chamber stages. Combined with machine learning, our method has great potential to enable discovery of hidden developmental mechanisms.
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Date Issued: 2016-01-06
Identifier: FSU_pmch_26732176, 10.1038/srep18850, PMC4702167, 26732176, 26732176, srep18850
Format: Citation

Title: Ca2+ Effects on ATP Production and Consumption Have Regulatory Roles on Oscillatory Islet Activity.
Creator: McKenna, Joseph P, Ha, Joon, Merrins, Matthew J, Satin, Leslie S, Sherman, Arthur, Bertram, Richard
Abstract/Description: Pancreatic islets respond to elevated blood glucose by secreting pulses of insulin that parallel oscillations in β-cell metabolism, intracellular Ca(2+) concentration, and bursting electrical activity. The mechanisms that maintain an oscillatory response are not fully understood, yet several models have been proposed. Only some can account for experiments supporting that metabolism is intrinsically oscillatory in β-cells. The dual oscillator model (DOM) implicates glycolysis as the source of...
Show morePancreatic islets respond to elevated blood glucose by secreting pulses of insulin that parallel oscillations in β-cell metabolism, intracellular Ca(2+) concentration, and bursting electrical activity. The mechanisms that maintain an oscillatory response are not fully understood, yet several models have been proposed. Only some can account for experiments supporting that metabolism is intrinsically oscillatory in β-cells. The dual oscillator model (DOM) implicates glycolysis as the source of oscillatory metabolism. In the companion article, we use recently developed biosensors to confirm that glycolysis is oscillatory and further elucidate the coordination of metabolic and electrical signals in the insulin secretory pathway. In this report, we modify the DOM by incorporating an established link between metabolism and intracellular Ca(2+) to reconcile model predictions with experimental observations from the companion article. With modification, we maintain the distinguishing feature of the DOM, oscillatory glycolysis, but introduce the ability of Ca(2+) influx to reshape glycolytic oscillations by promoting glycolytic efflux. We use the modified model to explain measurements from the companion article and from previously published experiments with islets.
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Date Issued: 2016-02-02
Identifier: FSU_pmch_26840737, 10.1016/j.bpj.2015.11.3526, PMC4744176, 26840737, 26840737, S0006-3495(15)04814-6
Format: Citation

Title: CAM Stochastic Volatility Model for Option Pricing.
Creator: Huang, Wanwan, Ewald, Brian, Oekten, Giray
Abstract/Description: The coupled additive and multiplicative (CAM) noises model is a stochastic volatility model for derivative pricing. Unlike the other stochastic volatility models in the literature, the CAM model uses two Brownian motions, one multiplicative and one additive, to model the volatility process. We provide empirical evidence that suggests a nontrivial relationship between the kurtosis and skewness of asset prices and that the CAM model is able to capture this relationship, whereas the traditional...
Show moreThe coupled additive and multiplicative (CAM) noises model is a stochastic volatility model for derivative pricing. Unlike the other stochastic volatility models in the literature, the CAM model uses two Brownian motions, one multiplicative and one additive, to model the volatility process. We provide empirical evidence that suggests a nontrivial relationship between the kurtosis and skewness of asset prices and that the CAM model is able to capture this relationship, whereas the traditional stochastic volatility models cannot. We introduce a control variate method and Monte Carlo estimators for some of the sensitivities (Greeks) of the model. We also derive an approximation for the characteristic function of the model.
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Date Issued: 2016
Identifier: FSU_libsubv1_wos_000376329800001, 10.1155/2016/5496945
Format: Citation

Title: A Confidence Building Exercise In Data And Identifiability: Modeling Cancer Chemotherapy As A Case Study.
Creator: Eisenberg, Marisa C., Jain, Harsh V.
Abstract/Description: Mathematical modeling has a long history in the field of cancer therapeutics, and there is increasing recognition that it can help uncover the mechanisms that underlie tumor response to treatment. However, making quantitative predictions with such models often requires parameter estimation from data, raising questions of parameter identifiability and estimability. Even in the case of structural (theoretical) identifiability, imperfect data and the resulting practical unidentifiability of...
Show moreMathematical modeling has a long history in the field of cancer therapeutics, and there is increasing recognition that it can help uncover the mechanisms that underlie tumor response to treatment. However, making quantitative predictions with such models often requires parameter estimation from data, raising questions of parameter identifiability and estimability. Even in the case of structural (theoretical) identifiability, imperfect data and the resulting practical unidentifiability of model parameters can make it difficult to infer the desired information, and in some cases, to yield biologically correct inferences and predictions. Here, we examine parameter identifiability and estimability using a case study of two compartmental, ordinary differential equation models of cancer treatment with drugs that are cell cycle-specific (taxol) as well as non-specific (oxaliplatin). We proceed through model building, structural identifiability analysis, parameter estimation, practical identifiability analysis and its biological implications, as well as alternative data collection protocols and experimental designs that render the model identifiable. We use the differential algebra/input-output relationship approach for structural identifiability, and primarily the profile likelihood approach for practical identifiability. Despite the models being structurally identifiable, we show that without consideration of practical identifiability, incorrect cell cycle distributions can be inferred, that would result in suboptimal therapeutic choices. We illustrate the usefulness of estimating practically identifiable combinations (in addition to the more typically considered structurally identifiable combinations) in generating biologically meaningful insights. We also use simulated data to evaluate how the practical identifiability of the model would change under alternative experimental designs. These results highlight the importance of understanding the underlying mechanisms rather than purely using parsimony or information criteria/goodness-of-fit to decide model selection questions. The overall roadmap for identifiability testing laid out here can be used to help provide mechanistic insight into complex biological phenomena, reduce experimental costs, and optimize model-driven experimentation. (C) 2017 Published by Elsevier Ltd.
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Date Issued: 10/27/2017
Identifier: FSU_libsubv1_wos_000410463600007, 10.1016/j.jtbi.2017.07.018
Format: Citation

Title: A confidence building exercise in data and identifiability: Modeling cancer chemotherapy as a case study..
Creator: Eisenberg, Marisa C, Jain, Harsh V
Abstract/Description: Mathematical modeling has a long history in the field of cancer therapeutics, and there is increasing recognition that it can help uncover the mechanisms that underlie tumor response to treatment. However, making quantitative predictions with such models often requires parameter estimation from data, raising questions of parameter identifiability and estimability. Even in the case of structural (theoretical) identifiability, imperfect data and the resulting practical unidentifiability of...
Show moreMathematical modeling has a long history in the field of cancer therapeutics, and there is increasing recognition that it can help uncover the mechanisms that underlie tumor response to treatment. However, making quantitative predictions with such models often requires parameter estimation from data, raising questions of parameter identifiability and estimability. Even in the case of structural (theoretical) identifiability, imperfect data and the resulting practical unidentifiability of model parameters can make it difficult to infer the desired information, and in some cases, to yield biologically correct inferences and predictions. Here, we examine parameter identifiability and estimability using a case study of two compartmental, ordinary differential equation models of cancer treatment with drugs that are cell cycle-specific (taxol) as well as non-specific (oxaliplatin). We proceed through model building, structural identifiability analysis, parameter estimation, practical identifiability analysis and its biological implications, as well as alternative data collection protocols and experimental designs that render the model identifiable. We use the differential algebra/input-output relationship approach for structural identifiability, and primarily the profile likelihood approach for practical identifiability. Despite the models being structurally identifiable, we show that without consideration of practical identifiability, incorrect cell cycle distributions can be inferred, that would result in suboptimal therapeutic choices. We illustrate the usefulness of estimating practically identifiable combinations (in addition to the more typically considered structurally identifiable combinations) in generating biologically meaningful insights. We also use simulated data to evaluate how the practical identifiability of the model would change under alternative experimental designs. These results highlight the importance of understanding the underlying mechanisms rather than purely using parsimony or information criteria/goodness-of-fit to decide model selection questions. The overall roadmap for identifiability testing laid out here can be used to help provide mechanistic insight into complex biological phenomena, reduce experimental costs, and optimize model-driven experimentation.
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Date Issued: 2017-10-27
Identifier: FSU_pmch_28733187, 10.1016/j.jtbi.2017.07.018, PMC6007023, 28733187, 28733187, S0022-5193(17)30345-4
Format: Citation

Title: Dual Detection System for Simultaneous Measurement of Intracellular Fluorescent Markers and Cellular Secretion.
Creator: Yi, Lian, Bandak, Basel, Wang, Xue, Bertram, Richard, Roper, Michael G
Abstract/Description: Glucose-stimulated insulin secretion from pancreatic β-cells within islets of Langerhans plays a critical role in maintaining glucose homeostasis. Although this process is essential for maintaining euglycemia, the underlying intracellular mechanisms that control it are still unclear. To allow simultaneous correlation between intracellular signal transduction events and extracellular secretion, an analytical system was developed that integrates fluorescence imaging of intracellular probes with...
Show moreGlucose-stimulated insulin secretion from pancreatic β-cells within islets of Langerhans plays a critical role in maintaining glucose homeostasis. Although this process is essential for maintaining euglycemia, the underlying intracellular mechanisms that control it are still unclear. To allow simultaneous correlation between intracellular signal transduction events and extracellular secretion, an analytical system was developed that integrates fluorescence imaging of intracellular probes with high-speed automated insulin immunoassays. As a demonstration of the system, intracellular [Ca] ([Ca]) was measured by imaging Fura-2 fluorescence simultaneously with insulin secretion from islets exposed to elevated glucose levels. Both [Ca] and insulin were oscillatory during application of 10 mM glucose with temporal and quantitative profiles similar to what has been observed elsewhere. In previous work, sinusoidal glucose levels have been used to test the entrainment of islets while monitoring either [Ca] or insulin levels; using this newly developed system, we show unambiguously that oscillations of both [Ca] and insulin release are entrained to oscillatory glucose levels and that the temporal correlation of these are maintained throughout the experiment. It is expected that the developed analytical system can be expanded to investigate a number of other intracellular messengers in islets or other stimulus-secretion pathways in different cells.
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Date Issued: 2016-11-01
Identifier: FSU_pmch_27712062, 10.1021/acs.analchem.6b02404, PMC5089909, 27712062, 27712062
Format: Citation

Title: The Effects of GABAergic Polarity Changes on Episodic Neural Network Activity in Developing Neural Systems.
Creator: Blanco, Wilfredo, Bertram, Richard, Tabak, Joël
Abstract/Description: Early in development, neural systems have primarily excitatory coupling, where even GABAergic synapses are excitatory. Many of these systems exhibit spontaneous episodes of activity that have been characterized through both experimental and computational studies. As development progress the neural system goes through many changes, including synaptic remodeling, intrinsic plasticity in the ion channel expression, and a transformation of GABAergic synapses from excitatory to inhibitory. What...
Show moreEarly in development, neural systems have primarily excitatory coupling, where even GABAergic synapses are excitatory. Many of these systems exhibit spontaneous episodes of activity that have been characterized through both experimental and computational studies. As development progress the neural system goes through many changes, including synaptic remodeling, intrinsic plasticity in the ion channel expression, and a transformation of GABAergic synapses from excitatory to inhibitory. What effect each of these, and other, changes have on the network behavior is hard to know from experimental studies since they all happen in parallel. One advantage of a computational approach is that one has the ability to study developmental changes in isolation. Here, we examine the effects of GABAergic synapse polarity change on the spontaneous activity of both a mean field and a neural network model that has both glutamatergic and GABAergic coupling, representative of a developing neural network. We find some intuitive behavioral changes as the GABAergic neurons go from excitatory to inhibitory, shared by both models, such as a decrease in the duration of episodes. We also find some paradoxical changes in the activity that are only present in the neural network model. In particular, we find that during early development the inter-episode durations become longer on average, while later in development they become shorter. In addressing this unexpected finding, we uncover a priming effect that is particularly important for a small subset of neurons, called the "intermediate neurons." We characterize these neurons and demonstrate why they are crucial to episode initiation, and why the paradoxical behavioral change result from priming of these neurons. The study illustrates how even arguably the simplest of developmental changes that occurs in neural systems can present non-intuitive behaviors. It also makes predictions about neural network behavioral changes that occur during development that may be observable even in actual neural systems where these changes are convoluted with changes in synaptic connectivity and intrinsic neural plasticity.
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Date Issued: 2017-09-29
Identifier: FSU_pmch_29085291, 10.3389/fncom.2017.00088, PMC5649201, 29085291, 29085291
Format: Citation

Title: Effects Of Nonuniform Viscosity On Ciliary Locomotion.
Creator: Shoele, Kourosh, Eastham, Patrick S.
Abstract/Description: The effect of nonuniform viscosity on the swimming velocity of a free swimmer at zero Reynolds number is examined. Using the generalized reciprocal relation for Stokes flow with nonuniform viscosity, we formulate the locomotion problem in a fluid medium with spatially varying viscosity. Assuming the limit of small variation in the viscosity of the fluid as a result of nonuniform distribution of nutrients around a swimmer, we derive a perturbation model to calculate the changes in the swimming...
Show moreThe effect of nonuniform viscosity on the swimming velocity of a free swimmer at zero Reynolds number is examined. Using the generalized reciprocal relation for Stokes flow with nonuniform viscosity, we formulate the locomotion problem in a fluid medium with spatially varying viscosity. Assuming the limit of small variation in the viscosity of the fluid as a result of nonuniform distribution of nutrients around a swimmer, we derive a perturbation model to calculate the changes in the swimming performance of a spherical swimmer as a result of position-dependent viscosity. The swimmer is chosen to be a spherical squirmer with a steady tangential motion on its surface modeling ciliary motion. The nutrient concentration around the body is described by an advection-diffusion equation. The roles of the surface stroke pattern, the specific relationship between the nutrient and viscosity, and the Peclet number of the nutrient in the locomotion velocity of the squirmer are investigated. Our results show that for a pure treadmill stroke, the velocity change is maximum at the limit of zero Peclet number and monotonically decreases toward zero at very high Peclet number. When higher surface stroke modes are present, larger modification in swimming velocity is captured at high Peclet number where two mechanisms of thinning the nutrient boundary layer and appearance of new stagnation points along the surface of squirmer are found to be the primary reasons behind the swimming velocity modifications. It is observed that the presence of nonuniform viscosity allows for optimal swimming speed to be achieved with stroke combinations other than pure treadmill.
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Date Issued: 2018-04-24
Identifier: FSU_libsubv1_wos_000430691900001, 10.1103/PhysRevFluids.3.043101
Format: Citation

Title: Enriched Galerkin Finite Elements For Coupled Poromechanics With Local Mass Conservation.
Creator: Choo, Jinhyun, Lee, Sanghyun
Abstract/Description: Robust and efficient discretization methods for coupled poromechanical problems are critical to address a wide range of problems related to civil infrastructure, energy resources, and environmental sustainability. In this work, we propose a new finite element formulation for coupled poromechanical problems that ensures local (element-wise) mass conservation. The proposed formulation draws on the so-called enriched Galerkin method, which augments piecewise constant functions to the classical...
Show moreRobust and efficient discretization methods for coupled poromechanical problems are critical to address a wide range of problems related to civil infrastructure, energy resources, and environmental sustainability. In this work, we propose a new finite element formulation for coupled poromechanical problems that ensures local (element-wise) mass conservation. The proposed formulation draws on the so-called enriched Galerkin method, which augments piecewise constant functions to the classical continuous Galerkin finite element method. These additional degrees of freedom allow us to obtain a locally conservative and nonconforming solution for the pore pressure field. The enriched and continuous Galerkin formulations are compared in several numerical examples ranging from a benchmark consolidation problem to a complex problem that involves plastic deformation due to unsaturated flow in a heterogeneous porous medium. The results of these examples show not only that the proposed method provides local mass conservation, but also that local mass conservation can be crucial to accurate simulation of deformation processes in fluid-infiltrated porous materials. (C) 2018 Elsevier B.V. All rights reserved.
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Date Issued: 2018-11-01
Identifier: FSU_libsubv1_wos_000442638700013, 10.1016/j.cma.2018.06.022
Format: Citation

Title: First Semester in Numerical Analysis with Julia.
Creator: Ökten, Giray
Abstract/Description: First Semester in Numerical Analysis with Julia presents the theory and methods, together with the implementation of the algorithms using the Julia programming language (version 1.1.0). The book covers computer arithmetic, root-finding, numerical quadrature and differentiation, and approximation theory. The reader is expected to have studied calculus and linear algebra. Some familiarity with a programming language is beneficial, but not required. The programming language Julia will be...
Show moreFirst Semester in Numerical Analysis with Julia presents the theory and methods, together with the implementation of the algorithms using the Julia programming language (version 1.1.0). The book covers computer arithmetic, root-finding, numerical quadrature and differentiation, and approximation theory. The reader is expected to have studied calculus and linear algebra. Some familiarity with a programming language is beneficial, but not required. The programming language Julia will be introduced in the book. The simplicity of Julia allows bypassing the pseudocode and writing a computer code directly after the description of a method while minimizing the distraction the presentation of a computer code might cause to the flow of the main narrative.
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Date Issued: 2019-04-23
Identifier: FSU_libsubv1_scholarship_submission_1556028278_15938059, 10.33009/jul
Format: Citation

Title: Generalized Mahalanobis Depth In Point Process And Its Application In Neural Coding.
Creator: Liu, Shuyi, Wu, Wei
Abstract/Description: In this paper, we propose to generalize the notion of depth in temporal point process observations. The new depth is defined as a weighted product of two probability terms: (1) the number of events in each process, and (2) the center-outward ranking on the event times conditioned on the number of events. In this study, we adopt the Poisson distribution for the first term and the Mahalanobis depth for the second term. We propose an efficient boot-strapping approach to estimate parameters in...
Show moreIn this paper, we propose to generalize the notion of depth in temporal point process observations. The new depth is defined as a weighted product of two probability terms: (1) the number of events in each process, and (2) the center-outward ranking on the event times conditioned on the number of events. In this study, we adopt the Poisson distribution for the first term and the Mahalanobis depth for the second term. We propose an efficient boot-strapping approach to estimate parameters in the defined depth. In the case of Poisson process, the observed events are order statistics where the parameters can be estimated robustly with respect to sample size. We demonstrate the use of the new depth by ranking realizations from a Poisson process. We also test the new method in classification problems using simulations as well as real neural spike train data. It is found that the new framework provides more accurate and robust classifications as compared to commonly used likelihood methods.
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Date Issued: 2017-06
Identifier: FSU_libsubv1_wos_000408732000021, 10.1214/17-AOAS1030
Format: Citation

Title: Genome-wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology.
Creator: Shaffer, John R., Orlova, Ekaterina, Lee, Myoung Keun, Leslie, Elizabeth J., Raffensperger, Zachary D., Heike, Carrie L., Cunningham, Michael L., Hecht, Jacqueline T., Kau,...
Show moreShaffer, John R., Orlova, Ekaterina, Lee, Myoung Keun, Leslie, Elizabeth J., Raffensperger, Zachary D., Heike, Carrie L., Cunningham, Michael L., Hecht, Jacqueline T., Kau, Chung How, Nidey, Nichole L., Moreno, Lina M., Wehby, George L., Murray, Jeffrey C., Laurie, Cecelia A., Laurie, Cathy C., Cole, Joanne, Ferrara, Tracey, Santorico, Stephanie, Klein, Ophir, Mio, Washington, Feingold, Eleanor, Hallgrimsson, Benedikt, Spritz, Richard A., Marazita, Mary L., Weinberg, Seth M.
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Abstract/Description: Numerous lines of evidence point to a genetic basis for facial morphology in humans, yet little is known about how specific genetic variants relate to the phenotypic expression of many common facial features. We conducted genome-wide association meta-analyses of 20 quantitative facial measurements derived from the 3D surface images of 3118 healthy individuals of European ancestry belonging to two US cohorts. Analyses were performed on just under one million genotyped SNPs (Illumina...
Show moreNumerous lines of evidence point to a genetic basis for facial morphology in humans, yet little is known about how specific genetic variants relate to the phenotypic expression of many common facial features. We conducted genome-wide association meta-analyses of 20 quantitative facial measurements derived from the 3D surface images of 3118 healthy individuals of European ancestry belonging to two US cohorts. Analyses were performed on just under one million genotyped SNPs (Illumina OmniExpress+Exome v1.2 array) imputed to the 1000 Genomes reference panel (Phase 3). We observed genome-wide significant associations (p < 5 x 10(-8)) for cranial base width at 14q21.1 and 20q12, intercanthal width at 21p13.3 and Xq13.2, nasal width at 20p11.22, nasal ala length at 14q11.2, and upper facial depth at 11q22.1. Several genes in the associated regions are known to play roles in craniofacial development or in syndromes affecting the face: MAFB, PAX9, MIPOL1, ALX3, HDAC8, and PAX1. We also tested genotype-phenotype associations reported in two previous genome-wide studies and found evidence of replication for nasal ala length and SNPs in CACNA2D3 and PRDM16. These results provide further evidence that common variants in regions harboring genes of known craniofacial function contribute to normal variation in human facial features. Improved understanding of the genes associated with facial morphology in healthy individuals can provide insights into the pathways and mechanisms controlling normal and abnormal facial morphogenesis.
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Date Issued: 2016-08
Identifier: FSU_libsubv1_wos_000382394500007, 10.1371/journal.pgen.1006149
Format: Citation

Title: Genome-Wide Association Study Reveals Multiple Loci Influencing Normal Human Facial Morphology.
Creator: Shaffer, John R, Orlova, Ekaterina, Lee, Myoung Keun, Leslie, Elizabeth J, Raffensperger, Zachary D, Heike, Carrie L, Cunningham, Michael L, Hecht, Jacqueline T, Kau, Chung How,...
Show moreShaffer, John R, Orlova, Ekaterina, Lee, Myoung Keun, Leslie, Elizabeth J, Raffensperger, Zachary D, Heike, Carrie L, Cunningham, Michael L, Hecht, Jacqueline T, Kau, Chung How, Nidey, Nichole L, Moreno, Lina M, Wehby, George L, Murray, Jeffrey C, Laurie, Cecelia A, Laurie, Cathy C, Cole, Joanne, Ferrara, Tracey, Santorico, Stephanie, Klein, Ophir, Mio, Washington, Feingold, Eleanor, Hallgrimsson, Benedikt, Spritz, Richard A, Marazita, Mary L, Weinberg, Seth M
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Abstract/Description: Numerous lines of evidence point to a genetic basis for facial morphology in humans, yet little is known about how specific genetic variants relate to the phenotypic expression of many common facial features. We conducted genome-wide association meta-analyses of 20 quantitative facial measurements derived from the 3D surface images of 3118 healthy individuals of European ancestry belonging to two US cohorts. Analyses were performed on just under one million genotyped SNPs (Illumina...
Show moreNumerous lines of evidence point to a genetic basis for facial morphology in humans, yet little is known about how specific genetic variants relate to the phenotypic expression of many common facial features. We conducted genome-wide association meta-analyses of 20 quantitative facial measurements derived from the 3D surface images of 3118 healthy individuals of European ancestry belonging to two US cohorts. Analyses were performed on just under one million genotyped SNPs (Illumina OmniExpress+Exome v1.2 array) imputed to the 1000 Genomes reference panel (Phase 3). We observed genome-wide significant associations (p < 5 x 10-8) for cranial base width at 14q21.1 and 20q12, intercanthal width at 1p13.3 and Xq13.2, nasal width at 20p11.22, nasal ala length at 14q11.2, and upper facial depth at 11q22.1. Several genes in the associated regions are known to play roles in craniofacial development or in syndromes affecting the face: MAFB, PAX9, MIPOL1, ALX3, HDAC8, and PAX1. We also tested genotype-phenotype associations reported in two previous genome-wide studies and found evidence of replication for nasal ala length and SNPs in CACNA2D3 and PRDM16. These results provide further evidence that common variants in regions harboring genes of known craniofacial function contribute to normal variation in human facial features. Improved understanding of the genes associated with facial morphology in healthy individuals can provide insights into the pathways and mechanisms controlling normal and abnormal facial morphogenesis.
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Date Issued: 2016-08-25
Identifier: FSU_pmch_27560520, 10.1371/journal.pgen.1006149, PMC4999139, 27560520, 27560520, PGENETICS-D-16-00511
Format: Citation

Title: Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape.
Creator: Cole, Joanne B., Manyama, Mange, Kimwaga, Emmanuel, Mathayo, Joshua, Larson, Jacinda R., Liberton, Denise K., Lukowiak, Ken, Ferrara, Tracey M., Riccardi, Sheri L., Li, Mao, Mio...
Show moreCole, Joanne B., Manyama, Mange, Kimwaga, Emmanuel, Mathayo, Joshua, Larson, Jacinda R., Liberton, Denise K., Lukowiak, Ken, Ferrara, Tracey M., Riccardi, Sheri L., Li, Mao, Mio, Washington, Prochazkova, Michaela, Williams, Trevor, Li, Hong, Jones, Kenneth L., Klein, Ophir D., Santorico, Stephanie A., Hallgrimsson, Benedikt, Spritz, Richard A.
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Abstract/Description: The human face is a complex assemblage of highly variable yet clearly heritable anatomic structures that together make each of us unique, distinguishable, and recognizable. Relatively little is known about the genetic underpinnings of normal human facial variation. To address this, we carried out a large genomewide association study and two independent replication studies of Bantu African children and adolescents from Mwanza, Tanzania, a region that is both genetically and environmentally...
Show moreThe human face is a complex assemblage of highly variable yet clearly heritable anatomic structures that together make each of us unique, distinguishable, and recognizable. Relatively little is known about the genetic underpinnings of normal human facial variation. To address this, we carried out a large genomewide association study and two independent replication studies of Bantu African children and adolescents from Mwanza, Tanzania, a region that is both genetically and environmentally relatively homogeneous. We tested for genetic association of facial shape and size phenotypes derived from 3D imaging and automated landmarking of standard facial morphometric points. SNPs within genes SCHIP1 and PDE8A were associated with measures of facial size in both the GWAS and replication cohorts and passed a stringent genomewide significance threshold adjusted for multiple testing of 34 correlated traits. For both SCHIP1 and PDE8A, we demonstrated clear expression in the developing mouse face by both whole-mount in situ hybridization and RNA-seq, supporting their involvement in facial morphogenesis. Ten additional loci demonstrated suggestive association with various measures of facial shape. Our findings, which differ from those in previous studies of European-derived whites, augment understanding of the genetic basis of normal facial development, and provide insights relevant to both human disease and forensics.
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Date Issued: 2016-08
Identifier: FSU_libsubv1_wos_000382394500010, 10.1371/journal.pgen.1006174
Format: Citation

Title: Genomewide Association Study of African Children Identifies Association of SCHIP1 and PDE8A with Facial Size and Shape.
Creator: Cole, Joanne B, Manyama, Mange, Kimwaga, Emmanuel, Mathayo, Joshua, Larson, Jacinda R, Liberton, Denise K, Lukowiak, Ken, Ferrara, Tracey M, Riccardi, Sheri L, Li, Mao, Mio,...
Show moreCole, Joanne B, Manyama, Mange, Kimwaga, Emmanuel, Mathayo, Joshua, Larson, Jacinda R, Liberton, Denise K, Lukowiak, Ken, Ferrara, Tracey M, Riccardi, Sheri L, Li, Mao, Mio, Washington, Prochazkova, Michaela, Williams, Trevor, Li, Hong, Jones, Kenneth L, Klein, Ophir D, Santorico, Stephanie A, Hallgrimsson, Benedikt, Spritz, Richard A
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Abstract/Description: The human face is a complex assemblage of highly variable yet clearly heritable anatomic structures that together make each of us unique, distinguishable, and recognizable. Relatively little is known about the genetic underpinnings of normal human facial variation. To address this, we carried out a large genomewide association study and two independent replication studies of Bantu African children and adolescents from Mwanza, Tanzania, a region that is both genetically and environmentally...
Show moreThe human face is a complex assemblage of highly variable yet clearly heritable anatomic structures that together make each of us unique, distinguishable, and recognizable. Relatively little is known about the genetic underpinnings of normal human facial variation. To address this, we carried out a large genomewide association study and two independent replication studies of Bantu African children and adolescents from Mwanza, Tanzania, a region that is both genetically and environmentally relatively homogeneous. We tested for genetic association of facial shape and size phenotypes derived from 3D imaging and automated landmarking of standard facial morphometric points. SNPs within genes SCHIP1 and PDE8A were associated with measures of facial size in both the GWAS and replication cohorts and passed a stringent genomewide significance threshold adjusted for multiple testing of 34 correlated traits. For both SCHIP1 and PDE8A, we demonstrated clear expression in the developing mouse face by both whole-mount in situ hybridization and RNA-seq, supporting their involvement in facial morphogenesis. Ten additional loci demonstrated suggestive association with various measures of facial shape. Our findings, which differ from those in previous studies of European-derived whites, augment understanding of the genetic basis of normal facial development, and provide insights relevant to both human disease and forensics.
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Date Issued: 2016-08-25
Identifier: FSU_pmch_27560698, 10.1371/journal.pgen.1006174, PMC4999243, 27560698, 27560698, PGENETICS-D-16-00752
Format: Citation

Title: Glucose Oscillations Can Activate an Endogenous Oscillator in Pancreatic Islets.
Creator: McKenna, Joseph P, Dhumpa, Raghuram, Mukhitov, Nikita, Roper, Michael G, Bertram, Richard
Abstract/Description: Pancreatic islets manage elevations in blood glucose level by secreting insulin into the bloodstream in a pulsatile manner. Pulsatile insulin secretion is governed by islet oscillations such as bursting electrical activity and periodic Ca2+ entry in β-cells. In this report, we demonstrate that although islet oscillations are lost by fixing a glucose stimulus at a high concentration, they may be recovered by subsequently converting the glucose stimulus to a sinusoidal wave. We predict with...
Show morePancreatic islets manage elevations in blood glucose level by secreting insulin into the bloodstream in a pulsatile manner. Pulsatile insulin secretion is governed by islet oscillations such as bursting electrical activity and periodic Ca2+ entry in β-cells. In this report, we demonstrate that although islet oscillations are lost by fixing a glucose stimulus at a high concentration, they may be recovered by subsequently converting the glucose stimulus to a sinusoidal wave. We predict with mathematical modeling that the sinusoidal glucose signal's ability to recover islet oscillations depends on its amplitude and period, and we confirm our predictions by conducting experiments with islets using a microfluidics platform. Our results suggest a mechanism whereby oscillatory blood glucose levels recruit non-oscillating islets to enhance pulsatile insulin output from the pancreas. Our results also provide support for the main hypothesis of the Dual Oscillator Model, that a glycolytic oscillator endogenous to islet β-cells drives pulsatile insulin secretion.
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Date Issued: 2016-10-27
Identifier: FSU_pmch_27788129, 10.1371/journal.pcbi.1005143, PMC5082885, 27788129, 27788129, PCOMPBIOL-D-16-00306
Format: Citation

Title: Human Facial Shape and Size Heritability and Genetic Correlations.
Creator: Cole, Joanne B, Manyama, Mange, Larson, Jacinda R, Liberton, Denise K, Ferrara, Tracey M, Riccardi, Sheri L, Li, Mao, Mio, Washington, Klein, Ophir D, Santorico, Stephanie A,...
Show moreCole, Joanne B, Manyama, Mange, Larson, Jacinda R, Liberton, Denise K, Ferrara, Tracey M, Riccardi, Sheri L, Li, Mao, Mio, Washington, Klein, Ophir D, Santorico, Stephanie A, Hallgrímsson, Benedikt, Spritz, Richard A
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Abstract/Description: The human face is an array of variable physical features that together make each of us unique and distinguishable. Striking familial facial similarities underscore a genetic component, but little is known of the genes that underlie facial shape differences. Numerous studies have estimated facial shape heritability using various methods. Here, we used advanced three-dimensional imaging technology and quantitative human genetics analysis to estimate narrow-sense heritability, heritability...
Show moreThe human face is an array of variable physical features that together make each of us unique and distinguishable. Striking familial facial similarities underscore a genetic component, but little is known of the genes that underlie facial shape differences. Numerous studies have estimated facial shape heritability using various methods. Here, we used advanced three-dimensional imaging technology and quantitative human genetics analysis to estimate narrow-sense heritability, heritability explained by common genetic variation, and pairwise genetic correlations of 38 measures of facial shape and size in normal African Bantu children from Tanzania. Specifically, we fit a linear mixed model of genetic relatedness between close and distant relatives to jointly estimate variance components that correspond to heritability explained by genome-wide common genetic variation and variance explained by uncaptured genetic variation, the sum representing total narrow-sense heritability. Our significant estimates for narrow-sense heritability of specific facial traits range from 28 to 67%, with horizontal measures being slightly more heritable than vertical or depth measures. Furthermore, for over half of facial traits, >90% of narrow-sense heritability can be explained by common genetic variation. We also find high absolute genetic correlation between most traits, indicating large overlap in underlying genetic loci. Not surprisingly, traits measured in the same physical orientation (i.e., both horizontal or both vertical) have high positive genetic correlations, whereas traits in opposite orientations have high negative correlations. The complex genetic architecture of facial shape informs our understanding of the intricate relationships among different facial features as well as overall facial development.
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Date Issued: 2017-02-01
Identifier: FSU_pmch_27974501, 10.1534/genetics.116.193185, PMC5289863, 27974501, 27974501, genetics.116.193185
Format: Citation

Title: Introduction to Financial Mathematics: Concepts and Computational Methods.
Creator: Fahim, Arash
Abstract/Description: Introduction to Financial Mathematics: Concepts and Computational Methods serves as a primer in financial mathematics with a focus on conceptual understanding of models and problem solving. It includes the mathematical background needed for risk management, such as probability theory, optimization, and the like. The goal of the book is to expose the reader to a wide range of basic problems, some of which emphasize analytic ability, some requiring programming techniques and others focusing on...
Show moreIntroduction to Financial Mathematics: Concepts and Computational Methods serves as a primer in financial mathematics with a focus on conceptual understanding of models and problem solving. It includes the mathematical background needed for risk management, such as probability theory, optimization, and the like. The goal of the book is to expose the reader to a wide range of basic problems, some of which emphasize analytic ability, some requiring programming techniques and others focusing on statistical data analysis. In addition, it covers some areas which are outside the scope of mainstream financial mathematics textbooks. For example, it presents marginal account setting by the CCP and systemic risk, and a brief overview of the model risk. Inline exercises and examples are included to help students prepare for exams on this book.
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Date Issued: 2019-07-08
Identifier: FSU_libsubv1_scholarship_submission_1562684770_1b3096ca_Comp, 10.33009/financialmath1
Format: Set of related objects

Title: Inverse Scattering Transform For The Nonlocal Nonlinear Schrodinger Equation With Nonzero Boundary Conditions.
Creator: Ablowitz, Mark J., Luo, Xu-Dan, Musslimani, Ziad H.
Abstract/Description: In 2013, a new nonlocal symmetry reduction of the well-known AKNS (an integrable system of partial differential equations, introduced by and named after Mark J. Ablowitz, David J. Kaup, and Alan C. Newell et al. (1974)) scattering problem was found. It was shown to give rise to a new nonlocal PT symmetric and integrable Hamiltonian nonlinear Schrodinger (NLS) equation. Subsequently, the inverse scattering transform was constructed for the case of rapidly decaying initial data and a family of...
Show moreIn 2013, a new nonlocal symmetry reduction of the well-known AKNS (an integrable system of partial differential equations, introduced by and named after Mark J. Ablowitz, David J. Kaup, and Alan C. Newell et al. (1974)) scattering problem was found. It was shown to give rise to a new nonlocal PT symmetric and integrable Hamiltonian nonlinear Schrodinger (NLS) equation. Subsequently, the inverse scattering transform was constructed for the case of rapidly decaying initial data and a family of spatially localized, time periodic one-soliton solutions was found. In this paper, the inverse scattering transform for the nonlocal NLS equation with nonzero boundary conditions at infinity is presented in four different cases when the data at infinity have constant amplitudes. The direct and inverse scattering problems are analyzed. Specifically, the direct problem is formulated, the analytic properties of the eigenfunctions and scattering data and their symmetries are obtained. The inverse scattering problem, which arises from a novel nonlocal system, is developed via a left-right Riemann-Hilbert problem in terms of a suitable uniformization variable and the time dependence of the scattering data is obtained. This leads to a method to linearize/solve the Cauchy problem. Pure soliton solutions are discussed, and explicit 1-soliton solution and two 2-soliton solutions are provided for three of the four different cases corresponding to two different signs of nonlinearity and two different values of the phase difference between plus and minus infinity. In another case, there are no solitons. Published by AIP Publishing.
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Date Issued: 2018-01
Identifier: FSU_libsubv1_wos_000424017000001, 10.1063/1.5018294
Format: Citation

Title: Investigation of drop impact on dry and wet surfaces with consideration of surrounding air.
Creator: Guo, Yisen, Lian, Yongsheng, Sussman, Mark
Abstract/Description: Numerical simulations were conducted to investigate drop impingement and splashing on both dry and wet surfaces at impact velocities greater than 50 m/s with the consideration of the effect of surrounding air. The Navier-Stokes equations were solved using the variable density pressure projection method on a dynamic block structured adaptive grid. The moment of fluid method was used to reconstruct interfaces separating different phases. A dynamic contact angle model was used to define the...
Show moreNumerical simulations were conducted to investigate drop impingement and splashing on both dry and wet surfaces at impact velocities greater than 50 m/s with the consideration of the effect of surrounding air. The Navier-Stokes equations were solved using the variable density pressure projection method on a dynamic block structured adaptive grid. The moment of fluid method was used to reconstruct interfaces separating different phases. A dynamic contact angle model was used to define the boundary condition at the moving contact line. Simulations showed that lowering the ambient gas density can suppress dry surface splashing, which is in agreement with the experiments. A recirculation zone was observed inside the drop after contact: a larger recirculation zone was formed earlier in the higher gas density case than in the lower gas density case. Increasing gas density also enhances the creation of secondary droplets from the lamella breakup. For high speed impact on a dry surface, lowering ambient gas density attenuates splashing. However, ambient air does not significantly affect splashing on a wet surface. Simulations showed that the splashed droplets are primarily from the exiting liquid film. Published by AIP Publishing.
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Date Issued: 2016-07
Identifier: FSU_libsubv1_wos_000382446200015, 10.1063/1.4958694
Format: Citation

Title: Iterated Elliptic And Hypergeometric Integrals For Feynman Diagrams.
Creator: Ablinger, J., Bluemlein, J., De Freitas, A., van Hoeij, M., Imamoglu, E., Raab, C. G., Radu, C.-S., Schneider, C.
Abstract/Description: We calculate 3-loop master integrals for heavy quark correlators and the 3-loop quantum chromodynamics corrections to the rho-parameter. They obey non-factorizing differential equations of second order with more than three singularities, which cannot be factorized in Mellin-N space either. The solution of the homogeneous equations is possible in terms of F-2(1) Gau beta hypergeometric functions at rational argument. In some cases, integrals of this type can be mapped to complete elliptic...
Show moreWe calculate 3-loop master integrals for heavy quark correlators and the 3-loop quantum chromodynamics corrections to the rho-parameter. They obey non-factorizing differential equations of second order with more than three singularities, which cannot be factorized in Mellin-N space either. The solution of the homogeneous equations is possible in terms of F-2(1) Gau beta hypergeometric functions at rational argument. In some cases, integrals of this type can be mapped to complete elliptic integrals at rational argument. This class of functions appears to be the next one arising in the calculation of more complicated Feynman integrals following the harmonic polylogarithms, generalized polylogarithms, cyclotomic harmonic polylogarithms, square-root valued iterated integrals, and combinations thereof, which appear in simpler cases. The inhomogeneous solution of the corresponding differential equations can be given in terms of iterative integrals, where the new innermost letter itself is not an iterative integral. A new class of iterative integrals is introduced containing letters in which (multiple) definite integrals appear as factors. For the elliptic case, we also derive the solution in terms of integrals over modular functions and also modular forms, using q-product and series representations implied by Jacobi's nu(i) functions and Dedekind's eta-function. The corresponding representations can be traced back to polynomials out of Lambert-Eisenstein series, having representations also as elliptic polylogarithms, a q-factorial 1/eta(k) (tau), logarithms, and polylogarithms of q and their q-integrals. Due to the specific form of the physical variable x(q) for different processes, different representations do usually appear. Numerical results are also presented. Published by AIP Publishing.
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Date Issued: 2018-06-01
Identifier: FSU_libsubv1_wos_000437094100030, 10.1063/1.4986417
Format: Citation

Title: Large Deviations And Applications For Markovian Hawkes Processes With A Large Initial Intensity.
Creator: Gao, Xuefeng, Zhu, Lingjiong
Abstract/Description: Hawkes process is a class of simple point processes that is self-exciting and has clustering effect. The intensity of this point process depends on its entire past history. It has wide applications in finance, insurance, neuroscience, social networks, criminology, seismology, and many other fields. In this paper, we study linear Hawkes process with an exponential kernel in the asymptotic regime where the initial intensity of the Hawkes process is large. We establish large deviations for...
Show moreHawkes process is a class of simple point processes that is self-exciting and has clustering effect. The intensity of this point process depends on its entire past history. It has wide applications in finance, insurance, neuroscience, social networks, criminology, seismology, and many other fields. In this paper, we study linear Hawkes process with an exponential kernel in the asymptotic regime where the initial intensity of the Hawkes process is large. We establish large deviations for Hawkes processes in this regime as well as the regime when both the initial intensity and the time are large. We illustrate the strength of our results by discussing the applications to insurance and queueing systems.
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Date Issued: 2018-11-01
Identifier: FSU_libsubv1_wos_000429696200015, 10.3150/17-BEJ948
Format: Citation

Title: Lung nodule malignancy classification using only radiologist-quantified image features as inputs to statistical learning algorithms: probing the Lung Image Database Consortium dataset with two statistical learning methods..
Creator: Hancock, Matthew C, Magnan, Jerry F
Abstract/Description: In the assessment of nodules in CT scans of the lungs, a number of image-derived features are diagnostically relevant. Currently, many of these features are defined only qualitatively, so they are difficult to quantify from first principles. Nevertheless, these features (through their qualitative definitions and interpretations thereof) are often quantified via a variety of mathematical methods for the purpose of computer-aided diagnosis (CAD). To determine the potential usefulness of...
Show moreIn the assessment of nodules in CT scans of the lungs, a number of image-derived features are diagnostically relevant. Currently, many of these features are defined only qualitatively, so they are difficult to quantify from first principles. Nevertheless, these features (through their qualitative definitions and interpretations thereof) are often quantified via a variety of mathematical methods for the purpose of computer-aided diagnosis (CAD). To determine the potential usefulness of quantified diagnostic image features as inputs to a CAD system, we investigate the predictive capability of statistical learning methods for classifying nodule malignancy. We utilize the Lung Image Database Consortium dataset and only employ the radiologist-assigned diagnostic feature values for the lung nodules therein, as well as our derived estimates of the diameter and volume of the nodules from the radiologists' annotations. We calculate theoretical upper bounds on the classification accuracy that are achievable by an ideal classifier that only uses the radiologist-assigned feature values, and we obtain an accuracy of 85.74 [Formula: see text], which is, on average, 4.43% below the theoretical maximum of 90.17%. The corresponding area-under-the-curve (AUC) score is 0.932 ([Formula: see text]), which increases to 0.949 ([Formula: see text]) when diameter and volume features are included and has an accuracy of 88.08 [Formula: see text]. Our results are comparable to those in the literature that use algorithmically derived image-based features, which supports our hypothesis that lung nodules can be classified as malignant or benign using only quantified, diagnostic image features, and indicates the competitiveness of this approach. We also analyze how the classification accuracy depends on specific features and feature subsets, and we rank the features according to their predictive power, statistically demonstrating the top four to be spiculation, lobulation, subtlety, and calcification.
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Date Issued: 2016-10-01
Identifier: FSU_pmch_27990453, 10.1117/1.JMI.3.4.044504, PMC5146644, 27990453, 27990453, 16150R
Format: Citation

Title: Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences..
Creator: Bucksch, Alexander, Atta-Boateng, Acheampong, Azihou, Akomian F, Battogtokh, Dorjsuren, Baumgartner, Aly, Binder, Brad M, Braybrook, Siobhan A, Chang, Cynthia, Coneva, Viktoirya...
Show moreBucksch, Alexander, Atta-Boateng, Acheampong, Azihou, Akomian F, Battogtokh, Dorjsuren, Baumgartner, Aly, Binder, Brad M, Braybrook, Siobhan A, Chang, Cynthia, Coneva, Viktoirya, DeWitt, Thomas J, Fletcher, Alexander G, Gehan, Malia A, Diaz-Martinez, Diego Hernan, Hong, Lilan, Iyer-Pascuzzi, Anjali S, Klein, Laura L, Leiboff, Samuel, Li, Mao, Lynch, Jonathan P, Maizel, Alexis, Maloof, Julin N, Markelz, R J Cody, Martinez, Ciera C, Miller, Laura A, Mio, Washington, Palubicki, Wojtek, Poorter, Hendrik, Pradal, Christophe, Price, Charles A, Puttonen, Eetu, Reese, John B, Rellán-Álvarez, Rubén, Spalding, Edgar P, Sparks, Erin E, Topp, Christopher N, Williams, Joseph H, Chitwood, Daniel H
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Abstract/Description: The geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of...
Show moreThe geometries and topologies of leaves, flowers, roots, shoots, and their arrangements have fascinated plant biologists and mathematicians alike. As such, plant morphology is inherently mathematical in that it describes plant form and architecture with geometrical and topological techniques. Gaining an understanding of how to modify plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems is vital to modeling a future with fewer natural resources. In this white paper, we begin with an overview in quantifying the form of plants and mathematical models of patterning in plants. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leaves in air streams. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.
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Date Issued: 2017-06-09
Identifier: FSU_pmch_28659934, 10.3389/fpls.2017.00900, PMC5465304, 28659934, 28659934
Format: Citation

Title: A morphometric analysis of vegetation patterns in dryland ecosystems.
Creator: Mander, Luke, Dekker, Stefan C, Li, Mao, Mio, Washington, Punyasena, Surangi W, Lenton, Timothy M
Abstract/Description: Vegetation in dryland ecosystems often forms remarkable spatial patterns. These range from regular bands of vegetation alternating with bare ground, to vegetated spots and labyrinths, to regular gaps of bare ground within an otherwise continuous expanse of vegetation. It has been suggested that spotted vegetation patterns could indicate that collapse into a bare ground state is imminent, and the morphology of spatial vegetation patterns, therefore, represents a potentially valuable source of...
Show moreVegetation in dryland ecosystems often forms remarkable spatial patterns. These range from regular bands of vegetation alternating with bare ground, to vegetated spots and labyrinths, to regular gaps of bare ground within an otherwise continuous expanse of vegetation. It has been suggested that spotted vegetation patterns could indicate that collapse into a bare ground state is imminent, and the morphology of spatial vegetation patterns, therefore, represents a potentially valuable source of information on the proximity of regime shifts in dryland ecosystems. In this paper, we have developed quantitative methods to characterize the morphology of spatial patterns in dryland vegetation. Our approach is based on algorithmic techniques that have been used to classify pollen grains on the basis of textural patterning, and involves constructing feature vectors to quantify the shapes formed by vegetation patterns. We have analysed images of patterned vegetation produced by a computational model and a small set of satellite images from South Kordofan (South Sudan), which illustrates that our methods are applicable to both simulated and real-world data. Our approach provides a means of quantifying patterns that are frequently described using qualitative terminology, and could be used to classify vegetation patterns in large-scale satellite surveys of dryland ecosystems.
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Date Issued: 2017-02-15
Identifier: FSU_pmch_28386414, 10.1098/rsos.160443, PMC5367281, 28386414, 28386414, rsos160443
Format: Citation

Title: Neuronal Intrinsic Physiology Changes During Development of a Learned Behavior.
Creator: Ross, Matthew T, Flores, Diana, Bertram, Richard, Johnson, Frank, Hyson, Richard L
Abstract/Description: Juvenile male zebra finches learn their songs over distinct auditory and sensorimotor stages, the former requiring exposure to an adult tutor song pattern. The cortical premotor nucleus HVC (acronym is name) plays a necessary role in both learning stages, as well as the production of adult song. Consistent with neural network models where synaptic plasticity mediates developmental forms of learning, exposure to tutor song drives changes in the turnover, density, and morphology of HVC synapses...
Show moreJuvenile male zebra finches learn their songs over distinct auditory and sensorimotor stages, the former requiring exposure to an adult tutor song pattern. The cortical premotor nucleus HVC (acronym is name) plays a necessary role in both learning stages, as well as the production of adult song. Consistent with neural network models where synaptic plasticity mediates developmental forms of learning, exposure to tutor song drives changes in the turnover, density, and morphology of HVC synapses during vocal development. A network's output, however, is also influenced by the intrinsic properties (e.g., ion channels) of the component neurons, which could change over development. Here, we use patch clamp recordings to show cell-type-specific changes in the intrinsic physiology of HVC projection neurons as a function of vocal development. Developmental changes in HVC neurons that project to the basal ganglia include an increased voltage sag response to hyperpolarizing currents and an increased rebound depolarization following hyperpolarization. Developmental changes in HVC neurons that project to vocal-motor cortex include a decreased resting membrane potential and an increased spike amplitude. HVC interneurons, however, show a relatively stable range of intrinsic features across vocal development. We used mathematical models to deduce possible changes in ionic currents that underlie the physiological changes and to show that the magnitude of the observed changes could alter HVC circuit function. The results demonstrate developmental plasticity in the intrinsic physiology of HVC projection neurons and suggest that intrinsic plasticity may have a role in the process of song learning.
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Date Issued: 2017-10-20
Identifier: FSU_pmch_29062887, 10.1523/ENEURO.0297-17.2017, PMC5649544, 29062887, 29062887, eN-NWR-0297-17
Format: Citation

Title: On The Evolution Of Partial Respect For Ownership.
Creator: Mesterton-Gibbons, Mike, Karabiyik, Tugba, Sherratt, Tom N.
Abstract/Description: An early prediction of game theory was that respect for ownership-"Bourgeois" or behavior-can arise as an arbitrary convention to avoid costly disputes. However, its mirror image-the dispute-avoiding "anti-Bourgeois" or behavior through which owners concede their property to intruders-also corresponds to an evolutionarily stable strategy (ESS) under the same conditions. It has since been found repeatedly that first finders of valuable resources are frequently left unchallenged in nature,...
Show moreAn early prediction of game theory was that respect for ownership-"Bourgeois" or behavior-can arise as an arbitrary convention to avoid costly disputes. However, its mirror image-the dispute-avoiding "anti-Bourgeois" or behavior through which owners concede their property to intruders-also corresponds to an evolutionarily stable strategy (ESS) under the same conditions. It has since been found repeatedly that first finders of valuable resources are frequently left unchallenged in nature, while evidence for ceding property to intruders without a contest is rare at best. An early verbal rationale for the observed rarity of was that two individuals employing such behavior over repeated rounds would be interchanging roles repeatedly, a potentially inefficient outcome known as "infinite regress." This argument was formalized only recently, through a Hawk-Dove model with ownership asymmetry and a fixed probability that two individuals meet again. The analysis showed that if and the cost of fighting exceed thresholds determined by the costs of assuming and relinquishing ownership, then becomes the only stable convention. However, contrary to expectation, and despite the inefficiency of the equilibrium, the analysis also showed that "infinite regress" does not invariably render unviable. Nevertheless, this model dealt only with ESSs at which respect for ownership is either absolute or entirely absent. Here, we extend the model to allow for polymorphic evolutionarily stable states, and we use it to explore the conditions that favor partial respect for ownership. In this way, we produce an analytic model that predicts a range of degrees of partial respect for ownership, dependent on model parameters. In particular, we identify a pathway through which any degree of respect for ownership can evolve from absolute disrespect under increasing with increasing costs of fighting.
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Date Issued: 2016-09
Identifier: FSU_libsubv1_wos_000381210600006, 10.1007/s13235-015-0152-4
Format: Citation

Title: OPTIMAL MODEL MANAGEMENT FOR MULTIFIDELITY MONTE CARLO ESTIMATION.
Creator: Peherstorfer, Benjamin, Willcox, Karen, Gunzburger, Max
Abstract/Description: This work presents an optimal model management strategy that exploits multifidelity surrogate models to accelerate the estimation of statistics of outputs of computationally expensive high-fidelity models. Existing acceleration methods typically exploit a multilevel hierarchy of surrogate models that follow a known rate of error decay and computational costs; however, a general collection of surrogate models, which may include projection-based reduced models, data-fit models, support vector...
Show moreThis work presents an optimal model management strategy that exploits multifidelity surrogate models to accelerate the estimation of statistics of outputs of computationally expensive high-fidelity models. Existing acceleration methods typically exploit a multilevel hierarchy of surrogate models that follow a known rate of error decay and computational costs; however, a general collection of surrogate models, which may include projection-based reduced models, data-fit models, support vector machines, and simplified-physics models, does not necessarily give rise to such a hierarchy. Our multifidelity approach provides a framework to combine an arbitrary number of surrogate models of any type. Instead of relying on error and cost rates, an optimization problem balances the number of model evaluations across the high-fidelity and surrogate models with respect to error and costs. We show that a unique analytic solution of the model management optimization problem exists under mild conditions on the models. Our multifidelity method makes occasional recourse to the high-fidelity model; in doing so it provides an unbiased estimator of the statistics of the high-fidelity model, even in the absence of error bounds and error estimators for the surrogate models. Numerical experiments with linear and nonlinear examples show that speedups by orders of magnitude are obtained compared to Monte Carlo estimation that invokes a single model only.
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Date Issued: 2016
Identifier: FSU_libsubv1_wos_000387347700070, 10.1137/15M1046472
Format: Citation

Title: OPTIMAL MODEL MANAGEMENT FOR MULTIFIDELITY MONTE CARLO ESTIMATION.
Creator: Peherstorfer, Benjamin, Willcox, Karen, Gunzburger, Max
Abstract/Description: This work presents an optimal model management strategy that exploits multifidelity surrogate models to accelerate the estimation of statistics of outputs of computationally expensive high-fidelity models. Existing acceleration methods typically exploit a multilevel hierarchy of surrogate models that follow a known rate of error decay and computational costs; however, a general collection of surrogate models, which may include projection-based reduced models, data-fit models, support vector...
Show moreThis work presents an optimal model management strategy that exploits multifidelity surrogate models to accelerate the estimation of statistics of outputs of computationally expensive high-fidelity models. Existing acceleration methods typically exploit a multilevel hierarchy of surrogate models that follow a known rate of error decay and computational costs; however, a general collection of surrogate models, which may include projection-based reduced models, data-fit models, support vector machines, and simplified-physics models, does not necessarily give rise to such a hierarchy. Our multifidelity approach provides a framework to combine an arbitrary number of surrogate models of any type. Instead of relying on error and cost rates, an optimization problem balances the number of model evaluations across the high-fidelity and surrogate models with respect to error and costs. We show that a unique analytic solution of the model management optimization problem exists under mild conditions on the models. Our multifidelity method makes occasional recourse to the high-fidelity model; in doing so it provides an unbiased estimator of the statistics of the high-fidelity model, even in the absence of error bounds and error estimators for the surrogate models. Numerical experiments with linear and nonlinear examples show that speedups by orders of magnitude are obtained compared to Monte Carlo estimation that invokes a single model only.
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Date Issued: 2016
Identifier: FSU_libsubv1_wos_000387347700070, 10.1137/15M1046472
Format: Citation

Title: The Persistent Homology Mathematical Framework Provides Enhanced Genotype-to-Phenotype Associations for Plant Morphology.
Creator: Li, Mao, Frank, Margaret H, Coneva, Viktoriya, Mio, Washington, Chitwood, Daniel H, Topp, Christopher N
Abstract/Description: Efforts to understand the genetic and environmental conditioning of plant morphology are hindered by the lack of flexible and effective tools for quantifying morphology. Here, we demonstrate that persistent-homology-based topological methods can improve measurement of variation in leaf shape, serrations, and root architecture. We apply these methods to 2D images of leaves and root systems in field-grown plants of a domesticated introgression line population of tomato (). We find that compared...
Show moreEfforts to understand the genetic and environmental conditioning of plant morphology are hindered by the lack of flexible and effective tools for quantifying morphology. Here, we demonstrate that persistent-homology-based topological methods can improve measurement of variation in leaf shape, serrations, and root architecture. We apply these methods to 2D images of leaves and root systems in field-grown plants of a domesticated introgression line population of tomato (). We find that compared with some commonly used conventional traits, (1) persistent-homology-based methods can more comprehensively capture morphological variation; (2) these techniques discriminate between genotypes with a larger normalized effect size and detect a greater number of unique quantitative trait loci (QTLs); (3) multivariate traits, whether statistically derived from univariate or persistent-homology-based traits, improve our ability to understand the genetic basis of phenotype; and (4) persistent-homology-based techniques detect unique QTLs compared to conventional traits or their multivariate derivatives, indicating that previously unmeasured aspects of morphology are now detectable. The QTL results further imply that genetic contributions to morphology can affect both the shoot and root, revealing a pleiotropic basis to natural variation in tomato. Persistent homology is a versatile framework to quantify plant morphology and developmental processes that complements and extends existing methods.
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Date Issued: 2018-08-01
Identifier: FSU_pmch_29871979, 10.1104/pp.18.00104, PMC6084663, 29871979, 29871979, pp.18.00104
Format: Citation

Title: Phase Analysis of Metabolic Oscillations and Membrane Potential in Pancreatic Islet β-Cells.
Creator: Merrins, Matthew J, Poudel, Chetan, McKenna, Joseph P, Ha, Joon, Sherman, Arthur, Bertram, Richard, Satin, Leslie S
Abstract/Description: Metabolism in islet β-cells displays oscillations that can trigger pulses of electrical activity and insulin secretion. There has been a decades-long debate among islet biologists about whether metabolic oscillations are intrinsic or occur in response to oscillations in intracellular Ca(2+) that result from bursting electrical activity. In this article, the dynamics of oscillatory metabolism were investigated using five different optical reporters. Reporter activity was measured...
Show moreMetabolism in islet β-cells displays oscillations that can trigger pulses of electrical activity and insulin secretion. There has been a decades-long debate among islet biologists about whether metabolic oscillations are intrinsic or occur in response to oscillations in intracellular Ca(2+) that result from bursting electrical activity. In this article, the dynamics of oscillatory metabolism were investigated using five different optical reporters. Reporter activity was measured simultaneously with membrane potential bursting to determine the phase relationships between the metabolic oscillations and electrical activity. Our experimental findings suggest that Ca(2+) entry into β-cells stimulates the rate of mitochondrial metabolism, accounting for the depletion of glycolytic intermediates during each oscillatory burst. We also performed Ca(2+) clamp tests in which we clamped membrane potential with the KATP channel-opener diazoxide and KCl to fix Ca(2+) at an elevated level. These tests confirm that metabolic oscillations do not require Ca(2+) oscillations, but show that Ca(2+) plays a larger role in shaping metabolic oscillations than previously suspected. A dynamical picture of the mechanisms of oscillations emerged that requires the restructuring of contemporary mathematical β-cell models, including our own dual oscillator model. In the companion article, we modified our model to account for these new data.
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Date Issued: 2016-02-02
Identifier: FSU_pmch_26840733, 10.1016/j.bpj.2015.12.029, PMC4744170, 26840733, 26840733, S0006-3495(15)04813-4
Format: Citation

Title: Predictive Computer Models for Biofilm Detachment Properties in Pseudomonas aeruginosa.
Creator: Cogan, Nick G., Harro, Janette M., Stoodley, Paul, Shirtliff, Mark E.
Abstract/Description: Microbial biofilm communities are protected against environmental extremes or clearance by antimicrobial agents or the host immune response. They also serve as a site from which microbial populations search for new niches by dispersion via single planktonic cells or by detachment by protected biofilm aggregates that, until recently, were thought to become single cells ready for attachment. Mathematically modeling these events has provided investigators with testable hypotheses for further...
Show moreMicrobial biofilm communities are protected against environmental extremes or clearance by antimicrobial agents or the host immune response. They also serve as a site from which microbial populations search for new niches by dispersion via single planktonic cells or by detachment by protected biofilm aggregates that, until recently, were thought to become single cells ready for attachment. Mathematically modeling these events has provided investigators with testable hypotheses for further study. Such was the case in the recent article by Kragh et al. (K. N. Kragh, J. B. Hutchison, G. Melaugh, C. Rodesney, A. E. Roberts, Y. Irie, P. O. Jensen, S. P. Diggle, R. J. Allen, V. Gordon, and T. Bjarnsholt, mBio 7: e00237-16, 2016, http://dx.doi.org/10.1128/mBio.00237-16), in which investigators were able to identify the differential competitive advantage of biofilm aggregates to directly attach to surfaces compared to the single-celled planktonic populations. Therefore, as we delve deeper into the properties of the biofilm mode of growth, not only do we need to understand the complexity of biofilms, but we must also account for the properties of the dispersed and detached populations and their effect on reseeding.
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Date Issued: 2016-06
Identifier: FSU_libsubv1_wos_000383440300066, 10.1128/mBio.00815-16
Format: Citation

Title: Predictive Computer Models for Biofilm Detachment Properties in Pseudomonas aeruginosa.
Creator: Cogan, Nick G, Harro, Janette M, Stoodley, Paul, Shirtliff, Mark E
Abstract/Description: Microbial biofilm communities are protected against environmental extremes or clearance by antimicrobial agents or the host immune response. They also serve as a site from which microbial populations search for new niches by dispersion via single planktonic cells or by detachment by protected biofilm aggregates that, until recently, were thought to become single cells ready for attachment. Mathematically modeling these events has provided investigators with testable hypotheses for further...
Show moreMicrobial biofilm communities are protected against environmental extremes or clearance by antimicrobial agents or the host immune response. They also serve as a site from which microbial populations search for new niches by dispersion via single planktonic cells or by detachment by protected biofilm aggregates that, until recently, were thought to become single cells ready for attachment. Mathematically modeling these events has provided investigators with testable hypotheses for further study. Such was the case in the recent article by Kragh et al. (K. N. Kragh, J. B. Hutchison, G. Melaugh, C. Rodesney, A. E. Roberts, Y. Irie, P. Ø. Jensen, S. P. Diggle, R. J. Allen, V. Gordon, and T. Bjarnsholt, mBio 7:e00237-16, 2016, http://dx.doi.org/10.1128/mBio.00237-16), in which investigators were able to identify the differential competitive advantage of biofilm aggregates to directly attach to surfaces compared to the single-celled planktonic populations. Therefore, as we delve deeper into the properties of the biofilm mode of growth, not only do we need to understand the complexity of biofilms, but we must also account for the properties of the dispersed and detached populations and their effect on reseeding.
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Date Issued: 2016-06-14
Identifier: FSU_pmch_27302761, 10.1128/mBio.00815-16, PMC4916383, 27302761, 27302761, mBio.00815-16
Format: Citation

Title: Quantifying the Relative Contributions of Divisive and Subtractive Feedback to Rhythm Generation.
Creator: Tabak-Sznajder, Joel, Rinzel, John, Bertram, R. (Richard)
Abstract/Description: Biological systems are characterized by a high number of interacting components. Determining the role of each component is difficult, addressed here in the context of biological oscillations. Rhythmic behavior can result from the interplay of positive feedback that promotes bistability between high and low activity, and slow negative feedback that switches the system between the high and low activity states. Many biological oscillators include two types of negative feedback processes:...
Show moreBiological systems are characterized by a high number of interacting components. Determining the role of each component is difficult, addressed here in the context of biological oscillations. Rhythmic behavior can result from the interplay of positive feedback that promotes bistability between high and low activity, and slow negative feedback that switches the system between the high and low activity states. Many biological oscillators include two types of negative feedback processes: divisive (decreases the gain of the positive feedback loop) and subtractive (increases the input threshold) that both contribute to slowly move the system between the high- and low-activity states. Can we determine the relative contribution of each type of negative feedback process to the rhythmic activity? Does one dominate? Do they control the active and silent phase equally? To answer these questions we use a neural network model with excitatory coupling, regulated by synaptic depression (divisive) and cellular adaptation (subtractive feedback). We first attempt to apply standard experimental methodologies: either passive observation to correlate the variations of a variable of interest to system behavior, or deletion of a component to establish whether a component is critical for the system. We find that these two strategies can lead to contradictory conclusions, and at best their interpretive power is limited. We instead develop a computational measure of the contribution of a process, by evaluating the sensitivity of the active (high activity) and silent (low activity) phase durations to the time constant of the process. The measure shows that both processes control the active phase, in proportion to their speed and relative weight. However, only the subtractive process plays a major role in setting the duration of the silent phase. This computational method can be used to analyze the role of negative feedback processes in a wide range of biological rhythms.
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Date Issued: 2011
Identifier: FSU_migr_math_faculty_publications-0003, 10.1371/journal.pcbi.1001124
Format: Citation

Title: Rapid automated landmarking for morphometric analysis of three-dimensional facial scans.
Creator: Li, Mao, Cole, Joanne B, Manyama, Mange, Larson, Jacinda R, Liberton, Denise K, Riccardi, Sheri L, Ferrara, Tracey M, Santorico, Stephanie A, Bannister, Jordan J, Forkert, Nils...
Show moreLi, Mao, Cole, Joanne B, Manyama, Mange, Larson, Jacinda R, Liberton, Denise K, Riccardi, Sheri L, Ferrara, Tracey M, Santorico, Stephanie A, Bannister, Jordan J, Forkert, Nils D, Spritz, Richard A, Mio, Washington, Hallgrimsson, Benedikt
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Abstract/Description: Automated phenotyping is essential for the creation of large, highly standardized datasets from anatomical imaging data. Such datasets can support large-scale studies of complex traits or clinical studies related to precision medicine or clinical trials. We have developed a method that generates three-dimensional landmark data that meet the requirements of standard geometric morphometric analyses. The method is robust and can be implemented without high-performance computing resources. We...
Show moreAutomated phenotyping is essential for the creation of large, highly standardized datasets from anatomical imaging data. Such datasets can support large-scale studies of complex traits or clinical studies related to precision medicine or clinical trials. We have developed a method that generates three-dimensional landmark data that meet the requirements of standard geometric morphometric analyses. The method is robust and can be implemented without high-performance computing resources. We validated the method using both direct comparison to manual landmarking on the same individuals and also analyses of the variation patterns and outlier patterns in a large dataset of automated and manual landmark data. Direct comparison of manual and automated landmarks reveals that automated landmark data are less variable, but more highly integrated and reproducible. Automated data produce covariation structure that closely resembles that of manual landmarks. We further find that while our method does produce some landmarking errors, they tend to be readily detectable and can be fixed by adjusting parameters used in the registration and control-point steps. Data generated using the method described here have been successfully used to study the genomic architecture of facial shape in two different genome-wide association studies of facial shape.
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Date Issued: 2017-04-01
Identifier: FSU_pmch_28078731, 10.1111/joa.12576, PMC5345630, 28078731, 28078731
Format: Citation

Title: Statistical Shape Analysis Of Simplified Neuronal Trees.
Creator: Duncan, Adam, Klassen, Eric, Srivastava, Anuj
Abstract/Description: Neuron morphology plays a central role in characterizing cognitive health and functionality of brain structures. The problem of quantifying neuron shapes and capturing statistical variability of shapes is difficult because neurons differ both in geometry and in topology. This paper develops a mathematical representation of neuronal trees, restricting to the trees that consist of: (1) a main branch viewed as a parameterized curve in R-3, and (2) some number of secondary branches-also...
Show moreNeuron morphology plays a central role in characterizing cognitive health and functionality of brain structures. The problem of quantifying neuron shapes and capturing statistical variability of shapes is difficult because neurons differ both in geometry and in topology. This paper develops a mathematical representation of neuronal trees, restricting to the trees that consist of: (1) a main branch viewed as a parameterized curve in R-3, and (2) some number of secondary branches-also parameterized curves in R-3-which emanate from the main branch at arbitrary points. It imposes a metric on the representation space, in order to compare neuronal shapes, and to obtain optimal deformations (geodesics) across arbitrary trees. The key idea is to impose certain equivalence relations that allow trees with different geometries and topologies to be compared efficiently. The combinatorial problem of matching side branches across trees is reduced to a linear assignment with well-known efficient solutions. This framework is then applied to comparing, clustering, and classifying neurons using fully automated algorithms. The framework is illustrated on three datasets of neuron reconstructions, specifically showing geodesics paths and cross-validated classification between experimental groups.
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Date Issued: 2018-09-01
Identifier: FSU_libsubv1_wos_000444259500002, 10.1214/17-AOAS1107
Format: Citation

Title: Twofold PT symmetry in doubly exponential optical lattices.
Creator: Cole, J. T., Makris, K. G., Musslimani, Z. H., Christodoulides, D. N., Rotter, S.
Abstract/Description: We introduce a family of non-Hermitian optical potentials that are given in terms of double-exponential periodic functions. The center of PT symmetry is not around zero and the potential satisfies a shifted PT-symmetry relation at two distinct locations. Motivated by wave transmission through thin phase screens and gratings, we examine these refractive index modulations from the perspective of optical lattices that are homogeneous along the propagation direction. The diffraction dynamics,...
Show moreWe introduce a family of non-Hermitian optical potentials that are given in terms of double-exponential periodic functions. The center of PT symmetry is not around zero and the potential satisfies a shifted PT-symmetry relation at two distinct locations. Motivated by wave transmission through thin phase screens and gratings, we examine these refractive index modulations from the perspective of optical lattices that are homogeneous along the propagation direction. The diffraction dynamics, abrupt phase transitions in the eigenvalue spectrum, and exceptional points in the band structure are examined in detail. In addition, the nonlinear properties of wave propagation in Kerr nonlinearity media are studied. In particular, coherent structures such as lattice solitons are numerically identified by applying the spectral renormalization method. The spatial symmetries of such lattice solitons follow the shifted PT-symmetric relations. Furthermore, such lattice solitons have a power threshold and their linear and nonlinear stabilities are critically dependent on their spatial symmetry point.
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Date Issued: 2016-01-04
Identifier: FSU_libsubv1_wos_000367658200014, 10.1103/PhysRevA.93.013803
Format: Citation

Title: Upregulation of an inward rectifying K+ channel can rescue slow Ca2+ oscillations in K(ATP) channel deficient pancreatic islets.
Creator: Yildirim, Vehpi, Vadrevu, Suryakiran, Thompson, Benjamin, Satin, Leslie S, Bertram, Richard
Abstract/Description: Plasma insulin oscillations are known to have physiological importance in the regulation of blood glucose. In insulin-secreting β-cells of pancreatic islets, K(ATP) channels play a key role in regulating glucose-dependent insulin secretion. In addition, they convey oscillations in cellular metabolism to the membrane by sensing adenine nucleotides, and are thus instrumental in mediating pulsatile insulin secretion. Blocking K(ATP) channels pharmacologically depolarizes the β-cell plasma...
Show morePlasma insulin oscillations are known to have physiological importance in the regulation of blood glucose. In insulin-secreting β-cells of pancreatic islets, K(ATP) channels play a key role in regulating glucose-dependent insulin secretion. In addition, they convey oscillations in cellular metabolism to the membrane by sensing adenine nucleotides, and are thus instrumental in mediating pulsatile insulin secretion. Blocking K(ATP) channels pharmacologically depolarizes the β-cell plasma membrane and terminates islet oscillations. Surprisingly, when K(ATP) channels are genetically knocked out, oscillations in islet activity persist, and relatively normal blood glucose levels are maintained. Compensation must therefore occur to overcome the loss of K(ATP) channels in K(ATP) knockout mice. In a companion study, we demonstrated a substantial increase in Kir2.1 protein occurs in β-cells lacking K(ATP) because of SUR1 deletion. In this report, we demonstrate that β-cells of SUR1 null islets have an upregulated inward rectifying K+ current that helps to compensate for the loss of K(ATP) channels. This current is likely due to the increased expression of Kir2.1 channels. We used mathematical modeling to determine whether an ionic current having the biophysical characteristics of Kir2.1 is capable of rescuing oscillations that are similar in period to those of wild-type islets. By experimentally testing a key model prediction we suggest that Kir2.1 current upregulation is a likely mechanism for rescuing the oscillations seen in islets from mice deficient in K(ATP) channels.
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Date Issued: 2017-07-27
Identifier: FSU_pmch_28749940, 10.1371/journal.pcbi.1005686, PMC5549769, 28749940, 28749940, PCOMPBIOL-D-17-00183
Format: Citation

Title: Visualizing phylogenetic tree landscapes.
Creator: Wilgenbusch, James C, Huang, Wen, Gallivan, Kyle A
Abstract/Description: Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential...
Show moreGenomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D projections significantly increase the fit between the tree-to-tree distances and can facilitate the interpretation of the relationship among phylogenetic trees. We demonstrate that the choice of dimensionality reduction method can significantly influence the spatial relationship among a large set of competing phylogenetic trees. We highlight the importance of selecting a dimensionality reduction method to visualize large multi-locus phylogenetic landscapes and demonstrate that 3D projections of mitochondrial tree landscapes better capture the relationship among the trees being compared.
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Date Issued: 2017-02-02
Identifier: FSU_pmch_28153045, 10.1186/s12859-017-1479-1, PMC5290614, 28153045, 28153045, 10.1186/s12859-017-1479-1
Format: Citation

Title: Vortices In Bose-einstein Condensates With Pt-symmetric Gain And Loss.
Creator: Schwarz, Lukas, Cartarius, Holger, Musslimani, Ziad H., Main, Joerg, Wunner, Guenter
Abstract/Description: We investigate vortex excitations in dilute Bose-Einstein condensates in the presence of complex PT symmetric potentials. These complex potentials are used to describe a balanced gain and loss of particles and allow an easier calculation of stationary states in open systems than in a full dynamical calculation including the whole environment. We examine the conditions under which stationary vortex states can exist and consider transitions from vortex to nonvortex states. In addition, we study...
Show moreWe investigate vortex excitations in dilute Bose-Einstein condensates in the presence of complex PT symmetric potentials. These complex potentials are used to describe a balanced gain and loss of particles and allow an easier calculation of stationary states in open systems than in a full dynamical calculation including the whole environment. We examine the conditions under which stationary vortex states can exist and consider transitions from vortex to nonvortex states. In addition, we study the influences of PT symmetry on the dynamics of nonstationary vortex states placed at off-center positions.
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Date Issued: 2017-05-12
Identifier: FSU_libsubv1_wos_000401189500012, 10.1103/PhysRevA.95.053613
Format: Citation

Title: Wave propagation through disordered media without backscattering and intensity variations.
Creator: Makris, Konstantinos G, Brandstötter, Andre, Ambichl, Philipp, Musslimani, Ziad H, Rotter, Stefan
Abstract/Description: A fundamental manifestation of wave scattering in a disordered medium is the highly complex intensity pattern the waves acquire due to multi-path interference. Here we show that these intensity variations can be entirely suppressed by adding disorder-specific gain and loss components to the medium. The resulting constant-intensity waves in such non-Hermitian scattering landscapes are free of any backscattering and feature perfect transmission through the disorder. An experimental...
Show moreA fundamental manifestation of wave scattering in a disordered medium is the highly complex intensity pattern the waves acquire due to multi-path interference. Here we show that these intensity variations can be entirely suppressed by adding disorder-specific gain and loss components to the medium. The resulting constant-intensity waves in such non-Hermitian scattering landscapes are free of any backscattering and feature perfect transmission through the disorder. An experimental demonstration of these unique wave states is envisioned based on spatially modulated pump beams that can flexibly control the gain and loss components in an active medium.
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Date Issued: 2017-09-08
Identifier: FSU_pmch_30167289, 10.1038/lsa.2017.35, PMC6062329, 30167289, 30167289
Format: Citation

Department of Mathematics (44)	+ -
Institute of Molecular Biophysics (6)	+ -
Program in Neuroscience (6)	+ -
Department of Statistics (3)	+ -
Department of Biological Science (2)	+ -

Department of Chemistry and Biochemistry (2)	+ -
Department of Mechanical Engineering (1)	+ -
Department of Psychology (1)	+ -
Department of Scientific Computing (1)	+ -

Animals (8)	+ -
Humans (8)	+ -
Face/anatomy & histology (4)	+ -
Calcium/metabolism (3)	+ -
Insulin-Secreting Cells/metabolism (3)	+ -

Insulin/metabolism (3)	+ -
Male (3)	+ -
Maxillofacial Development/genetics (3)	+ -
Mice (3)	+ -
Phenotype (3)	+ -
Adolescent (2)	+ -
Calcium Signaling (2)	+ -
Cells, Cultured (2)	+ -
Female (2)	+ -
Genetic Variation (2)	+ -
Genome-Wide Association Study (2)	+ -
Genotype (2)	+ -
Glucose/metabolism (2)	+ -
Insulin-Secreting Cells/physiology (2)	+ -
Islets of Langerhans/metabolism (2)	+ -
Models, Biological (2)	+ -
Models, Theoretical (2)	+ -
Polymorphism, Single Nucleotide (2)	+ -
3',5'-Cyclic-AMP Phosphodiesterases/genetics (1)	+ -
6-Cyano-7-nitroquinoxaline-2,3-dione/pharmacology (1)	+ -
Acoustic Stimulation (1)	+ -
Action Potentials (1)	+ -
Adenosine Triphosphate/metabolism (1)	+ -
Afferent Pathways/drug effects (1)	+ -
Afferent Pathways/physiology (1)	+ -

text (44)	+ -
journal article (29)	+ -
book (2)	+ -

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