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Predictive motor control of sensory dynamics in auditory active sensing.
Morillon B, Hackett TA, Kajikawa Y, Schroeder CE
(2015) Curr Opin Neurobiol 31: 230-8
MeSH Terms: Acoustic Stimulation, Animals, Attention, Auditory Cortex, Auditory Perception, Brain Mapping, Hearing, Humans, Motor Activity, Nonlinear Dynamics
Show Abstract · Added February 22, 2016
Neuronal oscillations present potential physiological substrates for brain operations that require temporal prediction. We review this idea in the context of auditory perception. Using speech as an exemplar, we illustrate how hierarchically organized oscillations can be used to parse and encode complex input streams. We then consider the motor system as a major source of rhythms (temporal priors) in auditory processing, that act in concert with attention to sharpen sensory representations and link them across areas. We discuss the circuits that could mediate this audio-motor interaction, notably the potential role of the somatosensory system. Finally, we reposition temporal predictions in the context of internal models, discussing how they interact with feature-based or spatial predictions. We argue that complementary predictions interact synergistically according to the organizational principles of each sensory system, forming multidimensional filters crucial to perception.
Copyright © 2015. Published by Elsevier Ltd.
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10 MeSH Terms
Mediation of cardiovascular risk factor effects through subclinical vascular disease: the Multi-Ethnic Study of Atherosclerosis.
Yeboah J, Delaney JA, Nance R, McClelland RL, Polak JF, Sibley CT, Bertoni A, Burke GL, Carr JJ, Herrington DM
(2014) Arterioscler Thromb Vasc Biol 34: 1778-83
MeSH Terms: Age Factors, Aged, Aged, 80 and over, Asymptomatic Diseases, Atherosclerosis, Body Mass Index, Brachial Artery, Cardiovascular Diseases, Carotid Artery Diseases, Carotid Intima-Media Thickness, Coronary Angiography, Coronary Artery Disease, Ethnic Groups, Female, Humans, Incidence, Male, Middle Aged, Nonlinear Dynamics, Obesity, Predictive Value of Tests, Proportional Hazards Models, Prospective Studies, Risk Factors, Sex Factors, Smoking, Tomography, X-Ray Computed, United States, Vascular Calcification, Vasodilation
Show Abstract · Added October 10, 2014
OBJECTIVE - It is unclear to what extent subclinical cardiovascular disease (CVD) such as coronary artery calcium (CAC), carotid intima-media thickness (CIMT), and brachial flow-mediated dilation (FMD) are mediators of the known associations between traditional cardiovascular risk factors and incident CVD events. We assessed the portion of the effects of risk factors on incident CVD events that are mediated through CAC, CIMT, and FMD.
APPROACH AND RESULTS - Six thousand three hundred fifty-five of 6814 Multi-Ethnic Study of Atherosclerosis participants were included. Nonlinear implementation of structural equation modeling (STATA mediation package) was used to assess whether CAC, CIMT, or FMD are mediators of the association between traditional risk factors and incident CVD event. Mean age was 62 years, with 47% men, 12% diabetics, and 13% current smokers. After a mean follow-up of 7.5 years, there were 539 CVD adjudicated events. CAC showed the highest mediation while FMD showed the least. Age had the highest percent of total effect mediated via CAC for CVD outcomes, whereas current cigarette smoking had the least percent of total effect mediated via CAC (percent [95% confidence interval]: 80.2 [58.8-126.7] versus 10.6 [6.1-38.5], respectively). Body mass index showed the highest percent of total effect mediated via CIMT (17.7 [11.6-38.9]); only a negligible amount of the association between traditional risk factors and CVD was mediated via FMD.
CONCLUSIONS - Many of the risk factors for incident CVD (other than age, sex, and body mass index) showed a modest level of mediation via CAC, CIMT, and FMD, suggesting that current subclinical CVD markers may not be optimal intermediaries for gauging upstream risk factor modification.
© 2014 American Heart Association, Inc.
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30 MeSH Terms
Nonlinear analyses of elicited modal, raised, and pressed rabbit phonation.
Awan SN, Novaleski CK, Rousseau B
(2014) J Voice 28: 538-47
MeSH Terms: Animals, Disease Models, Animal, Dysphonia, Glottis, Laryngeal Muscles, Male, Nonlinear Dynamics, Phonation, Rabbits, Sound Spectrography, Speech Acoustics, Voice Quality
Show Abstract · Added February 12, 2015
OBJECTIVES/HYPOTHESIS - The purpose of this study was to use nonlinear dynamic analysis methods such as phase space portraits and correlation dimension (D2) as well as descriptive spectrographic analyses to characterize acoustic signals produced during evoked rabbit phonation.
METHODS - Seventeen New Zealand white breeder rabbits were used to perform the study. A Grass S-88 stimulator (SA Instrumentation, Encinitas, CA) and constant current isolation unit (Grass Telefactor, model PSIU6; West Warwick, RI) were used to provide electrical stimulation to laryngeal musculature, and transglottal airflow rate and stimulation current (mA) were manipulated to elicit modal, raised intensity, and pressed phonations. Central 1 second portions of the most stable portion of the acoustic waveform for modal, raised intensity, and pressed phonations were edited and then analyzed via phase space portraits, Poincaré sections, and the estimation of the D2. In an attempt to limit the effects of the highly variable and nonstationary characteristics of some of the signals being analyzed, D2 analysis was also performed on the most stable central 200-millisecond portion of the acoustic waveform. Descriptive analysis of each phonation was also conducted using sound spectrograms.
RESULTS - Results showed that the complexity of phonation and the subsequent acoustic waveform is increased as transglottal airflow rate and degree of glottal adduction are manipulated in the evoked rabbit phonation model. In particular, phonatory complexity, as quantified via D2 analyses and demonstrated via spectrographic characteristics, increases from "modal" (ie, phonation elicited at just above the phonation threshold pressure) to raised intensity (phonation elicited by increasing transglottal airflow rate) to pressed (phonation elicited by increasing the stimulation current delivered to the larynx). Variations in a single dynamic dimension (airflow rate or adductory force) resulted in significantly increased productions of nonlinear phenomenon, including bifurcations from periodicity to regions of subharmonic content, fundamental frequency, and harmonic jumps, and evidence of periodicity within aperiodic regions ("chaos").
CONCLUSIONS - The evoked rabbit phonation model described in this study allows for the elicitation of various types of phonations under controlled conditions and, therefore, has the potential to provide insight regarding important variables that may elicit examples of nonlinear phenomena such as subharmonics and deterministic chaos.
Copyright © 2014 The Voice Foundation. Published by Elsevier Inc. All rights reserved.
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12 MeSH Terms
An efficient, nonlinear stability analysis for detecting pattern formation in reaction diffusion systems.
Holmes WR
(2014) Bull Math Biol 76: 157-83
MeSH Terms: Chemotaxis, Computer Simulation, Diffusion, GTP Phosphohydrolases, Kinetics, Linear Models, Mathematical Concepts, Models, Biological, Nonlinear Dynamics, Pattern Recognition, Automated, Phosphatidylinositols, Systems Biology
Show Abstract · Added February 26, 2016
Reaction diffusion systems are often used to study pattern formation in biological systems. However, most methods for understanding their behavior are challenging and can rarely be applied to complex systems common in biological applications. I present a relatively simple and efficient, nonlinear stability technique that greatly aids such analysis when rates of diffusion are substantially different. This technique reduces a system of reaction diffusion equations to a system of ordinary differential equations tracking the evolution of a large amplitude, spatially localized perturbation of a homogeneous steady state. Stability properties of this system, determined using standard bifurcation techniques and software, describe both linear and nonlinear patterning regimes of the reaction diffusion system. I describe the class of systems this method can be applied to and demonstrate its application. Analysis of Schnakenberg and substrate inhibition models is performed to demonstrate the methods capabilities in simplified settings and show that even these simple models have nonlinear patterning regimes not previously detected. The real power of this technique, however, is its simplicity and applicability to larger complex systems where other nonlinear methods become intractable. This is demonstrated through analysis of a chemotaxis regulatory network comprised of interacting proteins and phospholipids. In each case, predictions of this method are verified against results of numerical simulation, linear stability, asymptotic, and/or full PDE bifurcation analyses.
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12 MeSH Terms
Mechanistic analysis of challenge-response experiments.
Shotwell MS, Drake KJ, Sidorov VY, Wikswo JP
(2013) Biometrics 69: 741-7
MeSH Terms: Action Potentials, Animals, Biometry, Computer Simulation, Heart, Hypoxia, Least-Squares Analysis, Models, Cardiovascular, Models, Statistical, Monte Carlo Method, Nonlinear Dynamics, Rabbits, Regression Analysis, Systems Biology
Show Abstract · Added March 27, 2014
We present an application of mechanistic modeling and nonlinear longitudinal regression in the context of biomedical response-to-challenge experiments, a field where these methods are underutilized. In this type of experiment, a system is studied by imposing an experimental challenge, and then observing its response. The combination of mechanistic modeling and nonlinear longitudinal regression has brought new insight, and revealed an unexpected opportunity for optimal design. Specifically, the mechanistic aspect of our approach enables the optimal design of experimental challenge characteristics (e.g., intensity, duration). This article lays some groundwork for this approach. We consider a series of experiments wherein an isolated rabbit heart is challenged with intermittent anoxia. The heart responds to the challenge onset, and recovers when the challenge ends. The mean response is modeled by a system of differential equations that describe a candidate mechanism for cardiac response to anoxia challenge. The cardiac system behaves more variably when challenged than when at rest. Hence, observations arising from this experiment exhibit complex heteroscedasticity and sharp changes in central tendency. We present evidence that an asymptotic statistical inference strategy may fail to adequately account for statistical uncertainty. Two alternative methods are critiqued qualitatively (i.e., for utility in the current context), and quantitatively using an innovative Monte-Carlo method. We conclude with a discussion of the exciting opportunities in optimal design of response-to-challenge experiments.
© 2013, The International Biometric Society.
1 Communities
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14 MeSH Terms
A model for intracellular actin waves explored by nonlinear local perturbation analysis.
Mata MA, Dutot M, Edelstein-Keshet L, Holmes WR
(2013) J Theor Biol 334: 149-61
MeSH Terms: Actin Cytoskeleton, Actins, Algorithms, Animals, Cytoplasm, Cytoskeleton, Feedback, Physiological, Humans, Models, Biological, Nonlinear Dynamics
Show Abstract · Added February 26, 2016
Waves and dynamic patterns in chemical and physical systems have long interested experimentalists and theoreticians alike. Here we investigate a recent example within the context of cell biology, where waves of actin (a major component of the cytoskeleton) and its regulators (nucleation promoting factors, NPFs) are observed experimentally. We describe and analyze a minimal reaction diffusion model depicting the feedback between signalling proteins and filamentous actin (F-actin). Using numerical simulation, we show that this model displays a rich variety of patterning regimes. A relatively recent nonlinear stability method, the Local Perturbation Analysis (LPA), is used to map the parameter space of this model and explain the genesis of patterns in various linear and nonlinear patterning regimes. We compare our model for actin waves to others in the literature, and focus on transitions between static polarization, transient waves, periodic wave trains, and reflecting waves. We show, using LPA, that the spatially distributed model gives rise to dynamics that are absent in the kinetics alone. Finally, we show that the width and speed of the waves depend counter-intuitively on parameters such as rates of NPF activation, negative feedback, and the F-actin time scale.
© 2013 Published by Elsevier Ltd. All rights reserved.
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10 MeSH Terms
Ultrasonic characterization of the nonlinear properties of canine livers by measuring shear wave speed and axial strain with increasing portal venous pressure.
Rotemberg V, Byram B, Palmeri M, Wang M, Nightingale K
(2013) J Biomech 46: 1875-81
MeSH Terms: Animals, Biomechanical Phenomena, Dogs, Liver, Liver Circulation, Models, Cardiovascular, Nonlinear Dynamics, Portal Pressure, Portal Vein, Ultrasonography, Vascular Stiffness
Show Abstract · Added May 29, 2014
Elevated hepatic venous pressure is the primary source of complications in advancing liver disease. Ultrasound imaging is ideal for potential noninvasive hepatic pressure measurements as it is widely used for liver imaging. Specifically, ultrasound based stiffness measures may be useful for clinically monitoring pressure, but the mechanism by which liver stiffness increases with hepatic pressure has not been well characterized. This study is designed to elucidate the nonlinear properties of the liver during pressurization by measuring both hepatic shear wave speed (SWS) and strain with increasing pressure. Tissue deformation during hepatic pressurization was tracked in 8 canine livers using successively acquired 3-D B-mode volumes and compared with concurrently measured SWS. When portal venous pressure was increased from clinically normal (0-5mmHg) to pressures representing highly diseased states at 20mmHg, the liver was observed to expand with axial strain measures up to 10%. At the same time, SWS estimates were observed to increase from 1.5-2m/s at 0-5mmHg (baseline) to 3.25-3.5m/s at 20mmHg.
Copyright © 2013 Elsevier Ltd. All rights reserved.
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11 MeSH Terms
A Bayesian hierarchical nonlinear mixture model in the presence of artifactual outliers in a population pharmacokinetic study.
Choi L, Caffo BS, Kohli U, Pandharipande P, Kurnik D, Ely EW, Stein CM
(2011) J Pharmacokinet Pharmacodyn 38: 613-36
MeSH Terms: Aryl Hydrocarbon Hydroxylases, Bayes Theorem, Computer Simulation, Cytochrome P-450 CYP2A6, Dexmedetomidine, Dose-Response Relationship, Drug, Humans, Hypnotics and Sedatives, Nonlinear Dynamics, Research Design, Statistics as Topic
Show Abstract · Added December 10, 2013
The purpose of this study is to develop a statistical methodology to handle a large proportion of artifactual outliers in a population pharmacokinetic (PK) modeling. The motivating PK data were obtained from a population PK study to examine associations between PK parameters such as clearance of dexmedetomidine (DEX) and cytochrome P450 2A6 phenotypes. The blood samples were sparsely sampled from patients in intensive care units (ICUs) while different doses of DEX were continuously infused. Conventional population PK analysis of these data revealed several challenges and intricacies. Especially, there was strong evidence that some plasma drug concentrations were artifactually high and likely contaminated with the infused drug due to blood sampling processes that are sometimes unavoidable in an ICU setting. If not addressed, or if arbitrarily excluded, these outlying values could lead to biased estimates of PK parameters and miss important relationships between PK parameters and covariates due to increased variability. We propose a novel population PK model, a Bayesian hierarchical nonlinear mixture model, to accommodate the artifactual outliers using a finite mixture as the residual error model. Our results showed that the proposed model handles the outliers well. We also conducted simulation studies with a varying proportion of the outliers. These simulation results showed that the proposed model can accommodate the outliers well so that the estimated PK parameters are less biased.
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11 MeSH Terms
Automated refinement and inference of analytical models for metabolic networks.
Schmidt MD, Vallabhajosyula RR, Jenkins JW, Hood JE, Soni AS, Wikswo JP, Lipson H
(2011) Phys Biol 8: 055011
MeSH Terms: Algorithms, Computational Biology, Glycolysis, Kinetics, Metabolic Networks and Pathways, Models, Biological, Nonlinear Dynamics, Yeasts
Show Abstract · Added March 27, 2014
The reverse engineering of metabolic networks from experimental data is traditionally a labor-intensive task requiring a priori systems knowledge. Using a proven model as a test system, we demonstrate an automated method to simplify this process by modifying an existing or related model--suggesting nonlinear terms and structural modifications--or even constructing a new model that agrees with the system's time series observations. In certain cases, this method can identify the full dynamical model from scratch without prior knowledge or structural assumptions. The algorithm selects between multiple candidate models by designing experiments to make their predictions disagree. We performed computational experiments to analyze a nonlinear seven-dimensional model of yeast glycolytic oscillations. This approach corrected mistakes reliably in both approximated and overspecified models. The method performed well to high levels of noise for most states, could identify the correct model de novo, and make better predictions than ordinary parametric regression and neural network models. We identified an invariant quantity in the model, which accurately derived kinetics and the numerical sensitivity coefficients of the system. Finally, we compared the system to dynamic flux estimation and discussed the scaling and application of this methodology to automated experiment design and control in biological systems in real time.
1 Communities
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8 MeSH Terms
Distributed lag and spline modeling for predicting energy expenditure from accelerometry in youth.
Choi L, Chen KY, Acra SA, Buchowski MS
(2010) J Appl Physiol (1985) 108: 314-27
MeSH Terms: Adolescent, Aging, Algorithms, Ankle, Body Height, Body Weight, Calorimetry, Indirect, Child, Energy Metabolism, Female, Forecasting, Hip, Humans, Male, Metabolism, Models, Statistical, Monitoring, Physiologic, Motor Activity, Nonlinear Dynamics, Regression Analysis, Reproducibility of Results, Wakefulness, Wrist
Show Abstract · Added December 10, 2013
Movement sensing using accelerometers is commonly used for the measurement of physical activity (PA) and estimating energy expenditure (EE) under free-living conditions. The major limitation of this approach is lack of accuracy and precision in estimating EE, especially in low-intensity activities. Thus the objective of this study was to investigate benefits of a distributed lag spline (DLS) modeling approach for the prediction of total daily EE (TEE) and EE in sedentary (1.0-1.5 metabolic equivalents; MET), light (1.5-3.0 MET), and moderate/vigorous (> or = 3.0 MET) intensity activities in 10- to 17-year-old youth (n = 76). We also explored feasibility of the DLS modeling approach to predict physical activity EE (PAEE) and METs. Movement was measured by Actigraph accelerometers placed on the hip, wrist, and ankle. With whole-room indirect calorimeter as the reference standard, prediction models (Hip, Wrist, Ankle, Hip+Wrist, Hip+Wrist+Ankle) for TEE, PAEE, and MET were developed and validated using the fivefold cross-validation method. The TEE predictions by these DLS models were not significantly different from the room calorimeter measurements (all P > 0.05). The Hip+Wrist+Ankle predicted TEE better than other models and reduced prediction errors in moderate/vigorous PA for TEE, MET, and PAEE (all P < 0.001). The Hip+Wrist reduced prediction errors for the PAEE and MET at sedentary PA (P = 0.020 and 0.021) compared with the Hip. Models that included Wrist correctly classified time spent at light PA better than other models. The means and standard deviations of the prediction errors for the Hip+Wrist+Ankle and Hip were 0.4 +/- 144.0 and 1.5 +/- 164.7 kcal for the TEE, 0.0 +/- 84.2 and 1.3 +/- 104.7 kcal for the PAEE, and -1.1 +/- 97.6 and -0.1 +/- 108.6 MET min for the MET models. We conclude that the DLS approach for accelerometer data improves detailed EE prediction in youth.
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23 MeSH Terms