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PubMed1999

Guidelines for measurement validation in clinical trial design.

In the process of designing a clinical trial, the accuracy and precision of an endpoint is of critical importance in being able to determine valid results. In the creation and subsequent testing of the validity of an endpoint, it is desirable to show that on repeated measurements the endpoint can be measured precisely, and that it is reproducible with not only itself, but with any "gold standard" that can assess accuracy. Short of having this gold standard, we rely on showing that the endpoint is reliable. Agreement is the extent to which the measurement of the variable of interest yields the same results (consistency) on repeated trials. Thus the more consistent the results given by repeated measurements, the more reliable the measuring procedure. In this article, we examine the sensitivity to location and scale shift of different methods for assessing agreement. These tools include Pearson's correlation coefficient, the intraclass correlation coefficient, the concordance correlation coefficient, the Bradley-Blackwood procedure, and the within patient coefficient of variation. Our simulation studies showed that there are situations wherein the various methods for assessing agreement give conflicting results. On the basis of the results of the simulation studies, there are three important components to consider when deciding whether two sets of measurements are in agreement or not. The first component is the degree of linear relationship between the two sets; the second is the amount of bias as represented by the difference in the means; and the third is the difference between the two variances. The purpose of this article is to help interpret numerical results from the measures of agreement and to establish a criterion or range of values for each agreement measure that we consider to indicate agreement. We clarify what is meant by agreement by placing the measures in context based on scale and location shifts. Furthermore, we present guidelines for assessing agreement or endpoint validation when there are plans to design a clinical trial, and we give an actual example from a recent study.

Biometry↗
PubMed1998

Monte Carlo calculations of electron beam output factors for a medical linear accelerator.

The purpose of this study was to investigate the application of the Monte Carlo technique to the calculation and analysis of output factors for electron beams used in radiotherapy. The code EGS4/BEAM was used to obtain phase-space files for 6, 12 and 20 MeV clinical electron beams from a scattering-foil linac (Varian Clinac 2100C) for a clinically representative range of applicator and square or rectangular insert combinations. The source-to-surface distance used was 100 cm. The field sizes ranged from 1 x 1 cm2 to 20 x 20 cm2. These phase-space files were analysed to study the intrinsic beam characteristics and used as source input for relative dose and output factor computations in homogeneous water phantoms using the code EGS4/DOSXYZ. The calculated relative central-axis depth-dose and transverse dose profiles at various depths of clinical interest agreed with the corresponding measured dose profiles to within 2% of the maximum dose. Calculated output factors for the fields studied agreed with measured output factors to about 2%. This demonstrated that for the Varian Clinac 2100C linear accelerator, electron beam dose calculations in homogeneous water phantoms can be performed accurately at the 2% level using Monte Carlo simulations.

Computer Simulation↗
PubMed2006

Application of wavelet-based tools to study the dynamics of biological processes.

The article makes use of three different examples (sensory information processing in the rat trigeminal complex, intracellular interaction in snail neurons and multimodal dynamics in nephron autoregulation) to demonstrate how modern approaches to time-series analysis based on the wavelet-transform can provide information about the underlying complex biological processes.

Animals↗
PubMed2000

Self-organization and competition in the immune response to cancer invasion: a phase-orientated computational model of oncogenesis.

MOTIVATION: Recent studies indicate that fractal dimensions can uncover aspects of cellular dynamics prior to pathological manifestation. In this respect we are interested in building a computational model of oncogenesis able to generate patterns with the same fractal dimension spectrum as the in vivo tumor. RESULTS: A new theoretical model incorporating a systemic view of oncogenesis in a computational model was proposed. The tumor growth is viewed as competition for resources between the two self-organizing subsystems: the neoplastic and the immune. Numerical simulations revealed that tumor escape can be uncovered in some earlier stage of the immune-system-tumor interaction using multifractal measures. The described computational model is able to simulate also the case of immune, surgical, chemical and radiotherapeutical treatment, as well as their effects. AVAILABILITY: T The software used is available on request from the authors. CONTACT: Sorinel Oprisan, University of New Orleans, Department of Psychology, Ne w Orleans, LA 70148, USA. soprisan@uno.edu

Computer Simulation↗
PubMed2004

Voltage refinement by deficit HOLZ line geometry.

A method of refining electron beam voltage from deficit line intersections, using a quasi-kinematic scattering approximation, is described and applied to a silicon standard. It is shown that dynamical corrections are necessary for higher-index zone axes, such as 310 and 411, where a single deficit line associated with one dominant Bloch state is visible. This leads to a substantial difference in the refined voltage compared with that obtained from a purely kinematic approximation. Neglect of this dynamical correction term effectively invokes a systematic error that may lead to high precision but poor accuracy in higher-order Laue zone measurements of beam voltage or lattice parameters. Although relatively small, differences in the dynamical correction necessary for these two zones are confirmed experimentally for 100-300 keV electrons.

Computer Simulation↗
PubMed2005

Using ergodic theory to assess the performance of ecosystem models.

Ecosystem simulation models are designed to assess the flux of energy, water, carbon and nitrogen according to a given vegetation type. The reliability of the modeled results is determined by model validations. Model validations are typically done using classical statistical methods like regression analysis of predicted versus observed values, paired t statistics and error assessment procedures to characterize the quality of current and future model predictions. All these validation efforts concentrate on static aspects of the model but fail to describe the model dynamics. In this paper, we introduce methods from ergodic theory to analyze the dynamic behavior of ecosystem models. We describe (1) how the attractor representation of model behavior can be reconstructed from a time series of model outputs, and (2) what we can learn from the attractor to assess the model dynamics. As an application example, we provide simulation results for two important pine forest ecosystems in Austria, i.e., 23 Cembran pine and 16 Scots pine stands. These stands were simulated with three model parameterizations: one representing a generic, evergreen needle-leaf forest, and two species- specific parameter sets, one for Cembran pine and one for Scots pine. First, we applied standard validation methods to get static measures of model accuracy and precision. Next, we used ergodic theory to assess model dynamics. A comparison of both analyses reveals important issues related to model dynamics, such as the finding that the occurrence of instabilities in model behavior may not be detected by standard validation methods. Using ergodic theory, we were able to reconstruct the attractors of model behavior. In the attractor describing model dynamics for Cembran pine, simulated with the generic, evergreen needle-leaf forest parameter set, we detected instability in model behavior. We identified this instability as a riddled basin configuration, which is a strong indicator for the occurrence of a chaotic model behavior that may result in random predictions. Our results suggest that ergodic theory is a useful tool for assessing inconsistencies in the dynamics of ecosystem model simulations that have not been detected by standard statistical validation methods.

Climate↗
PubMed1990

Application of a LaserJet printer to plot the Farnsworth-Munsell 100-hue color test.

This paper presents a quick method of computing Farnsworth-Munsell (FM-100) scores and displaying these values on the polar coordinate scale usually associated with this test. The displayed results also present the clinician with a graph of the extended normalized score against cap number and a D-15 panel plot. The output is printed at high resolution on a Hewlett-Packard (HP) LaserJet or a similar printer compatible with or able to emulate the HP. The program is written and compiled in Microsoft-C 5.0. The code can be easily modified either to be customized, or to be moved across compilers.

Color Perception Tests↗
PubMed2003

A radiologic study of the tympanic bone: anatomy and surgery.

OBJECTIVE: The aim of this study was to obtain data on the anatomic structure of the tympanic bone using parasagittal reformatted images created from high-resolution axial computed tomographic scans. In particular, the thickness of the bone in the region of the temporomandibular joint and the floor of the external auditory canal was assessed. The findings are discussed with particular emphasis on the relevance to surgery in this area. BACKGROUND: Surgical management of the tympanic bone forms the basis of canalplasty, which is an essential step in the management of disorders of the external auditory canal. Adequate canalplasty is also crucial in the provision of access for tympanoplasty and to ensure optimal cavity geometry in canal wall down mastoidectomy. Tympanic bone removal is a major step in approaches to the lateral skull base and infratemporal fossa. The tympanic bone is also important because it has critical neurovascular relations in this region of the skull base. METHODS: Computed tomography of the tympanic bone (parasagittal reformatted images) in 54 consecutive adults. RESULTS: The mean thickness of the anterosuperior, anteroinferior, and inferior aspects of the tympanic bone are 2.6, 2.8, and 8 mm, respectively. CONCLUSION: Canalplasty is safely performed in the regions outlined. The technique of canalplasty described in this article is essential for good exposure in external ear, middle ear, mastoid, and skull base surgery.

Adult↗
PubMed2005

Hybrid molecular-continuum fluid models: implementation within a general coupling framework.

Over the past three years we have been developing a new approach for the modelling and simulation of complex fluids. This approach is based on a multiscale hybrid scheme, in which two or more contiguous subdomains are dynamically coupled together. One subdomain is described by molecular dynamics while the other is described by continuum fluid dynamics; such coupled models are of considerable importance for the study of fluid dynamics problems in which only a restricted aspect requires a fully molecular representation. Our model is representative of the generic set of coupled models whose algorithmic structure presents interesting opportunities for deployment on a range of architectures including computational grids. Here we describe the implementation of our HybridMD code within a coupling framework that facilitates flexible deployment on such architectures.

Computer Simulation↗
PubMed1994

Combined statistical study of joint angles and ground reaction forces using component and multiple correspondence analysis.

The purpose of this research is to propose a general methodology to draw gait patterns when including hip, knee and ankle angle excursions in the sagital plane and the three components of the ground reaction force. The multidimensional signal analysis procedure is divided into three main stages: 1) describing the six signals of each step through sliding averages computed for successive time windows, 2) analyzing separately the six step-by-window tables obtained for each signal through principal component analysis to reduce the excessive quantity of data, and 3) analyzing the most informative time windows of the six signals at the same time. To emphasize both linear and nonlinear relationships between the respective time windows, the signal range within a window is cut into fuzzy modalities such as, "low" "medium" and "large." The resulting table is investigated using multiple correspondence analysis. The outcomes are gait patterns combining both time and space aspects. The factor planes obtained from multiple correspondence analysis constitute initial data models so that new data obtained from pathological gait can be directly projected onto them. Such an operation can be used to show how the rehabilitation of a particular subject evolves in relation to normal gait patterns.

Biomechanical Phenomena↗
PubMed2001

Ultrasonic integrated backscatter coefficient profiling of human coronary arteries in vitro.

A theoretical formulation for the profile of the integrated backscatter coefficient (IBC) is derived. This new formulation is based on a theoretical treatment by Chen et al. [1]. It includes correction for the diffraction of the ultrasonic beam and correction for the non-ideal nature of the reference signal. The inclusion of these correction factors permits accurate quantitative profiling of the IBC over the transducer focal zone. Experimental measurements are first performed on well-calibrated vessel-equivalent phantom materials and subsequently on human coronary arteries in vitro. A spherically focused 50.0 MHz f/1.83 transducer is used. IBC profiles are shown for three samples that are representative of early, mid, and advanced atherosclerotic coronary disease. The IBC profiles clearly differentiate the arterial tissues. However, variation between samples with histologically confirmed intimal thickening (N = 24) was large. The mean IBC (+/- 1 standard deviation), in (Sr.mm)-1, for media, adventitia, and thickened intima were 3.86 x 10(-3), 1.53 x 10(-2), and 2.24 x 10(-2), respectively. The mean IBC of thickened intima is larger than previous measurements obtained from femoral arteries, and the mean IBC for media and adventitia layers are lower, reflecting differences in tissue composition between coronary and femoral vessels.

Adult↗
PubMed1990

Computer-assisted linearization of the von Krogh Curve for the measurement of serum complement titre.

Computer simulations of complement titre measurement in sera by linearizing the sigmoidal curve of complement dose response were performed, to simplify the logarithmic calculations of CH50 values. CH50 titres of large variety of human sera including healthy donors and immune deficiency patients were estimated. The values obtained were compared with the hand-simulated results using the Y/(1-Y) conversion table and a log-log graphic paper. Using computer simulation, CH50 can be determined with great ease.

Complement Hemolytic Activity Assay↗
PubMed2005

Do computer-assisted, morphometric-derived sperm characteristics reflect DNA status in canine spermatozoa?

It is widely accepted that sperm morphology is a strong indicator of semen quality. As the sperm head mainly comprises the sperm DNA, it is have been proposed that subtle changes in sperm morphology may be related to abnormal DNA content. Semen from four mongrel dogs was used to investigate DNA quality by means of the sperm chromatin structure assay (SCSA), and for computerized sperm morphometry (CASMA). Each sperm head was measured for nine primary parameters [head area (A), head perimeter (P), head length (L), head width (W), midpiece width (w), midpiece area (a), distance (d) between the major axes of the head and midpiece, angle (theta) of divergence of the midpiece from the head axis] and four parameters of head shape [FUN1, L/W; FUN2, 4piA/P(2); FUN3, (L - W)/(L + W); FUN4, piLW/4A]. Significant differences were found in all CASMA-derived parameters among dogs (p < 0.001). Linear regression models including sperm head shape factors 1, 3 and 4 predicted the extent of DNA denaturation (p < 0.001). We conclude that the CASMA analysis can be considered a powerful tool to improve the spermiogram.

Animals↗
PubMed2001

High-speed digital imaging of the medial surface of the vocal folds.

High-speed digital imaging of the medial surface of the vocal folds was performed in excised canine larynx experiments. Building on the excised larynx investigations of Baer [Ph.D. dissertation, MIT, Boston, MA (1975)] and hemilarynx investigations of Jiang and Titze [Laryngoscope 103, 872-882 (1993)], nine vocal fold fleshpoints were tracked simultaneously along the medial surface of one coronal plane of the left vocal fold using a Kodak EktaPro 4540 high-speed digital imaging system. By imaging from two distinct views, 3D reconstructions of fleshpoint trajectories were performed with a sampling frequency of 4.5 kHz and a spatial resolution of approximately 0.08 mm. Quantitative results were derived from a typical example of periodic chestlike vibrations. Furthermore, these data were decomposed into empirical eigenfunctions, the building blocks of vocal fold vibration, illuminating basic mechanisms of self-sustained oscillation. Previously, such mechanisms have only been explored theoretically using computer models of vocal fold vibration [Berry et al., J. Acoust. Soc. Am. 95, 3595-3604 (1994)]. Similar to the theoretical studies, two eigenfunctions captured 98% of the variance of the data. Because this investigation utilized high-speed technology, the methodology may also be used to examine complex, aperiodic vibrations. Thus, this technique allows mechanisms of regular and irregular vocal fold vibration to be explored using direct observations of vibrating tissues in the laboratory.

Animals↗
PubMed2003

Time-frequency model for echo-delay resolution in wideband biosonar.

A time/frequency model of the bat's auditory system was developed to examine the basis for the fine (approximately 2 micros) echo-delay resolution of big brown bats (Eptesicus fuscus), and its performance at resolving closely spaced FM sonar echoes in the bat's 20-100-kHz band at different signal-to-noise ratios was computed. The model uses parallel bandpass filters spaced over this band to generate envelopes that individually can have much lower bandwidth than the bat's ultrasonic sonar sounds and still achieve fine delay resolution. Because fine delay separations are inside the integration time of the model's filters (approximately 250-300 micros), resolving them means using interference patterns along the frequency dimension (spectral peaks and notches). The low bandwidth content of the filter outputs is suitable for relay of information to higher auditory areas that have intrinsically poor temporal response properties. If implemented in fully parallel analog-digital hardware, the model is computationally extremely efficient and would improve resolution in military and industrial sonar receivers.

Animals↗
PubMed2004

Eigenfunction analysis of stochastic backscatter for characterization of acoustic aberration in medical ultrasound imaging.

Presented here is a characterization of aberration in medical ultrasound imaging. The characterization is optimal in the sense of maximizing the expected energy in a modified beamformer output of the received acoustic backscatter. Aberration correction based on this characterization takes the form of an aberration correction filter. The situation considered is frequently found in applications when imaging organs through a body wall: aberration is introduced in a layer close to the transducer, and acoustic backscatter from a scattering region behind the body wall is measured at the transducer surface. The scattering region consists of scatterers randomly distributed with very short correlation length compared to the acoustic wavelength of the transmit pulse. The scatterer distribution is therefore assumed to be delta correlated. This paper shows how maximizing the expected energy in a modified beamformer output signal naturally leads to eigenfunctions of a Fredholm integral operator, where the associated kernel function is a spatial correlation function of the received stochastic signal. Aberration characterization and aberration correction are presented for simulated data constructed to mimic aberration introduced by the abdominal wall. The results compare well with what is obtainable using data from a simulated point source.

Artifacts↗
PubMed2004

Ultrasonic wave propagation in human cancellous bone: application of Biot theory.

Ultrasonic wave propagation in human cancellous bone is considered. Reflection and transmission coefficients are derived for a slab of cancellous bone having an elastic frame using Biot's theory modified by the model of Johnson et al. [J. Fluid Mech. 176, 379-402 (1987)] for viscous exchange between fluid and structure. Numerical simulations of transmitted waves in the time domain are worked out by varying the modified Biot parameters. The variation is applied to the governing parameters and is about 20%. From this study, we can gain an insight into the sensitivity of each physical parameter used in this theory. Some parameters play an important role in slow-wave wave form, such as the viscous characteristic length lambda and pore fluid bulk modulus Kf. However, other parameters play an important role in the fast-wave wave form, such as solid density rhos and shear modulus N. We also note from these simulations that some parameters such as porosity phi, tortuosity alpha(infinty), thickness, solid bulk modulus Ks, and skeletal compressibility frame Kb, play an important role simultaneously in both fast and slow wave forms compared to other parameters which act on the wave form of just one of the two waves. The sensitivity of the modified Biot parameters with respect to the transmitted wave depends strongly on the coupling between the solid and fluid phases of the cancellous bone. Experimental results for slow and fast waves transmitted through human cancellous bone samples are given and compared with theoretical predictions.

Bone Density↗