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PubMed2005

Calculation of partition functions by measuring component distributions.

A new algorithm is presented, which allows us to calculate numerically the partition function Z for systems, which can be described by arbitrary interaction graphs and lattices, e.g., Ising models or Potts models (for arbitrary values q>0), including random or diluted models. The new approach is suitable for large systems. The basic idea is to measure the distribution of the number of connected components in the corresponding Fortuin-Kasteleyn representation and to compare with the case of zero degrees of freedom, where the exact result Z=1 is known. As an application, d=2 and d=3 dimensional ferromagnetic Potts models are studied, and the critical values qc, where the transition changes from second to first order, are determined. Large systems of sizes N=1000(2) and N=100(3) are treated. The critical value qc(d=2)=4 is confirmed and qc(d=3)=2.35(5) is found.

Journal Article↗
PubMed2005

Airway wall thickness in cigarette smokers: quantitative thin-section CT assessment.

PURPOSE: To design and validate a dedicated software tool to measure airway dimensions on thin-section computed tomographic (CT) images and to use the tool to prospectively compare airway wall thickness in nonsmokers with normal lung function with that in smokers with and without chronic obstructive pulmonary disease (COPD). MATERIALS AND METHODS: All subjects gave written informed consent. The study was approved by local ethics committee. With Laplacian of Gaussian algorithm, software was tested in phantom and excised sheep lung fixed in inflation and validated with Bland-Altman analysis. Study prospectively included nine nonsmokers (six women, three men; mean age, 53 years +/- 5.6 [standard error of the mean]) with normal lung function (group 1), seven smokers (three women, four men; mean age, 56 years +/- 5.6) with normal lung function (group 2), and eight smokers (zero women, eight men; mean age, 65 years +/- 4.0) with COPD. Calculations were determined with spirometrically gated CT: For each selected bronchus, the wall area (WA), internal area (IA), airway caliber (sum of IA and WA), and WA/IA ratio were calculated. For each patient, summation of WA to summation of IA (SigmaWA/SigmaIA) ratio, which reflected normalized airway wall thickness, was calculated. Groups were compared by using analysis of variance with generalized linear model and unpaired t test. Pearson correlation coefficient was used to assess correlation between software measurements and pulmonary function test results. RESULTS: Comparison of measurements in phantom and excised sheep lung with algorithm measurements revealed that the latter were reliable and repeatable. In clinical study, SigmaWA/SigmaIA ratio was significantly different among three groups (P < .001). Normalized airway wall thickness and IA were significantly related to lung function test data, including forced expiratory volume in 1 second (r = -0.54, P = .006), specific airway conductance (r = -0.45, P = .03), and forced expiratory flow between 25% and 75% of vital capacity (r = -0.65, P < .001). CONCLUSION: This software provides accurate and reproducible measurements of IA and WA of bronchi on thin-section CT images and demonstrates that in vivo normalized airway wall thickness was larger in smokers with COPD than it was in smokers or nonsmokers without COPD.

Animals↗
PubMed2001

Comparative analysis of multiple-casualty incident triage algorithms.

STUDY OBJECTIVE: We sought to retrospectively measure the accuracy of multiple-casualty incident (MCI) triage algorithms and their component physiologic variables in predicting adult patients with critical injury. METHODS: We performed a retrospective review of 1,144 consecutive adult patients transported by ambulance and admitted to 2 trauma centers. Association between first-recorded out-of-hospital physiologic variables and a resource-based definition of severe injury appropriate to the MCI context was determined. The association between severe injury and Triage Sieve, Simple Triage and Rapid Treatment, modified Simple Triage and Rapid Treatment, and CareFlight Triage was determined in the patient population. RESULTS: Of the physiologic variables, the Motor Component of the Glasgow Coma Scale had the strongest association with severe injury, followed by systolic blood pressure. The differences between CareFlight Triage, Simple Triage and Rapid Treatment, and modified Simple Triage and Rapid Treatment were not dramatic, with sensitivities of 82% (95% confidence interval [CI] 75% to 88%), 85% (95% CI 78% to 90%), and 84% (95% CI 76% to 89%), respectively, and specificities of 96% (95% CI 94% to 97%), 86% (95% CI 84% to 88%), and 91% (95% CI 89% to 93%), respectively. Both forms of Triage Sieve were significantly poorer predictors of severe injury. CONCLUSION: Of the physiologic variables used in the triage algorithms, the Motor Component of the Glasgow Coma Scale and systolic blood pressure had the strongest association with severe injury. CareFlight Triage, Simple Triage and Rapid Treatment, and modified Simple Triage and Rapid Treatment had similar sensitivities in predicting critical injury in designated trauma patients, but CareFlight Triage had better specificity. Because patients in a true mass casualty situation may not be completely comparable with designated trauma patients transported to emergency departments in routine circumstances, the best triage instrument in this study may not be the best in an actual MCI. These findings must be validated prospectively before their accuracy can be confirmed.

Adolescent↗
PubMed1995

Measurement of a photon penumbra-generating kernel for a convolution-adapted ratio-TAR algorithm for 3D treatment planning.

A method has been developed to measure a photon penumbra-generating kernel using dosimetry equipment available in most radiation therapy departments. The kernel is used in a convolution-adapted ratio-TAR algorithm in our three-dimensional treatment planning system. The kernel is assumed to be invariant with respect to off-axis position, axially symmetric, and is divided into short- and long-range components, with a different measurement technique for each. The data required to obtain the short-range component are measured by scanning across a split-field geometry incident on a water phantom. The derivative of the measured profile is proportional to one-dimensional projections across the kernel. Because the kernel is axially symmetric, only one profile measurement is required for each depth. A CT reconstruction technique is used to extract the radial dependence of the kernel from the strip integrals. Electronic noise in the acquisition system yields significant uncertainties in the kernel shape for distances beyond 3 cm. The long-range portion of the kernel is obtained by examining tissue-air ratios (TARs). The derivative of the TAR at the center of a circular field is proportional to the kernel value at the distance corresponding to the radius of the field. The kernel measurement method was tested by comparing measured and calculated square-field profiles at a variety of depths. Agreement was within 1% within the field boundary and 3% outside the field boundary for all depths.

Algorithms↗
PubMed2002

Retrieval of atmospheric-temperature and water-vapor profiles by use of combined satellite and ground-based infrared spectral-radiance measurements.

A nonlinear sounding retrieval algorithm is used to produce vertical-temperature and water-vapor profiles from coincident observations taken by the airborne High-resolution Interferometer Sounder (HIS) and the ground-based Atmospheric Emitted Radiance Interferometer (AERI) during the SUbsonic Contrails and Clouds Effects Special Study (SUCCESS). Also, clear sky Geostationary Operational Environmental Satellite (GOES) and AERI radiance measurements, achieved on a daily real-time basis at the Department of Energy's Oklahoma CART (Cloud and Radiation Testbed) site, are used to demonstrate the current profiling capability by use of simultaneous geostationary satellite and ground-based remote sensing observations under clear-sky conditions. The discrepancy principle, a method to find the proper smoothing parameters from the minimum value between the normalized spectral residual norm and the a priori upper bound, is used to demonstrate the feasibility and effectiveness of on-line simultaneous tuning of the multiple weighting and smoothing parameters from the combined satellite/airborne and ground-based measurements for the temperature and water-vapor retrieval in this nonlinear-retrieval process. An objective method to determine the degrees of freedom (d.f.) of the observation signal is derived. The d.f. of the radiance signal for the combined GOES and AERI measurements is larger than that for either instrument alone; while the d.f. of the observation signal for the combined GOES and AERI measurements is larger than that for either instrument alone and of the combined GOES and AERI measurements. The use of simultaneous clear-sky AERI and GOES data now provides improved vertical temperature and moisture soundings on an hourly basis for use in the Atmospheric Radiation Measurement program [J. Appl. Meteorol. 37, 875 (1998)].

Journal Article↗
PubMed1994

Bacteria identification of otitis media with fluorescence spectroscopy.

We have investigated the fluorescence profiles of four common pathogens: S. pneumoniae, S. aureus, M. catarrhalis, and H. influenzae. The steady-state auto fluorescence spectra of bacteria are measured as a function of the incident light from 200 to 700 nm. The spectra for each bacterium are combined into a fluorescence profile or fluorescence finger print. Each bacterium produces a unique in vitro fluorescence profile when measured in a saline suspension. The profiles are reproducible. Suspensions of a bacterial strain, where the identification is not known, can be correctly matched to a small library of previously measured fluorescence profiles using a linear least-squares fitting algorithm. In addition, we have measured the fluorescence and absorption spectrum of the tympanic membrane removed from a chinchilla. The optical properties of the tympanic membrane and the least-squares identification process form precept for a non-invasive, fluorescence based bacterial diagnosis technique to be used in otitis media.

Algorithms↗
PubMed2004

Measure profile surrogates: a method to validate the performance of epileptic seizure prediction algorithms.

In a growing number of publications it is claimed that epileptic seizures can be predicted by analyzing the electroencephalogram (EEG) with different characterizing measures. However, many of these studies suffer from a severe lack of statistical validation. Only rarely are results passed to a statistical test and verified against some null hypothesis H0 in order to quantify their significance. In this paper we propose a method to statistically validate the performance of measures used to predict epileptic seizures. From measure profiles rendered by applying a moving-window technique to the electroencephalogram we first generate an ensemble of surrogates by a constrained randomization using simulated annealing. Subsequently the seizure prediction algorithm is applied to the original measure profile and to the surrogates. If detectable changes before seizure onset exist, highest performance values should be obtained for the original measure profiles and the null hypothesis. "The measure is not suited for seizure prediction" can be rejected. We demonstrate our method by applying two measures of synchronization to a quasicontinuous EEG recording and by evaluating their predictive performance using a straightforward seizure prediction statistics. We would like to stress that the proposed method is rather universal and can be applied to many other prediction and detection problems.

Algorithms↗
PubMed1994

A comparison of three electron planning algorithms for a 16 MeV electron beam.

PURPOSE: We report results of a comparison of three electron planning algorithms, an Age-Diffusion Pencil beam algorithm and two (2-D) and three dimensional (3-D) Hogstrom pencil beam algorithms, using simple 2 x 2 cm air and hard bone inhomogeneities and a complex anthropomorphic head and neck phantom. METHODS AND MATERIALS: The simple inhomogeneities have variable dimensions outside the plane of calculation to test the effects of out of plane scattering on 2-D algorithms, compared with dose measured by film below the inhomogeneity in the dose fall-off range. Comparisons are also made of a parotid treatment field for 16 MeV electrons, and the dose measured by high sensitivity thermoluminescent dosimeters in the head and neck phantom. RESULTS: Behind the simple inhomogeneities, the electron algorithms are found to underestimate the dose behind the air cavity by up to 40% and overestimated the dose behind bone by up to 30%. In the head phantom, the presence of inhomogeneities also presents problems for the algorithms, with overestimations of dose of up to 20% found behind bone-tissue interfaces, apparently due to shielding by high density bone. Overestimations of up to 17% are also found beside interfaces parallel to the beam. Underestimations of dose of up to 10% are found on the beam-side of interfaces, due to under-prediction of backscattered electrons. All three investigated algorithms underestimate the dose by up to 20% behind extreme surface curvature. One algorithm is found to underestimate the dose in the falloff region while another overestimates the dose around the 90% isodose. CONCLUSION: Clinicians should be aware of the limitations of their planning systems.

Algorithms↗
PubMed1990

An algorithm for the interpretation of cardiopulmonary exercise tests.

We have developed and are using an algorithm for the interpretation of cardiopulmonary exercise tests that are performed in our Pulmonary Diagnostic Service Department. As its decision points, this algorithm uses routinely obtained measurements from the results of these exercise tests, such as VO2, VCO2, VE, SaO2, HR, and AT. Using the algorithm results in an objective determination of limitation to exercise and allows for the differentiation between pulmonary and cardiac or circulatory limitation. This straightforward technique for arriving at an interpretation of these tests has resulted in a more consistent approach to interpretation and an excellent teaching guide for physicians and technicians.

Algorithms↗
PubMed2006

Algorithm for multi-curve-fitting with shared parameters and a possible application in evoked compound action potential measurements.

BACKGROUND: Experimental results are commonly fitted by determining parameter values of suitable mathematical expressions. In case a relation exists between different data sets, the accuracy of the parameters obtained can be increased by incorporating this relationship in the fitting process instead of fitting the recordings separately. METHODS: An algorithm to fit multiple measured curves simultaneously was developed. The method accounts for parameters that are shared by some curves. It can be applied to either linear or nonlinear equations. Simulated noisy "measurement results" were created to compare the introduced method to the "straight forward" way of fitting the curves separately. RESULTS: The analysis of the simulated measurements confirm, that the introduced method yields more accurate parameters compared to the ones gained by fitting the measurements separately. Therefore it needs more computer time. As an example, the new fitting algorithm is applied to the measurements of the evoked compound action potentials (ECAP) of the auditory nerve: This leads to promising ideas to reduce artefacts generated by the measuring process. CONCLUSION: The introduced fitting algorithm uses the relationship between multiple measurement results to increase the accuracy of the parameters. Its application in the field of ECAP measurements is promising and should be further investigated.

Action Potentials↗
PubMed2004

On the use of the derivative of electroglottographic signals for characterization of nonpathological phonation.

Electroglottography is a common method for providing noninvasive measurements of glottal activity. The derivative of the electroglottographic signal, however, has not attracted much attention, although it yields reliable indicators of glottal closing instants. The purpose of this paper is to provide a guide to the usefulness of this signal. The main features that are to be found in this signal are presented on the basis of an extensive analysis of a database of items sung by 18 trained singers. Glottal opening and closing instants are related to peaks in the signal; the latter can be used to measure glottal parameters such as fundamental frequency and open quotient. In some cases, peaks are doubled or imprecise, which points to special (but by no means uncommon) glottal configurations. A correlation-based algorithm for the automatic measurement of fundamental frequency and open quotient using the derivative of electroglottographic signals is proposed. It is compared to three other electroglottographic-based methods with regard to the measurement of open quotient in inverse-filtered derived glottal flow. It is shown that agreement with the glottal-flow measurements is much better than most threshold-based measurements in the case of sustained sounds.

Algorithms↗
PubMed2004

Physical activity in low-income postpartum women.

PURPOSE: To validate the 7-day physical activity recall (PAR), including alternative PAR scoring algorithms, using pedometer readings with low-income postpartum women, and to describe physical activity patterns of a low-income population of postpartum women. METHODS: Forty-four women (13 African American, 19 Hispanic, and 12 White) from the Austin New Mothers Study (ANMS) were interviewed at 3 months postpartum. Data were scored alternatively according to the Blair (sitting treated as light activity) and Welk (sitting excluded from light activity and treated as rest) algorithms. Step counts based on 3 days of wearing pedometers served as the validation measure. FINDINGS: Using the Welk algorithm, PAR components significantly correlated with step counts were: minutes spent in light activity, total activity (sum of light to very hard activity), and energy expenditure. Minutes spent in sitting were negatively correlated with step counts. No PAR component activities derived with the Blair algorithm were significantly related to step counts. The largest amount of active time was spent in light activity: 384.4 minutes with the Welk algorithm. Mothers averaged fewer than 16 minutes per day in moderate or high intensity activity. Step counts measured by pedometers averaged 6,262 (SD = 2,712) per day. CONCLUSIONS: The findings indicate support for the validity of the PAR as a measure of physical activity with low-income postpartum mothers when scored according to the Welk algorithm. On average, low-income postpartum women in this study did not meet recommendations for amount of moderate or high intensity physical activity.

Activities of Daily Living↗
PubMed2007

Dispersion multiplexing with broadband filtering for miniature spectrometers.

We replace the traditional grating used in a dispersive spectrometer with a multiplex holographic grating to increase the spectral range sensed by the instrument. The multiplexed grating allows us to measure three different, overlapping spectral bands on a color digital focal plane. The detector's broadband color filters, along with a computational inversion algorithm, let us disambiguate measurements made from the three bands. The overlapping spectral bands allow us to measure a greater spectral bandwidth than a traditional spectrometer with the same sized detector. Additionally, our spectrometer uses a static coded aperture mask in the place of a slit. The aperture mask allows increased light throughput, offsetting the photon loss at the broadband filters. We present our proof-of-concept dispersion multiplexing spectrometer design with experimental measurements to verify its operation.

Algorithms↗
PubMed2002

Retrieval of CO from nadir remote-sensing measurements in the infrared by use of four different inversion algorithms.

Four inversion schemes based on various retrieval approaches (digital gas correlation, nonlinear least squares, global fit adjustment, and neural networks) developed to retrieve CO from nadir radiances measured by such downward-looking satelliteborne instruments as the Measurement of Pollution in the Troposphere (MOPITT), the Tropospheric Emission Spectrometer (TES), and the Infrared Atmospheric Sounding Interferometer (IASI) instruments were compared both for simulated cases and for atmospheric spectra recorded by the Interferometric Monitor for Greenhouse Gases (IMG). The sensitivity of the retrieved CO total column amount to properties that may affect the inversion accuracy (noise, ancillary temperature profile, and water-vapor content) was investigated. The CO column amounts for the simulated radiance spectra agreed within 4%, whereas larger discrepancies were obtained when atmospheric spectra recorded by the IMG instrument were analyzed. The assumed vertical temperature profile is shown to be a critical parameter for accurate CO retrieval. The instrument's line shape was also identified as a possible cause of disagreement among the result provided by the groups of scientist who are participating in this study.

Journal Article↗
PubMed2006

A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.

MOTIVATION: Comparing two or more complex protein mixtures using liquid chromatography mass spectrometry (LC-MS) requires multiple analysis steps to locate and quantitate natural peptides within a single experiment and to align and normalize findings across multiple experiments. RESULTS: We describe msInspect, an open-source application comprising algorithms and visualization tools for the analysis of multiple LC-MS experimental measurements. The platform integrates novel algorithms for detecting signatures of natural peptides within a single LC-MS measurement and combines multiple experimental measurements into a peptide array, which may then be mined using analysis tools traditionally applied to genomic array analysis. The platform supports quantitation by both label-free and isotopic labeling approaches. The software implementation has been designed so that many key components may be easily replaced, making it useful as a workbench for integrating other novel algorithms developed by a growing research community. AVAILABILITY: The msInspect software is distributed freely under an Apache 2.0 license. The software as well as a Zip file with all peptide feature files and scripts needed to generate the tables and figures in this article are available at http://proteomics.fhcrc.org/.

Algorithms↗
PubMed2000

Validation of partial tissue segmentation of single-channel magnetic resonance images of the brain.

We describe and evaluate a practical, automated algorithm based on local statistical mixture modeling for segmenting single-channel, T1-weighted volumetric magnetic resonance images of the brain into gray matter, white matter, and cerebrospinal fluid. We employed a stereological sampling method to assess, prospectively, the performance of the method with respect to human experts on 10 normal T1-weighted brain scans acquired with a three-dimensional gradient echo pulse sequence. The overall kappa statistic for the concordance of the algorithm with the human experts was 0.806, while that among raters, excluding the algorithm, was 0.802. The algorithm had better agreement with the modal expert decision (kappa = 0.878). The algorithm could not be distinguished from the experts by this measure. We also validated the algorithm on a simulated MR scan of a digital brain phantom with known tissue composition. Global gray matter and white matter errors were 1% and <1%, respectively, and correlation coefficients with the underlying tissue model were 0.95 for gray matter, 0.98 for white matter, and 0.95 for cerebrospinal fluid. In both approaches to validation, we evaluated both local and global performance of the algorithm. Human experts generated slightly higher global gray matter proportion estimates on the test brain scans relative to the algorithm (3.7%) and on the simulated MR scan relative to the true tissue model (4.4%). The algorithm underestimated gray in some subcortical nuclei which contain admixed gray and white matter. We demonstrate the reliability of the method on individual 1 NEX data sets of the test subjects, and its insensitivity to the precise values of initial model parameters. The output of this algorithm is suitable for quantifying cerebral cortical tissue, using a commonly performed commercial pulse sequence.

Algorithms↗
PubMed2002

Noninvasive total hemoglobin measurement.

Wavelength selection and prediction algorithm for determining total hemoglobin concentration are investigated. A model based on the difference in optical density induced by the pulsation of the heart beat is developed by taking an approximation of Twersky's theory on the assumption that the variation of blood vessel size is small during arterial pulsing. A device is constructed with a five-wavelength light emitting diode array as the light source. The selected wavelengths are two isobestic points and three in compensation for tissue scattering. Data are collected from 129 outpatients who are randomly grouped as calibration and prediction sets. The ratio of the variations of optical density between systole and diastole at two different wavelengths is used as a variable. We selected several such variables that show high reproducibility among all variables. Multiple linear regression analysis is made in order to predict total hemoglobin concentration. The correlation coefficient is 0.804 and the standard deviation is 0.864 g/dL for the calibration set. The relative percent error and standard deviation of the prediction set are 8.5% and 1.142 g/dL, respectively. We successfully demonstrate the possibility of noninvasive hemoglobin measurement, particularly, using the wavelengths below 1000 nm.

Algorithms↗