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Results for “Measuring algorithm”

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PubMed1997

Partial depletion of sarcoplasmic reticulum calcium does not prevent calcium sparks in rat ventricular myocytes.

1. The exact nature of calcium sparks in the heart remains highly controversial. We sought to determine whether calcium sparks arise from a single or multiple calcium release channels/ ryanodine receptors in the sarcoplasmic reticulum (SR). If their genesis involves a calcium-coupled recruitment of multiple channels, calcium sparks might be abolished by a modest depletion of SR calcium (because of the decrease in unitary calcium flux and hence a decrease in the gain of local calcium-induced calcium release). If, on the other extreme, calcium sparks are produced despite severe SR depletion, the single-channel origin will be preferred. 2. Spontaneous calcium sparks were studied in rat ventricular myocytes using confocal microscopy and the fluorescent calcium probe fluo-3. A computer algorithm was developed to count and measure objectively calcium sparks in linescan images. 3. Thapsigargin (25-150 nM) depleted caffeine-releasable SR calcium by up to 64%, in a dose- and time-dependent manner, without altering the resting cytosolic calcium level. During SR depletion, calcium sparks were robustly observed, albeit at reduced frequency (> or = 30% of control) and amplitude (> or = 60% of control). 4. Due to the reduced detectability of small sparks against noise background, the observed data would overestimate reduction in spark frequency but underestimate amplitude reduction. After correction for this detection bias, we found that the spark frequency was independent of SR load, whereas the amplitude was proportional to load. 5. We conclude that, although spark amplitude depends on SR filling status, the frequency of spark generation is independent of SR calcium load, and therefore independent of the local calcium release rate. This implies that sparks are single-channel events, or collective events that are well above threshold for local regeneration. Additionally, our results suggest that intraluminal SR calcium, at normal or low loads, does not play a major role in the regulation of on-gating of the ryanodine receptor.

Adamantane↗

PubMed2006

Genetic analysis of growth curves using the SAEM algorithm.

The analysis of nonlinear function-valued characters is very important in genetic studies, especially for growth traits of agricultural and laboratory species. Inference in nonlinear mixed effects models is, however, quite complex and is usually based on likelihood approximations or Bayesian methods. The aim of this paper was to present an efficient stochastic EM procedure, namely the SAEM algorithm, which is much faster to converge than the classical Monte Carlo EM algorithm and Bayesian estimation procedures, does not require specification of prior distributions and is quite robust to the choice of starting values. The key idea is to recycle the simulated values from one iteration to the next in the EM algorithm, which considerably accelerates the convergence. A simulation study is presented which confirms the advantages of this estimation procedure in the case of a genetic analysis. The SAEM algorithm was applied to real data sets on growth measurements in beef cattle and in chickens. The proposed estimation procedure, as the classical Monte Carlo EM algorithm, provides significance tests on the parameters and likelihood based model comparison criteria to compare the nonlinear models with other longitudinal methods.

Algorithms↗

PubMed1988

Semi-automated analysis of manually reconstructed tracks of progressively motile human spermatozoa.

Several alternative algorithms for computer-assisted derivation of measurements of movement characteristics from manually reconstructed tracks of progressively motile human spermatozoa were compared. Fifty tracks were reconstructed at 30 Hz from video recordings and analysed using traditional manual methods and by four combinations of computer algorithms. The best algorithm set was identified ('Videomot.mdpt') and the values for the curvilinear, average path and linear velocities (VCVL, VAVE and VLIN respectively), the amplitude of lateral displacement of the sperm head about the axis of progression (AH) and the number of times the sperm head crossed the average path (the 'beat/cross frequency', BXF) obtained using it were compared to those obtained by manual analysis. There was a considerable time saving when the computer-assisted method was used and the values it gave for the various movement characteristics showed good correspondence with those obtained manually. In addition, repeated data entry and analysis was found to be highly reproducible. When the tracks were re-plotted at 6 Hz (as used by the multiple-exposure photomicrography method for sperm motility analysis) insufficient information remained in the tracks for reliable determination of anything other than VLIN. We conclude that the Videomot.mdpt program provides reliable values for the movement characteristics of progressively motile human spermatozoa, and believe it will be of great value in the validation of commercial systems providing automated sperm movement analysis and in laboratories which do not have access to such costly equipment.

Algorithms↗

PubMed2005

Microphysical aerosol parameters from multiwavelength lidar.

The hybrid regularization technique developed at the Institute of Mathematics of Potsdam University (IMP) is used to derive microphysical properties such as effective radius, surface-area concentration, and volume concentration, as well as the single-scattering albedo and a mean complex refractive index, from multiwavelength lidar measurements. We present the continuation of investigations of the IMP method. Theoretical studies of the degree of ill-posedness of the underlying model, simulation results with respect to the analysis of the retrieval error of microphysical particle properties from multiwavelength lidar data, and a comparison of results for different numbers of backscatter and extinction coefficients are presented. Our analysis shows that the backscatter operator has a smaller degree of ill-posedness than the operator for extinction. This fact underlines the importance of backscatter data. Moreover, the degree of ill-posedness increases with increasing particle absorption, i.e., depends on the imaginary part of the refractive index and does not depend significantly on the real part. Furthermore, an extensive simulation study was carried out for logarithmic-normal size distributions with different median radii, mode widths, and real and imaginary parts of refractive indices. The errors of the retrieved particle properties obtained from the inversion of three backscatter (355, 532, and 1064 nm) and two extinction (355 and 532 nm) coefficients were compared with the uncertainties for the case of six backscatter (400, 710, 800 nm, additionally) and the same two extinction coefficients. For known complex refractive index and up to 20% normally distributed noise, we found that the retrieval errors for effective radius, surface-area concentration, and volume concentration stay below approximately 15% in both cases. Simulations were also made with unknown complex refractive index. In that case the integrated parameters stay below approximately 30%, and the imaginary part of the refractive index stays below 35% for input noise up to 10% in both cases. In general, the quality of the retrieved aerosol parameters depends strongly on the imaginary part owing to the degree of ill-posedness. It is shown that under certain constraints a minimum data set of three backscatter coefficients and two extinction coefficients is sufficient for a successful inversion. The IMP algorithm was finally tested for a measurement case.

Journal Article↗

PubMed2003

Chamber for indirect calorimetry with accurate measurement and time discrimination of metabolic plateaus of over 20 min.

A robust algorithm for pull-calorimeters that provides a rapid response to changes in respiratory gas exchange has been implemented. Metabolic plateaus (over 20 min), such as that generated by steady treadmill exercise, can be measured accurately (< 2.0% error for an energy expenditure level of 16.7 kJ min(-1)). The time resolution for changes between plateaus can be accurately found with 1 min discrimination. Implementation required only software changes but no structural or instrumentation changes to the chamber. The algorithm was based on the one developed for the push-calorimeter at the Sahlgrenska Hospital in Sweden. The method utilises published equations for the rate of O2 consumption and CO2 production in the chamber, along with techniques for suppressing noise and identifying trends. Using the exact solution of the equations for steady state, the O2 concentrations from the preceding 30 min period are fitted to two connected exponential segments, of variable length, using the least-squares method. The smoothed O2 concentration and associated time derivative are then determined for the time point 15 min earlier and substituted into the respiration equations. The CO2 concentrations are subjected to the same analysis. The process is repeated every minute, and the newly computed rates of O2 consumption and CO2 production, as well as metabolic rate, are then presented. Gas injection tests proved that the chamber can respond instantaneously to a change from one steady state of respiration to another and correctly averages repeated changes in respiration with periods less than 15min (< 1.4% error for simulated, alternating O2 consumption levels of 0.81 min (-1) and 0.01 min). The successful integration of the algorithm into the Pennington chambers allows for traditional 24 h energy expenditure measurements and various metabolic experiments requiring rapid responses.

Algorithms↗

PubMed1995

An algorithm for analysing probed partial digestion experiments.

A partial digestion of DNA (e.g. cosmid. Lambda, YAC, chromosome) is performed and the lengths of thoses fragments which hybridize to a labeled probe are measured using gel electrophoresis. We give an efficient algorithm that takes as input this experimental data and proposes one or more candidate solutions. Each solution designates the location of each restriction site and specifies the endpoints of each fragment. (Further experiments can then be designed to select the correct solution from this small set of candidates.) The algorithm works well even when the experiment gives inexact values for the lengths.

Algorithms↗

PubMed2004

Scanning laser polarimetry of the retinal nerve fiber layer in perimetrically unaffected eyes of glaucoma patients.

PURPOSE: To compare scanning laser polarimetry (SLP) measurements of retinal nerve fiber layer (RNFL) thickness in perimetrically unaffected eyes of glaucoma patients with those in their fellow eyes with field loss and eyes of healthy subjects. DESIGN: Observational case-control study. PARTICIPANTS AND CONTROLS: Twenty-three glaucoma patients with a reproducible visual field (VF) defect in one eye (mean mean deviation [MD], -5.71 decibels [dB]) and a normal VF in the other one (i.e., < or =1 VF test point below the 5% probability level [mean MD, -0.01 dB]) and 73 control eyes of as many age-matched healthy subjects (mean MD, 0.39 dB). The MDs and pattern standard deviations of the glaucoma patients' eyes with normal VFs and the control eyes did not statistically significantly differ (independent samples t test, P = 0.15 and P = 0.61, respectively). METHODS: All subjects were measured in both eyes with the GDxVCC, a commercially available instrument featuring SLP with automated variable corneal compensation. Standard automated perimetry was assessed by means of the Humphrey Field Analyzer (24-2 Full Threshold or Swedish interactive threshold algorithm Standard achromatic test program). MAIN OUTCOME MEASURES: The standard GDxVCC parameters TSNIT (temporal, superior, nasal, inferior, temporal) Average, Superior Average, Inferior Average, TSNIT Std. Dev., and Nerve Fiber Indicator (NFI) were determined. We also assessed the thickness values in 6 parapapillary sectors. In addition, we calculated the proportion of eyes per group with an NFI of > or =40. RESULTS: GDxVCC measurements showed more RNFL thinning in the perimetrically unaffected eyes of glaucoma patients than in the healthy control eyes. The RNFL in the perimetrically unaffected eyes of glaucoma patients was thicker than that in their fellow eyes with field loss. The NFI had a value of > or =40 in 11 of 23 (47.8%) perimetrically unaffected eyes of glaucoma patients, 19 of 23 (82.6%) eyes with VF loss of glaucoma patients, and 3 of 73 (4.1%) healthy control eyes. CONCLUSION: With the GDxVCC, thinning of the RNFL may be detected in perimetrically unaffected eyes of glaucoma patients with field loss in their fellow eyes.

Adult↗

PubMedDate not supplied

Comparison of keratometry and videokeratography after penetrating keratoplasty.

BACKGROUND: As new methods for corneal curvature measurement have evolved, users of videokeratscopes need to know the practical limitations of these instruments. We assessed agreement between keratometry and videokeratography in measuring highly astigmatic corneas. METHODS: Two independent examiners made three keratometric and videokeratographic measurements on each of 33 corneas after penetrating keratoplasty. The non-orthogonal keratometric readings obtained with a Zeiss 10 SL/O keratometer (Carl Zeiss Ltd.) were compared to the non-orthogonal simK readings (maxK, minK) calculated by the algorithms of a TMS-1 videokeratoscope (Tomey). Measurement agreement was evaluated for steep and flat meridian power and location, and astigmatism magnitude (D). RESULTS: A systematic bias of the TMS-1 in measuring steeper than keratometry for the steep meridian was demonstrated (95% confidence interval: -0.34 to -1.20 D). The limits of agreement (d - 2SD to d + 2SD) between the two instruments were found to be unacceptable for clinical purposes in measuring steep meridian power (-3.17 to +1.63 D), flat meridian power (-4.92 to +4.48 D) and astigmatism magnitude (-5.84 to +4.87 D). Clinically acceptable differences were observed in identification of steep and flat meridian location. CONCLUSIONS: The Zeiss 10 SL/O keratometer and the TMS-1 videokeratoscope showed poor measurement agreement for irregular corneal surfaces, despite the good correlation previously shown between keratometry and videokeratography in calibrated spheres and regular corneas. The TMS-1 showed a systematic bias, measuring a greater power in the steeper meridian than the Zeiss 10 SL/O keratometer. It is suggested that the two instruments cannot be used interchangeably in comparing the curvature of corneas after penetrating keratoplasty.

Adult↗

PubMed2002

Rapid large-scale oligonucleotide selection for microarrays.

We present the first algorithm that selects oligonucleotide probes (e.g. 25-mers) for microarray experiments on a large scale. For example, oligos for human genes can be found within 50 hours. This becomes possible by using the longest common substring as a specificity measure for candidate oligos. We present an algorithm based on a suffix array with additional information that is efficient both in terms of memory usage and running time to rank all candidate oligos according to their specificity. We also introduce the concept of master sequences to describe the sequences from which oligos are to be selected. Constraints such as oligo length, melting temperature, and self-complementarity are incorporated in the master sequence at a preprocessing stage and thus kept separate from the main selection problem. As a result, custom oligos can now be designed for any sequenced genome, just as the technology for on-site chip synthesis is becoming increasingly mature.

Algorithms↗

PubMed2006

The impact of in vitro binding on in vitro-in vivo extrapolations, projections of metabolic clearance and clinical drug-drug interactions.

This review provides a vista of the current opportunities and remaining challenges in the area of in vitro-in vivo extrapolation, with particular emphasis on drug binding terms in predictive models, which has been the source of much controversy. Although the importance of fu(inc) (fraction unbound in in vitro incubations) has been acknowledged for decades, it is not always applied in practice. This is somewhat disappointing, since although it may be onerous to measure this term for large numbers of compounds, algorithms to estimate the term from logD(7.4) or logP have been detailed in the literature. These are sufficiently robust to negate routine measurement in early drug discovery. Several groups have recently established convincing relationships between unbound in vivo and in vitro metabolic intrinsic clearance (CL(int)). In the authors' laboratory, correlations of this type have been constructed for rat, dog and Man. The use and interpretation of these models within a drug discovery setting is discussed. The quantitative prediction of drug-drug interactions from in vitro cytochrome P450 (CYP) inhibition data remains a challenge. Although extensive literature databases are at last emerging, apparent ad hoc use of terms for in vivo inhibitor concentrations and only occasional consideration of fu(inc) may only have confused matters. The effect of accounting for drug binding on the accuracy of predictions is reviewed. Other themes including the impact of fu(inc) on relative activity factors (RAFs) and how in vitro data quality and inter-laboratory differences can confound quantitative human pharmacokinetic predictions are also developed.

Animals↗

PubMedDate not supplied

Guidelines for assessing performance of ST analysers.

This paper proposes principles and methods for assessing performance of ST analysers and algorithms. We describe an evaluation protocol and performance measures suitable for assessing the accuracy of: (1) detecting episodes of ischaemic ST changes, (2) distinguishing between ischaemic and non-ischaemic ST change episodes, and (3) measuring ST deviation and ischaemia duration. There is generally not a one-to-one correspondence between reference and analyser-annotated ST episodes, nor can non-events be counted. Sensitivity and positive predictivity measures which assess the accuracy of detecting ischaemic ST episodes and total ischaemic time are based on the concepts of matching and overlap, respectively. To address the question of predicting performance in a clinical environment, we have utilized the bootstrap statistical procedure, which estimates the mean as well as the standard deviation of the analyser's expected performance. We illustrate the use of the evaluation protocol and performance measures by a case study in which we present an evaluation of our 2-channel Karhunen-Loève transform based ST change detection algorithm using the European Society of Cardiology ST-T database.

Algorithms↗

PubMed1984

On the construction of functional maps in positron emission tomography.

A linear algorithm for the rapid calculation of local rate constants is proposed. The method is applicable to the three-compartment models currently used in the analysis of positron camera measurements with [11C]methionine, [11C]deoxyglucose, and [11C]glucose. The same technique can also be used for the regional measurement of local blood flow with the aid of a freely diffusible tracer. The algorithm was applied to measurements on humans with [11C]glucose. As a comparison, the same data were also analyzed with a standard nonlinear technique. Good agreement between the two methods was obtained.

Brain↗

PubMed1997

Doppler myocardial imaging vs. B-mode grey-scale imaging: a comparative in vitro and in vivo study into their relative efficacy in endocardial boundary detection.

Doppler myocardial imaging (DMI) is a new ultrasound imaging modality in which colour Doppler algorithms are adapted to visualise the myocardium. It allows measurement of regional intramyocardial velocities and quantification of intramural left ventricular function. However promising the technique is, to date the accuracy of endocardial boundary detection by DMI has not been validated. As Doppler velocity estimation is based on measurement of phase shift rather than signal strength, the technique is relatively independent of chest wall attenuation. In the current study, a series of in vitro and in vivo studies was performed to compare standard B-mode grey-scale imaging (GSI) and DMI techniques in endocardial boundary detection. In vitro, the minimum and maximum volumes of a single-chamber tissue-mimicking phantom were calculated using both imaging techniques. In vivo, left ventricular end-diastolic (ED) volume and end-systolic (ES) volume indices were measured from GSI and DMI images in a group of 40 volunteers. All images were obtained in the freeze-frame mode with the Doppler display turned on and off so that simultaneous DMI and GSI information was obtained. In vitro, the limits of agreement between the minimum volume of the phantom and the minimum volume measured by GSI and DMI was 4% and 3%, respectively. For maximum volumes, limits of agreement were 3% for GSI and 2% for DMI. In vivo, the limits of agreement between the two imaging techniques in volume measurements were 6 mL (9%) for ED and 4 mL (11%) for ES. The comparison of the endocardial boundary detection by GSI vs. DMI showed DMI to be significantly superior: ED (72 +/- 16% vs. 85 +/- 8%, respectively; p < 0.05) and ES (71 +/- 13% vs. 88 +/- 7%, respectively; p < 0.05). The results of the study show that: (1) in vitro, based on two-dimensional algorithms, DMI provides as accurate volume measurements as GSI; and (2) in vivo, there is a very good agreement of left ventricular volume measurements between GSI and DMI. However, the endocardial boundary is more reliably displayed and visually easier to detect using DMI than GSI.

Adult↗

PubMed1994

Quantification of atherosclerotic plaques in carotid arteries by three-dimensional ultrasound.

The aim of this study was to develop three-dimensional (3D) ultrasound imaging of the carotid arteries in order to reduce intraexaminer and interexaminer variabilities of volume measurements in follow-up scans of atherosclerotic plaques. The non-invasive quantification of human atherosclerosis by 3D ultrasound was performed using a three-dimensional computer based image reconstruction. The linear movements of the transducer were driven by a motor triggered by electrocardiography. The method included an option to change angle of insonation and a correction of skin contact adaptation. Repeated measurements were performed at weekly intervals in 70 patients. Variabilities and ranges of three newly developed evaluation procedures of plaque volumes (manual tracing, threshold procedure, watershed algorithm) were used. Intraexaminer variability varied between 2.8% (watershed algorithm) and 4.1% (threshold procedure). Interexaminer variability ranged from 4.2% (manual tracing) to 7.6% (threshold procedure), follow-up measurements from 5.2% (watershed algorithm) to 9.4% (threshold procedure). Pearson correlation coefficients of interexaminer agreement and also those between all three measurement procedures were highly significant (p < 0.01). We conclude that the newly developed 3D computer based image reconstruction allows repeated quantification of moderate atherosclerosis with a high reliability.

Arteriosclerosis↗

PubMed1994

3D ultrasound measurement of atherosclerotic plaque volume in carotid arteries.

The aim of the present study was to measure the volume of atherosclerotic plaques using three-dimensional (3D) ultrasound imaging of the carotid arteries and to reduce intra- and interexaminer variabilities in follow-up scans of atherosclerotic plaques. The noninvasive quantification of human atherosclerosis by 3D ultrasound was performed by a 3D computer-based image reconstruction (3D ultrasound). The linear movements of the transducer were driven by a motor triggered by ECG. The method included an option to change angle insonation and a correction of skin contact adaptation. Repeated measurements were performed in a weekly interval in 60 patients. Three evaluation procedures (manual tracing, threshold procedure, watershed algorithm) were developed. Intraexaminer mean variability varied between 2.8 (watershed algorithm) and 4.4% (threshold procedure). Interexaminer mean variability ranged from 3.8 (manual tracing) to 6.8% (threshold procedure), follow-up measurements from 5.3 (watershed algorithm) to 8.9% (threshold procedure). The newly developed 3D computer-based image reconstruction allows repeated quantification of moderate atherosclerosis with a low variability and will be applied in prospective studies of the regression or progression of atherosclerosis.

Aged↗

PubMed2005

Effective grading of termhood in biomedical literature.

The ever-increasing amount of textual information in biomedicine calls for effective procedures for automatic terminology extraction which assist biomedical researchers and professionals in gathering and organizing terminological knowledge encoded in text documents. In this study, we propose a new, linguistically grounded measure for automatically identifying multi-word terms from the biomedical literature. Our approach is based on the limited paradigmatic modifiability of terms and is tested on bigram, trigram and quadgram noun phrases extracted from a 104-million-word text corpus comprised of Medline abstracts. Using the UMLS Metathesaurus as a gold standard, we show that our algorithm substantially outperforms the standard term identification measures and, therefore, qualifies as a high-performing building block for any biomedical terminology mining system.

Algorithms↗

PubMed2001

Comparing the similarity of time-series gene expression using signal processing metrics.

Many algorithms have been used to cluster genes measured by microarray across a time series. Instead of clustering, our goal was to compare all pairs of genes to determine whether there was evidence of a phase shift between them. We describe a technique where gene expression is treated as a discrete time-invariant signal, allowing the use of digital signal-processing tools, including power spectral density, coherence, and transfer gain and phase shift. We used these on a public RNA expression set of 2467 genes measured every 7 min for 119 min and found 18 putative associations. Two of these were known in the biomedical literature and may have been missed using correlation coefficients. Digital signal processing tools can be embedded and enhance existing clustering algorithms.

Algorithms↗

PubMed1979

Automated scene analysis of CT scans.

Since the advent of computed tomography, there has been an increasing realization that CT scans contain quantitative as well as qualitative information useful in the diagnostic process. Often however, the use of this information is impeded by the tedious manual outlining of the areas of interest in the scan. To alleviate this problem, we have developed a scene segmentation algorithm which will automatically delineate areas of interest in a CT scan. This procedure uses known information about the expected objects in the scan in conjuction with an algorithm to label those objects. The resultant scene segmentation divides the scan into four anatomical areas: skull, normal brain, high density lesions and CSF. After an area of interest is interactively selected by the clinician, volume, density or other quantitative measures may be computed. Limitations of the algorithm and its clinical applications are discussed.

Absorptiometry, Photon↗