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PubMed2004

Class of 4 + 1-phase algorithms with error compensation.

It is well known that phase-shifting interferometry suffers from inaccuracy in the presence of phase-shifting errors. We have proved the limitation of using a 4-phase algorithm to reduce the phase-measurement error in the presence of the phase-shifting error. A class of 4 + 1-phase error compensating algorithms is formulated. It is shown that the proposed algorithms can effectively minimize the effects of the constant phase-shifting error and possess a superior performance than existing error-compensating algorithms. The effectiveness of the proposed algorithm is demonstrated by computer simulations and experiments.

Journal Article↗

PubMed2006

AutoNR: an automated system that measures ECAP thresholds with the Nucleus Freedom cochlear implant via machine intelligence.

OBJECTIVE: AutoNRT is an automated system that measures electrically evoked compound action potential (ECAP) thresholds from the auditory nerve with the Nucleus Freedom cochlear implant. ECAP thresholds along the electrode array are useful in objectively fitting cochlear implant systems for individual use. This paper provides the first detailed description of the AutoNRT algorithm and its expert systems, and reports the clinical success of AutoNRT to date. METHODS: AutoNRT determines thresholds by visual detection, using two decision tree expert systems that automatically recognise ECAPs. The expert systems are guided by a dataset of 5393 neural response measurements. The algorithm approaches threshold from lower stimulus levels, ensuring recipient safety during postoperative measurements. Intraoperative measurements use the same algorithm but proceed faster by beginning at stimulus levels much closer to threshold. When searching for ECAPs, AutoNRT uses a highly specific expert system (specificity of 99% during training, 96% during testing; sensitivity of 91% during training, 89% during testing). Once ECAPs are established, AutoNRT uses an unbiased expert system to determine an accurate threshold. Throughout the execution of the algorithm, recording parameters (such as implant amplifier gain) are automatically optimised when needed. RESULTS: In a study that included 29 intraoperative and 29 postoperative subjects (a total of 418 electrodes), AutoNRT determined a threshold in 93% of cases where a human expert also determined a threshold. When compared to the median threshold of multiple human observers on 77 randomly selected electrodes, AutoNRT performed as accurately as the 'average' clinician. CONCLUSIONS: AutoNRT has demonstrated a high success rate and a level of performance that is comparable with human experts. It has been used in many clinics worldwide throughout the clinical trial and commercial launch of Nucleus Custom Sound Suite, significantly streamlining the clinical procedures associated with cochlear implant use.

Algorithms↗

PubMed1990

How to study the kinetic depth effect experimentally.

Sperling, Landy, Dosher, and Perkins (1989) proposed an objective 3D shape identification task with 2D artifactual cues removed and with full feedback (FB) to the subjects to measure KDE and to circumvent algorithmically equivalent KDE-alternative computations and artifactual non-KDE processing. (1) The 2D velocity flow-field was necessary and sufficient for true KDE. (2) Only the first-order (Fourier-based) perceptual motion system could solve our task because the second-order (rectifying) system could not simultaneously process more than two locations. (3) To ensure first-order motion processing, KDE tasks must require simultaneous processing at more than two locations. (4) Practice with FB is essential to measure ultimate capacity (aptitude) and, thereby, to enable comparisons with ideal observers. Experiments without FB measure ecological achievement--the ability of subjects to extrapolate their past experience to the current stimuli.

Algorithms↗

PubMed1992

Prenatal screening for Down's syndrome with use of maternal serum markers.

BACKGROUND: Approximately 35 percent of all cases of Down's syndrome in fetuses can be detected by measuring maternal serum alpha-fetoprotein during the second trimester in the general population of pregnant women. Recent case-control studies indicate that this detection rate could be approximately doubled by measuring serum levels of unconjugated estriol and chorionic gonadotropin, which are abnormally low and abnormally high, respectively, in women carrying fetuses affected by Down's syndrome. METHODS: We prospectively screened 25,207 women and adolescents in the second trimester of pregnancy and assigned each a risk of fetal Down's syndrome with an algorithm that took into account measurements of all three serum markers in combination with maternal age. On this basis, 1661 subjects (6.6 percent) were initially assigned a second-trimester risk of fetal Down's syndrome of at least 1 in 190, and 962 (3.8 percent) were offered amniocentesis for chromosomal analysis after verification of gestational age. Gestational age was determined on the basis of the first day of the last menstrual period or, when available, by ultrasonography. RESULTS: Among the 760 women and adolescents who chose amniocentesis, 20 cases of fetal Down's syndrome were detected, along with 7 other chromosomal disorders. There was 1 additional case of fetal Down's syndrome among the 202 women who chose not to have amniocentesis. The rate of detection of Down's syndrome was thus 58 percent (21 of 36 expected cases), and the frequency of identifying a fetus with Down's syndrome in women undergoing amniocentesis was 1 per 38 amniocenteses (95 percent confidence interval, 1 in 25 to 1 in 62). CONCLUSIONS: Measuring serum alpha-fetoprotein, chorionic gonadotropin, and estriol is more effective in screening for fetal Down's syndrome than measuring maternal serum alpha-fetoprotein alone. Such an expanded protocol can readily be incorporated into existing prenatal screening programs.

Adolescent↗

PubMed2001

Precise onset detection of human motor responses using a whitening filter and the log-likelihood-ratio test.

Investigation of the human motor system frequently requires precise determination of the motor response onset indicating the time of movement initiation (e.g., in reaction time experiments). This paper presents a new model-based algorithm for computerized response onset detection in kinematic signals (e.g., joint angle). The response onset is identified as an abrupt change in the (time-varying) parameters of a statistical process model adapted to the measured signal. The accuracy of the algorithm is assessed by statistical simulations, and the performance of the method is compared to the performance of conventional onset detection methods using simulated as well as real kinematic signals. Results show that onset detection can substantially be improved by including a priori knowledge on the physiological background of the measured signals to the decision process.

Algorithms↗

PubMed1998

Interpretive algorithms for the symptom-limited exercise test: assessing dyspnea in Persian Gulf war veterans.

Interpretation of symptom-limited exercise testing requires analysis of a large body of simultaneously recorded cardiopulmonary data. Karlman Wasserman has recommended an algorithmic approach to interpretation (WA) that leads to a dichotomous choice between pulmonary and cardiovascular impairment. An alternative algorithm published by William Eschenbacher (EA) provides for concurrent assessment of cardiovascular and pulmonary exercise impairment. We analyzed a group of 29 individuals referred to the Pulmonary Physiology Laboratory at the Washington Veterans Affairs Medical Center for evaluation of dyspnea following service in the Persian Gulf War to assess the concordance of the two algorithms in determining the cause of dyspnea and exercise impairment in these individuals. They each performed a progressive, ramped, symptom-limited exercise test on a bike for a minimum of 6 min. Exercise measurements were analyzed by both interpretive algorithms. Concordance was found in 28% of tests. The greatest discordance occurred in identifying pulmonary limitation. Eleven had pulmonary limitation by EA; of these, WA found 1 to have pulmonary limitation, 5 to be normal, 4 indeterminate, and 1 musculoskeletal limitation. Of the 11 with pulmonary limitation by EA, but not by WA, 5 had abnormal resting pulmonary function measurements. Analysis of the differences between these two interpretive approaches is given. The EA algorithm may be more sensitive for detecting exercise impairment of pulmonary origin, but its specificity remains to be determined.

Adult↗

PubMed2002

Determination of glucose concentration in a scattering medium based on selected wavelengths by use of an overtone absorption band.

A method and device for measuring glucose concentration in a scattering medium have been developed. A spectral range of 800-1800 nm is considered for wavelength selection because of its deeper penetration into biological tissue and the presence of a glucose absorption band. An algorithm based on selected wavelengths is proposed to minimize interference from other components. The optimal distance between the light source and the detector for diffuse reflectance measurement minimizes the influence of medium scattering. The proposed algorithm and measuring device are tested with a solution containing milk with added glucose. Glucose concentrations between 0 and 2000 mg/dl are determined with a correlation coefficient of 0.977. We also investigate the influence of concentration variations of other substances such as water, hemoglobin, albumin, and cholesterol when they are mixed in a scattering medium.

Algorithms↗

PubMed2006

CGHScan: finding variable regions using high-density microarray comparative genomic hybridization data.

BACKGROUND: Comparative genomic hybridization can rapidly identify chromosomal regions that vary between organisms and tissues. This technique has been applied to detecting differences between normal and cancerous tissues in eukaryotes as well as genomic variability in microbial strains and species. The density of oligonucleotide probes available on current microarray platforms is particularly well-suited for comparisons of organisms with smaller genomes like bacteria and yeast where an entire genome can be assayed on a single microarray with high resolution. Available methods for analyzing these experiments typically confine analyses to data from pre-defined annotated genome features, such as entire genes. Many of these methods are ill suited for datasets with the number of measurements typical of high-density microarrays. RESULTS: We present an algorithm for analyzing microarray hybridization data to aid identification of regions that vary between an unsequenced genome and a sequenced reference genome. The program, CGHScan, uses an iterative random walk approach integrating multi-layered significance testing to detect these regions from comparative genomic hybridization data. The algorithm tolerates a high level of noise in measurements of individual probe intensities and is relatively insensitive to the choice of method for normalizing probe intensity values and identifying probes that differ between samples. When applied to comparative genomic hybridization data from a published experiment, CGHScan identified eight of nine known deletions in a Brucella ovis strain as compared to Brucella melitensis. The same result was obtained using two different normalization methods and two different scores to classify data for individual probes as representing conserved or variable genomic regions. The undetected region is a small (58 base pair) deletion that is below the resolution of CGHScan given the array design employed in the study. CONCLUSION: CGHScan is an effective tool for analyzing comparative genomic hybridization data from high-density microarrays. The algorithm is capable of accurately identifying known variable regions and is tolerant of high noise and varying methods of data preprocessing. Statistical analysis is used to define each variable region providing a robust and reliable method for rapid identification of genomic differences independent of annotated gene boundaries.

Algorithms↗

PubMedDate not supplied

Effect of a pharmacist-managed diabetes care program in a free medical clinic.

Diabetes care, morbidity, and mortality are usually worse in poor minority populations compared with non-minority ones. This report evaluates evidence-based process and outcome measures of diabetes care in diabetic patients followed in a free medical clinic and compares them to published results. The following process measures compared favorably with measures of the general population: dilated eye and foot exams and measurements of glycated hemoglobin levels; concentrations of total cholesterol; fasting triglycerides and low density lipoprotein (LDL) cholesterol; and proteinuria (by dipstick). Process and outcome measures in 89 diabetic patients referred to a Diabetes Management Program in which diabetes care was delivered by pharmacists following detailed algorithms (experimental group) were compared with measures in 92 diabetic patients who received diabetes care in the general clinic setting (control group). The patients in the experimental group had a slightly longer duration of diabetes and more microvascular and neuropathic complications, and more diabetic patients were taking insulin than were patients in the control group. All of the process measures listed above were more frequent in the experimental group. Compared with the control group, the initial glycated hemoglobin level (% +/- SE) in the experimental group was significantly (P < .001) higher (8.8 +/- 0.2 versus 7.9 +/- 0.2) but fell significantly (P < .03) more (-0.8 +/- 0.2 versus -0.05 +/- 0.3). The lack of a greater decrease in the glycated hemoglobin levels in the experimental group was not related to the inability of the pharmacists to follow the algorithms, the patients' refusal to follow the recommended medication adjustments, or the lack of appropriate self-monitoring of blood glucose in insulin-requiring patients. It was inversely related (r = -0.36, P < .03) to the number of missed visits, i.e., the greater the number of broken appointments, the less the glycated hemoglobin fell. In conclusion, diabetes care for a poor minority population in a free clinic setting can compare favorably to care in the general population. Pharmacists following detailed algorithms can enhance this care further. Administrative and support system changes that minimize the number of missed visits might further improve diabetes care in this population.

California↗

PubMed2001

Deadspace free ventilatory measurements in newborns during mechanical ventilation.

OBJECTIVE: To improve the accuracy of ventilatory measurements in ventilated newborns by means of a numerical correction when a deadspace free differential measuring method using two pneumotachographs (PNTs) is applied and to investigate the clinical usefulness of this correction procedure. DESIGN: In vitro study and prospective animal study. SETTING: Research laboratory of the Clinic of Neonatology and the Animal Research Laboratory, Charité Hospital Berlin. SUBJECTS: Ten newborn piglets, weighing 610-1340 g (median, 930 g), age <12 hrs. INTERVENTIONS: The accuracy of both the deadspace free method and the endotracheal flow measurements (conventional method) was investigated using mechanical lung models. A correction procedure for the deadspace free method was developed considering signal delay time and tube compliance between both PNTs. This method was applied to the piglets measured during partial liquid ventilation (PLV). Measurements were done before and after lung lavage and during 30 and 120 mins of PLV (30 mL/kg body weight perfluorocarbon). MEASUREMENTS AND MAIN RESULTS: In vitro measurements showed volume differences between both methods of 8%, 12%, 16%, and 17%, respectively, depending on the distance between the PNTs of 10, 60, 120, and 180 cm. After applying the correction algorithm, the differences decreased to 3%, 0%, -2%, and -8%, respectively. The piglets were measured with 120-cm tube length between the PNTs. The correction algorithm reduced the measured tidal volume before lavage by 7%, after lavage by 14%, 30-min PLV by 12%, and 120-min PLV by 10%, corresponding to the changes in respiratory compliance of 1.2, 0.6, 1.0, and 1.1 mL/cm H2O. CONCLUSIONS: The deadspace free method can be advantageously used for continuous measurements in newborns despite much higher technical expense. The correcting procedure improved the accuracy of the volume measurement remarkably, especially for lower respiratory compliance.

Algorithms↗

PubMed1996

Comparison of different quantitative coronary analysis systems: ARTREK, CAAS, and CMS.

It has been known that the first generation quantitative coronary analysis systems overestimate small vessel sizes. In the 2nd generation the contour detection algorithms, e.g., of the new Cardiovascular Measurement System (CMS), were modified to correct for the limited resolution of the X-ray imaging chain. This study validated and compared the CMS with the well-known Coronary Angiography Analysis System (CAAS) and the vessel tracking program ARTREK in a phantom study and a clinical study. In addition, the influence of different acquisition media (cinefilm vs. digitally acquired angiograms) on the accuracy of quantitative analysis was examined. The phantom study comprised 19 stenotic or non-stenotic glass tubes with a diameter range from 0.54 mm to 4.9 mm. In the clinical study the mean diameters of 322 coronary segments were analysed and the results of the systems were compared among each other. The results of the phantom study were presented in terms of the mean difference (accuracy) between true and measured values. In the phantom study the overall accuracy of the CMS was -6 microns (ARTREK: 85 microns; CAAS: 35 microns) with an overestimation of small vessels of only -11 microns (ARTREK: 97 microns: CAAS: 51 microns). The clinical study showed that the CMS corrected the usually occurring overestimation of small coronary arteries and that the influence on the accuracy of different acquisition media is minor. Due to the modified algorithms the new CMS is able to measure coronary diameters down to 0.5 mm accurately. Therefore, the CMS seems to provide more precise measurements in quantitative analysis of small coronary diameters than CAAS and ARTREK.

Coronary Angiography↗

PubMed2004

Identification of Hammerstein models with cubic spline nonlinearities.

This paper considers the use of cubic splines, instead of polynomials, to represent the static nonlinearities in block structured models. It introduces a system identification algorithm for the Hammerstein structure, a static nonlinearity followed by a linear filter, where cubic splines represent the static nonlinearity and the linear dynamics are modeled using a finite impulse response filter. The algorithm uses a separable least squares Levenberg-Marquardt optimization to identify Hammerstein cascades whose nonlinearities are modeled by either cubic splines or polynomials. These algorithms are compared in simulation, where the effects of variations in the input spectrum and distribution, and those of the measurement noise are examined. The two algorithms are used to fit Hammerstein models to stretch reflex electromyogram (EMG) data recorded from a spinal cord injured patient. The model with the cubic spline nonlinearity provides more accurate predictions of the reflex EMG than the polynomial based model, even in novel data.

Algorithms↗

PubMed2001

Scene illuminant classification: brighter is better.

Knowledge of the scene illuminant spectral power distribution is useful for many imaging applications, such as color image reproduction and automatic algorithms for image database applications. In many applications accurate spectral characterization of the illuminant is impossible because the input device acquires only three spectral samples. In such applications it is sensible to set a more limited objective of classifying the illuminant as belonging to one of several likely types. We describe a data set of natural images with measured illuminants for testing illuminant classification algorithms. One simple type of algorithm is described and evaluated by using the new data set. The empirical measurements show that illuminant information is more reliable in bright regions than in dark regions. Theoretical predictions of the algorithm's classification performance with respect to scene illuminant blackbody color temperature are tested and confirmed by using the natural-image data set.

Journal Article↗

PubMed2004

Theoretical evaluation of accuracy in position and size of brain activity obtained by near-infrared topography.

Near-infrared (NIR) topography can obtain a topographical distribution of the activated region in the brain cortex. Near-infrared light is strongly scattered in the head, and the volume of tissue sampled by a source-detector pair on the head surface is broadly distributed in the brain. This scattering effect results in poor resolution and contrast in the topographic image of the brain activity. In this study, a one-dimensional distribution of absorption change in a head model is calculated by mapping and reconstruction methods to evaluate the effect of the image reconstruction algorithm and the interval of measurement points for topographic imaging on the accuracy of the topographic image. The light propagation in the head model is predicted by Monte Carlo simulation to obtain the spatial sensitivity profile for a source-detector pair. The measurement points are one-dimensionally arranged on the surface of the model, and the distance between adjacent measurement points is varied from 4 mm to 28 mm. Small intervals of the measurement points improve the topographic image calculated by both the mapping and reconstruction methods. In the conventional mapping method, the limit of the spatial resolution depends upon the interval of the measurement points and spatial sensitivity profile for source-detector pairs. The reconstruction method has advantages over the mapping method which improve the results of one-dimensional analysis when the interval of measurement points is less than 12 mm. The effect of overlapping of spatial sensitivity profiles indicates that the reconstruction method may be effective to improve the spatial resolution of a two-dimensional reconstruction of topographic image obtained with larger interval of measurement points. Near-infrared topography with the reconstruction method potentially obtains an accurate distribution of absorption change in the brain even if the size of absorption change is less than 10 mm.

Algorithms↗

PubMed2004

Determination of a unique solution to parallel proton transfer reactions using the genetic algorithm.

Kinetic analysis of the dynamics as measured in multiequilibria systems is readily attained by curve-fitting methodologies, a treatment that can accurately retrace the shape of the measured signal. Still, these reconstructions are not related to the detailed mechanism of the process. In this study we subjected multiple proton transfer reactions to rigorous kinetic analysis, which consists of solving a set of coupled-nonlinear differential rate equations. The manual analysis of such systems can be biased by the operator; thus the analysis calls for impartial corroboration. What is more, there is no assurance that such a complex system has a unique solution. In this study, we used the Genetic Algorithm to investigate whether the solution of the system will converge into a single global minimum in the multidimensional parameter space. The experimental system consisted of proton transfer between four proton-binding sites with seven independent adjustable parameters. The results of the search indicate that the solution is unique and all adjustable parameters converge into a single minimum in the multidimensional parameter space, thus corroborating the accuracy of the manual analysis.

Algorithms↗

PubMed2002

3D CT imaging method for measuring temporal bone aeration.

OBJECTIVE: 3D volume reconstruction of CT images can be used to measure temporal bone aeration. This study evaluates the technique with respect to reproducibility and acquisition parameters. MATERIAL AND METHODS: Helical CT images acquired from patients with radiographically normal temporal bones using standard clinical protocols were retrospectively analyzed. 3D image reconstruction was performed to measure the volume of air within the temporal bone. The appropriate threshold values for air were determined from reconstruction of a phantom with a known air volume imaged using the same clinical protocols. The appropriate air threshold values were applied to the clinical material. RESULTS: Air volume was measured according to an acquisition algorithm. The average volume in the temporal bone CT group was 5.56 ml, compared to 5.19 ml in the head CT group (p = 0.59). The correlation coefficient between examiners was > 0.92. There was a wide range of aeration volumes among individual ears (0.76-18.84 ml); however, paired temporal bones differed by an average of just 1.11 ml. CONCLUSIONS: The method of volume measurement from 3D reconstruction reported here is widely available, easy to perform and produces consistent results among examiners. Application of the technique to archival CT data is possible using corrections for air segmentation thresholds according to acquisition parameters.

Adult↗

PubMed2004

Automatic and quantitative measurement of protein-protein colocalization in live cells.

We introduce a novel statistical approach that quantifies, for the first time, the amount of colocalization of two fluorescent-labeled proteins in an image automatically, removing the bias of visual interpretation. This is done by estimating simultaneously the maximum threshold of intensity for each color below which pixels do not show any statistical correlation. The sensitivity of the method was illustrated on simulated data by statistically confirming the existence of true colocalization in images with as little as 3% colocalization. This method was then tested on a large three-dimensional set of fixed cells cotransfected with CFP/YFP pairs of proteins that either co-compartmentalized, interacted, or were just randomly localized in the nucleolus. In this test, the algorithm successfully distinguished random color overlap from colocalization due to either co-compartmentalization or interaction, and results were verified by fluorescence resonance energy transfer. The accuracy and consistency of our algorithm was further illustrated by measuring, for the first time in live cells, the dissociation rate (k(d)) of the HIV-1 Rev/CRM1 export complex induced by the cytotoxin leptomycin B. Rev/CRM1 colocalization in nucleoli dropped exponentially after addition of leptomycin B at a rate of 1.25 x 10(-3) s(-1). More generally, this algorithm can be used to answer a variety of biological questions involving protein-protein interactions or co-compartmentalization and can be generalized to colocalization of more than two colors.

Fatty Acids, Unsaturated↗

PubMed1994

Phylogenetic inference under the pure drift model.

When pairwise genetic distances are used for phylogenetic reconstruction, it is usually assumed that the genetic distance between two taxa contains information about the time after the two taxa diverged. As a result, upon an appropriate transformation if necessary, the distance usually can be fitted to a linear model such that it is expressed as the sum of lengths of all branches that connect the two taxa in a given phylogeny. This kind of distance is referred to as "additive distance." For a phylogenetic tree exclusively driven by random genetic drift, genetic distances related to coancestry coefficients (theta XY) between any two taxa are more suitable. However, these distances are fundamentally different from the additive distance in that coancestry does not contain any information about the time after two taxa split from a common ancestral population; instead, it reflects the time before the two taxa diverged. In other words, the magnitude of theta XY provides information about how long the two taxa share the same evolutionary pathways. The fundamental difference between the two kinds of distances has led to a different algorithm of evaluating phylogenetic trees when theta XY and related distance measures are used. Here we present the new algorithm using the ordinary-least-squares approach but fitting to a different linear model. This treatment allows genetic variation within a taxon to be included in the model. Monte Carlo simulation for a rooted phylogeny of four taxa has verified the efficacy and consistency of the new method. Application of the method to human population was demonstrated.

Animals↗