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PubMed1994

The SBASE protein domain library, release 3.0: a collection of annotated protein sequence segments.

SBASE 3.0 is the third release of SBASE, a collection of annotated protein domain sequences. SBASE entries represent various structural, functional, ligand-binding and topogenic segments of proteins as defined by their publishing authors. SBASE can be used for establishing domain homologies using different database-search tools such as FASTA [Lipman and Pearson (1985) Science, 227, 1436-1441], and BLAST3 [Altschul and Lipman (1990) Proc. Natl. Acad. Sci. USA, 87, 5509-5513] which is especially useful in the case of loosely defined domain types for which efficient consensus patterns can not be established. The present release contains 41,749 entries provided with standardized names and cross-referenced to the major protein and nucleic acid databanks as well as to the PROSITE catalogue of protein sequence patterns. The entries are clustered into 2285 groups using the BLAST algorithm for computing similarity measures. SBASE 3.0 is freely available on request to the authors or by anonymous 'ftp' file transfer from < ftp.icgeb.trieste.it >. Individual records can be retrieved with the gopher server at < icgeb.trieste.it > and with a www-server at < http:@www.icgeb.trieste.it >. Automated searching of SBASE by BLAST can be carried out with the electronic mail server < sbase@icgeb.trieste.it >. Another mail server < domain@hubi.abc.hu > assigns SBASE domain homologies on the basis of SWISS-PROT searches. A comparison of pertinent search strategies is presented.

Amino Acid Sequence↗

PubMed2006

An objective procedure for evaluation of adaptive antifeedback algorithms in hearing aids.

OBJECTIVE: This study evaluated the performance of nine adaptive antifeedback algorithms. There were two goals: first, to identify objective procedures that are useful for evaluating these algorithms, and second, to identify strengths and weaknesses of existing algorithms. DESIGN: The algorithms were evaluated in behind-the-ear implementations on the Knowles Electronics Manikin for Acoustic Research (KEMAR). Different acoustic conditions were created by placing a telephone handset or a hat on KEMAR. Electroacoustic techniques were devised to measure the following performance aspects of each algorithm: (1) additional gain made available before oscillation, (2) gain lost in specific frequency regions, (3) reduction of suboscillatory peaks in the frequency response, (4) speed of adaptation to changing acoustic conditions, and (5) robustness in the presence of tonal input signals. RESULTS: For each measurement, performance varied widely across algorithms. No single algorithm was clearly superior or inferior to the others. Generally, the feedback cancellation algorithms were less likely to sacrifice gain in specific frequency regions and better at reducing suboscillatory peaks, whereas the algorithms that used noncancellation techniques were more tolerant of tonal input signals. For those algorithms equipped with special operational modes intended for music listening, the music mode improved the response to tonal inputs but sometimes sacrificed other performance aspects. Algorithms that required an acoustic measurement for initialization purposes tended to perform poorly in acoustic conditions dissimilar to the condition in which initialization was performed. CONCLUSIONS: The objective methods devised for this study appear useful for evaluating the performance of adaptive antifeedback algorithms. Currently available algorithms demonstrate a wide range of performance, and further research is required to develop new algorithms that combine the best features of existing algorithms.

Acoustics↗

PubMed2003

Three-dimensional forward solver and its performance analysis for magnetic resonance electrical impedance tomography (MREIT) using recessed electrodes.

In magnetic resonance electrical impedance tomography (MREIT), we try to reconstruct a cross-sectional resistivity (or conductivity) image of a subject. When we inject a current through surface electrodes, it generates a magnetic field. Using a magnetic resonance imaging (MRI) scanner, we can obtain the induced magnetic flux density from MR phase images of the subject. We use recessed electrodes to avoid undesirable artefacts near electrodes in measuring magnetic flux densities. An MREIT image reconstruction algorithm produces cross-sectional resistivity images utilizing the measured internal magnetic flux density in addition to boundary voltage data. In order to develop such an image reconstruction algorithm, we need a three-dimensional forward solver. Given injection currents as boundary conditions, the forward solver described in this paper computes voltage and current density distributions using the finite element method (FEM). Then, it calculates the magnetic flux density within the subject using the Biot-Savart law and FEM. The performance of the forward solver is analysed and found to be enough for use in MREIT for resistivity image reconstructions and also experimental designs and validations. The forward solver may find other applications where one needs to compute voltage, current density and magnetic flux density distributions all within a volume conductor.

Algorithms↗

PubMed2001

A general algorithm for optimal sampling schedule design in nuclear medicine imaging.

Optimal sampling schedule (OSS) is of great interest in biomedical experiment design, as it can improve the physiological parameter estimation precision and significantly reduce the samples required. A number of well designed algorithms and software packages have been developed, which deal with the instantaneous measurements at discrete times. However, in nuclear medicine tracer kinetic studies, the imaging systems, such as positron emission tomography (PET) and single photon emission computed tomography (SPECT), take measurements (images) based on continuous accumulation over time intervals. In this case, the existing algorithms cannot be used to design OSS so as to reduce the image frame numbers. In this paper, a general OSS design algorithm for the accumulative measurement is proposed. The potential usefulness of the algorithm is demonstrated by its designing OSS in [18F] fluoro-2-deoxy-D-glucose (FDG) studies with PET to estimate the local cerebral metabolic rate of glucose. The robustness of parameter estimation using the OSS with respect to intra-subject and inter-subject parameter variations is also presented.

Algorithms↗

PubMed2005

Optimal prediction of bone mineral density with ultrasonic measurements in excised human femur.

Bone mineral density (BMD) measured with dual energy X-ray absorptiometry (DXA) techniques is the current gold standard for osteoporotic fracture risk prediction. Quantitative ultrasound (QUS) techniques in transmission measurements are, however, increasingly recognized as an alternative approach. It is feasible to select different QUS methods, one type being optimized to assess microarchitectural properties of bone structure and another to assess BMD. Broadband ultrasonic attenuation (BUA) and ultrasonic velocity (UV) measured on the proximal human femur have been shown to be both significantly correlated with BMD. However, a great diversity of algorithms has been reported to measure the time-of-flight used to derive UV values. The purpose of this study was to determine which procedure results in the optimal BMD prediction at the proximal femur from ultrasound measurements. Thirty-eight excised human femurs were measured in transmission with a pair of focused 0.5-MHz central frequency transducers. Two-dimensional scans were performed and radiofrequency (RF) signals were recorded digitally at each scan position. BUA was estimated and eight different signal processing techniques were performed to estimate UV. For each signal-processing technique UV was compared to BMD. We show that the best prediction of BMD was obtained with signal-processing techniques taking into account only the first part of the transmitted signal (r2BMD-SOS = 0.86). Moreover, we show that a linear multiple regression using both BUA and speed of sound (SOS) and applied to site-matched regions of interest improved the accuracy of BMD predictions (r2BMD-SOS/BUA = 0.95). Our results demonstrate that selecting specific signal-processing methods for QUS variables allows optimal assessment of BMD. Correlation is sufficiently high that this specific QUS method can be considered as a good surrogate of BMD.

Absorptiometry, Photon↗

PubMed2004

A real-time articulated human motion tracking using tri-axis inertial/magnetic sensors package.

A basic requirement in virtual environments is the tracking of objects, especially humans. A real time motion-tracking system was presented and evaluated in this paper. System sensors were built using tri-axis microelectromechanical accelerometers, rate gyros, and magnetometers. A Kalman-based fusion algorithm was applied to obtain dynamic orientations and further positions of segments of the subject's body. The system with the proposed algorithm was evaluated via dynamically measuring Euler orientation and comparing with other two conventional methods. An arm motion experiment was demonstrated using the developed system and algorithm. The results validated the effectiveness of the proposed method.

Acceleration↗

PubMed2006

Pharmacokinetic profile of once daily intravenous tobramycin in children with cystic fibrosis.

AIM: Once-daily tobramycin in patients with cystic fibrosis (CF) is a more convenient dosing regimen than thrice daily dosing. There are limited data on the pharmacokinetic (PK) profile for once-daily tobramycin in patients with CF. The aim of this study was to define the PK parameters for once-daily tobramycin in children with CF and develop an algorithm for therapeutic drug monitoring dosing. METHODS: CF patients admitted to hospital were commenced on once-daily intravenous tobramycin (12 mg/kg/day) and ticarcillin/clavulinic acid. Serum tobramycin levels were taken at 30 min, 2-4 h and 12 h post dose. Data points for the PK model included: age, sex, weight, tobramycin dose, time of tobramycin doses and levels, tobramycin levels. WinNonMix was used to obtain the PK parameters. RESULTS: Forty-four children with 86 admissions who were aged 9 months-20 years were included. A one-compartment intravenous infusion model with first order elimination kinetics produced the best model. Population parameters were: volume of distribution (V(d)) = 0.267 L/kg (95% confidence interval (CL) 0.260-0.272), clearance (CL) 0.103 L/kg/h (95% CI 0.098-0.107) and half-life (t(1/2)) 1.82 (95% CI 1.77-1.88) h. Once the population model was established post hoc analysis was used to calculate individual subject predictions. Plots of individual prediction curves agreed well with observed values. CONCLUSION: This study has established an algorithm for routine monitoring of once-daily tobramycin in children with CF. Satisfactory serum levels of tobramycin were obtained with a dose of 12 mg/kg/day and a regimen algorithm that uses only one measurement to monitor the plasma concentration is suggested.

Adolescent↗

PubMed2006

Quantitative flow visualization in supersonic jets through tomographic inversion of wavefronts estimated through shadow casting.

We present a simple method with which to reconstruct wavefronts that are transilluminating supersonic jets through measurement of their local slopes. The wavefront slopes are measured in two orthogonal directions by use of the average displacements suffered by a random-dot pattern in its shadow cast by the wavefront in front of it. A smooth wavefront is estimated from its measured slopes by a least-squares curve fitting technique. The calculated wavefront distortion is tomographically inverted to yield the density distributions of the object. The results are comparable to that obtained by use of a phase-retrieval algorithm from axial intensity transport measurements.

Algorithms↗

PubMed1998

A new autosomal-dominant locus (DFNA12) is responsible for a nonsyndromic, midfrequency, prelingual and nonprogressive sensorineural hearing loss.

OBJECTIVE: This study aimed to report on the audiologic findings of a nonsyndromic autosomal-dominant hearing loss of which the gene (DFNA 12) recently was found to map to chromosome 11q22-24. The study also aimed to propose and evaluate an algorithm based on the audiometric findings to discriminate between affected and unaffected family members before genetic linkage analysis. STUDY DESIGN: The study design was a retrospective analysis of the audiometric data of genetically affected and unaffected patients. SETTING: The study was conducted at a tertiary referral center. PATIENTS: A total of 17 genetically affected and 54 unaffected family members were studied. INTERVENTIONS: Pure-tone audiometry with air and bone conduction and construction and evaluation of an algorithm were performed. MAIN OUTCOME MEASURES: The type and degree of hearing loss as compared to age and gender-dependent values according to the International Organization for Standardization 7029 standard were measured. For this comparison, the variable "hearing standard deviations" (HSD) is introduced and is defined as the number of standard deviations that a hearing threshold is lying above the age and gender-related median at the given frequency. A description of the algorithm and an evaluation in terms of alpha- and beta-error also were measured. RESULTS: The hearing loss is nonsyndromic, sensorineural, moderate-to-moderately severe (pure-tone average, 51 dB at age 18 years), with an early onset (probably prelingual) and no progression. It affects all frequencies but mainly the midfrequencies (500, 1,000, and 2,000 Hz). The algorithm consists of an analysis of variance to determine the frequency that is most sensitive for the genetic trait under study and on the ranking of the family members according to their hearing loss (HSD) at this frequency. Individual persons are labeled as "affected" or "unaffected" according to this ranking.

Adolescent↗

PubMed2003

Semi-automated software for the three-dimensional delineation of complex vascular networks.

The understanding of tumour angiogenesis is of great importance in cancer research, as is the tumour response to vascular-targeted drugs. This paper presents software aimed at aiding these investigations and other situations where linear or dendritic structures are to be delineated from three-dimensional (3D) data sets. This software application was written to analyse the data from 3D data sets by allowing the manual and semi-automated tracking and delineation of the vascular tree, including the measurement of vessel diameter. A new algorithm, CHARM, based on a compact Hough transform and the formation of a radial map, has been used to locate vessel centres and measure diameters automatically. The robustness of this algorithm to image smoothing and noise has been investigated.

Blood Vessels↗

PubMed1998

Calculation of absorbed dose distributions from dynamic wedges.

In radiotherapy with photon beams, the use of dynamic wedges, which are obtained by the movement of one of the jaws, offers an increasing flexibility relative to the traditional use of metal wedges. But it is a disadvantage for the measurement of absorbed dose distributions, because the absorbed dose at each measurement point can only be obtained after a complete movement of the jaw. Consequently, for radiotherapy planning, an algorithm should be available that does not require measurements for any specific dynamically wedged beam, but is based on only a modest number of measurements. In this paper, an algorithm for the calculation of the dose distribution from dynamic wedges is described. This algorithm uses the convolution of pencil beam kernels with a non-uniform field function. These pencil beam kernels are derived from empirical data resulting from measurements of the open beam only.

Algorithms↗

PubMed1994

Glare-correction in DNA image cytometry.

We tested the reproducibility of a simple method for glare correction in a modern video-based optical densitometer (CYDOK) by performing repeated measurements of the DNA content on identical sets of different rat hepatocyte DNA-classes and lymphocytes. Using a computer-controlled scanning stage of the microscope we were able to re-localize each nucleus of air-dried Feulgen-stained preparations with different microscope settings. The proposed microscope-adjusted glare-correction algorithm is based on the measurement of the transmittance of opaque bars a standard micrometric glass. The procedure gives local glare errors and allows calculation of the mean glare error which is applicable for the entire view field. Subtraction of this mean glare transmittance from each object and normalization of the background allows the user to eliminate errors due to different nuclear Feulgen-staining intensities. The method eliminates the need to use cell-type-dependent constants to correct the known DNA disproportionalities in air-dried, Feulgen-stained preparations. An additional advantage of the glare correction algorithm is the low coefficients of variation (CV, < 3%) within each nuclear DNA-class which reflect the highly reproducible DNA measurements.

Algorithms↗

PubMed1985

[Separate measurements of compact and spongy bone density using a transverse rotation scanner. Determination of mineral content of the radius using a least squares algorithm].

The absorption profile of the distal forearm, which depends on bone mineralisation, was measured using a high resolution microcomputer-controlled transverse rotational scanner with a tightly collimated I-125 photon source and a scintillation counter. Reconstruction of the anatomical structures within the measured area occurred in two stages. Subsequently the linear attenuation coefficient for soft tissues, compacta and spongiosa was obtained by a "least-square" algorithm. The absorption coefficient of the compacta and spongiosa provided a measure of bone mineralisation. Correlation between the reconstructed images and the calculated results and measurements was tested by calculation. Ten measurements of a model and of in vivo bones resulted in a coefficient of variation of 1.8% and 3.3% for the compacta and 2.5% and 3.8% for the spongiosa. Relative deviation from the standard varied from +1.3% to -1.0%, depending on mineral content. This new, technically simple procedure for the separate determination of the compacta and spongiosa in the distal radius is useful for the early recognition of changes in bone mineralisation which are usually apparent first in the spongiosa.

Bone and Bones↗

PubMed2002

An expectation maximization algorithm for training hidden substitution models.

We derive an expectation maximization algorithm for maximum-likelihood training of substitution rate matrices from multiple sequence alignments. The algorithm can be used to train hidden substitution models, where the structural context of a residue is treated as a hidden variable that can evolve over time. We used the algorithm to train hidden substitution matrices on protein alignments in the Pfam database. Measuring the accuracy of multiple alignment algorithms with reference to BAliBASE (a database of structural reference alignments) our substitution matrices consistently outperform the PAM series, with the improvement steadily increasing as up to four hidden site classes are added. We discuss several applications of this algorithm in bioinformatics.

Algorithms↗

PubMed2002

Automated sulcal segmentation using watersheds on the cortical surface.

The human cortical surface is a highly complex, folded structure. Sulci, the spaces between the folds, define location on the cortex and provide a parcellation into anatomically distinct areas. A topic that has recently received increased attention is the segmentation of these sulci from magnetic resonance images, with most work focusing on extracting either the sulcal spaces between the folds or curve representations of sulci. Unlike these methods, we propose a technique that extracts actual regions of the cortical surface that surround sulci, which we call "sulcal regions." The method is based on a watershed algorithm applied to a geodesic depth measure on the cortical surface. A well-known problem with the watershed algorithm is a tendency toward oversegmentation, meaning that a single region is segmented as several pieces. To address this problem, we propose a postprocessing algorithm that merges appropriate segments from the watershed algorithm. The sulcal regions are then manually labeled by simply selecting the appropriate regions with a mouse click and a preliminary study of sulcal depth is reported. Finally, a scheme is presented for computing a complete parcellation of the cortical surface.

Automation↗

PubMed2001

A new method for quantification of spatial and temporal parameters of endocardial motion: evaluation of experimental infarction using magnetic resonance imaging.

BACKGROUND: With the development of high-resolution myocardial imaging there has evolved a need for automated techniques that can accurately quantify regional function. OBJECTIVE: To develop a new method for quantification of spatial and temporal parameters of endocardial motion. DESIGN: Magnetic resonance images were analyzed using a unique, shape-based approach that tracks endocardial surface motion at defined points through the cardiac cycle by minimizing the bending energy. SETTING: Animal instrumentation was performed in the Nuclear Cardiology Experimental Research Laboratory at Yale University, New Haven, Connecticut. Magnetic resonance imaging was performed at the Yale New Haven Hospital Center. ANIMALS: Eight mongrel canines were used. INTERVENTIONS: Electrocardiograph-gated gradient-echo magnetic resonance images were obtained before and after occlusion of the left anterior descending coronary. Thirty-two points along automatically defined endocardial contours were tracked. Average displacements and cumulative path lengths were computed from end-diastole for each point over the entire cardiac cycle. The average cumulative path length was computed for each of four quarters of systole for the normal, border and infarct zones. Shape-based parameters of systolic motion were compared with the centreline approach. Infarct zone was defined by postmortem histochemical staining. MAIN RESULTS: Displacement and cumulative path length over the cardiac cycle decreased significantly in the infarct and border zones (P<0.05), but did not change in the normal zone (P was not significant). Temporal changes in motion were observed in all zones. Displacement measured using the shape-based algorithm was more consistent than cumulative path length when compared with systolic motion measured using the centreline method. CONCLUSIONS: An automated, shape-based approach permits quantitative evaluation of both spatial and temporal parameters of regional endocardial motion from high-resolution electrocardiograph-gated images. Analysis of endocardial motion and cumulative motion over the entire cardiac cycle discriminated infarcted from normal and border regions.

Animals↗

PubMed1999

Feature selection for optimized skin tumor recognition using genetic algorithms.

In this paper, a new approach to computer supported diagnosis of skin tumors in dermatology is presented. High resolution skin surface profiles are analyzed to recognize malignant melanomas and nevocytic nevi (moles), automatically. In the first step, several types of features are extracted by 2D image analysis methods characterizing the structure of skin surface profiles: texture features based on cooccurrence matrices, Fourier features and fractal features. Then, feature selection algorithms are applied to determine suitable feature subsets for the recognition process. Feature selection is described as an optimization problem and several approaches including heuristic strategies, greedy and genetic algorithms are compared. As quality measure for feature subsets, the classification rate of the nearest neighbor classifier computed with the leaving-one-out method is used. Genetic algorithms show the best results. Finally, neural networks with error back-propagation as learning paradigm are trained using the selected feature sets. Different network topologies, learning parameters and pruning algorithms are investigated to optimize the classification performance of the neural classifiers. With the optimized recognition system a classification performance of 97.7% is achieved.

Algorithms↗

PubMed1998

Predicting patients' utilities from quality of life items: an improved scoring system for the UBQ-H.

The Utility-based Quality of Life--Heart Questionnaire (UBQ-H) is a cardiovascular extension of the Health Measurement Questionnaire. It is a multidimensional instrument that can be scored to yield a utility estimate using the Rosser Index and a classification algorithm developed for the Health Measurement Questionnaire. The aim of this study was to employ a statistical modelling approach to devise an improved scoring system. A sample of 201 cardiovascular patients completed the UBQ-H and assessed the utility of their own health state using standard gamble and time trade-off questions in an interview. Two new scoring methods were devised by regressing the UBQ-H data against patients' self-assessed utilities. The new methods gave utility estimates that correlated with angina/dyspnoea grades, life satisfaction scores and General Health Questionnaire (GHQ) scores. In a second sample of 1,112 cardiovascular patients, the UBQ-H utilities were able to distinguish between patients who had/had not experienced an adverse event (e.g. myocardial infarction) and were responsive to changes in health over time. The new scoring methods were not particularly more sensitive to quality of life effects than the original method based on the Rosser Index. However, they produced significantly lower estimates and more accurately reflected patients' self-assessed utilities.

Cardiovascular Diseases↗