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PubMed2006

Automatic measure of the split in the second cardiac sound by using the wavelet transform technique.

This paper is concerned with the identification and automatic measure of the split in the second heart sound (S2) of the phonocardiogram signal (PCGs) for normal or pathological case. The second heart sound S2 consists of two acoustic components A2 and P2, the former is due to the closure of the aortic valve and the latter is due to the closure of the pulmonary valve. The aortic valve usually closes before the pulmonary valve, introducing a time delay known as "split". A automatic technique based on the discrete wavelet transform (DWT) and the continuous wavelet transform (CWT) is developed in this paper to measure the split of the second cardiac sound (S2) for the normal and pathological cases of the PCG signals. To quantify the splitting, the two components in S2 (i.e. A2 and P2) are identified and, the delay between the two components can be estimated. It is shown that the wavelet transform can provide best information and features of the split of S2 and the major components (A2 and P2) and consequently aid in medical diagnosis.

Aortic Valve↗
PubMed2004

Automatic spinal disease diagnoses assisted by 3D unaligned transverse CT slices.

This paper describes a three-dimensional (3D) reconstruction method and an automatic diagnosis method for spinal diseases using unaligned transverse slices that have arbitrary angles and intervals but do not intersect to each other at regions of interest. The 3D reconstruction method extends the marching cube algorithm to generate triangulated isosurfaces for these unaligned slices. The automatic spinal disease diagnostic method analyses boundaries of discs and vertebral bodies on unaligned transverse slices to estimate the presence and extent of disc herniation and canal compression, and deformities in the spinal curve. The prototype system can be used as a qualitative and quantitative tool for the diagnosis of various spinal diseases using unaligned transverse slices.

Aged↗
PubMed2006

An automatic variational level set segmentation framework for computer aided dental X-rays analysis in clinical environments.

An automatic variational level set segmentation framework for Computer Aided Dental X-rays Analysis (CADXA) in clinical environments is proposed. Designed for clinical environments, the segmentation contains two stages: a training stage and a segmentation stage. During the training stage, first, manually chosen representative images are segmented using hierarchical level set region detection. Then the window based feature extraction followed by principal component analysis (PCA) is applied and results are used to train a support vector machine (SVM) classifier. During the segmentation stage, dental X-rays are classified first by the trained SVM. The classifier provides initial contours which are close to correct boundaries for three coupled level sets driven by a proposed pathologically variational modeling which greatly accelerates the level set segmentation. Based on the segmentation results and uncertainty maps that are built based on a proposed uncertainty measurement, a computer aided analysis scheme is applied. The experimental results show that the proposed method is able to provide an automatic pathological segmentation which naturally segments those problem areas. Based on the segmentation results, the analysis scheme is able to provide indications of possible problem areas of bone loss and decay to the dentists. As well, the experimental results show that the proposed segmentation framework is able to speed up the level set segmentation in clinical environments.

Algorithms↗
PubMed2006

Automatic arm removal in PET and CT images for deformable registration.

Positron emission tomography (PET) imaging is rapidly expanding its role in clinical practice for cancer management. The high sensitivity of PET for functional abnormalities associated with cancer can be confounded by the minimal anatomical information it provides for cancer localization. Computed tomography (CT) provides detailed anatomical information but is less sensitive to pathologies than PET. Thus, combining (i.e., registering) PET and CT images would enable both accurate and sensitive cancer localization with respect to detailed patient anatomy. An additional application area of registration is to align CT-CT scans from serial studies on a patient on a PET/CT scanner to facilitate accurate assessment of therapeutic response from the co-aligned PET images. To facilitate image fusion, we are developing a deformable registration software system using mutual information and a B-spline model of the deformation. When applying deformable registration to whole body images, one of the obstacles is that the arms are present in PET images but not in CT images or are in different positions in serial CT images. This feature mismatch requires a preprocessing step to remove the arms where present and thus adds a manual step in an otherwise automatic algorithm. In this paper, we present a simple yet effective method for automatic arm removal. We demonstrate the efficiency and robustness of this algorithm on both clinical PET and CT images. By streamlining the entire registration process, we expect that the fusion technology will soon find its way into clinics, greatly benefiting cancer diagnosis, staging, therapy planning and treatment monitoring.

Algorithms↗
PubMed2005

Plasma leptin status in young calves: effects of pre-term birth, age, glucocorticoid status, suckling, and feeding with an automatic feeder or by bucket.

Plasma leptin concentrations depend on energy intake and fat stores and are modified by hormones, such as glucocorticoids. We have measured plasma leptin concentrations in pre-term calves (born on day 277 of gestation) during the first week of life, in full-term calves (290 days of gestation), fed similar amounts of nutrients with colostrum or a milk-derived formula, combined with or without dexamethasone treatment (to simulate a high glucocorticoid status), during the first five days of life, and in calves fed with an automatic feeder or by bucket or suckling on dams up to day 28. Leptin concentrations increased (P<0.05) from birth to day 7 in pre-term calves. In full-term calves leptin concentrations were stable from day 1 to day 4 in colostrum-fed animals, but decreased (P<0.05) and were lower (P<0.05) if fed a formula with similar amounts of energy and macronutrients as colostrum. Concentrations increased (P<0.05) from day 1 to day 2 in calves suckling on dams and then remained elevated, but did not change and were lower in calves fed with the automatic feeder or by bucket than in suckling calves. Dexamethasone only slightly elevated leptin concentrations. There was no episodic secretion pattern, and there were no consistent associations of leptin with various metabolites and hormones. In conclusion, plasma leptin in young calves with respect to effects of nutrition (low energy intake) and hormones (glucocorticoids) and in association with metabolic changes behaved differently from what is known in mature cattle.

Animals↗
PubMed2005

Automatic ankle pressure measurements using PPG in ankle-brachial pressure index determination.

OBJECTIVE: To evaluate a new technique using a photoplethysmographic (PPG) probe for automatic ankle pressure measurements. DESIGN: Comparative study on two techniques for ankle pressure measurement. SETTING: University hospital. MATERIAL: Thirty-five patients with leg arterial disease and eight healthy volunteers. Ankle-brachial indices (ABPI) were measured using conventional CW Doppler technique and PPG-based prototype equipment for the ankle pressure recordings. CHIEF OUTCOME MEASURES: ABPIs calculated from CW Doppler and PPG ankle pressure measurements. The PPG signals were analysed both by visual judgement and by a software based, automatic algorithm. MAIN RESULTS: The mean difference between ABPIs calculated from CW Doppler recordings and PPG (visual analysis) was -0.01 (limits of agreement (+/-two standard deviations) +0.16 to -0.19). The correlation coefficient was 0.93. When the algorithm was used, the mean difference (CW Doppler-PPG) was 0.05 (limits of agreement 0.28 to -0.18, r=0.89). CONCLUSIONS: The PPG method is a promising technique with an inherent potential for automatisation of the ankle pressure measurements, thereby reducing the observer-dependency in ABPI recordings.

Adult↗
PubMed2004

On compensation of mismatched recording conditions in the Bayesian approach for forensic automatic speaker recognition.

This paper deals with a procedure to compensate for mismatched recording conditions in forensic speaker recognition, using a statistical score normalization. Bayesian interpretation of the evidence in forensic automatic speaker recognition depends on three sets of recordings in order to perform forensic casework: reference (R) and control (C) recordings of the suspect, and a potential population database (P), as well as a questioned recording (QR) . The requirement of similar recording conditions between suspect control database (C) and the questioned recording (QR) is often not satisfied in real forensic cases. The aim of this paper is to investigate a procedure of normalization of scores, which is based on an adaptation of the Test-normalization (T-norm) [2] technique used in the speaker verification domain, to compensate for the mismatch. Polyphone IPSC-02 database and ASPIC (an automatic speaker recognition system developed by EPFL and IPS-UNIL in Lausanne, Switzerland) were used in order to test the normalization procedure. Experimental results for three different recording condition scenarios are presented using Tippett plots and the effect of the compensation on the evaluation of the strength of the evidence is discussed.

Bayes Theorem↗
PubMed2005

The automatic detection of known beta-propeller structural motifs from protein tertiary structure.

Following our previous work on the analysis of 'structural plasticity' associated with the beta-propeller structural motifs, we have now developed a simple method that can automatically detect all the known beta-propellers in protein tertiary structure, given a list of Protein Data Bank (PDB) codes as input to the computer program. Our beta-propeller detection (BPD) method identifies the location of beta-propellers in the protein structure, specifies the beta-propeller type, the beta-sheet associated beta-strand pattern and the structurally similar beta-propellers observed in other proteins. When tested on 21,566 proteins in the PDB, the BPD method was capable of correctly identifying all the known 245 beta-propellers described in the structural classification of proteins (SCOP) with the number of false positives detected being less than 0.2%. Forty-one false positives were detected that correspond to eight known protein families. When compared with some of the popular web-based programs that can automatically detect 'structural similarities' between the query and target proteins, our method has the advantage of also being capable of detecting beta-propellers associated with 'structural plasticity' and in situations where the target and query proteins differ in amino acid sequence length.

Amino Acid Motifs↗
PubMed2006

Automatic lexeme acquisition for a multilingual medical subword thesaurus.

PURPOSE: We present a method for the automated acquisition of a multilingual medical lexicon (for Spanish, French and Swedish) to be used within the framework of a medical cross-language text retrieval system. METHODS: For the lexical acquisition process, we incorporate seed lexicons and lists of trusted term translations derived from the UMLS Metathesaurus. The seed lexicons for Spanish, French and Swedish are automatically generated from (previously manually constructed) Portuguese, German and English sources by simple string transformations. Lexical and semantic hypotheses are then validated by processing pairs of term translations. In a last step, we use the cleaned list of "approved" translations in order to augment, step by step, the target dictionaries by processing the parallel corpora in terms of co-occurrence patterns of hypothesized translation equivalents which cannot be derived by simple character substitutions. RESULTS: An existing multilingual lexicon for the medical domain with about 60,000 entries for English, German, and Portuguese was automatically augmented by more then 17,000 new lexemes for Spanish, French, and Swedish. CONCLUSIONS: Our approach constitutes a promising method for the automated creation of new lexicon entries and their linkage to semantic identifiers.

Electronic Data Processing↗
PubMed2004

Automatic quantification of light sleep shows differences between apnea patients and healthy subjects.

A fully automatic method to quantify sleep depth during the night was developed in the present work. The method was tested using 20 all-night recordings from 10 healthy control subjects and 10 sleep apnea patients. The results showed statistically significant differences in sleep depth between control subjects and sleep apnea patients. The overall sleep was lighter in apnea patients than in healthy control subjects, most likely indicating a disturbed sleep caused by apneas. The automatic parameters presented provide a method to quantify the light sleep and could in the future possibly be used in clinical sleep studies and follow-up of treatment.

Adult↗
PubMed2005

Atlas-based automatic segmentation of MR images: validation study on the brainstem in radiotherapy context.

PURPOSE: Brain tumor radiotherapy requires the volume measurements and the localization of several individual brain structures. Any tool that can assist the physician to perform the delineation would then be of great help. Among segmentation methods, those that are atlas-based are appealing because they are able to segment several structures simultaneously, while preserving the anatomy topology. This study aims to evaluate such a method in a clinical context. METHODS AND MATERIALS: The brain atlas is made of two three-dimensional (3D) volumes: the first is an artificial 3D magnetic resonance imaging (MRI); the second consists of the segmented structures in this artificial MRI. The elastic registration of the artificial 3D MRI against a patient 3D MRI dataset yields an elastic transformation that can be applied to the labeled image. The elastic transformation is obtained by minimizing the sum of the square differences of the image intensities and derived from the optical flow principle. This automatic delineation (AD) enables the mapping of the segmented structures onto the patient MRI. Parameters of the AD have been optimized on a set of 20 patients. Results are obtained on a series of 6 patients' MRI. A comprehensive validation of the AD has been conducted on performance of atlas-based segmentation in a clinical context with volume, position, sensitivity, and specificity that are compared by a panel of seven experimented physicians for the brain tumor treatments. RESULTS: Expert interobserver volume variability ranged from 16.70 cm(3) to 41.26 cm(3). For patients, the ratio of minimal to maximal volume ranged from 48% to 70%. Median volume varied from 19.47 cm(3) to 27.66 cm(3) and volume of the brainstem calculated by AD varied from 17.75 cm(3) to 24.54 cm(3). Medians of experts ranged, respectively, for sensitivity and specificity, from 0.75 to 0.98 and from 0.85 to 0.99. Median of AD were, respectively, 0.77 and 0.97. Mean of experts ranged, respectively, from 0.78 to 0.97 and from 0.86 to 0.99. Mean of AD were, respectively, 0.76 and 0.97. CONCLUSIONS: Results demonstrate that the method is repeatable, provides a good trade-off between accuracy and robustness, and leads to reproducible segmentation and labeling. These results can be improved by enriching the atlas with the rough information of tumor or by using different laws of deformation for the different structures. Qualitative results also suggest that this method can be used for automatic segmentation of other organs such as neck, thorax, abdomen, pelvis, and limbs.

Algorithms↗
PubMed2005

Predictive value of ventricular arrhythmia inducibility for subsequent ventricular tachycardia or ventricular fibrillation in Multicenter Automatic Defibrillator Implantation Trial (MADIT) II patients.

UNLABELLED: In the Multicenter Automatic Defibrillator Implantation Trial (MADIT) II, implantable cardioverter-defibrillator (ICD)-randomized patients underwent electrophysiologic testing. Both inducible and noninducible patients received an ICD. We correlated inducibility with the occurrence of subsequent ventricular tachycardia (VT) or ventricular fibrillation (VF). Intracardiac ICD electrograms for subsequent events were analyzed to categorize the spontaneous arrhythmia as VT or VF. The two-year Kaplan-Meier event rate for VT in inducible patients was 29.0% versus 19.3% in noninducible patients. However, ICD therapy for spontaneous VF was less common at two years in inducible patients (3.2%) than in noninducible patients (8.6%). In the MADIT II study, inducibility predicted an increased likelihood of VT but decreased VF. OBJECTIVES: We correlated electrophysiologic inducibility with spontaneous ventricular tachycardia (VT) or ventricular fibrillation (VF) in the Multicenter Automatic Defibrillator Implantation Trial (MADIT) II. BACKGROUND: In the MADIT II study, 593 (82%) of 720 implantable cardioverter-defibrillator (ICD) randomized patients underwent electrophysiologic testing. Patients received an ICD whether they were inducible or not. METHODS: A "standard" inducibility definition included sustained monomorphic or polymorphic VT induced with three or fewer extrastimuli or VF induced with two or fewer extrastimuli. We compared a narrow inducibility definition (only monomorphic VT) and a broad definition (standard definition plus VF with three extrastimuli). We used ICD-stored electrograms to categorize spontaneous VT or VF. RESULTS: Inducible patients (standard definition) had a greater likelihood of experiencing ICD therapy for VT than noninducible patients (p = 0.023). Unexpectedly, ICD therapy for spontaneous VF was less common (p = 0.021) in inducible patients than in noninducible patients. The two-year Kaplan-Meier event rate for VT or VF was 29.4% for inducible patients and 25.5% for noninducible patients. Standard inducibility did not predict the combined end point of VT or VF (p = 0.280, by log-rank analysis). The narrow inducibility definition outperformed the standard definition, whereas the broad definition appeared inferior to the standard definition. CONCLUSIONS: In the MADIT II study patients, inducibility was associated with an increased likelihood of VT. Noninducible MADIT II study subjects using this electrophysiologic protocol had a considerable VT event rate and a higher VF event rate than inducible patients. Induction of polymorphic VT or VF, even with double extrastimuli, appears less relevant than induction of monomorphic VT.

Aged↗
PubMed2005

WaveRead: automatic measurement of relative gene expression levels from microarrays using wavelet analysis.

Gene expression microarrays monitor the expression levels of thousands of genes in an experiment simultaneously. To utilize the information generated, each of the thousands of spots on a microarray image must be properly quantified, including background correction. Most present methods require manual alignment of grids to the image data, and still often require additional minor adjustments on a spot by spot basis to correct for spotting irregularities. Such intervention is time consuming and also introduces inconsistency in the handling of data. A fully automatic, tested system would increase throughput and reliability in this field. In this paper, we describe WaveRead, a fully automated, standalone, open-source system for quantifying gene expression array images. Through the use of wavelet analysis to identify the spot locations and diameters, the system is able to automatically grid the image and quantify signal intensities and background corrections without any user intervention. The ability of WaveRead to perform proper quantification is demonstrated by analysis of both simulated images containing spots with donut shapes, elliptical shapes, and Gaussian intensity distributions, as well as of standard images from the National Cancer Institute.

Algorithms↗
PubMed2006

Automatic atom type and bond type perception in molecular mechanical calculations.

In molecular mechanics (MM) studies, atom types and/or bond types of molecules are needed to determine prior to energy calculations. We present here an automatic algorithm of perceiving atom types that are defined in a description table, and an automatic algorithm of assigning bond types just based on atomic connectivity. The algorithms have been implemented in a new module of the AMBER packages. This auxiliary module, antechamber (roughly meaning "before AMBER"), can be applied to generate necessary inputs of leap-the AMBER program to generate topologies for minimization, molecular dynamics, etc., for most organic molecules. The algorithms behind the manipulations may be useful for other molecular mechanical packages as well as applications that need to designate atom types and bond types.

Algorithms↗
PubMed2004

Automatic alignment of individual peaks in large high-resolution spectral data sets.

Pattern recognition techniques are effective tools for reducing the information contained in large spectral data sets to a much smaller number of significant features which can then be used to make interpretations about the chemical or biochemical system under study. Often the effectiveness of such approaches is impeded by experimental and instrument induced variations in the position, phase, and line width of the spectral peaks. Although characterizing the cause and magnitude of these fluctuations could be important in its own right (pH-induced NMR chemical shift changes, for example) in general they obscure the process of pattern discovery. One major area of application is the use of large databases of (1)H NMR spectra of biofluids such as urine for investigating perturbations in metabolic profiles caused by drugs or disease, a process now termed metabonomics. Frequency shifts of individual peaks are the dominant source of such unwanted variations in this type of data. In this paper, an automatic procedure for aligning the individual peaks in the data set is described and evaluated. The proposed method will be vital for the efficient and automatic analysis of large metabonomic data sets and should also be applicable to other types of data.

Animals↗
PubMed2005

Quantitative study of the effects of chemical shift tolerances and rates of SA cooling on structure calculation from automatically assigned NOE data.

The calculation of protein structures from nuclear magnetic resonance (NMR) data has been greatly facilitated by improvements in software for the automatic assignment of NOESY spectra. Nevertheless, for larger proteins, resonance overlap may lead to an overwhelming number of assignment options per peak. Although most software for automatic NOESY assignment can deal with a certain level of assignment ambiguity, structure calculations fail when this becomes too high. Reducing the number of assignment options per peak by reducing the chemical shift tolerances can lead to correct assignments being excluded, and thus also to incorrect structures. We have investigated, systematically, for three proteins of different size, the influence of the chemical shift tolerance limits (Delta) and of the number of simulated annealing (SA) cooling steps on the performance of the software ARIA. Large tolerance windows, and the correspondingly high levels of ambiguity, did not cause problems when appropriately slower cooling was used in our SA protocol. In cases where a high percentage of well-converged structures was not achieved, we demonstrate that it is more productive to calculate fewer structures whilst applying slow cooling, than to calculate many structures with fast cooling. In this way, high-quality structures were obtained even for proteins whose NMR spectra showed great degeneracy, and where there was much inconsistency in peak alignment between different samples. The method described herein opens the way to the automated structure determination of larger proteins from NMR data.

Algorithms↗
PubMed2004

Automatic recognition of alertness level by using wavelet transform and artificial neural network.

We propose a novel method for automatic recognition of alertness level from full spectrum electroencephalogram (EEG) recordings. This procedure uses power spectral density (PSD) of discrete wavelet transform (DWT) of full spectrum EEG as an input to an artificial neural network (ANN) with three discrete outputs: alert, drowsy and sleep. The error back propagation neural network is selected as a classifier to discriminate the alertness level of a subject. EEG signals were obtained from 30 healthy subjects. The group consisted of 14 females and 16 males with ages ranging from 18 to 65 years and a mean age of 33.5 years, and a body mass index (BMI) of 32.4 +/- 7.3 kg/m2. Alertness level and classification properties of ANN were tested using the data recorded in 12 healthy subjects, whereby the EEG recordings were not used been used to train the ANN. The statistics were used as a measure of potential applicability of the ANN. The accuracy of the ANN was 96 +/- 3% alert, 95 +/- 4% drowsy and 94 +/- 5% sleep. The results suggest that the automatic recognition algorithm is applicable for distinguishing between alert, drowsy and sleep state in recordings that have not been used for the training.

Adolescent↗
PubMed2005

Automatic detection of movement disorders using recordings of rapid alternating movements.

The present work assesses the potential of rapid alternating movement analysis for detecting movement disorders like Parkinson's disease. Rapid alternating wrist movements were recorded by a diadochokinesimeter for patients with Parkinson's disease (n=10) and healthy controls (n=20). An index of irregularity was computed for each individual as the density of jerk singularities (i.e. zero-crossings) during the movements. Several scales of analysis (i.e. "coarseness") were used for detecting the jerk events and two methods were compared for all of these scales: (1) automatic classification by means of a threshold that optimally separates the indexes of irregularity of the patients from those of the controls, and (2) statistical decision (normal or abnormal) based upon a distribution of indexes of irregularity obtained from a large population of normal subjects. The results showed that (1) two scales of analysis were sufficient and that (2) both methods presented similar performances (e.g. sensitivity=1.00, specificity=0.85, efficiency=0.90). However, statistical decision should be preferred because of its simplicity. The possibility of automatic detection of movement disorders from alternating movements is discussed.

Adult↗