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PubMedDate not supplied

Probity: a protein identification algorithm with accurate assignment of the statistical significance of the results.

An algorithm for protein identification based on mass spectrometric proteolytic peptide mapping and genome database searching is presented. The algorithm ranks database proteins based on direct calculation of the probability of random matching and assigns the statistical significance to each result. We investigate the performance of the algorithm by simulation and show that the algorithm responds to random data in the desired manner and that the statistical significance computed indicates the risk that a particular identification result is false.

Algorithms↗

PubMedDate not supplied

Open mass spectrometry search algorithm.

Large numbers of MS/MS peptide spectra generated in proteomics experiments require efficient, sensitive and specific algorithms for peptide identification. In the Open Mass Spectrometry Search Algorithm (OMSSA), specificity is calculated by a classic probability score using an explicit model for matching experimental spectra to sequences. At default thresholds, OMSSA matches more spectra from a standard protein cocktail than a comparable algorithm. OMSSA is designed to be faster than published algorithms in searching large MS/MS datasets.

Algorithms↗

PubMed1997

An algorithm for real-time, continuous evaluation of left ventricular mechanics by single-beat estimation of arterial and ventricular elastance.

We describe a computer algorithm that allows continuous, real-time evaluation of ventricular elastance (Ees), arterial elastance (Ea), and their coupling ratio in a clinical setting. In the conventional pressure-volume analysis of left ventricular (LV) contractility, invasive methods of volume determination and a significant, rapid preload reduction are required to generate Ees. With the help of automated border detection by transesophageal echocardiography, and a technique of estimating peak LV isovolumic pressure, Ea and Ees were determined from a single cardiac beat without the need for preload reduction. A comparison of results obtained by a conventional approach and the new algorithm technique, showed good correlation for Ea (r = 0.86, p < 0.001) and Ees (r = 0.74, p = 0.001). Bias analysis showed a bias (d) of 1.47 mmHg/cm2 for Ea with a standard deviation (SD) of 7.03 mmHg/cm2, and upper (d+2SD) and lower(d-2SD) limits of agreement of 15.24 mmHg/cm2 and -12.31 mmHg/cm2, respectively. Bias analysis showed a bias of -1.42 mmHg/cm2 for Ees with a SD of 4.88 mmHg/cm2, and limits of agreement of 8.15 mmHg/cm2 and -10.98 mmHg/cm2. The algorithm's stability to artifacts was also analyzed by comparing magnitudes of residuals of Ea and Ees from source signals with and without noise. With Ea differing by an average of 1.036 mmHg/cm2 and Ees differing by an average of 0.836 mmHg/cm2, the algorithm was found to be stable to artifacts in the source signals.

Algorithms↗

PubMed1998

A real-time algorithm to improve the response time of a clinical multigas analyser.

OBJECTIVE: An algorithm to improve the response time of a clinical respiratory multigas analyser is presented. METHODS: The algorithm involves the application of a second order differential equation to the analyser gas output signals in real-time. The adjusted analyser output signals are compared with those of a quadrupole respiratory mass spectrometer sampling and analysing simultaneously. RESULTS: Our results show a close correlation between the adjusted clinical gas analyser and the mass spectrometer signals. Lung volumes derived from a non-invasive sinusoidal inert gas forcing technique, in a model test lung, using the adjusted clinical gas analyser and the mass spectrometer signals demonstrated comparable results. CONCLUSIONS: The algorithm provides an improvement on the relatively slow response times of the clinical gas analyser for breath-by-breath time-dependent applications. The same algorithm can also be applied to other instruments which have slow response times.

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PubMedDate not supplied

[Application of neural networks using the volume learning algorithm for the study of structure-activity relationship in chemical compounds].

A volume learning algorithm for artificial neural networks was developed to quantitatively describe the three-dimensional structure-activity relationships using as an example N-benzylpiperidine derivatives. The new algorithm combines two types of neural networks, the Kohonen and the feed-forward artificial neural networks, which are used to analyze the input grid data generated by the comparative molecular field approach. Selection of the most informative parameters using the algorithm helped to reveal the most important spatial properties of the molecules, which affect their biological activities. Cluster regions determined using the new algorithm adequately predicted the activity of molecules from a control data set.

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PubMed2001

Clinical validation of an automated boundary tracking algorithm on cardiac MR images.

The goal of this research was to develop an automated algorithm for tracking the borders of the left ventricle (LV) in a cine-MRI gradient-echo temporal data set. The algorithm was validated on four patient populations: healthy volunteers and patients with dilated cardiomyopathy (DCM), left ventricular hypertrophy (LVH), or left ventricular aneurysm (LVA). A full tomographic set (approximately 11 slices/case) of short-axis images through systole was obtained for each patient. Initial endocardial and epicardial contours for the end-diastolic (ED) and end-systolic (ES) frames were manually traced on the computer by an experienced radiologist. The ED tracings were used as the starting point for the algorithm. The borders were tracked through each phase of the temporal data set, until the ES frame was reached (approximately 7 phases/slice). Peak gradients along equally spaced chords calculated perpendicular to a centerline determined midway between the endocardial and epicardial borders were used for border detection. This approach was tested by comparing the LV epicardial and endocardial volumes calculated at ES to those based on the manual tracings. The results of the algorithm compared favorably with both the endocardial (r2 = 0.72 - 0.98) and epicardial (r2 = 0.96 - 0.99) volumes of the tracer.

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PubMed2002

Performance assessment of an algorithm for the alignment of fMRI time series.

This paper reports on performance assessment of an algorithm developed to align functional Magnetic Resonance Image (fMRI) time series. The algorithm is based on the assumption that the human brain is subject to rigid-body motion and has been devised by pipelining fiducial markers and tensor based registration methodologies. Feature extraction is performed on each fMRI volume to determine tensors of inertia and gradient image of the brain. A head coordinate system is determined on the basis of three fiducial markers found automatically at the head boundary by means of the tensors and is used to compute a point-based rigid matching transformation. Intensity correction is performed with sub-voxel accuracy by trilinear interpolation. Performance of the algorithm was preliminarily assessed by fMR brain images in which controlled motion has been simulated. Further experimentation has been conducted with real fMRI time series. Rigid-body transformations were retrieved automatically and the value of motion parameters compared to those obtained with the Statistical Parametric Mapping (SPM99) and the Automatic Image Registration (AIR 3.08). Results indicate that the algorithm offers sub-voxel accuracy in performing both misalignment and intensity correction of fMRI time series.

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PubMed2003

Development and testing of a de novo drug-design algorithm.

In this article we present an implementation of a de novo drug-design algorithm. The algorithm starts with a molecule placed in the binding site of a protein and then modifies it using a sequential growth approach. This involves successive cycles of suppression of randomly picked groups in the molecule and their replacement by other groups chosen from databanks of linear or cyclic fragments. The algorithm has been coupled with the DYNAMO library which allows the simulation of macromolecules using molecular mechanical and quantum chemical methods. The main body of the article describes the methodologies we use to create, characterize and evaluate putative ligands. We also consider briefly an application of the algorithm to a protein of pharmacological interest, the neuraminidase of the influenza virus, and discuss the strengths and weaknesses of our approach.

Algorithms↗

PubMed2004

An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments.

We report an automated procedure for high-throughput NMR resonance assignment for a protein of known structure, or of an homologous structure. Our algorithm performs Nuclear Vector Replacement (NVR) by Expectation/Maximization (EM) to compute assignments. NVR correlates experimentally-measured NH residual dipolar couplings (RDCs) and chemical shifts to a given a priori whole-protein 3D structural model. The algorithm requires only uniform (15)N-labelling of the protein, and processes unassigned H(N)-(15)N HSQC spectra, H(N)-(15)N RDCs, and sparse H(N)-H(N) NOE's (d(NN)s). NVR runs in minutes and efficiently assigns the (H(N),(15)N) backbone resonances as well as the sparse d(NN)s from the 3D (15)N-NOESY spectrum, in O (n(3)) time. The algorithm is demonstrated on NMR data from a 76-residue protein, human ubiquitin, matched to four structures, including one mutant (homolog), determined either by X-ray crystallography or by different NMR experiments (without RDCs). NVR achieves an average assignment accuracy of over 99%. We further demonstrate the feasibility of our algorithm for different and larger proteins, using different combinations of real and simulated NMR data for hen lysozyme (129 residues) and streptococcal protein G (56 residues), matched to a variety of 3D structural models.

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PubMed2005

The precision of in vitro methods and algorithms for predicting the bioavailability of dietary iron.

Three factors determine how much iron will be absorbed from a meal. They are the physiological mechanisms that regulate uptake by and transfer through the enterocytes in the upper small intestine, the quantity of iron in the meal, and its availability to the cellular iron transporters. Established methods exist for predicting the effect of physiological regulation and for measuring or estimating meal iron content. Three approaches to estimating bioavailability have been advocated. Two are in vitro screening procedures: measurement of dialyzable iron and Caco-2 cell uptake, both carried out after in vitro simulated gastric and pancreatic digestion. The third is the use of algorithms based on the predicted effects of specific meal components on absorption derived from isotopic studies in human volunteers. The in vitro procedures have been very useful for identifying and characterizing factors that affect non-heme iron absorption, but direct comparisons between absorption predicted from the in vitro tests and measurements in human volunteers have only been made in a limited number of published studies. The available data indicate that dialysis and Caco-2 cell uptake are useful for ranking meals and single food items in terms of predicted iron bioavailability, but may not reflect the magnitudes of the effects of factors that influence absorption accurately. Algorithms based on estimates of the amounts of heme iron and of enhancers and inhibitors of non-heme iron absorption in foods make it possible to classify meals or diets as being of high, medium, or low bioavailability. The precision with which meal iron bioavailability can be predicted in a population, for which a specific algorithm has been developed, is improved by measuring the content of the most important enhancers and inhibitors. However, the accuracy of such predictions appears to be much lower when the algorithm is applied to meals eaten by different populations.

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PubMed2003

Algorithms for accurate 3D registration of neuronal images acquired by confocal scanning laser microscopy.

This paper presents automated and accurate algorithms based on high-order transformation models for registering three-dimensional (3D) confocal images of dye-injected neurons. The algorithms improve upon prior methods in several ways, and meet the more stringent image registration needs of applications such as two-view attenuation correction recently developed by us. First, they achieve high accuracy ( approximately 1.2 voxels, equivalent to 0.4 micro m) by using landmarks, rather than intensity correlations, and by using a high-dimensional affine and quadratic transformation model that accounts for 3D translation, rotation, non-isotropic scaling, modest curvature of field, distortions and mechanical inconsistencies introduced by the imaging system. Second, they use a hierarchy of models and iterative algorithms to eliminate potential instabilities. Third, they incorporate robust statistical methods to achieve accurate registration in the face of inaccurate and missing landmarks. Fourth, they are fully automated, even estimating the initial registration from the extracted landmarks. Finally, they are computationally efficient, taking less than a minute on a 900-MHz Pentium III computer for registering two images roughly 70 MB in size. The registration errors represent a combination of modelling, estimation, discretization and neuron tracing errors. Accurate 3D montaging is described; the algorithms have broader applicability to images of vasculature, and other structures with distinctive point, line and surface landmarks.

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PubMed2001

Conduct of an algorithm in quantifying simulated palatal surface tooth erosion.

In order to test the ability of an algorithm to quantify simulated palatal erosion, a total of 10 extracted permanent upper central incisors were mounted in brass blocks. Baseline impressions were recorded using an addition cured silicone impression material in a metal impression tray. Once set and removed from the teeth, the impressions were coated twice with a high silver content electroconductive paint, applied using a brush, before being backed up with die stone to form an electroconductive replica. Each tooth was then subject to three treatments: application of phosphoric acid etchant gel for 60 s, application of etchant gel for 120 s and immersion for 3 h in Diet Coca-Cola*. After each one the replication process was repeated. Thereafter all replicas were mapped using a computer controlled electrical probe and the resultant digital terrain models (DTMS) compared using a surface matching and difference detection algorithm (SMADDA). Surface matching was unsuccessful only in one instance. As the duration of the insult increased, so did the proportion of the surface that underwent change to a maximum of 33.3%. Anatomical site was significantly (P < 0.05) associated with the susceptibility to erosion. The cingulum periphery appeared most resistant to this. The algorithmic approach offers much scope for monitoring dental erosion as acid dissolution of the tooth's surface appears to occur gradually. The cingulum region appears relatively more resistant to this process than other tooth sites and thus facilitates the process of surface matching. Further testing is however, required to determine precisely the algorithm's upper tolerance level.

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PubMed2001

Contribution of a pacemaker bradycardia detection algorithm in the study of patients with carotid sinus syndrome.

While carotid sinus syndrome (CSS) is often suspected as a cause of syncope in the elderly, whether it represents an indication for cardiac pacing may remain uncertain. Bradycardia algorithms included in pacemakers are now able to establish a precise relationship between spontaneous asystole and occurrence of symptoms and strengthen the indication for permanent pacing. This study included seven men and three women (70.5 +/- 7.3 years of age) who, over an average period of 54.1 +/- 17 months, had suffered from syncope (12.6 episodes/patient) and presyncope (11.2 episodes/patient) attributed to pure cardioinhibition (2 patients) or mixed CSS (8 patients). Other sources of symptoms were excluded by thorough clinical evaluations, including Holter monitoring, echocardiography, and electrophysiological testing. All patients received a CHORUS 6234 pacemaker, the memory of which includes a dedicated bradycardia detection algorithm capable of storing atrial and ventricular chains, and date and time of the last ten pauses and/or bradycardic events. After a initial period of 14.7 +/- 8 months, during which symptoms were suppressed, the bradycardia algorithm was activated. From then on, a cumulative increase in the number of patients presenting with diurnal pauses was measured (1 month, n = 0; 3 months, n = 6; 9 months, n = 7; 2 years, n = 8). Fourteen episodes of diurnal asystole were recorded. The mean duration of the longest episodes of spontaneous ventricular standstill was 6,319 +/- 1,615 ms and was due to sinoatrial block (n = 7), atrioventricular block (n = 5), and a combination of both (n = 2). In conclusion, activation of the CHORUS bradycardia algorithm allowed confirmation of the appropriateness of permanent pacing in a majority of patients suffering from CSS.

Aged↗

PubMed2002

Failure of atrial flutter detection by a pacemaker with a dedicated atrial flutter detection algorithm.

Detection of atrial flutter may be difficult for pacemakers with automatic mode switching algorithms. The Medtronic Kappa 700 device pacemakerfamily offers a dedicated Blanked Flutter Search algorithm specifically designed for the detection of atrial flutter. This report describes how spontaneous atrioventricular conduction, resulting in a sensed QRS complex at a critical time, inhibited the function of the Blanked Flutter Search algorithm to sense "concealed" or "blanked" atrialflutter. This observation underscores the need for further refinement of pacemaker algorithms for the detection of atrial tachyarrhythmias.

Aged↗

PubMed2003

Effect of modern pacing algorithms on generator longevity: a predictive analysis.

Pulse generator (PG) longevity is of major importance to the quality of care of pacemaker patients. A series of automatic algorithms affect PG longevity. This study investigated the individual and combined effects of three algorithms incorporated in the Medtronic Kappa 700 pacemaker series: Capture Management periodically measures the stimulation threshold and adjusts the PG output, Sinus Preference allows the sinus rate to prevail in a specified range below the sensor rate, and Search AV allows an extension of the AV interval if spontaneous conduction is observed. The effects of Capture Management, Sinus Preference, and Search AV on device longevity were studied in 21 consecutive patients treated in the VDD and DDDR modes. Patients were followed for 1 year. The data were analyzed using an equation provided by the manufacturer. Capture Management was activated in 20 patients. For 11 PGs at the basic settings, longevity was extended by 5.2%, whereas reprogrammed PGs had no gain. Sinus Preference was active in four DDDR patients, who gained 12.0 +/- 5.3%atrial sensing from it, with a resultant longevity gain of1.4 +/- 0.45 months(NS). Search AV was active in 19 patients and 8 responders gained 7.8 +/- 4.4 months PG longevity. The overall longevity in this study was 106.3 +/- 8.4 months with all features as programmed, whereas the longevity without Capture Management and Search AV algorithms would be 98.2 +/- 4.9 months, saving 8.1 +/- 5.8 months(range 0-18) of battery life. Thus, two algorithms: Capture Management and Search AV, have clinical relevance in the extension of PG longevity.

Algorithms↗

PubMed2000

Outcome indicators for stroke: application of an algorithm treatment across the continuum of postacute rehabilitation services.

OBJECTIVE: To determine the feasibility and utility of applying a case-mix adjusted algorithm for treatment across the continuum of stroke rehabilitation. DESIGN: Implementation of a clinical algorithm developed through national expert panels to standardize rehabilitation assessment and treatment of veterans with stroke. Stroke patients were stratified into initial severity groups using FIM instrument-Function Related Groups (FIM-FRG) classifications and were followed up from first rehabilitation referral to completion of all active restorative functional goals. FIM-FRG assignments were used to establish case-mix adjusted outcome indicators for the continuum of rehabilitation services. SETTING: Rehabilitation services in medical and surgical units, intermediate care units, inpatient rehabilitation bed units, and outpatient settings in 10 participating Veterans Affairs (VA) medical centers. PATIENTS: Stroke patients (n = 421) who received rehabilitation in the 10 participating VA centers. MAIN OUTCOME MEASURES: Patients' functional gains, length of treatment (LOT), functional status at discharge, LOT efficiency, costs, cost efficiency, and disposition location. RESULTS: Two hundred twenty-three patients began rehabilitation while in acute medical or surgical units, 171 in inpatient rehabilitation units, 24 in intermediate care, and the remainder while in other settings. With cases compiled across all settings, average total rehabilitation costs for patients in the lowest FRG class (most severe disabilities) were more than twice those for patients assigned to the highest FRG class (least severe disabilities). FIM gains were greatest in the subset of younger stroke patients with the most severe disabilities. CONCLUSIONS: Implementing a standard algorithm of rehabilitation care that includes outcome indicators adjusted to patients' disability severity is feasible. The algorithm's utility is evident because it encompasses rehabilitation care provided across the full continuum, promotes access to care by advocating assessment of all stroke patients, encourages early initiation of treatment, and promotes a smooth transition though various levels of care while encouraging cost containment.

Aged↗

PubMed2001

Initial clinical experience with a new arrhythmia detection algorithm in dual chamber implantable cardioverter defibrillators.

AIM: Inappropriate therapy, due to poor discrimination of supraventricular tachycardia (SVT) from ventricular tachycardia (VT) remains a major problem in patients with an implantable cardioverter defibrillator (ICD). Theoretically, the addition of atrial sensing in discrimination algorithms should improve this differentiation. The aim of the study is to evaluate the performance of a new tachycardia discrimination algorithm, SMART Detection. METHODS AND RESULTS: Twenty-six patients received a non-thoracotomy ICD system (Phylax AV, Biotronik, Germany). All documented spontaneous arrhythmia episodes were analyzed. During a mean follow-up of 8 months, a total number of 139 events with stored electrograms were recorded in 12 patients. The final diagnosis was ventricular fibrillation (VF) or polymorphic VT (n=20), monomorphic VT (n=69), SVT (n=26), other ventricular arrhythmia (n=3) and T wave oversensing (n=21). In 6 episodes a dual tachycardia was present. Considering SVT episodes, inappropriate therapy occurred in 2 cases of atrial flutter due to stable ventricular rate (<30 ms), 1 case of atrial tachycardia and 2 cases of sinus tachycardia due to a sudden onset (> 10%). CONCLUSION: With the SMART Detection algorithm, discrimination of VT from SVT achieved a sensitivity of 100%, with an accuracy of 95.6% for all ventricular arrhythmias. In the case of SVT, the algorithm appropriately detected and inhibited therapy in 88% of atrial fibrillation.

Adult↗

PubMed2002

[First clinical experience with a full-size, flat-panel detector for imaging the peripheral skeleton - Part II: Post-processing with a newly developed adaptive autowindow algorithm].

PURPOSE: of the second part of the investigation was the evaluation of a newly developed adaptive autowindow algorithm in comparison to the system processing radiographs of the wrist and ankle to further optimize the image quality with softcopy reading. MATERIAL AND METHODS: All 120 radiographs of the wrist and all 100 radiographs of the ankle used in the 1st part of this paper were processed with the adaptive autowindow algorithm. The evaluation was again performed by 5 radiologists with softcopy reading. For the data analysis a variation of the Visual Grading Analysis (VGA) was used. RESULTS: Up to 19 % of the wrist radiographs and 2 % of the ankle radiographs processed with the system software had to be processed manually afterwards to get acceptable results. By the application of the adaptive autowindow algorithm a manual post-processing was no longer necessary. Highly significant (p less-than-or-equal 0.001) differences for all criteria to be evaluated were found for the wrist radiographs and in the case of the ankle radiographs for the bone contrast, the contrast in soft-tissue regions, the fine details in the bone and the artifacts, the adaptive autowindow algorithm performed always better than the system software. CONCLUSION: Using half of the exposition dose on a flat-panel detector, an optimized post-processing leads to comparable or better results compared to the conventional film-screen-system concerning the image quality.

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