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At least 1,423 records · Page 79Linked to original sources

PubMed2006

An algorithm for detecting startle state based on physiological signals.

To construct safe workspaces or daily life environments, it is important to develop a technology for automatically recording dangerous environmental situations. Based on increased finger skin conductance and decreased instantaneous heart (pulse) rate, we developed an algorithm for detecting the startle state of humans when encountering dangerous situations. The parameter values in the algorithm were optimized by tuning them with experimental results obtained in a virtual reality system, in which dangerous scenarios were presented to 21 subjects. The detection sensitivity of the optimized algorithm was 100% during a static standing condition and also while cycling. The detection specificity attained 90% and 87% for the static and exercising conditions, respectively. The optimized algorithm was applied to a real world situation such as car driving, and relatively high sensitivity of 87% and specificity of 80% were obtained.

Adolescent↗

PubMed2006

Comparing cardiac ejection fraction estimation algorithms without a gold standard.

RATIONALE AND OBJECTIVES: Imaging and estimation of left ventricular function have major diagnostic and prognostic importance in patients with coronary artery disease. It is vital that the method used to estimate cardiac ejection fraction (EF) allows the observer to best perform this task. To measure task-based performance, one must clearly define the task in question, the observer performing the task, and the patient population being imaged. In this report, the task is to accurately and precisely measure cardiac EF, and the observers are human-assisted computer algorithms that analyze the images and estimate cardiac EF. It is very difficult to measure the performance of an observer by using clinical data because estimation tasks typically lack a gold standard. A solution to this "no-gold-standard" problem recently was proposed, called regression without truth (RWT). MATERIALS AND METHODS: Results of three different software packages used to analyze gated, cardiac, and nuclear medicine images, each of which uses a different algorithm to estimate a patient's cardiac EF, are compared. The three methods are the Emory method, Quantitative Gated Single-Photon Emission Computed Tomographic method, and the Wackers-Liu Circumferential Quantification method. The same set of images is used as input to each of the three algorithms. Data were analyzed from the three different algorithms by using RWT to determine which produces the best estimates of cardiac EF in terms of accuracy and precision. RESULTS AND DISCUSSION: In performing this study, three different consistency checks were developed to ensure that the RWT method is working properly. The Emory method of estimating EF slightly outperformed the other two methods. In addition, the RWT method passed all three consistency checks, garnering confidence in the method and its application to clinical data.

Algorithms↗

PubMed2005

A brief readiness to change drinking algorithm: concurrent validity in female VA primary care patients.

Brief primary care interventions for alcohol use should be tailored to patients' readiness to change; however, validated measures of readiness to change are too lengthy to be practical in most primary care settings. We compared a readiness to change drinking algorithm (RTC Algorithm) based on three standardized questions to a validated 12-item readiness to change questionnaire (Rollnick RTCQ) in 85 hazardous drinking female Veterans Affairs (VA) patients. Results from comparisons of mean Rollnick RTCQ scale scores across RTC Algorithm categories suggest good concurrent validity. Regular assessment using the RTC Algorithm questions may help primary care providers tailor alcohol-related discussions with hazardous drinking patients.

Adult↗

PubMed2005

Management of patients infected with airborne-spread diseases: an algorithm for infection control professionals.

BACKGROUND: Many US hospitals lack the capacity to house safely a surge of potentially infectious patients, increasing the risk of secondary transmission. Respiratory protection and negative-pressure rooms are needed to prevent transmission of airborne-spread diseases, but US hospitals lack available and/or properly functioning negative-pressure rooms. Creating new rooms or retrofitting existing facilities is time-consuming and expensive. METHODS: Safe methods of managing patients with airborne-spread diseases and establishing temporary negative-pressure and/or protective environments were determined by a literature review. Relevant data were analyzed and synthesized to generate a response algorithm. RESULTS: Ideal patient management and placement guidelines, including instructions for choosing respiratory protection and creating temporary negative-pressure or other protective environments, were delineated. Findings were summarized in a treatment algorithm. CONCLUSION: The threat of bioterrorism and emerging infections increases health care's need for negative-pressure and/or protective environments. The algorithm outlines appropriate response steps to decrease transmission risk until an ideal protective environment can be utilized. Using this algorithm will prepare infection control professionals to respond more effectively during a surge of potentially infectious patients following a bioterrorism attack or emerging infectious disease outbreak.

Air Microbiology↗

PubMed2006

Base deficit estimation in umbilical cord blood is influenced by gestational age, choice of fetal fluid compartment, and algorithm for calculation.

OBJECTIVE: The purpose of this study was to explore the influences of gestational age, the choice of fetal fluid compartment, and the algorithm for calculation on the estimation of the base deficit in umbilical cord arterial blood at birth. STUDY DESIGN: From 1995 to 2002, cord arterial blood gases and obstetric data were available for 43,551 newborn infants at 37+ weeks of gestation (cohort I). The mean base deficit in blood and the base deficit in extracellular fluid were estimated from pH and PCO2 values in 28,213 newborn infants with a 5-minute Apgar score of > or = 9 (cohort II) with the use of 3 different calculation algorithms (base deficit in blood, base deficit in extracellular fluid [A], and base deficit in extracellular fluid [B]). RESULTS: In cohort II, the base deficit in blood, the base deficit in extracellular fluid (A), and the base deficit in extracellular fluid (B) increased with advancing gestational age (linear regression; P < .0001). The curves run almost parallel, with the base deficit in blood being higher than the base deficit in extracellular fluid (A) and (B). With the use of receiver operating characteristic curves in cohort I, the area under curve to indicate a 5-minute Apgar score of < 7 and < 4 showed the area under curve-pH to be greater than the area under curve-base deficit in extracellular fluid (A) and (B), the area under curve-base deficit in blood to be greater than the area under curve-base deficit in extracellular fluid (A) and (B) for a 5-minute Apgar score of < 7, and the area under curve-base deficit in blood to be greater than the area under curve-base deficit in extracellular fluid (A) and (B) for an Apgar score of < 4. The cutoffs with highest sensitivity and lowest false-positive rate for a 5-minute Apgar score of < 7 and < 4 were, for both scores, a pH value of 7.15, a base deficit in blood of 10 mmol/L, a base deficit in extracellular fluid (A) of 8 mmol/L, and a base deficit in extracellular fluid (B) of 6 mmol/L. CONCLUSION: The calculated values of the base deficit in umbilical cord arterial blood are influenced decisively by gestational age, the choice of fetal fluid compartment, and the calculation algorithms that are used. The power of the base deficit to indicate neonatal distress depends on the choices of fluid compartment and the algorithm that is used to calculate the base deficit.

Acidosis↗

PubMed2006

Relation of QT interval measurements to evolving automated algorithms from different manufacturers of electrocardiographs.

QT-interval measurements have clinical importance for the electrocardiographic recognition of congenital and acquired heart disease and as markers of arrhythmogenic risk during drug therapy, but software algorithms for the automated measurement of electrocardiographic durations differ among manufacturers and evolve within manufacturers. To compare automated QT-interval measurements, simultaneous paired electrocardiograms were obtained in 218 subjects using digital recorders from the 2 major manufacturers of electrocardiographs used in the United States and analyzed by 2 currently used versions of each manufacturer's software. The 4 automated QT and QTc durations were examined by repeated-measures analysis of variance with post hoc testing. Significantly larger automated QT-interval measurements were found with the most recent software of each manufacturer (12- to 24-ms mean differences from earlier algorithms). Systematic differences in QT measurements between manufacturers were significant for the earlier algorithms (11-ms mean difference) but not for the most recent software (1.3-ms mean difference). Similar relations were found for the rate-corrected QTc, with large mean differences between earlier and later algorithms (15 to 26 ms). Although there was a <2-ms mean difference between the most recent automated QTc measurements of the 2 manufacturers, the SD of the difference was 12 ms. In conclusion, reference values for automated electrocardiographic intervals and serial QT measurements vary among electrocardiographs and analysis software. Technically based differences in automated QT and QTc measurements must be considered when these intervals are used as markers of heart disease, prognosis, or arrhythmogenic risk.

Algorithms↗

PubMed2004

Early mortality in coronary bypass surgery: the EuroSCORE versus The Society of Thoracic Surgeons risk algorithm.

BACKGROUND: We compare two widely used risk algorithms for coronary bypass surgery: The European System for Cardiac Operative Risk Evaluation (EuroSCORE) and The Society of Thoracic Surgeons (STS) risk stratification algorithm. METHODS: Risk factors for all adult patients undergoing heart surgery at the University Hospital of Lund between 1996 and 2001 were collected prospectively at preoperative admission. Predictive accuracy for 30-day mortality was assessed by comparing the observed and the expected mortality for equal-sized quintiles of risk by using the Hosmer-Lemeshow goodness-of-fit test. The discriminatory power was evaluated by calculating the areas under receiver operating characteristics (ROC) curves. RESULTS: The study included 4497 coronary artery bypass-only operations. The average age was 66.4 +/- 9.3 years (range 31 to 90 years). Most patients were men (77.0% versus 23.0%). The actual 30-day mortality was 1.89%. The Hosmer-Lemeshow goodness-of-fit test gave a p value of 0.81 (EuroSCORE) and 0.83 (STS), which indicates a good accuracy of both models. The area under the ROC curve was 0.84 (95% confidence interval [CI] 0.80 to 0.88) for EuroSCORE and 0.71 (95% CI 0.66 to 0.77) for STS. The discriminatory power (area under the ROC curve) was significantly larger for EuroSCORE compared with STS (p < 0.00005). CONCLUSIONS: In this large, single institution study the additive EuroSCORE algorithm had a significantly better discriminatory power to predict 30-day mortality than the STS risk algorithm for patients undergoing coronary artery bypass.

Adult↗

PubMed2005

Automatic intraaortic balloon pump timing using an intrabeat dicrotic notch prediction algorithm.

PURPOSE: The efficacy of intraaortic balloon counterpulsation (IABP) during arrhythmic episodes is questionable. A novel algorithm for intrabeat prediction of the dicrotic notch was used for real time IABP inflation timing control. DESCRIPTION: A windkessel model algorithm was used to calculate real-time aortic flow from aortic pressure. The dicrotic notch was predicted using a percentage of calculated peak flow. Automatic inflation timing was set at intrabeat predicted dicrotic notch and was combined with automatic IAB deflation. EVALUATION: Prophylactic IABP was applied in 27 patients with low ejection fraction (< 35%) undergoing cardiac surgery. Analysis of IABP at a 1:4 ratio revealed that IAB inflation occurred at a mean of 0.6 +/- 5 ms from the dicrotic notch. In all patients accurate automatic timing at a 1:1 assist ratio was performed. Seventeen patients had episodes of severe arrhythmia, the novel IABP inflation algorithm accurately assisted 318 of 320 arrhythmic beats at a 1:1 ratio. CONCLUSIONS: The novel real-time intrabeat IABP inflation timing algorithm performed accurately in all patients during both regular rhythms and severe arrhythmia, allowing fully automatic intrabeat IABP timing.

Aged↗

PubMed2006

A guest molecule-host cavity fitting algorithm to mine PDB for small molecule targets.

Inhaled anesthetic molecule occupancy of a protein internal cavity depends in part on the volumes of the guest molecule and the host site. Current algorithms to determine volume and surface area of cavities in proteins whose structures have been determined and cataloged make no allowance for shape or small degrees of shape adjustment to accommodate a guest. We developed an algorithm to determine spheroid dimensions matching cavity volume and surface area and applied it to screen the cavities of 6,658 nonredundant structures stored in the Protein Data Bank (PDB) for potential targets of halothane (2-bromo-2-chloro-1,1,1-trifluoroethane). Our algorithm determined sizes of prolate and oblate spheroids matching dimensions of each cavity found. If those spheroids could accommodate halothane (radius 2.91 A) as a guest, we determined the packing coefficient. 394,766 total cavities were identified. Of 58,681 cavities satisfying the fit criteria for halothane, 11,902 cavities had packing coefficients in the range of 0.46-0.64. This represents 20.3% of cavities large enough to hold halothane, 3.0% of all cavities processed, and found in 2,432 protein structures. Our algorithm incorporates shape dependence to screen guest-host relationships for potential small molecule occupancy of protein cavities. Proteins with large numbers of such cavities are more likely to be functionally altered by halothane.

Algorithms↗

PubMed2004

Memetic algorithms for the unconstrained binary quadratic programming problem.

This paper presents a memetic algorithm, a highly effective evolutionary algorithm incorporating local search for solving the unconstrained binary quadratic programming problem (BQP). To justify the approach, a fitness landscape analysis is conducted experimentally for several instances of the BQP. The results of the analysis show that recombination-based variation operators are well suited for the evolutionary algorithms with local search. Therefore, the proposed approach includes--besides a highly effective randomized k-opt local search--a new variation operator that has been tailored specially for the application in the hybrid evolutionary framework. The operator is called innovative variation and is fundamentally different from traditional crossover operators, since new genetic material is included in the offspring which is not contained in one of the parents. The evolutionary heuristic is tested on 35 publicly available BQP instances, and it is shown experimentally that the algorithm is capable of finding best-known solutions to large BQPs in a short time and with a high frequency. In comparison to other approaches for the BQP, the approach appears to be much more effective, particularly for large instances of 1000 or 2500 binary variables.

Algorithms↗

PubMed2004

Simulation of rat behavior by a reinforcement learning algorithm in consideration of appearance probabilities of reinforcement signals.

Brown and Wanger [Brown, R.T., Wanger, A.R., 1964. Resistance to punishment and extinction following training with shock or nonreinforcement. J. Exp. Psychol. 68, 503-507] investigated rat behaviors with the following features: (1) rats were exposed to reward and punishment at the same time, (2) environment changed and rats relearned, and (3) rats were stochastically exposed to reward and punishment. The results are that exposure to nonreinforcement produces resistance to the decremental effects of behavior after stochastic reward schedule and that exposure to both punishment and reinforcement produces resistance to the decremental effects of behavior after stochastic punishment schedule. This paper aims to simulate the rat behaviors by a reinforcement learning algorithm in consideration of appearance probabilities of reinforcement signals. The former algorithms of reinforcement learning were unable to simulate the behavior of the feature (3). We improve the former reinforcement learning algorithms by controlling learning parameters in consideration of the acquisition probabilities of reinforcement signals. The proposed algorithm qualitatively simulates the result of the animal experiment of Brown and Wanger.

Algorithms↗

PubMed2005

On the use of multi-objective evolutionary algorithms for the induction of fuzzy classification rule systems.

Extracting comprehensible and general classifiers from data in the form of rule systems is an important task in many problem domains. This study investigates the utility of a multi-objective evolutionary algorithm (MOEA) for this task. Multi-objective evolutionary algorithms are capable of finding several trade-off solutions between different objectives in a single run. In the context of the present study, the objectives to be optimised are the complexity of the rule systems, and their fit to the data. Complex rule systems are required to fit the data well. However, overly complex rule systems often generalise poorly on new data. In addition they tend to be incomprehensible. It is, therefore, important to obtain trade-off solutions that achieve the best possible fit to the data with the lowest possible complexity. The rule systems produced by the proposed multi-objective evolutionary algorithm are compared with those produced by several other existing approaches for a number of benchmark datasets. It is shown that the algorithm produces less complex classifiers that perform well on unseen data.

Algorithms↗

PubMed2005

DNA algorithm for an unbounded fan-in Boolean circuit.

In this paper, we present a new DNA-based evaluation algorithm for a Boolean circuit that employs standard bio-molecular techniques. The algorithm operates on an unbounded fan-in Boolean circuit consisting of AND and OR gates. The whole simulation of our algorithm is proposed in a single test tube in O(1) time complexity and is much easier to implement in the laboratory than previously described models. Furthermore, the algorithm allows for evaluating any number of Boolean circuits in parallel in a single test tube.

Algorithms↗

PubMed2006

Algorithmic and complexity results for decompositions of biological networks into monotone subsystems.

A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions which are optimal in an appropriate sense. In graph-theoretic language, the problems can be recast in terms of maximal sign-consistent subgraphs. The theoretical results include polynomial-time approximation algorithms as well as constant-ratio inapproximability results. One of the algorithms, which has a worst-case guarantee of 87.9% from optimality, is based on the semidefinite programming relaxation approach of Goemans-Williamson [Goemans, M., Williamson, D., 1995. Improved approximation algorithms for maximum cut and satisfiability problems using semidefinite programming. J. ACM 42 (6), 1115-1145]. The algorithm was implemented and tested on a Drosophila segmentation network and an Epidermal Growth Factor Receptor pathway model, and it was found to perform close to optimally.

Algorithms↗

PubMed2006

Evaluation of an algorithm of tagging SNPs selection by linkage disequilibrium.

BACKGROUND: Single nucleotide polymorphisms (SNPs) are the most abundant kind of genetic polymorphism in the human genome. They are important in both genetic research and genetic testing in a clinical setting, such as in the area of pharmacogenetics. In order to improve efficiency, tagging SNPs (tagSNPs) are selected in genes of interest to represent other co-related SNPs in linkage disequilibrium (LD) with the tagSNPs. Various algorithms have been proposed to identify a subset of single nucleotide polymorphisms as tagSNPs. Most algorithms of tagSNPs selection are haplotype-based, in which the spatial relationship between SNPs is considered. Currently, a more efficient cluster-based algorithm is proposed which clusters SNPs solely by a LD parameter, such as r(2). Here, we evaluated the sample distribution of r(2) and its effect on the cluster-based tagSNPs selection. DESIGN AND METHODS: The genotype data of 198 individual within a 500-kb region on 5q31 was used to evaluate the sample distribution of r(2) and its effect on the cluster-based tagSNPs selection. RESULTS: It was found that the degree of variation of LD depends on the LD structure of genes. CONCLUSION: As a cluster-based tagSNPs selection algorithm does not take into account the spatial position of SNPs, a more stringent r(2) threshold is required to achieve more reliable tagSNPs selection.

Algorithms↗

PubMed2004

An efficient filling algorithm for counting regions.

Region filling has many applications in computer graphics and image analysis. Some region filling tasks can be performed by fast scan line filling algorithms. Other region filling tasks require seed filling algorithms which are more general but slower. This paper introduces a seed filling algorithm that is designed to count regions irrespective of their shape. The method is described and its performance is compared with three alternative algorithms by applying them to a collection of 34 test images. The four methods showed complete agreement with respect to the counted numbers of regions. The proposed method was found to be fastest and requiring least memory.

Algorithms↗

PubMed2004

Reduced bio basis function neural network for identification of protein phosphorylation sites: comparison with pattern recognition algorithms.

Protein phosphorylation is a post-translational modification performed by a group of enzymes known as the protein kinases or phosphotransferases (Enzyme Commission classification 2.7). It is essential to the correct functioning of both proteins and cells, being involved with enzyme control, cell signalling and apoptosis. The major problem when attempting prediction of these sites is the broad substrate specificity of the enzymes. This study employs back-propagation neural networks (BPNNs), the decision tree algorithm C4.5 and the reduced bio-basis function neural network (rBBFNN) to predict phosphorylation sites. The aim is to compare prediction efficiency of the three algorithms for this problem, and examine knowledge extraction capability. All three algorithms are effective for phosphorylation site prediction. Results indicate that rBBFNN is the fastest and most sensitive of the algorithms. BPNN has the highest area under the ROC curve and is therefore the most robust, and C4.5 has the highest prediction accuracy. C4.5 also reveals the amino acid 2 residues upstream from the phosporylation site is important for serine/threonine phosphorylation, whilst the amino acid 3 residues upstream is important for tyrosine phosphorylation.

Algorithms↗

PubMed2006

An RNA folding algorithm including pseudoknots based on dynamic weighted matching.

On the basis of maximum weighted matching (MWM) algorithm, we introduced a dynamic weight related with stem length and used a recursive algorithm to predict RNA secondary structures by searching the stem structure with maximum weight summation step-by-step. This algorithm not only avoids the complicated free energy calculation, but also it could attain higher prediction accuracy. Moreover, our algorithm can predict most types of potential pseudoknots in the RNA structure.

Algorithms↗