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At least 379 records · Page 21Linked to original sources

PubMed2001

A simple algorithm to infer gene duplication and speciation events on a gene tree.

MOTIVATION: When analyzing protein sequences using sequence similarity searches, orthologous sequences (that diverged by speciation) are more reliable predictors of a new protein's function than paralogous sequences (that diverged by gene duplication), because duplication enables functional diversification. The utility of phylogenetic information in high-throughput genome annotation ('phylogenomics') is widely recognized, but existing approaches are either manual or indirect (e.g. not based on phylogenetic trees). Our goal is to automate phylogenomics using explicit phylogenetic inference. A necessary component is an algorithm to infer speciation and duplication events in a given gene tree. RESULTS: We give an algorithm to infer speciation and duplication events on a gene tree by comparison to a trusted species tree. This algorithm has a worst-case running time of O(n(2)) which is inferior to two previous algorithms that are approximately O(n) for a gene tree of sequences. However, our algorithm is extremely simple, and its asymptotic worst case behavior is only realized on pathological data sets. We show empirically, using 1750 gene trees constructed from the Pfam protein family database, that it appears to be a practical (and often superior) algorithm for analyzing real gene trees. AVAILABILITY: http://www.genetics.wustl.edu/eddy/forester.

Algorithms↗

PubMed1988

A finite state machine algorithm for finding restriction sites and other pattern matching applications.

Existing algorithms for finding restriction endonuclease recognition sites use brute-force algorithms which run in time 0(NM) where N is the number of nucleotides in the sequence under analysis and M is the total number of nucleotides in all the different sites being searched for. This paper presents a deterministic finite state machine algorithm which runs in time 0(N). Memory use can be as high as 0(M4) but a slight modification to the basic algorithm can impose a theoretical upper bound of 0(M) at the cost of some added complexity in the execution of the state machine. The algorithm can operate with a single pass through the sequence under analysis, with no need to back up or (for non-circular sequences) store more than a single input character at a time. This type of algorithm can be adapted to many pattern-matching tasks and is simple enough to implement in hardware that it could, for example, be built into a disk controller as part of a specialized database machine.

Algorithms↗

PubMed1991

Improved algorithms for searching restriction maps.

We present algorithms for searching a DNA restriction enzyme map for a region that best matches a shorter 'probe' map. Our algorithms utilize a new model of map alignments, and extensive experiments prove our model superior to earlier approaches for certain applications. Let M be the number of map sites and P be the number of probe sites. Our first algorithm, which optimizes only over a restricted class of alignments, requires O(MP log P) worst-case time and O(M + P) space. Our second algorithm, which optimizes over all alignments, runs in O(MP3) time and O(M + P2) space, under reasonable assumptions about the distribution of restriction enzyme cleavage sites. Combining the algorithms gives a map-searching method that optimizes over all alignments in O(MP log P) time in practice. The algorithms' effectiveness is illustrated by searches involving a genomic restriction map of Escherichia coli.

Algorithms↗

PubMed2000

The use of a genetic algorithm for simultaneous mapping of multiple interacting quantitative trait loci.

Here we describe a general method for improving computational efficiency in simultaneous mapping of multiple interacting quantitative trait loci (QTL). The method uses a genetic algorithm to search for QTL in the genome instead of an exhaustive enumerative ("step-by-step") search. It can be used together with any method of QTL mapping based on a genomic search, since it only provides a more efficient way to search the genome for QTL. The computational demand decreases by a factor of approximately 130 when using genetic algorithm-based mapping instead of an exhaustive enumerative search for two QTL in a genome size of 2000 cM using a resolution of 1 cM. The advantage of using a genetic algorithm increases further for larger genomes, higher resolutions, and searches for more QTL. We show that a genetic algorithm-based search has efficiency higher than or equal to a search method conditioned on previously identified QTL for all epistatic models tested and that this efficiency is comparable to that of an exhaustive search for multiple QTL. The genetic algorithm is thus a powerful and computationally tractable alternative to the exhaustive enumerative search for simultaneous mapping of multiple interacting QTL. The use of genetic algorithms for simultaneous mapping of more than two QTL and for determining empirical significance thresholds using permutation tests is also discussed.

Algorithms↗

PubMed1994

How to find a wombmate: validation of an algorithm to identify twin pairs in Linked Birth/Infant Death Files.

Linked Birth/Infant Death Files available from the National Center for Health Statistics identify an infant as a twin, but do not identify twin pairs. An algorithm based on maternal, paternal, and infant characteristics has been used to identify twin pairs, but the validity of this algorithm has never been tested. The Missouri linked birth/infant death file from 1980 to 1990 identifies twin pairs by a sequence number. The authors tested the rate and accuracy with which the algorithm identified true pairs in the Missouri file and whether estimates of risk and possible risk factors calculated from pairs of twins identified by the algorithm agreed with these characteristics as calculated from known twin pairs. The algorithm identified 96% (8,273 of 8,620) of true pairs and one false pair. Despite incomplete pair identification, and even identification of a false pair, estimates from the subset identified by the algorithm generally agreed well with characteristics measured from all twin pairs. Nonetheless, incorporation of a multiple birth sequence number into Linked Birth/Infant Death Files would enhance their utility.

Algorithms↗

PubMed1997

Effective use of a novel rate-smoothing algorithm in atrial fibrillation by ventricular pacing.

BACKGROUND: It is still unknown whether a fast heart rate or an irregular ventricular response in atrial fibrillation causes tachycardiomyopathy. Reduction in the variability of RR intervals without an increase in heart rate might be an alternative treatment when antiarrhythmic drugs fail to control the irregularity accompanying atrial fibrillation. SUBJECTS AND METHODS: Eight patients underwent temporary right ventricular pacing, using a novel rate-smoothing algorithm prior to DC cardioversion or His bundle ablation. A rate-smoothing algorithm was utilized by right ventricular apical stimulation. Spontaneous and paced RR intervals during atrial fibrillation were quantified and processed for statistical analysis. RESULTS: The rate-smoothing algorithm resulted in a substantial reduction in the variance of the RR intervals (slow mode 73.1%, fast mode 40.0%) and RR range (slow mode 49.3%, fast mode 34.3%). In contrast to previous algorithms, the mean heart rate during pacing intervention in atrial fibrillation did not change significantly to the heart rate directly preceding the pacemaker intervention (+2%). CONCLUSIONS: This initial study of the novel rate-smoothing algorithm shows that pacing intervention is a relatively safe, rapid and reliable alternative therapy for controlling irregular ventricular rhythms due to atrial fibrillation. Incorporation of the algorithm in implantable pacemakers appears justified, but demands further prospective studies in patients to evaluate relief of symptoms and reduction of tachycardiomyopathy due to atrial fibrillation.

Aged↗

PubMed2002

Comparison of TLD algorithms for monochromatic fluorescent radiation and continuous spectrum X rays.

A personal dosimetry system is required to measure the personal dose equivalent accurately in a wide range of radiation fields. However, the dose evaluation algorithm at the Korea Atomic Energy Research Institute (KAERI) has been developed with the spectral X ray fields described in the American National Standards Institute (ANSI) Standard N13.11 and the actual fields to be monitored may be significantly different from these. To evaluate the dose more accurately when workers are exposed to non-ANSI N13.11 radiation fields, a dose evaluation algorithm using monochromatic radiation (monochromatic algorithm) was developed using the experimental data of the energy responses of CaSO4:Dy thermoluminescent materials irradiated by monochromatic fluorescent X ray fields recently established at KAERI; this was compared with another algorithm developed on the basis of the ANSI N13.11 continuous spectrum X ray fields (spectrum algorithm). The paper concludes with discussions about some results of the algorithm test, including mixed field irradiation and angular response, conducted in an International Atomic Energy Authority/Regional Cooperation of Asia (IAEA/RCA) intercomparison study.

Algorithms↗

PubMed1997

Diagnosing left ventricular dysfunction after myocardial infarction: the Dundee algorithm.

Large-scale trials of angiotensin converting enzyme (ACE) inhibitors after acute myocardial infarction (AMI) suggest that the benefits are greatest in patients with left ventricular (LV) dysfunction. However, early evaluation of LV function in all patients after AMI by current methods can be difficult due to a lack of resources and skilled personnel. Thus a clinical algorithm that could be used at the bedside to reliably identify patients with a left ventricular ejection fraction (LVEF) < or = 40% would be helpful as an occasional alternative to echocardiography. We have devised such an algorithm based on the presence of one of: (i) clinical signs of heart failure; (ii) an index Q-wave anterior myocardial infarction; (iii) lack of thrombolytic therapy when there is a history of two or more previous myocardial infarctions and a CK rise > 1000 U/l. We tested this new algorithm prospectively in the coronary care units of two hospitals (one UK and one USA). In the UK centre, the sensitivity and specificity of the algorithm at identifying patients with a LVEF < or = 40% were 82% and 72%, respectively. In the US centre, the sensitivity of the algorithm was 91% and the specificity 78% at identifying patients with LV dysfunction. We have validated a simple clinical algorithm which can be used at the bedside for identifying patients who would benefit from an ACE inhibitor after AMI.

Aged↗

PubMed1997

A digital filterbank hearing aid: three digital signal processing algorithms--user preference and performance.

OBJECTIVE: Three digital signal processing algorithms named RangeEar, DynEar, and LinEar were compared with regard to user preference and performance when a wearable digital filterbank hearing aid was used. All three algorithms provided individual frequency shaping via a seven-band filterbank. Compression was used in a low-frequency (LF) and a high-frequency (HF) channel. RangeEar and DynEar used wide dynamic range syllabic compression in the LF channel, whereas LinEar used compression limiting. In the HF channel, RangeEar used a slow acting automatic volume control, whereas DynEar and LinEar used compression limiting. The subjects had access to a manual volume control when using the LinEar or DynEar options. DESIGN: The study included 13 hearing aid users with symmetrical sensorineural losses. In a 1 mo long blind field test, the RangeEar algorithm was compared with the preferred algorithm from an earlier study, DynEar or LinEar. A data logger function was included for objective recording of the total time each algorithm was used and how the volume controls were used. The preference was based on the time used for each algorithm and from subjective statements. Threshold signal-to-noise ratio (S/N-threshold) for speech was tested, and sound quality ratings were obtained through a questionnaire. RESULTS: Of the 13 subjects, six preferred the RangeEar fitting and another four preferred the DynEar fitting. Two subjects preferred the LinEar fitting and one had equal preference for RangeEar and LinEar. The results from the questionnaire showed that the preferred fittings were rated higher concerning overall impression of sound quality and clearness, whereas the S/N for the speech test did not show any differences. Preferences, where stated, could be predicted from auditory dynamic range measurements in the LF and HF frequency ranges. The mean dynamic range was broader for low and narrower for high frequencies for those who preferred the RangeEar or DynEar fitting as compared with those who preferred the LinEar fitting. The preference between RangeEar and DynEar was predicted by differences in the HF range, with the narrower dynamic range for the DynEar preference subjects. CONCLUSION: Most subjects preferred the option of having a wide dynamic range syllabic compressor in the LF channel and having the overall gain in the HF channel adjustable, either manually (DynEar) or automatically (RangeEar).

Adult↗

PubMed1999

Usability of semiautomatic segmentation algorithms for tumor volume determination.

RATIONALE AND OBJECTIVES: Tumor volume is an important parameter for clinical decision making. At present, semiautomatic image segmentation is not a standard for tumor volumetry. The aim of this work was to investigate the usability of semiautomatic algorithms for tumor volume determination. METHODS: Semiautomatic region- and volume-growing, isocontour, snakes, hierarchical, and histogram-based segmentation algorithms were tested for accuracy, contour variability, and time performance. The test were performed on a newly developed organic phantom for the simulation of a human liver and liver metastases. The real tumor volumes were measured by water displacement. These measured volumes were used as the gold standard for determining the accuracy of the algorithms. RESULTS: Variability of the segmented volumes ranging from 3.9 +/- 3.2% (isocontour algorithm) to 11.5 +/- 13.9% (hierarchical segmentation) was observed. The segmentation time per slice varied between 32 (volume-growing) and 72 seconds (snakes) on an IBM/RS6000 workstation. CONCLUSIONS: Only the region-growing and isocontour algorithms have the potential to be used for tumor volumetry. However, further improvements of these algorithms are necessary before they can be placed into clinical use.

Algorithms↗

PubMed1999

The Texas Children's Medication Algorithm Project: report of the Texas Consensus Conference Panel on Medication Treatment of Childhood Major Depressive Disorder.

OBJECTIVES: To develop consensus guidelines for medication treatment algorithms for childhood major depressive disorder (MDD) based on scientific evidence and clinical opinion when science is lacking. The ultimate goal of this approach is to synthesize research and clinical experience for the practitioner and to increase the uniformity of preferred treatment for childhood MDD. A final goal is to develop an approach that can be tested as to whether it improves clinical outcomes for children and adolescents with MDD. METHOD: A consensus conference was held. Participants included academic clinicians and researchers, practicing clinicians, administrators, consumers, and families. The focus was to review and use clinical evidence to recommend specific pharmacological approaches for treatment of MDD in children and adolescents. After a series of presentations of current research evidence and panel discussion, the consensus panel met, agreed on assumptions, and drafted the algorithms. The process initially addressed strategies of treatment and then tactics to implement the strategies. RESULTS: Consensually agreed-upon algorithms for major depressions (with and without psychosis) and comorbid attention deficit disorders were developed. Treatment strategies emphasized the use of selective serotonin reuptake inhibitors. The algorithm consists of systematic strategies for treatment interventions and recommended tactics for implementation of the strategies, including medication augmentation and medication combinations. Participants recommended prospective evaluation of the algorithms in various public sector settings, and many volunteered as sites for such an evaluation. CONCLUSIONS: Using scientific and clinical experience, consensus-derived algorithms for children and adolescents with MDD can be developed.

Adolescent↗

PubMedDate not supplied

CT reconstruction algorithm selection in the evaluation of solitary pulmonary nodules.

OBJECTIVE: We have observed a significant CT artifact in the evaluation of lung nodules that occurred with the use of high-spatial-frequency reconstruction algorithms. We have seen this lead to a false-positive diagnosis of calcification in a small uncalcified lung nodule. Because of the seriousness of misinterpretation of benign calcification in an uncalcified nodule, we reviewed the various effects of several reconstruction algorithms on different scanners. MATERIALS AND METHODS: Using high-spatial-frequency, smoothing, and intermediate reconstruction algorithms, we studied standardized cylinders in a CT reference phantom and lung nodules in eight patients. Algorithms on four CT scanners were analyzed. RESULTS: We found peripheral edge enhancement artifact on some CT images of phantom cylinders and uncalcified lung nodules. The images with edge enhancement artifact were obtained from two scanners with the use of high-spatial-frequency algorithms (Picker 1200 SX and GE HiSpeed Advantage). CONCLUSION: Use of high-spatial-frequency reconstruction algorithms for the analysis of lung nodules with thin-section CT may lead to an erroneous diagnosis of calcification.

Algorithms↗

PubMed1998

Comparison of professional judgment versus an algorithm for nutrition status classification.

OBJECTIVES: The classification of a patient's nutrition status is important for identifying patients who require nutrition care, for designing effective nutrition interventions, and for measuring severity of illness. The objective of this study was to evaluate the reliability and validity of two variants of the Department of Veterans Affairs' nutrition status classification: professional judgment versus an algorithm. METHODS: The study consisted of two phases, both of which included providing a sample of approximately 60 registered dietitians and 60 clinical dietetic technicians with data on 16 (phase I) and 20 (phase II) patients, to which they assigned nutrition statuses using both professional judgment and the algorithm. Improvements in instructions and training were implemented between the two phases. Interrater reliability of the responses was calculated, and content validity was measured by comparing the staff's responses with those of an expert panel. RESULTS: Reliability improved significantly between phases for both professional judgment and the algorithm. Greater reliability and validity were observed with use of the algorithm, by both dietitians and technicians, during both phases. CONCLUSION: Classification of a patient's nutrition status is important in the delivery of cost-effective health care. The Department of Veterans Affairs' nutrition status classification is a good one for assessing nutrition status quickly and reliably, especially when an algorithm is used. The results underscore the advantages of a classification system based on an algorithm when the system is designed to be used by many different staff across multiple facilities.

Adult↗

PubMed2000

Simplified algorithms for the estimation of 99Tcm-MAG3 clearance.

The aim of this study was to evaluate two formulae allowing the determination of MAG3 clearance by means of a single blood sample, namely Bubeck's formula and Russell's formula. As a first step, a simulation study was performed with the two single-sample algorithms to predict MAG3 clearance as a function of plasma concentration, using various times for blood sampling and various body surface areas. As a second step, a validation study on 47 adult patients with varying renal function allowed a clinical comparison between the reference technique, namely the multiple blood sample technique, and the two simplified techniques. The simplified algorithms were calculated using the fitted value at 44 min. In the simulation study, whatever the time of blood sampling or the level of correction introduced for body surface area, the results obtained by means of Bubeck's algorithm diverged significantly from those of Russell's algorithm, for low clearance values as well as for high clearance values. The curve of the differences between the two methods had a typical boomerang shape. In the clinical study, the difference between Russell's algorithm and the reference method was generally within 20 ml.min-1, with no systematic bias; with Bubeck's algorithm there was a marked underestimation, both in the low and high clearance ranges. We suggest Russell's single-sample method is the method of choice.

Adult↗

PubMed2001

Risk-based versus alternative algorithms for antibiotic prophylaxis among women seeking early suction abortion: a cost-effectiveness simulation.

BACKGROUND: Particularly in resource-poor settings, simple, inexpensive, and cost-effective algorithms are needed to direct antibiotic prophylaxis to prevent sequelae of infections with Chlamydia trachomatis, Neisseria gonorrhoeae, and bacterial vaginosis-associated organisms among women undergoing abortion. GOAL: To assess the prevalence of and risk factors for infections among women seeking abortion in Bali, Indonesia, and to use these data in designing a cost-effective risk-based prophylaxis algorithm. STUDY DESIGN: A cross-sectional analysis and data-based simulation of risk-based and alternative prophylaxis algorithms were performed. RESULTS: The risk-based algorithm would have provided prophylaxis to 70% (95% CI, 53-83%) of women with cervical infection, 64% (95% CI, 54-74%) of those with bacterial vaginosis, and 57% (95% CI, 42-72%) of those with trichomoniasis. For cervical infection, the algorithm was more cost effective than all others evaluated. The cost-effectiveness was acceptable for bacterial vaginosis. CONCLUSIONS: Risk-based algorithms may be cost effective in identifying women likely to benefit from preabortion prophylaxis. Prospective evaluation is needed to validate these findings.

Abortion, Induced↗

PubMed2003

Assessment of the validity of and adherence to sexually transmitted infection algorithms at a female sex worker clinic in Abidjan, Côte d'Ivoire.

BACKGROUND: Algorithms for sexually transmitted infection (STI) case management were designed in a female sex worker (FSW) clinic in Abidjan, Côte d'Ivoire, in 1993. GOAL: The goal was to evaluate the long-term validity of the algorithms for returning clients of the clinic and to assess the adherence of the health workers to their application. STUDY DESIGN: A cross-sectional study was conducted from 1999 to 2000 among FSWs attending as returning clients. RESULTS: The prevalences of genital infections were as follows: Neisseria gonorrhoeae and/or Chlamydia trachomatis, 8.2%; Trichomonas vaginalis, 16.7%; bacterial vaginosis, 62.3%; and Candida albicans, 6.2%. The sensitivity of the algorithms was 20% and the positive predictive value was 14% for cervical infection. The proportion of cases for which all steps of the algorithm were correctly applied was 30%. CONCLUSION: Algorithms for the treatment of STIs in FSWs should be periodically reevaluated and adapted to the changing population. To maintain healthcare workers' adherence to the algorithms, supervision should be ongoing and reinforced.

Adolescent↗

PubMed2001

Validation of a new algorithm for the BPM-100 electronic oscillometric office blood pressure monitor.

BACKGROUND: To test the accuracy of a new algorithm for the BPM-100, an automated oscillometric blood pressure (BP) monitor, using stored data from an independently conducted validation trial comparing the BPM-100(Beta) with a mercury sphygmomanometer. DESIGN: Raw pulse wave and cuff pressure data were stored electronically using embedded software in the BPM-100(Beta), during the validation trial. The 391 sets of measurements were separated objectively into two subsets. A subset of 136 measurements was used to develop a new algorithm to enhance the accuracy of the device when reading higher systolic pressures. The larger subset of 255 measurements (three readings for 85 subjects) was used as test data to validate the accuracy of the new algorithm. METHODS: Differences between the new algorithm BPM-100 and the reference (mean of two observers) were determined and expressed as the mean difference +/- SD, plus the percentage of measurements within 5, 10, and 15 mmHg. RESULTS: The mean difference between the BPM-100 and reference systolic BP was -0.16 +/- 5.13 mmHg, with 73.7% < or = 5 mmHg, 94.9% < or = 10 mmHg and 98.8% < or = 15 mmHg. The mean difference between the BPM-100 and reference diastolic BP was -1.41 +/- 4.67 mmHg, with 78.4% < or = 5 mmHg, 92.5% < or = 10 mmHg, and 99.2% < or = 15 mmHg. These data improve upon that of the BPM-100(Beta) and pass the AAMI standard, and 'A' grade BHS protocol. CONCLUSION: This study illustrates a new method for developing and testing a change in an algorithm for an oscillometric BP monitor utilizing collected and stored electronic data and demonstrates that the new algorithm meets the AAMI standard and BHS protocol.

Adolescent↗

PubMed2000

Evaluation of an algorithm for treatment of status epilepticus in adult patients undergoing video/EEG monitoring.

Convulsive or generalized tonic clonic status epilepticus (SE) is a neurological emergency that can lead to transient or permanent brain damage or even death. An algorithm was designed to aid nursing and medical staff members in decision making about the type of SE and pharmacological intervention needed to stop prolonged or repetitive seizures. Fifteen registered nurses at a northern New England medical center's epilepsy unit participated in educational sessions on classification of seizures and status epilepticus prior to use of the algorithm. A pretest-posttest design with an investigator-developed tool was used to measure SE knowledge before and after educational intervention. There was a significant improvement in scores on the posttest of the classification of status epilepticus (Z = -2.93, p = .003). Twenty-nine medical records of patients who had experienced SE between February 1992 and December 1997 were reviewed. Nineteen patients experienced SE before the algorithm was implemented, and 10 patients experienced SE after the algorithm was implemented. A total of 16 patients experienced generalized convulsive SE with 12 episodes occurring before and 4 episodes after algorithm implementation. The mean time taken to stop the episode of SE after pharmacologic treatment began was compared in both groups using a t-test. The mean difference between the groups was 235 minutes (t = 2.57, p = .026). The findings of this project demonstrate that combining a treatment algorithm with education of staff members on its use has benefits in the practice setting of an inpatient comprehensive epilepsy program. Episodes of SE are more accurately classified and successful treatment of the episodes occurs earlier.

Adolescent↗