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PubMed1999

Patients with newly diagnosed carcinoma of the breast: validation of a claim-based identification algorithm.

The objectives of this study were to validate a claims-based algorithm for identification of patients with newly diagnosed carcinoma of the breast and to optimize the algorithm. Claims data from all females aged 21 years or older who enrolled in a large California health maintenance organization during the study period from October 1, 1994 through March 31, 1996 were analyzed. Medical records of the patients identified through the claims-based algorithm were reviewed to determine whether the patients were correctly identified. The initial algorithm had a positive predictive value of 84% which was similar to the previous study. The percentages of correct identification significantly increased with the patient's age at diagnosis. Other patient demographic characteristics and facility characteristics were not related to the accuracy of the identification. Using a classification tree procedure and additional information from the false-positive cases, the initial algorithm was modified for improvement. The best-modified algorithm had a positive predictive value of 92% while only 0.5% (4/837) of the true-positive cases were excluded. The results once again demonstrated that patients with newly diagnosed carcinomas of the breast can be identified using claims data. These databases provide an efficient and effective tool for performing health services studies on large patient populations.

Adult↗

PubMed1998

Multiresolution texture based adaptive clustering algorithm for breast lesion segmentation.

OBJECTIVE: A specific algorithm is presented for the automatic extraction of breast tumors in ultrasonic imaging. METHOD: The algorithm involves two-dimensional adaptive K-means clustering of the gray scale and textural feature images. The segmentation problem is formulated as a maximum a posteriori (MAP) estimation problem. The MAP estimation is achieved using Besag's iterated conditional modes algorithm for the minimization of an energy function. This function has three components: the first constrains the region to be close to the data; the second imposes spatial continuity; and the third takes into consideration the texture of the various regions. A multiresolution implementation of the algorithm is performed using a waveless basis. RESULTS: Experiments were carried out on synthetic images and on in vivo breast ultrasound images. Various parameters involved in the algorithm are discussed to evaluate the robustness and accuracy of the segmentation method. CONCLUSION: Including textural features in the segmentation of ultrasonic data improves the robustness of the algorithm and makes the segmentation result less parameter dependent.

Adenocarcinoma↗

PubMed2003

Electrical impedance tomography of human brain function using reconstruction algorithms based on the finite element method.

Electrical impedance tomography (EIT) is a recently developed technique which enables the internal conductivity of an object to be imaged using rings of external electrodes. In a recent study, EIT during cortical evoked responses showed encouraging changes in the raw impedance measurements, but reconstructed images were noisy. A simplified reconstruction algorithm was used which modelled the head as a homogeneous sphere. In the current study, the development and validation of an improved reconstruction algorithm are described in which realistic geometry and conductivity distributions have been incorporated using the finite element method. Data from computer simulations and spherical or head-shaped saline-filled tank phantoms, in which the skull was represented by a concentric shell of plaster of Paris or a real human skull, have been reconstructed into images. There were significant improvements in image quality as a result of the incorporation of accurate geometry and extracerebral layers in the reconstruction algorithm. Image quality, assessed by blinded subjective expert observers, also improved significantly when data from the previous evoked response study were reanalysed with the new algorithm. In preliminary images collected during epileptic seizures, the new algorithm generated EIT conductivity changes which were consistent with the electrographic ictal activity. Incorporation of realistic geometry and conductivity into the reconstruction algorithm significantly improves the quality of EIT images and lends encouragement to the belief that EIT may provide a low-cost, portable functional neuroimaging system in the foreseeable future.

Adult↗

PubMed2002

Spike detection: a review and comparison of algorithms.

For algorithm developers, this review details recent approaches to the problem, compares the accuracy of various algorithms, identifies common testing issues and proposes some solutions. For the algorithm user, e.g. electroencephalograph (EEG) technician or neurologist, this review provides an estimate of algorithm accuracy and comparison to that of human experts. Manuscripts dated from 1975 are reviewed. Progress since Frost's 1985 review of the state of the art is discussed. Twenty-five manuscripts are reviewed. Many novel methods have been proposed including neural networks and high-resolution frequency methods. Algorithm accuracy is less than that of experts, but the accuracy of experts is probably less than what is commonly believed. Larger record sets will be required for expert-level detection algorithms.

Action Potentials↗

PubMed2003

The EIM algorithm in the joint segregation analysis of quantitative traits.

In this article, a new algorithm for obtaining the maximum likelihood estimators (MLEs) of parameters in the joint segregation analysis (JSA) of multiple generations of P1, F1, P2, F2 and F2:3 (MG5) for quantitative traits was set up. Firstly, owing to the fact that the component variance of the heterogeneous genotype in F2:3 included both the first-order genetic parameters (denoted by the means of distributions) and the second-order parameters, a simple closed form for the MLEs of the means of component distributions did not exist while the expectation and maximization (EM) algorithm was used. To simplify the estimation of parameters, the first partial derivative of the above variance on the mean in the sample log-likelihood function was omitted. However, this would be remedied by the iterated method. Then, variances of component distributions for segregating populations were partitioned into major-gene, polygenic and environmental variances so that the generally iterated formulae for estimating the means as well as polygenic and environmental variances of component distributions in the maximization step (M-step) of the EM algorithm were obtained. Therefore, the EM algorithm for estimating parameters in the JSA model for the MG5 was simplified. This is called the expectation and iterated maximization (EIM) algorithm. Finally, an example of the inheritance of the resistance of soybean to beanfly showed that the results of mixed inheritance analysis in this paper coincided with those in both Wang & Gai (2001) and Wei et al. (1989), so the EIM algorithm was appropriate.

Algorithms↗

PubMed2005

Does provider adherence to a treatment guideline change clinical outcomes for patients with bipolar disorder? Results from the Texas Medication Algorithm Project.

BACKGROUND: Despite increasing adoption of clinical practice guidelines in psychiatry, there is little measurement of provider implementation of these recommendations, and the resulting impact on clinical outcomes. The current study describes one effort to measure these relationships in a cohort of public sector out-patients with bipolar disorder. METHOD: Participants were enrolled in the algorithm intervention of the Texas Medication Algorithm Project (TMAP). Study methods and the adherence scoring algorithm have been described elsewhere. The current paper addresses the relationships between patient characteristics, provider experience with the algorithm, provider adherence, and clinical outcomes. Measurement of provider adherence includes evaluation of visit frequency, medication choice and dosing, and response to patient symptoms. An exploratory composite 'adherence by visit' score was developed for these analyses. RESULTS: A total of 1948 visits from 141 subjects were evaluated, and utilized a two-stage declining effects model. Providers with more experience using the algorithm tended to adhere less to treatment recommendations. Few patient factors significantly impacted provider adherence. Increased adherence to algorithm recommendations was associated with larger decreases in overall psychiatric symptoms and depressive symptoms over time, but did not impact either immediate or long-term reductions in manic symptoms. CONCLUSIONS: Greater provider adherence to treatment guideline recommendations was associated with greater reductions in depressive symptoms and overall psychiatric symptoms over time. Additional research is needed to refine measurement and to further clarify these relationships.

Adolescent↗

PubMed1989

Limited sampling of conformational space by the distance geometry algorithm: implications for structures generated from NMR data.

Calculations with a metric matrix distance geometry algorithm were performed that show that the standard implementation of the algorithm generally samples a very limited region of conformational space. This problem is most severe when only a small amount of distance information is used as input for the algorithm. Control calculations were performed on linear peptides, disulfide-linked peptides, and a double-stranded DNA decamer where only distances defining the covalent structures of the molecules (as well as the hydrogen bonds for the base pairs in the DNA) were included as input. Since the distance geometry algorithm is commonly used to generate structures of biopolymers from distance data obtained from NMR experiments, simulations were performed on the small globular protein basic pancreatic trypsin inhibitor (BPTI) that mimic calculations performed with actual NMR data. The results on BPTI and on the control peptides indicate that the standard implementation of the algorithm has two main problems: first, that it generates extended structures; second, that it has a tendency to consistently produce similar structures instead of sampling all structures consistent with the input distance information. These results also show that use of a simple root-mean-square deviation for evaluating the quality of the structures generated from NMR data may not be generally appropriate. The main sources of these problems are identified, and our results indicate that the problems are not a fundamental property of the distance geometry algorithm but arise from the implementations presently used to generate structures from NMR data. Several possible methods for alleviating these problems are discussed.

Algorithms↗

PubMed2005

Maximal use of minimal libraries through the adaptive substituent reordering algorithm.

This paper describes an adaptive algorithm for interpolation over a library of molecules subjected to synthesis and property assaying. Starting with a coarse sampling of the library compounds, the algorithm finds the optimal substituent orderings on all of the functionalized scaffold sites to allow for accurate property interpolation over all remaining compounds in the full library space. A previous paper introduced the concept of substituent reordering and a smoothness-based criterion to search for optimal orderings (Shenvi, N.; Geremia, J. M.; Rabitz, H. J. Phys. Chem. A 2003, 107, 2066). Here, we propose a data-driven root-mean-squared (RMS) criteria and a combined RMS/smoothness criteria as alternative methods for the discovery of optimal substituent orderings. Error propagation from the property measurements of the sampled compounds is determined to provide confidence intervals on the interpolated molecular property values, and a substituent rescaling technique is introduced to manage poorly designed/sampled libraries. Finally, various factors are explored that can influence the applicability and interpolation quality of the algorithm. An adaptive methodology is proposed to iteratively and efficiently use laboratory experiments to optimize these algorithmic factors, so that the accuracy of property predictions is maximized. The enhanced algorithm is tested on copolymer and transition metal complex libraries, and the results demonstrate the capability of the algorithm to accurately interpolate various properties of both molecular libraries.

Algorithms↗

PubMed2006

Performance evaluation of existing de novo sequencing algorithms.

Two methods have been developed for protein identification from tandem mass spectra: database searching and de novo sequencing. De novo sequencing identifies peptide directly from tandem mass spectra. Among many proposed algorithms, we evaluated the performance of the five de novo sequencing algorithms, AUDENS, Lutefisk, NovoHMM, PepNovo, and PEAKS. Our evaluation methods are based on calculation of relative sequence distance (RSD), algorithm sensitivity, and spectrum quality. We found that de novo sequencing algorithms have different performance in analyzing QSTAR and LCQ mass spectrometer data, but in general, perform better in analyzing QSTAR data than LCQ data. For the QSTAR data, the performance order of the five algorithms is PEAKS > Lutefisk, PepNovo > AUDENS, NovoHMM. The performance of PEAKS, Lutefisk, and PepNovo strongly depends on the spectrum quality and increases with an increase of spectrum quality. However, AUDENS and NovoHMM are not sensitive to the spectrum quality. Compared with other four algorithms, PEAKS has the best sensitivity and also has the best performance in the entire range of spectrum quality. For the LCQ data, the performance order is NovoHMM > PepNovo, PEAKS > Lutefisk > AUDENS. NovoHMM has the best sensitivity, and its performance is the best in the entire range of spectrum quality. But the overall performance of NovoHMM is not significantly different from the performance of PEAKS and PepNovo. AUDENS does not give a good performance in analyzing either QSTAR and LCQ data.

Algorithms↗

PubMed2005

Application of obesity treatment algorithms to Canadian adults.

OBJECTIVE: The purpose of this study was to apply obesity treatment algorithms to a representative sample of Canadians to determine their potential impact on the population. DESIGN: The Canadian Heart Health Surveys (1986-1992) were used to describe the prevalence of adults (18-64 y) that would be eligible for weight loss treatment according to the US NIH algorithm, which uses body mass index (BMI), waist circumference (WC), and the presence of two or more cardiovascular disease (CVD) risk factors. Similar algorithms based on CVD risk factors and a single measure of either BMI or WC alone were also evaluated. RESULTS: Using the NIH algorithm, 24% of Canadians (28% men, 19% women) would be identified for weight loss treatment. Virtually, all subjects received the same treatment recommendations when using BMI and CVD risk factors only, while 22% (23% men, 21% women) would meet the criteria for treatment using WC and CVD risk factors only. CONCLUSIONS: Approximately one in four Canadians would be eligible for weight loss treatment using the NIH obesity treatment algorithm. However, the algorithm may be improved through the incorporation of more sensitive WC thresholds.

Adolescent↗

PubMed2002

Analysis of mode switching algorithms in dual chamber pacemakers.

Dual chamber systems are currently implanted in an increasing number of patients with a pacing indication and paroxysmal atrial tachyarrhythmias (ATAs). To avoid tracking of high atrial rates during ATA while providing AV synchronous pacing during sinus rhythm and AV block, automatic mode switching (MS) to a nontracking mode has been developed. Several concepts of MS algorithms have been introduced differing in sensitivity and specificity of ATA detection, delay between ATA onset and MS, pacing mode during MS, rapidity of MS termination upon detection of sinus rhythm, and special algorithms pertinent to MS. This review classifies and analyzes algorithms that are integrated into MS concepts and outlines considerations on optimal MS performance. Based on simulations and clinical studies, fast MS concepts avoiding high paced ventricular rates seem preferable but require special functions to avoid loss of AV synchrony by inappropriate MS. Similarly, fast return to tracking mode after ATA cessation seems preferable but requires algorithms to prevent mode oscillations. Sudden ventricular rate changes have to be avoided by rate smoothing functions, and an appropriate ventricular rate during nontracking mode has to be provided by rate responsive pacing. Programming of the device includes individual optimization of atrial sensitivity, atrial blanking times, and tachycardia detection rates. In addition, a high signal-to-noise ratio by careful atrial lead implantation, narrowly spaced bipolar atrial leads and a good sensing amplifier, together with special algorithms for atrial sensing adjustment improve the performance of MS algorithms.

Algorithms↗

PubMed2003

A new algorithm for closed-loop stimulation: a feasibility study.

Closed-loop stimulation (CLS) is a physiological system for adaptive rate pacing based on monitoring and processing of the intracardiac impedance. The "standard" CLS algorithm (SCLS) requires continuous ventricular pacing. A new, enhanced CLS algorithm (ECLS) provides rate modulation during sensed and paced ventricular depolarizations. The aim of this study was to validate ECLS and to compare its effectiveness with that of SCLS. Ten patients received Inos2+ CLS pulse generators. SCLS and ECLS were uploaded to the device and evaluated in a randomized, crossover fashion at 30 and 45 days after pacemaker implantation. At each follow-up visit, ambulatory and posture tests were performed. Heart rate (HR) during daily activity was evaluated based on 24-hour Holter recordings. During all phases of the ambulatory test, both algorithms provided physiologically appropriate rates in all patients. The proportion of sensed ventricular events was significantly higher in ECLS (93.9%) than in SCLS (0.7%). The proportion of paced ventricular events during 24 hours was substantially lower with ECLS (25.7%) than with SCLS (98.4%). Postural changes did not influence HR with either algorithm. The Holter recordings indicated prompt, safe, and effective rate modulation appropriate to patients activity. In conclusion, analysis of these clinical data demonstrated the safety and effectiveness of the ECLS algorithm. Moreover, with this algorithm the ventricle is paced only when required, which may be expected to retard battery depletion and retain the natural ventricular activation pattern whenever possible.

Aged↗

PubMed2002

Performance reassessment of a real-time seizure-detection algorithm on long ECoG series.

PURPOSE: Automated seizure detection and blockage requires highly sensitive and specific algorithms. This study reassessed the performance of an algorithm by using a more extensive database than that of a previous study and its suitability for safety/efficacy closed-loop studies to block seizures in humans. METHODS: Up to eight electrocorticography (EcoG) channels from 15 subjects were analyzed off-line. Visual and computerized analyses of the data were performed by different (blinded) investigators. Independent visual analysis also was performed for clinical seizures and for detections identified only by the algorithm. The following were computed: FP rate, number of FNs, latency to automated detection, warning rate for clinical onset and warning times, seizure duration/intensity, and interrater agreement. Adaptations to improve performance were performed when indicated. RESULTS: Fourteen subjects met inclusion criteria. Generic algorithm "relative sensitivity" for clinical seizures was 100%; two undetected subclinical seizures and two unclassified seizures were captured after adaptation. FPs/day were zero in seven and fewer than one in an additional three subjects. Adaptations for four subjects with greater than 1 FP/day (7.7-66.6/day) reduced the rate to 0 in one subject and to fewer than five FP/day (1.7-4.2/day) in the remainder. Generic latency to automated detection was <5 s in eight of 13 subjects, and in 12 of 13 after adaptation. Detections provided warning of clinical onset in three of four subjects in whom it always followed electrographic onset, and in four of four after adaptation. Interrater agreement was low for FPs and EDs. CONCLUSIONS: The generic algorithm demonstrated high sensitivity, specificity, and speed, characteristics further enhanced by adaptation. This algorithm is well suited for seizure detection/warning and use in safety/efficacy closed-loop therapy studies.

Adolescent↗

PubMed2002

Recognising vascular causes of leg complaints in endurance athletes. Part 1: validation of a decision algorithm.

Flow limitations in the iliac arteries of endurance athletes during exercise were previously ascribed solely to intravascular lesions. We postulate that functional kinking of the arteries can also result in flow limitations. However, the diagnostic tools in routine practice are not effective in diagnosing such flow limitations in a substantial proportion of athletes, mainly because these diagnostic tools do not measure in the provocative situations. Ninety-two symptomatic legs in 80 endurance athletes were examined with newly developed, sports-specific vascular tests. Thirty-five asymptomatic cyclists matched for working capacity served as the control subjects. Legs were classified as vascular or non-vascular following a decision algorithm, based upon the results of these diagnostic tests, excluding orthopaedic causes by the effects of specific treatment. Independently of this clinical classification, an alternative method was applied to find stable characteristics in the total patient group using factor analysis. This characterisation was based on scores on 14 test variables deriving from diagnostic tests that were not used in the decision algorithm, thus avoiding dependency between the clinical categorisation and the statistical categorisation. The hypothesis was that these characteristics were sufficiently sensitive to classify patients with vascular and non-vascular complaints. If so, these characteristics should correspond with the one derived from the decision algorithm. Following the decision algorithm, 58 legs (63%) were classified as vascular, 29 (32%) as non-vascular and 5 (5%) as inconclusive. The latter were considered non-vascular. In a substantial proportion of the vascular patients, kinking of the iliac arteries was identified as the major cause of flow limitation. The characteristics derived from factor analysis proved to classify 87% in agreement with the decision algorithm (kappa 0.56). The agreement is sufficient for validation of the clinical classification. The algorithm can therefore be applied in clinical situations to diagnose endurance athletes with flow limitations due to both intravascular lesions and kinking of the arteries.

Adult↗

PubMed2003

Algorithms for optimizing the treatment of depression: making the right decision at the right time.

Medication algorithms for the treatment of depression are designed to optimize both treatment implementation and the appropriateness of treatment strategies. Thus, they are essential tools for treating and avoiding refractory depression. Treatment algorithms are explicit treatment protocols that provide specific therapeutic pathways and decision-making tools at critical decision points throughout the treatment process. The present article provides an overview of major projects of algorithm research in the field of antidepressant therapy. The Berlin Algorithm Project and the Texas Medication Algorithm Project (TMAP) compare algorithm-guided treatments with treatment as usual. The Sequenced Treatment Alternatives to Relieve Depression Project (STAR*D) compares different treatment strategies in treatment-resistant patients.

Algorithms↗

PubMed2005

[Emergency room management of multiple injured patients. A multislice computed tomography orientated treatment algorithm].

INTRODUCTION: In the treatment of the seriously injured patient, time is crucial. Clarke et al. showed that in the hypotensive patient with blunt abdominal trauma and bleeding a delay in the surgical treatment over 90 min increases mortality of 1 % every 3 minutes. So called trauma algorithms are used as systematic approach to the seriously injured patient that can be easily reviewed and practiced. One impact of this algorithm is to shorten time in the emergency room and may improve outcome of the patient. The patient outcome is directly related to the length of time between the injury and the beginning to proper definitive care. OBJECTIVE: Are improvements still necessary and possible in the care of the seriously injured patient? New technical developments like multislice-CT are able to shorten time until definitive care. The practicability of an multislice-CT orientated treatment algorithm was evaluated. METHODS: After integration of an multislice-CT into the emergency room the treatment of the seriously injured patient (ISS >16) was changed. Therefore an algorithm which puts the CT diagnostics in the first minutes of the clinical care was developed. RESULTS: 50 patients were treated following the new algorithm. The time in the emergency room decreased from 87 min to 36 min. CONCLUSION: This algorithm requires a differing from previous surgical standards, but it proved to be timesaving, effective and practicable. It makes the beginning of the definitive care possible within the first 40 min after patient arrival in the emergency room.

Algorithms↗

PubMed1989

A new algorithm for diagnosis of anemia.

Studies of the cognitive processes of diagnosis have shown that use of heuristics (eg, shortcuts, rules of thumb) dominates clinical problem solving. Thus, an algorithmic approach to diagnosis can be particularly useful. Because the sensitivity and specificity of many tests are not known, however, this approach is not perfect. Therefore, algorithms should be taken as a general guide to diagnosis but should not be applied too rigidly. In the past, algorithms for anemia did not apply any principles of decision analysis. The algorithm presented in this article is based on test operating characteristics reported in the literature. Disease is excluded by highly sensitive tests (screening tests) and confirmed by highly specific tests (pathognomonic findings). This algorithm can reduce the need for expensive, complex procedures, including radioisotope studies (eg, chromium 51 red blood cell study, ferrokinetics). It provides a rational and semiquantitative estimation of diagnostic possibilities. Alternate pathways to diagnosis may arise in individual cases. Also, the algorithm is difficult to apply to multifactorial anemias.

Algorithms↗

PubMed2004

Performance of a screening algorithm for chlamydial infection in 2 samples of patients in general practice.

This paper evaluates the performance of an algorithm developed for opportunistic, selective screening of women for chlamydial infection in general practice in Antwerp, Belgium. Its performance was examined in 2 independent sets of patients: A) a cohort of 326 women participating in a pilot screening study, and B) a sample of 25 Chlamydia positive women, identified from the records of a laboratory of clinical microbiology. For group A, positive and negative predictive values were calculated and the accuracy of the algorithm was assessed. For group B, we examined the proportion of patients complying with the algorithm. In group A, the screening algorithm would have detected 73% of the cases in 35.6% of the population. The positive and negative predictive values were 7.7% and 98.4%, respectively. In group B, 84% of patients complied with the algorithm. The screening algorithm worked reasonably well in 2 datasets from a similar population studied 2 y later, but needs further validation.

Adult↗