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PubMed2003

An algorithm for three-way data analysis that alternatively minimizes coupled vector (COV) resolution error and PARAFAC error.

A novel algorithm, alternatively minimizing coupled vector (COV) resolution error and PARAFAC error algorithm, is proposed in this paper. This algorithm can overcome the problem of slow convergence and is insensitive to the estimation of component number, such problems are unavoidable while using the traditional parallel factors analysis (PARAFAC) algorithm. In other words, this algorithm is capable of improving the computing speed and providing accurate resolutions provided that the number of factors used in the computation is no less than that of the actual underlying ones. The characteristic performances were demonstrated with a novel fluorescence data array.

Journal Article↗

PubMed1983

Accuracy of deconvolution algorithms assessed by simulation studies: concise communication.

Deconvolution has been used to correct first-pass radionuclide angiocardiography for the time course of the delivery of radiopharmaceutical into the cardiopulmonary system. The extreme sensitivity of deconvolution to random errors in the data may account for some of the problems encountered in practice. We implemented several deconvolution algorithms that were suitable for use with the unimodal and multimodal superior vena caval and pulmonary curves found in left-to-right shunt quantification. The sensitivity of the algorithms to random errors was assessed using mathematical test problems degraded with pseudorandom noise. An algorithm that constrained the deconvolved pulmonary curve to be expressable as the non-negative sum of a set of lagged normal curves was found to have the smallest maximum error on the curves tested. Comparison with results from a previously published test problem indicated an error reduction of greater than 50% over previously used algorithms. Use of this algorithm may permit more accurate deconvolution of pulmonary time-activity curves and thereby improve shunt quantification.

Heart↗

PubMed1980

[Differential diagnosis of endometrial diseases by scrapings based on setting up an algorithm of the histological study].

In order to facilitate the diagnostic analysis of histologic changes in biopsies of endometrial diseases, it is suggested that the use should be made of the first order algorithm developed on the basis of the experience gained so far. This algorithm excludes the oversight of visible changes and predetermines the subsequent activities of an assistant. During differential diagnosis of endometrial diseases the staged synthesis is effected by making up the second order algorithm from the first order algorithmic elements. The suggested diagnostic procedure developed on the basis of algorithmization and probable concepts is time-saving and creats conditions for more successful verification of the pathological process.

Biopsy↗

PubMed1981

Evaluating antimicrobial use with an algorithm.

An algorithm (integrated series of screening criteria) for evaluating antimicrobial use is described. The algorithm was initially designed during a survey of the antimicrobial use for 117 patients. After the survey, the criteria in the algorithm were refined by a literature search; 10 criteria in the algorithm were added, six of which concerned the prophylactic use of antimicrobials. Two hospitals used the algorithm and reported that it reduced the number of hours needed to establish final audit criteria.

Anti-Infective Agents↗

PubMed2003

Texas Medication Algorithm Project, phase 3 (TMAP-3): clinical results for patients with a history of mania.

BACKGROUND: The Texas Medication Algorithm Project (TMAP) assessed the clinical and economic impact of algorithm-driven treatment (ALGO) as compared with treatment-as-usual (TAU) in patients served in public mental health centers. This report presents clinical outcomes in patients with a history of mania (BD), including bipolar I and schizoaffective disorder, bipolar type, during 12 months of treatment beginning March 1998 and ending with the final active patient visit in April 2000. METHOD: Patients were diagnosed with bipolar I disorder or schizoaffective disorder, bipolar type, according to DSM-IV criteria. ALGO was comprised of a medication algorithm and manual to guide treatment decisions. Physicians and clinical coordinators received training and expert consultation throughout the project. ALGO also provided a disorder-specific patient and family education package. TAU clinics had no exposure to the medication algorithms. Quarterly outcome evaluations were obtained by independent raters. Hierarchical linear modeling, based on a declining effects model, was used to assess clinical outcome of ALGO versus TAU. RESULTS: ALGO and TAU patients showed significant initial decreases in symptoms (p =.03 and p <.001, respectively) measured by the 24-item Brief Psychiatric Rating Scale (BPRS-24) at the 3-month assessment interval, with significantly greater effects for the ALGO group. Limited catch-up by TAU was observed over the remaining 3 quarters. Differences were also observed in measures of mania and psychosis but not in depression, side-effect burden, or functioning. CONCLUSION: For patients with a history of mania, relative to TAU, the ALGO intervention package was associated with greater initial and sustained improvement on the primary clinical outcome measure, the BPRS-24, and the secondary outcome measure, the Clinician-Administered Rating Scale for Mania (CARS-M). Further research is planned to clarify which elements of the ALGO package contributed to this between-group difference.

Adolescent↗

PubMedDate not supplied

Nasal tip overprojection: algorithm of surgical deprojection techniques and introduction of medial crural overlay.

OBJECTIVES: To discuss the evaluation of the overprojected nasal tip, present an algorithm of various treatments for deprojection of the nasal tip, and introduce our experience of greater than 10 years with medial crural overlay. DESIGN: Retrospective review of a large sequential series of patients undergoing rhinoplasty who were treated with various deprojection techniques by the senior author (R.W.H.K.) from January 1, 1991, through December 31, 2002. Patients underwent preoperative and postoperative evaluation during this period on a regular basis to record the effects of various approaches on nasal projection, rotation, need for revision, and patient satisfaction. Medical records and photographic documentation were reviewed. The occurrence of postoperative complications and secondary revision procedures were noted. We used the information obtained to evaluate and expound on an algorithmic paradigm for treatment of nasal tip overprojection. RESULTS: From 1991 to 2002, 130 cases used 1 or more of the senior author's preferred methods for deprojection. Ten patients were excluded owing to the primarily reconstructive nature of their surgery. Of the remaining 120 patients, 3 (2.5%) underwent minor revision of dorsal irregularities and another 5 (4.2%) underwent tip revision. Only 9 patients (7.5%) required concomitant alar base reduction. One patient had postoperative epistaxis, and there were no cases of postoperative functional complaints. CONCLUSIONS: Deprojection of the overprojected nasal tip can be accomplished successfully with a handful of properly used techniques. Once proper analysis has been accomplished, an algorithm can be used to help simplify the approach to deprojection. These techniques offer sound functional approaches to effect deprojection while controlling the level of rotation. The beneficial effects observed using this algorithm are attested to by the minimal number of complications, the relatively low number of patients requiring revision, and the overall long-term patient satisfaction with their results.

Algorithms↗

PubMed2005

Accuracy of a pharmacovigilance algorithm in diagnosing drug hypersensitivity reactions.

BACKGROUND: This study was performed to evaluate the diagnostic accuracy of a pharmacovigilance algorithm in patients with 1 or more histories suggestive of drug hypersensitivity. METHODS: We performed a retrospective analysis of a clinic case series. We analyzed patients with suspected clinical reactions of drug hypersensitivity. Patients with severe skin reactions were excluded. Patients with history of drug allergy were subjected to additional testing to validate this history. Following a detailed clinical history, skin tests were performed. If skin tests were not available or validated, drug provocation tests were conducted. Assessment of causality was established by an investigator unaware of drug testing results using a pharmacovigilance algorithm that was then compared with the final diagnosis. RESULTS: A total of 677 consecutive patients with 1001 reactions were analyzed. No score could be given because of the absence of 1 of the criteria required for 204 reactions (20.4%). For 720 reactions (71.9%), a dubious causality assessment score was given. Drug hypersensitivity was confirmed by drug testing in 175 reactions (17.5%) and eliminated in 826 reactions (82.5%). Sensitivity of the algorithm was 10.3% and specificity was 76.9%. Although there were 1.7% false-positive scores, there were no false-negative scores. The logistic regression that was performed to look for independent clinical risk factors linked to the drug hypersensitivity diagnosis found 3 parameters: likely causality assessment score, drug reintroduction in clinical history, and delay between reaction and last drug intake of less than 1 hour. CONCLUSION: A pharmacovigilance algorithm is not accurate for the diagnosis of drug hypersensitivity reactions and cannot replace drug allergy testing.

Adolescent↗

PubMed1991

Comparison of analytic algorithms for detecting glaucomatous visual field loss.

The sensitivity and specificity of alternate analytic strategies for recognizing glaucomatous visual field loss from automated threshold perimetry (C-30-2 test of the Humphrey Field Analyzer) were compared among one eye each of 106 patients with glaucoma and 249 normal subjects. Algorithms included commercially available global indexes and cross-meridional differences (Statpac 1 and Statpac 2), as well as cross-meridional and cluster analyses that were developed independently for natural history studies and clinical trials. The sensitivity of most algorithms was high, except for those that used only diffuse loss as an indicator of abnormality. Specificity was acceptably high for all algorithms. Subjects who failed to meet the manufacturer's standard for reliability had much reduced specificity, but sensitivity was also affected. Algorithms that were based on any of the alternate definitions of localized reduction in retinal sensitivity performed equally well, which suggests that any of these approaches is useful in searching for glaucomatous visual loss as typified by this database. Availability, familiarity, and convenience may govern the selection of any one analytic approach for use in a particular setting.

Algorithms↗

PubMed1999

Improving protein identification from peptide mass fingerprinting through a parameterized multi-level scoring algorithm and an optimized peak detection.

We have developed a new algorithm to identify proteins by means of peptide mass fingerprinting. Starting from the matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) spectra and environmental data such as species, isoelectric point and molecular weight, as well as chemical modifications or number of missed cleavages of a protein, the program performs a fully automated identification of the protein. The first step is a peak detection algorithm, which allows precise and fast determination of peptide masses, even if the peaks are of low intensity or they overlap. In the second step the masses and environmental data are used by the identification algorithm to search in protein sequence databases (SWISS-PROT and/or TrEMBL) for protein entries that match the input data. Consequently, a list of candidate proteins is selected from the database, and a score calculation provides a ranking according to the quality of the match. To define the most discriminating scoring calculation we analyzed the respective role of each parameter in two directions. The first one is based on filtering and exploratory effects, while the second direction focuses on the levels where the parameters intervene in the identification process. Thus, according to our analysis, all input parameters contribute to the score, however with different weights. Since it is difficult to estimate the weights in advance, they have been computed with a generic algorithm, using a training set of 91 protein spectra with their environmental data. We tested the resulting scoring calculation on a test set of ten proteins and compared the identification results with those of other peptide mass fingerprinting programs.

Algorithms↗

PubMed2001

Generalized-ensemble algorithms for molecular simulations of biopolymers.

In complex systems with many degrees of freedom such as peptides and proteins, there exists a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review uses of the generalized-ensemble algorithms in biomolecular systems. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present three new generalized-ensemble algorithms that combine the merits of the above methods. The effectiveness of the methods for molecular simulations in the protein folding problem is tested with short peptide systems.

Algorithms↗

PubMed2002

Confocal DNA cytometry: a contour-based segmentation algorithm for automated three-dimensional image segmentation.

BACKGROUND: Confocal laser scanning microscopy (CLSM) presents the opportunity to perform three-dimensional (3D) DNA content measurements on intact cells in thick histological sections. So far, these measurements have been performed manually, which is quite time-consuming. METHODS: In this study, an intuitive contour-based segmentation algorithm for automatic 3D CLSM image cytometry of nuclei in thick histological sections is presented. To evaluate the segmentation algorithm, we measured the DNA content and volume of human liver and breast cancer nuclei in 3D CLSM images. RESULTS: A high percentage of nuclei could be segmented fully automatically (e.g., human liver, 92%). Comparison with (time-consuming) interactive measurements on the same CLSM images showed that the results were well correlated (liver, r = 1.00; breast, r = 0.92). CONCLUSIONS: Automatic 3D CLSM image cytometry enables measurement of volume and DNA content of large numbers of nuclei in thick histological sections within an acceptable time. This makes large-scale studies feasible, whereby the advantages of CLSM can be exploited fully. The intuitive modular segmentation algorithm presented in this study detects and separates overlapping objects, also in two-dimensional (2D) space. Therefore, this algorithm may also be suitable for other applications.

Algorithms↗

PubMed2001

A fast impingement detection algorithm for computer-aided orthopedic surgery.

OBJECTIVE: For simulation of computer-aided orthopedic interventions, the detection of impingement between parts of the patient's anatomy and/or implants is often of key importance. The impingement (collision) detection methods used in the existing literature seem to be unsuitable for two reasons. First, a polyhedral approximation of an anatomical model is not appropriate because medical images are quite irregular and are geometrically complex. Second, geometric and temporal coherences are not always available, because only the final results may be of interest. This article describes the development of a fast and accurate impingement detection algorithm for medical applications. MATERIALS AND METHODS: The presented algorithm takes implicit object models from reconstructions of anatomical CT data that represent complicated anatomical structures. To speed up the detection procedure, a lookup table and a linear transform are used so that searching for impingement between any two objects becomes a problem of calculating spatial indices and checking the lookup table. RESULTS: For any given transformation, the algorithm could perform impingement detection of two objects within 0.1 s on a 167 MHz Sun UltraSPARC1 workstation. Experimental results concerning accuracy, reliability and speed are given for a phantom and for a patient's data set. CONCLUSIONS: This algorithm provides a general-purpose impingement detection method in the sense that objects can be of any shape, and it can be extended to any number of objects in the scene.

Algorithms↗

PubMed2004

Algorithms based on prostate-specific antigen (PSA), free PSA, digital rectal examination and prostate volume reduce false-positive PSA results in prostate cancer screening.

Our objective was to determine whether multivariate algorithms based on serum total PSA, the free proportion of PSA, age, digital rectal examination and prostate volume can reduce the rate of false-positive PSA results in prostate cancer screening more effectively than the proportion of free PSA alone at 95% sensitivity. A total of 1,775 consecutive 55- to 67-year-old men with a serum PSA of 4-10 microg/l in the European Randomized Study of Screening for Prostate Cancer were included. To predict the presence of cancer, multivariate algorithms were constructed using logistic regression (LR) and a multilayer perceptron neural network with Bayesian regularization (BR-MLP). A prospective setting was simulated by dividing the data set chronologically into one set for training and validation (67%, n = 1,183) and one test set (33%, n = 592). The diagnostic models were calibrated using the training set to obtain 95% sensitivity. When applied to the test set, the LR model, the BR-MLP model and the proportion of free PSA reached 92%, 87% and 94% sensitivity and reduced 29%, 36% and 22% of the false-positive PSA results, respectively. At a fixed sensitivity of 95% in the test set, the LR model eliminated more false-positive PSA results (22%) than the proportion of free PSA alone (17%) (p < 0.001), whereas the BR-MLP model did not (19%) (p = 0.178). The area under the ROC curve was larger for the LR model (0.764, p = 0.030) and the BR-MLP model (0.760, p = 0.049) than for the proportion of free PSA (0.718). A multivariate algorithm can be used to reduce unnecessary prostate biopsies in screening more effectively than the proportion of free PSA alone, but the algorithms will require updating when clinical practice develops with time.

Aged↗

PubMed2003

Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms.

Multiple time step (MTS) algorithms present an effective integration approach to reduce the computational cost of dynamics simulations. By using force splitting to allow larger time steps for the more slowly varying force components, computational savings can be realized. The Particle-Mesh-Ewald (PME) method has been independently devised to provide an effective and efficient treatment of the long-range electrostatics interactions. Here we examine the performance of a combined MTS/PME algorithm previously developed for AMBER on a large polymerase beta/DNA complex containing 40,673 atoms. Our goal is to carefully combine the robust features of the Langevin/MTS (LN) methodology implemented in CHARMM-which uses position rather than velocity Verlet with stochasticity to make possible outer time steps of 150 fs-with the PME formulation. The developed MTS/PME integrator removes fast terms from the reciprocal-space Ewald component by using switch functions. We analyze the advantages and limitations of the resulting scheme by comparing performance to the single time step leapfrog Verlet integrator currently used in AMBER by evaluating different time-step protocols using three assessors for accuracy, speedup, and stability, all applied to long (i.e., nanosecond) simulations to ensure proper energy conservation. We also examine the performance of the algorithm on a parallel, distributed shared-memory computer (SGI Origin 2000 with 8 300-MHz R12000 processors). Good energy conservation and stability behavior can be demonstrated, for Newtonian protocols with outer time steps of up to 8 fs and Langevin protocols with outer time steps of up to 16 fs. Still, we emphasize the inherent limitations imposed by the incorporation of MTS methods into the PME formulation that may not be widely appreciated. Namely, the limiting factor on the largest outer time-step size, and hence speedup, is an intramolecular cancellation error inherent to PME. This error stems from the excluded-nonbonded correction term contained in the reciprocal-space component. This cancellation error varies in time and introduces artificial frequencies to the governing dynamics motion. Unfortunately, we find that this numerical PME error cannot be easily eliminated by refining the PME parameters (grid resolution and/or order of interpolating polynomial). We suggest that methods other than PME for fast electrostatics may allow users to reap the full advantages from MTS algorithms.

Algorithms↗

PubMed2004

An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots.

Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base-pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base-pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure.

Algorithms↗

PubMed2005

Lattice models of peptide aggregation: evaluation of conformational search algorithms.

We present a series of conformational search calculations on the aggregation of short peptide fragments that form fibrils similar to those seen in many protein mis-folding diseases. The proteins were represented by a face-centered cubic lattice model with the conformational energies calculated using the Miyazawa-Jernigan potential. The searches were performed using algorithms based on the Metropolis Monte Carlo method, including simulated annealing and replica exchange. We also present the results of searches using the tabu search method, an algorithm that has been used for many optimization problems, but has rarely been used in protein conformational searches. The replica exchange algorithm consistently found more stable structures then the other algorithms, and was particularly effective for the octamers and larger systems.

Algorithms↗

PubMed2006

A search algorithm for fixed-composition protein design.

We present a computational protein design algorithm for finding low-energy sequences of fixed amino acid composition. The search algorithms used in protein design typically do not restrict amino acid composition. However, the random energy model of Shakhnovich suggests that the use of fixed-composition sequences may circumvent defects in the modeling of the denatured state. Our algorithm, FC_FASTER, links fixed-composition versions of Monte Carlo and the FASTER algorithm. As proof of principle, FC_FASTER was tested on an experimentally validated, full-sequence design of the beta1 domain of protein G. For the wild-type composition, FC_FASTER found a lower energy sequence than the experimentally validated sequence. Also, for a different composition, FC_FASTER found the hypothetical lowest-energy sequence in 14 out of 32 trials.

Algorithms↗

PubMed2006

Minimum sequence requirements for selective RNA-ligand binding: a molecular mechanics algorithm using molecular dynamics and free-energy techniques.

In vitro evolution techniques allow RNA molecules with unique functions to be developed. However, these techniques do not necessarily identify the simplest RNA structures for performing their functions. Determining the simplest RNA that binds to a particular ligand is currently limited to experimental protocols. Here, we introduce a molecular-mechanics based algorithm employing molecular dynamics simulations and free-energy methods to predict the minimum sequence requirements for selective ligand binding to RNA. The algorithm involves iteratively deleting nucleotides from an experimentally determined structure of an RNA-ligand complex, performing energy minimizations and molecular dynamics on each truncated structure, and assessing which truncations do not prohibit RNA binding to the ligand. The algorithm allows prediction of the effects of sequence modifications on RNA structural stability and ligand-binding energy. We have implemented the algorithm in the AMBER suite of programs, but it could be implemented in any molecular mechanics force field parameterized for nucleic acids. Test cases are presented to show the utility and accuracy of the methodology.

Algorithms↗