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PubMed1994

Phosphorescence lifetime analysis with a quadratic programming algorithm for determining quencher distributions in heterogeneous systems.

A new method for analysis of phosphorescence lifetime distributions in heterogeneous systems has been developed. This method is based on decomposition of the data vector to a linearly independent set of exponentials and uses quadratic programming principles for x2 minimization. Solution of the resulting algorithm requires a finite number of calculations (it is not iterative) and is computationally fast and robust. The algorithm has been tested on various simulated decays and for analysis of phosphorescence measurements of experimental systems with descrete distributions of lifetimes. Critical analysis of the effect of signal-to-noise on the resolving capability of the algorithm is presented. This technique is recommended for resolution of the distributions of quencher concentration in heterogeneous samples, of which oxygen distributions in tissue is an important example. Phosphors of practical importance for biological oxygen measurements: Pd-meso-tetra (4-carboxyphenyl) porphyrin (PdTCPP) and Pd-meso-porphyrin (PdMP) have been used to provide experimental test of the algorithm.

Algorithms↗

PubMed1989

Nonparametric comparison of entire ROC curves for computerized ECG left ventricular hypertrophy algorithms using data from the Framingham Heart Study.

A computer program may be capable of several different statements for left ventricular hypertrophy (eg, possible LVH, probable LVH, consistent with LVH), but such statements resulting from discretized levels of sensitivity/specificity would represent only isolated points on a receiver-operating characteristic (ROC) curve, which is a plot of all levels of sensitivity versus specificity. Even if two algorithms use the same discrete scales, their performances may not readily be compared. The authors present a comparison methodology for ROC curves using ROC area as a nonparametric measure of the ability of the algorithm to separate the two populations; the ROC area ranges from 0.5 (no ability) to 1.0 (perfect separation) and is unbiased if the normal versus abnormal populations have no common values for the measurement. The methodology compares the performance of ECG algorithms on the same population of cases by testing for significant differences of ROC areas and incorporating correlation of the algorithms in a nonparametric way. To illustrate this methodology, they use ECG and echocardiographic data from the Framingham Heart Study.

Algorithms↗

PubMed1987

An algorithmic approach to diagnosis of hypoglycemia.

An algorithm has been devised to facilitate the diagnostic approach to the causes of hypoglycemia. This systematic approach enables the physician to reach the final diagnosis in a logical way without subjecting the child to unnecessary and possibly hazardous investigations. The algorithm is based on the following measurements as required by each patient: concentrations of blood glucose, lactate, ketone bodies, and glucose-regulating hormones. These measurements are performed with the patient in the fasting state and after loading tests (glycerol and galactose) as needed. If indicated, an enzymatic test is performed to establish the final diagnosis. Eighteen children aged 1 month to 7 years who had persistent or recurrent hypoglycemia have been examined according to this algorithm. The correct diagnosis was arrived at in 17 patients. The diagnosis was not reached in one neonate who had glucose-6-phosphatase deficiency and initially did not have lactic acidosis; once lactic acidosis developed, his illness fitted perfectly into the algorithm.

Algorithms↗

PubMed1993

Screening and managing abdominal aortic aneurysms at the Ochsner Clinic: suggested algorithm and method of derivation. Department of Surgery and Ochsner Clinic Quality Assurance Committee.

An algorithm for screening and management of abdominal aortic aneurysms was developed at the Ochsner Medical Institutions to address the considerable variation identified in clinical practice. A consensus panel of physicians whose opinions differed regarding the management of abdominal aortic aneurysms was convened to develop the algorithm. Based on a literature review and clinical experience, the panel established criteria to determine how frequently and by which methodologies patients with abdominal aortic aneurysms should be followed and when a referral to a vascular surgeon is appropriate. The algorithm developed by the consensus panel method was used to establish practice guidelines that are flexible enough to address individual patient needs yet structured enough to eliminate inappropriate care. Data are being collected and analyzed in real time to determine whether elements of the algorithm should be revised.

Aftercare↗

PubMed1987

Developing a clinical algorithm for early management of cervical spine injury in child trauma victims.

To define a subset of injured children for whom emergency cervical spine radiography may be unnecessary, we performed a retrospective chart and radiologic review. Two entry methods were used: All injured children, from birth through 16 years, who had received cervical spine radiographs at The Children's Memorial Hospital from September 1983, to September 1984, were included. All patients from birth to 16 years with proven or suspected cases of cervical spine injury who had received cervical spine radiographs and who had been treated at either the Children's Memorial Hospital or the Northwestern University Spine Trauma Unit during period 1974 to 1984 also were included. Each child's chart was reviewed, and 84 clinical variables were recorded. All radiographs were reviewed by a pediatric neuroradiologist. Of 206 children studied, 59 had cervical spine injuries. A clinical algorithm was derived using the following eight variables: neck pain; neck tenderness; limitation of neck mobility; history of trauma to the neck; and abnormalities of reflexes, strength, sensation, or mental status. The following decision rule was selected: Positive findings in any of these eight variables mandates cervical spine radiography. This algorithm correctly identified 58 of 59 children with cervical spine injury, yielding a sensitivity of 98% and specificity of 54%. Cervical spine radiographs could have been avoided in 79 children (38% of the entire sample). This algorithm performed better than did models derived from logistic regression analysis of the same data. Validation trials are required prior to the implementation of this or other clinical decision algorithms in practice.

Accidents↗

PubMed1989

Development of a decision algorithm for a semiautomatic defibrillator.

A decision algorithm was developed for a semiautomatic defibrillator. The function of the algorithm is to evaluate the ECG of a patient and determine whether a defibrillation shock should be delivered. The development process included establishment of defibrillation criteria, creation of ECG databases, algorithm design, development of test protocols, and clinical testing. The result was an algorithm with sensitivity and specificity sufficiently accurate to allow a defibrillation shock to be delivered safely outside the hospital.

Algorithms↗

PubMed1978

Resuscitation algorithm for management of acute emergencies.

Assuming that unrecognized or inadequately corrected hypovolemia results in higher mortality and morbidity rates, we developed a systematic approach to resuscitation that would: 1) identify criteria to aid in the recognition of hypovolemia and ensure the expeditious correction of this defect without interfering with diagnostic workup and management; 2) define criteria to prevent fluid overload which may jeopardize the patient's course, and 3) express these criteria in an explicit, systematic, patient care algorithm, ie, protocol, useful to both the resident and the practicing physician. We are now conducting prospective clinical trials with one service using the algorithm and the others acting as the control group. Preliminary results comparing patient outcomes suggest that the algorithm improves patient care by shortening resuscitation time and results in fewer hospital days, intensive care unit days, febrile days, and days on mechanical ventilation as well as reduced mortality. The algorithm provides a systematic plan to organize patient care so that the most urgently needed procedures are not delayed or overlooked.

Algorithms↗

PubMed1991

New joint prediction algorithm (Q7-JASEP) improves the prediction of protein secondary structure.

The classical problem of secondary structure prediction is approached by a new joint algorithm (Q7-JASEP) that combines the best aspects of six different methods. The algorithm includes the statistical methods of Chou-Fasman, Nagano, and Burgess-Ponnuswamy-Scheraga, the homology method of Nishikawa, the information theory method of Garnier-Osgurthope-Robson, and the artificial neural network approach of Qian-Sejnowski. Steps in the algorithm are (i) optimizing each individual method with respect to its correlation coefficient (Q7) for assigning a structural type from the predictive score of the method, (ii) weighting each method, (iii) combining the scores from different methods, and (iv) comparing the scores for alpha-helix, beta-strand, and coil conformational states to assign the secondary structure at each residue position. The present application to 45 globular proteins demonstrates good predictive power in cross-validation testing (with average correlation coefficients per test protein of Q7, alpha = 0.41, Q7, beta = 0.47, Q7,c = 0.41 for alpha-helix, beta-strand, and coil conformations). By the criterion of correlation coefficient (Q7) for each type of secondary structure, Q7-JASEP performs better than any of the component methods. When all protein classes are included for training and testing (by cross-validation), the results here equal the best in the literature, by the Q7 criterion. More generally, the basic algorithm can be applied to any protein class and to any type of structure/sequence or function/sequence correlation for which multiple predictive methods exist.

Algorithms↗

PubMedDate not supplied

Graph automorphism perception algorithms in computer-enhanced structure elucidation.

The concept of graph symmetry is explained in terms of the vertex automorphism group, which is a subgroup of the complete vertex permutation group. The automorphism group can be deduced from the automorphism partition of graph vertices. An algorithm is described which constructs the automorphism group of a graph from the automorphism vertex partitioning. The algorithm is useful especially for graphs which contain more than one vertex-partition set. Several well-known topological symmetry perception algorithms that yield automorphism partitions are compared. The comparison is favorable to the Shelley-Munk algorithm, developed in the framework of the SESAMI system for computer-enhanced structure elucidation.

Algorithms↗

PubMed1989

An algorithm for the treatment of pain in advanced cancer.

An algorithm is presented that has been developed over the past three years to provide pain relief in advanced cancer. The hospital records of 92 patients were reviewed to evaluate the validity of the algorithm. The algorithm is as follows: the 24 hour oral consumption of opioids was converted to sustained release morphine. If ineffective usually over 360 mg daily the total 24 hour oral dose was divided by 6 to convert to I.V. If this was ineffective, usually over 10 mg/hr of morphine, the intravenous dose was divided by 10 and infused epidurally. Local anesthetic was added for plexus involvement. After four days, the patient was weaned from local anesthetic solution. If sharp pain or pain to movement persisted, 6% phenol in 1 to 2 ml aliquots was injected every 8-12 hours to a total of 5-8 ml. While the conversion from intravenous to epidural morphine was 10:1 that from epidural to intravenous was only 1:3. Intravenous dose converts directly to the subcutaneous. The conversion from intravenous to oral is 1:3. There view showed that the dosages at which the conversions were made varied considerably. The reasons for the wide variation are presented. In summary the algorithm is a good practical guide for treatment of cancer pain.

Adult↗

PubMed1995

An algorithm for predicting tissue: blood partition coefficients of organic chemicals from n-octanol: water partition coefficient data.

The objectives of the present study were (1) to develop an algorithm to predict tissue:blood partition coefficients (PCs) of organic chemicals from n-octanol: water (Ko/w) PC data, and (2) to apply this algorithm to predict the rat tissue:blood PCs of some relatively hydrophilic organics, particularly ketones, alcohols, and acetate esters. The algorithm, developed by modifying a previously published one, involved predicting tissue:blood PCs of chemicals by dividing their partitioning into tissues by the sum of their partitioning into erythrocytes and plasma. The partitioning of a chemical into tissues, erythrocytes, and plasma was expressed as an additive function of its partitioning into neutral lipids, phospholipids, and water contained in them. The muscle, liver, and adipose tissue:blood PCs predicted with the present method were compared with the experimental values obtained from the literature for five ketones, eight alcohols, and eight acetate esters. The predicted muscle:blood and liver:blood PCs for the set of 21 hydrophilic organics were within a factor of 1.01 and 0.99 (on an average), respectively, of the experimental values. However, the predicted adipose tissue:blood PCs of the hydrophilic organics were greater than the experimental values by a factor of 4.13, which improved when vegetable oil:saline (Ko/s) PCs were used instead of Ko/w PCs (factor of 1.51). Overall, the use of the present algorithm should enable the prediction of tissue:blood PCs for organic chemicals for which Ko/w or Ko/s data are available.

Acetates↗

PubMed1988

The enhancement of radiographic images from a multiwire camera using a maximum entropy algorithm.

The multiwire camera (MWC) produces high speed, quantitative autoradiography of radiolabelled substances in two-dimensional systems. While greatly superior to film-based systems in respect of speed and quantitativity the MWC has significantly poorer spatial resolution (particularly for high energy beta-emitting radiolabels) and the performance is ultimately limited by the noise induced in the images by Poisson statistics and counter background. Processing the MWC images with a maximum entropy algorithm significantly improves the performance of the system in these respects. The algorithm has been tested using one-dimensional data taken from images of known tritium, 14C and 125I distributions. Processed images are visually more acceptable with improved quantitative accuracy and spatial resolution. Quantitative accuracy, calculated as the root mean square deviation between an image and the known sample activities, is 10-40% lower for processed images compared with original camera images. Spatial resolution, calculated from slopes in the images representing edges of activity in the sources, is improved by 20-40% for the processed images. The algorithm is used to improve a two-dimensional image from a biological study. The source distribution consisted of a set of circular dots of varying activity. The dots with lowest activity were barely discernible in the raw MWC image but are clearly resolved after processing. The algorithm used is simple and effective and executes acceptably quickly on a personal computer. It should prove useful in any context where the imaging performance of a system is limited by Poisson statistics.

Algorithms↗

PubMed1989

A two-dimensional pencil-beam algorithm for calculation of arc electron dose distributions.

A two-dimensional pencil-beam algorithm is presented for the calculation of arc electron dose distributions in any plane that is perpendicular to the axis of rotation. The dose distributions are calculated by modelling the arced beam as a single broad beam defined by the irradiated surface of the patient. The algorithm is two-dimensional in that the anatomical cross section of the patient and the skin collimators are assumed identical in parallel planes outside the plane of calculation. The broad beam is modelled as a collection of strip beams, each strip beam being characterised by its planar fluence, mean projected angular direction and a root-mean-square spread about the mean direction. Using these parameters, the dose distribution is calculated using pencil-beam theory. Examples of strip-beam parameters and resulting dose distributions for patient geometries are presented. Features of the algorithm, which include (1) incorporation of pencil-beam theory for the calculation of dose in heterogeneous tissue, (2) run times of only about twice that of comparable-sized fixed electron fields and (3) the input requirement of only a single depth dose and four off-axis dose profiles of measured data, make the algorithm practical for clinical use.

Algorithms↗

PubMed1991

Effect of dimensionality of heterogeneity corrections on the implementation of a three-dimensional electron pencil-beam algorithm.

Electron beam dose distributions were calculated on a three-dimensional grid using three pencil-beam algorithms, each taking into account irregularities in field shape. The algorithms differ in that patient anatomy in either one, two, or three dimensions is used in the calculation of dose to a point. Algorithms were optimized for speed by such techniques as precalculation and storage of several quantities, reordering of pencil-beam and grid-point loops, selection of cut-off values for some calculated quantities, and invoking error function symmetries. Execution times for optimized versions of each of the algorithms as implemented on a three-dimensional treatment planning system were comparable for both the one- and two-dimensional heterogeneity correction requires an additional calculational loop over fan lines. Execution times for the three-dimensional heterogeneity correction were approximately a factor of four longer than those for the two-dimensional correction. For certain geometries, three-dimensional heterogeneity corrections were necessary to calculate dose distributions accurately, in spite of the additional cost in calculation times.

Algorithms↗

PubMed1992

An algorithm for maximizing the probability of complication-free tumour control in radiation therapy.

New radiobiological models are used to describe tumour and normal tissue reactions and to account for their dependence on the irradiated volume and inhomogeneities of the delivered dose distribution and cell sensitivity. The probability of accomplishing complication-free tumour control is maximized by an iterative algorithm. The algorithm is demonstrated by applying it to a one-dimensional (1D) tumour model but also to a more clinically relevant 2D case. The new algorithm is n-dimensional so it could simultaneously optimize the dose delivery in a 3D volume and in principle also select the ideal beam orientations, beam modalities (photons, electrons, neutrons, etc) and optimal spectral distributions of the corresponding modalities. To make calculation time reasonable, 2D-3D problems are most practical, and suitable beam orientations are preselected by the choice of irradiation kernel. The energy deposition kernel should therefore be selected in order to avoid irradiation through organs at risk. Clinically established dose response parameters for the tissues of interest are used to make the optimization as relevant as possible to the clinical problems at hand. The algorithm can be used even with a poorly selected kernel because it will always, as far as possible, avoid irradiating organs at risk. The generated dose distribution will be optimal with respect to the spatial distribution and assumed radiobiological properties of the tumour and normal tissues at risk for the kernel chosen. More specifically the probability of achieving tumour control without fatal complications in normal tissues is maximized. In the clinical examples a reduced tumour dose is seen at the border to sensitive organs at risk, but instead an increased dose just inside the tumour border is generated. The increased tumour dose has the effect that the dose fall-off is as steep as possible at the border to organs at risk.

Algorithms↗

PubMed1994

A filtered backprojection algorithm for pinhole SPECT with a displaced centre of rotation.

In this paper the importance of correcting a small centre-of-rotation displacement (approximately 1 mm) in single-photon-emission computed tomography (SPECT) using high-resolution pinhole collimation is demonstrated. A filtered backprojection (FBP) algorithm is derived for a pinhole geometry that has a displaced centre-of-rotation. The centre-of-rotation displacement, or mechanical shift (MS), is the displacement of the midplane of the pinhole collimator from the rotation centre. It is characterized by two orthogonal components: the shift eta of the midplane of the pinhole collimator along the direction of the axis of rotation, and the distance tau between the midline of the pinhole collimator and the axis of rotation. This algorithm is fast and corrects the centre-of-rotation displacement directly by incorporating this displacement into the algorithm. This new algorithm is evaluated using both a three-line source and a micro-SPECT cold rod phantom. The results demonstrate that the pinhole FBP with mechanical shift correction is able to correct the 'doughnut'-type artifacts caused by the mechanical shift and restore the expected system resolution.

Algorithms↗

PubMed1994

Data bank homology search algorithm with linear computation complexity.

A new algorithm for data bank homology search is proposed. The principal advantages of the new algorithm are: (i) linear computation complexity; (ii) low memory requirements; and (iii) high sensitivity to the presence of local region homology. The algorithm first calculates indicative matrices of k-tuple 'realization' in the query sequence and then searches for an appropriate number of matching k-tuples within a narrow range in database sequences. It does not require k-tuple coordinates tabulation and in-memory placement for database sequences. The algorithm is implemented in a program for execution on PC-compatible computers and tested on PIR and GenBank databases with good results. A few modifications designed to improve the selectivity are also discussed. As an application example, the search for homology of the mouse homeotic protein HOX 3.1 is given.

Algorithms↗

PubMed1986

DNAMAT: an efficient graphic matrix sequence homology algorithm and its application to structural analysis.

We present a fast algorithm to produce a graphic matrix representation of sequence homology. The algorithm is based on lexicographical ordering of fragments. It preserves most of the options of a simple naive algorithm with a significant increase in speed. This algorithm was the bais for a program, called DNAMAT, that has been extensively tested during the last three years at the Weizmann Institute of Science and has proven to be very useful. In addition we suggest a way to extend our approach to analyse a series of related DNA or RNA sequences, in order to determine certain common structural features. The analysis is done by 'summing' a set of dot-matrices to produce an overall matrix that displays structural elements common to most of the sequences. We give an example of this procedure by analysing tRNA sequences.

Algorithms↗