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PubMed2003

Sexually transmitted infections among female sex workers in Kupang, Indonesia: searching for a screening algorithm to detect cervical gonococcal and chlamydial infections.

BACKGROUND AND GOAL: Notifications of HIV infection in Indonesia are increasing, but there are few data on other sexually transmitted infections (STIs), especially in the eastern islands of Indonesia. We aimed to measure the prevalence of STIs among female sex workers (FSWs) in Kupang, West Timor, and to develop screening algorithms to detect cervical infections with Neisseria gonorrhoeae and/or Chlamydia trachomatis (NG/CT). STUDY DESIGN: During 6 months in 1999, we recruited all the FSWs at Kupang's only brothel complex and a smaller number of independent FSWs. The women were examined at dedicated clinics and most laboratory tests were performed at provincial laboratories. Algorithms based on the strongest associations of variables with NG/CT were compared with the laboratory diagnoses. RESULTS: We recruited 288 women. The prevalence of N gonorrhoeae infection was 31%, that of C trachomatis infection was 24%, that of Trichomonas vaginalis infection was 5%, and that of syphilis was 13%. No case of HIV infection was detected. Few women had symptoms of STI. The only variables significantly associated with NG/CT after logistic regression analysis were the presence of cervical discharge (either yellow or clear) and a high count of polymorphonuclear leukocytes on gram-stained endocervical smear. Several algorithms to screen for NG/CT achieved high (>80%) sensitivity, but the highest specificity among these was only 50%. CONCLUSIONS: Although several of the generated algorithms may be useful in the absence of simple, accurate, affordable diagnostic tests, the high rates of STIs in this population could justify a more aggressive strategy incorporating periodic presumptive treatment to rapidly reduce prevalence.

Adolescent↗

PubMed2003

Effectiveness of physical therapy for patients with neck pain: an individualized approach using a clinical decision-making algorithm.

OBJECTIVE: The purpose of this study was to determine the effectiveness of an individualized physical therapy intervention in treating neck pain based on a clinical reasoning algorithm. Treatment effectiveness was examined by assessing changes in impairment, physical performance, and disability in response to intervention. DESIGN: One treatment group of 30 patients with neck pain completed physical therapy treatment. The control group of convenience was formed by a cohort group of 27 subjects who also had neck pain but did not receive treatment for various reasons. There were no significant differences between groups in demographic data and the initial test scores of the outcome measures. A quasi-experimental, nonequivalent, pretest-posttest control group design was used. A physical therapist rendered an eclectic intervention to the treatment group based on a clinical decision-making algorithm. Treatment outcome measures included the following five dependent variables: cervical range of motion, numeric pain rating, timed weighted overhead endurance, the supine capital flexion endurance test, and the Patient Specific Functional Scale. Both the treatment and control groups completed the initial and follow-up examinations, with an average duration of 4 wk between tests. RESULTS: Five mixed analyses of variance with follow-up tests showed a significant difference for all outcome measures in the treatment group compared with the control group. After an average 4 wk of physical therapy intervention, patients in the treatment group demonstrated statistically significant increases of cervical range of motion, decrease of pain, increases of physical performance measures, and decreases in the level of disability. The control group showed no differences in all five outcome variables between the initial and follow-up test scores. CONCLUSIONS: This study delineated algorithm-based clinical reasoning strategies for evaluating and treating patients with cervical pain. The algorithm can help clinicians classify patients with cervical pain into clinical patterns and provides pattern-specific guidelines for physical therapy interventions. An organized and specific physical therapy program was effective in improving the status of patients with neck pain.

Adult↗

PubMed2002

Suture algorithm for the broad or bulbous nasal tip.

The history and current status of suture techniques to correct a broad or bulbous nasal tip are reviewed. General principles for suture techniques to control tip shape are discussed; they include leaving an approximately 6-mm-wide lateral crus. The algorithm presented includes four sutures, all of which are not necessary in every case. These sutures include (1) the transdomal suture (to narrow the individual domes), (2) the interdomal suture (to provide symmetry and tip strength and sometimes to narrow the tip complex), (3) the lateral crural mattress suture (to reduce lateral crural convexity), and (4) the columella-septal suture (to prevent tip drop and adjust tip projection). The lateral crural mattress suture is the newest of these sutures. It specifically controls undesirable convexity of the lateral crus. The four-suture algorithm is principally designed for primary open rhinoplasties. However, it is also recommended for secondary rhinoplasties. A minor modification is suggested for use in closed rhinoplasties. The algorithm is intended to reduce the difficulty of determining which of the currently available rhinoplasty sutures are useful and in what order they should be used. Illustrative cases are provided. The advantages and disadvantages of this particular algorithm, compared with others that have been proposed, are also reviewed.

Algorithms↗

PubMed2005

Prevalence of transmitted HIV-1 drug resistance and the role of resistance algorithms: data from seroconverters in the CASCADE collaboration from 1987 to 2003.

OBJECTIVES: To examine factors influencing the rate of transmitted drug resistance (TDR) among seroconverters, with particular emphasis on 3 widely used genotypic drug resistance algorithms. METHODS: The study used data from CASCADE (Concerted Action on Seroconversion to AIDS and Death in Europe), a collaboration of seroconverter cohorts in Europe and Canada. Genotypic resistance data were derived within 18 months of the last seronegative test or date of laboratory evidence of acute infection and before the initiation of antiretroviral therapy. The Stanford algorithm was used to analyze each individual's nucleotide sequence. A multivariate logistic model was used to assess independent relationships between the presence of TDR and exposure category, sex, age at seroconversion, and year of seroconversion. The paper also describes 3 alternative definitions of resistance: the Stanford algorithm, the key resistance mutations defined by the International AIDS Society, and the Agence Nationale de Recherches sur le Sida (ANRS) algorithm. RESULTS: Forty-five of 438 patients (10.3%) seroconverting between 1987 and 2003 were infected with a drug-resistant HIV-1 variant. Forty patients (9.1%) showed resistance mutations to only 1 class of antiretroviral drugs, 2 (0.5%) to 2 classes, and 3 (0.7%) to 3 classes of antiretroviral therapy. It was suggested that individuals seroconverting later in calendar time were more likely to have TDR (relative risk 3.89 and 95% CI: 0.84 to 18.02, and relative risk 4.69 and 95% CI: 1.03 to 21.31, for 1996-1999 and 2000-2003, respectively, compared with pre-1996; P trend = 0.08). This trend was apparent regardless of the definition of TDR used. The total estimated proportion of individuals with TDR varied between 10.3% and 15.5% according to which definition was used. CONCLUSIONS: Evidence was found for the rise of TDR over time. A specific definition of what constitutes TDR rather than a simple list of mutations is needed.

Adolescent↗

PubMed2006

Extending the dynamic range of phase contrast magnetic resonance velocity imaging using advanced higher-dimensional phase unwrapping algorithms.

Phase contrast magnetic resonance velocity imaging is a powerful technique for quantitative in vivo blood flow measurement. Current practice normally involves restricting the sensitivity of the technique so as to avoid the problem of the measured phase being 'wrapped' onto the range -pi to +pi. However, as a result, dynamic range and signal-to-noise ratio are sacrificed. Alternatively, the true phase values can be estimated by a phase unwrapping process which consists of adding integral multiples of 2pi to the measured wrapped phase values. In the presence of noise and data undersampling, the phase unwrapping problem becomes non-trivial. In this paper, we investigate the performance of three different phase unwrapping algorithms when applied to three-dimensional (two spatial axes and one time axis) phase contrast datasets. A simple one-dimensional temporal unwrapping algorithm, a more complex and robust three-dimensional unwrapping algorithm and a novel velocity encoding unwrapping algorithm which involves unwrapping along a fourth dimension (the 'velocity encoding' direction) are discussed, and results from the three are presented and compared. It is shown that compared to the traditional approach, both dynamic range and signal-to-noise ratio can be increased by a factor of up to five times, which demonstrates considerable promise for a possible eventual clinical implementation. The results are also of direct relevance to users of any other technique delivering time-varying two-dimensional phase images, such as dynamic speckle interferometry and synthetic aperture radar.

Algorithms↗

PubMed1991

An algorithm for associating the features of two images.

In this paper we describe an algorithm that operates on the distances between features in the two related images and delivers a set of correspondences between them. The algorithm maximizes the inner product of two matrices, one of which is the desired 'pairing matrix' and the other a 'proximity matrix' with elements exp (-rij2/2 sigma 2), where rij is the distance between two features, one in each image, and sigma is an adjustable scale parameter. The output of the algorithm may be compared with the movements that people perceive when viewing two images in quick succession, and it is found that an increase in sigma affects the computed correspondences in much the same way as an increase in interstimulus interval alters the perceived displacements. Provided that sigma is not too small the algorithm will recover the feature mappings that result from image translation, expansion or shear deformation--transformations of common occurrence in image sequences--even when the displacements of individual features depart slightly from the general trend.

Algorithms↗

PubMed2005

Identification of polymorphic motifs using probabilistic search algorithms.

The problem of identifying motifs comprising nucleotides at a set of polymorphic DNA sites, not necessarily contiguous, arises in many human genetic problems. However, when the sites are not contiguous, no efficient algorithm exists for polymorphic motif identification. A search based on complete enumeration is computationally inefficient. We have developed probabilistic search algorithms to discover motifs of known or unknown lengths. We have developed statistical tests of significance for assessing a motif discovery, and a statistical criterion for simultaneously estimating motif length and discovering it. We have tested these algorithms on various synthetic data sets and have shown that they are very efficient, in the sense that the "true" motifs can be detected in the vast majority of replications and in a small number of iterations. Additionally, we have applied them to some real data sets and have shown that they are able to identify known motifs. In certain applications, it is pertinent to find motifs that contain contrasting nucleotides at the sites included in the motif (e.g., motifs identified in case-control association studies). For this, we have suggested appropriate modifications. Using simulations, we have discovered that the success rate of identification of the correct motif is high in case-control studies except when relative risks are small. Our analyses of evolutionary data sets resulted in the identification of some motifs that appear to have important implications on human evolutionary inference. These algorithms can easily be implemented to discover motifs from multilocus genotype data by simple numerical recoding of genotypes.

Africa↗

PubMed1989

The use of adaptive algorithms for obtaining optimal electrical shimming in magnetic resonance imaging (MRI).

A method of determining the dc coil current values to electrically shim the static magnetic fields used in magnetic resonance imaging (MRI) using modified steepest descent adaptive algorithm is described. Using a 32 cm diameter by a 40 cm long water phantom as the test volume, the algorithm achieved field homogeneities of 0.2 parts per million (ppm) peak-to-peak within a 20 cm diameter spherical imaging volume, and 1.3 ppm peak-to-peak within the entire phantom. The algorithm achieved an inhomogeneity variance of 0.18 ppm2. The shim system was successfully modeled as a sum of adaptive linear combiners. The model contains 13 parameters that can be varied, 12 shim coil currents, and the receiver mixer frequency. The model was then used to predict key adaptive algorithm parameters. Experimental verification of these parameters lends support to the accuracy of the model.

Algorithms↗

PubMed1990

A comparison of the noise sensitivity of nine QRS detection algorithms.

The noise sensitivities for nine different QRS detection algorithms were measured for a normal, single-channel lead II, synthesized ECG corrupted with five different types of synthesized noise. The noise types were electromyographic interference, 60 Hz powerline interference, baseline drift due to respiration, abrupt baseline shift, and a composite noise constructed from all of the other noise types. The percentage of QRS complexes detected, the number of false positives, and the detection delay were measured. None of the algorithms were able to detect all QRS complexes without any false positives for all of the noise types at the highest noise level. Algorithms based on amplitude and slope had the highest performance for EMG-corrupted ECG. An algorithm using a digital filter had the best performance for the composite noise corrupted data.

Algorithms↗

PubMed1991

A semiclosed-loop algorithm for the control of blood glucose levels in diabetics.

In this paper, a theoretical analysis of the control of plasma glucose levels in diabetic individuals is undertaken using a simple mathematical model of the dynamics of glucose and insulin interaction in the blood system. Mathematical optimization techniques are applied to the mathematical model to derive insulin infusion programs for the control of blood levels in diabetic individuals. Based on the results of the mathematical optimization, a semiclosed-loop algorithm is proposed for continuous insulin delivery to diabetic patients. The algorithm is based on three hourly plasma glucose samples. A theoretical evaluation of the effectiveness of this algorithm shows that it is superior to two existing algorithms in controlling hyperglycemia. A glucose infusion term representing the effect of glucose intake resulting from a meal is then introduced into the model equations. Various insulin infusion programs for the control of plasma glucose levels following a meal are then assessed. The theoretical results suggest that the most effective short-term control is achieved by an insulin infusion program which incorporates an injection to coincide with the meal.

Algorithms↗

PubMed1999

A low-complexity intracardiac electrogram compression algorithm.

Implantable cardioverter defibrillators (ICD's) detect, diagnose and treat the potentially fatal heart arrhythmias known as bradycardia, ventricular tachycardia (VT), and ventricular fibrillation (VF) in cases where these arrhythmias are resistant to surgical and drug-based treatments by direct sensing and electrical stimulation of the heart muscle. Since the ICD is implanted, power consumption, reliability, and size are severe design constraints. This paper targets the problems associated with increasing the signal recording capabilities of an ICD. A data-compression algorithm is described which has been optimized for low power consumption and high reliability implementation. Reliance on a patients morphology or that of a population of patients is avoided by adapting to the intracardiac electrogram (ICEG) amplitude and phase variations and by using adaptive scalar quantization. The algorithm is compared to alternative compression algorithms which are also patient independent using a subset of VT arrhythmias from a data base of 146 patients. At low distortion the algorithm is closest to the Shannon lower bound achieving an average of 3.5 b/sample at 5% root mean square distortion for a 250-Hz sample rate. At higher distortion vector quantization and Karhunen-Loeve Transform approaches are superior but at the cost of considerable additional computational complexity.

Algorithms↗

PubMed2002

An efficient coding algorithm for the compression of ECG signals using the wavelet transform.

A wavelet-based electrocardiogram (ECG) data compression algorithm is proposed in this paper. The ECG signal is first preprocessed, the discrete wavelet transform (DWT) is then applied to the preprocessed signal. Preprocessing guarantees that the magnitudes of the wavelet coefficients be less than one, and reduces the reconstruction errors near both ends of the compressed signal. The DWT coefficients are divided into three groups, each group is thresholded using a threshold based on a desired energy packing efficiency. A binary significance map is then generated by scanning the wavelet decomposition coefficients and outputting a binary one if the scanned coefficient is significant, and a binary zero if it is insignificant. Compression is achieved by 1) using a variable length code based on run length encoding to compress the significance map and 2) using direct binary representation for representing the significant coefficients. The ability of the coding algorithm to compress ECG signals is investigated, the results were obtained by compressing and decompressing the test signals. The proposed algorithm is compared with direct-based and wavelet-based compression algorithms and showed superior performance. A compression ratio of 24:1 was achieved for MIT-BIH record 117 with a percent root mean square difference as low as 1.08%.

Algorithms↗

PubMed2002

Feature analysis and centromere segmentation of human chromosome images using an iterative fuzzy algorithm.

Classification of homologous chromosomes is essential to advanced studies of cancer genetics. Centromere intensities are believed to be an important differentiating feature between homologs. Therefore, segmentation of centromeres is a major step toward the realization of homolog classification. This paper describes an iterative fuzzy algorithm which successfully segments centromeres from images of human chromosomes prepared using fluorescence in-situ hybridization technique. The algorithm is based on assigning a fuzzy membership value to each pixel in the centromere image. An iterative algorithm then updates and minimizes a defined error function. Chromosome 22, a highly heteromorphic chromosome, is used to verify the centromere segmentation method. Homologs of this chromosome are classified based on their segmented centromere intensities as well as their morphological differences. The classification results of these two methods agree completely and are used to validate our developed algorithm.

Algorithms↗

PubMed1997

Sampling concerns in scanline algorithms.

This paper investigates the problem of providing suitable interpolation for scanline algorithms. These algorithms are of interest, as they are parallelizable. A structure for analyzing the problem is given. The theory in regard to resampling is developed in the context of a scanline algorithm for image rotation. The theory is compared to results arrived at in practice. Alternative interpolation schemes are discussed, including the use of a cubic Hermite interpolator. The paper points to theoretical limitations of scanline algorithms.

Algorithms↗

PubMed1998

A harmonic decomposition reconstruction algorithm for spatially varying focal length collimators.

Spatially varying focal length fan-beam collimators can be used in single photon emission computed tomography to improve detection efficiency and to reduce reconstruction artifacts resulting from the truncation of projection data. It has been proven that there exists no convolution backprojection algorithm for this type of collimator, so a complicated interpolation between two nonparallel projection rays is necessary for existing algorithms. The interpolation may generate blurring and artifacts in the reconstructed images. Based on a harmonic decomposition technique and the translation property of Fourier series, a semifrequency resampling technique is proposed to avoid the above mentioned interpolations. By this technique, the harmonic decomposition of projection data for spatially varying focal length fan-beam collimators has the same form as that for parallel-beam collimators in the semifrequency domain (Fourier transform with respect to angular variables only). An alternative version of the inverse Cormack transform is then proposed to reconstruct the images. The derived reconstruction algorithm was implemented in a Pentium II/266 PC computer. Numerical simulations demonstrated its efficiency (3 s for 128 x 128 reconstruction arrays) and its robust performance (compared to the existing algorithms).

Algorithms↗

PubMed1999

An adaptive segmentation algorithm for time-of-flight MRA data.

A three-dimensional (3-D) representation of cerebral vessel morphology is essential for neuroradiologists treating cerebral aneurysms. However, current imaging techniques cannot provide such a representation. Slices of MR angiography (MRA) data can only give two-dimensional (2-D) descriptions and ambiguities of aneurysm position and size arising in X-ray projection images can often be intractable. To overcome these problems, we have established a new automatic statistically based algorithm for extracting the 3-D vessel information from time-of-flight (TOF) MRA data. We introduce distributions for the data, motivated by a physical model of blood flow, that are used in a modified version of the expectation maximization (EM) algorithm. The estimated model parameters are then used to classify statistically the voxels into vessel or other brain tissue classes. The algorithm is adaptive because the model fitting is performed recursively so that classifications are made on local subvolumes of data. We present results from applying our algorithm to several real data sets that contain both artery and aneurysm structures of various sizes.

Algorithms↗

PubMed2000

Evaluating performance of reconstruction algorithms for 3-D [15O] water PET using subtraction analysis.

Positron emission tomography (PET) [15O] activation studies have benefited significantly from three-dimensional (3-D) data acquisition. However, they have been slow to take advantage of new 3-D reconstruction techniques. Compared with the widely used 3-D reprojection reconstruction (3DRP), the advantage of signal and noise for iterative algorithms has been outweighed by concern about long and complicated reconstruction procedures and inconsistent performance. Most pseudo-3-D algorithms, such as rebinning methods, aim at increasing the speed of reconstruction but lack further resolution improvement or noise control. Although many evaluations have been conducted through simulations and phantom experiments, the spatially varying nature of signal and noise and the complexity of biological effects have complicated the interpretation of real data based on simulation or phantom results. We have taken a different approach and used the analysis of real data directly as a measure with which to compare three reconstruction algorithms: 3DRP, iterative filtered backprojection with median root prior (IFBP-MRP), and Fourier rebinning followed by two-dimensional (2-D) filtered backprojection (FORE-FBP) for [15O] PET. Two subjects, each with 32 scans acquired in four sessions during a finger opposition motor task, are analyzed using subtraction. A fixed volume-of-interest (VOI) measurement in regions related to the task demonstrates that at high resolution, IFBP-MRP has the best signal-to-noise performance followed by 3DRP and FORE-FBP; however, this advantage gradually diminishes as the resolution decreases. For a voxel measurement derived from the image of each reconstruction, all three algorithms are capable of detecting highly activated regions. Although there are some differences in the size, shape, and center location of the activated foci, our preliminary results suggest that IFBP-MRP does offer enhanced signal with some noise control compared with 3DRP for the analysis of high-resolution images. If images are to be analyzed at an intermediate to lower resolution, FORE-FBP provides a significant reduction of reconstruction time compared with 3DRP.

Algorithms↗

PubMed2001

The design and implementation of COSEM, an iterative algorithm for fully 3-D listmode data.

In this paper,we present coincidence-list-ordered sets expectation-maximization (COSEM), an algorithm for iterative image reconstruction directly from list-mode coincidence acquisition data. The COSEM algorithm is based on the ordered sets EM algorithm for binned data but has several extensions that makes it suitable for rotating two planar detector tomographs. We develop the COSEM algorithm and extend it to include analytic calculation of detection probability, noise reducing iterative filtering schemes, and on-the-fly attenuation correction methods. We present an adaptation of COSEM to the Varicam\VG camera and show results from clinical and phantom studies.

Algorithms↗