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At least 1,243 records · Page 69Linked to original sources
PubMed2005

Influence of positional and angular variation of automatically planned short-axis stacks on quantification of left ventricular dimensions and function with cardiovascular magnetic resonance.

PURPOSE: To theoretically and experimentally investigate the influence of the automated cardiovascular magnetic resonance (CMR) scan planning pitfalls, namely inaccurate positioning and tilting of short-axis (SA) imaging planes, on quantification of the left ventricular (LV) dimensions and function. MATERIALS AND METHODS: Eleven healthy subjects and eight patients underwent CMR. Manually and automatically planned SA sets were acquired. To obtain the quantitative measurements of LV function, one observer performed image analysis twice. The agreement between planning methods, as well as the decomposition of the total variation into interstudy and intraobserver components was measured. RESULTS: The decomposition of the total variation showed that the interstudy factor accounts for 70-85% of the total variation, while the rest is due to the intraobserver factor. Moreover, the relative contribution of the interstudy factor remains independent from errors in slice positioning and small angular deviation of SA stacks from the optimal orientation. Good agreement between the theoretical and measured variability factors was observed. CONCLUSION: Global LV function derived from the automatically planned CMR acquisitions yield accurate quantification of the human cardiovascular system. Inaccurate positioning and tilting of SA images does not affect the quantitative measurements of LV function. The computer-aided system for automated CMR has proven clinical applicability.

Adult↗
PubMed2006

Automatic identification of the left ventricle in cardiac cine-MR images: dual-contrast cluster analysis and scout-geometry approaches.

PURPOSE: To evaluate the technical feasibility of two approaches--dual-contrast (DC) cluster analysis, and scout geometry (SG)--for automatic identification of the left ventricular (LV) cavity in short-axis (SA) cine-MR images. MATERIALS AND METHODS: The DC algorithm uses Fuzzy C-Means (FCM) cluster analysis of SA images from a black-blood double-inversion recovery turbo spin-echo (dual IR TSE) sequence, and bright-blood images from a steady-state free precession (SSFP) sequence. The SG algorithm employs geometric information from scout views (i.e., vertical long-axis (VLA) and four-chamber (4CH) views). Both algorithms incorporate additional geometric continuity constraints along with LV region segmentation to identify the LV. The performance of both algorithms was compared on images of eight healthy volunteers, and the SG algorithm was further evaluated on images of 13 clinical patients. RESULTS: The DC algorithm identified the LV in 89% (72/75 at end-diastole (ED) and 47/59 at end-systole (ES)) of the images from healthy volunteers, compared to 98% (74/75 at ED and 57/59 at ES) by the SG algorithm. Both methods are robust against interslice signal variations and misalignment. The DC method suffers from misregistration between the dual IR TSE and SSFP images near the apex at ES. The SG method identified the LV in 91% (112/122 at ED and 91/102 at ES) of the images from clinical patients. CONCLUSION: The SG method requires no additional scan, is robust and accurate, and performs better than the DC method for automatic identification of the LV.

Adult↗
PubMed2006

Automatic vessel wall contour detection and quantification of wall thickness in in-vivo MR images of the human aorta.

PURPOSE: To develop an automated technique to trace the contours of the lumen and outer boundary of the aortic wall, and measure aortic wall thickness in axial MR images. MATERIALS AND METHODS: The algorithm uses prior knowledge of vessel wall morphology. A geometrical model (ellipse) is deformed, translated and rotated to obtain a rough approximation of the contours. Model-matching is based on image gradient measurements. To enhance edges, the images were preprocessed using gray-level stretching. Refinement is performed by means of dynamic programming. Wall thickness is computed by measuring the distance between inner and outer contour of the aortic wall. RESULTS: The algorithm has been tested on high-resolution axial MR images from 28 human subjects of the descending thoracic aorta. The results demonstrate: High correspondence between automatic and manual area measurements: lumen (r = 0.99), outer (r = 0.96), and wall thickness (r = 0.85). CONCLUSION: Though further optimization is required, our algorithm is a powerful tool to automatically draw the boundaries of the aortic wall and measure aortic wall thickness in aortic wall devoid of major lesions. J. Magn. Reson. Imaging 2006. (c) 2006 Wiley-Liss, Inc.

Aged↗
PubMed1983

Subcutaneous administration of inactivated hepatitis B vaccine by automatic jet injection.

To assess the feasibility of jet injection for mass immunization against hepatitis B virus, inactivated, alum-adsorbed hepatitis B vaccine (Merck, Sharp, and Dohme Research Laboratories, West Point, PA) was administered subcutaneously by automatic jet injection to 19 volunteers lacking antibody to hepatitis B surface antigen (anti-HBs). Three 20-microgram doses were given at 0, 1, and 6 months. Of 19 volunteers, 5 (26%) developed anti-HBs by 1 month after the first injection, and 15 of 19 (79%) were anti-HBs-positive 6 to 8 weeks after the first booster administration. Following the second booster, 16 of 19 (84%) recipients had detectable anti-HBs. Possible systemic reactions were limited to low-grade fever (37.8 degrees C) in one volunteer following one injection, and mild lethargy in a second recipient. Local reactions to jet injection of vaccine occurred more frequently, with indurated, nodular lesions 3-10 mm in diameter developing at the site of 19 of 57 (33%) vaccine injections, compared with 2 of 57 (3%) saline placebo injections. Such nodules were generally painless. Sore arms were noted in 11 of 57 (19%) vaccine injections. With the exception of frequent but minor local reactions, subcutaneous administration of inactivated hepatitis B vaccine by automatic jet injection is safe, and results in vaccine immunogenicity approximating that associated with intramuscular needle injection.

Adult↗
PubMed1989

Atropine absorption after intramuscular administration with 2-pralidoxime chloride by two automatic injector devices.

Compared with manual intramuscular injection, automatic injector delivery substantially enhances drug absorption rate. We examined the effect of two types of automatic injector delivery of two drugs which are components of the standard antidote to anticholinesterase poisoning and which have been previously shown to have a reduced absorption rate when mixed together in a manual injection. In crossover experiments one week apart, 20 nonsmoking healthy young male humans (ages 20-30) were studied after citrated atropine (6.9 mumol/0.7 mL) and pralidoxime chloride (3.5 mmol/2.0 mL; PAMCL) were injected sequentially into a single intramuscular site by either a multichambered autoinjector or a device which delivers the drugs into two separate intramuscular sites (MARK I). Atropine absorption was assessed by the appearance of atropine in the serum and by changes in heart rate, salivary secretion, pupil diameters, and near vision accommodation. Atropine absorption was significantly greater in the first 30 min following injection with the MARK I. The results of this study suggest that: (1) the MARK I device produces a faster absorption of atropine, probably through some combination of its broader dispersal of atropine in the muscle site and its separation of atropine from the PAMCL; (2) salivary secretion may be the most convenient and sensitive marker of atropine action; and (3) the 6.9- mumol (2-mg) dose of atropine delivered by either autoinjector gives near maximal antisialogogue activity in normal male humans.

Accommodation, Ocular↗
PubMed2002

Automatic selection of mask and arterial phase images for temporally resolved MR digital subtraction angiography.

For time-resolved background-subtracted contrast-enhanced magnetic resonance angiography, the bright and sparse arterial signal allows unique identification of contrast bolus arrival in the arteries. This article presents an automatic filtering algorithm using such arterial characterization for selecting arterial phase images and mask images to generate an optimal summary arteriogram. A paired double-blinded comparison demonstrated that this automatic algorithm is as effective as the manual process.

Adult↗
PubMed2003

Control characteristics of an automatic matching control system for in vivo EPR spectroscopy.

A method for estimating the characteristics of an automatic matching control (AMC) system for in vivo electron paramagnetic resonance (EPR) spectroscopy is described. AMC is also known as automatic coupling control (ACC) and is used to compensate for perturbation due to movement of the subject animal. The open-loop function of the AMC system is derived and the characteristics (gain, phase margin, steady-state error, system bandwidth, and disturbance rejection) of the system are examined. The proposed method is supported by experimental findings. The frequency response of perturbation due to the movement of an anesthetized rat was measured with a 1.1-GHz continuous-wave EPR spectrometer. Disturbance rejection with the AMC system was also considered for respiratory motion and the heartbeat of the anesthetized rat, and these perturbations were reduced by about 40 dB in the power spectrum of the output of the diode detector in the spectrometer.

Abdomen↗
PubMed1992

Automatic in vivo NMR data processing based on an enhancement procedure and linear prediction method.

A new data processing method for in vivo NMR data quantitation is presented. This method (EPLPSVD) is based on the enhancement procedure (EP) proposed by J. A. Cadzow (IEEE Trans. Acoust. Speech Signal Process. 36, 49, 1988) followed by the usual linear prediction method using the singular value decomposition (LPSVD). The evaluation of this protocol is performed using synthesized 31P signals with different signal-to-noise ratios. A Monte-Carlo simulation as a function of signal-to-noise ratio (SNR) has proved that EPLPSVD leads to unbiased estimated values of parameters. Then the Cramer-Rao method yields reliable confidence intervals for the estimated parameters. The estimates of NMR parameters using EPLPSVD are reliable and accurate for SNR > or = 1.2 while the LPSVD method failed for SNR < or = 4. This protocol is applied to analyze automatically a series of 31P free induction decays obtained from the human gastrocnemius muscle during exercise. Spectral parameters with their confidence intervals, curves of relative intensity variations in phosphocreatine and inorganic phosphate, and pH curves are automatically provided.

Adenosine Triphosphate↗
PubMed1998

Automatic probe tuning and matching.

The problem of automatically tuning and matching a probe is considered, and attention is drawn to the main cause of difficulty: the interaction of tuning and matching mechanisms. The use of a doubly resonant, inductively coupled probe is therefore advocated, for to first order, tuning, and matching are then orthogonal for small perturbations. It is shown that when such a probe is equipped with negative feedback control of tuning and matching elements, driven by error signals derived from a bridge and the NMR spectrometer, stable and rapid automatic tuning and matching are achieved. The importance of approximately correct phasing of the error signals is emphasized, but the restriction of having to have specific cable lengths to achieve this task is removed. The effects of small errors of phasing are then considered and shown to be unimportant for the chosen probe, in contrast to the situation for other, nonorthogonal probe types. Suggestions for orthogonalization of two common capacitively coupled probe designs are made, and a practical instrument design is then given that, with the addition of external components, can also be used if the NMR receiver cannot be pressed into service.

Equipment Design↗
PubMed1998

Automatic segmentation of gadolinium-enhanced multiple sclerosis lesions.

Automatic detection and quantitation of contrast-enhanced lesions on MRI is expected to be useful in characterizing the disease state in multiple sclerosis (MS). The enhancing structures such as cerebral vasculature and regions with no blood-brain barrier complicate automated analysis of lesion enhancement. A pulse sequence that incorporates both stationary and marching saturation bands and gradient dephasing is described for suppressing the enhancements within the cerebral vasculature. A postprocessing technique based on automatic image segmentation is implemented for eliminating enhancing structures such as choroid plexus. All MS lesions larger than 5 mm3 have been successfully identified. The automated analysis produced no false-positives or false-negative lesions above this volume in 13 patients with MS who were evaluated using the acquisition and evaluation techniques described.

Algorithms↗
PubMed2001

Effect of degenerate spherical harmonics and a method for automatic shimming of oblique slices.

Several spherical harmonics degenerate on an oblique plane. Two-dimensional field mapping of an oblique slice causes ambiguity in determination of the degenerate spherical harmonics terms. Therefore, automatic shimming of oblique slices may lead to erroneous adjustment of shims corresponding to the degenerate spherical harmonics. In this paper an automatic slice shimming technique derived from the FASTMAP method (Gruetter R. Magn. Reson. Med. 1993; 29, 804-811) is proposed. This new method unequivocally determines and corrects all of the first- and the second-order shims for slices of arbitrary orientation.

Diagnostic Imaging↗
PubMed2001

Automatic quantitation of localized in vivo 1H spectra with LCModel.

The LCModel method analyzes an in vivo spectrum as a Linear Combination of Model in vitro spectra from individual metabolite solutions. Complete model spectra, rather than individual resonances, are used in order to incorporate maximum prior information into the analysis. A nearly model-free constrained regularization method automatically accounts for the baseline and lineshape in vivo without imposing a restrictive parameterized form on them. LCModel is automatic (non-interactive) with no subjective input. Approximately maximum-likelihood estimates of the metabolite concentrations and their uncertainties (Cramér-Rao lower bounds) are obtained. LCModel analyses of spectra from users with fields from 1.5 to 9.4 T and a wide range of sequences, particularly with short TE, are used here to illustrate the capabilities and limitations of LCModel and proton MRS.

Algorithms↗
PubMed2004

Decoupling of automatic control systems in a continuous-wave electron paramagnetic resonance spectrometer for biomedical applications.

This article describes a systematic approach to decoupling automatic tuning control (ATC) and automatic matching control (AMC) systems in continuous-wave (CW) electron paramagnetic resonance (EPR) spectroscopy for animal experiments. This technique enables us to improve the stability of CW-EPR spectroscopy even if the animal is moving during the data acquisition of EPR spectra. The control systems are formulated to allow the behavior of interference between them to be investigated, since they are generally coupled due to the characteristics of the microwave resonator. The stability of the entire control system in a 1.1 GHz CW-EPR spectrometer is evaluated with the generalized Nyquist stability criterion. We compare the EPR spectra of a triarylmethyl (TAM) radical that is dosed in anesthetized mice in terms of the signal-to-noise ratio (SNR) to test the precompensator for decoupling the ATC and AMC systems. The experimental findings suggest that the present technique is useful for improving the SNR of EPR spectra in animal experiments. The SNR of the measured EPR spectra was improved by about 50% with the precompensator.

Algorithms↗
PubMed1987

Morphometry of bladder carcinoma: I. The automatic delineation of urothelial nuclei in tissue sections using an IBAS II image array processor.

Semi-automatic methods of morphometry require the boundaries of the objects under study to be drawn by hand. This is slow, tedious and does not guarantee accuracy. Complete automation, with recognition, detection and verification by computer is not yet feasible. Automatic detection of nuclear boundaries with observer verification provides a means of obtaining large amounts of data for analysis, quickly and with similar accuracy to manual tracing.

Cell Nucleus↗
PubMed2005

Automatic annotation of matrix-assisted laser desorption/ionization N-glycan spectra.

Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) is the pre-eminent technique for mass mapping of glycans. In order to make this technique practical for high-throughput screening, reliable automatic methods of annotating peaks must be devised. We describe an algorithm called Cartoonist that labels peaks in MALDI spectra of permethylated N-glycans with cartoons which represent the most plausible glycans consistent with the peak masses and the types of glycans being analyzed. There are three main parts to Cartoonist. (i) It selects annotations from a library of biosynthetically plausible cartoons. The library we currently use has about 2800 cartoons, but was constructed using only about 300 archetype cartoons entered by hand. (ii) It determines the precision and calibration of the machine used to generate the spectrum. It does this automatically based on the spectrum itself. (iii) It assigns a confidence score to each annotation. In particular, rather than making a binary yes/no decision when annotating a peak, it makes all plausible annotations and associates them with scores indicating the probability that they are correct.

Algorithms↗
PubMed1995

An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins.

With a growing number of structures available in the Brookhaven Protein Data Bank, automatic methods for domain identification are required for the construction of databases. Domains are considered to be clusters of secondary structure elements. Thus, helices and strands are first clustered using intersecondary structural distances between C alpha positions, and dendrograms based on this distance measure are used to identify domains. Individual domains are recognized by a disjoint factor, which enables the automatic identification and classification into disjoint, interacting, and conjoint domains. Application to a database of 83 protein families and 18 unique structures shows that the approach provides an effective delineation of boundaries and identifies those proteins that can be considered as a single domain. A quantitative estimate of the interaction between domains has been proposed. The database of protein domains is a useful tool for understanding protein folding, for recognizing protein folds, and for understanding structure-activity relationships.

Algorithms↗
PubMed2003

Automatic annotation of protein function based on family identification.

Although genomes are being sequenced at an impressive rate, the information generated tells us little about protein function, which is slow to characterize by traditional methods. Automatic protein function annotation based on computational methods has alleviated this imbalance. The most powerful current approach for inferring the function of new proteins is by studying the annotations of their homologues, since their common origin is assumed to be reflected in their structure and function. Unfortunately, as proteins evolve they acquire new functions, so annotation based on homology must be carried out in the context of orthologues or subfamilies. Evolution adds new complications through domain shuffling: homology (or orthology) frequently corresponds to domains rather than complete proteins. Moreover, the function of a protein may be seen as the result of combining the functions of its domains. Additionally, automatic annotation has to deal with problems related to the annotations in the databases: errors (which are likely to be propagated), inconsistencies, or different degrees of function specification. We describe a method that addresses these difficulties for the annotation of protein function. Sequence relationships are detected and measured to obtain a map of the sequence space, which is searched for differentiated groups of proteins (similar to islands on the map), which are expected to have a common function and correspond to groups of orthologues or subfamilies. This mapmaking is done by applying a clustering algorithm based on Normalized cuts in graphs. The domain problem is addressed in a simple way: pairwise local alignments are analyzed to determine the extent to which they cover the entire sequence lengths of the two proteins. This analysis determines both what homologues are preferred for functional inheritance and the level of confidence of the annotation. To alleviate the problems associated with database annotations, the information on all the homologues that are grouped together with the query protein are taken into account to select the most representative functional descriptors. This method has been applied for the annotation of the genome of Buchnera aphidicola (specific host Baizongia pistaciae). Human inspection of the annotations allowed an estimation of accuracy of 94%; the different kinds of error that may appear when using this approach are described. Results can be accessed at http://www.pdg.cnb.uam.es/funcut.html. The programs are available upon request, although installation in other systems may be complicated.

Algorithms↗
PubMed2005

CASP6 data processing and automatic evaluation at the protein structure prediction center.

We present a short overview of the system governing data processing and automatic evaluation of predictions in CASP6, implemented at the Livermore Protein Structure Prediction Center. The system incorporates interrelated facilities for registering participants, collecting prediction targets from crystallographers and NMR spectroscopists and making them available to the CASP6 participants, accepting predictions and providing their preliminary evaluation, and finally, storing and visualizing results. We have automatically evaluated predictions submitted to CASP6 using criteria and methods developed over the successive CASP experiments. Also, we have tested a new evaluation technique based on non-rigid-body type superpositions. Approximately the same number of predictions has been submitted to CASP6 as to all previous CASPs combined, making navigation through and understanding of the data particularly challenging. To facilitate this, we have substantially modernized all data handling procedures, including implementation of a dedicated relational database. An overview of our redesigned website is also presented (http://predictioncenter.org/casp6/).

Algorithms↗