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PubMed1999

[High-resolution magnetoencephalography--studies with a small-volume phantom].

To investigate the spatiotemporal organisation of neuronal processes in an animal model using magnetoencephalography (MEG), a high temporal resolution (ms) and an appropriate spatial resolution of about 1 mm is necessary. With the aim of determining the localization error and the resolution power of high-resolution MEG systems, we developed a phantom capable of simulating the characteristics of animal models. The phantom enables us to variably position at least two magnetic field sources to within 0.1 mm. For source localization on the basis of the magnetic field data, a spatial filtering algorithm was used. The investigation of a 16-channel micro SQUID-MEG system with a current dipole orientated tangentially to the phantom surface produced the following localization data (min ... max, x, y--horizontal plane, z--depth); systematic localization error e(x) = 1.16 ... 1.67 mm, e(y) = -1.01 ... -1.28 mm, e(z) = -5.22 ... -7.64 mm, standard deviation of the individual measurements perpendicular to the dipole axis s(perp) = 0.05 ... 0.22 mm, along this axis s(long) = 0.20 ... 1.73 mm, in the depths sz = 0.17 ... 3.17 mm. The "goodness of fit" was > 95%. Separation of two dipoles was still possible for parallel dipoles at a distance apart of d(parallel) = 0.03 mm and for those oriented perpendicularly to each other at a distance apart of d(perp) = 0.10 mm. On the basis of these results we conclude that the MEG system can achieve a resolution sufficient to permit the investigation of neuronal microstructures. The spatial errors detected were related to sensor position in the cryostatic vessel as well as to external low-frequency noise.

Magnetoencephalography↗
PubMed2005

Image reconstruction in SNR units: a general method for SNR measurement.

The method for phased array image reconstruction of uniform noise images may be used in conjunction with proper image scaling as a means of reconstructing images directly in SNR units. This facilitates accurate and precise SNR measurement on a per pixel basis. This method is applicable to root-sum-of-squares magnitude combining, B(1)-weighted combining, and parallel imaging such as SENSE. A procedure for image reconstruction and scaling is presented, and the method for SNR measurement is validated with phantom data. Alternative methods that rely on noise only regions are not appropriate for parallel imaging where the noise level is highly variable across the field-of-view. The purpose of this article is to provide a nuts and bolts procedure for calculating scale factors used for reconstructing images directly in SNR units. The procedure includes scaling for noise equivalent bandwidth of digital receivers, FFTs and associated window functions (raw data filters), and array combining.

Algorithms↗
PubMed1988

Binding of the bovine basic pancreatic trypsin inhibitor (Kunitz) to human alpha-, beta- and gamma-thrombin; a kinetic and thermodynamic study.

Kinetic and thermodynamic parameters for the binding of the bovine basic pancreatic trypsin inhibitor (BPTI, Kunitz inhibitor) to human alpha-, beta- and gamma-thrombin have been determined, between 5 and 45 degrees C, at pH 7.5. BPTI-binding properties to human thrombins have been analyzed in parallel with those of serine (pro)enzymes acting on cationic and non-cationic substrates, with particular reference to the bovine beta-trypsin/BPTI system. The observed binding behaviour of BPTI to human alpha-, beta- and gamma-thrombin has been related to the inferred stereochemistry of the enzyme/inhibitor contact region(s).

Algorithms↗
PubMed2006

Statistical analysis of intrahelical ionic interactions in alpha-helices and coiled coils.

There are many controversies concerning whether ionic interactions in alpha-helices and coiled coils actually contribute to the stabilisation and formation of these structures. Here we used a statistical approach to probe this question. We extracted unique alpha-helical and coiled coil structures from the protein database and analysed the ionic interactions between positively and negatively charged residues. The ionic interactions were categorized according to the type, spacing and order of the residues involved. Separate datasets were produced depending on the number of alpha-helices in the coiled coils and the mutual orientation of the helices. We compared the frequency of residue configurations able to form ionic interactions with their probability to form the interaction. We found a correlation between the two variables in alpha-helices, antiparallel two-stranded coiled coils and parallel two-stranded coiled coils. This indicates that some ionic interactions are indeed important for the formation and stabilisation of alpha-helices and coiled coils. We concluded that the configurations, which have simultaneously a large probability to form the ionic interaction and a frequent occurrence, are those, which have the most stabilising effect. These are the 4RE, 3ER and 4ER interactions.

Algorithms↗
PubMed2001

Quantitative analysis of three-dimensional-resolved fiber architecture in heterogeneous skeletal muscle tissue using nmr and optical imaging methods.

The determination of principal fiber directions in structurally heterogeneous biological tissue substantially contributes to an understanding of its mechanical function in vivo. In this study we have depicted structural heterogeneity through the model of the mammalian tongue, a tissue comprised of a network of highly interwoven fibers responsible for producing numerous variations of shape and position. In order to characterize the three-dimensional-resolved microscopic myoarchitecture of the intrinsic musculature of the tongue, we viewed its fiber orientation at microscopic and macroscopic length scales using NMR (diffusion tensor MRI) and optical (two-photon microscopy) imaging methods. Diffusion tensor imaging (DTI) of the excised core region of the porcine tongue resulted in an array of 3D diffusion tensors, in which the leading eigenvector corresponded to the principal fiber orientation at each location in the tissue. Excised axially oriented lingual core tissues (fresh or paraffin-embedded) were also imaged with a mode-locked Ti-Sapphire laser, (76 MHz repetition rate, 150 femtosecond pulse width), allowing for the visualization of individual myofibers at in situ orientation. Fiber orientation was assessed by computing the 3D autocorrelation of discrete image volumes, and deriving the minimal eigenvector of the center voxel Hessian matrix. DTI of the fibers, comprising the intrinsic core of the tongue, demonstrated directional heterogeneity, with two distinct populations of fibers oriented orthogonal to each other and in-plane to the axial perspective. Microscopic analysis defined this structural heterogeneity as discrete regions of in-plane parallel fibers, with an angular separation of ~80 degrees, thereby recapitulating the macroscopic angular relationship. This analysis, conceived at two different length scales, demonstrates that the lingual core is a spatially complex tissue, composed of repeating orthogonally oriented and in-plane fiber patches, which are capable of jointly producing hydrostatic elongation and displacement.

Algorithms↗
PubMed2002

HeinzelCluster: accelerated reconstruction for FORE and OSEM3D.

Using iterative three-dimensional (3D) reconstruction techniques for reconstruction of positron emission tomography (PET) is not feasible on most single-processor machines due to the excessive computing time needed, especially so for the large sinogram sizes of our high-resolution research tomograph (HRRT). In our first approach to speed up reconstruction time we transform the 3D scan into the format of a two-dimensional (2D) scan with sinograms that can be reconstructed independently using Fourier rebinning (FORE) and a fast 2D reconstruction method. On our dedicated reconstruction cluster (seven four-processor systems, Intel PIII@700 MHz, switched fast ethernet and Myrinet, Windows NT Server), we process these 2D sinograms in parallel. We have achieved a speedup > 23 using 26 processors and also compared results for different communication methods (RPC, Syngo, Myrinet GM). The other approach is to parallelize OSEM3D (implementation of C Michel), which has produced the best results for HRRT data so far and is more suitable for an adequate treatment of the sinogram gaps that result from the detector geometry of the HRRT. We have implemented two levels of parallelization for four dedicated cluster (a shared memory fine-grain level on each node utilizing all four processors and a coarse-grain level allowing for 15 nodes) reducing the time for one core iteration from over 7 h to about 35 min.

Algorithms↗
PubMed2005

Home blood glucose prediction: validation, safety, and efficacy testing in clinical diabetes.

BACKGROUND: Patients with diabetes do daily self-monitoring of blood glucose (SMBG). For such patients, we devised an engine that predicts not only the expected blood glucose level at the next meal but also the pending risks of hypoglycemia. The purpose of this study was to validate the predictions and provide evidence of the safety and efficacy of using predicted data in dosing decision support for routine patient care. RESEARCH DESIGN AND METHODS: The prediction engine is a computer program that accesses a central database into which daily records of self-monitored blood glucose data are captured by direct access either across the WWW or by an interactive voice response service on-line 24/7. Validation was done by comparison of predicted values to the subsequently observed data using a Clarke Error Grid. Safety focused on body weight and the frequency of hypoglycemia. Efficacy was judged according to glycated hemoglobin and daily insulin dosages. The experimental design contrasted patients in the tight control (TC) group who had been recently converted to intensified (basal-bolus) therapy with patients in the poor control (PC) group on conventional therapy and who were referred to begin intensified therapy. Both groups accessed the remote database to report their daily SMBG. Predicted glucose values were used in dosing decision support for the PC but not the TC group. RESULTS: Over the 6-month study period a total of 30,129 blood glucose levels were reported by the 54 study patients, and some 24,953 blood glucose predictions were made. Of these, 83% were in the clinically acceptable zones of the Clarke Error Grid. When these data were used for dosing decision support in the PC group, glycated hemoglobin levels fell significantly from 9.7 +/- 1.7% to 7.9 +/- 1.2%, and hypoglycemia dropped fourfold. Total daily insulin doses declined 22%, while body weight remained constant. In the parallel TC group (n = 24), glycated hemoglobin also fell, but only slightly from 7.6 +/- 0.9% to 7.2 +/- 1.1%, while daily insulin doses, rates of hypoglycemia and body weight remained constant. CONCLUSIONS: A novel engine is capable of generating meaningful predictions of blood glucose levels. Use of these validated predictions in decision support for managing medication doses proved safe and efficacious.

Algorithms↗
PubMed2005

Parallelising the MARS15 code with MPI for shielding applications.

The MARS15 Monte Carlo code capabilities to deal with time-consuming deep penetration shielding problems and other computationally tough tasks in accelerator, detector and shielding applications, have been enhanced by a parallel processing option. It has been developed, implemented and tested on the Fermilab Accelerator Division Linux cluster and network of Sun workstations. The code uses a message passing interface MPI. It is scalable and demonstrates good performance. The general architecture of the code, specific uses of message passing and effects of a scheduling on the performance and fault tolerance are described.

Algorithms↗
PubMed2006

Three-dimensional cerebral contrast-enhanced magnetic resonance venography at 3.0 Tesla: initial results using highly accelerated parallel acquisition.

OBJECTIVE: The objective of this study was to evaluate a high spatial resolution 3-dimensional (3D) contrast-enhanced magnetic resonance (CE-MR) venography protocol for evaluation of intracranial venous system using highly accelerated parallel imaging at 3.0 T. MATERIALS AND METHODS: Ten patients (4 male, 6 female; age, 38-76 years) with suspected cerebrovascular disease were prospectively studied on a 32-channel 3.0 T MR system. After a single intravenous contrast injection, high spatial resolution 3D CE-MR angiography of the entire supraaortic arteries was performed followed immediately by 3D cerebral CE-MR venography. By using a fast 3D gradient-recalled-echo sequence with elliptic centric k-space ordering and highly accelerated parallel acquisition (acceleration factor 3 and 2 in phase and slice encoding direction, respectively), 3D cerebral CE-MR venography was acquired with voxel dimensions of 0.7 x 0.7 x 0.8 mm in 24 seconds. Image evaluation was performed independently by 2 neuroradiologists for overall image quality, presence of noise, and artifacts. The image quality of 30 venous segments was evaluated in each subject using a 1 to 4 scoring scale. In 2 patients, catheter angiography was available for correlation. Statistical analysis of data was performed by using Wilcoxon rank sum test and kappa coefficient. RESULTS: All studies were determined to be of diagnostic image quality by both observers. The majority (90%) of cerebral venous segments were evaluated to be of diagnostic image quality (median, 3; range, 3-4) by both readers and with excellent interobserver agreement (kappa = 0.86; 95% confidence interval, 0.79-0.93). One meningioma invading the superior sagittal sinus and one superior sagittal sinus fistula were detected subsequently confirmed by conventional angiography. CONCLUSION: High spatial resolution 3D cerebral CE-MR venography is feasible and promising. Using a 32-channel 3.0 T system combined with multichannel array coils effectively supports highly accelerated parallel imaging, enabling subsequent acquisition of both high spatial resolution CE-MR angiography and CE-MR venography after a single contrast injection without impairing the image quality. More extensive clinical studies are warranted to establish the range of applications and confirm the accuracy of this technique.

Adult↗
PubMed2003

FAME--a flexible appearance modeling environment.

Combined modeling of pixel intensities and shape has proven to be a very robust and widely applicable approach to interpret images. As such the active appearance model (AAM) framework has been applied to a wide variety of problems within medical image analysis. This paper summarizes AAM applications within medicine and describes a public domain implementation, namely the flexible appearance modeling environment (FAME). We give guidelines for the use of this research platform, and show that the optimization techniques used renders it applicable to interactive medical applications. To increase performance and make models generalize better, we apply parallel analysis to obtain automatic and objective model truncation. Further, two different AAM training methods are compared along with a reference case study carried out on cross-sectional short-axis cardiac magnetic resonance images and face images. Source code and annotated data sets needed to reproduce the results are put in the public domain for further investigation.

Algorithms↗
PubMed1993

A hardware efficient cascadable chip set for ANN's with on-chip backpropagation.

In this paper, an analogue, cascadable, CMOS chip set for artificial neural networks is presented. The chip set (a synapse chip and a neuron chip) offer on-chip back-propagation learning in a fully parallel, layered, feedforward network of arbitrary size and topology. The learning scheme is implemented with no extra circuits at the synapse sites (compared to the system without the learning scheme) and extra circuits of a complexity only about the same as the neurons at the neuron sites. Also, no additional wiring is required by the learning scheme. Measurements on an experimental chip set are presented.

Algorithms↗
PubMed2004

[Natriuretic peptides--new diagnostic markers in heart disease].

In patients with heart failure, increased wall stretch due to volume and pressure overload leads to an increase in circulating natriuretic peptides (ANP and BNP and their N-terminal fragments NT-proANP and NT-proBNP). Plasma BNP levels commonly considered normal (< 20 pg/ml) are influenced by age, sex, and also by genetic factors. ANP and BNP are synthesized and released by atrial and ventricular myocytes (Figure 1). In subjects with acute dyspnea, a BNP plasma concentration of 100 pg/ml has been established as a cutoff value for the diagnosis of heart failure yielding a very high negative predictive value coupled with an acceptable positive predictive value (Figure 3). However, recent evidence suggests that much more subtle elevations of plasma BNP may also indicate an increased long-term risk of cardiovascular events and death (Figure 2). In acute heart failure, natriuretic peptides correlate with ventricular pressure and volume overload, as well as with NYHA functional class. They can, however, not reliably discriminate between heart failure due to reduced ejection fraction and heart failure with preserved systolic function (Figure 4). Thus, elevated BNP or NT-proBNP levels always demand further clarification of heart failure etiology using echocardiography as the method of choice. As indicated by the algorithm for a BNP-based differential diagnosis of acute heart failure symptoms (Figure 5), a variety of noncardiac causes may also lead to moderate elevations of the markers (BNP plasma concentrations of 100-400 pg/ml). In addition, normal marker levels may be observed in > 20% of patients with long-term stable heart failure. Thus, increased plasma concentrations of natriuretic peptides are not strictly specific for heart diseases and also lack sensitivity in the chronic compensated state. Diuretics, angiotensin-converting enzyme (ACE) inhibitors, angiotensin receptor antagonists, and spironolactone have been shown to decrease BNP and NT-proBNP in parallel with clinical and hemodynamic improvement. In patients hospitalized for decompensated heart failure, predischarge plasma BNP levels reflect the risk of future death and rehospitalization (Figure 6). Although adjusting heart failure treatment to reduce plasma NT-proBNP levels may improve outcome, a general recommendation for monitoring drug therapy using this marker should not be derived from this observation. General practitioners may, in the future, use BNP or NT-proBNP as a rule-out test for heart failure and preselect patients for further diagnostic work-up on the basis of an elevated plasma level. Within the framework of the German network for heart failure the multicentric "Handheld-BNP Study" will clarify, whether echocardiography using low-price simple handcarried devices could be used as an alternative or, more likely, as a complementary diagnostic tool to further improve heart failure diagnosis in primary care.

Biomarkers↗
PubMed2003

[Artificial neural networks. Theory and applications in anesthesia, intensive care and emergency medicine].

Artificial neural networks (ANN) are constructed to simulate processes of the central nervous system of higher creatures. An ANN consists of a set of processing units (nodes) which simulate neurons and are interconnected via a set of "weights" (analogous to synaptic connections in the nervous system) in a way which allows signals to travel through the network in parallel. The nodes (neurons) are simple computing elements. They accumulate input from other neurons by means of a weighted sum. If a certain threshold is reached the neuron sends information to all other connected neurons otherwise it remains quiescent. One major difference compared with traditional statistical or rule-based systems is the learning aptitude of an ANN. At the very beginning of a training process an ANN contains no explicit information. Then a large number of cases with a known outcome are presented to the system and the weights of the inter-neuronal connections are changed by a training algorithm designed to minimise the total error of the system. A trained network has extracted rules that are represented by the matrix of the weights between the neurons. This feature is called generalisation and allows the ANN to predict cases that have never been presented to the system before. Artificial neural networks have shown to be useful predicting various events. Especially complex, non-linear, and time depending relationships can be modelled and forecasted. Furthermore an ANN can be used when the influencing variables on a certain event are not exactly known as it is the case in financial or weather forecasts. This article aims to give a short overview on the function of ANN and their previous use and possible future applications in anaesthesia, intensive care, and emergency medicine.

Anesthesiology↗
PubMed2005

A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions.

Classical molecular dynamics simulations of biological macromolecules in explicitly modeled solvent typically require the evaluation of interactions between all pairs of atoms separated by no more than some distance R, with more distant interactions handled using some less expensive method. Performing such simulations for periods on the order of a millisecond is likely to require the use of massive parallelism. The extent to which such simulations can be efficiently parallelized, however, has historically been limited by the time required for interprocessor communication. This article introduces a new method for the parallel evaluation of distance-limited pairwise particle interactions that significantly reduces the amount of data transferred between processors by comparison with traditional methods. Specifically, the amount of data transferred into and out of a given processor scales as O(R(3/2)p(-1/2)), where p is the number of processors, and with constant factors that should yield a substantial performance advantage in practice.

Algorithms↗
PubMed2006

Proteome informatics II: bioinformatics for comparative proteomics.

The present review attempts to cover the most recent initiatives directed towards representing, storing, displaying and processing protein-related data suited to undertake "comparative proteomics" studies. Data interpretation is brought into focus. Efforts invested into analysing and interpreting experimental data increasingly express the need for adding meaning. This trend is perceptible in work dedicated to determining ontologies, modelling interaction networks, etc. In parallel, technical advances in computer science are spurred by the development of the Web and the growing need to channel and understand massive volumes of data. Biology benefits from these advances as an application of choice for many generic solutions. Some examples of bioinformatics solutions are discussed and directions for on-going and future work conclude the review.

Algorithms↗
PubMed1997

Developments in cardiovascular ultrasound: Part 1: Signal processing and instrumentation.

One of the major contributions to the improvement of spectral Doppler and colour flow imaging instruments has been the development of advanced signal-processing techniques made possible by increasing computing power. Model-based or parametric spectral estimators, time-frequency transforms, station-arising algorithms and spectral width correction techniques have been investigated as possible improvements on the FFT-based estimators currently used for real-time spectral estimation of Doppler signals. In colour flow imaging some improvement on velocity estimation accuracy has been achieved by the use of new algorithms but at the expense of increased computational complexity compared with the conventional autocorrelation method. Polynomial filters have been demonstrated to have some advantages over IIR filters for stationary echo cancellation. Several methods of velocity vector estimation to overcome the problem of angle dependence have been studied, including 2D feature tracking, two and three beam approaches and the use of spectral width in addition to mean frequency. 3D data acquisition and display and Doppler power imaging have also been investigated. The use of harmonic imaging, using the second harmonic generated by encapsulated bubble contrast media, seems promising particularly for imaging slow flow. Parallel image data acquisition using non-sequential scanning or broad beam transmission, followed by simultaneous reception along a number of beams, has been studied to speed up 'real-time' imaging.

Blood Flow Velocity↗
PubMed1994

A variable-resolution rotate-only computed tomography scanner.

The Rotoscan is a computed tomography scanner that combines the advantages of variable geometric resolution and adjustable size of measurement diameter of translate-rotate scanners with the improved speed of rotate-only scanners. Because of the small number of only 26 detectors used for this scanner, a special data collection scheme of multiple rotations with interleaved detector positions was employed. In order to avoid angular data interpolation after reordering of the projections from the fan- to a parallel-beam geometry, the detectors were incrementally moved at a right angle to the centerline of the fan rather than rotated about the source. The measurement time of 40 s for one cross-section is comparable to that of second-generation systems. However, for longer measurement diameters, the measurement time for second-generation systems increases, whereas that of the Rotoscan remains constant.

Algorithms↗
PubMed1994

Nutrition support, supplementation, and replacement.

Nutrition support in acute, chronic, or home care settings can be implemented successfully by the well-informed primary care physician, who often is the first to identify poor nutritional health in his or her patients. Using established protocols for the identification or of risk factors and indicators of malnutrition, specific alerts to the need for nutrition support are presented. The logical approach to nutrition support interventions through four stages representing the gradual increase in complexity and cost, paralleling the progressive inability to use regular foods and the gastrointestinal tract are discussed. Specific, practical measures that can be recommended and implemented by the primary care physician managing the older person are presented. The ethical, legal, and home health aspects of nutrition support in the care of the older American by the primary care physician are also reviewed.

Aged↗