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PubMed2005

Imaging anisotropic and viscous properties of breast tissue by magnetic resonance-elastography.

MR-elastography is a new technique for assessing the viscoelastic properties of tissue. One current focus of elastography is the provision of new physical parameters for improving the specificity in breast cancer diagnosis. This analysis describes a technique to extend the reconstruction to anisotropic elastic properties in terms of a so-called transversely isotropic model. Viscosity is treated as being isotropic. The particular model chosen for the anisotropy is appealing because it is capable of describing elastic shear anisotropy of parallel fibers. The dependence of the reconstruction on the particular choice of Poisson's ratio is eliminated by extracting the compressional displacement contribution using the Helmholtz-Hodge decomposition. Results are presented for simulations, a polyvinyl alcohol breast phantom, excised beef muscle, and measurements in two patients with breast lesions (invasive ductal carcinoma and fibroadenoma). The results show enhanced anisotropic and viscous properties inside the lesions and an indication for preferred fiber orientation.

Algorithms↗
PubMed2005

Combination of optimized transmit arrays and some receive array reconstruction methods can yield homogeneous images at very high frequencies.

Image inhomogeneity related to high radiofrequencies is one of the major challenges for high field imaging. This inhomogeneity can be thought of as having 2 radiofrequency-field related contributors: the transmit field distribution and the reception field distribution. Adjusting magnitude and phase of currents in elements of a transmit array can significantly improve flip angle homogeneity at high field. Effective application of some well-known parallel imaging and other receive array post-processing methods removes receptivity patterns from the intensity distribution in the final image, though noise then becomes a function of position in the final image. Here simulations are used to show that, assuming high signal-to-noise ratio, very homogeneous images in the human head can be acquired with the combination of transmit arrays and some receive array reconstruction methods at frequencies as high as 600 MHz.

Algorithms↗
PubMed2004

Sequence context and modified hydrophobic moment plots help identify 'horizontal' surface helices in transmembrane protein structure prediction.

Transmembrane proteins make up at least one-fifth of the genome of most organisms and are critical components of key pathways for cell survival and interactions with the environment. The function of helices found at the membrane surface in transmembrane proteins has not been greatly explored, but it is likely that they play an ancillary role to membrane spanning helices and are analogous to the surface active helices of peripheral membrane proteins, being involved in: lipid association, membrane perturbation, transmembrane signal transduction and regulation, and transmembrane helical bundle formation. Due to the difficulties in obtaining high-resolution structural data for this class of proteins, structure-from-sequence predictive methods continue to be developed as a means to obtain structural models for these largely intractable systems. A simple but effective variant of the hydrophobic moment analysis of amino acid sequences is described here as part of a protocol for distinguishing helical sequences that are parallel to or 'horizontal' at the membrane bilayer/aqueous phase interface from helices that are membrane-embedded or located in extra-membranous domains. This protocol when tested on transmembrane spanning protein amino acid sequences not used in its development, was found to be 84-91% accurate when the results were compared to the partition locations in the corresponding structures determined by X-ray crystallography, and 72% accurate in determining which helices lie horizontal or near horizontal at the lipid interface.

Algorithms↗
PubMedDate not supplied

Hybrid visualization for white matter tracts using triangle strips and point sprites.

Diffusion tensor imaging is of high value in neurosurgery, providing information about the location of white matter tracts in the human brain. For their reconstruction, streamline techniques commonly referred to as fiber tracking model the underlying fiber structures and have therefore gained interest. To meet the requirements of surgical planning and to overcome the visual limitations of line representations, a new real-time visualization approach of high visual quality is introduced. For this purpose, textured triangle strips and point sprites are combined in a hybrid strategy employing GPU programming. The triangle strips follow the fiber streamlines and are textured to obtain a tube-like appearance. A vertex program is used to orient the triangle strips towards the camera. In order to avoid triangle flipping in case of fiber segments where the viewing and segment direction are parallel, a correct visual representation is achieved in these areas by chains of point sprites. As a result, a high quality visualization similar to tubes is provided allowing for interactive multimodal inspection. Overall, the presented approach is faster than existing techniques of similar visualization quality and at the same time allows for real-time rendering of dense bundles encompassing a high number of fibers, which is of high importance for diagnosis and surgical planning.

Algorithms↗
PubMed2006

Aggregation during fruiting body formation in Myxococcus xanthus is driven by reducing cell movement.

When starved, Myxococcus xanthus cells assemble themselves into aggregates of about 10(5) cells that grow into complex structures called fruiting bodies, where they later sporulate. Here we present new observations on the velocities of the cells, their orientations, and reversal rates during the early stages of fruiting body formation. Most strikingly, we find that during aggregation, cell velocities slow dramatically and cells orient themselves in parallel inside the aggregates, while later cell orientations are circumferential to the periphery. The slowing of cell velocity, rather than changes in reversal frequency, can account for the accumulation of cells into aggregates. These observations are mimicked by a continuous agent-based computational model that reproduces the early stages of fruiting body formation. We also show, both experimentally and computationally, how changes in reversal frequency controlled by the Frz system mutants affect the shape of these early fruiting bodies.

Algorithms↗
PubMedDate not supplied

Neural networks in clinical medicine.

Neural networks are parallel, distributed, adaptive information-processing systems that develop their functionality in response to exposure to information. This paper is a tutorial for researchers intending to use neural nets for medical decision-making applications. It includes detailed discussion of the issues particularly relevant to medical data as well as wider issues relevant to any neural net application. The article is restricted to back-propagation learning in multilayer perceptrons, as this is the neural net model most widely used in medical applications.

Algorithms↗
PubMed1990

Distributed parallel processing in the vertical vestibulo-ocular reflex: learning networks compared to tensor theory.

The vestibulo-ocular reflex (VOR) is capable of producing compensatory eye movements in three dimensions. It utilizes the head rotational velocity signals from the semicircular canals to control the contractions of the extraocular muscles. Since canal and muscle coordinate frames are not orthogonal and differ from one another, a sensorimotor transformation must be produced by the VOR neural network. Tensor theory has been used to construct a linear transformation that can model the three-dimensional behavior of the VOR. But tensor theory does not take the distributed, redundant nature of the VOR neural network into account. It suggests that the neurons subserving the VOR, such as vestibular nucleus neurons, should have specific sensitivity-vectors. Actual data, however, are not in accord. Data from the cat show that the sensitivity-vectors of vestibular nucleus neurons, rather than aligning with any specific vectors, are dispersed widely. As an alternative to tensor theory, we modeled the vertical VOR as a three-layered neural network programmed using the back-propagation learning algorithm. Units in mature networks had divergent sensitivity-vectors which resembled those of actual vestibular nucleus neurons in the cat. This similarity suggests that the VOR sensorimotor transformation may be represented redundantly rather than uniquely. The results demonstrate how vestibular nucleus neurons can encode the VOR sensorimotor transformation in a distributed manner.

Animals↗
PubMed2006

Comparison of possible arrangements of five identical columns in preparative chromatography.

Goal of the paper is to demonstrate how configuration of a certain number of identical HPLC columns influences on the effectiveness of the isolation of a target component. There are two extreme configurations: all the available columns are operated in parallel (provided there are enough pumps available) or all the columns are connected in series. Various combinations of columns connected parallel and in series are possible. Besides batch operation more sophisticated multicolumn arrangements allowing continuous separation are considered. In particular, in this work different configurations of five columns were examined. For illustration the separation of a binary mixture was considered. As the objective function the productivity of the less retained component has been used. A standard model capable to describe the propagation of chromatographic bands has been used to optimize the operating conditions for various possible multicolumn arrangements.

Algorithms↗
PubMed2006

Using two-dimensional spatial information in decomposition of surface EMG signals.

Recently, high-density surface EMG electrode grids and multi-channel amplifiers became available for non-invasive recording of human motor units (MUs). We present a way to decompose surface EMG signals into MU firing patterns, whereby we concentrate on the importance of two-dimensional spatial differences between the MU action potentials (MUAPs). Our method is exemplified with high-density EMG data from the vastus lateralis muscle of a single subject. Bipolar and Laplacian spatial filtering was applied to the monopolar raw signals. From the single recording in this subject six different simultaneously active MUs could be distinguished using the spatial differences between MUAPs in the direction perpendicular to the muscle fiber direction. After spike-triggered averaging, 125-channel two-dimensional MUAP templates were obtained. Template-matching allowed tracking of all MU firings. The impact of spatial information was measured by using subsets of the MUAP templates, either in parallel or perpendicular to the muscle fiber direction. The use of one-dimensional spatial information perpendicular to the muscle fiber direction was superior to the use of a linear array electrode in the longitudinal direction. However, to detect the firing events of the MUs with a high accuracy, as needed for instance for estimation of firing synchrony, two-dimensional information from the complete grid electrode appears essential.

Action Potentials↗
PubMed1994

Pinhole collimation for ultra-high-resolution, small-field-of-view SPECT.

The objective of this investigation was to evaluate small-field-of-view, ultra-high-resolution pinhole collimation for a rotating-camera SPECT system that could be used to image small laboratory animals. Pinhole collimation offers distinct advantages over conventional parallel-hole collimation when used to image small objects. Since geometric sensitivity increases markedly for points close to the pinhole, small-diameter and high-magnification pinhole geometries may be useful for selected imaging tasks when used with large-field-of-view scintillation cameras. The use of large magnifications can minimize the loss of system resolution caused by the intrinsic resolution of the scintillation camera. A pinhole collimator has been designed and built that can be mounted on one of the scintillation cameras of a triple-head SPECT system. Three pinhole inserts with approximate aperture diameters of 0.6, 1.2 and 2.0 mm have been built and can be mounted individually on the collimator housing. When a ramp filter is used with a three-dimensional (3D) filtered backprojection (FBP) algorithm, the three apertures have in-plane SPECT spatial resolutions (FWHM) at 4 cm of 1.5, 1.9 and 2.8 mm, respectively. In-air point source sensitivities at 4 cm from the apertures are 0.9, 2.6 and 5.7 counts s(-1) microCi(-1) (24, 70 and 154 counts s(-1) MBq(-1)) for the 0.6, 1.2 and 2.0 mm apertures, respectively. In vitro image quality was evaluated with a micro-cold-rod phantom and a micro-Defrise phantom using both the 3D FBP algorithm and a 3D maximum likelihood-expectation maximization (ML-EM) algorithm. In vivo image quality was evaluated using two (315 and 325 g) rats. Ultra-high-resolution pinhole SPECT is an inexpensive and simple approach for imaging small animals that can be used with existing rotating-camera SPECT system.

Algorithms↗
PubMed2006

Volume measurement variability in three-dimensional high-frequency ultrasound images of murine liver metastases.

The identification and quantification of tumour volume measurement variability is imperative for proper study design of longitudinal non-invasive imaging of pre-clinical mouse models of cancer. Measurement variability will dictate the minimum detectable volume change, which in turn influences the scheduling of imaging sessions and the interpretation of observed changes in tumour volume. In this paper, variability is quantified for tumour volume measurements from 3D high-frequency ultrasound images of murine liver metastases. Experimental B16F1 liver metastases were analysed in different size ranges including less than 1 mm3, 1-4 mm3, 4-8 mm3 and 8-70 mm3. The intra- and inter-observer repeatability was high over a large range of tumour volumes, but the coefficients of variation (COV) varied over the volume ranges. The minimum and maximum intra-observer COV were 4% and 14% for the 1-4 mm3 and <1 mm3 tumours, respectively. For tumour volumes measured by segmenting parallel planes, the maximum inter-slice distance that maintained acceptable measurement variability increased from 100 to 600 microm as tumour volume increased. Comparison of free breathing versus ventilated animals demonstrated that respiratory motion did not significantly change the measured volume. These results enable design of more efficient imaging studies by using the measured variability to estimate the time required to observe a significant change in tumour volume.

Algorithms↗
PubMed1993

Multiple alignment of sequences on parallel computers.

A software package that allows one to carry out multiple alignment of protein and nucleic acid sequences of almost unlimited length and number of sequences is developed on C-DAC parallel computer--a transputer-based machine. The farming approach is used for data parallelization. The speed gains are almost linear when the number of transputers is increased from 4 to 64. The software is used to carry out multiple alignment of 100 sequences each of alpha-chain and beta-chain of hemoglobin and 83 cytochrome c sequences. The signature sequence of cytochrome c was found to be PGTKMXF. The single parameter, multiple alignment score, S, has been used to categorize proteins in different subfamilies and groups.

Algorithms↗
PubMed2002

Evaluation of complex joint motion with computer-based analysis of fluoroscopic sequences.

RATIONALE AND OBJECTIVES: To develop a computer-assisted analysis of complex joint motion based on standard fluoroscopic sequences. MATERIALS AND METHODS: Fluoroscopic sequences of 10 normal shoulders and 20 patients after total shoulder arthroplasty were recorded during abduction and adduction. The analysis of the shoulder motion was based on automated tracking of selected components (models) of the shoulder joint. After processing the digitized images with an edge-detection procedure, visible edges were defined as base models. These models were tracked frame by frame. Several automated postprocessing evaluation procedures were developed and tested. RESULTS: The amounts of rotation and translation of the glenohumeral joint can be quantified and related. The mean translation parallel to the glenoid in the normal shoulder joints was 2.8 mm and 1.9 mm in joints after shoulder arthroplasty. The mean translation perpendicular to the glenoid was 0.9 mm and 0.8 mm, respectively. In complex motion patterns (ie, combined glenohumeral and thoracoscapular motion), electronic stabilization of an object (ie, stabilization of scapula) and, thus, separate analysis of each component. CONCLUSION: Computer assisted analysis allows automated evaluation of complex joint motion based on standard fluoroscopic sequences.

Algorithms↗
PubMed2004

Conversion of brain SPECT images between different collimators and reconstruction processes for analysis using statistical parametric mapping.

To make it possible to share a normal database in single photon emission computed tomography (SPECT) studies, we developed a new method for converting a SPECT image in one physical condition to that in another condition for data acquisition and reconstruction. A Hoffman 3-dimensional brain phantom experiment was conducted to determine systematic differences between collimators and reconstruction processes. SPECT images for the brain phantom were obtained using fan-beam collimators with scatter and attenuation corrections and using parallel-hole collimators without any correction. Dividing these two phantom images after anatomical standardization by Statistical Parametric Mapping 99 (SPM99) created a 3-dimensional conversion map. This conversion map was applied to convert an anatomically standardized SPECT image using parallel-hole collimators without any correction to that using fan-beam collimators with scatter and attenuation corrections in eleven subjects who underwent sequential SPECT measurements using different collimators after injection of 99mTc ethyl cysteinate dimer. The SPM99 demonstrated adequate validity of this conversion in comparative analyses of these sequential SPECT images with different collimators. This may be a promising approach for further sharing of a normal database in SPECT imaging between different cameras.

Adult↗
PubMed2002

Enhancement of L-cystine transport activity and its relation to xCT gene induction at the blood-brain barrier by diethyl maleate treatment.

The purpose of the present study was to elucidate the mechanism of enhancement of L-cystine uptake at the blood-brain barrier (BBB). The uptake of [(14)C]L-cystine and [(3)H]L-glutamic acid (L-Glu) was determined using a mouse brain endothelial cell line (MBEC4) as an in vitro BBB model. The mRNA levels of L-cystine/L-Glu exchanger, system x(c)(-), which consists of xCT and 4F2hc, were determined by quantitative real-time reverse transcription-polymerase chain reaction analysis. The [(14)C]L-cystine uptake by MBEC4 cells appeared to be mediated via an Na(+)-independent saturable process. The corresponding Michaelis-Menten constant (K(m)) was 63.7 microM. In the presence of L-Glu, there was competitive inhibition with an inhibition constant (K(i)) of 83.5 microM. [(3)H]L-Glu uptake in the absence of Na(+) was saturable with a K(m) of 48.1 microM, and it exhibited competitive inhibition with a K(i) of 24.9 microM in the presence of L-cystine. The mutual inhibition between L-cystine and L-Glu and the type of inhibition suggest that system x(c)(-) operates in MBEC4 cells. The xCT and 4F2hc mRNAs were expressed in MBEC4 cells and, following diethyl maleate (DEM) treatment, the xCT mRNA level and L-cystine uptake in MBEC4 cells were enhanced in parallel with an increase in DEM concentration (up to 500 microM). Concomitantly, the glutathione concentration in MBEC4 cells was increased. In conclusion, system x(c)(-)-mediated L-cystine uptake takes place in MBEC4 cells. L-Cystine transport via system x(c)(-) at the BBB is likely to be induced under oxidative stress conditions following DEM treatment due to enhanced transcription of the xCT gene.

Algorithms↗
PubMed1994

Performance assessment of coupled tests: the effects of statistical non-independence.

Limited to two-test associations (series and parallel schemes), the effects of statistical non-independence were studied through a mathematical approach and an experimentally-based evaluation. Both procedures were applied to results for total hormones and free fractions in euthyroid and dysthyroid subjects. Assuming independence, the sensitivity of combined tests was found to increase in parallel coupling, and to decrease, symmetrically, in series coupling, depending critically on the degree of between-test correlation and on the value of single test sensitivity (the opposite modifications obviously occur for specificity). A more complicated situation resulted for the predictive value of test associations, where a prediction based on a mathematical model was found not to be generally valid; in this case, calculations using the correct values of conditional probabilities of coupled tests seemingly remain the safest procedure.

Algorithms↗
PubMed2004

Relationship between follicle-stimulating hormone levels at the beginning of the human menstrual cycle, length of the follicular phase and excreted estrogens: the FREEDOM study.

Although reproductive aging has been separately related to elevated FSH and shorter follicular phase (FP), the direct association between both parameters has not been investigated. Also, the exact effects of increased FSH on estrogen production are yet to be established.A large database of daily urinary concentrations of FSH, LH, and estrone 3-glucuronide (E1G) from 37 regularly menstruating women (median 11 cycles per patient) was used. Initial FSH levels (iFSH) were estimated as the mean value of d 1-5. The day of E1G take-off (ETO) was determined by an algorithm, and accordingly, the FP was divided into early (d 1 to ETO) and late (ETO+1 to LH peak). FP maximum and integrated E1G were calculated. Subjects were distributed according to their mean iFSH into three categories (</=5, >5 to 10, and >10 IU/liter). There was a gradual decrease in FP length with increasing category (15.2 +/- 3.8, 14.1 +/- 3.6, and 13 +/- 2.6 d, respectively; P < 0.0001). A similar effect occurred in early FP (7.5 +/- 4, 6.4 +/- 3.7, and 5.4 +/- 2.7; P < 0.0001); in contrast, late FP was unaffected (7.7 +/- 2.1, 7.7 +/- 2.1, and 7.6 +/- 2.4; P = 0.86). No consistent increase in E1G was found with advancing iFSH category; however, women with mean initial LH higher than 6 IU/liter had significantly elevated maximum (P < 0.0001) and integrated (P = 0.002) E1G.FP length decreases in parallel with increasing iFSH, with a selective effect on the early FP. Increased FSH does not affect E1G; however, elevated initial LH level was related to higher E1G.

Adult↗
PubMed2004

MCDE: a new Monte Carlo dose engine for IMRT.

A new accurate Monte Carlo code for IMRT dose computations, MCDE (Monte Carlo dose engine), is introduced. MCDE is based on BEAMnrc/DOSXYZnrc and consequently the accurate EGSnrc electron transport. DOSXYZnrc is reprogrammed as a component module for BEAMnrc. In this way both codes are interconnected elegantly, while maintaining the BEAM structure and only minimal changes to BEAMnrc.mortran are necessary. The treatment head of the Elekta SLiplus linear accelerator is modelled in detail. CT grids consisting of up to 200 slices of 512 x 512 voxels can be introduced and up to 100 beams can be handled simultaneously. The beams and CT data are imported from the treatment planning system GRATIS via a DICOM interface. To enable the handling of up to 50 x 10(6) voxels the system was programmed in Fortran95 to enable dynamic memory management. All region-dependent arrays (dose, statistics, transport arrays) were redefined. A scoring grid was introduced and superimposed on the geometry grid, to be able to limit the number of scoring voxels. The whole system uses approximately 200 MB of RAM and runs on a PC cluster consisting of 38 1.0 GHz processors. A set of in-house made scripts handle the parallellization and the centralization of the Monte Carlo calculations on a server. As an illustration of MCDE, a clinical example is discussed and compared with collapsed cone convolution calculations. At present, the system is still rather slow and is intended to be a tool for reliable verification of IMRT treatment planning in the case of the presence of tissue inhomogeneities such as air cavities.

Adenocarcinoma↗