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An objective function for radiation treatment optimization based on local biological measures.

The implementation of biological optimization of radiation treatment plans is impeded by both computational and modelling problems. We derive an objective function from basic model assumptions which includes the normal tissue constraints as interior penalty functions. For organs that are composed of parallel subunits, a mean response model is proposed which leads to constraints similar to dose-volume constraints. This objective function is convex in the case when no parallel organs lie in the treatment volume. Otherwise, an argument is given to show that a number of local minima may exist which are near degenerate to the global minimum. Thus, together with the measure quality of the objective function, highly efficient gradient algorithms can be used. The number of essential biological model parameters could be reduced to a minimum. However, if the optimization constraints are given as TCP/NTCP values, Lagrange multiplier updates have to be performed by invoking comprehensive biological models.

Humans↗

Input minimization: a model of cerebellar learning without climbing fiber error signals.

The cerebellum is critical for motor learning. Current cerebellar learning models follow the Marr/Albus paradigm, in which climbing fibers provide error signals that shape plastic synapses between parallel fibers and Purkinje cells. However, climbing fibers have slow and largely random discharge, and seem unlikely to provide error signals with resolution sufficient to guide cerebellar learning. Parallel fibers carry error signals and could direct the plasticity of their own synapses, but the error signals are carried along with other signals. This report presents the new input minimization (InMin) model, in which Purkinje cells reduce error by minimizing their overall parallel fiber input. The slowly, randomly firing climbing fiber provides only synchronization pulses. InMin offers an alternative that can unify cerebellar findings.

Action Potentials↗

Implementation of FFT convolution and multigrid superposition models in the FOCUS RTP system.

In radiotherapy treatment planning, convolution/superposition algorithms currently represent the best practical approach for accurate photon dose calculation in heterogeneous tissues. In this work, the implementation, accuracy and performance of the FFT convolution (FFTC) and multigrid superposition (MGS) algorithms are presented. The FFTC and MGS models use the same 'TERMA' calculation and are commissioned using the same parameters. Both models use the same spectra, incorporate the same off-axis softening and base incident lateral fluence on the same measurements. In addition, corrections are explicitly applied to the polyenergetic and parallel kernel approximations, and electron contamination is modelled. Spectra generated by Monte Carlo (MC) modelling of treatment heads are used. Calculations using the MC spectra were in excellent agreement with measurements for many linear accelerator types. To speed up the calculations, a number of calculation techniques were implemented, including separate primary and scatter dose calculation, the FFT technique which assumes kernel invariance for the convolution calculation and a multigrid (MG) acceleration technique for the superposition calculation. Timing results show that the FFTC model is faster than MGS by a factor of 4 and 8 for small and large field sizes, respectively. Comparisons with measured data and BEAM MC results for a wide range of clinical beam setups show that (a) FFTC and MGS doses match measurements to better than 2% or 2 mm in homogeneous media; (b) MGS is more accurate than FFTC in lung phantoms where MGS doses are within 3% or 3 mm of BEAM results and (c) FFTC overestimates the dose in lung by a maximum of 9% compared to BEAM.

Algorithms↗

Toward computerized morphometric facilities: a review of 58 software packages for computer-aided three-dimensional reconstruction, quantification, and picture generation from parallel serial sections.

This review gives an inventory of 58 computer-aided three-dimensional reconstruction applications in the domain of biomedical research. It is devoted to the formulation of a set of recommendations thought to be necessary for improved performance of software packages in this field. These recommendations can be used to select packages and to guide future developments of existing reconstruction systems. The survey is restricted to three-dimensional reconstructions based upon a series of parallel sections of an object. Subjects treated are programming languages, resolution and sampling, input preparation, realignment, local deformation of slices, numerical quantifications, topological complexity, internal representation, display complexity (hidden surfaces, shading, smoothing), structure extraction, descriptive elements, database, data compression, time efficiency of systems and algorithms, hardware configuration, input devices, input media, interactive aids, display devices, and output devices. Information for this survey comes from articles that appeared between 1965 and 1985.

Computers↗

Clinical management of acute and chronic cocaine poisoning.

At the Haight-Ashbury Free Medical Clinics in San Francisco, the recreational use of cocaine is on a precipitous incline of popularity. Intensified symptoms of intoxication and the possibility of overdose parallel the current fad of smoking "freebase." We examined the "cocaine reaction," an adrenergic storm affecting CNS, respiratory and cardiovascular systems, which may proceed to generalized collapse and death within minutes. The physiologic and pharmacologic mechanisms of the reaction are elaborated, and a logical algorithm of treatment is outlined. The psychodynamics of the "armed" cocaine personality is discussed, as is the proper psychological approach to these patients. A specific indicated technical and pharmacologic approach, as well as several caveats of therapy that have been clinically developed in the treatment of several hundred cases of cocaine overdose, are presented.

Brain↗

A triple-head SPECT system with parallel-hole collimators of different acceptance angles.

We proposed to use three different parallel-hole collimators for a triple-head SPECT system. One of the collimators had a small collimator acceptance angle to provide ultra-high spatial resolution and the other two had larger collimator acceptance angles to achieve high counts. A new 2D reconstruction algorithm that combined the data acquired from different collimators was derived to take advantages of both high resolution and high sensitivity. The algorithm was evaluated using a computer-simulated matrix of spherical sources. For noise-free data, the accuracy (mainly determined by spatial resolution) obtained from combination of the collimator acceptance angles of 1.35, 4.05 and 6.75 degrees (or 1.35, 5.40 and 9.45 degrees) was slightly inferior to that obtained from three same LEHR collimators (with a 2.70 degrees collimator acceptance angle). This is because the modulation transfer function (MTF) resulting from three different collimators decreases more quickly at low frequencies but becomes comparable at high frequencies as compared with the MTF of the 2.70 degrees collimator. With noisy data, however, the image quality obtained with three different collimators was better than that resulting from any combinations of three same collimators. The improvement was only achieved by using the derived algorithm, while the conventional FBP algorithm did not improve image quality even with the same collimator configuration.

Algorithms↗

The plastic coupled map lattice: A novel image-processing paradigm.

Coupled map lattices (CML) can describe many relaxation and optimization algorithms currently used in image processing. We recently introduced the "plastic-CML" as a paradigm to extract (segment) objects in an image. Here, the image is applied by a set of forces to a metal sheet which is allowed to undergo plastic deformation parallel to the applied forces. In this paper we present an analysis of our "plastic-CML" in one and two dimensions, deriving the nature and stability of its stationary solutions. We also detail how to use the CML in image processing, how to set the system parameters and present examples of it at work. We conclude that the plastic-CML is able to segment images with large amounts of noise and large dynamic range of pixel values, and is suitable for a very large scale integration (VLSI) implementation.

Journal Article↗

Subsystem identification through dimensionality reduction of large-scale gene expression data.

The availability of parallel, high-throughput biological experiments that simultaneously monitor thousands of cellular observables provides an opportunity for investigating cellular behavior in a highly quantitative manner at multiple levels of resolution. One challenge to more fully exploit new experimental advances is the need to develop algorithms to provide an analysis at each of the relevant levels of detail. Here, the data analysis method non-negative matrix factorization (NMF) has been applied to the analysis of gene array experiments. Whereas current algorithms identify relationships on the basis of large-scale similarity between expression patterns, NMF is a recently developed machine learning technique capable of recognizing similarity between subportions of the data corresponding to localized features in expression space. A large data set consisting of 300 genome-wide expression measurements of yeast was used as sample data to illustrate the performance of the new approach. Local features detected are shown to map well to functional cellular subsystems. Functional relationships predicted by the new analysis are compared with those predicted using standard approaches; validation using bioinformatic databases suggests predictions using the new approach may be up to twice as accurate as some conventional approaches.

Algorithms↗

Dynamic tracking in interventional MRI using wavelet-encoded gradient-echo sequences.

This work describes a newly developed magnetic resonance imaging (MRI) data-acquisition strategy which replaces the standard Fourier phase-encoding with the spatially localized coefficients of wavelet-encoding and offers a new technique for image guidance when combined with a dynamic tracking algorithm. By using this new technique, only a specific fraction of the entire raw data set needs to be updated and reconstructed to visualize the movement of an interventional device during an MR guided procedure. The combination of wavelet-encoding and a dynamic tracking algorithm was implemented in two-dimensional and three-dimensional gradient-echo sequences on a 0.2-T open C-arm-shaped MR system (Siemens, Erlangen Germany) and tested in phantom and in vitro experiments. When applying the wavelet-encoding direction parallel to the movement of a straight interventional device, only those spatially localized wavelet-coefficients mainly affected by the interventional device are updated. This led to potential increases of the image frame rate by a factor of up to seven.

Animals↗

Using the Potts glass for solving the clustering problem.

We present an application of a Potts glass to the clustering problem. Simulated annealing in the mean field approximation is used in order to avoid local minima. The resulting updating equations are completely parallel, and very easy to implement. The model has no free parameters except for the annealing parameters. We show how the model can be implemented for some special clustering problems. The T-->0 limit of the Potts glass is identical to the vector quantization algorithm with certain increments. A comparative study of the Potts glass and vector quantization is also made, and it is shown that for difficult clustering problems, the Potts glass is far better than vector quantization.

Algorithms↗

Bilateral inhibition generates neuronal responses tuned to interaural level differences in the auditory brainstem of the barn owl.

I investigated the neural algorithms by which neurons gain selectivity for interaural level difference in the brainstem of the barn owl (Tyto alba). Differences in the timing and in the level of sounds at the ears are used by this owl to encode, respectively, azimuthal and vertical position of sound sources in space. These two cues are processed in two parallel neural pathways. Below the level of the inferior colliculus, all neurons in the pathway that processes level differences show responses to this cue that are monotonic, and thus not selective for a particular level difference. Only in the inferior colliculus, which contains a map of auditory space, are neurons sharply tuned to specific interaural level differences. How are these response properties generated from those of the nuclei that provide input to the inferior colliculus? I show that the posterior subdivision of the nucleus ventralis lemnisci lateralis (VLVp) projects bilaterally to the lateral shell of the central nucleus of the inferior colliculus, the input stage to the map of auditory space. Both these nuclei are part of the pathway that processes interaural level differences. Manipulations of the responses in VLVp affected the responses to level differences in the inferior colliculus; responses to time differences were unaffected. By systematically increasing or decreasing neural activity in VLVp, I show that the VLVp on each side provides inhibition to the colliculus at large level differences. This results in a peaked response that is tuned to level differences in the inferior colliculus. Some cells in the lateral shell of the inferior colliculus appear to receive direct GABAergic inhibition from VLVp. I suggest that this circuitry and the algorithms it supports are the neural substrates that allow the barn owl to exploit level differences for computation of sound source elevation.

Acoustic Stimulation↗

The cellular computer DNA: program or data.

The classical metaphor of the genetic program written in the DNA nucleotidic sequences is reconsidered. Recent works on algorithmic complexity and logical properties of computer programs and data are used to question the explanatory value of that metaphor. Structural properties of strings are looked for which would be necessary to apply to DNA sequences if the metaphor is to be taken literally. The notion of sophistication is used to quantify meaningful complexity and to distinguish it from classical computational complexity. In this context, the distinction between program and data becomes relevant and an alternative metaphor of DNA as data to a parallel computing network embedded in the global geometrical and biochemical structure of the cell is discussed. An intermediate picture of an evolving network emerges as the most likely where the output of the cellular computing network can produce, at a different time scale, changes in the structure of the network itself by means of changes in the DNA activity patterns.

Algorithms↗

New approaches to high-throughput phasing.

Recent progress in macromolecular phasing, in part stimulated by the high-throughput structural biology initiatives, has made this crucial stage of the elucidation of crystal structures easier and more automatic. A quick soak in various salts leads to the rapid incorporation of the anomalously scattering ions, suitable for phasing by MAD (multiwavelength anomalous dispersion), SAD (single-wavelength anomalous dispersion) or MIR (multiple isomorphous replacement) methods. The availability of stable synchrotron beam lines equipped with elaborate hardware control and sophisticated data processing programs makes it possible to collect very accurate diffraction data and to solve structures from the very weak anomalous signal of such atoms as sulfur or phosphorus, inherently present in macromolecules. The current progress in phasing, coupled with the parallel advances in protein crystallization, diffraction data collection and so on, suggests that, in the near future, the process of macromolecular crystal structure elucidation may become fully automatic.

Algorithms↗

A distributed, developmental model of word recognition and naming.

A parallel distributed processing model of visual word recognition and pronunciation is described. The model consists of sets of orthographic and phonological units and an interlevel of hidden units. Weights on connections between units were modified during a training phase using the back-propagation learning algorithm. The model simulates many aspects of human performance, including (a) differences between words in terms of processing difficulty, (b) pronunciation of novel items, (c) differences between readers in terms of word recognition skill, (d) transitions from beginning to skilled reading, and (e) differences in performance on lexical decision and naming tasks. The model's behavior early in the learning phase corresponds to that of children acquiring word recognition skills. Training with a smaller number of hidden units produces output characteristic of many dyslexic readers. Naming is simulated without pronunciation rules, and lexical decisions are simulated without accessing word-level representations. The performance of the model is largely determined by three factors: the nature of the input, a significant fragment of written English; the learning rule, which encodes the implicit structure of the orthography in the weights on connections; and the architecture of the system, which influences the scope of what can be learned.

Dyslexia↗

A synchrotron radiation microtomography system for the analysis of trabecular bone samples.

X-ray computed microtomography is particularly well suited for studying trabecular bone architecture, which requires three-dimensional (3-D) images with high spatial resolution. For this purpose, we describe a three-dimensional computed microtomography (microCT) system using synchrotron radiation, developed at ESRF. Since synchrotron radiation provides a monochromatic and high photon flux x-ray beam, it allows high resolution and a high signal-to-noise ratio imaging. The principle of the system is based on truly three-dimensional parallel tomographic acquisition. It uses a two-dimensional (2-D) CCD-based detector to record 2-D radiographs of the transmitted beam through the sample under different angles of view. The 3-D tomographic reconstruction, performed by an exact 3-D filtered backprojection algorithm, yields 3-D images with cubic voxels. The spatial resolution of the detector was experimentally measured. For the application to bone investigation, the voxel size was set to 6.65 microm, and the experimental spatial resolution was found to be 11 microm. The reconstructed linear attenuation coefficient was calibrated from hydroxyapatite phantoms. Image processing tools are being developed to extract structural parameters quantifying trabecular bone architecture from the 3-D microCT images. First results on human trabecular bone samples are presented.

Aged↗

Arterial imaging with a new forward-viewing intravascular ultrasound catheter, II. Three-dimensional reconstruction and display of data.

BACKGROUND: Current intravascular ultrasound (IVUS) catheters provide transverse imaging at the level of the ultrasound transducer. This limits imaging to large-diameter segments without critical atherosclerotic narrowings. We have developed a prototype 20-MHz forward-viewing IVUS catheter that provides two-dimensional sector imaging distal to the catheter tip. A present limitation of this technique is that the catheter must be manually rotated to obtain multiple longitudinal views required to integrate the segment into a three-dimensional matrix. To overcome this, we have developed an algorithm that reconstructs these multiple two-dimensional forward-viewing IVUS images into a three-dimensional matrix for more complete depiction of the segment distal to the ultrasound catheter. This algorithm allows display and multidimensional slicing of the three-dimensional reconstruction. METHODS AND RESULTS. To test our algorithms, five arterial segments (three canine aortas, two human femoral arteries) were evaluated in vitro. In each segment, 36 forward-viewing longitudinal slices were collected, digitized, processed, and reoriented to produce a three-dimensional reconstruction (3DR) matrix. The matrix data were sliced into parallel transverse sections and compared with morphometric interpretation of histological sections (Histo). As a result, image data could be reconstructed for a distance of 2.0 cm ahead of the catheter. 3DR easily demonstrated wall and luminal morphology and provided transverse IVUS images comparable to the histological specimens. A good correlation was noted between Histo- and 3DR-determined luminal diameters (LD) and luminal areas: 3DR LD = 1.4 Histo LD-0.4, r = .86; 3DR LD = 0.7 +/- 0.20 cm (mean +/- SD); and Histo LD = 0.7 +/- 0.13 cm. CONCLUSIONS: These preliminary data demonstrate the feasibility of 3DR of forward-viewing IVUS data. This method allows rapid, detailed analysis of diseased arterial segments previously unavailable with standard IVUS and may permit better targeting of interventional techniques.

Animals↗

Anatomy and physiology of a color system in the primate visual cortex.

Staining for the mitochondrial enzyme cytochrome oxidase reveals an array of dense regions (blobs) in the primate primary visual cortex. They are most obvious in the upper layers, 2 and 3, but can also be seen in layers 4B, 5, and 6, in register with the blobs in layers 2 and 3. We compared cells inside and outside blobs in macaque and squirrel monkeys, looking at their physiological responses and anatomical connections. Cells within blobs did not show orientation selectivity, whereas cells between blobs were highly orientation selective. Receptive fields of blob cells had circular symmetry and were of three main types, Broad-Band Center-Surround, Red-Green Double-Opponent, and Yellow-Blue Double-Opponent. Double-Opponent cells responded poorly or not at all to white light in any form, or to diffuse light at any wavelength. In contrast to blob cells, none of the cells recorded in layer 4C beta were Double-Opponent: like the majority of cells in the parvocellular geniculate layers, they were either Broad-Band or Color-Opponent Center-Surround, e.g., red-on-center green-off-surround. To our surprise cells in layer 4C alpha were orientation selective. In tangential penetrations throughout layers 2 and 3, optium orientation, when plotted against electrode position, formed long, regular, usually linear sequences, which were interrupted but not perturbed by the blobs. Staining area 18 for cytochrome oxidase reveals a series of alternating wide and narrow dense stripes, separated by paler interstripes. After small injections of horseradish peroxidase into area 18, we saw a precise set of connections from the blobs in area 17 to thin stripes in area 18, and from the interblob regions in area 17 to interstripes in area 18. Specific reciprocal connections also ran from thin stripes to blobs and from interstripes to interblobs. We have not yet determined the area 17 connections to thick stripes in area 18. In addition, within area 18 there are stripe-to-stripe and interstripe-to-interstripe intrinsic connections. These results suggest that a system involved in the processing of color information, especially color-spatial interactions, runs parallel to and separate from the orientation-specific system. Color, encoded in three coordinates by the major blob cell types, red-green, yellow-blue, and black-white, can be transformed into the three coordinates, red, green, and blue, of the Retinex algorithm of Land.

Animals↗

Analysis of interaction between number of implant catheters and dose-volume histograms in prostate high- dose-rate brachytherapy using a computer model.

PURPOSE: In prostate high-dose-rate brachytherapy, to determine before implant, using the standard geometric optimization algorithm, whether there is an optimal number of catheters. MATERIALS AND METHODS: Transrectal ultrasound images of the prostate from 24 patients were transferred into the brachytherapy planning system. Urethra and prostate contours were digitized onto each axial slice of a CT scan, as well as hypothetical locations of the catheters (2/3 of the catheters along the prostate contour, 1/3 around the urethra). Each prostate was implanted with 9, 12, 15, 18, and 21 catheters. Dosimetry was optimized using a geometric optimization algorithm; prescription isodose was chosen so that 95% of planning target volume was covered by the 100% isodose. RESULTS: A significant increase in mean volume of prostate receiving 150% of the dose (V150) when the number of catheters decreased (p < 0.0001). The 9-catheter group significantly differed from each of the other groups; no difference was seen in V150 among the 21-, 18-, and 15-catheter groups. Parallel results were observed for urethra V150 and homogeneity index; there was no difference in conformity index by catheter group. CONCLUSION: V150 increased when fewer catheters were used. There was no significant difference among the 21-, 18-, and 15-catheter groups: the geometric optimization routine probably compensated for the larger distance between dwell positions. Based on the technique described in our study, we conclude that 15 to 21 catheters seem to cover the prostate adequately without creating excess hot spots.

Algorithms↗