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Insect motion perception.

The first step in this work of reconstruction of a theory of insect vision was to demonstrate that visual behaviour relies on scanning by self-motion and apparently involves measurement of angular velocities of contrasts moving across the eye. The next step was to demonstrate that parallax is also significant as a way of segmenting the visual scene into separate objects. There followed a series of experiments to rule out the existing theory that motion perception depends on autocorrelation, and at the same time an alternative theory was developed. The new theory assumes that at the level of the optic medulla there are numerous parallel channels on each visual axis, representing different neurons, all looking out for their specific combination of signals. The combinations are formed by positive, negative or no-change temporal contrasts at two adjacent visual axes at two successive times, forming 3(4) = 81 possible templates. Simulation of this highly parallel system shows that it can represent the moving image in a compact form that would be adequate to explain what is known for motion and form vision (but not colour vision) in insects. Form, like colour, would be seen as the ratio of numbers of responses of particular templates, in the same way that colours are seen as ratios of responses of receptors for different wavelengths.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms

Assessment of the vasomotility of epicardial coronary arteries with quantitative coronary angiography.

Quantitative in vivo analysis of the vasomotility of epicardial coronary arteries is based on the measurement of changes of the vessel diameters. Vessel contours can be determined with the help of a precision caliper by the investigator or with computer-assisted geometrical analysis systems applying a contour detection algorithm; the variability of the results from repeated coronary diameter measurements in the identical film frame is comparably low with all systems (less than or equal to 0.12 mm standard deviation). When investigating the influence of an intervention on coronary vasomotility the variability of the measurements can only be kept low by careful standardization of the entire method. Repeated coronary angiograms are performed in identical angiographic projections (mono- or biplane) with standardization of the inspiratory status of the patient and of the rate of contrast material injection (automatic injection pump). For quantitative analysis all coronary segments with a diameter greater than 1 mm which are clearly outlined, free from overlaps, and mainly run parallel to the image plane, are selected by the investigator in preferably end-diastolic cineframes. Whereas with a caliper and with most of the semi-automatic edge detection systems the segment diameter can only be measured at particular sites defined by the investigator, few systems are able to analyze and average the diameter over the entire segment length. The variability of measurements of the minimal diameters of coronary stenoses in different cine frames is particularly high; therefore, only distinct changes of this parameter (e.g. with the CAAS-system greater than 0.24 mm) may be considered significant.(ABSTRACT TRUNCATED AT 250 WORDS)

Cineangiography

Combination (multiple) testing for myocardial infarction using myoglobin, creatine kinase-2 (mass), and troponin T.

We retrospectively determined the mass concentrations of myoglobin, creatine kinase-2 (CK-2), and troponin T in serial samples from 80 patients with confirmed myocardial infarction (MI) and 60 non-MI patients. Results from receiver operating characteristic curve analyses show that all three tests are comparable in their diagnostic utility within the first 12 h of infarction. Decision thresholds were selected at a constant rule-in specificity of 95% and rule-out sensitivities of 95% at, respectively, 3-6, 6-9, and 9-12 h intervals after the onset of symptoms. Test sensitivities and specificities were compared for each, used as: a single test; two-test parallel combination; three-test parallel combination; two-test series combination; and three-test series combination. Our results from combination testing indicate what for the early diagnosis of MI, a single serum myoglobin measurement has diagnostic utility at 3 h after the onset of symptoms, and myoglobin and CK-2 (mass) in combination later than 3 h following the onset of symptoms. Serum troponin T is diagnostically similar to CK-2 (mass), although it has superior cardiac-tissue specificity, but it is not as yet commercially available as a "stat" test. Therefore, we recommend using troponin T as a confirmatory test 9 h after the onset of MI. Based on our findings, we suggest a testing algorithm for the early biochemical diagnosis of MI.

Adult

FFC: a scalable FASTA compressor.

SUMMARY: FASTA is a widely used text-based format for storing nucleotide and protein sequences. The existing FASTA compressors usually focus on (slightly) improving the compression ratio, not on practical performance. We present FFC, a scalable FASTA compressor that achieves average compression speeds 4.7× and 11.4× higher than two high-performance compressors, zstd and NAF, respectively, across a benchmark set of seven single genomes. It also delivers average decompression speeds 3.5× and 2.7× higher than zstd and NAF, respectively. Although a chunk-based zstd variant with parallel decompression, pzstd, almost matches FFC speed, its compression ratio is on average by 23% worse than FFC's. For the experiment, a 14-core workstation and a RAM disk (to reduce the impact of I/O) were used. AVAILABILITY AND IMPLEMENTATION: FFC is freely available at github.com/kowallus/ffc and also as a Zenodo repository at 10.5281/zenodo.18892353, and the used datasets at 10.5281/zenodo.18873744.

Data Compression

Criticality and parallelism in combinatorial optimization.

Local search methods constitute one of the most successful approaches to solving large-scale combinatorial optimization problems. As these methods are increasingly parallelized, optimization performance initially improves but then abruptly degrades to no better than that of random search beyond a certain point. The existence of this transition is demonstrated for a family of generalized spin-glass models and the traveling salesman problem. Finite-size scaling is used to characterize size-dependent effects near the transition, and analytical insight is obtained through a mean-field approximation.

Algorithms

An evaluation of lesion detectability with cone-beam, fanbeam and parallel-beam collimation in SPECT by continuous ROC study.

UNLABELLED: To evaluate lesion detectability for clinical evaluation of cone-beam (CB), fanbeam (FB) and parallel-beam (PB) collimator sensitivity, experimentally acquired phantom data were used to assess the advantage of CB collimation over conventional collimation. METHODS: Lesion detectability with CB, FB and PB collimation in SPECT was compared using a three-dimensional brain phantom and continuous receiver operating characteristic (CROC) analysis. A simulated cold lesion was located near the posterior portion of the thalamus. High count density scans of this phantom were acquired with CB, FB and PB collimators with similar resolution. These projections were scaled to count levels which reflected the measured sensitivities of the three collimators. Computer-generated Poisson noise was added to the projections to produce uncorrelated data sets. Images were reconstructed using a filtered backprojection algorithm. All reconstructions used a Hann filter with multiplicative attenuation correction. Each of seven trained observers viewed 288 sets of images and indicated the certainty of perceiving a cold lesion at a specified location by a rating of 0-100. Each image set contained four adjacent slices centered on the lesion to minimize partial volume effects. The program LABROC4 was used to fit CROC curves to individual observers' ratings. A t-test for paired data was performed on the individual areas. RESULTS: The average areas (standard deviations) under CROC curves for CB, FB and PB were 0.89 (0.03), 0.83 (0.05) and 0.76 (0.04), respectively. The differences of the areas were statistically significant with all two-tailed p values < 0.02. CONCLUSION: These results demonstrate that cold lesions in the posterior portion of the thalamus are best detected by images obtained using CB followed by FB and PB collimation.

Brain

3D base: a geometrical data base system for the analysis and visualisation of 3D-shapes obtained from parallel serial sections including three different geometrical representations.

In this paper we discuss a geometrical data base that includes three different geometrical representations of one and the same reconstructed 3D shape: the contour-pile, the voxel enumeration, and the triangulation of a surface. The data base is tailored for 3D shapes obtained from plan-parallel serial sections. It is explained how this geometrical data base is useful with the different processing approaches of a 3D shape, such as analysis and visualisation. Methods of conversion between the geometrical representations are discussed. Examples of the operation of the data base as it is embedded in a data base management system are given by illustrations of retrieval of geometrical information.

Algorithms

Recognition of Telugu characters using neural networks.

The aim of the present work is to recognize printed and handwritten Telugu characters using artificial neural networks (ANNs). Earlier work on recognition of Telugu characters has been done using conventional pattern recognition techniques. We make an initial attempt here of using neural networks for recognition with the aim of improving upon earlier methods which do not perform effectively in the presence of noise and distortion in the characters. The Hopfield model of neural network working as an associative memory is chosen for recognition purposes initially. Due to limitation in the capacity of the Hopfield neural network, we propose a new scheme named here as the Multiple Neural Network Associative Memory (MNNAM). The limitation in storage capacity has been overcome by combining multiple neural networks which work in parallel. It is also demonstrated that the Hopfield network is suitable for recognizing noisy printed characters as well as handwritten characters written by different "hands" in a variety of styles. Detailed experiments have been carried out using several learning strategies and results are reported. It is shown here that satisfactory recognition is possible using the proposed strategy. A detailed preprocessing scheme of the Telugu characters from digitized documents is also described.

Algorithms

Calculation of site affinity constants and cooperativity coefficients for binding of ligands and/or protons to macromolecules. I. Generation of partition functions and mass balance equations.

The thermodynamics of binding of a ligand A and/or proton H to a macromolecule M is treated by the partition function method. In complex systems, the representation of the equilibria by means of cumulative constants beta PQR used as coefficients in partition functions ZM, ZA, and ZH is ill-suited to least-squares refinement procedures because the cumulative constants are interrelated by common cooperativity functions gamma j(i) and common site affinity constants kappa j. There is therefore the need to express ZM, ZA, ZH as functions of site constants kappa j and cooperativity coefficients bj. This is done by developing an algebra of partition functions based on the following concepts: (i) factorability of partition functions; (ii) binary generating function Jj = (1 + kappa j[Y])i tau for each class j of sites, represented by column (Jj) and row (Jj) vectors; (iii) cooperativity between sites of one class described by functions gamma j(i), represented by diagonal matrices gamma j; (iv) probability of finding microspecies represented by elements of tensor product matrix Ll = (J1)[J2]; (v) statistical factors mij obtained from Newton polynomials, Jj; (vi) power operators Oi', O(i-l)', and O(i tau-l)', transforming vectors Jj; and (vii) operators Oi or O(i-l) indicating tensor products of i or (i-l) vectors Jj. Vectors Jj combined in tensors Ll give rise to both an affinity/cooperativity space and a parallel index space. The partition functions ZM, ZA, and ZH and the total amounts TM, TA, and TH can be obtained as an appropriate sum of elements of matrices Ll, each of which is represented in an index space by a combination p1, p2,...q1, q2,...r1, r2,... of indices ij. From these indices the contribution of that element to partition function ZM, ZA, or ZH and to total amount TM, TA, or TH is calculated in the affinity/cooperativity space as product of factors: [i tau !/i !(i tau-i)!]kappa ij(exp[bj (i-1)i])[X]i, i being any index p, q, r and X any component M, A, or H. Future applications of this algorithm to practical problems of macromolecule-ligand-proton equilibria are outlined.

Binding Sites

Higher-order structure in regularity detection.

In three experiments a simple Euclidean transformation (reflection, translation, rotation) was applied to collections of twelve dots in such a way that they contained equal lower-order structure, defined on the pairwise grouping of elements with their partner following transformation (e.g. parallel virtual lines), but differed in the presence vs absence of higher-order structure, defined on pairs of pairwise groupings (e.g. virtual quadrangles with correlated angles). Based on the much better performance levels (d') in the case of additional higher-order structure, we conclude that global regularities are easier to detect when the local correspondences are supported by higher-order ones formed between them. These enable the lower-order groupings to spread out across the whole pattern very rapidly (called bootstrapping). As a preliminary attempt to specify these principles, we proposed a working model with two basic components: first, a function expressing the cost of a perceptual grouping or the lack of regularity, and, secondly, an algorithm based on simulated annealing to minimize the cost function. The simulation results obtained with our current implementation of these principles showed satisfactory qualitative agreement with human regularity detection performance. Finally, the theory was shown to capture the essence of a large number of grouping phenomena taken from diverse domains such as detection of symmetry in dot patterns, global structure in Glass and vector patterns, correspondence in stereoscopic transparency and apparent motion. Therefore, we are convinced that, in principle, the mechanism used by the human visual system to detect regularity incorporates something like bootstrapping based on higher-order structure. We regard this as a promising step towards unraveling the intriguing mechanisms of classic Gestalt phenomena.

Cues

Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer.

Rapid growth of protein structures database in recent years requires an effective approach for objective comparison and classification of deposited protein structures. We describe a novel method for structure comparison and classification based on the alignment of one-dimensional structure profiles. These profiles are obtained by calculating the OCCO pseudodihedral angles (formed by O-C-C-O atoms of carbonyl groups of consecutive amino acid residues) from protein three-dimensional coordinates. These angle measurements are then converted into a 24 letter alphabet, and the protein structures are represented by sequences of letter from this alphabet. The BioSCAN parallel computer, designed for primary sequence alignment, is used to rapidly align and classify these one-dimensional structure profiles. We have developed and implemented weighted scoring matrix to identify structural classes based on commonly found structural motifs. The results of our experiments are in good agreement with the traditional protein structure classification schemes. One-dimensional structure profiles significantly improve efficiency of structure comparison and classification.

Algorithms

ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool.

Many advanced software tools fail to reach a wide audience because they require specialized hardware, installation expertise, or an abundance of CPU cycles. The worldwide web offers a new opportunity for distributing such systems. One such program, MEME, discovers repeated patterns, called motifs, in sets of DNA or protein sequences. This tool is now available to biologists over the worldwide web, using an asynchronous, single-program multiple-data version of the program called ParaMEME that runs on an Intel Paragon XP/S parallel computer at the San Diego Super-computer Center. ParaMEME scales gracefully to 64 nodes on the Paragon with efficiencies > 72% for large data sets. The worldwide web interface to ParaMEME accepts a set of sequences interactively from a user, submits the sequences to the Paragon for analysis, and e-mails the results back to the user. ParaMEME is available for free public use at http://@www.sdsc.edu/CompSci/Biomed/ MEME.

Algorithms

Molecular modeling of the amphipathic helices of the plasma apolipoproteins.

In this paper we propose a classification of the amphipathic helical repeats occurring in the plasma apolipoprotein sequences. It is based upon the calculation of the molecular hydrophobicity potential around the helical segments. The repeats were identified using a new autocorrelation matrix, based upon similarities of hydrophobic and hydrophilic properties of the amino acid residues within the apolipoprotein sequences. The helices were constructed by molecular modeling, the molecular hydrophobicity potential was calculated, and isopotential contour lines drawn around the helices yielded a three-dimensional visualization of the hydrophobicity potential. Two classes of apolipoproteins could be differentiated by comparing the hydrophobic angles obtained by projection of the isopotential contour lines on a plane perpendicular to the long axis of the helix. The isopotential contour lines around apo AI, AIV, and E are more hydrophilic than hydrophobic, whereas they are of similar intensity for apo AII, CI, and CIII. In both cases discoidal lipid-protein complexes are generated, with the amphipathic helices around the edge of the lipid core. The long axis of the helices is oriented parallel to the phospholipid acyl chains and the hydrophilic side of the helix toward the aqueous phase. As a result of the differences in hydrophobicity potential, the contact between the hydrophobic side of the helices and the phospholipid acyl chains is larger for apo AII, CI, and CIII than for the other apolipoproteins. This might account for the greater stability of the discoidal complexes generated between phospholipids and these apoproteins.

Algorithms

A new motion responsive pacemaker: first clinical experience with an acceleration sensor pacemaker.

A new accelerometer-based adaptive rate pacemaker (EXCEL VR) was evaluated to investigate its behavior at nominal settings during treadmill exercise testing and postural changes. Eight patients with sinus rhythm were selected to compare intrinsic heart rate to sensor mediated rate. Throughout exercise treadmill testing, changes in the sensor mediated rate closely paralleled actual physiological changes. The Pearson product moment correlation of pacing rate with sinus frequency, calculated for all patients, was r = 0.82 (P = 0.001). Change in the patient's physical position resulted in immediate change in sensor rate, which corresponded appropriately to the type of position change and activity level. Average (+/- SD) pacing rate was 62.4 +/- 2.7 beats/min supine; 67 +/- 3.8 beats/min sitting; 69.8 +/- 6.4 beats/min standing; 81.6 +/- 8.7 beats/min slow walking; and 96.8 +/- 1.3 beats/min fast walking. After 4 minutes of recovery, the average pacing rate dropped to 65 +/- 3 beats/min. The interaction between the accelerometer and the pulse generator at nominal settings was accurate and infrequently required the use of its many programming options. The accelerometer sensor and pulse generator algorithm in this device during postural change and exercise resulted in physiological-like changes in sensor mediated heart rate.

Acceleration

Retrieval of clinical science information using an interactive activation and competition network.

A method for storing and retrieving tabulated clinical science information is described. This method uses the interactive activation and competition network and belongs to the realm of parallel distributed processing. The advantages of this method are that information is readily retrievable by name and by any content, and that the best matched information is automatically returned when partially incorrect cues are given. Furthermore, it allows a variable degree of association among different units of information. The basic principles of this method are illustrated through a simple example from clinical bacteriology. In addition an application of this method to the retrieval of information in cardiology is presented.

Algorithms

Two-dimensional 1H NMR study of human ubiquitin: a main chain directed assignment and structure analysis.

The 1H resonances of human ubiquitin were studied by two-dimensional nuclear magnetic resonance techniques. A recently introduced assignment algorithm termed the main chain directed (MCD) assignment [Englander, S. W., & Wand, A. J. (1987) Biochemistry 26, 5953-5958] was applied. This approach relies on an ordered series of searches for prescribed patterns of connectivities in two-dimensional J-correlated and nuclear Overhauser effect spectra and centers on the dipolar interactions involving main-chain amide NH, alpha-CH, and beta-CH. Unlike the sequential assignment procedure, the MCD approach does not rest upon definition of side-chain J-coupled networks and is generally not sequential with the primary sequence of the protein. The various MCD patterns and the general algorithm are reiterated and applied to the analysis of human ubiquitin. With this algorithm, the vast majority of amino acid residue amide NH-C alpha H-C beta H J-coupled subspin systems could be associated with and aligned within units of secondary structure without any knowledge of the identity of the side chains. This greatly simplified recognition of side-chain spin systems by restricting their identity. Essentially complete resonance assignments are presented. The MCD method is compared with the sequential assignment method in some detail. The MCD method is highly amenable to automation. Human ubiquitin is found, at pH 5.8 and 30 degrees C, to be composed of an extensive beta-sheet structure involving five strands. Three of these strands form an antiparallel set sharing a common strand and have a parallel orientation to two antiparallel strands. Two helical segments were also observed. The largest, spanning 13 residues, shows dipolar interactions consistent with an alpha-helix while the smaller 4-residue helical segment appears, on the basis of observed nuclear Overhauser effects, to be a 3(10) helix. Five classical tight turns could be demonstrated.

Humans

[Roentgenologically wasted time in bronchial carcinoma -a review (author's transl)].

The importance of roentgenologically wasted time, its frequency, causes and relation to specific characteristics of bronchial carcinoma are discussed in details along the literature. A short casuistic will show the actuality of the problem. There may be gained some important conclusions from the literature, but the differences in methods and the missing security in some definitions don't allow reliable answers to some detailproblems. The following conclusion could be derived from literature: 1. The roentgenologically protracted rate amounts to more than 30% on average. It decreases with increasing in experience of the readers of fluorographies. But even among them in the part of protracted cases amounts up to 10%. 2. Late protracted roentgenologic roentgenologic diagnosis is caused by -overlooking minimal lesions, -false algorithm in diagnostic procedure, -false diagnosis, -inadequate techniques, -the misinterpretation of developing malign lesion on the basis of existing alterations aetiologically known, -the delay on the patient's part. 3. The most important cause of all protracted x-ray findings is misinterpreted obstructive pneumonitis; it is followed by parenchymal cloudy densities, by striped atelectasis, old tuberculous processes, peripheral coin lesions and hilus alterations. 4. The time roentgenologically wasted is differing in wide range up to some years. 5. With increasing wasted time the portion of central tumors is also rising. 6. Even in patients considered as radically resected there exists still a negative correlation between the roentgenologically wasted time and prognosis. 7. The average of wasted time in x-ray lesions is running parallel to the screening intervals. 8. There seem to exist some differences between the different histological types in view of the roentgenologically wasted time. 9. There are no correlations between the age of the patients and the roentgenologically wasted time.

Adenocarcinoma

Atlas-level single-cell integration and clustering-free differential expression analysis with GEDI 2.0.

MOTIVATION: GEDI is a generative framework for multi-sample, multi-condition single-cell analysis that performs batch correction, latent representation learning, and clustering-free differential expression within a unified model. However, the original implementation suffered from prohibitive memory use and runtime, preventing its application to modern atlas-scale datasets. RESULTS: We present GEDI 2.0, a complete high-performance reimplementation featuring a standalone C++ computational core with pre-allocated workspaces, strict sparse-matrix preservation, optimized BLAS routines, and multi-threaded block-coordinate descent. Across extensive benchmarks spanning up to 500 000 cells and 10 000 features, GEDI 2.0 achieves 40%-63.6% mean reduction in peak memory, 2.98&#xd7; mean single-threaded speedups, and up to 11.5&#xd7; acceleration with parallel execution, while maintaining full numerical equivalence to the original method. These improvements enable GEDI 2.0 to analyze million-cell datasets, a scale not achievable with the legacy implementation. GEDI 2.0 provides R and Python interfaces and seamless interoperability with common single-cell workflows. AVAILABILITY AND IMPLEMENTATION: Source code, documentation, reproducible codebase, and tutorials are available at https://github.com/csglab/gedi2.

Single-Cell Analysis