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An improved estimator of spontaneous mutation rates in Luria-Delbrück fluctuation experiments.

In estimating the spontaneous mutation rate, mu, in cultured mammalian cells, the number of mutant cells in several parallel cultures, each a clone from a single cell, is determined. Luria and Delbrück (1943), and subsequently Lea and Coulson (1949), proposed several estimators of mu using data from such experiments. These methods of analysis were originally proposed to apply to mutants arising in microbial cultures, and some of the limitations in applying them to mammalian cell cultures have been outlined by Featherstone et al. (1987), and by Kendal and Frost (1988). For a given value of mu, the number of mutants, r, found in a culture is exceedingly variable, so that r contains very little information concerning mu. It is important, therefore, that an estimator of mu be efficient; that it not waste the limited information available in the experimental data. To this end, a new estimator is proposed which compounds the information previously utilized by the so-called P0 and median estimators. Using a spreadsheet program such as that available with MINITAB, the algorithm can be programmed in as few as 26 instructions. Tested against simulated data across a range of values of mu, the proposed compound estimator is more efficient than the currently used estimators.

Algorithms

Simultaneous reconstruction, segmentation, and edge enhancement of relatively piecewise continuous images with intensity-level information.

A multinomial image model is proposed which uses intensity-level information for reconstruction of contiguous image regions. The intensity-level information assumes that image intensities are relatively constant within contiguous regions over the image-pixel array and that intensity levels of these regions are determined either empirically or theoretically by information criteria. These conditions may be valid, for example, for cardiac blood-pool imaging, where the intensity levels (or radionuclide activities) of myocardium, blood-pool, and background regions are distinct and the activities within each region of muscle, blood, or background are relatively uniform. To test the model, a mathematical phantom over a 64 x 64 array was constructed. The phantom had three contiguous regions. Each region had a different intensity level. Measurements from the phantom were simulated using an emission-tomography geometry. Fifty projections were generated over 180 degrees, with 64 equally spaced parallel rays per projection. Projection data were randomized to contain Poisson noise. Image reconstructions were performed using an iterative maximum a posteriori probability procedure. The contiguous regions corresponding to the three intensity levels were automatically segmented. Simultaneously, the edges of the regions were sharpened. Noise in the reconstructed images was significantly suppressed. Convergence of the iterative procedure to the phantom was observed. Compared with maximum likelihood and filtered-backprojection approaches, the results obtained using the maximum a posteriori probability with the intensity-level information demonstrated qualitative and quantitative improvement in localizing the regions of varying intensities.

Algorithms

Tomography using a rotating slant-hole collimator and a large number of projections.

A tomographic method using a limited-view angle has been evaluated. In studies using a gamma camera and a rotating 30-degree slant-hole (RSH) collimator, 64 projection images were registered. A special filtered backprojection technique was used for reconstruction of section images parallel to the collimator face. Resolution within such sections was 0.6 cm, 3 cm from the collimator face and 1.3 cm at 18 cm. Depth resolution was 2.2 cm at 3 cm and 5.1 cm at 18 cm. Spacing between section images was regular and geometric distortion negligible. Short-axis section images of a myocardium in vivo were qualitatively comparable or better than those obtained with single-photon emission computed tomography. Degradation in the posterior wall due to attenuation and scatter was less. Section images of the facial bones and a hip joint further demonstrated the tomographic capability of the method.

Algorithms

Nonlinear parameter estimation by linear association: application to a five-parameter passive neuron model.

Linear associative memories (LAM) have been intensely used in the areas of pattern recognition and parallel processing for the past two decades. Application of LAM to nonlinear parameter estimation, however, has only been recently attempted. The process consists in converting the nonlinear function in the parameters into a set of linear algebraic equations. The nature of the linearized system and the factors influencing the accuracy of the parameter estimates have not yet been fully investigated. In this paper, LAM is applied to a nonlinear five-parameter model of the neuron. Ill-conditioning, which is often exhibited in LAM, is treated with the method of regularization as well as by the singular value decomposition (SVD). Simulation results indicate that the parameters estimated by LAM exhibit a remarkable robustness against additive white noise in comparison with the classical gradient optimization technique. Moreover, it is shown that regularization can be superior to SVD under certain conditions. Our results suggest that LAM can be used both as a noise reduction technique and as a stand-alone nonlinear parameter estimation algorithm. The comparison between LAM and a gradient technique show that, for this estimation problem, the LAM method can give more reliable estimates. Further improvements in estimation quality may still be achieved by the use of other forms of regularizing functions.

Linear Models

Cranial CT artifacts and gantry angulation.

Computed tomographic investigation of the brain is frequently accomplished by scanning parallel to the canthomeatal line. In these scans, evaluation of the brain stem and neighboring structures is often compromised by streak artifacts from bone-induced beam hardening. These artifacts may be reduced by introducing a change in gantry angulation. Results from a phantom study as well as from a clinical trial offer evidence that may be helpful in assessing different scanning planes. An inclination of 5 degrees below Reid baseline is suggested to minimize the interpetrous artifact. Variations in slice thickness and exposure parameters do not appear to affect significantly this typical posterior fossa artifact.

Algorithms

Kinetics of reactivation during refolding of guanidine-denatured pancreatic ribonuclease A.

The method aforementioned (Liu, W. and Tsou, C.L. (1987) Biochim. Biophys. Acta 916, 455-464) for the study of the kinetics of irreversible modification of enzyme activity has been applied to the reactivation of guanidine-denatured ribonuclease A, by following the hydrolysis of cyclic CMP during refolding upon diluting a guanidine-denatured enzyme with a substrate-containing buffer. Appropriate equations have been derived to deal with the kinetics of the substrate reaction during the course of activation, while the product formed, 3'CMP, is a competitive inhibitor. When the overall process consists of multiple first-order reactions, the individual rate constants could be obtained by suitable semilogarithmic plots. Moreover, in certain cases, it can be distinguished from the shapes of the plots, whether the overall process consists of parallel or consecutive first-order reactions. The kinetics for the reactivation reaction has been compared to that for the refolding of the substrate binding site, as indicated by complex formation with the competitive inhibitor, 2'CMP, and for the refolding of the molecule as a whole. At pH 6.0 and 25 degrees C, only monophasic first-order reactions could be detected by manual mixing for both the reactivation and the refolding processes. At lower temperatures (0-10 degrees C), both processes consist of two first-order reactions. In all cases, the same rate constants have been obtained for the refolding and reactivation reactions.

Algorithms

Size estimation and magnification error in radiographic imaging: implications for classification of arteriovenous malformations.

PURPOSE: To assess magnification error in digital subtraction angiography as it pertains to arteriovenous malformation (AVM) size. METHODS: A rectangular grid phantom with equally spaced markers mounted in a stereotactic frame was imaged with digital angiographic equipment. The location and orientation of the grid was altered relative to the central plane of the phantom. Both linear and area measurements were made according to the perceived location of phantom markers using a standard catheter calibration technique and compared with stereotactically derived estimates. Finally, a single case example of an angiographically imaged rolandic AVM was used to compare linear dimensions obtained with both described techniques. RESULTS: The determination of location and size with standard angiographic imaging is subject to error because of the divergent geometry of the incident x-ray beam. The resulting nonconstant geometric magnification causes errors in linear measurements of 10% to 13% at depths of 7 cm from the calibration plane. Errors in area measurements at the same position increase by 20% to 25%. Measurements of maximum diameter or cross-sectional area may have an additional error when nonspherical objects are inclined to the viewing direction (40% at 45 degrees inclination). These errors are reduced to less than 1 mm using the stereotactic technique. Some commercial angiographic systems have internal software to enable a spatial calibration based on known distances in the image or on the diameter of a catheter. The catheter technique was accurate in the calibration direction (perpendicular to the catheter axis) but had a 12% error in the direction parallel to the catheter because of a nonunity aspect ratio in the video system. Measurement of the dimensions of a rolandic AVM using the catheter calibration technique had an error that ranged from -3% to +26% (standard error, 20%) with respect to the stereotactic technique. CONCLUSIONS: Numerous nonstereotactic referential systems for determining linear distances are inherently erroneous by varying degrees compared with the stereotactic technique. Area and volume determinations naturally increase this error further. To the extent that no standardized method for determining linear distances exists, significant variations in estimation of AVM size result. Classification schemes for AVMs have been hampered by this technical error.

Algorithms

Parallel computation of genetic likelihoods using CRI-MAP, PVM, and a network of distributed workstations.

We have developed a version of the CRI-MAP computer program for genetic likelihood computations that runs the FLIPS and ALL functions of CRI-MAP in parallel on a distributed network of workstations. The performance of CRI-MAP-PVM was assessed in several linkage analyses using the FLIPS option of CRI-MAP on a map of 85 microsatellite markers for human chromosome 1. These analyses showed excellent speedup and efficiency and low distribution overhead. In addition, we have adapted the MultiMap program for automated construction of linkage maps to use CRI-MAP-PVM. These improvements significantly reduce the time required to compare likelihoods of different marker orders. Thus, the construction of linkage maps can proceed in a more timely fashion, in keeping with recent advances in genotyping technology.

Algorithms

The amplitude and periodicity of synchronized renal sympathetic nerve discharges in anesthetized cats: differential effect of baroreceptor activity.

We applied a computerized peak detection algorithm to recordings of synchronized sympathetic nerve discharges from anesthetized cats to retrieve information about the characteristics of renal nerve activity (RNA) during changes in baroreceptor activity. The algorithm scanned the series of RNA voltages for significant increases followed by significant decreases in a small cluster of voltage values. Once each synchronized RNA peak had been detected, its corresponding amplitude, width and peak-to-peak interval were calculated. The peak-to-peak interval periodicity showed two modes of synchronized discharge, one between 200-500 ms accounting for 47% of intervals, and a higher 20-180 ms frequency (49% of intervals). Baroreceptor stimulation decreased the occurrence of the high frequencies while increasing the probability of the lower frequency components. The overall occurrence of synchronized peaks per second fell linearly to zero with increases in blood pressure. The peak amplitude of RNA was unimodally distributed and was not affected by baroreceptor stimulation until an increase in mean arterial pressure reached a threshold (mean 142 +/- 5 mmHg) whereupon it fell quickly to zero. Sino-aortic vagal denervation did not affect the distribution of peak height. The width of synchronized discharges was also unimodal, mean 82 +/- 1 ms, and was almost unchanged during baroreflex stimulation acting in parallel with changes in the peak amplitude and decreasing at high blood pressures. Sino-aortic vagal denervation did not affect the synchronized width. There was no relationship between the periodicity and amplitude or width of synchronized discharges under all conditions. The results indicate that the periodicity and amplitude of renal synchronized discharges appear to be independent of each other and are differentially affected by baroreceptor input.

Animals

An instrument using parallel filtering of acoustic signals to record fetal heart rate.

A novel portable instrument for long-term recording of fetal heart rate has been developed, based on the detection and evaluation of maternal abdominal acoustic signals. Multichannel, adaptive digital filtering using different frequency characteristics yields a reliable indication of fetal heart beats even at a high level of noise. The evaluation system statistically processes the acoustic signals, controls amplitude limits, and adjusts filter characteristics. Heart-rate variations of as much as 25/min/sec have been accurately registered. High-level integration enables the realization of the method in a very small, belt-mounted instrument with low power consumption, thus convenient for home use. The more than 40 hours of recorded detections stored in the built-in flash memory can be read back into a personal computer for medical inspection and analysis.

Abdomen

A study of interface effects in 60Co beams using a thin-walled parallel plate ionization chamber.

A large plane-parallel ionization chamber has been constructed to investigate interface effects in 60Co beam. The designed geometry yields negligible perturbation from the side walls, as opposed to the large effects existing in commercially available plane-parallel chambers. The chamber has been used to investigate interface phenomena in transition zones using a wide range of elements (Z = 4-82) as front- and back-scattering media and a clinically relevant 60Co gamma-ray field size. The effects of varying the chamber height discretely (0.5-11 mm) and increasing the wall thickness (1-9 mg/cm2) have been investigated. The variation of the measured ionization with the experimental setup (air gap between backscatter material and chamber wall, measurements at dmax and at 5-cm depth, varying the material both in front of and behind the chamber, etc.) has also been investigated. The simple geometry of the ion chamber has been found optimum for benchmark studies of Monte Carlo calculations. The ion chamber is suited for investigating experimentally the effects of varying transport parameters used in Monte Carlo simulations. The results presented show that the complex physical mechanisms governing 60Co interface dosimetry still make Monte Carlo condensed-history (macroscopic) techniques uncertain. It has been found that the EGS4 Monte Carlo system, together with the user code DOSRZ V4.0 and the PRESTA algorithm, yields good agreement with experiments for low and medium Z (main interest in dosimetry and radiotherapy), but may underestimate up to 10% the backscatter from high-Z materials even when transport parameters are optimized.

Algorithms

Topographic relations between ocular dominance and orientation columns in the cat striate cortex.

In the visual cortex of four adult cats ocular dominance and orientation columns were visualized with (3H)proline and (14C)deoxyglucose autoradiography. The two columnar systems were reconstructed from serial horizontal sections or from flat-mount preparations and graphically superimposed. They share a number of characteristic features: In both systems the columns have a tendency to form regularly spaced parallel bands whose main trajectory is perpendicular to the border between areas 17 and 18. These bands frequently bifurcate or terminate in blind endings. The resulting irregularities are much more pronounced in the ocular dominance than in the orientation system. The periodicity of the columnar patterns was assessed along trajectories perpendicular to the main orientation of the bands and differed in the two columnar systems. The spacing of the ocular dominance stripes was significantly narrower than the spacing of orientation bands. The mean periodicity of a particular columnar system was virtually identical in the two hemispheres of the same animal but it differed substantially in different animals. However, the spacing of orientation columns covaried with that of the ocular dominance columns, the ratios of the mean spacings of the two columnar systems being similar in the four cats. The superposition of the two columnar systems revealed no obvious topographic relation between any of the organizational details such as the location of bifurcations, blind endings and intersections. We suggest the following conclusions: 1. The developmental processes generating the two columnar systems seem to obey the same algorithms but they act independently of each other. 2. The space constants of the two systems are rigorously specified and appear to depend on a common variable. 3. The main orientation of the bands in both columnar systems is related to a) the representation of the vertical meridian, b) the anisotropy of the cortical magnification factor, and c) the tangential spread of intracortical connections.

Animals

Impossible objects and the things we do first in vision.

Interpreting an image involves postulating that it represents a structure drawn from some class C. Attention tends to focus on methods where C is large (e.g. 'rigid structures') or small (e.g. 'faces'). However scene analysis programs where C is intermediate have interesting properties. In particular it is often neither easy nor worthwhile to establish the full consequences of the postulates underlying analysis. The price of this incompleteness is that inconsistent interpretations are occasionally accepted. This parallels the psychological phenomenon of seeing 'Impossible Objects', so Impossible Objects may indicate that human vision too uses intermediate postulates and develops only a key subset of their implications. If this interpretation is correct, and demonstrations suggest that it is, then the particular pictures which cause us such problems should indicate what the relevant postulates are and to what level they are developed. Experiments and demonstrations suggest that the postulates concern angles between edges and that implications about edges' orientations, but not their depths, are automatically derived and checked. This makes sense ecologically and computationally. Ecologically, precise depth information would only help in cases involving improbable alignments. Computationally, a description of edge orientation paves the way to obtain various other types of information as required.

Algorithms

Elucidation of non-parallel EIA curves.

Quantitative determinations by EIA can be only obtained by reverse regression when linear portions of sample and standard curves are parallel. However, analysis of complex biological fluids often yields sigmoid curves displaying lower slopes, thus invalidating any quantitative interpretation. We hypothesized that this phenomenon was due to a competition effect between the target (for example an antigen) and related molecules for the binding sites (for example a capture antibody) immobilized onto the solid phase. This has been confirmed experimentally using various target-to-competitor ratios and formulated as a mathematical model. The slope decrease in target detection was related to the proportion of competitor, not in a linear, but in an exponential manner. This mathematical model has been computerized and can be used to correct aberrant sample curves provided the relevant parameters have been previously determined in the same systems.

Algorithms

Bicarbonate secretion modulates ammonium absorption in rat distal colon in vivo.

Although the mammalian colon is thought to absorb large quantities of total ammonia, principally in the form of NH3, quantitative support for this hypothesis is lacking. In rat distal colon, we observed that NH3 was approximately 400 times more permeant than NH+4. In addition, colonic HCO-3 secretion influenced total ammonia (NH3 plus NH+4) absorption; that is, alteration of HCO-3 secretion caused a parallel change in total ammonia absorption. Perfusion with total ammonia also caused net HCO-3 secretion to switch to net absorption, and, in the setting of preexisting HCO-3 absorption, perfusate containing total ammonia enhanced HCO-3 absorption. These events suggest that colonic HCO-3 secretion titrates luminal NH+4 to NH3, permitting NH3 to diffuse from the lumen, while HCO-3 is titrated to carbon dioxide and also diffuses from the lumen. In support of titration of NH+4 and HCO-3, the magnitude of induced HCO-3 absorption approximated total ammonia absorption. This titration relationship suggests that, in kinetic studies, total ammonia absorption will be limited by a fixed rate of HCO-3 secretion. A model was developed that simulated these events.

Algorithms

SAIGE-GPU: accelerating genome- and phenome-wide association studies using GPUs.

MOTIVATION: Genome-wide association studies (GWAS) at biobank scale are computationally intensive, especially for admixed populations requiring robust statistical models. SAIGE is a widely used method for generalized linear mixed-model GWAS but is limited by its CPU-based implementation, making phenome-wide association studies impractical for many research groups. RESULTS: We developed SAIGE-GPU, a GPU-accelerated version of SAIGE that replaces CPU-intensive matrix operations with GPU-optimized kernels. The core innovation is distributing genetic relationship matrix calculations across GPUs and communication layers. Applied to 2068 phenotypes from 635 969 participants in the Million Veteran Program, including diverse and admixed populations, SAIGE-GPU achieved a 5-fold speedup in mixed model fitting on supercomputing infrastructure and cloud platforms. We further optimized the variant association testing step through multi-core and multi-trait parallelization. Deployed on Google Cloud Platform and Azure, the method provided substantial cost and time savings. AVAILABILITY AND IMPLEMENTATION: Source code and binaries are available for download at https://github.com/saigegit/SAIGE/tree/SAIGE-GPU-1.3.3. A code snapshot is archived at Zenodo for reproducibility (DOI: [10.5281/zenodo.17642591]). SAIGE-GPU is available in a containerized format for use across HPC and cloud environments and is implemented in R/C++ and runs on Linux systems.

Genome-Wide Association Study

Inhibition of porcine pepsin by two substrate analogues containing statine. The effect of histidine at the P2 subsite on the inhibition of aspartic proteinases.

Two new inhibitors, 4 and 5, of the aspartic proteinase porcine pepsin were synthesized. These compounds, which span the P4-P'3 binding subsites of the enzyme, were derived by replacing the Nph-Phe dipeptidyl unit of a good pepsin substrate, H2N-Phe-Gly-His-Nph-Phe-Ala-Phe-OMe (3), with statine [(3S,4S)-4-amino-3-hydroxy-6-methylheptanoic acid, Sta]. Hexapeptide 5, H2N-Phe-Gly-Val-(S,S)-Sta-Ala-Phe-OMe, is an extremely potent inhibitor of pepsin with a Ki value less than 1 nM. This result is consistent with the proposal that statine functions as a bioisosteric replacement for a substrate dipeptidyl unit. Compound 4, which contains His at P2, is 2 orders of magnitude less active than the valine analogue 5 (Ki = 150 nM). The factor for the decrease in binding to pepsin effected by replacement of Val by His at P2 parallels the ratio of protonated vs unprotonated imidazole group in peptide 4 at pH 4, according to the Henderson-Hasselbach equation. This result suggests that a positively charged side chain at P2 is undesirable for maximum pepsin inhibition. Kinetic constants for several known inhibitors of pepsin and renin are presented that demonstrate that the effect of His incorporation at P2 on pepsin inhibition depends upon the peptide sequence and that the effect is considerably different for renin inhibitors. We further suggest that the high selectivity of potent renin inhibitors known to be only weak pepsin and cathepsin D inhibitors is due in part to the extent of histidine protonation at P2 arising from pH differences in the inhibition kinetics assay of renin (neutral conditions) compared to other aspartic proteinases (acid pH 2-4).

Algorithms

A model for the spatio-temporal organization of DNA replication in mammalian cells.

The spatio-temporal organization of chromosomal DNA replication was analyzed using a model based on a "DNA unit" (or decondensation unit) hypothesis. The model is an extension of the fork movement theory of Huberman & Riggs (1968) and can account for a partially deterministic and partially stochastic order of DNA replication in chromosomes. It presumes that each chromosome is composed of DNA units that are arranged in sequence and that are replicated in parallel. A deterministic wave of chromatin decondensation propagates along the DNA unit continuously and progressively providing a field for the random activation of replication origin. Assignment of replication times to DNA compartments by a Monte Carlo method was programmed based on the model and the program was used to stimulate DNA synthesis rate curves that can be measured by the method of Dolbeare et al. (1983, 1985). The shape of the curve is shown to constrain possible parameter values of the model, which include the rate of fork movement, the fraction of chromatin that is decondensed at the start of S-phase, the initial number of origins activated, the rate at which new origins are activated, etc. The chromosomal organization that controls the molecular level of DNA replication is briefly reviewed and its relevance to the model is also discussed.

Algorithms