Dreams, Twilight Dreams

https://digitalcommons.library.umaine.edu/mmb-vp/2863/thumbnail.jp

If the Rose of my Dream, was You

https://digitalcommons.library.umaine.edu/mmb-vp/1819/thumbnail.jp

Opposing effects of final population density and stress on Escherichia coli mutation rate

Evolution depends on mutations. For an individual genotype, the rate at which mutations arise is known to increase with various stressors (stress-induced mutagenesis-SIM) and decrease at high final population density (density-associated mutation-rate plasticity-DAMP). We hypothesised that these two forms of mutation-rate plasticity would have opposing effects across a nutrient gradient. Here we test this hypothesis, culturing Escherichia coli in increasingly rich media. We distinguish an increase in mutation rate with added nutrients through SIM (dependent on error-prone polymerases Pol IV and Pol V) and an opposing effect of DAMP (dependent on MutT, which removes oxidised G nucleotides). The combination of DAMP and SIM results in a mutation rate minimum at intermediate nutrient levels (which can support 7 × 10  cells ml ). These findings demonstrate a strikingly close and nuanced relationship of ecological factors-stress and population density-with mutation, the fuel of all evolution

Modeling the Distance-Dependent Blurring in Transmission Imaging in the Ordered-Subset Transmission (OSTR) Algorithm by Using an Unmatched Projector/Backprojector Pair

In SPECT, accurate emission reconstruction requires attenuation compensation with high-quality attenuation maps. Resolution loss in transmission maps could cause blurring and artifacts in emission reconstruction. For a transmission system employing parallel-hole collimators and a sheet source, distance-dependent blurring is caused by the non-ideal source and camera collimations, and the finite intrinsic resolution of the detector. These can be approximately modeled by an incremental-blurring model. To compensate for this blurring in iterative transmission reconstruction, we incorporated the incremental blurring model in the forward projector of the OSTR algorithm but did not include the blur in the backprojector. To evaluate our approach, we simulated transmission projections of the MCAT phantom using a ray-tracing projector, in which the rays coming out from a source point form a narrow cone. The geometric blurring due to the non-ideal source and camera collimations was simulated by multiplying the counts along each cone-beam ray with a weight calculated from the overall geometric response function (assumed a two-dimensional Gaussian function), and then summing the weighted counts into projections. The resulting projections were convolved with the intrinsic response (another two-dimensional Gaussian) to simulate the total system blurring of transmission imaging. Poisson noise was then added to the projection data. We also acquired two sets of transmission measurements of an air-filled Data Spectrum Deluxe SPECT phantom on a Prism 2000 scanning-line-source transmission system. We reconstructed the simulations using the OSTR algorithm, with and without modeling of the incremental blur in the projector. The scaling parameter of the penalty prior was optimized in each case by minimizing the root-mean-square error (RMSE). Reconstructions showed that modeling the incremental blur improved the resolution of the attenuation map and quantitative accuracy.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/85829/1/Fessler211.pd

Spontaneous mutation rate is a plastic trait associated with population density across domains of life

Rates of random, spontaneous mutation can vary plastically, dependent upon the environment. Such plasticity affects evolutionary trajectories and may be adaptive. We recently identified an inverse plastic association between mutation rate and population density at 1 locus in 1 species of bacterium. It is unknown how widespread this association is, whether it varies among organisms, and what molecular mechanisms of mutagenesis or repair are required for this mutation-rate plasticity. Here, we address all 3 questions. We identify a strong negative association between mutation rate and population density across 70 years of published literature, comprising hundreds of mutation rates estimated using phenotypic markers of mutation (fluctuation tests) from all domains of life and viruses. We test this relationship experimentally, determining that there is indeed density-associated mutation-rate plasticity (DAMP) at multiple loci in both eukaryotes and bacteria, with up to 23-fold lower mutation rates at higher population densities. We find that the degree of plasticity varies, even among closely related organisms. Nonetheless, in each domain tested, DAMP requires proteins scavenging the mutagenic oxidised nucleotide 8-oxo-dGTP. This implies that phenotypic markers give a more precise view of mutation rate than previously believed: having accounted for other known factors affecting mutation rate, controlling for population density can reduce variation in mutation-rate estimates by 93%. Widespread DAMP, which we manipulate genetically in disparate organisms, also provides a novel trait to use in the fight against the evolution of antimicrobial resistance. Such a prevalent environmental association and conserved mechanism suggest that mutation has varied plastically with population density since the early origins of life

A Multi-Wavelength Mass Analysis of RCS2 J232727.6-020437, a ~3x1015^{15}M⊙_{\odot} Galaxy Cluster at z=0.7

We present an initial study of the mass and evolutionary state of a massive and distant cluster, RCS2 J232727.6-020437. This cluster, at z=0.6986, is the richest cluster discovered in the RCS2 project. The mass measurements presented in this paper are derived from all possible mass proxies: X-ray measurements, weak-lensing shear, strong lensing, Sunyaev Zel'dovich effect decrement, the velocity distribution of cluster member galaxies, and galaxy richness. While each of these observables probe the mass of the cluster at a different radius, they all indicate that RCS2 J232727.6-020437 is among the most massive clusters at this redshift, with an estimated mass of M_200 ~3 x10^15 h^-1 Msun. In this paper, we demonstrate that the various observables are all reasonably consistent with each other to within their uncertainties. RCS2 J232727.6-020437 appears to be well relaxed -- with circular and concentric X-ray isophotes, with a cool core, and no indication of significant substructure in extensive galaxy velocity data.Comment: 19 pages, 15 figures, submitted to ApJ on March 5, 2015; in press. Manuscript revised following the referee revie

Deterministic Partial Differential Equation Model for Dose Calculation in Electron Radiotherapy

Treatment with high energy ionizing radiation is one of the main methods in modern cancer therapy that is in clinical use. During the last decades, two main approaches to dose calculation were used, Monte Carlo simulations and semi-empirical models based on Fermi-Eyges theory. A third way to dose calculation has only recently attracted attention in the medical physics community. This approach is based on the deterministic kinetic equations of radiative transfer. Starting from these, we derive a macroscopic partial differential equation model for electron transport in tissue. This model involves an angular closure in the phase space. It is exact for the free-streaming and the isotropic regime. We solve it numerically by a newly developed HLLC scheme based on [BerCharDub], that exactly preserves key properties of the analytical solution on the discrete level. Several numerical results for test cases from the medical physics literature are presented.Comment: 20 pages, 7 figure

Estimation of the rigid-body motion from three-dimensional images using a generalized center-of-mass points approach

We present an analytical method for the estimation of rigid-body motion in sets of three-dimensional (3-D) SPECT and PET slices. This method utilizes mathematically defined generalized center-of-mass points in images, requiring no segmentation. It can be applied to compensation of the rigid-body motion in both SPECT and PET, once a series of 3-D tomographic images are available. We generalized the formula for the center-of-mass to obtain a family of points comoving with the object\u27s rigid-body motion. From the family of possible points we chose the best three points which resulted in the minimum root-mean-square difference between images as the generalized center-of-mass points for use in estimating motion. The estimated motion was used to sum the sets of tomographic images, or incorporated in the iterative reconstruction to correct for motion during reconstruction of the combined projection data. For comparison, the principle-axes method was also applied to estimate the rigid-body motion from the same tomographic images. To evaluate our method for different noise levels, we performed simulations with the MCAT phantom. We observed that though noise degraded the motion-detection accuracy, our method helped in reducing the motion artifact both visually and quantitatively. We also acquired four sets of the emission and transmission data of the Data Spectrum Anthropomorphic Phantom positioned at four different locations and/or orientations. From these we generated a composite acquisition simulating periodic phantom movements during acquisition. The simulated motion was calculated from the generalized center-of-mass points calculated from the tomographic images reconstructed from individual acquisitions. We determined that motion-compensation greatly reduced the motion artifact. Finally, in a simulation with the gated MCAT phantom, an exaggerated rigid-body motion was applied to the end-systolic frame. The motion was estimated from the end-diastolic and end-systolic images, and used to sum them into a summed image without obvious artifact. Compared to the principle-axes method, in two of the three comparisons with anthropomorphic phantom data our method estimated the motion in closer agreement to the Polaris system than the principal-axes method, while the principle-axes method gave a more accurate estimation of motion in most cases for the MCAT simulations. As an image-driven approach, our method assumes angularly com plete data sets for each state of motion. We expert this method to be applied in correction of respiratory motion in respiratory gated SPECT, and respiratory or other rigid-body motion in PET. © 2006 IEEE