137 research outputs found
Diffusion Coefficients of Endogenous Cytosolic Proteins from Rabbit Skinned Muscle Fibers
AbstractEfflux time courses of endogenous cytosolic proteins were obtained from rabbit psoas muscle fibers skinned in oil and transferred to physiological salt solution. Proteins were separated by gel electrophoresis and compared to load-matched standards for quantitative analysis. A radial diffusion model incorporating the dissociation and dissipation of supramolecular complexes accounts for an initial lag and subsequent efflux of glycolytic and glycogenolytic enzymes. The model includes terms representing protein crowding, myofilament lattice hindrance, and binding to the cytomatrix. Optimization algorithms returned estimates of the apparent diffusion coefficients, D(r,t), that were very low at the onset of diffusion (∼10−10 cm2 s−1) but increased with time as cytosolic protein density, which was initially high, decreased. D(r,t) at later times ranged from 2.11 × 10−7 cm2 s−1 (parvalbumin) to 0.20 × 10−7 cm2 s−1 (phosphofructose kinase), values that are 3.6- to 12.3-fold lower than those predicted in bulk water. The low initial values are consistent with the presence of complexes in situ; the higher later values are consistent with molecular sieving and transient binding of dissociated proteins. Channeling of metabolic intermediates via enzyme complexes may enhance production of adenosine triphosphate at rates beyond that possible with randomly and/or sparsely distributed enzymes, thereby matching supply with demand
Self-similar scaling and evolution in the galaxy cluster X-ray Luminosity-Temperature relation
We investigate the form and evolution of the X-ray luminosity-temperature
(LT) relation of a sample of 114 galaxy clusters observed with Chandra at
0.1<z<1.3. The clusters were divided into subsamples based on their X-ray
morphology or whether they host strong cool cores. We find that when the core
regions are excluded, the most relaxed clusters (or those with the strongest
cool cores) follow an LT relation with a slope that agrees well with simple
self-similar expectations. This is supported by an analysis of the gas density
profiles of the systems, which shows self-similar behaviour of the gas profiles
of the relaxed clusters outside the core regions. By comparing our data with
clusters in the REXCESS sample, which extends to lower masses, we find evidence
that the self-similar behaviour of even the most relaxed clusters breaks at
around 3.5keV. By contrast, the LT slopes of the subsamples of unrelaxed
systems (or those without strong cool cores) are significantly steeper than the
self-similar model, with lower mass systems appearing less luminous and higher
mass systems appearing more luminous than the self-similar relation. We argue
that these results are consistent with a model of non-gravitational energy
input in clusters that combines central heating with entropy enhancements from
merger shocks. Such enhancements could extend the impact of central energy
input to larger radii in unrelaxed clusters, as suggested by our data. We also
examine the evolution of the LT relation, and find that while the data appear
inconsistent with simple self-similar evolution, the differences can be
plausibly explained by selection bias, and thus we find no reason to rule out
self-similar evolution. We show that the fraction of cool core clusters in our
(non-representative) sample decreases at z>0.5 and discuss the effect of this
on measurements of the evolution in the LT relation.Comment: 21 pages, 15 figures. Submitted to MNRAS. Comments welcom
A Chromosome-Scale Assembly of the Garden Orach (Atriplex hortensis L.) Genome Using Oxford Nanopore Sequencing
Atriplex hortensis (2n = 2x = 18, 1C genome size 1.1 gigabases), also known
as garden orach and mountain-spinach, is a highly nutritious, broadleaf annual of
the Amaranthaceae-Chenopodiaceae alliance (Chenopodiaceae sensu stricto, subfam.
Chenopodioideae) that has spread in cultivation from its native primary domestication
area in Eurasia to other temperate and subtropical regions worldwide. Atriplex L. is a
highly complex but, as understood now, a monophyletic group of mainly halophytic
and/or xerophytic plants, of which A. hortensis has been a vegetable of minor
importance in some areas of Eurasia (from Central Asia to the Mediterranean) at least
since antiquity. Nonetheless, it is a crop with tremendous nutritional potential due
primarily to its exceptional leaf and seed protein quantities (approaching 30%) and
quality (high levels of lysine). Although there is some literature describing the taxonomy
and production of A. hortensis, there is a general lack of genetic and genomic data
that would otherwise help elucidate the genetic variation, phylogenetic positioning, and
future potential of the species. Here, we report the assembly of the first high-quality,
chromosome-scale reference genome for A. hortensis cv. “Golden.” Long-read data
from Oxford Nanopore’s MinION DNA sequencer was assembled with the program
Canu and polished with Illumina short reads. Contigs were scaffolded to chromosome
scale using chromatin-proximity maps (Hi-C) yielding a final assembly containing 1,325
scaffolds with a N50 of 98.9 Mb – with 94.7% of the assembly represented in the nine
largest, chromosome-scale scaffolds. Sixty-six percent of the genome was classified
as highly repetitive DNA, with the most common repetitive elements being Gypsy-
(32%) and Copia-like (11%) long-terminal repeats. The annotation was completed using
MAKER which identified 37,083 gene models and 2,555 tRNA genes. Completeness of the genome, assessed using the Benchmarking Universal Single Copy Orthologs
(BUSCO) metric, identified 97.5% of the conserved orthologs as complete, with only
2.2% being duplicated, reflecting the diploid nature of A. hortensis. A resequencing
panel of 21 wild, unimproved and cultivated A. hortensis accessions revealed three
distinct populations with little variation within subpopulations. These resources provide
vital information to better understand A. hortensis and facilitate future study
Joint analysis of X-ray and Sunyaev Zel'dovich observations of galaxy clusters using an analytic model of the intra-cluster medium
We perform a joint analysis of X-ray and Sunyaev Zel'dovich (SZ) effect data
using an analytic model that describes the gas properties of galaxy clusters.
The joint analysis allows the measurement of the cluster gas mass fraction
profile and Hubble constant independent of cosmological parameters. Weak
cosmological priors are used to calculate the overdensity radius within which
the gas mass fractions are reported. Such an analysis can provide direct
constraints on the evolution of the cluster gas mass fraction with redshift. We
validate the model and the joint analysis on high signal-to-noise data from the
Chandra X-ray Observatory and the Sunyaev-Zel'dovich Array for two clusters,
Abell 2631 and Abell 2204.Comment: ApJ in pres
The Mysterious Merger of NGC6868 and NGC6861 in the Telescopium Group
We use Chandra X-ray observations of the hot gas in and around NGC6868 and
NGC6861 in the Telescopium galaxy group (AS0851) to probe the interaction
history between these galaxies. Mean surface brightness profiles for NGC6868
and NGC6861 are each well described by double beta-models, suggesting that they
are each the dominant galaxy in a galaxy subgroup about to merge. Surface
brightness and temperature maps of the brightest group galaxy NGC6868 show a
cold front edge ~23 kpc to the north, and a cool 0.62 keV spiral-shaped tail to
the south. Analysis of the temperature and density across the cold front
constrains the relative motion between NGC6868 and the ambient group gas to be
at most transonic; while the spiral morphology of the tail strongly suggests
that the cold front edge and tail are the result of gas sloshing due to the
subgroup merger. The cooler central region of NGC6861 is surrounded by a sheath
of hot gas to the east and hot, bifurcated tails of X-ray emission to the west
and northwest. We discuss supersonic infall of the NGC6861 subroup, sloshing
from the NGC6868 and NGC6861 subgroup merger, and AGN heating as possible
explanations for these features, and discuss possible scenarios that may
contribute to the order of magnitude discrepancy between the Margorrian and
black hole mass - sigma predictions for its central black hole.Comment: 17 pages, 23 figures, submitted to Ap
LoCuSS: A Comparison of Sunyaev-Zel'dovich Effect and Gravitational Lensing Measurements of Galaxy Clusters
We present the first measurement of the relationship between the
Sunyaev-Zel'dovich effect signal and the mass of galaxy clusters that uses
gravitational lensing to measure cluster mass, based on 14 X-ray luminous
clusters at z~0.2 from the Local Cluster Substructure Survey. We measure the
integrated Compton y-parameter, Y, and total projected mass of the clusters
(M_GL) within a projected clustercentric radius of 350 kpc, corresponding to
mean overdensities of 4000-8000 relative to the critical density. We find
self-similar scaling between M_GL and Y, with a scatter in mass at fixed Y of
32%. This scatter exceeds that predicted from numerical cluster simulations,
however, it is smaller than comparable measurements of the scatter in mass at
fixed T_X. We also find no evidence of segregation in Y between disturbed and
undisturbed clusters, as had been seen with T_X on the same physical scales. We
compare our scaling relation to the Bonamente et al. relation based on mass
measurements that assume hydrostatic equilibrium, finding no evidence for a
hydrostatic mass bias in cluster cores (M_GL = 0.98+/-0.13 M_HSE), consistent
with both predictions from numerical simulations and lensing/X-ray-based
measurements of mass-observable scaling relations at larger radii. Overall our
results suggest that the Sunyaev-Zel'dovich effect may be less sensitive than
X-ray observations to the details of cluster physics in cluster cores.Comment: Minor changes to match published version: 2009 ApJL 701:114-11
Infrared skin damage thresholds from 1319-nm continous-wave laser exposures
A series of experiments were conducted in vivo using Yucatan miniature pigs (Sus scrofa domestica) to determine thermal damage thresholds to the skin from 1319-nm continuous-wave Nd:YAG laser irradiation. Experiments employed exposure durations of 0.25, 1.0, 2.5, and 10 s and beam diameters of ∼0.6 and 1 cm. Thermal imagery data provided a time-dependent surface temperature response from the laser. A damage endpoint of fifty percent probability of a minimally visible effect was used to determine threshold for damage at 1 and 24 h postexposure. Predicted thermal response and damage thresholds are compared with a numerical model of opticalthermal interaction. Resultant trends with respect to exposure duration and beam diameter are compared with current standardized exposure limits for laser safety. Mathematical modeling agreed well with experimental data, predicting that though laser safety standards are sufficient for exposuress, they may become less safe for very long exposures. © The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. Distribution or reproduction of this work in whole or in part requires full attribution of the original publication, including its DOI. [DOI: 10.1117/1.JBO.18.12.125002
LoCuSS: The Sunyaev-Zel'dovich Effect and Weak Lensing Mass Scaling Relation
We present the first weak-lensing-based scaling relation between galaxy
cluster mass, M_wl, and integrated Compton parameter Y_sph. Observations of 18
galaxy clusters at z~0.2 were obtained with the Subaru 8.2-m telescope and the
Sunyaev-Zel'dovich Array. The M_wl-Y_sph scaling relations, measured at
Delta=500, 1000, and 2500 rho_c, are consistent in slope and normalization with
previous results derived under the assumption of hydrostatic equilibrium (HSE).
We find an intrinsic scatter in M_wl at fixed Y_sph of 20%, larger than both
previous measurements of M_HSE-Y_sph scatter as well as the scatter in true
mass at fixed Y_sph found in simulations. Moreover, the scatter in our
lensing-based scaling relations is morphology dependent, with 30-40% larger
M_wl for undisturbed compared to disturbed clusters at the same Y_sph at r_500.
Further examination suggests that the segregation may be explained by the
inability of our spherical lens models to faithfully describe the
three-dimensional structure of the clusters, in particular, the structure along
the line-of-sight. We find that the ellipticity of the brightest cluster
galaxy, a proxy for halo orientation, correlates well with the offset in mass
from the mean scaling relation, which supports this picture. This provides
empirical evidence that line-of-sight projection effects are an important
systematic uncertainty in lensing-based scaling relations.Comment: Accepted versio
Image-based consensus molecular subtyping in rectal cancer biopsies and response to neoadjuvant chemoradiotherapy
The development of deep learning (DL) models to predict the consensus molecular subtypes (CMS) from histopathology images (imCMS) is a promising and cost-effective strategy to support patient stratification. Here, we investigate whether imCMS calls generated from whole slide histopathology images (WSIs) of rectal cancer (RC) pre-treatment biopsies are associated with pathological complete response (pCR) to neoadjuvant long course chemoradiotherapy (LCRT) with single agent fluoropyrimidine. DL models were trained to classify WSIs of colorectal cancers stained with hematoxylin and eosin into one of the four CMS classes using a multi-centric dataset of resection and biopsy specimens (n = 1057 WSIs) with paired transcriptional data. Classifiers were tested on a held out RC biopsy cohort (ARISTOTLE) and correlated with pCR to LCRT in an independent dataset merging two RC cohorts (ARISTOTLE, n = 114 and SALZBURG, n = 55 patients). DL models predicted CMS with high classification performance in multiple comparative analyses. In the independent cohorts (ARISTOTLE, SALZBURG), cases with WSIs classified as imCMS1 had a significantly higher likelihood of achieving pCR (OR = 2.69, 95% CI 1.01–7.17, p = 0.048). Conversely, imCMS4 was associated with lack of pCR (OR = 0.25, 95% CI 0.07–0.88, p = 0.031). Classification maps demonstrated pathologist-interpretable associations with high stromal content in imCMS4 cases, associated with poor outcome. No significant association was found in imCMS2 or imCMS3. imCMS classification of pre-treatment biopsies is a fast and inexpensive solution to identify patient groups that could benefit from neoadjuvant LCRT. The significant associations between imCMS1/imCMS4 with pCR suggest the existence of predictive morphological features that could enhance standard pathological assessment
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