219 research outputs found
Hierarchical graphs for rule-based modeling of biochemical systems
<p>Abstract</p> <p>Background</p> <p>In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions. A rule that specifies addition (removal) of an edge represents a class of association (dissociation) reactions, and a rule that specifies a change of a vertex attribute represents a class of reactions that affect the internal state of a molecular component. A set of rules comprises an executable model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system.</p> <p>Results</p> <p>For purposes of model annotation, we propose the use of hierarchical graphs to represent structural relationships among components and subcomponents of molecules. We illustrate how hierarchical graphs can be used to naturally document the structural organization of the functional components and subcomponents of two proteins: the protein tyrosine kinase Lck and the T cell receptor (TCR) complex. We also show that computational methods developed for regular graphs can be applied to hierarchical graphs. In particular, we describe a generalization of Nauty, a graph isomorphism and canonical labeling algorithm. The generalized version of the Nauty procedure, which we call HNauty, can be used to assign canonical labels to hierarchical graphs or more generally to graphs with multiple edge types. The difference between the Nauty and HNauty procedures is minor, but for completeness, we provide an explanation of the entire HNauty algorithm.</p> <p>Conclusions</p> <p>Hierarchical graphs provide more intuitive formal representations of proteins and other structured molecules with multiple functional components than do the regular graphs of current languages for specifying rule-based models, such as the BioNetGen language (BNGL). Thus, the proposed use of hierarchical graphs should promote clarity and better understanding of rule-based models.</p
Probing the extreme realm of AGN feedback in the massive galaxy cluster, RX J1532.9+3021
We present a detailed Chandra, XMM-Newton, VLA and HST analysis of one of the
strongest cool core clusters known, RX J1532.9+3021 (z=0.3613). Using new, deep
90 ks Chandra observations, we confirm the presence of a western X-ray cavity
or bubble, and report on a newly discovered eastern X-ray cavity. The total
mechanical power associated with these AGN-driven outflows is (22+/-9)*10^44
erg/s, and is sufficient to offset the cooling, indicating that AGN feedback
still provides a viable solution to the cooling flow problem even in the
strongest cool core clusters. Based on the distribution of the optical
filaments, as well as a jet-like structure seen in the 325 MHz VLA radio map,
we suggest that the cluster harbours older outflows along the north to south
direction. The jet of the central AGN is therefore either precessing or
sloshing-induced motions have caused the outflows to change directions. There
are also hints of an X-ray depression to the north aligned with the 325 MHz
jet-like structure, which might represent the highest redshift ghost cavity
discovered to date. We further find evidence of a cold front (r=65kpc) that
coincides with the outermost edge of the western X-ray cavity and the edge of
the radio mini-halo. The common location of the cold front with the edge of the
radio mini-halo supports the idea that the latter originates from electrons
being reaccelerated due to sloshing induced turbulence. Alternatively, its
coexistence with the edge of the X-ray cavity may be due to cool gas being
dragged out by the outburst. We confirm that the central AGN is highly
sub-Eddington and conclude that a >10^10M_Sun or a rapidly spinning black hole
is favoured to explain both the radiative-inefficiency of the AGN and the
powerful X-ray cavities.Comment: Accepted for publication to ApJ (minor corrections), 16 pages, 16
figures, 5 tables. Full resolution at http://www.stanford.edu/~juliehl/M1532
Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism
We investigate the ability of algorithms developed for reverse engineering of
transcriptional regulatory networks to reconstruct metabolic networks from
high-throughput metabolite profiling data. For this, we generate synthetic
metabolic profiles for benchmarking purposes based on a well-established model
for red blood cell metabolism. A variety of data sets is generated, accounting
for different properties of real metabolic networks, such as experimental
noise, metabolite correlations, and temporal dynamics. These data sets are made
available online. We apply ARACNE, a mainstream transcriptional networks
reverse engineering algorithm, to these data sets and observe performance
comparable to that obtained in the transcriptional domain, for which the
algorithm was originally designed.Comment: 14 pages, 3 figures. Presented at the DIMACS Workshop on Dialogue on
Reverse Engineering Assessment and Methods (DREAM), Sep 200
Uplift, Feedback, and Buoyancy: Radio Lobe Dynamics in NGC 4472
© 2017. The American Astronomical Society. All rights reserved. We present results from deep (380 ks) Chandra observations of the active galactic nucleus (AGN) outburst in the massive early-type galaxy NGC 4472. We detect cavities in the gas coincident with the radio lobes and estimate the eastern and western lobe enthalpy to be (1.1 ± 0.5) × 10 56 erg and (3 ± 1) × 10 56 erg and the average power required to inflate the lobes to be (1.8 ± 0.9) × 10 41 erg s -1 and (6 ± 3) × 10 41 erg s -1 , respectively. We also detect enhanced X-ray rims around the radio lobes with sharp surface brightness discontinuities between the shells and the ambient gas. The temperature of the gas in the shells is less than that of the ambient medium, suggesting that they are not AGN-driven shocks but rather gas uplifted from the core by the buoyant rise of the radio bubbles. We estimate the energy required to lift the gas to be up to (1.1 ± 0.3) × 10 56 erg and (3 ± 1) × 10 56 erg for the eastern and western rims, respectively, constituting a significant fraction of the total outburst energy. A more conservative estimate suggests that the gas in the rim was uplifted at a smaller distance, requiring only 20%-25% of this energy. In either case, if a significant fraction of this uplift energy is thermalized via hydrodynamic instabilities or thermal conduction, our results suggest that it could be an important source of heating in cool core clusters and groups. We also find evidence for a central abundance drop in NGC 4472. The iron abundance profile shows that the region along the cavity system has a lower metallicity than the surrounding undisturbed gas, similar to the central region. This also shows that bubbles have lifted low-metallicity gas from the center
Star-Forming Brightest Cluster Galaxies at 0.25 < z < 1.25: A Transitioning Fuel Supply
We present a multi-wavelength study of 90 brightest cluster galaxies (BCGs)
in a sample of galaxy clusters selected via the Sunyaev Zel'dovich effect by
the South Pole Telescope, utilizing data from various ground- and space-based
facilities. We infer the star formation rate (SFR) for the BCG in each cluster,
based on the UV and IR continuum luminosity, as well as the [O II] emission
line luminosity in cases where spectroscopy is available, finding 7 systems
with SFR > 100 Msun/yr. We find that the BCG SFR exceeds 10 Msun/yr in 31 of 90
(34%) cases at 0.25 < z < 1.25, compared to ~1-5% at z ~ 0 from the literature.
At z > 1, this fraction increases to 92(+6)(-31)%, implying a steady decrease
in the BCG SFR over the past ~9 Gyr. At low-z, we find that the specific star
formation rate in BCGs is declining more slowly with time than for field or
cluster galaxies, most likely due to the replenishing fuel from the cooling ICM
in relaxed, cool core clusters. At z > 0.6, the correlation between cluster
central entropy and BCG star formation - which is well established at z ~ 0 -
is not present. Instead, we find that the most star-forming BCGs at high-z are
found in the cores of dynamically unrelaxed clusters. We investigate the
rest-frame near-UV morphology of a subsample of the most star-forming BCGs
using data from the Hubble Space Telescope, finding complex, highly asymmetric
UV morphologies on scales as large as ~50-60 kpc. The high fraction of
star-forming BCGs hosted in unrelaxed, non-cool core clusters at early times
suggests that the dominant mode of fueling star formation in BCGs may have
recently transitioned from galaxy-galaxy interactions to ICM cooling.Comment: 20 pages, 10 figures. Submitted for publication in ApJ. Comments
welcom
Current Estimates for HIV-1 Production Imply Rapid Viral Clearance in Lymphoid Tissues
It has recently been estimated that a single HIV-1 infected cell produces between and more than viral particles over its life span. Since body-wide estimates of the ratio of free virus to productively infected cells are smaller than and much smaller than , individual virions must be cleared rapidly. This seems difficult to reconcile with the fact that most of the total body virus is trapped on follicular dendritic cells where it can survive for many months. It has also been difficult to reconcile the vast difference in the rates at which the virus is cleared from the blood in rhesus macaques and in chronically infected patients. Here we attempt to reconcile these seemingly contradictory observations by considering the virion clearance rate in various organs and the virion exchange rates between them. The main results are that the per capita clearance rate of free virus in lymphoid tissue should be fast, the virion exchange rate between lymphoid tissue and the blood should be slow, and the comparatively slow previous estimates for the virion clearance rate from the blood correspond to the rate of virion efflux from the blood to other organs where the virus is ultimately cleared
Testing for X-Ray–SZ Differences and Redshift Evolution in the X-Ray Morphology of Galaxy Clusters
We present a quantitative study of the X-ray morphology of galaxy clusters, as a function of their detection method and redshift. We analyze two separate samples of galaxy clusters: a sample of 36 clusters at 0.35 < z < 0.9 selected in the X-ray with the ROSAT PSPC 400 deg 2 survey, and a sample of 90 clusters at 0.25 < z < 1.2 selected via the Sunyaev-Zel'dovich (SZ) effect with the South Pole Telescope. Clusters from both samples have similar-quality Chandra observations, which allow us to quantify their X-ray morphologies via two distinct methods: centroid shifts (w) and photon asymmetry (A phot ). The latter technique provides nearly unbiased morphology estimates for clusters spanning a broad range of redshift and data quality. We further compare the X-ray morphologies of X-ray- and SZ-selected clusters with those of simulated clusters. We do not find a statistically significant difference in the measured X-ray morphology of X-ray and SZ-selected clusters over the redshift range probed by these samples, suggesting that the two are probing similar populations of clusters. We find that the X-ray morphologies of simulated clusters are statistically indistinguishable from those of X-ray- or SZ-selected clusters, implying that the most important physics for dictating the large-scale gas morphology (outside of the core) is well-approximated in these simulations. Finally, we find no statistically significant redshift evolution in the X-ray morphology (both for observed and simulated clusters), over the range of z ∼ 0.3 to z ∼ 1, seemingly in contradiction with the redshift-dependent halo merger rate predicted by simulations.United States. National Aeronautics and Space Administration (Award 13800883)United States. National Aeronautics and Space Administration (Award 16800690
Mass Calibration and Cosmological Analysis of the SPT-SZ Galaxy Cluster Sample Using Velocity Dispersion and X-ray Measurements
We present a velocity dispersion-based mass calibration of the South Pole
Telescope Sunyaev-Zel'dovich effect survey (SPT-SZ) galaxy cluster sample.
Using a homogeneously selected sample of 100 cluster candidates from 720 deg2
of the survey along with 63 velocity dispersion () and 16 X-ray Yx
measurements of sample clusters, we simultaneously calibrate the
mass-observable relation and constrain cosmological parameters. The
calibrations using and Yx are consistent at the level,
with the calibration preferring ~16% higher masses. We use the full
cluster dataset to measure . The
SPT cluster abundance is lower than preferred by either the WMAP9 or
Planck+WMAP9 polarization (WP) data, but assuming the sum of the neutrino
masses is eV, we find the datasets to be consistent at the
1.0 level for WMAP9 and 1.5 for Planck+WP. Allowing for larger
further reconciles the results. When we combine the cluster and
Planck+WP datasets with BAO and SNIa, the preferred cluster masses are
higher than the Yx calibration and higher than the
calibration. Given the scale of these shifts (~44% and ~23% in mass,
respectively), we execute a goodness of fit test; it reveals no tension,
indicating that the best-fit model provides an adequate description of the
data. Using the multi-probe dataset, we measure and
. Within a CDM model we find eV. We present a consistency test of the cosmic growth rate.
Allowing both the growth index and the dark energy equation of state
parameter to vary, we find and ,
demonstrating that the expansion and the growth histories are consistent with a
LCDM model ().Comment: Accepted by ApJ (v2 is accepted version); 17 pages, 6 figure
- …