142 research outputs found
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A multi-modal data resource for investigating topographic heterogeneity in patient-derived xenograft tumors.
Patient-derived xenografts (PDXs) are an essential pre-clinical resource for investigating tumor biology. However, cellular heterogeneity within and across PDX tumors can strongly impact the interpretation of PDX studies. Here, we generated a multi-modal, large-scale dataset to investigate PDX heterogeneity in metastatic colorectal cancer (CRC) across tumor models, spatial scales and genomic, transcriptomic, proteomic and imaging assay modalities. To showcase this dataset, we present analysis to assess sources of PDX variation, including anatomical orientation within the implanted tumor, mouse contribution, and differences between replicate PDX tumors. A unique aspect of our dataset is deep characterization of intra-tumor heterogeneity via immunofluorescence imaging, which enables investigation of variation across multiple spatial scales, from subcellular to whole tumor levels. Our study provides a benchmark data resource to investigate PDX models of metastatic CRC and serves as a template for future, quantitative investigations of spatial heterogeneity within and across PDX tumor models
Galaxy Zoo: Disentangling the Environmental Dependence of Morphology and Colour
We analyze the environmental dependence of galaxy morphology and colour with
two-point clustering statistics, using data from the Galaxy Zoo, the largest
sample of visually classified morphologies yet compiled, extracted from the
Sloan Digital Sky Survey. We present two-point correlation functions of spiral
and early-type galaxies, and we quantify the correlation between morphology and
environment with marked correlation functions. These yield clear and precise
environmental trends across a wide range of scales, analogous to similar
measurements with galaxy colours, indicating that the Galaxy Zoo
classifications themselves are very precise. We measure morphology marked
correlation functions at fixed colour and find that they are relatively weak,
with the only residual correlation being that of red galaxies at small scales,
indicating a morphology gradient within haloes for red galaxies. At fixed
morphology, we find that the environmental dependence of colour remains strong,
and these correlations remain for fixed morphology \textit{and} luminosity. An
implication of this is that much of the morphology--density relation is due to
the relation between colour and density. Our results also have implications for
galaxy evolution: the morphological transformation of galaxies is usually
accompanied by a colour transformation, but not necessarily vice versa. A
spiral galaxy may move onto the red sequence of the colour-magnitude diagram
without quickly becoming an early-type. We analyze the significant population
of red spiral galaxies, and present evidence that they tend to be located in
moderately dense environments and are often satellite galaxies in the outskirts
of haloes. Finally, we combine our results to argue that central and satellite
galaxies tend to follow different evolutionary paths.Comment: 19 pages, 18 figures. Accepted for publication in MNRA
Walking and Walkability: Is Wayfinding a Missing Link? Implications for Public Health Practice
Research on walking and walkability has yet to focus on wayfinding, the interactive, problem-solving process by which people use environmental information to locate themselves and navigate through various settings
Galaxy Zoo: The large-scale spin statistics of spiral galaxies in the Sloan Digital Sky Survey
We re-examine the evidence for a violation of large-scale statistical
isotropy in the distribution of projected spin vectors of spiral galaxies. We
have a sample of spiral galaxies from the Sloan Digital Sky
Survey, with their line of sight spin direction confidently classified by
members of the public through the online project Galaxy Zoo. After establishing
and correcting for a certain level of bias in our handedness results we find
the winding sense of the galaxies to be consistent with statistical isotropy.
In particular we find no significant dipole signal, and thus no evidence for
overall preferred handedness of the Universe. We compare this result to those
of other authors and conclude that these may also be affected and explained by
a bias effect.Comment: Accepted for publication in MNRAS. 8 pages, 5 figure
The Extended Star Formation History of the Andromeda Spheroid at 35 Kpc on the Minor Axis
Using the HST ACS, we have obtained deep optical images reaching well below
the oldest main sequence turnoff in fields on the southeast minor-axis of the
Andromeda Galaxy, 35 kpc from the nucleus. These data probe the star formation
history in the extended halo of Andromeda -- that region beyond 30 kpc that
appears both chemically and morphologically distinct from the metal-rich,
highly-disturbed inner spheroid. The present data, together with our previous
data for fields at 11 and 21 kpc, do not show a simple trend toward older ages
and lower metallicities, as one might expect for populations further removed
from the obvious disturbances of the inner spheroid. Specifically, the mean
ages and [Fe/H] values at 11 kpc, 21 kpc, and 35 kpc are 9.7 Gyr and -0.65,
11.0 Gyr and -0.87, and 10.5 Gyr and -0.98, respectively. In the best-fit model
of the 35 kpc population, one third of the stars are younger than 10 Gyr, while
only ~10% of the stars are truly ancient and metal-poor. The extended halo thus
exhibits clear evidence of its hierarchical assembly, and the contribution from
any classical halo formed via early monolithic collapse must be small.Comment: Accepted for publication in The Astrophysical Journal Letters. 4
pages, latex, 2 color figure
Galaxy Zoo: Reproducing Galaxy Morphologies Via Machine Learning
We present morphological classifications obtained using machine learning for
objects in SDSS DR6 that have been classified by Galaxy Zoo into three classes,
namely early types, spirals and point sources/artifacts. An artificial neural
network is trained on a subset of objects classified by the human eye and we
test whether the machine learning algorithm can reproduce the human
classifications for the rest of the sample. We find that the success of the
neural network in matching the human classifications depends crucially on the
set of input parameters chosen for the machine-learning algorithm. The colours
and parameters associated with profile-fitting are reasonable in separating the
objects into three classes. However, these results are considerably improved
when adding adaptive shape parameters as well as concentration and texture. The
adaptive moments, concentration and texture parameters alone cannot distinguish
between early type galaxies and the point sources/artifacts. Using a set of
twelve parameters, the neural network is able to reproduce the human
classifications to better than 90% for all three morphological classes. We find
that using a training set that is incomplete in magnitude does not degrade our
results given our particular choice of the input parameters to the network. We
conclude that it is promising to use machine- learning algorithms to perform
morphological classification for the next generation of wide-field imaging
surveys and that the Galaxy Zoo catalogue provides an invaluable training set
for such purposes.Comment: 13 Pages, 5 figures, 10 tables. Accepted for publication in MNRAS.
Revised to match accepted version
Galaxy Zoo 1 : Data Release of Morphological Classifications for nearly 900,000 galaxies
Morphology is a powerful indicator of a galaxy's dynamical and merger
history. It is strongly correlated with many physical parameters, including
mass, star formation history and the distribution of mass. The Galaxy Zoo
project collected simple morphological classifications of nearly 900,000
galaxies drawn from the Sloan Digital Sky Survey, contributed by hundreds of
thousands of volunteers. This large number of classifications allows us to
exclude classifier error, and measure the influence of subtle biases inherent
in morphological classification. This paper presents the data collected by the
project, alongside measures of classification accuracy and bias. The data are
now publicly available and full catalogues can be downloaded in electronic
format from http://data.galaxyzoo.org.Comment: Accepted by MNRAS, 14 pages. Updated to match final version; problem
with table 7 header fixed. Full tables available at http://data.galaxyzoo.or
The SPLASH Survey: A Spectroscopic Portrait of Andromeda's Giant Southern Stream
The giant southern stream (GSS) is the most prominent tidal debris feature in
M31's stellar halo. The GSS is composed of a relatively metal-rich, high
surface-brightness "core" and a lower metallicity, lower surface brightness
"envelope." We present Keck/DEIMOS spectroscopy of red giant stars in six
fields in the vicinity of M31's GSS and one field on Stream C, an arc-like
feature on M31's SE minor axis at R=60 kpc. Several GSS-related findings and
measurements are presented here. We present the innermost kinematical detection
of the GSS core to date (R=17 kpc). This field also contains the continuation
of a second kinematically cold component originally seen in a GSS core field at
R=21 kpc. The velocity gradients of the GSS and the second component in the
combined data set are parallel over a radial range of 7 kpc, suggesting a
possible bifurcation in the line-of-sight velocities of GSS stars. We also
present the first kinematical detection of substructure in the GSS envelope.
Using kinematically identified samples, we show that the envelope debris has a
~0.7 dex lower mean photometric metallicity and possibly higher intrinsic
velocity dispersion than the GSS core. The GSS is also identified in the field
of the M31 dSph satellite And I; the GSS in this field has a metallicity
distribution identical to that of the GSS core. We confirm the presence of two
kinematically cold components in Stream C, and measure intrinsic velocity
dispersions of ~10 and ~4 km/s. This compilation of the kinematical (mean
velocity, intrinsic velocity dispersion) and chemical properties of stars in
the GSS core and envelope, coupled with published surface brightness
measurements and wide-area star-count maps, will improve constraints on the
orbit and internal structure of the dwarf satellite progenitor.Comment: Accepted for publication in Ap
The ACS Survey of Galactic Globular Clusters. IX. Horizontal Branch Morphology and the Second Parameter Phenomenon
The horizontal branch (HB) morphology of globular clusters (GCs) is most
strongly influenced by metallicity. The second parameter phenomenon
acknowledges that metallicity alone is not enough to describe the HB morphology
of all GCs. In particular, the outer Galactic halo contains GCs with redder HBs
at a given metallicity than are found inside the Solar circle. Thus, at least a
second parameter is required to characterize HB morphology. Here we analyze the
median color difference between the HB and the red giant branch (RGB), d(V-I),
measured from HST ACS photometry of 60 GCs within ~20 kpc of the Galactic
Center. Analysis of this homogeneous data set reveals that, after the influence
of metallicity has been removed, the correlation between d(V-I) and age is
stronger than that of any other parameter considered. Expanding the sample to
include HST photometry of the 6 most distant Galactic GCs lends additional
support to the correlation between d(V-I) and age. This result is robust with
respect to the adopted metallicity scale and the method of age determination,
but must bear the caveat that high quality, detailed abundance information is
not available for a significant fraction of the sample. When a subset of GCs
with similar metallicities and ages are considered, a correlation between
d(V-I) and central luminosity density is exposed. With respect to the existence
of GCs with anomalously red HBs at a given metallicity, we conclude that age is
the second parameter and central density is most likely the third. Important
problems related to HB morphology in GCs, notably multi-modal distributions and
faint blue tails, remain to be explained. (Abridged)Comment: Accepted for publication in ApJ; 49 pages, 19 figure
Galaxy Zoo: Dust in Spirals
We investigate the effect of dust on spiral galaxies by measuring the
inclination-dependence of optical colours for 24,276 well-resolved SDSS
galaxies visually classified in Galaxy Zoo. We find clear trends of reddening
with inclination which imply a total extinction from face-on to edge-on of 0.7,
0.6, 0.5 and 0.4 magnitudes for the ugri passbands. We split the sample into
"bulgy" (early-type) and "disky" (late-type) spirals using the SDSS fracdeV (or
f_DeV) parameter and show that the average face-on colour of "bulgy" spirals is
redder than the average edge-on colour of "disky" spirals. This shows that the
observed optical colour of a spiral galaxy is determined almost equally by the
spiral type (via the bulge-disk ratio and stellar populations), and reddening
due to dust. We find that both luminosity and spiral type affect the total
amount of extinction, with "disky" spirals at M_r ~ -21.5 mags having the most
reddening. This decrease of reddening for the most luminous spirals has not
been observed before and may be related to their lower levels of recent star
formation. We compare our results with the latest dust attenuation models of
Tuffs et al. We find that the model reproduces the observed trends reasonably
well but overpredicts the amount of u-band attenuation in edge-on galaxies. We
end by discussing the effects of dust on large galaxy surveys and emphasize
that these effects will become important as we push to higher precision
measurements of galaxy properties and their clustering.Comment: MNRAS in press. 25 pages, 22 figures (including an abstract comparing
GZ classifications with common automated methods for selecting disk/early
type galaxies in SDSS data). v2 corrects typos found in proof
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