1,316 research outputs found
Novel continuum modeling of crystal surface evolution
We propose a novel approach to continuum modeling of the dynamics of crystal
surfaces. Our model follows the evolution of an ensemble of step
configurations, which are consistent with the macroscopic surface profile.
Contrary to the usual approach where the continuum limit is achieved when
typical surface features consist of many steps, our continuum limit is
approached when the number of step configurations of the ensemble is very
large. The model can handle singular surface structures such as corners and
facets. It has a clear computational advantage over discrete models.Comment: 4 pages, 3 postscript figure
Automatic segmentation of multiple cardiovascular structures from cardiac computed tomography angiography images using deep learning.
OBJECTIVES:To develop, demonstrate and evaluate an automated deep learning method for multiple cardiovascular structure segmentation. BACKGROUND:Segmentation of cardiovascular images is resource-intensive. We design an automated deep learning method for the segmentation of multiple structures from Coronary Computed Tomography Angiography (CCTA) images. METHODS:Images from a multicenter registry of patients that underwent clinically-indicated CCTA were used. The proximal ascending and descending aorta (PAA, DA), superior and inferior vena cavae (SVC, IVC), pulmonary artery (PA), coronary sinus (CS), right ventricular wall (RVW) and left atrial wall (LAW) were annotated as ground truth. The U-net-derived deep learning model was trained, validated and tested in a 70:20:10 split. RESULTS:The dataset comprised 206 patients, with 5.130 billion pixels. Mean age was 59.9 ± 9.4 yrs., and was 42.7% female. An overall median Dice score of 0.820 (0.782, 0.843) was achieved. Median Dice scores for PAA, DA, SVC, IVC, PA, CS, RVW and LAW were 0.969 (0.979, 0.988), 0.953 (0.955, 0.983), 0.937 (0.934, 0.965), 0.903 (0.897, 0.948), 0.775 (0.724, 0.925), 0.720 (0.642, 0.809), 0.685 (0.631, 0.761) and 0.625 (0.596, 0.749) respectively. Apart from the CS, there were no significant differences in performance between sexes or age groups. CONCLUSIONS:An automated deep learning model demonstrated segmentation of multiple cardiovascular structures from CCTA images with reasonable overall accuracy when evaluated on a pixel level
Measuring D_A and H at z=0.35 from the SDSS DR7 LRGs using baryon acoustic oscillations
We present measurements of the angular diameter distance D_A(z) and the
Hubble parameter H(z) at z=0.35 using the anisotropy of the baryon acoustic
oscillation (BAO) signal measured in the galaxy clustering distribution of the
Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) Luminous Red Galaxies
(LRG) sample. Our work is the first to apply density-field reconstruction to an
anisotropic analysis of the acoustic peak. Reconstruction partially removes the
effects of non-linear evolution and redshift-space distortions in order to
sharpen the acoustic signal. We present the theoretical framework behind the
anisotropic BAO signal and give a detailed account of the fitting model we use
to extract this signal from the data. Our method focuses only on the acoustic
peak anisotropy, rather than the more model-dependent anisotropic information
from the broadband power. We test the robustness of our analysis methods on 160
LasDamas DR7 mock catalogues and find that our models are unbiased at the ~0.2%
level in measuring the BAO anisotropy. After reconstruction we measure
D_A(z=0.35)=1050+/-38 Mpc and H(z=0.35)=84.4+/-7.0 km/s/Mpc assuming a sound
horizon of r_s=152.76 Mpc. Note that these measurements are correlated with a
correlation coefficient of 0.58. This represents a factor of 1.4 improvement in
the error on D_A relative to the pre-reconstruction case; a factor of 1.2
improvement is seen for H.Comment: 30 pages, 21 figures, accepted by MNRAS, updated to version accepted
by journa
Cosmological Non-Linearities as an Effective Fluid
The universe is smooth on large scales but very inhomogeneous on small
scales. Why is the spacetime on large scales modeled to a good approximation by
the Friedmann equations? Are we sure that small-scale non-linearities do not
induce a large backreaction? Related to this, what is the effective theory that
describes the universe on large scales? In this paper we make progress in
addressing these questions. We show that the effective theory for the
long-wavelength universe behaves as a viscous fluid coupled to gravity:
integrating out short-wavelength perturbations renormalizes the homogeneous
background and introduces dissipative dynamics into the evolution of
long-wavelength perturbations. The effective fluid has small perturbations and
is characterized by a few parameters like an equation of state, a sound speed
and a viscosity parameter. These parameters can be matched to numerical
simulations or fitted from observations. We find that the backreaction of
small-scale non-linearities is very small, being suppressed by the large
hierarchy between the scale of non-linearities and the horizon scale. The
effective pressure of the fluid is always positive and much too small to
significantly affect the background evolution. Moreover, we prove that
virialized scales decouple completely from the large-scale dynamics, at all
orders in the post-Newtonian expansion. We propose that our effective theory be
used to formulate a well-defined and controlled alternative to conventional
perturbation theory, and we discuss possible observational applications.
Finally, our way of reformulating results in second-order perturbation theory
in terms of a long-wavelength effective fluid provides the opportunity to
understand non-linear effects in a simple and physically intuitive way.Comment: 84 pages, 3 figure
Functional analysis of structural variants in single cells using Strand-seq
Somatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations
PER2 Variation is Associated with Diurnal Preference in a Korean Young Population
The PER2 gene has been reported to influence diurnal preference. In this study, we have attempted to characterize the associations between the PER2 gene polymorphisms and diurnal preference in a population of healthy young subjects, controlling for the social and environmental confounding factors. Subjects were 299 students in a college, carefully selected to be mentally and physically healthy. All subjects completed the 13-item composite scale for morningness (CSM). PER2 gene polymorphisms were genotyped by PCR-based methods. Genotype and allele carrier status of a PER2 G3853A polymorphism (rs934945) were associated with CSM scores. Carriers of the 3853G allele showed significantly higher CSM scores (P = 0.004, P = 0.009, and P = 0.001; total, morningness, and activity plan, respectively). There were no significant differences on CSM scores among genotypes and allele status of PER2 rs2304672. This result indicates that rs934945 of PER2 may be associated with diurnal preference in a Korean healthy population
Early Planet Formation in Embedded Disks (eDisk) X: Compact Disks, Extended Infall, and a Fossil Outburst in the Class I Oph IRS43 Binary
We present the first results from the Early Planet Formation in Embedded
Disks (eDisk) ALMA Large Program toward Oph IRS43, a binary system of solar
mass protostars. The 1.3 mm dust continuum observations resolve a compact disk,
~6au radius, around the northern component and show that the disk around the
southern component is even smaller, <~3 au. CO, 13CO, and C18O maps reveal a
large cavity in a low mass envelope that shows kinematic signatures of rotation
and infall extending out to ~ 2000au. An expanding CO bubble centered on the
extrapolated location of the source ~130 years ago suggests a recent outburst.
Despite the small size of the disks, the overall picture is of a remarkably
large and dynamically active region.Comment: Paper 10 of the ALMA eDisk Large Program. Accepted for publication in
Ap
Early Planet Formation in Embedded Disks (eDisk). VIII. A Small Protostellar Disk around the Extremely Low-Mass and Young Class 0 Protostar, IRAS 15398-3359
Protostellar disks are a ubiquitous part of the star formation process and
the future sites of planet formation. As part of the Early Planet Formation in
Embedded Disks (eDisk) large program, we present high-angular resolution dust
continuum (mas) and molecular line (mas) observations of
the Class 0 protostar, IRAS 15398-3359. The dust continuum is small, compact,
and centrally peaked, while more extended dust structures are found in the
outflow directions. We perform a 2D Gaussian fitting to find the deconvolved
size and radius of the dust disk to be
and , respectively. We estimate the gas+dust disk mass
assuming optically thin continuum emission to be ,
indicating a very low-mass disk. The CO isotopologues trace components of the
outflows and inner envelope, while SO traces a compact, rotating disk-like
component. Using several rotation curve fittings on the PV diagram of the SO
emission, the lower limits of the protostellar mass and gas disk radius are
and from our Modified 2 single power-law
fitting. A conservative upper limit of the protostellar mass is inferred to be
. The protostellar mass-accretion rate and the specific angular
momentum at the protostellar disk edge are found to be between
and
, respectively, with an age
estimated between yr. At this young age with no clear
substructures in the disk, planet formation would likely not yet have started.
This study highlights the importance of high-resolution observations and
systematic fitting procedures when deriving dynamical properties of deeply
embedded Class 0 protostars.Comment: 28 pages, 16 figures. Accepted for publication in ApJ as one of the
first-look papers of the eDisk ALMA Large Progra
Performance of the CMS Cathode Strip Chambers with Cosmic Rays
The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device
in the CMS endcaps. Their performance has been evaluated using data taken
during a cosmic ray run in fall 2008. Measured noise levels are low, with the
number of noisy channels well below 1%. Coordinate resolution was measured for
all types of chambers, and fall in the range 47 microns to 243 microns. The
efficiencies for local charged track triggers, for hit and for segments
reconstruction were measured, and are above 99%. The timing resolution per
layer is approximately 5 ns
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