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 ($\sim40\,$mas) and molecular line ($\sim150\,$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 $2\sigma$ radius of the dust disk to be $4.5\times2.8\,\mathrm{au}$ and $3.8\,\mathrm{au}$, respectively. We estimate the gas+dust disk mass assuming optically thin continuum emission to be $0.6-1.8\,M_\mathrm{jup}$, 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 $0.022\,M_\odot$ and $31.2\,\mathrm{au}$ from our Modified 2 single power-law fitting. A conservative upper limit of the protostellar mass is inferred to be $0.1\,M_\odot$. The protostellar mass-accretion rate and the specific angular momentum at the protostellar disk edge are found to be between $1.3-6.1\times10^{-6}\,M_\odot\,\mathrm{yr^{-1}}$ and $1.2-3.8\times10^{-4}\,\mathrm{km\,s^{-1}\,pc}$, respectively, with an age estimated between $0.4-7.5\times10^{4}\,$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