A sensitive APEX and ALMA CO(1-0), CO(2-1), CO(3-2), and [CI](1-0) spectral survey of 40 local (U)LIRGs

We present a high sensitivity spectral line survey of CO(1-0), CO(2-1), CO(3-2) and [CI](1-0) in 40 local (ultra) luminous infrared galaxies ((U)LIRGs), all with previous Herschel OH119 $\mu$m observations. We use single-dish observations (PI and archival) conducted with APEX, complemented with ALMA and ACA data. We study the total emission and pay special attention to the extended low-surface brightness components. We find a tight correlation between low-J CO and [CI] line luminosities suggesting their emission arise from similar regions, at least when averaged over galactic scales. We estimate a median CO-to-H$_2$ conversion factor of $1.7\pm 0.5$ M$_{\odot}$ (K km s$^{-1}$ pc$^2)^{-1}$ for ULIRGs, using [CI] as an independent tracer. We derive median galaxy-integrated CO line ratios ($r_{21}$, $r_{31}$ and $r_{32}$), as well as $r_{CICO}$, significantly higher than normal star forming galaxies, confirming the exceptional molecular gas properties of ULIRGs. We find that $r_{21}$ and $r_{32}$ are poor tracers of CO excitation in ULIRGs, while $r_{31}$ shows a positive trend with $L_{IR}$ and SFR, and a negative trend with the H$_2$ gas depletion timescales ($\tau_{dep}$). When studying CO line ratios as a function of gas kinematics, we find a positive relation between $r_{21}$ and $\sigma_v$, which can be explained by CO opacity effects. We find that the linewidths of [CI] lines are ~10% narrower than CO lines, which may suggest that the low optical depth of [CI] can challenge its detection in diffuse, low-surface brightness outflows, and so its use as a tracer of CO-dark H$_2$ gas in these components. Finally, we find that higher $L_{AGN}$ are associated to longer $\tau_{dep}$, consistent with the hypothesis that AGN feedback may reduce the efficiency of star formation.Comment: Accepted for publication by A&A. 42 pages, 22 figures. Abstract summarised for arXiv submissio

Algebraic Comparison of Partial Lists in Bioinformatics

The outcome of a functional genomics pipeline is usually a partial list of genomic features, ranked by their relevance in modelling biological phenotype in terms of a classification or regression model. Due to resampling protocols or just within a meta-analysis comparison, instead of one list it is often the case that sets of alternative feature lists (possibly of different lengths) are obtained. Here we introduce a method, based on the algebraic theory of symmetric groups, for studying the variability between lists ("list stability") in the case of lists of unequal length. We provide algorithms evaluating stability for lists embedded in the full feature set or just limited to the features occurring in the partial lists. The method is demonstrated first on synthetic data in a gene filtering task and then for finding gene profiles on a recent prostate cancer dataset

User Interaction in Semi-Automatic Segmentation of Organs at Risk: a Case Study in Radiotherapy

Accurate segmentation of organs at risk is an important step in radiotherapy planning. Manual segmentation being a tedious procedure and prone to inter- and intra-observer variability, there is a growing interest in automated segmentation methods. However, automatic methods frequently fail to provide satisfactory result, and post-processing corrections are often needed. Semi-automatic segmentation methods are designed to overcome these problems by combining physicians’ expertise and computers’ potential. This study evaluates two semi-automatic segmentation methods with different types of user interactions, named the “strokes” and the “contour”, to provide insights into the role and impact of human-computer interaction. Two physicians participated in the experiment. In total, 42 case studies were carried out on five different types of organs at risk. For each case study, both the human-computer interaction process and quality of the segmentation results were measured subjectively and objectively. Furthermore, different measures of the process and the results were correlated. A total of 36 quantifiable and ten non-quantifiable correlations were identified for each type of interaction. Among those pairs of measures, 20 of the contour method and 22 of the strokes method were strongly or moderately correlated, either directly or inversely. Based on those correlated measures, it is concluded that: (1) in the design of semi-automatic segmentation methods, user interactions need to be less cognitively challenging; (2) based on the observed workflows and preferences of physicians, there is a need for flexibility in the interface design; (3) the correlated measures provide insights that can be used in improving user interaction design

ZeChipC: Time Series Interpolation Method Based on Lebesgue Sampling

In this paper, we present an interpolation method based on Lebesgue sampling that could help to develop systems based time series more efficiently. Our methods can transmit times series, frequently used in health monitoring, with the same level of accuracy but using much fewer data. Our method is based in Lebesgue sampling, which collects information depending on the values of the signal (e.g. the signal output is sampled when it crosses specific limits). Lebesgue sampling contains additional information about the shape of the signal in-between two sampled points. Using this information would allow generating an interpolated signal closer to the original one. In our contribution, we propose a novel time-series interpolation method designed explicitly for Lebesgue sampling called ZeChipC. ZeChipC is a combination of Zero-order hold and Piecewise Cubic Hermite Interpolating Polynomial (PCHIP) interpolation. ZeChipC includes new functionality to adapt the reconstructed signal to concave/convex regions. The proposed methods have been compared with state-of-the-art interpolation methods using Lebesgue sampling and have offered higher average performance.Enterprise Irelan

A New Method for Morphometric Analysis of Tissue Distribution of Mobile Cells in Relation to Immobile Tissue Structures

The distribution of cells in stained tissue sections provides information that may be analyzed by means of morphometric computation. We developed an algorithm for automated analysis for the purpose of answering questions pertaining to the relative densities of wandering cells in the vicinity of comparatively immobile tissue structures such as vessels or tumors. As an example, we present the analysis of distribution of CD56-positive cells and of CXCR3-positive cells (relative densities of peri-vascular versus non-vascular cell populations) in relation to the endothelium of capillaries and venules of human parietal decidua tissue of first trimester pregnancy. In addition, the distibution of CD56-positive cells (mostly uterine NK cells) in relation to spiral arteries is analyzed. The image analysis is based on microphotographs of two-color immunohistological stainings. Discrete distances (10–50 µm) from the fixed structures were chosen for the purpose of definining the extent of neighborhood areas. For the sake of better comparison of cell distributions at different overall cell densities a model of random distribution of “cells” in relation to neighborhood areas and rest decidua of a specific sample was built. In the chosen instances, we found increased perivascular density of CD56-positive cells and of CXCR3-positive cells. In contrast, no accumulation of CD56-positive cells was found in the neighborhood of spiral arteries

MASCOT: molecular gas depletion times and metallicity gradients – evidence for feedback in quenching active galaxies

We present results from the first public data release of the MaNGA-ARO Survey of CO Targets (MASCOT), focusing our study on galaxies whose star formation rates and stellar masses place them below the ridge of the star-forming main sequence. In optically selected type 2 AGN/low-ionization nuclear emission regions (LINERs)/Composites, we find an empirical relation between gas-phase metallicity gradients ∇Z and global molecular gas depletion times tdep=MH2/SFR with ‘more quenched’ systems showing flatter/positive gradients. Our results are based on the O3N2 metallicity diagnostic (applied to star-forming regions within a given galaxy), which was recently suggested to also be robust against emission by diffuse ionized gas (DIG) and LINERs. We conduct a systematic investigation into possible drivers of the observed ∇Z − tdep relation (ouflows, gas accretion, in situ star formation, mergers, and morphology). We find a strong relation between ∇Z or tdep and centralized outflow strength traced by the [O III] velocity broadening. We also find signatures of suppressed star formation in the outskirts in AGN-like galaxies with long depletion times and an enhancement of metals in the outer regions. We find no evidence of inflows impacting the metallicity gradients, and none of our results are found to be significantly affected by merger activity or morphology. We thus conclude that the observed ∇Z–tdep relation may stem from a combination of metal redistribution via weak feedback, and a connection to in situ star formation via a resolved mass-metallicity–SFR relation. © 2022 The Author(s) Published by Oxford University Press on behalf of Royal Astronomical Society.DW and CB are supported through the Emmy Noether Programme of the German Research Foundation. MA acknowledges support from FONDECYT grant 1211951, CONICYT + PCI + INSTITUTO MAX PLANCK DE ASTRONOMIA MPG190030, CONICYT+PCI + REDES 190194, and ANID BASAL project FB210003. WB acknowledges support from the ERC Advanced Grant 695671, ‘QUENCH’ and from the Science and Technology Facilities Council (STFC). Funding for the Sloan Digital Sky Survey IV has been provided by the Alfred P. Sloan Foundation, the U.S. Department of Energy Office of Science, and the Participating Institutions. SDSS-IV acknowledges support and resources from the Center for High Performance Computing at the University of Utah.With funding from the Spanish government through the "Severo Ochoa Centre of Excellence" accreditation (CEX2021-001131-S).Peer reviewe