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  1. Cowen, Lenore (Ed.)
    Abstract Motivation Biclustering has emerged as a powerful approach to identifying functional patterns in complex biological data. However, existing tools are limited by their accuracy and efficiency to recognize various kinds of complex biclusters submerged in ever large datasets. We introduce a novel fast and highly accurate algorithm RecBic to identify various forms of complex biclusters in gene expression datasets. Results We designed RecBic to identify various trend-preserving biclusters, particularly, those with narrow shapes, i.e. clusters where the number of genes is larger than the number of conditions/samples. Given a gene expression matrix, RecBic starts with a column seed, andmore »grows it into a full-sized bicluster by simply repetitively comparing real numbers. When tested on simulated datasets in which the elements of implanted trend-preserving biclusters and those of the background matrix have the same distribution, RecBic was able to identify the implanted biclusters in a nearly perfect manner, outperforming all the compared salient tools in terms of accuracy and robustness to noise and overlaps between the clusters. Moreover, RecBic also showed superiority in identifying functionally related genes in real gene expression datasets. Availability and implementation Code, sample input data and usage instructions are available at the following websites. Code: https://github.com/holyzews/RecBic/tree/master/RecBic/. Data: http://doi.org/10.5281/zenodo.3842717. Supplementary information Supplementary data are available at Bioinformatics online.« less
  2. A fundamental understanding of the flow of polymer solutions through the pore spaces of porous media is relevant and significant to enhanced oil recovery and groundwater remediation. We present in this work an experimental study of the fluid rheological effects on non-Newtonian flows in a simple laboratory model of the real-world pores—a rectangular sudden contraction–expansion microchannel. We test four different polymer solutions with varying rheological properties, including xanthan gum (XG), polyvinylpyrrolidone (PVP), polyethylene oxide (PEO), and polyacrylamide (PAA). We compare their flows against that of pure water at the Reynolds ( R e ) and Weissenburg ( W i )more »numbers that each span several orders of magnitude. We use particle streakline imaging to visualize the flow at the contraction–expansion region for a comprehensive investigation of both the sole and the combined effects of fluid shear thinning, elasticity and inertia. The observed flow regimes and vortex development in each of the tested fluids are summarized in the dimensionless W i − R e and χ L − R e parameter spaces, respectively, where χ L is the normalized vortex length. We find that fluid inertia draws symmetric vortices downstream at the expansion part of the microchannel. Fluid shear thinning causes symmetric vortices upstream at the contraction part. The effect of fluid elasticity is, however, complicated to analyze because of perhaps the strong impact of polymer chemistry such as rigidity and length. Interestingly, we find that the downstream vortices in the flow of Newtonian water, shear-thinning XG and elastic PVP solutions collapse into one curve in the χ L − R e space.« less
  3. ABSTRACT The ATOMS, standing for ALMA Three-millimeter Observations of Massive Star-forming regions, survey has observed 146 active star-forming regions with ALMA band 3, aiming to systematically investigate the spatial distribution of various dense gas tracers in a large sample of Galactic massive clumps, to study the roles of stellar feedback in star formation, and to characterize filamentary structures inside massive clumps. In this work, the observations, data analysis, and example science of the ATOMS survey are presented, using a case study for the G9.62+0.19 complex. Toward this source, some transitions, commonly assumed to trace dense gas, including CS J = 2−1,more »HCO+J = 1−0, and HCN J = 1−0, are found to show extended gas emission in low-density regions within the clump; less than 25 per cent of their emission is from dense cores. SO, CH3OH, H13CN, and HC3N show similar morphologies in their spatial distributions and reveal well the dense cores. Widespread narrow SiO emission is present (over ∼1 pc), which may be caused by slow shocks from large–scale colliding flows or H ii regions. Stellar feedback from an expanding H ii region has greatly reshaped the natal clump, significantly changed the spatial distribution of gas, and may also account for the sequential high-mass star formation in the G9.62+0.19 complex. The ATOMS survey data can be jointly analysed with other survey data, e.g. MALT90, Orion B, EMPIRE, ALMA_IMF, and ALMAGAL, to deepen our understandings of ‘dense gas’ star formation scaling relations and massive protocluster formation.« less