bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenylethanoid glycosides extract from Cistanche deserticola ameliorates atherosclerosis in apolipoprotein E-deficient mice and regulates intestinal PPARγ-LXRα-ABCA1 pathway
Authors: Jia Xiubin , Liu Boyan , Xue Junli , Liu Yunchao , Zhang Jingjun , Qin Shucun , Zhang Ying 
Published: February 2023

Abstract

Objectives
This study was aimed to evaluate the protective effects of phenylethanoid glycosides extract from Cistanche deserticola against atherosclerosis and its molecular mechanism.

Methods
Total phenylethanoid glycosides were extracted and purified from C. deserticola, and the C. deserticola extract (CDE) was used to treat a mice model of atherosclerosis.

Key findings
CDE containing 81.00% total phenylethanoid glycosides, with the contents of echinacoside and acteoside being 31.36% and 7.23%, respectively. A 13-week of CDE supplementation (1000 mg/kg body weight/day) significantly reduced atherosclerotic lesions in the aortic sinus and entire aorta in ApoE−/− mice fed with a high-fat diet. In addition, varying doses of CDE (250, 500 and 1000 mg/kg body weight/day) lowered plasma total cholesterol, triglyceride and non-high-density lipoprotein cholesterol levels. Transcriptomic analysis of the small intestine revealed the changes enriched in cholesterol metabolic pathway and the activation of Abca1 gene. Further validation using real-time quantitative PCR and western blot confirmed that CDE significantly increased the mRNA levels and protein expressions of ABCA1, LXRα and PPARγ.

Conclusions
Our results demonstrate the beneficial effects of C. deserticola on atherosclerotic plaques and lipid homeostasis, and it is, at least partially, by activating PPARγ-LXRα-ABCA1 pathway in small intestine.
Disentangling positive and negative partisanship in social media interactions using a coevolving latent space network with attractors model
Authors: Zhu Xiaojing , Caliskan Cantay , Christenson Dino P , Spiliopoulos Konstantinos , Walker Dylan , Kolaczyk Eric D 
Published: February 2023

Abstract
We develop a broadly applicable class of coevolving latent space network with attractors (CLSNA) models, where nodes represent individual social actors assumed to lie in an unknown latent space, edges represent the presence of a specified interaction between actors, and attractors are added in the latent level to capture the notion of attractive and repulsive forces. We apply the CLSNA models to understand the dynamics of partisan polarization in US politics on social media, where we expect Republicans and Democrats to increasingly interact with their own party and disengage with the opposing party. Using longitudinal social networks from the social media platforms Twitter and Reddit, we quantify the relative contributions of positive (attractive) and negative (repulsive) forces among political elites and the public, respectively.
Growth–defence trade-off in rice: fast-growing and acquisitive genotypes have lower expression of genes involved in immunity
Authors: de Tombeur Felix , Pélissier Rémi , Shihan Ammar , Rahajaharilaza Koloina , Fort Florian , Mahaut Lucie , Lemoine Taïna , Thorne Sarah J , Hartley Sue E , Luquet Delphine , Fabre Denis , Lambers Hans , Morel Jean-Benoît , Ballini Elsa , Violle Cyrille 
Published: February 2023

Abstract
Plant ecologists and molecular biologists have long considered the hypothesis of a trade-off between plant growth and defence separately. In particular, how genes thought to control the growth–defence trade-off at the molecular level relate to trait-based frameworks in functional ecology, such as the slow–fast plant economics spectrum, is unknown. We grew 49 phenotypically diverse rice genotypes in pots under optimal conditions and measured growth-related functional traits and the constitutive expression of 11 genes involved in plant defence. We also quantified the concentration of silicon (Si) in leaves to estimate silica-based defences. Rice genotypes were aligned along a slow–fast continuum, with slow-growing, late-flowering genotypes versus fast-growing, early-flowering genotypes. Leaf dry matter content and leaf Si concentrations were not aligned with this axis and negatively correlated with each other. Live-fast genotypes exhibited greater expression of OsNPR1, a regulator of the salicylic acid pathway that promotes plant defence while suppressing plant growth. These genotypes also exhibited greater expression of SPL7 and GH3.2, which are also involved in both stress resistance and growth. Our results do not support the hypothesis of a growth–defence trade-off when leaf Si and leaf dry matter content are considered, but they do when hormonal pathway genes are considered. We demonstrate the benefits of combining ecological and molecular approaches to elucidate the growth–defence trade-off, opening new avenues for plant breeding and crop science.
Ex vivowound model on porcine skin for the evaluation of the antibiofilm activity of polyhexamethylene biguanide and ciprofloxacin
Authors: Guedes Glaucia Morgana de Melo , Pinheiro Rodrigo Machado , Freitas Alyne Soares , Pereira Vinicius Carvalho , Gomes Francisco Ivanilsom Firmiano , Cordeiro Rossana de Aguiar , Sidrim José Júlio Costa , Rocha Marcos Fábio Gadelha , Castelo-Branco Debora de Souza Collares Maia 
Published: February 2023

AbstractThis study aimed to standardize the use of an ex vivo wound model for the evaluation of compounds with antibiofilm activity. The in vitro susceptibility of Staphylococcus aureus ATCC 29213 and Pseudomonas aeruginosa ATCC 27853 to ciprofloxacin and polyhexamethylene biguanide (PHMB) was evaluated in planktonic and biofilm growth. The effects of ciprofloxacin and PHMB on biofilms grown on porcine skin explants were evaluated by colony-forming unit (CFU) counting and confocal microscopy. Minimum inhibitory concentrations (MICs) against S. aureus and P. aeruginosa were, respectively, 0.5 and 0.25 µg mL−1 for ciprofloxacin, and 0.78 and 6.25 µg mL−1 for PHMB. Minimum biofilm eradication concentrations (MBECs) against S. aureus and P. aeruginosa were, respectively, 2 and 8 µg mL−1 for ciprofloxacin, and 12.5 and &gt;25 µg mL−1 for PHMB. Ciprofloxacin reduced (P &lt; 0.05) log CFU counts of the biofilms grown ex vivo by 3 and 0.96 for S. aureus and P. aeruginosa, respectively, at MBEC, and by 0.58 and 8.12 against S. aureus and P. aeruginosa, respectively, at 2xMBEC. PHMB (100 µg/mL) reduced (P &lt; 0.05) log CFU counts by 0.52 for S. aureus and 0.68 log for P. aeruginosa, leading to an overall decrease (P &lt; 0.05) in biofilm biomass. The proposed methodology to evaluate the susceptibility of biofilms grown ex vivo led to reproducible and reliable results.
Splitting the lentils: Clues to galaxy/black hole coevolution from the discovery of offset relations for non-dusty versus dusty (wet-merger-built) lenticular galaxies in theMbh–M*,spheroid andMbh–M*,galaxy diagrams
Authors: Graham Alister W 
Published: February 2023

ABSTRACTThis work advances the (galaxy morphology)-dependent (black hole mass, Mbh)–(spheroid/galaxy stellar mass, M*) scaling relations by introducing ‘dust bins’ for lenticular (S0) galaxies. Doing so has led to the discovery of Mbh–M*,sph and Mbh–M*,gal relations for dusty S0 galaxies – built by major wet mergers and comprising half the S0 sample – offset from the distribution of dust-poor S0 galaxies. The situation is reminiscent of how major dry mergers of massive S0 galaxies have created an offset population of ellicular and elliptical galaxies. For a given Mbh, the dust-rich S0 galaxies have 3–4 times higher M*,sph than the dust-poor S0 galaxies, and the steep distributions of both populations in the Mbh–M*,sph diagram bracket the $M_{\rm bh} \propto M_{\rm *,sph}^{2.27+/-0.48}$ relation defined by the spiral galaxies, themselves renovated through minor mergers. The new relations offer refined means to estimate Mbh in other galaxies and should aid with: (i) constructing (galaxy morphology)-dependent black hole mass functions; (ii) estimating the masses of black holes associated with tidal disruption events; (iii) better quantifying evolution in the scaling relations via improved comparisons with high-z data by alleviating the pickle of apples versus oranges; (iv) mergers and long-wavelength gravitational wave science; (v) simulations of galaxy/black hole coevolution and semi-analytic works involving galaxy speciation; plus (vi) facilitating improved extrapolations into the intermediate-mass black hole landscape. The role of the galaxy’s environment is also discussed, and many potential projects that can further explore the morphological divisions are mentioned.
Limits on compression of cosmic rays in supernova remnants
Authors: Sushch Iurii , Brose Robert 
Published: February 2023

ABSTRACTThe spectral shape of the gamma-ray emission observed for dynamically old supernova remnants that interact with molecular clouds triggered an exciting scenario of adiabatic compression and farther re-acceleration of Galactic cosmic rays (GCRs) in radiative shells of the remnants, which was extensively discussed and applied to various sources over recent years. Indeed, the observed gamma-ray spectrum from a number of remnants strongly resembles the expected spectrum of the gamma-ray emission from the compressed population of GCRs. In the following we discuss the feasibility of this scenario and show that it is very unlikely that compressed GCRs could produce sufficient amount of gamma-rays and that the observed spectral shape is putting strong limits on the allowed compression factors. Further, absence of curvature in featureless power-law spectra of evolved supernova remnants at radio wavelengths is strongly disfavouring the compression scenario for electrons and hence for hadrons. Our calculations show that the contribution of compressed electrons to the observed radio flux could reach at most $\sim 10\,$ per cent.
Coherent and incoherent structures in fuzzy dark matter haloes
Authors: Liu I-Kang , Proukakis Nick P , Rigopoulos Gerasimos 
Published: February 2023

ABSTRACTWe show that fuzzy dark matter haloes exhibit spatial differentiation in the coherence of the field configuration, ranging from completely coherent in the central solitonic core to incoherent outside it, with a significant drop of the dimensionless phase-space density with increasing radius. The core is a pure condensate, overlapping perfectly with the Penrose-Onsager mode corresponding to the largest eigenvalue of the one-particle density matrix. The virialized outer halo exhibits no clear coherence as a whole upon radial and temporal averaging but can be described as a collection of local, short-lived quasi-condensate lumps, exhibiting suppressed fluctuations, which can be identified with the structures commonly referred to as granules. These localized regions are separated by vortices that form a dynamical web, inhibiting phase coherence across the entire halo. We further examine the core oscillations, finding that they are accurately described by two time-dependent parameters characterizing the size of the core, rc(t), and a crossover region, rt(t). For the haloes in our merger simulations, this feature is reflected in the (anti-)correlated oscillation of the peak value of the density power-spectrum. The halo’s turbulent vortex tangle appears to reach a quasi-equilibrium state over probed time-scales, with the incompressible component of the kinetic energy exhibiting a characteristic k−3 tail in its spectrum, indicative of a ρ ∼ r2 density profile around the quantum vortex cores. Comparison of the peak wavenumbers in the corresponding power-spectra shows the inter-vortex spacing and the granule length scale in the outer halo to be very similar and slightly above the core size.
The AGNIFS survey: spatially resolved observations of hot molecular and ionized outflows in nearby active galaxies
Authors: Riffel R A , Storchi-Bergmann T , Riffel R , Bianchin M , Zakamska N L , Ruschel-Dutra D , Bentz M C , Burtscher L , Crenshaw D M , Dahmer-Hahn L G , Dametto N Z , Davies R I , Diniz M R , Fischer T C , Harrison C M , Mainieri V , Revalski M , Rodriguez-Ardila A , Rosario D J , Schönell A J 
Published: February 2023

ABSTRACTWe present the hot molecular and warm ionized gas kinematics for 33 nearby (0.001 ≲ z ≲ 0.056) X-ray selected active galaxies using the H$_2\, 2.1218\, \mu$m and Br γ emission lines observed in the K band with the Gemini near-infrared integral field spectrograph. The observations cover the inner 0.04–2 kpc of each active galactic nucleus at spatial resolutions of 4–250 pc with a velocity resolution of σinst ≈ 20 ${\rm km\, s^{-1}}$. We find that 31 objects (94 per cent) present a kinematically disturbed region (KDR) seen in ionized gas, while such regions are observed in hot molecular gas for 25 galaxies (76 per cent). We interpret the KDR as being due to outflows with masses of 102–107 and 100–104 M⊙ for the ionized and hot molecular gas, respectively. The ranges of mass-outflow rates ($\dot{M}_{\rm out}$) and kinetic power ($\dot{E}_{\rm K}$) of the outflows are 10−3–101 M⊙ yr−1 and ∼1037–1043 erg s−1 for the ionized gas outflows, and 10−5–10−2 M⊙ yr−1 and 1035–1039 erg s−1 for the hot molecular gas outflows. The median coupling efficiency in our sample is $\dot{E}_{\mathrm{K}}/L_{\rm bol}\approx 1.8\times 10^{-3}$ and the estimated momentum fluxes of the outflows suggest they are produced by radiation-pressure in low-density environment, with possible contribution from shocks.
The study of thermonuclear X-ray bursts in accreting millisecond pulsar MAXI J1816−195 with NuSTAR and NICER
Authors: Mandal Manoj , Pal Sabyasachi , Chauhan Jaiverdhan , Lohfink Anne , Bharali Priya 
Published: February 2023

ABSTRACT
The millisecond pulsar MAXI J1816−195 was recently discovered in an outburst by the Monitor of All-sky X-ray Image (MAXI) in 2022 May. We study different properties of the pulsar using data from the Nuclear Spectroscopic Telescope Array (NuSTAR) and the Neutron Star Interior Composition Explorer (NICER) observations. The unstable burning of accreted material on the surface of neutron stars induces thermonuclear (Type-I) bursts. Several such thermonuclear bursts have been detected by MAXI J1816−195 during its outburst. We investigate the evolution of the burst profiles with flux and energy using NuSTAR and NICER observations. During the NuSTAR observation, a total of four bursts were detected from the source. The duration of each burst is around ∼30 s and the ratio of peak to persistent count rate is ∼26 as seen from the NuSTAR data. The burst profiles are modelled using a sharp linear rise and exponential decay function to determine the burst timing parameters. The burst profiles show a relatively long tail at lower energies. The broad-band time-resolved spectra during the burst periods are successfully modelled with a combination of an absorbed blackbody along with a non-thermal component to account for the persistent emission. From our modelling results, we are able to estimate the maximum apparent emitting area of the blackbody of the neutron star to be ∼12.5 km during the peak of the outburst and the maximum distance to the object to be 8.7 kpc. Our findings for the mass accretion rate and the α factor indicate the stable burning of hydrogen via a hot CNO cycle during the bursts.
PINION: physics-informed neural network for accelerating radiative transfer simulations for cosmic reionization
Authors: Korber Damien , Bianco Michele , Tolley Emma , Kneib Jean-Paul 
Published: February 2023

ABSTRACTWith the advent of the Square Kilometre Array Observatory (SKAO), scientists will be able to directly observe the Epoch of Reionization by mapping the distribution of neutral hydrogen at different redshifts. While physically motivated results can be simulated with radiative transfer codes, these simulations are computationally expensive and cannot readily produce the required scale and resolution simultaneously. Here we introduce the Physics-Informed neural Network for reIONization (PINION), which can accurately and swiftly predict the complete 4D hydrogen fraction evolution from the smoothed gas and mass density fields from pre-computed N-body simulation. We trained PINION on the C2-Ray simulation outputs and a physics constraint on the reionization chemistry equation is enforced. With only five redshift snapshots, PINION can accurately predict the entire reionization history between z = 6 and 12. We evaluate the accuracy of our predictions by analyzing the dimensionless power spectra and morphology statistics estimations against C2-Ray results. We show that while the network’s predictions are in very good agreement with simulation to redshift z &gt; 7, the network’s accuracy suffers for z &lt; 7. We motivate how PINION performance could be improved using additional inputs and potentially generalized to large-scale simulations.
Tests of photometry: the case of the NGC 3370 ACS field
Authors: Jang In Sung 
Published: February 2023

ABSTRACT
A critical analysis and comparison of different methods for obtaining point spread function (PSF) photometry are carried out. Deep ACS observations of NGC 3370 were reduced using four distinct approaches. These reductions explore a number of methodological differences: software packages (DAOPHOT and DOLPHOT), input images (individual and stacked frames), PSF models (synthetic and empirical), and aperture correction methods (automatic and manual). A comparison of the photometry leads to the following results: (1) Photometric incompleteness between individual reductions shows only a minimal difference (&lt;10 per cent). (2) Statistical errors are 20 per cent to 30 per cent smaller for DAOPHOT runs on stacked frames than DOLPHOT runs on individual frames. (3) Statistical errors assigned directly by the photometry codes are 25 per cent to 50 per cent smaller than the errors measured from artificial star tests. (4) Systematic errors are magnitude dependent and become larger at the faint end, at the level of σs ∼ 0.1 mag. (5) The automatic aperture correction routines in DOLPHOT result in a significant systematic error (σs ∼ 0.05 mag). (6) Individual reductions agree well at the 0.02-mag level when the systematic errors are properly corrected through artificial star tests. The reasonable agreement between the reductions leads to important implications that (i) the reduction-dependent errors can be reduced to a 1 per cent level in the luminosity distance scale, and (ii) the stacked frame photometry can be a good means to study non-variable stars in external galaxies.
Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging
Authors: Sabaté Thomas , Lelandais Benoît , Bertrand Edouard , Zimmer Christophe 
Published: February 2023

AbstractGenome-wide chromosome conformation capture (Hi-C) has revealed the organization of chromatin into topologically associating domains (TADs) and loops, which are thought to help regulate genome functions. TADs and loops are understood as the result of DNA extrusion mediated by the cohesin complex. However, despite recent efforts, direct visualization and quantification of this process in single cells remains an open challenge. Here, we use polymer simulations and dedicated analysis methods to explore if, and under which conditions, DNA loop extrusion can be detected and quantitatively characterized by imaging pairs of fluorescently labeled loci located near loop or TAD anchors in fixed or living cells. We find that under realistic conditions, extrusion can be detected and the frequency of loop formation can be quantified from fixed cell images alone, while the lifetime of loops and the speed of extrusion can be estimated from dynamic live-cell data. Our delineation of appropriate imaging conditions and the proposed analytical methods lay the groundwork for a systematic quantitative characterization of loop extrusion in fixed or living cells.
Incoherent merger network for robust ratiometric gene expression response
Authors: Kwon Ukjin , Huang Hsin-Ho , Chávez Jorge L , Beabout Kathryn , Harbaugh Svetlana , Del Vecchio Domitilla 
Published: February 2023

AbstractA ratiometric response gives an output that is proportional to the ratio between the magnitudes of two inputs. Ratio computation has been observed in nature and is also needed in the development of smart probiotics and organoids. Here, we achieve ratiometric gene expression response in bacteria Escherichia coli with the incoherent merger network. In this network, one input molecule activates expression of the output protein while the other molecule activates an intermediate protein that enhances the output’s degradation. When degradation rate is first order and faster than dilution, the output responds linearly to the ratio between the input molecules’ levels over a wide range with R2 close to 1. Response sensitivity can be quantitatively tuned by varying the output’s translation rate. Furthermore, ratiometric responses are robust to global perturbations in cellular components that influence gene expression because such perturbations affect the output through an incoherent feedforward loop. This work demonstrates a new molecular signal processing mechanism for multiplexed sense-and-respond circuits that are robust to intra-cellular context.
Actinobacillus pleuropneumoniae encodes multiple phase-variable DNA methyltransferases that control distinct phasevarions
Authors: Nahar Nusrat , Tram Greg , Jen Freda E-C , Phillips Zachary N , Weinert Lucy A , Bossé Janine T , Jabbari Jafar S , Gouil Quentin , Du Mei R M , Ritchie Matthew E , Bowden Rory , Langford Paul R , Tucker Alexander W , Jennings Michael P , Turni Conny , Blackall Patrick J , Atack John M 
Published: February 2023

Abstract
Actinobacillus pleuropneumoniae is the cause of porcine pleuropneumonia, a severe respiratory tract infection that is responsible for major economic losses to the swine industry. Many host-adapted bacterial pathogens encode systems known as phasevarions (phase-variable regulons). Phasevarions result from variable expression of cytoplasmic DNA methyltransferases. Variable expression results in genome-wide methylation differences within a bacterial population, leading to altered expression of multiple genes via epigenetic mechanisms. Our examination of a diverse population of A. pleuropneumoniae strains determined that Type I and Type III DNA methyltransferases with the hallmarks of phase variation were present in this species. We demonstrate that phase variation is occurring in these methyltransferases, and show associations between particular Type III methyltransferase alleles and serovar. Using Pacific BioSciences Single-Molecule, Real-Time (SMRT) sequencing and Oxford Nanopore sequencing, we demonstrate the presence of the first ever characterised phase-variable, cytosine-specific Type III DNA methyltransferase. Phase variation of distinct Type III DNA methyltransferase in A. pleuropneumoniae results in the regulation of distinct phasevarions, and in multiple phenotypic differences relevant to pathobiology. Our characterisation of these newly described phasevarions in A. pleuropneumoniae will aid in the selection of stably expressed antigens, and direct and inform development of a rationally designed subunit vaccine against this major veterinary pathogen.