bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of the matter-radiation equality scale using the extended baryon oscillation spectroscopic survey quasar sample
Authors: Bahr-Kalus Benedict , Parkinson David , Mueller Eva-Maria 
Published: June 2023

ABSTRACTThe position of the peak of the matter power spectrum, the so-called turnover scale, is set by the horizon size at the epoch of matter-radiation equality. It can easily be predicted in terms of the physics of the universe in the relativistic era, and so can be used as a standard ruler, independent of other features present in the matter power spectrum, such as baryon acoustic oscillations (BAOs). We use the distribution of quasars measured by the extended Baryon Oscillation Spectroscopic Survey (eBOSS) to determine the turnover scale in a model-independent fashion statistically. We avoid modelling the BAO by down-weighting affected scales in the covariance matrix using the mode deprojection technique. We measure the wavenumber of the peak to be $k_\mathrm{TO} = \left(17.6^{+1.9}_{-1.8} \right) \times 10^{-3}h/\mathrm{Mpc}$, corresponding to a dilation scale of $D_\mathrm{V}(z_\mathrm{eff} = 1.48) = \left(31.1^{+4.1}_{-3.4}\right)r_\mathrm{H}$. This is not competitive with current BAO distance measures in terms of determining the expansion history but does provide a useful cross-check. We combine this measurement with low-redshift distance measurements from type-Ia supernova data from Pantheon and BAO data from eBOSS to make a sound-horizon free estimate of the Hubble–Lemaître parameter and find it to be $H_0=64.8^{+8.4}_{-7.8} \ \mathrm{km/s/Mpc}$ with Pantheon, and $H_0=63.3^{+8.2}_{-6.9} \ \mathrm{km/s/Mpc}$ with eBOSS BAO. We make predictions for the measurement of the turnover scale by the Dark Energy Spectroscopic Instrument (DESI) survey, the Maunakea Spectroscopic Explorer (MSE), and MegaMapper, which will make more precise and accurate distance determinations.
Cooling-driven coagulation
Authors: Gronke Max , Oh S Peng 
Published: June 2023

ABSTRACT
Astrophysical gases such as the interstellar-, circumgalactic-, or intracluster-medium are commonly multiphase, which poses the question of the structure of these systems. While there are many known processes leading to fragmentation of cold gas embedded in a (turbulent) hot medium, in this work, we focus on the reverse process: coagulation. This is often seen in wind-tunnel and shearing layer simulations, where cold gas fragments spontaneously coalesce. Using 2D and 3D hydrodynamical simulations, we find that sufficiently large (≫cstcool), perturbed cold gas clouds develop pulsations which ensure cold gas mass growth over an extended period of time (≫r/cs). This mass growth efficiently accelerates hot gas which in turn can entrain cold droplets, leading to coagulation. The attractive inverse square force between cold gas droplets has interesting parallels with gravity; the ‘monopole’ is surface area rather than mass. We develop a simple analytic model which reproduces our numerical findings.
A high-resolution extinction mapping technique for face-on disc galaxies
Authors: Faustino Vieira Helena , Duarte-Cabral Ana , Davis Timothy A , Peretto Nicolas , Smith Matthew W L , Querejeta Miguel , Colombo Dario , Anderson Michael 
Published: June 2023

ABSTRACT
We present a new dust extinction technique with which we are able to retrieve parsec-scale gas surface density maps for entire nearby galaxies. The method measures the dust attenuation in optical bands on a pixel-by-pixel basis against a smoothed, reconstructed stellar distribution. The contribution of foreground light along the line-of-sight is calibrated using dust emission observations, assuming that the dust sits in a layer close to the mid-plane of the face-on galaxy. Here, we apply this technique to M51 (NGC 5194) as a proof-of-concept, obtaining a resolution of 0.14 arcsec (5 pc). Our dust (and gas) surface density map is consistent with independent dust- and CO-based studies at lower resolution. We find that discrepancies between our estimates of surface density and other studies stem primarily from the choice of dust model (i.e. different dust absorption coefficients). When assuming the same dust opacity law, our technique produces surface densities that are consistent with independent studies. This dust extinction technique provides us with gas surface density maps at an unprecedented resolution for full disc coverage studies of nearby galaxies. The resulting well-resolved spatial information opens the possibility for more in-depth examination of the influence of large-scale dynamics (and also stellar feedback mechanisms) on the interstellar medium at parsec-scales, and consequently star formation in nearby galaxies.
Observability of low-luminosity AGNs in the early Universe with JWST
Authors: Jeon Junehyoung , Liu Boyuan , Bromm Volker , Finkelstein Steven L 
Published: June 2023

ABSTRACT
Active galactic nuclei (AGNs) in the early Universe are thought to be prominent sources of energy and ionizing photons that affected the growth of their host galaxy and their environment. However, it is still unclear how the supermassive black holes (SMBHs) that fuel these AGNs grew to the observed high masses already at high redshifts. Observations of high-redshift SMBH progenitors or lower luminosity AGNs will thus help characterize the evolution of SMBHs and their impact on the surroundings. With the launch of the JWST, fainter objects at high redshifts can now be detected, including lower luminosity AGNs. We assess the observability of such low-luminosity AGNs, using the cosmological simulation code gizmo to provide a realistic environment for black hole growth in the early Universe. Soon after the first stars are born in the simulation run, we insert stellar-remnant black hole seeds of various initial masses, between 300 and 104 M⊙, at the centre of a dark matter halo and follow their growth until z ∼ 6. Such stellar black hole seeds placed in a typical high-z environment do not significantly accrete and grow to reach masses that can be observed with the JWST under conditions of standard Bondi–Hoyle accretion, as energy input from stellar feedback and chaotic dynamics prevent efficient gas accretion on to the black holes. To be observed with the JWST, rarer but still physically feasible growth regimes, involving Eddington or super-Eddington accretion, would be required. Alternatively, AGN observability may be boosted under even rarer conditions of extreme gravitational lensing.
Probing dark fluids and modified gravity with gravitational lensing
Authors: Perivolaropoulos Leandros , Antoniou Ioannis , Papadopoulos Demetrios 
Published: June 2023

ABSTRACT
We generalize the result of Rindler-Ishak for the lensing deflection angle in a Schwarzschild–deSitter (SdS) space–time, to the case of a general spherically symmetric fluid beyond the cosmological constant. We thus derive an analytic expression to first post-Newtonian order for the lensing deflection angle in a general static spherically symmetric metric of the form $\mathrm{ d}s^2 = f(r)\mathrm{ d}t^{2} -\frac{\mathrm{ d}r^{2}}{f(r)}-r^{2}(\mathrm{ d}\theta ^2 +\sin ^2 \theta \mathrm{ d}\phi ^2)$ with $f(r) = 1 - \frac{2m}{r}-\sum _{i} b_\mathrm{ i}\,\, r_0^{-q_i}\,\, \left(\frac{r_0}{r}\right)^{q_i}$, where r0 is the lensing impact parameter, $b_i\ll r_0^{q_i}$, m is the mass of the lens, and qi are real arbitrary constants related to the properties of the fluid that surrounds the lens or to modified gravity. This is a generalization of the well known Kiselev black hole metric. The approximate analytic expression of the deflection angle is verified by an exact numerical derivation and in special cases it reduces to results of previous studies. The density and pressure of the spherically symmetric fluid that induces this metric is derived in terms of the constants bi. The Kiselev case of a Schwarzschild metric perturbed by a general spherically symmetric dark fluid (e.g. vacuum energy) is studied in some detail and consistency with the special case of Rindler-Ishak result is found for the case of a cosmological constant background. Observational data of the Einstein radii from distant clusters of galaxies lead to observational constraints on the constants bi and through them on the density and pressure of dark fluids, field theories, or modified gravity theories that could induce this metric.
Ask the machine: systematic detection of wind-type outflows in low-mass X-ray binaries
Authors: Mata Sánchez D , Muñoz-Darias T , Casares J , Huertas-Company M , Panizo-Espinar G 
Published: June 2023

ABSTRACT
The systematic discovery of outflows in the optical spectra of low-mass X-ray binaries opened a new avenue for the study of the outburst evolution in these extreme systems. However, the efficient detection of such features in a continuously growing data base requires the development of new analysis techniques with a particular focus on scalability, adaptability, and automatization. In this pilot study, we explore the use of machine learning algorithms to perform the identification of outflows in spectral line profiles observed in the optical range. We train and test the classifier on a simulated data base constructed through a combination of disc emission line profiles and outflow signatures, emulating typical observations of low-mass X-ray binaries. The final, trained classifier is applied to two sets of spectra taken during two bright outbursts that were particularly well covered, those of V404 Cyg (2015) and MAXI J1820+070 (2018). The resulting classification gained by this novel approach is overall consistent with that obtained through traditional techniques, while simultaneously providing a number of key advantages over the latter, including the access to low-velocity outflows. This study sets the foundations for future studies on large samples of spectra from low-mass X-ray binaries and other compact binaries.
Morpho-kinematic and photoionization models of the multipolar structures in planetary nebula NGC 6572
Authors: Bandyopadhyay Rahul , Das Ramkrishna , Parthasarathy Mudumba , Kar Subhajit 
Published: June 2023

ABSTRACT
We have studied planetary nebula (PN) NGC 6572 through 3D morpho-kinematic and photoionization modelling. The 3D morphology is reconstructed from the Hubble Space Telescope images in different narrow-band filters and position–velocity spectra. The PN has a multipolar morphology consisting of highly collimated outflows. The nebular image shows signatures of multiple lobes within a spiral-ring-like structure. The multipolar structure is modelled with two bipolar shells (axes ratios ∼5.5:1 and ∼3:1), having closed and open lobes, respectively. A toroidal structure (radius:height ∼ 1:3) surrounds the shells at the waist. The toroidal axis aligns with the major axes of the bipolar shells. Our study reveals the nebula to have a history of collimated polar outflow perpendicular to a higher density equatorial wind with the outflow seemingly having episodes of changing direction of ejection. We construct a photoionization model of NGC 6572 using the optical spectra obtained at the 2 m Himalayan Chandra Telescope. For the photoionization model, we configure the input shell geometry in the form of a highly bipolar nebular shell with reference to the 3D morphology. Our photoionization model satisfactorily reproduces the observables. We estimate nebular elemental abundances, and important characteristic parameters of the central star (e.g. effective temperature, luminosity, gravity, mass, etc.) and the nebula (e.g. hydrogen density profiles, radii, etc.). We compare the resolved H β, [O iii], and [N ii] profiles obtained using the 4.2 m William Herschel Telescope with that from the photoionization model and find a good characteristic match.
Recent Evolution of a Maternally Acting Sex-Determining Supergene in a Fly with Single-Sex Broods
Authors: Baird Robert B , Urban John M , Mongue Andrew J , Jaron Kamil S , Hodson Christina N , Grewoldt Malte , Martin Simon H , Ross Laura 
Published: June 2023

Abstract
Sex determination is a key developmental process, yet it is remarkably variable across the tree of life. The dipteran family Sciaridae exhibits one of the most unusual sex determination systems in which mothers control offspring sex through selective elimination of paternal X chromosomes. Whereas in some members of the family females produce mixed-sex broods, others such as the dark-winged fungus gnat Bradysia coprophila are monogenic, with females producing single-sex broods. Female-producing females were previously found to be heterozygous for a large X-linked paracentric inversion (X′), which is maternally inherited and absent from male-producing females. Here, we assembled and characterized the X′ sequence. As close sequence homology between the X and X′ made identification of the inversion challenging, we developed a k-mer–based approach to bin genomic reads before assembly. We confirmed that the inversion spans most of the X′ chromosome (∼55 Mb) and encodes ∼3,500 genes. Analysis of the divergence between the inversion and the homologous region of the X revealed that it originated very recently (&lt;0.5 Ma). Surprisingly, we found that the X′ is more complex than previously thought and is likely to have undergone multiple rearrangements that have produced regions of varying ages, resembling a supergene composed of evolutionary strata. We found functional degradation of ∼7.3% of genes within the region of recombination suppression, but no evidence of accumulation of repetitive elements. Our findings provide an indication that sex-linked inversions are driving turnover of the strange sex determination system in this family of flies.
Long-Term Impact of Daily E-cigarette Exposure on the Lungs of Asthmatic Mice
Authors: Song Min-Ae , Wold Loren E , Aslaner David M , Archer Kellie J , Patel Devki , Jeon Hyeongseon , Chung Dongjun , Shields Peter G , Christman John W , Chung Sangwoon 
Published: June 2023

AbstractIntroductionAlthough the greater popularity of electronic cigarettes (EC) among asthmatics is alarming, there is limited knowledge of the long-term consequences of EC exposure in asthmatics.Aims and MethodsMild asthmatic C57/BL6J adult male and female mice were established by intranasal insufflation with three combined allergens. The asthmatic and age and sex-matched’ naïve mice were exposed to air, nicotine-free (propylene glycol [PG]/vegetable glycerin [VG]-only), or PG/VG+Nicotine, 4 hours daily for 3 months. The effects of EC exposure were accessed by measuring cytokines in bronchoalveolar lavage, periodic acid-schiff (PAS) staining, mitochondrial DNA copy numbers (mtCN), and the transcriptome in the lung. Significance was false discovery rate &lt;0.2 for transcriptome and 0.05 for the others.ResultsIn asthmatic mice, PG/VG+Nicotine increased PAS-positive cells and IL-13 compared to mice exposed to air and PG/VG-only. In naïve mice exposed to PG/VG+Nicotine and PG/VG-only, higher INF-γ was observed compared to mice exposed only to air. PG/VG-only and PG/VG+Nicotine had significantly higher mtCN compared to air exposure in asthmatic mice, while the opposite pattern was observed in non-asthmatic naïve mice. Different gene expression patterns were profoundly found for asthmatic mice exposed to PG/VG+Nicotine compared to PG/VG-only, including genes involved in mitochondrial dysfunction, oxidative phosphorylation, and p21-activated kinase (PAK) signaling.ConclusionsThis study provides experimental evidence of the potential impact of nicotine enhancement on the long-term effects of EC in asthmatics compared to non-asthmatics.ImplicationsThe findings from this study indicate the potential impact of EC in asthmatics by addressing multiple biological markers. The long-term health outcomes of EC in the susceptible group can be instrumental in supporting policymaking and educational campaigns and informing the public, healthcare providers, and EC users about the underlying risks of EC use.
WUSCHEL controls genotype-dependent shoot regeneration capacity in potato
Authors: Park Ji-Sun , Park Kwang Hyun , Park Su-Jin , Ko Seo-Rin , Moon Ki-Beom , Koo Hyunjin , Cho Hye Sun , Park Sang Un , Jeon Jae-Heung , Kim Hyun-Soon , Lee Hyo-Jun 
Published: June 2023

Abstract
Plant cells can reprogram their fate. The combinatorial actions of auxin and cytokinin dedifferentiate somatic cells to regenerate organs, which can develop into individual plants. As transgenic plants can be generated from genetically modified somatic cells through these processes, cell fate transition is an unavoidable step in crop genetic engineering. However, regeneration capacity closely depends on the genotype, and the molecular events underlying these variances remain elusive. In the present study, we demonstrated that WUSCHEL (WUS)—a homeodomain transcription factor—determines regeneration capacity in different potato (Solanum tuberosum) genotypes. Comparative analysis of shoot regeneration efficiency and expression of genes related to cell fate transition revealed that WUS expression coincided with regeneration rate in different potato genotypes. Moreover, in a high-efficiency genotype, WUS silencing suppressed shoot regeneration. Meanwhile, in a low-efficiency genotype, regeneration could be enhanced through the supplementation of a different type of cytokinin that promoted WUS expression. Computational modeling of cytokinin receptor–ligand interactions suggested that the docking pose of cytokinins mediated by hydrogen bonding with the core residues may be pivotal for WUS expression and shoot regeneration in potatoes. Furthermore, our whole-genome sequencing analysis revealed core sequence variations in the WUS promoters that differentiate low- and high-efficiency genotypes. The present study revealed that cytokinin responses, particularly WUS expression, determine shoot regeneration efficiency in different potato genotypes.
Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots
Authors: Liu Li , Heidecker Michel , Depuydt Thomas , Manosalva Perez Nicolas , Crespi Martin , Blein Thomas , Vandepoele Klaas 
Published: June 2023

Abstract
Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in plant genomes. While some lincRNAs have been characterized as important regulators in different biological processes, little is known about the transcriptional regulation for most plant lincRNAs. Through the integration of 8 annotation resources, we defined 6,599 high-confidence lincRNA loci in Arabidopsis (Arabidopsis thaliana). For lincRNAs belonging to different evolutionary age categories, we identified major differences in sequence and chromatin features, as well as in the level of conservation and purifying selection acting during evolution. Spatiotemporal gene expression profiles combined with transcription factor (TF) chromatin immunoprecipitation (ChIP) data were used to construct a TF-lincRNA regulatory network containing 2,659 lincRNAs and 15,686 interactions. We found that properties characterizing lincRNA expression, conservation, and regulation differ between plants and animals. Experimental validation confirmed the role of 3 TFs, KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4, as key regulators controlling root-specific lincRNA expression, demonstrating the predictive power of our network. Furthermore, we identified 58 lincRNAs, regulated by these TFs, showing strong root cell type-specific expression or chromatin accessibility, which are linked with genome-wide association studies genetic associations related to root system development and growth. The multilevel genome-wide characterization covering chromatin state information, promoter conservation, and chromatin immunoprecipitation-based TF binding, for all detectable lincRNAs across 769 expression samples, permits rapidly defining the biological context and relevance of Arabidopsis lincRNAs through regulatory networks.
The functions of a 5′ tRNA-Ala-derived fragment in gene expression
Authors: Li Yuanyuan , Gao Junping , Wang Ying , Cai Jun , Wu Dousheng , Wang Long , Pu Wenxuan , Yu Feng , Zhu Sirui 
Published: June 2023

Abstract
Transfer RNA (tRNA) can produce smaller RNA fragments called tRNA-derived fragments (tRFs). tRFs play critical roles in multiple cellular programs, although the functional mechanisms of tRFs remain largely unknown in plants. In this study, we examined the phenotype associated with 5′ tRF-Ala (tRF-Ala, produced from tRNA-Ala) overexpression and knockdown lines (tDR-Ala-OE and tDR-Ala-kd, respectively) and the mechanisms by which tRF-Ala affects mRNA levels in Arabidopsis (Arabidopsis thaliana). We investigated the candidate proteins associated with tRF-Ala by quantitative proteomics and confirmed the direct interaction between tRF-Ala and the splicing factor SERINE-ARGININE RICH PROTEIN 34 (SR34). A transcriptome sequencing analysis showed that 318 genes among all the genes (786) with substantial alternative splicing (AS) variance in tDR-Ala-OE lines are targets of SR34. tRF-Ala diminished the binding affinity between SR34 and its targets by direct competition for interaction with SR34. These findings reveal the critical roles of tRF-Ala in regulating mRNA levels and splicing.
Evaporation-driven internal hydraulic redistribution alleviates root drought stress: Mechanisms and modeling
Authors: Liu Yang , Nadezhdina Nadezhda , Hu Wei , Clothier Brent , Duan Jie , Li Ximeng , Xi Benye 
Published: June 2023

AbstractMany tree species have developed extensive root systems that allow them to survive in arid environments by obtaining water from a large soil volume. These root systems can transport and redistribute soil water during drought by hydraulic redistribution (HR). A recent study revealed the phenomenon of evaporation-driven hydraulic redistribution (EDHR), which is driven by evaporative demand (transpiration). In this study, we confirmed the occurrence of EDHR in Chinese white poplar (Populus tomentosa) through root sap flow measurements. We utilized microcomputed tomography technology to reconstruct the xylem network of woody lateral roots and proposed conceptual models to verify EDHR from a physical perspective. Our results indicated that EDHR is driven by the internal water potential gradient within the plant xylem network, which requires 3 conditions: high evaporative demand, soil water potential gradient, and special xylem structure of the root junction. The simulations demonstrated that during periods of extreme drought, EDHR could replenish water to dry roots and improve root water potential up to 38.9% to 41.6%. This highlights the crucial eco-physiological importance of EDHR in drought tolerance. Our proposed models provide insights into the complex structure of root junctions and their impact on water movement, thus enhancing our understanding of the relationship between xylem structure and plant hydraulics.