bluuebunny/crossref_metadata_2025_split huggingface dataset:
The formation of cores in galaxies across cosmic time – the existence of cores is not in tension with the ΛCDM paradigm
Authors: Jackson R A , Kaviraj S , Yi S K , Peirani S , Dubois Y , Martin G , Devriendt J E G , Slyz A , Pichon C , Volonteri M , Kimm T , Kraljic K 
Published: January 2024

ABSTRACT
The ‘core-cusp’ problem is considered a key challenge to the ΛCDM paradigm. Haloes in dark matter only simulations exhibit ‘cuspy’ profiles, where density continuously increases towards the centre. However, the dark matter profiles of many observed galaxies (particularly in the dwarf regime) deviate strongly from this prediction, with much flatter central regions (‘cores’). We use NewHorizon (NH), a hydrodynamical cosmological simulation, to investigate core formation, using a statistically significant number of galaxies in a cosmological volume. Haloes containing galaxies in the upper (M⋆ ≥ 1010.2 M⊙) and lower (M⋆ ≤ 108 M⊙) ends of the stellar mass distribution contain cusps. However, Haloes containing galaxies with intermediate (108 M⊙ ≤ M⋆ ≤ 1010.2 M⊙) stellar masses are generally cored, with typical halo masses between 1010.2 M⊙ and 1011.5 M⊙. Cores form through supernova-driven gas removal from halo centres, which alters the central gravitational potential, inducing dark matter to migrate to larger radii. While all massive (M⋆ ≥ 109.5 M⊙) galaxies undergo a cored-phase, in some cases cores can be removed and cusps reformed. This happens if a galaxy undergoes sustained star formation at high redshift, which results in stars (which, unlike the gas, cannot be removed by baryonic feedback) dominating the central gravitational potential. After cosmic star formation peaks, the number of cores, and the mass of the Haloes they are formed in, remain constant, indicating that cores are being routinely formed over cosmic time after a threshold halo mass is reached. The existence of cores is, therefore, not in tension with the standard paradigm.
Star-forming environments in smoothed particle magnetohydrodynamics simulations II: re-simulating isolated clumps to determine equivalence of extracted clumps and parent simulations
Authors: Wurster James , Rowan Connar 
Published: January 2024

ABSTRACT
What is the numerical reproducibility of a stellar system (including its discs) when evolving only a subset of (partially-evolved) smoothed particle hydrodynamics (SPH) particles? To investigate this, we modelled the evolution of 29 star-forming clumps that were extracted from our previous simulations that investigated the formation and early evolution of low-mass star clusters. These clumps were evolved using a three-dimensional smoothed particle radiation magnetohydrodynamics code, where we included or excluded non-ideal magnetohydrodynamics to match the cluster simulation. While star formation proceeded as expected, we were unable to identically reproduce any of the systems present at the end of the cluster simulations. However, the final distributions of stellar mass, stellar system mass, disc mass, and disc radii were reproduced statistically; unfortunately, the distribution of average magnetic field strengths in the discs was not reproduced statistically, but this may be a result of our updated algorithms governing the evolution of the magnetic field. Therefore, given that our clumps yield stellar masses that are statistically similar to those in the original low-mass star clusters, we have demonstrated that we can statistically reproduce systems (aside from their magnetic field strength) by evolving a subset of SPH particles. Therefore, clumps such as these can be used as initial conditions to investigate the formation of isolated stars from less-contrived initial environments.
Off-axis MeV and very-high-energy gamma-ray emissions from structured gamma-ray burst jets
Authors: Bošnjak Željka , Zhang B Theodore , Murase Kohta , Ioka Kunihito 
Published: January 2024

ABSTRACT
Very-high-energy (VHE) photons around TeV energies from a gamma-ray burst (GRB) jet will play an essential role in the multimessenger era, with a fair fraction of the events being observed off-axis to the jet. We show that different energy photons (MeV and TeV photons in particular) arrive from different emission zones for off-axis observers even if the emission radius is the same. The location of the emission region depends on the jet structure of the surface brightness, and the structures are generally different at different energies, mainly due to the attenuation of VHE photons by electron–positron pair creation. This off-axis zone-shift effect does not justify the usual assumption of the one emission zone at a certain radius and also produces a time delay of VHE photons comparable to the GRB duration, which is crucial for future VHE observations, such as by the Cherenkov Telescope Array.
Cosmological gas accretion history on to the stellar discs of Milky Way-like galaxies in the Auriga simulations – II. The inside–out growth of discs
Authors: Iza Federico G , Nuza Sebastián E , Scannapieco Cecilia , Grand Robert J J , Gómez Facundo A , Springel Volker , Pakmor Rüdiger , Marinacci Federico , Fragkoudi Francesca 
Published: January 2024

ABSTRACT
We investigate the growth of stellar discs in Milky Way-mass galaxies using the magnetohydrodynamical simulations of the Auriga Project in a full cosmological context. We focus on the gas accretion process along the discs, calculating the net, infall and outflow rates as a function of galactocentric distance, and investigate the relation between them and the star formation activity. The stellar distributions of around 70 per cent of the simulated galaxies exhibit an ‘inside–out’ pattern, with older (younger) stellar populations preferentially located in the inner (outer) disc regions. In all cases, we find a very tight correlation between the infall, outflow, and net accretion rates, as well as between these three quantities and the star formation rate. This is because the amount of gas which is ultimately available for star formation in each radial ring depends not only on the infall rates, but also on the amount of gas leaving the disc in outflows, which directly relates to the local star formation level. Therefore, any of these rates can be used to identify galaxies with inside–out growth. For these galaxies, the correlation between the dominant times of accretion/star formation and disc radius is well fitted by a linear function. We also find that, when averaged over galaxies with formation histories similar to the Milky Way, the simulated accretion rates show a similar evolution (both temporally and radially integrated) to the usual accretion prescriptions used in chemical evolution models, although some major differences arise at early times and in the inner disc regions.
The distribution of stellar orbits in eagle galaxies – the effect of mergers, gas accretion, and secular evolution
Authors: Santucci Giulia , Lagos Claudia Del P , Harborne Katherine E , Ludlow Aaron , Proctor Katy L , Foster Caroline , McDermid Richard , Poci Adriano , Thater Sabine , van de Ven Glenn , Zhu Ling , Walo Martín Daniel 
Published: January 2024

ABSTRACT
The merger history of a galaxy is thought to be one of the major factors determining its internal dynamics, with galaxies having undergone different types or mergers (e.g. dry, minor, or major mergers) predicted to show different dynamical properties. We study the instantaneous orbital distribution of galaxies in the eagle simulation, colouring the orbits of the stellar particles by their stellar age, in order to understand whether stars form in particular orbits (e.g. in a thin or thick disc). We first show that eagle reproduces well the observed stellar mass fractions in different stellar orbital families as a function of stellar mass and spin parameter at z = 0. We find that the youngest stars reside in a thin disc component that can extend to the very inner regions of galaxies, and that older stars have warmer orbits, with the oldest ones showing orbits consistent with both hot and counter-rotating classifications, which is consistent with the trend found in the Milky Way and other disc galaxies. We also show that counter-rotating orbits trace galaxy mergers – in particular dry mergers, and that in the absence of mergers, counter-rotating orbits can also be born from highly misaligned gas accretion that leads to star formation.
From Hubble to snap parameters: a Gaussian process reconstruction
Authors: Jesus J F , Benndorf D , Escobal A A , Pereira S H 
Published: January 2024

ABSTRACT
By using recent H(z) and supernovae Type Ia (SNe Ia) data, we reconstruct the evolution of kinematic parameters H(z), q(z), jerk, and snap, using a model-independent, non-parametric method, namely, the Gaussian processes. Throughout the present analysis, we have allowed for a spatial curvature prior, based on Planck 18 constraints. In the case of SNe Ia, we modify a python package (gapp) in order to obtain the reconstruction of the fourth derivative of a function, thereby allowing us to obtain the snap from comoving distances. Furthermore, using a method of importance sampling, we combine H(z) and SNe Ia reconstructions in order to find joint constraints for the kinematic parameters. We find for the current values of the parameters: H0 = 67.2 ± 6.2 km s−1 Mpc−1, $q_0 = -0.54^{+0.06}_{-0.05}$, $j_0=0.94^{+0.20}_{-0.18}$, and $s_0=-0.62^{+0.26}_{-0.25}$ at 1σ c.l. We find that these reconstructions are compatible with the predictions from flat lambda-cold dark matter model, at least for 2σ confidence intervals.
X-ray polarization in magnetar atmospheres – effects of mode conversion
Authors: Kelly Ruth M E , Zane Silvia , Turolla Roberto , Taverna Roberto 
Published: January 2024

ABSTRACT
Magnetars, the most strongly magnetized neutron stars, are among the most promising targets for X-ray polarimetry. Imaging X-ray Polarimetry Explorer (IXPE), the first satellite devoted to exploring the sky in polarized X-rays, has observed four magnetars to date. A proper interpretation of IXPE results requires the development of new atmospheric models that can take into proper account the effects of the magnetized vacuum on par with those of the plasma. Here we investigate the effects of mode conversion at the vacuum resonance on the polarization properties of magnetar emission by computing plane-parallel atmospheric models under varying conditions of magnetic field strength/orientation, effective temperature, and allowing for either complete or partial adiabatic mode conversion. Complete mode conversion results in a switch of the dominant polarization mode, from the extraordinary (X) to the ordinary (O) one, below an energy that decreases with increasing magnetic field strength, occurring at $\approx 0.5\, \mathrm{keV}$ for a magnetic field strength of $B=10^{14}\, \mathrm{G}$. Partial adiabatic mode conversion results in a reduced polarization degree when compared with a standard plasma atmosphere. No dominant mode switch occurs for $B=10^{14}\, \mathrm{G}$, while there are two switches for lower fields of $B=3\times 10^{13}\, \mathrm{G}$. Finally, by incorporating our models in a ray-tracing code, we computed the expected polarization signal at infinity for different emitting regions on the star surface and for different viewing geometries. The observability of quantum electrodynamics signatures with IXPE and with future soft X-ray polarimeters as Rocket Experiment Demonstration of a Soft X-ray Polarimeter is discussed.
Less-is-more: selecting transcription factor binding regions informative for motif inference
Authors: Xu Jinrui , Gao Jiahao , Ni Pengyu , Gerstein Mark 
Published: January 2024

Abstract
Numerous statistical methods have emerged for inferring DNA motifs for transcription factors (TFs) from genomic regions. However, the process of selecting informative regions for motif inference remains understudied. Current approaches select regions with strong ChIP-seq signal for a given TF, assuming that such strong signal primarily results from specific interactions between the TF and its motif. Additionally, these selection approaches do not account for non-target motifs, i.e. motifs of other TFs; they presume the occurrence of these non-target motifs infrequent compared to that of the target motif, and thus assume these have minimal interference with the identification of the target. Leveraging extensive ChIP-seq datasets, we introduced the concept of TF signal ‘crowdedness’, referred to as C-score, for each genomic region. The C-score helps in highlighting TF signals arising from non-specific interactions. Moreover, by considering the C-score (and adjusting for the length of genomic regions), we can effectively mitigate interference of non-target motifs. Using these tools, we find that in many instances, strong ChIP-seq signal stems mainly from non-specific interactions, and the occurrence of non-target motifs significantly impacts the accurate inference of the target motif. Prioritizing genomic regions with reduced crowdedness and short length markedly improves motif inference. This ‘less-is-more’ effect suggests that ChIP-seq region selection warrants more attention.
A super minigene with a short promoter and truncated introns recapitulates essential features of transcription and splicing regulation of the SMN1 and SMN2 genes
Authors: Ottesen Eric W , Seo Joonbae , Luo Diou , Singh Natalia N , Singh Ravindra N 
Published: January 2024

Abstract
Here we report a Survival Motor Neuron 2 (SMN2) super minigene, SMN2Sup, encompassing its own promoter, all exons, their flanking intronic sequences and the entire 3′-untranslated region. We confirm that the pre-mRNA generated from SMN2Sup undergoes splicing to produce a translation-competent mRNA. We demonstrate that mRNA generated from SMN2Sup produces more SMN than an identical mRNA generated from a cDNA clone. We uncover that overexpression of SMN triggers skipping of exon 3 of SMN1/SMN2. We define the minimal promoter and regulatory elements associated with the initiation and elongation of transcription of SMN2. The shortened introns within SMN2Sup preserved the ability of camptothecin, a transcription elongation inhibitor, to induce skipping of exons 3 and 7 of SMN2. We show that intron 1-retained transcripts undergo nonsense-mediated decay. We demonstrate that splicing factor SRSF3 and DNA/RNA helicase DHX9 regulate splicing of multiple exons in the context of both SMN2Sup and endogenous SMN1/SMN2. Prevention of SMN2 exon 7 skipping has implications for the treatment of spinal muscular atrophy (SMA). We validate the utility of the super minigene in monitoring SMN levels upon splicing correction. Finally, we demonstrate how the super minigene could be employed to capture the cell type-specific effects of a pathogenic SMN1 mutation.
Homology recognition without double-stranded DNA-strand separation in D-loop formation by RecA
Authors: Shibata Takehiko , Ikawa Shukuko , Iwasaki Wakana , Sasanuma Hiroyuki , Masai Hisao , Hirota Kouji 
Published: January 2024

Abstract
RecA protein and RecA/Rad51 orthologues are required for homologous recombination and DNA repair in all living creatures. RecA/Rad51 catalyzes formation of the D-loop, an obligatory recombination intermediate, through an ATP-dependent reaction consisting of two phases: homology recognition between double-stranded (ds)DNA and single-stranded (ss)DNA to form a hybrid-duplex core of 6–8 base pairs and subsequent hybrid-duplex/D-loop processing. How dsDNA recognizes homologous ssDNA is controversial. The aromatic residue at the tip of the β-hairpin loop (L2) was shown to stabilize dsDNA-strand separation. We tested a model in which dsDNA strands were separated by the aromatic residue before homology recognition and found that the aromatic residue was not essential to homology recognition, but was required for D-loop processing. Contrary to the model, we found that the double helix was not unwound even a single turn during search for sequence homology, but rather was unwound only after the homologous sequence was recognized. These results suggest that dsDNA recognizes its homologous ssDNA before strand separation. The search for homologous sequence with homologous ssDNA without dsDNA-strand separation does not generate stress within the dsDNA; this would be an advantage for dsDNA to express homology-dependent functions in vivo and also in vitro.
Uromodulin biology
Authors: Karagiannidis Artemios G , Theodorakopoulou Marieta P , Pella Eva , Sarafidis Pantelis A , Ortiz Alberto 
Published: January 2024

ABSTRACT
Uromodulin is a kidney-specific glycoprotein which is exclusively produced by the epithelial cells lining the thick ascending limb and early distal convoluted tubule. It is currently recognized as a multifaceted player in kidney physiology and disease, with discrete roles for intracellular, urinary, interstitial and serum uromodulin. Among these, uromodulin modulates renal sodium handling through the regulation of tubular sodium transporters that reabsorb sodium and are targeted by diuretics, such as the loop diuretic–sensitive Na+-K+-2Cl− cotransporter type 2 (NKCC2) and the thiazide-sensitive Na+/Cl− cotransporter (NCC). Given these roles, the contribution of uromodulin to sodium-sensitive hypertension has been proposed. However, recent studies in humans suggest a more complex interaction between dietary sodium intake, uromodulin and blood pressure. This review presents an updated overview of the uromodulin's biology and its various roles, and focuses on the interaction between uromodulin and sodium-sensitive hypertension.
Conductive catalysis by subsurface transition metals
Authors: Deng Xin , Zheng Caiyan , Li Yangsheng , Zhou Zeyu , Wang Jiamin , Ran Yihua , Hu Zhenpeng , Yang Fan , Li Landong 
Published: January 2024

ABSTRACT
The nature of catalysis has been hotly pursued for over a century, and current research is focused on understanding active centers and their electronic structures. Herein, the concept of conductive catalysis is proposed and verified by theoretical simulations and experimental observations. Metallic systems containing buried catalytically active transitional metals and exposed catalytically inert main group metals are constructed, and the electronic interaction between them via metallic bonding is disclosed. Through the electronic interaction, the catalytic properties of subsurface transitional metals (Pd or Rh) can be transferred to outermost main group metals (Al or Mg) for several important transformations like semi-hydrogenation, Suzuki-coupling and hydroformylation. The catalytic force is conductive, in analogy with the magnetic force and electrostatic force. The traditional definition of active centers is challenged by the concept of conductive catalysis and the electronic nature of catalysis is more easily understood. It might provide new opportunities for shielding traditional active centers against poisoning or leaching and allow for precise regulation of their catalytic properties by the conductive layer.
Lesser Woodcreepers excavate nest cavities in trees
Authors: Cockle Kristina L , Gomez Milka R , Ferreyra Carlos A , Di Sallo Facundo G , Bodrati Alejandro 
Published: January 2024

Abstract
To understand the evolution, life-history tradeoffs, and population ecology of cavity nesters, it is critical to identify the avian lineages and circumstances in which birds excavate tree cavities. Woodcreepers (Furnariidae: Dendrocolaptinae; 56 species) are considered non-excavators dependent on existing cavities. We overturn this assumption by providing definitive evidence that the Lesser Woodcreeper (Xiphorhynchus fuscus, 23 g) is a facultative tree-cavity excavator. From 2007 to 2022 in the Atlantic forest of Misiones, Argentina, Lesser Woodcreepers nested in preexisting tree crevices (4 nests), or excavated cavities in trunks of large-diameter trees in advanced stages of decay (mean diameter: 58 cm, range: 22–121 cm, 22 nests). Nest entrances were vertically elongated and chambers were usually pocket like, excavated in the exterior of the trees (sapwood), with floors that curved along the trees’ circumference. Excavating woodcreepers pulled out elongated pieces of spongy, fibrous decayed wood, tapping only when inside cavities. Published and online photographs of nests of Xiphorhynchus species suggest that excavation may be widespread in the genus. Our observations that woodcreepers tore out elongated pieces of spongy wood (rather than hammering) are consistent with the idea that their long, thin bills are more resistant to torsion and less resistant to impact compared to the stouter bills of other excavators in Passeriformes and Piciformes. Research has tended to focus on birds with chisel-shaped bills, perforating harder sapwood to create nesting chambers in the center of heartrot-infected trees (resulting in typical woodpecker cavities, with circular floors). We hypothesize that Lesser Woodcreepers have adopted an alternative strategy, selecting large trunks with soft outer wood (sapwood), stopping their excavation radially if they reach harder wood, and then expanding the nest chamber laterally. Furnariidae may offer a useful model family for understanding ecological and evolutionary factors that influence cavity excavation. We provide a Spanish translation in Supplementary Material.
The impact of light and thioredoxins on the plant thiol-disulfide proteome
Authors: Hou Liang-Yu , Sommer Frederik , Poeker Louis , Dziubek Dejan , Schroda Michael , Geigenberger Peter 
Published: January 2024

Abstract
Thiol-based redox regulation is a crucial posttranslational mechanism to acclimate plants to changing light availability. Here, we conducted a biotin switch–based redox proteomics study in Arabidopsis (Arabidopsis thaliana) to systematically investigate dynamics of thiol–redox networks in response to temporal changes in light availability and across genotypes lacking parts of the thioredoxin (Trx) or NADPH-Trx-reductase C (NTRC) systems in the chloroplast. Time-resolved dynamics revealed light led to marked decreases in the oxidation states of many chloroplast proteins with photosynthetic functions during the first 10 min, followed by their partial reoxidation after 2 to 6 h into the photoperiod. This involved f, m, and x-type Trx proteins showing similar light-induced reduction–oxidation dynamics, while NTRC, 2-Cys peroxiredoxins, and Trx y2 showed an opposing pattern, being more oxidized in light than dark. In Arabidopsis trxf1f2, trxm1m2, or ntrc mutants, most proteins showed increased oxidation states in the light compared to wild type, suggesting their light-dependent dynamics were related to NTRC/Trx networks. While NTRC deficiency had a strong influence in all light conditions, deficiencies in f- or m-type Trxs showed differential impacts on the thiol–redox proteome depending on the light environment, being higher in constant or fluctuating light, respectively. The results indicate plant redox proteomes are subject to dynamic changes in reductive and oxidative pathways to cooperatively fine-tune photosynthetic and metabolic processes in the light. The importance of the individual elements of the NTRC/Trx networks mediating these responses depend on the extent of light variability, with NTRC playing a crucial role to balance protein–redox states in rapidly fluctuating light.