bluuebunny/crossref_metadata_2025_split huggingface dataset:
ΛCDM with baryons versus MOND: The time evolution of the universal acceleration scale in the Magneticum simulations
Authors: Mayer Alexander C , Teklu Adelheid F , Dolag Klaus , Remus Rhea-Silvia 
Published: October 2022

ABSTRACT
MOdified Newtonian Dynamics (MOND) is an alternative to the standard Cold Dark Matter (CDM) paradigm which proposes an alteration of Newton’s laws of motion at low accelerations, characterized by a universal acceleration scale a0. It attempts to explain observations of galactic rotation curves and predicts a specific scaling relation of the baryonic and total acceleration in galaxies, referred to as the Rotational Acceleration Relation (RAR), which can be equivalently formulated as a Mass Discrepancy Acceleration Relation (MDAR). The appearance of these relations in observational data such as SPARC has lead to investigations into the existence of similar relations in cosmological simulations using the standard ΛCDM model. Here, we report the existence of an RAR and MDAR similar to that predicted by MOND in ΛCDM using a large sample of galaxies extracted from a cosmological, hydrodynamical simulation (Magneticum). Furthermore, by using galaxies in Magneticum at different redshifts, a prediction for the evolution of the inferred acceleration parameter a0 with cosmic time is derived by fitting a MOND force law to these galaxies. In Magneticum, the best fit for a0 is found to increase by a factor ≃3 from redshift z = 0 to z = 2.3. This offers a powerful test from cosmological simulations to distinguish between MOND and ΛCDM observationally.
Probing particle acceleration at trans-relativistic shocks with off-axis gamma-ray burst afterglows
Authors: Takahashi Kazuya , Ioka Kunihito , Ohira Yutaka , van Eerten Hendrik J 
Published: October 2022

ABSTRACT
Particle acceleration is expected to be different between relativistic and non-relativistic collisionless shocks. We show that electromagnetic counterparts to gravitational waves (GWs), gamma-ray burst (GRB) afterglows, are ideal targets for observing trans-relativistic evolution of accelerated electron distribution because the GWs spot nearby GRBs with off-axis jets, otherwise missed in gamma-ray observations. We find that the relativistic spectral slope begins to change steeply near the peak time of the light curve and approaches the non-relativistic limit in about 10 times the peak time. The trans-relativistic evolution of the afterglow synchrotron spectrum is consistent with GRB 170817A observations within errors, and will be measurable in similar but more distant events at a GW horizon ∼200 Mpc in a denser environment. We roughly estimate that such events represent a fraction of 10–50 per cent of the GRB 170817A-like off-axis short GRBs. We also find that the spectral evolution does not depend on the jet structure if their light curves are similar to each other.
CS-ROMER: a novel compressed sensing framework for Faraday depth reconstruction
Authors: Cárcamo Miguel , Scaife Anna M M , Alexander Emma L , Leahy J Patrick 
Published: October 2022

ABSTRACT
The reconstruction of Faraday depth structure from incomplete spectral polarization radio measurements using the RM synthesis technique is an underconstrained problem requiring additional regularization. In this paper, we present cs-romer: a novel object-oriented compressed sensing framework to reconstruct Faraday depth signals from spectropolarization radio data. Unlike previous compressed sensing applications, this framework is designed to work directly with data that are irregularly sampled in wavelength-squared space and to incorporate multiple forms of compressed sensing regularization. We demonstrate the framework using simulated data for the VLA telescope under a variety of observing conditions, and we introduce a methodology for identifying the optimal basis function for reconstruction of these data, using an approach that can also be applied to data sets from other telescopes and over different frequency ranges. In this work, we show that the delta basis function provides optimal reconstruction for VLA L-band data and we use this basis with observations of the low-mass galaxy cluster Abell 1314 in order to reconstruct the Faraday depth of its constituent cluster galaxies. We use the cs-romer framework to de-rotate the Galactic Faraday depth contribution directly from the wavelength-squared data and to handle the spectral behaviour of different radio sources in a direction-dependent manner. The results of this analysis show that individual galaxies within Abell 1314 deviate from the behaviour expected for a Faraday-thin screen such as the intra-cluster medium and instead suggest that the Faraday rotation exhibited by these galaxies is dominated by their local environments.
Accurate dark-matter halo elongation from weak-lensing stacking analysis
Authors: Gonzalez Elizabeth J , Hoffmann Kai , Gaztañaga Enrique , García Lambas Diego R , Fosalba Pablo , Crocce Martin , Castander Francisco J , Makler Martín 
Published: October 2022

ABSTRACT
Shape estimates that quantifying the halo anisotropic mass distribution are valuable parameters that provide information on their assembly process and evolution. Measurements of the mean shape estimates for a sample of cluster-sized haloes can be used to test halo formation scenarios, as well as improving the modelling of potential biases in constraining cosmological parameters using these systems. In this work, we test the recovery of halo cluster shapes and masses applying weak-lensing stacking techniques. To this end, we use lensing shear and a new dark-matter halo catalogue, derived from the light-cone output of the cosmological simulation MICE-GC. We perform this study by combining the lensing signals obtained for several samples of haloes, selected according to their mass and redshift, taking into account the main directions of the dark-matter distributions. In the analysis, we test the impact of several potential introduced systematics, such as the adopted modelling, the contribution of the neighbouring mass distribution, miscentring, and misalignment effects. Our results show that when some considerations regarding the halo relaxation state are taken into account, the lensing semi-axial ratio estimates are in agreement within a 5 per cent with the mean shapes of the projected dark-matter particle distribution of the stacked haloes. The presented methodology provides a useful tool to derive reliable shapes of galaxy clusters and to contrast them with those expected from numerical simulations. Furthermore, our proposed modelling, that takes into account the contribution of neighbouring haloes, allows to constraint the elongation of the surrounding mass distribution.
Properties of atomic hydrogen gas in the Galactic plane from THOR 21-cm absorption spectra: a comparison with the high latitude gas
Authors: Basu Arghyadeep , Roy Nirupam , Beuther Henrik , Syed Jonas , Ott Jürgen , Soler Juan D , Stil Jeroen , Rugel Michael R 
Published: October 2022

ABSTRACT
The neutral hydrogen 21-cm line is an excellent tracer of the atomic interstellar medium in the cold and the warm phases. Combined 21-cm emission and absorption observations are very useful to study the properties of the gas over a wide range of density and temperature. In this work, we have used 21-cm absorption spectra from recent interferometric surveys, along with the corresponding emission spectra from earlier single dish surveys to study the properties of the atomic gas in the Milky Way. In particular, we focus on a comparison of properties between lines of sight through the gas disc in the Galactic plane and high Galactic latitude lines of sight through more diffuse gas. As expected, the analysis shows a lower average temperature for the gas in the Galactic plane compared to that along the high latitude lines of sight. The gas in the plane also has a higher molecular fraction, showing a sharp transition and flattening in the dust–gas correlation. On the other hand, the observed correlation between 21-cm brightness temperature and optical depth indicates some intrinsic difference in spin temperature distribution and a fraction of gas in the Galactic plane having intermediate optical depth (for 0.02 &lt; τ &lt; 0.2) but higher spin temperature, compared to that of the diffuse gas at high latitude with the same optical depth. This may be due to a small fraction of cold gas with slightly higher temperature and lower density present on the Galactic plane.
Zonal winds in the gas planets driven by convection above a stably stratified layer
Authors: Wulff Paula N , Dietrich W , Christensen U R , Wicht J 
Published: October 2022

ABSTRACT
The analysis of the recent gravity measurements of Jupiter and Saturn reveal that the zonal winds observed on their surfaces reach several thousand kilometres deep into their atmospheres. However, it remains unclear which mechanism prevents them from penetrating deeper. Recent models suggest that a stably stratified region would yield the desired effect. In this numerical study we systematically explore the dynamics of flow in a rotating spherical shell where the lower third is stably stratified while convection in the outer region drives multiple zonal winds, similar to those observed on Jupiter or Saturn. When using a rigid lower boundary condition, only an equatorial jet pair is formed without an underlying stable layer. When including a stable layer, fierce multiple jets also develop at mid to high latitudes, once the stable stratification is strong enough to effectively decouple the jet dynamics from the lower boundary. We find that the decay of the jet amplitude near the stable layer boundary is controlled by Ω/N, where Ω is the rotation rate and N the Brunt-Väisälä frequency that quantifies the degree of stable stratification. Furthermore, the penetration distance of the jets is proportional to the jet width. In the convective region, the winds are invariant along the axis of rotation, whereas their extension in the stable layer tends to become radially aligned.
Infrared variability of young solar analogues in the Lagoon Nebula
Authors: Ordenes-Huanca C , Zoccali M , Bayo A , Cuadra J , Contreras Ramos R , Hillenbrand L A , Lacerna I , Abarzua S , Avendaño C , Diaz P , Fernandez I , Lara G 
Published: October 2022

ABSTRACT
T Tauri stars are low-mass pre-main sequence stars that are intrinsically variable. Due to the intense magnetic fields they possess, they develop dark spots on their surface that, because of rotation, introduce a periodic variation of brightness. In addition, the presence of surrounding discs could generate flux variations by variable extinction or accretion. Both can lead to a brightness decrease or increase, respectively. Here, we have compiled a catalogue of light curves for 379 T Tauri stars in the Lagoon Nebula (M8) region, using VVVX survey data in the Ks-band. All these stars were already classified as pre-MS stars based on other indicators. The data presented here are spread over a period of about eight years, which gives us a unique follow-up time for these sources at this wavelength. The light curves were classified according to their degree of periodicity and asymmetry, to constrain the physical processes responsible for their variation. Periods were compared with the ones found in literature, on a much shorter baseline. This allowed us to prove that for 126 stars, the magnetically active regions remain stable for several years. Besides, our near-IR data were compared with the optical Kepler/K2 light curves, when available, giving us a better understanding of the mechanisms responsible for the brightness variations observed and how they manifest at different bands. We found that the periodicity in both bands is in fairly good agreement, but the asymmetry will depend on the amplitude of the bursts or dips events and the observation cadence.
The eccentricity distribution of wide binaries
Authors: Benisty David , Evans N Wyn , Davis Anne-Christine 
Published: October 2022

ABSTRACT
Future Gaia and Legacy Survey of Space and Time data releases, together with wide area spectroscopic surveys, will deliver large samples of resolved binary stars with phase space coordinates, albeit with low-cadence. Given an eccentricity law f(ϵ), we derive properties of (i) the velocity distribution $v/\sqrt{G M/r}$ normalized by the value for a circular orbit at the measured separation r; (ii) the astrometric acceleration distributions a/(GM/r2) again normalized to the circular orbit value. Our formulation yields analytic predictions for the full statistical distribution for some commonly used eccentricity laws, if the time-scale of data sampling is comparable to or exceeds the binary period. In particular, the velocity distribution for the linear eccentricity law is surprisingly simple. With Bayesian analysis, we suggest a method to infer the eccentricity distribution based on the measured velocity distribution.
Functional Attenuation of UCP1 as the Potential Mechanism for a Thickened Blubber Layer in Cetaceans
Authors: Zhou Ming , Wu Tianzhen , Chen Yue , Xu Shixia , Yang Guang 
Published: October 2022

Abstract
Uncoupling protein 1 (UCP1) is an essential protein in the mitochondrial inner membrane that mediates nonshivering thermogenesis (NST) and plays an important role in thermoregulation and fat deposition. However, the relationship between the evolution of UCP1 and fat deposition in the blubber layer in cetaceans remains unclear. Here, frameshift mutations, premature termination, and relaxed selection pressure (ω = 0.9557, P &lt; 0.05) were detected in UCP1 in cetaceans, suggesting that UCP1 was inactivated during cetacean evolution. By time estimation, it was found that the inactivation of UCP1 in cetaceans occurred between 53.1 and 50.2 Ma. However, combined with findings from immunohistochemical analysis of the blubber layer of the Yangtze finless porpoise and in vitro functional assays, a premature termination of cetacean UCP1 resulted in a reduction of UCP1-mediated NST capacity (about 50%) and lipolytic capacity (about 40%), both of which were beneficial to maintain blubber layer and body temperature without excessive fat consumption. This study provides new insights into the molecular mechanisms of the blubber thickening in cetaceans and highlights the importance of UCP1 attenuation in cetaceans for secondary aquatic adaptation.
Prokaryotic Pangenomes Act as Evolving Ecosystems
Authors: McInerney James O 
Published: October 2022

Abstract
Understanding adaptation to the local environment is a central tenet and a major focus of evolutionary biology. But this is only part of the adaptionist story. In addition to the external environment, one of the main drivers of genome composition is genetic background. In this perspective, I argue that there is a growing body of evidence that intra-genomic selective pressures play a significant part in the composition of prokaryotic genomes and play a significant role in the origin, maintenance and structuring of prokaryotic pangenomes.
Single-cell and bulk ICP–MS investigation of accumulation patterns of Pt-based metallodrugs in cisplatin-sensitive and -resistant cell models
Authors: Lim Si Ying , Low Zhi En , Tan Regina Pei Woon , Lim Zhi Chiaw , Ang Wee Han , Kubota Tetsuo , Yamanaka Michiko , Pang Steven , Simsek Erhan , Li Sam Fong Yau 
Published: October 2022

Abstract
In research enabling preclinical development and attaining a deeper understanding of the behavior of metallodrugs in cancer cells with acquired resistance, intracellular Pt accumulation could be considered an important biomarker and analytical focus. In this work, Pt accumulation patterns in terms of the number of cells and Pt mass in single cells were precisely defined by using inductively coupled plasma-mass spectrometry (ICP–MS) operating in a fast time-resolved analysis mode. This technique is otherwise known as single-cell (SC)–ICP–MS. By applying the nascent and validated SC–ICP–MS technique, comparisons across three Pt drugs (cisplatin, carboplatin, and oxaliplatin) in the A2780 and A2780cis ovarian cancer cell models could be made. Additional roles of transporters on top of passive diffusion and the drugs’ bioactivity could be postulated. The SC–ICP–MS-based observations also served as a cross-validation point to augment preexisting research findings on Pt-resistance mechanisms. Conjectures regarding S and Fe metabolism were also derived based on an additional and direct ICP–MS analysis of endogenous elements. Overall, our work not only confirms the utility of SC–ICP–MS in chemotherapeutic research, but also provided insights into further ICP–MS-based analytical capacities to be developed.
Molecular basis for lethal cross-talk between two unrelated bacterial transcription factors - the regulatory protein of a restriction-modification system and the repressor of a defective prophage
Authors: Wisniewska Aleksandra , Wons Ewa , Potrykus Katarzyna , Hinrichs Rebecca , Gucwa Katarzyna , Graumann Peter L , Mruk Iwona 
Published: October 2022

AbstractBacterial gene expression depends on the efficient functioning of global transcriptional networks, however their interconnectivity and orchestration rely mainly on the action of individual DNA binding proteins called transcription factors (TFs). TFs interact not only with their specific target sites, but also with secondary (off-target) sites, and vary in their promiscuity. It is not clear yet what mechanisms govern the interactions with secondary sites, and how such rewiring affects the overall regulatory network, but this could clearly constrain horizontal gene transfer. Here, we show the molecular mechanism of one such off-target interaction between two unrelated TFs in Escherichia coli: the C regulatory protein of a Type II restriction-modification system, and the RacR repressor of a defective prophage. We reveal that the C protein interferes with RacR repressor expression, resulting in derepression of the toxic YdaT protein. These results also provide novel insights into regulation of the racR-ydaST operon. We mapped the C regulator interaction to a specific off-target site, and also visualized C protein dynamics, revealing intriguing differences in single molecule dynamics in different genetic contexts. Our results demonstrate an apparent example of horizontal gene transfer leading to adventitious TF cross-talk with negative effects on the recipient's viability. More broadly, this study represents an experimentally-accessible model of a regulatory constraint on horizontal gene transfer.
PlantExp: a platform for exploration of gene expression and alternative splicing based on public plant RNA-seq samples
Authors: Liu Jinding , Zhang Yaru , Zheng Yiqing , Zhu Yali , Shi Yapin , Guan Zhuoran , Lang Kun , Shen Danyu , Huang Wen , Dou Daolong 
Published: October 2022

Abstract
Over the last decade, RNA-seq has produced a massive amount of plant transcriptomic sequencing data deposited in public databases. Reanalysis of these public datasets can generate additional novel hypotheses not included in original studies. However, the large data volume and the requirement for specialized computational resources and expertise present a barrier for experimental biologists to explore public repositories. Here, we introduce PlantExp (https://biotec.njau.edu.cn/plantExp), a database platform for exploration of plant gene expression and alternative splicing profiles based on 131 423 uniformly processed publicly available RNA-seq samples from 85 species in 24 plant orders. In addition to two common retrieval accesses to gene expression and alternative splicing profiles by functional terms and sequence similarity, PlantExp is equipped with four online analysis tools, including differential expression analysis, specific expression analysis, co-expression network analysis and cross-species expression conservation analysis. With these online analysis tools, users can flexibly customize sample groups to reanalyze public RNA-seq datasets and obtain new insights. Furthermore, it offers a wide range of visualization tools to help users intuitively understand analysis results. In conclusion, PlantExp provides a valuable data resource and analysis platform for plant biologists to utilize public RNA-seq. datasets.
Molecular basis of cyclic tetra-oligoadenylate processing by small standalone CRISPR-Cas ring nucleases
Authors: Molina Rafael , Garcia-Martin Ricardo , López-Méndez Blanca , Jensen Anne Louise Grøn , Ciges-Tomas J Rafael , Marchena-Hurtado Javier , Stella Stefano , Montoya Guillermo 
Published: October 2022

Abstract
Standalone ring nucleases are CRISPR ancillary proteins, which downregulate the immune response of Type III CRISPR-Cas systems by cleaving cyclic oligoadenylates (cA) second messengers. Two genes with this function have been found within the Sulfolobus islandicus (Sis) genome. They code for a long polypeptide composed by a CARF domain fused to an HTH domain and a short polypeptide constituted by a CARF domain with a 40 residue C-terminal insertion. Here, we determine the structure of the apo and substrate bound states of the Sis0455 enzyme, revealing an insertion at the C-terminal region of the CARF domain, which plays a key role closing the catalytic site upon substrate binding. Our analysis reveals the key residues of Sis0455 during cleavage and the coupling of the active site closing with their positioning to proceed with cA4 phosphodiester hydrolysis. A time course comparison of cA4 cleavage between the short, Sis0455, and long ring nucleases, Sis0811, shows the slower cleavage kinetics of the former, suggesting that the combination of these two types of enzymes with the same function in a genome could be an evolutionary strategy to regulate the levels of the second messenger in different infection scenarios.
Fungal names: a comprehensive nomenclatural repository and knowledge base for fungal taxonomy
Authors: Wang Fang , Wang Ke , Cai Lei , Zhao Mingjun , Kirk Paul M , Fan Guomei , Sun Qinglan , Li Bo , Wang Shuai , Yu Zhengfei , Han Dong , Ma Juncai , Wu Linhuan , Yao Yijian 
Published: October 2022

AbstractFungal taxonomy is a complex and rapidly changing subject, which makes proper naming of fungi challenging for taxonomists. A registration platform with a standardized and information-integrated database is a powerful tool for efficient research on fungal taxonomy. Fungal Names (FN, https://nmdc.cn/fungalnames/; launched in 2011) is one of the three official fungal nomenclatural repositories authorized by the International Nomenclature Committee for Fungi (NCF). Currently, FN includes &gt;567 000 taxon names from &gt;10 000 related journals and books published since 1596 and covers &gt;147 000 collection records of type specimens/illustrations from &gt;5000 preserving agencies. FN is also a knowledge base that integrates nomenclature information with specimens, culture collections and herbaria/fungaria, publications and taxonomists, and represents a summary of the history and recent advances in fungal taxonomy. Published fungal names are categorized based on well-accepted nomenclature rules and can be readily searched with different keywords and strategies. In combination with a standardized name checking tool and a sequence alignment-based identification package, FN makes the registration and typification of nomenclatural novelties of fungi convenient and accurate.