bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of Streptomyces species CS-62, a novel producer of the Acinetobacter baumannii selective antibiotic factumycin
Authors: Alwali Amir Y , Santos Diane , Aguilar César , Birch Audrey , Rodriguez-Orduña Lorena , Roberts Carson B , Modi Ramya , Licona-Cassani Cuauhtemoc , Parkinson Elizabeth I 
Published: April 2024

Abstract
Narrow-spectrum antibiotics are of great interest given their ability to spare the microbiome and decrease widespread antibiotic resistance compared to broad-spectrum antibiotics. Herein, we screened an in-house library of Actinobacteria strains for selective activity against Acinetobacter baumannii and successfully identified Streptomyces sp. CS-62 as a producer of a natural product with this valuable activity. Analysis of the cultures via high-resolution mass spectrometry and tandem mass spectrometry, followed by comparison with molecules in the Natural Product Atlas and the Global Natural Products Social Molecular Networking platform, suggested a novel natural product. Genome mining analysis initially supported the production of a novel kirromycin derivative. Isolation and structure elucidation via mass spectrometry and Nuclear Magnetic Resonance (NMR) analyses revealed that the active natural product was the known natural product factumycin, exposing omissions and errors in the consulted databases. While public databases are generally very useful for avoiding rediscovery of known molecules, rediscovery remains a problem due to public databases either being incomplete or having errors that result in failed dereplication. Overall, the work describes the ongoing problem of dereplication and the continued need for public database curation.
Hydrodynamical simulations of merging galaxy clusters: giant dark matter particle colliders, powered by gravity
Authors: Sirks Ellen L , Harvey David , Massey Richard , Oman Kyle A , Robertson Andrew , Frenk Carlos , Everett Spencer , Gill Ajay S , Lagattuta David , McCleary Jacqueline 
Published: April 2024

ABSTRACT
Terrestrial particle accelerators collide charged particles, then watch the trajectory of outgoing debris – but they cannot manipulate dark matter. Fortunately, dark matter is the main component of galaxy clusters, which are continuously pulled together by gravity. We show that galaxy cluster mergers can be exploited as enormous, natural dark matter colliders. We analyse hydrodynamical simulations of a universe containing self-interacting dark matter (SIDM) in which all particles interact via gravity, and dark matter particles can also scatter off each other via a massive mediator. During cluster collisions, SIDM spreads out and lags behind cluster member galaxies. Individual systems can have quirky dynamics that makes them difficult to interpret. Statistically, however, we find that the mean or median of dark matter’s spatial offset in many collisions can be robustly modelled, and is independent of our viewing angle and halo mass even in collisions between unequal-mass systems. If the SIDM cross-section were σ/m = 0.1 cm2 g−1 = 0.18 barn GeV−1, the ‘bulleticity’ lag would be ∼5 per cent that of gas due to ram pressure, and could be detected at 95 per cent confidence level in weak lensing observations of ∼100 well-chosen clusters.
Maser flares driven by isothermal shock waves
Authors: Gray M D , Etoka S , Pimpanuwat B , Richards A M S 
Published: April 2024

ABSTRACT
We use 3D computer modelling to investigate the time-scales and radiative output from maser flares generated by the impact of shock waves on astronomical unit-scale clouds in interstellar and star-forming regions, and in circumstellar regions in some circumstances. Physical conditions are derived from simple models of isothermal hydrodynamic (single-fluid) and C-type (ionic and neutral fluid) shock waves, and based on the ortho-H2O 22-GHz transition. Maser saturation is comprehensively included, and we find that the most saturated maser inversions are found predominantly in the shocked material. We study the effect on the intensity, flux density, and duration of flares of the following parameters: the pre-shock level of saturation, the observer’s viewpoint, and the shock speed. Our models are able to reproduce observed flare rise times of a few times 10 d, specific intensities of up to 105 times the saturation intensity and flux densities of order 100(R/d)2 Jy from a source of radius R astronomical units at a distance of d kiloparsec. We found that flares from C-type shocks are approximately five times more likely to be seen by a randomly placed observer than flares from hydrodynamically shocked clouds of similar dimensions. We computed intrinsic beaming patterns of the maser emission, finding substantial extension of the pattern parallel to the shock front in the hydrodynamic models. Beaming solid angles for hydrodynamic models can be as small as 1.3 × 10−5 sr, but are an order of magnitude larger for C-type models.
Dense stellar clump formation driven by strong quasar winds in the FIRE cosmological hydrodynamic simulations
Authors: Mercedes-Feliz Jonathan , Anglés-Alcázar Daniel , Oh Boon Kiat , Hayward Christopher C , Cochrane Rachel K , Richings Alexander J , Faucher-Giguère Claude-André , Wellons Sarah , Terrazas Bryan A , Moreno Jorge , Su Kung Yi , Hopkins Philip F 
Published: April 2024

ABSTRACT
We investigate the formation of dense stellar clumps in a suite of high-resolution cosmological zoom-in simulations of a massive, star-forming galaxy at z ∼ 2 under the presence of strong quasar winds. Our simulations include multiphase ISM physics from the Feedback In Realistic Environments (FIRE) project and a novel implementation of hyper-refined accretion disc winds. We show that powerful quasar winds can have a global negative impact on galaxy growth while in the strongest cases triggering the formation of an off-centre clump with stellar mass ${\rm M}_{\star }\sim 10^{7}\, {\rm M}_{\odot }$, effective radius ${\rm R}_{\rm 1/2\, \rm Clump}\sim 20\, {\rm pc}$, and surface density $\Sigma _{\star } \sim 10^{4}\, {\rm M}_{\odot }\, {\rm pc}^{-2}$. The clump progenitor gas cloud is originally not star-forming, but strong ram pressure gradients driven by the quasar winds (orders of magnitude stronger than experienced in the absence of winds) lead to rapid compression and subsequent conversion of gas into stars at densities much higher than the average density of star-forming gas. The AGN-triggered star-forming clump reaches ${\rm SFR} \sim 50\, {\rm M}_{\odot }\, {\rm yr}^{-1}$ and $\Sigma _{\rm SFR} \sim 10^{4}\, {\rm M}_{\odot }\, {\rm yr}^{-1}\, {\rm kpc}^{-2}$, converting most of the progenitor gas cloud into stars in ∼2 Myr, significantly faster than its initial free-fall time and with stellar feedback unable to stop star formation. In contrast, the same gas cloud in the absence of quasar winds forms stars over a much longer period of time (∼35 Myr), at lower densities, and losing spatial coherency. The presence of young, ultra-dense, gravitationally bound stellar clumps in recently quenched galaxies could thus indicate local positive feedback acting alongside the strong negative impact of powerful quasar winds, providing a plausible formation scenario for globular clusters.
Mapping the intracluster medium in the era of high-resolution X-ray spectroscopy
Authors: Zhang Congyao , Zhuravleva Irina , Markevitch Maxim , ZuHone John , Mernier François , Biffi Veronica , Bogdán Ákos , Chakraborty Priyanka , Churazov Eugene , Dolag Klaus , Ettori Stefano , Forman William R , Hernquist Lars , Jones Christine , Khabibullin Ildar , Kilbourne Caroline , Kraft Ralph , Lau Erwin T , Lin Sheng-Chieh , Nagai Daisuke , Nelson Dylan , Ogorzałek Anna , Rasia Elena , Sarkar Arnab , Simionescu Aurora , Su Yuanyuan , Vogelsberger Mark , Walker Stephen 
Published: April 2024

ABSTRACT
High-resolution spectroscopy in soft X-rays will open a new window to map multiphase gas in galaxy clusters and probe physics of the intracluster medium (ICM), including chemical enrichment histories, circulation of matter and energy during large-scale structure evolution, stellar and black hole feedback, halo virialization, and gas mixing processes. An eV-level spectral resolution, large field of view, and effective area are essential to separate cluster emissions from the Galactic foreground and efficiently map the cluster outskirts. Several mission concepts that meet these criteria have been proposed recently, e.g. LEM, HUBS, and Super DIOS. This theoretical study explores what information on ICM physics could be recovered with such missions and the associated challenges. We emphasize the need for a comprehensive comparison between simulations and observations to interpret the high-resolution spectroscopic observations correctly. Using Line Emission Mapper (LEM) characteristics as an example, we demonstrate that it enables the use of soft X-ray emission lines (e.g. O vii/viii and Fe-L complex) from the cluster outskirts to measure the thermodynamic, chemical, and kinematic properties of the gas up to r200 and beyond. By generating mock observations with full backgrounds, analysing their images/spectra with observational approaches, and comparing the recovered characteristics with true ones from simulations, we develop six key science drivers for future missions, including the exploration of multiphase gas in galaxy clusters (e.g. temperature fluctuations, phase-space distributions), metallicity, ICM gas bulk motions and turbulence power spectra, ICM-cosmic filament interactions, and advances for cluster cosmology.
Investigating cosmic homogeneity using multifractal analysis of the SDSS-IV eBOSS DR16 quasar catalogue
Authors: Goyal Priya , Malik Sunil , Yadav Jaswant K , Seshadri T R 
Published: April 2024

ABSTRACT
We analyse the volume-limited subsamples extracted from the sixteenth data release of the Sloan Digital Sky Survey-IV (SDSS-IV) eBOSS quasar survey spanning a redshift interval of 0.8 &lt; z &lt; 2.2, to estimate the scale of transition to homogeneity in the Universe. The multifractal analysis used for this purpose considers the scaling behaviour of different moments of quasar distribution in different density environments. This analysis gives the spectrum of generalized dimension Dq, where positive values of q characterize the scaling behaviour in overdense regions and the negative ones in underdense regions. We expect fractal correlation dimension Dq(r) = 3, for a homogeneous, random point distribution in 3-Dimensions. The fractal correlation dimension Dq(r), corresponding to q = 2 obtained in our study stabilizes in the range (2.8–2.9) for scales r &gt; 80 h−1 Mpc. The observed quasar distribution shows consistency with the simulated mock data and the random distribution of quasars within one sigma. Further, the generalized dimension spectrum Dq(r) also reveals transition to homogeneity beyond &gt;110 h−1 Mpc, and the dominance of clustering at small scales r &lt; 80 h−1 Mpc. Consequently, our study provides strong evidence for the homogeneity in SDSS quasar distribution, offering insights into large-scale structure properties and, thus can play a pivotal role in scrutinizing the clustering properties of quasars and its evolution in various upcoming surveys such as Dark Energy Spectroscopic Instrument and Extremely Large Telescope.
Effects of particle creation rate in two-fluid interacting cosmologies
Authors: Banerjee Trishit , Mandal Goutam , Biswas Atreyee , Biswas Sujay Kr 
Published: April 2024

ABSTRACT
In this work, a two-fluid interacting model in a flat FLRW universe has been studied considering particle creation mechanism with a particular form of particle creation rate $\Gamma =\Gamma _0 H+\frac{\Gamma _1}{H}$ from different aspects. Statistical analysis with a combined data set of SNe Ia (Supernovae Type Ia) and Hubble data is performed to achieve the best-fitting values of the model parameters, and the model is compatible with current observational data. We also perform a dynamical analysis of this model to get an overall qualitative description of the cosmological evolution by converting the governing equations into a system of ordinary differential equations considering a proper transformation of variables. We find some non-isolated sets of critical points, among which some usually are normally hyperbolic sets of points that describe the present acceleration of the universe dominated by dark energy mimicking cosmological constant or phantom fluid. Scaling solutions are also obtained from this analysis, and they can alleviate the coincidence problem successfully. Statefinder diagnosis is also carried out for this model to compare it with the ΛCDM, and any other dark energy models byfinding various statefinder parameters. Finally, the thermodynamic analysis shows that the generalized second law of thermodynamics is valid in an irreversible thermodynamic context.
Beyond the rings: Polar ring galaxy NGC 4262 and its globular cluster system
Authors: Akhil Krishna R , Kartha Sreeja S , Mathew Blesson 
Published: April 2024

ABSTRACT
In the context of the hierarchical model of galaxy evolution, polar ring galaxies (PRGs) are considered the intermediate phase between ongoing mergers and quiescent galaxies. This study explores the globular cluster system (GCS) and its properties in the nearest PRG, NGC4262, serving as a pilot investigation to study GCS in nearby PRGs. We utilize wide and deep-field observations of the CFHT as part of the NGVS to investigate the GCS of NGC4262. We presented the first optical image of NGC4262 with an optically faint ring component. The photometric analysis of the GCS displays a distinct colour bimodality. We estimate the total number of GCs for NGC4262 to be 266 $\pm$ 16 GCs with a specific frequency of 4.2 $\pm$ 0.8 and a specific mass of 0.23 $\pm$ 0.01, which is relatively high compared to other galaxies of similar mass and environmental conditions. The spatial and azimuthal distributions of subpopulations reveal strong evidence of previous interactions within the host galaxy. The colour distribution of GCS in NGC4262 shows a gradient of –0.05 $\pm$ 0.01 within 5.5$^\prime$, supporting the notion of past interactions and evolutionary transitions. PRG NGC4262 conforms to the overall trend of the GCS mass with respect to the halo mass. Furthermore, our investigation of the global scaling relations between GCS and host galaxy parameters provides further support for the hypothesis that PRGs are an intermediate phase connecting ongoing mergers and quiescent galaxies.
Observation of the L5 Kordylewski dust cloud with a portable imaging polarimetric telescope in the Namibian Khomas Highland
Authors: Slíz-Balogh Judit , Mádai Attila , Sári Pál , Barta András , Horváth Gábor 
Published: April 2024

ABSTRACT
The Kordylewski dust clouds (KDCs) around the L5 and L4 Lagrange points of the Earth–Moon system have been first observed by imaging polarimetry in 2017 and 2022 in a Hungarian astronomical observatory. Due to the non-ideal (almost always hazy, aerosol-polluted) astroclimate of Hungary and the extremely low intensity of dust-scattered sunlight, the polarimetric hunt after both KDCs lasted 2–7 yr. Waiting for cloud- and aerosol-free atmosphere and appropriate astronomical conditions (e.g. moonless sky with above-horizon KDC) in our Hungarian observatory takes a long time. Thus, our goal was to build a portable imaging polarimetric, wide field-of-view telescope and use it in the very good astroclimate of the Isabis Astro Lodge in the Khomas Highland of Namibia. Our long term aim is to study the dynamics of KDCs with this instrument in Namibian 1-month astropolarimetric campaigns in the next decade. In this work, we describe our portable imaging polarimetric telescope and present our first KDC observation achieved with it in Namibia during our 4-week astropolarimetric campaign between 2023 July 18 and August 15. We conclude that our portable polarimetric telescope functions well. Using it in Namibia, we corroborated the existence of the L5 KDC, the polarization characteristics (polarization degree and angle) of which refer to an inhomogeneous dust cloud composed of several particle agglomerations that scatter and linearly polarize the illuminating sunlight.
Transit spectroscopy of K2-33b with subaru/IRD: Spin-Orbit alignment and tentative atmospheric helium
Authors: Hirano Teruyuki , Gaidos Eric , Harakawa Hiroki , Hodapp Klaus W , Kotani Takayuki , Kudo Tomoyuki , Kurokawa Takashi , Kuzuhara Masayuki , Mann Andrew W , Nishikawa Jun , Omiya Masashi , Serizawa Takuma , Tamura Motohide , Thao Pa Chia , Ueda Akitoshi , Vievard Sebastien 
Published: April 2024

ABSTRACT
Exoplanets in their infancy are ideal targets to probe the formation and evolution history of planetary systems, including the planet migration and atmospheric evolution and dissipation. In this paper, we present spectroscopic observations and analyses of two planetary transits of K2-33b, which is known to be one of the youngest transiting planets (age ≈ 8–11 Myr) around a pre-main-sequence M-type star. Analysing K2-33’s near-infrared spectra obtained by the IRD instrument on Subaru, we investigate the spin-orbit angle and transit-induced excess absorption for K2-33b. We attempt both classical modelling of the Rossiter–McLaughlin (RM) effect and Doppler-shadow analyses for the measurements of the projected stellar obliquity, finding a low angle of $\lambda =-6_{-58}^{+61}$ deg (for RM analysis) and $\lambda =-10_{-24}^{+22}$ deg (for Doppler-shadow analysis). In the modelling of the RM effect, we allow the planet-to-star radius ratio to float freely to take into account the possible smaller radius in the near infrared, but the constraint we obtain ($R_p/R_s=0.037_{-0.017}^{+0.013}$) is inconclusive due to the low radial-velocity precision. Comparison spectra of K2-33 of the 1083 nm triplet of metastable ortho-He I obtained in and out of the 2021 transit reveal excess absorption that could be due to an escaping He-rich atmosphere. Under certain conditions on planet mass and stellar XUV emission, the implied escape rate is sufficient to remove an Earth-mass H/He in ∼1 Gyr, transforming this object from a Neptune to a super-Earth.
Computationally Efficient Demographic History Inference from Allele Frequencies with Supervised Machine Learning
Authors: Tran Linh N , Sun Connie K , Struck Travis J , Sajan Mathews , Gutenkunst Ryan N 
Published: April 2024

Abstract
Inferring past demographic history of natural populations from genomic data is of central concern in many studies across research fields. Previously, our group had developed dadi, a widely used demographic history inference method based on the allele frequency spectrum (AFS) and maximum composite-likelihood optimization. However, dadi’s optimization procedure can be computationally expensive. Here, we present donni (demography optimization via neural network inference), a new inference method based on dadi that is more efficient while maintaining comparable inference accuracy. For each dadi-supported demographic model, donni simulates the expected AFS for a range of model parameters then trains a set of Mean Variance Estimation neural networks using the simulated AFS. Trained networks can then be used to instantaneously infer the model parameters from future genomic data summarized by an AFS. We demonstrate that for many demographic models, donni can infer some parameters, such as population size changes, very well and other parameters, such as migration rates and times of demographic events, fairly well. Importantly, donni provides both parameter and confidence interval estimates from input AFS with accuracy comparable to parameters inferred by dadi’s likelihood optimization while bypassing its long and computationally intensive evaluation process. donni’s performance demonstrates that supervised machine learning algorithms may be a promising avenue for developing more sustainable and computationally efficient demographic history inference methods.
The structure assessment web server: for proteins, complexes and more
Authors: Waterhouse Andrew M , Studer Gabriel , Robin Xavier , Bienert Stefan , Tauriello Gerardo , Schwede Torsten 
Published: April 2024

Abstract
The ‘structure assessment’ web server is a one-stop shop for interactive evaluation and benchmarking of structural models of macromolecular complexes including proteins and nucleic acids. A user-friendly web dashboard links sequence with structure information and results from a variety of state-of-the-art tools, which facilitates the visual exploration and evaluation of structure models. The dashboard integrates stereochemistry information, secondary structure information, global and local model quality assessment of the tertiary structure of comparative protein models, as well as prediction of membrane location. In addition, a benchmarking mode is available where a model can be compared to a reference structure, providing easy access to scores that have been used in recent CASP experiments and CAMEO. The structure assessment web server is available at https://swissmodel.expasy.org/assess.
m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq
Authors: Ye Haokai , Li Tenglong , Rigden Daniel J , Wei Zhen 
Published: April 2024

Abstract
We present m6ACali, a novel machine-learning framework aimed at enhancing the accuracy of N6-methyladenosine (m6A) epitranscriptome profiling by reducing the impact of non-specific antibody enrichment in MeRIP-Seq. The calibration model serves as a genomic feature-based classifier that refines the identification of m6A sites, distinguishing those genuinely present from those that can be detected in in-vitro transcribed (IVT) control experiments. We find that m6ACali effectively identifies non-specific binding peaks reported by exomePeak2 and MACS2 in novel MeRIP-Seq datasets without the need for paired IVT controls. The model interpretation revealed that off-target antibody binding sites commonly occur at short exons and short mRNAs, originating from high read coverage regions that share the motif sequence with true m6A sites. We also reveal that the ML strategy can efficiently adjust differentially methylated peaks and other antibody-dependent, base-resolution m6A detection techniques. As a result, m6ACali offers a promising method for the universal enhancement of m6A profiles generated by MeRIP-Seq experiments, elevating the benchmark for omics-level m6A data integration.