bluuebunny/crossref_metadata_2025_split huggingface dataset:
Signatures of gas flows – II. Connecting the kinematics of the multiphase circumgalactic medium to galaxy rotation
Authors: Nateghi Hasti , Kacprzak Glenn G , Nielsen Nikole M , Sameer  , Murphy Michael T , Churchill Christopher W , Charlton Jane C 
Published: September 2024

ABSTRACT
The multiphase circumgalactic medium (CGM) hosts critical processes that affect galaxy evolution such as accretion and outflows. We searched for evidence of these phenomena by using the EW co-rotation fraction ($f_{\rm EWcorot}$) to study the kinematic connection between the multiphase CGM and host galaxy rotation. We examined CGM absorption from Hubble Space Telescope /Cosmic Origins Spectrograph (including, but not limited to, Si ii, C ii, Si iii, C iii, and O vi) within $21\le D\le ~276$ kpc of 27 galaxies. We find the median $f_{\rm EWcorot}$ for all ions is consistent within errors and the $f_{\rm EWcorot}$ increases with increasing N$({{{\rm H} \rm{\small I}}})$. The $f_{\rm EWcorot}$ of lower ionization gas decreases with increasing $D/R_{\rm vir}$, while O vi and H i are consistent with being flat. The $f_{\rm EWcorot}$ varies minimally as a function of azimuthal angle and is similar for all ions at a fixed azimuthal angle. The larger number of O vi detections enabled us to investigate where the majority of co-rotating gas is found. Highly co-rotating O vi primarily resides along the galaxies’ major axis. Looking at the $f_{\rm EWcorot}$ as a function of ionization potential (${{\rm d}{({f_{\rm EWcorot}})}}/{{\rm d}{(\rm eV)}}$), we find a stronger co-rotation signature for lower ionization gas. There are suggestions of a connection between the CGM metallicity and major axis co-rotation where low-ionization gas with higher $f_{\rm EWcorot}$ exhibits lower metallicity and may trace large-scale filamentary inflows. Higher ionization gas with higher $f_{\rm EWcorot}$ exhibits higher metallicity and may instead trace co-planar recycled gas accretion. Our results stress the importance of comparing absorption originating from a range of ionization phases to differentiate between various gas flow scenarios.
McFine: python-based Monte Carlo multicomponent hyperfine structure fitting
Authors: Williams Thomas G , Watkins Elizabeth J 
Published: September 2024

ABSTRACT
Modelling complex line emission in the interstellar medium (ISM) is a degenerate high-dimensional problem. Here, we present McFine, a tool for automated multicomponent fitting of emission lines with complex hyperfine structure, in a fully automated way. We use Markov chain Monte Carlo (MCMC) to efficiently explore the complex parameter space, allowing for characterizing model denegeracies. This tool allows for both local thermodynamic equilibrium (LTE) and radiative-transfer (RT) models. McFine can fit individual spectra and data cubes, and for cubes encourage spatial coherence between neighbouring pixels. It is also built to fit the minimum number of distinct components, to avoid overfitting. We have carried out tests on synthetic spectra, where in around 90 per cent of cases it fits the correct number of components, otherwise slightly fewer components. Typically, $T_{\rm ex}$ is overestimated and $\tau$ underestimated, but accurate within the estimated uncertainties. The velocity and line widths are recovered with extremely high accuracy, however. We verify McFine by applying to a large Atacama Large Millimeter/submillimeter Array (ALMA) N$_2$H$^+$ mosaic of an high-mass star forming region, G316.75−00.00. We find a similar quality of fit to our synthetic tests, aside from in the active regions forming O-stars, where the assumptions of Gaussian line profiles or LTE may break down. To show the general applicability of this code, we fit CO(J = 2-1) observations of NGC 3627, a nearby star-forming galaxy, again obtaining excellent fit quality. McFine provides a fully automated way to analyse rich data sets from interferometric observations, is open source, and pip-installable.
Using neural network models to estimate stellar ages from lithium equivalent widths: an eagles expansion
Authors: Weaver G , Jeffries R D , Jackson R J 
Published: September 2024

ABSTRACT
We present an artificial neural network (ANN) model of photospheric lithium depletion in cool stars ($3000\lt T_{\rm eff}/{\rm K} \lt 6500$), producing estimates and probability distributions of age from $^7$Li 6708 Å equivalent width (LiEW) and effective temperature data inputs. The model is trained on the same sample of 6200 stars from 52 open clusters, observed in the Gaia-ESO spectroscopic survey, and used to calibrate the previously published analytical eagles model, with ages 2–6000 Myr and $-0.3 \lt $ [Fe/H] $\lt 0.2$. The additional flexibility of the ANN provides some improvements, including better modelling of the ‘lithium dip’ at ages $\lt 50$ Myr and $T_{\rm eff}\sim 3500$ K, and of the intrinsic dispersion in LiEW at all ages. Poor age discrimination is still an issue at ages &gt;1 Gyr, confirming that additional modelling flexibility is not sufficient to fully represent the LiEW–age–T$_{\text{eff}}$ relationship, and suggesting the involvement of further astrophysical parameters. Expansion to include such parameters–rotation, accretion, and surface gravity–is discussed, and the use of an ANN means these can be more easily included in future iterations, alongside more flexible functional forms for the LiEW dispersion. Our methods and ANN model are provided in an updated version 2.0 of the eagles software.
The PIPER survey. II. The globular cluster systems of low surface brightness galaxies in the Perseus cluster
Authors: Janssens Steven R , Forbes Duncan A , Romanowsky Aaron J , Gannon Jonah , Pfeffer Joel , Couch Warrick J , Brodie Jean P , Harris William E , Durrell Patrick R , Bekki Kenji 
Published: September 2024

ABSTRACT
We present Hubble Space Telescope ACS/WFC and WFC3/UVIS imaging for a sample of 50 low-surface brightness (LSB) galaxies in the $\sim 10^{15}$ M$_{\odot }$ Perseus cluster, which were originally identified in ground-based imaging. We measure the structural properties of these galaxies and estimate the total number of globular clusters (GCs) they host. Around half of our sample galaxies meet the strict definition of an ultra-diffuse galaxy (UDG), while the others are UDG-like but are either somewhat more compact or slightly brighter. A small number of galaxies reveal systems with many tens of GCs, rivalling some of the richest GC systems known around UDGs in the Coma cluster. We find the sizes of rich GC systems, in terms of their half-number radii, extending to $\sim$1.2 times the half-light radii of their host galaxy on average. The mean colours of the GC systems are the same, within the uncertainties, as those of their host galaxy stars. This suggests that GCs and galaxy field stars may have formed at the same epoch from the same enriched gas. It may also indicate a significant contribution from disrupted GCs to the stellar component of the host galaxy as might be expected in the ‘failed galaxy’ formation scenario for UDGs.
Prospect of precision cosmology and testing general relativity using binary black holes – galaxies cross-correlation
Authors: Afroz Samsuzzaman , Mukherjee Suvodip 
Published: September 2024

ABSTRACT
Modified theories of gravity predict deviations from general relativity (GR) in the propagation of gravitational waves (GWs) across cosmological distances. A key prediction is that the GW luminosity distance will vary with redshift, differing from the electromagnetic (EM) luminosity distance due to varying effective Planck mass. We introduce a model-independent, data-driven approach to explore these deviations using multimessenger observations of dark standard sirens [binary black holes (BBH)]. By combining GW luminosity distance measurements from dark sirens with baryon acoustic oscillation measurements, BBH redshifts inferred from cross-correlation with spectroscopic or photometric galaxy surveys, and sound horizon measurements from the cosmic microwave background, we can make a data-driven test of GR (jointly with the Hubble constant) as a function of redshift. Using the multimessenger technique with the spectroscopic DESI galaxy survey, we achieve precise measurements of deviations in the effective Planck mass variation with redshift. For the Cosmic Explorer and Einstein Telescope (CEET), the best precision is approximately 3.6 per cent, and for LIGO–Virgo–KAGRA (LVK), it is 7.4 per cent at a redshift of $\rm {z = 0.425}$. Additionally, we can measure the Hubble constant with a precision of about 1.1 per cent from CEET and 7 per cent from LVK over 5 yr of observation with a 75 per cent duty cycle. We also explore the potential of cross-correlation with photometric galaxy surveys from the Rubin Observatory, extending measurements up to a redshift of $\rm {z \sim 2.5}$. This approach can reveal potential deviations from models affecting GW propagation using numerous dark standard sirens in synergy with DESI and the Rubin Observatory.
One-point statistics in various cosmic environments in the presence of massive neutrinos
Authors: Khoshtinat Mohadese , Hatamnia Hossein , Baghram Shant 
Published: September 2024

ABSTRACT
Studying the structures (haloes and galaxies) within the cosmic environments (void, sheet, filament, and node) where they reside is an ongoing attempt in cosmological studies. The link between the properties of structures and the cosmic environments may help to unravel the nature of the dark sector of the Universe. In this paper, we study the cosmic web environments from the spatial pattern perspective in the context of Lambda cold dark matter ($\Lambda$CDM) and $\nu \Lambda$CDM as an example of an extension to the vanilla model. To do this, we use the T-web classification method and classify the cosmic environments for the catalogues from the gevolution N-body simulations for $\Lambda$CDM and $\nu \Lambda$CDM cosmology. Then, we compute the first nearest neighbour cumulative distribution function, spherical contact cumulative distribution function, and $J$-function for every cosmic environment. In the context of the standard model, the results indicate that these functions can differentiate the various cosmic environments. In association with distinguishing between extensions of the standard model of cosmologies, these functions within the cosmic environment seem beneficial as a complementary probe.
Vertical shear instability with partially reflecting boundary conditions
Authors: Wu Yuzi , Yu Cong , Cui Can 
Published: September 2024

ABSTRACT
The vertical shear instability (VSI) is widely believed to be effective in driving turbulence in protoplanetary discs (PPDs). Prior studies on VSI exclusively exploit the reflecting boundary conditions (BCs) at the disc surfaces. VSI depends critically on the boundary behaviours of waves at the disc surfaces. We extend earlier studies by performing a comprehensive numerical analysis of VSI with partially reflecting BCs for both the axisymmetric and non-axisymmetric unstable VSI modes. We find that the growth rates of the unstable modes diminish when the outgoing component of the flow is greater than the incoming one for high-order body modes. When the outgoing wave component dominates, the growth of VSI is notably suppressed. We find that the non-axisymmetric modes are unstable and they grow at a rate that decreases with the azimuthal wavenumber. The different BCs at the lower and upper disc surfaces naturally lead to non-symmetric modes relative to the disc mid-plane. The potential implications of our studies for further understanding planetary formation and evolution in PPDs are also briefly discussed.
Why Naturalism? Translating Homo Natura Back into Nietzsche’s Text
Authors: Janaway Christopher 
Published: September 2024

ABSTRACT
This article questions a common reading of Section 230 of Beyond Good and Evil as containing a canonical statement of Nietzsche’s naturalism. The section cannot be read simply as the programmatic statement of an investigative task, and is relatively vague as to its nature. Nietzsche’s aim is aporetic. He presents the naturalist task as involving mental self-cruelty and a struggle with unconscious vanity, suggesting that thinkers have found no way to justify why they choose this task, unless they invoke self-descriptions which are false and belong to a metaphysical conception of truth and inquiry that naturalism must resist. In the Genealogy, Nietzsche revisits this theme and announces his task as that of calling into question these justifications of naturalist inquiry.
Nietzsche’s Curse on Christianity
Authors: Tevenar Gudrun von 
Published: September 2024

Abstract
This paper explores background features in the development of Nietzsche’s criticism of Christianity by following him through what I have termed his conventional stage, his critical stage, and his stage of outrage. Next to examining some of his various criticisms during those stages, I also ask what the challenges were to which these criticisms responded and why Nietzsche eventually responded to these challenges with outrage. Outrage towards Christianity is unmistakably expressed in Nietzsche’s late work The Antichrist: A Curse on Christianity. To understand Nietzsche’s outrage better we need to explore the role of ‘Antichrist’ in the title of that work and the meaning of ‘curse’ in its subtitle.
Nanoscale elemental and morphological imaging of nitrogen-fixing cyanobacteria
Authors: Duersch Bobby G , Soini Steven A , Luo Yanqi , Liu Xiaoyang , Chen Si , Merk Vivian M 
Published: September 2024

Abstract
Nitrogen-fixing cyanobacteria bind atmospheric nitrogen and carbon dioxide using sunlight. This experimental study focused on a laboratory-based model system, Anabaena sp., in nitrogen-depleted culture. When combined nitrogen is scarce, the filamentous prokaryotes reconcile photosynthesis and nitrogen fixation by cellular differentiation into heterocysts. To better understand the influence of micronutrients on cellular function, 2D and 3D synchrotron X-ray fluorescence mappings were acquired from whole biological cells in their frozen-hydrated state at the Bionanoprobe, Advanced Photon Source. To study elemental homeostasis within these chain-like organisms, biologically relevant elements were mapped using X-ray fluorescence spectroscopy and energy-dispersive X-ray microanalysis. Higher levels of cytosolic K+, Ca2+, and Fe2+ were measured in the heterocyst than in adjacent vegetative cells, supporting the notion of elevated micronutrient demand. P-rich clusters, identified as polyphosphate bodies involved in nutrient storage, metal detoxification, and osmotic regulation, were consistently co-localized with K+ and occasionally sequestered Mg2+, Ca2+, Fe2+, and Mn2+ ions. Machine-learning-based k-mean clustering revealed that P/K clusters were associated with either Fe or Ca, with Fe and Ca clusters also occurring individually. In accordance with XRF nanotomography, distinct P/K-containing clusters close to the cellular envelope were surrounded by larger Ca-rich clusters. The transition metal Fe, which is a part of nitrogenase enzyme, was detected as irregularly shaped clusters. The elemental composition and cellular morphology of diazotrophic Anabaena sp. was visualized by multimodal imaging using atomic force microscopy, scanning electron microscopy, and fluorescence microscopy. This paper discusses the first experimental results obtained with a combined in-line optical and X-ray fluorescence microscope at the Bionanoprobe.
Using nucleolytic toxins as restriction enzymes enables new RNA applications
Authors: Rothweiler Ulli , Gundesø Sigurd Eidem , Mikalsen Emma Wu , Svenning Steingrim , Singh Mahavir , Combes Francis , Pettersson Frida J , Mangold Antonia , Piotrowski Yvonne , Schwab Felix , Lanes Olav , Striberny Bernd Ketelsen 
Published: September 2024

Abstract
Over the past five decades, DNA restriction enzymes have revolutionized biotechnology. While these enzymes are widely used in DNA research and DNA engineering, the emerging field of RNA and mRNA therapeutics requires sequence-specific RNA endoribonucleases. Here, we describe EcoToxN1, a member of the type III toxin-antitoxin family of sequence-specific RNA endoribonucleases, and its use in RNA and mRNA analysis. This enzyme recognizes a specific pentamer in a single-stranded RNA and cleaves the RNA within this sequence. The enzyme is neither dependent on annealing of guide RNA or DNA oligos to the template nor does it require magnesium. Furthermore, it performs over a wide range of temperatures. With its unique functions and characteristics, EcoToxN1 can be classified as an RNA restriction enzyme. EcoToxN1 enables new workflows in RNA analysis and biomanufacturing, meeting the demand for faster, cheaper, and more robust analysis methods.
Mei5–Sae3 stabilizes Dmc1 nucleating clusters for efficient Dmc1 assembly on RPA-coated single-stranded DNA
Authors: Wei Chin-Dian , Chang Hao-Yen , Lu Chia-Hua , Chang Chih-Chun , Furukohri Asako , Mwaniki Stephen , Shinohara Akira , Chi Peter , Li Hung-Wen 
Published: September 2024

Abstract
Interhomolog recombination in meiosis requires a meiosis-specific recombinase, Dmc1. In Saccharomyces cerevisiae, the Mei5–Sae3 complex facilitates the loading of Dmc1 onto the replication protein A (RPA)-coated single-stranded DNA (ssDNA) to form nucleoprotein filaments. In vivo, Dmc1 and Mei5–Sae3 are interdependent in their colocalization on the chromosomes. However, the mechanistic role of Mei5–Sae3 in mediating Dmc1 activity remains unclear. We used single-molecule fluorescence resonance energy transfer and colocalization single-molecule spectroscopy experiments to elucidate how Mei5–Sae3 stimulates Dmc1 assembly on ssDNA and RPA-coated ssDNA. We showed that Mei5–Sae3 stabilized Dmc1 nucleating clusters with two to three molecules on naked DNA by preferentially reducing Dmc1 dissociation rates. Mei5–Sae3 also stimulated Dmc1 assembly on RPA-coated DNA. Using green fluorescent protein-labeled RPA, we showed the coexistence of an intermediate with Dmc1 and RPA on ssDNA before RPA dissociation. Moreover, the displacement efficiency of RPA depended on Dmc1 concentration, and its dependence was positively correlated with the stability of Dmc1 clusters on short ssDNA. These findings suggest a molecular model that Mei5–Sae3 mediates Dmc1 binding on RPA-coated ssDNA by stabilizing Dmc1 nucleating clusters, thus altering RPA dynamics on DNA to promote RPA dissociation.
Reconstruction of a robust bacterial replication module
Authors: Wang Tao , He Fan , He Ting , Lin Chen , Guan Xin , Qin Zhongjun , Xue Xiaoli 
Published: September 2024

Abstract
Chromosomal DNA replication is a fundamental process of life, involving the assembly of complex machinery and dynamic regulation. In this study, we reconstructed a bacterial replication module (pRC) by artificially clustering 23 genes involved in DNA replication and sequentially deleting these genes from their naturally scattered loci on the chromosome of Escherichia coli. The integration of pRC into the chromosome, moving from positions farther away to close to the replication origin, leads to an enhanced efficiency in DNA synthesis, varying from lower to higher. Strains containing replication modules exhibited increased DNA replication by accelerating the replication fork movement and initiating chromosomal replication earlier in the replication cycle. The minimized module pRC16, containing only replisome and elongation encoding genes, exhibited chromosomal DNA replication efficiency comparable to that of pRC. The replication module demonstrated robust and rapid DNA replication, regardless of growth conditions. Moreover, the replication module is plug-and-play, and integrating it into Mb-sized extrachromosomal plasmids improves their genetic stability. Our findings indicate that DNA replication, being a fundamental life process, can be artificially reconstructed into replication functional modules. This suggests potential applications in DNA replication and the construction of synthetic modular genomes.
DrugMAP 2.0: molecular atlas and pharma-information of all drugs
Authors: Li Fengcheng , Mou Minjie , Li Xiaoyi , Xu Weize , Yin Jiayi , Zhang Yang , Zhu Feng 
Published: September 2024

Abstract
The escalating costs and high failure rates have decelerated the pace of drug development, which amplifies the research interests in developing combinatorial/repurposed drugs and understanding off-target adverse drug reaction (ADR). In other words, it is demanded to delineate the molecular atlas and pharma-information for the combinatorial/repurposed drugs and off-target interactions. However, such invaluable data were inadequately covered by existing databases. In this study, a major update was thus conducted to the DrugMAP, which accumulated (a) 20831 combinatorial drugs and their interacting atlas involving 1583 pharmacologically important molecules; (b) 842 repurposed drugs and their interacting atlas with 795 molecules; (c) 3260 off-targets relevant to the ADRs of 2731 drugs and (d) various types of pharmaceutical information, including diverse ADMET properties, versatile diseases, and various ADRs/off-targets. With the growing demands for discovering combinatorial/repurposed therapies and the rapidly emerging interest in AI-based drug discovery, DrugMAP was highly expected to act as an indispensable supplement to existing databases facilitating drug discovery, which was accessible at: https://idrblab.org/drugmap/.
IRescue: uncertainty-aware quantification of transposable elements expression at single cell level
Authors: Polimeni Benedetto , Marasca Federica , Ranzani Valeria , Bodega Beatrice 
Published: September 2024

Abstract
Transposable elements (TEs) are mobile DNA repeats known to shape the evolution of eukaryotic genomes. In complex organisms, they exhibit tissue-specific transcription. However, understanding their role in cellular diversity across most tissues remains a challenge, when employing single-cell RNA sequencing (scRNA-seq), due to their widespread presence and genetic similarity. To address this, we present IRescue (Interspersed Repeats single-cell quantifier), a software capable of estimating the expression of TE subfamilies at the single-cell level. IRescue incorporates a unique UMI deduplication algorithm to rectify sequencing errors and employs an Expectation-Maximization procedure to effectively redistribute the counts of multi-mapping reads. Our study showcases the precision of IRescue through analysis of both simulated and real single cell and nuclei RNA-seq data from human colorectal cancer, brain, skin aging, and PBMCs during SARS-CoV-2 infection and recovery. By linking the expression patterns of TE signatures to specific conditions and biological contexts, we unveil insights into their potential roles in cellular heterogeneity and disease progression.