bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection and genotyping of zoonotic microsporidia in the endangered Iberian lynx (Lynx pardinus)
Authors: Ávalos Gabriel , Caballero-Gómez Javier , Matas-Méndez Pablo , Castro-Scholten Sabrina , Jiménez-Martín Débora , Köster Pamela C , Santín Mónica , Bailo Begoña , Cano-Terriza David , González-Barrio David , Mateo Marta , García-Bocanegra Ignacio , Dashti Alejandro , Nájera Fernando , Carmena David 
Published: March 2024

Abstract
Microsporidia is a diverse group of obligate, intracellular, and spore-forming parasites that infect a wide range of animals. Among them, Enterocytozoon bieneusi and Encephalitozoon spp. are the most frequently reported species in humans. Limited information is available about the presence and molecular diversity of microsporidian species in the endangered Iberian lynx (Lynx pardinus). Presence of Enterocytozoon bieneusi and Encephalitozoon spp. was investigated by molecular methods in wild and captive Iberian lynxes from Spain. Overall, E. bieneusi was detected in 3.2% (8/251) of the animals examined. None of the samples tested were positive for Encephalitozoon spp. Four known (D, EbfelA, PigEBITS7, and Type IV) and a novel (named as LynxSpEb1) E. bieneusi genotypes were identified. All the genotypes found belonged to the zoonotic Group 1 of E. bieneusi. This study provides the first genotyping data of E. bieneusi in Iberian lynx in Spain. Our result indicate that the Iberian lynx does not seem to play a relevant role in the epidemiology of Encephalitozoon spp., and that this endangered felid is likely acting as spillover host rather than a true reservoir of E. bieneusi. Additional studies should be conducted to assess the impact of this parasite in the health status of the endangered Iberian lynx.
Cliff collapse on Comet 67P/Churyumov–Gerasimenko – II. Imhotep and Hathor
Authors: Davidsson Björn J R 
Published: March 2024

ABSTRACT
Cliff collapses on Comet 67P/Churyumov–Gerasimenko expose relatively pristine nucleus matter and offer rare opportunities to characterize ice-rich comet material. Here, Microwave Instrument for Rosetta Orbiter (MIRO) observations of two collapsed or crumbling cliffs in the Imhotep and Hathor regions have been assembled. The empirical diurnal antenna temperature curves are analysed with thermophysical and radiative transfer models in order to place constraints on the physical properties and degrees of stratification in the near-surface material. The Imhotep site consists of an exposed dust/water-ice mixture with thermal inertia 100–$160\, \mathrm{J\, m^{-2}\, K^{-1}\, s^{-1/2}}$, having sublimating CO2 ice located $11\pm 4\, \mathrm{cm}$ below the surface. Its estimated age is consistent with an outburst observed on 2014 April 27–30. The Hathor site has a $0.8\pm 0.2\, \mathrm{cm}$ dust mantle, a thermal inertia of $40\pm 20\, \mathrm{J\, m^{-2}\, K^{-1}\, s^{-1/2}}$, no CO2 ice to within $1.0\, \mathrm{m}$ depth, and a mantle bulk density of $340\pm 80\, \mathrm{kg\, m^{-3}}$ that is higher than the theoretically expected $180\pm 10\, \mathrm{kg\, m^{-3}}$, suggesting that compression has taken place.
The bright black hole X-ray binary 4U 1543-47 during 2021 outburst. A clear state transition from super-Eddington to sub-Eddington accretion revealed by Insight-HXMT
Authors: Jin Pei , Zhang Guobao , Zhang Yuexin , Méndez Mariano , Qu Jinlu , Russell David M , Wang Jiancheng , Zhang Shuangnan , Yang Yi-Jung , Jia Shumei , Yang Zixu , Liu Hexin 
Published: March 2024

ABSTRACT
We present a detailed analysis of the observations with the Hard X-ray Modulation Telescope of the black hole X-ray transient 4U 1543-47 during its outburst in 2021. We find a clear state transition during the outburst decay of the source. Using previous measurements of the black hole mass and distance to the source, the source luminosity during this transition is close to the Eddington limit. The light curves before and after the transition can be fitted by two exponential functions with short (∼16 d) and long (∼130 d) decay time-scales, respectively. We detect strong reflection features in all observations that can be described with either the relxillns or reflionx_bb reflection models, both of which have a black-body incident spectrum. In the super-Eddington state, we observe a Comptonized component characterized by a low electron temperature of approximately 2.0 keV. We suggest that this component appears exclusively within the inner radiation-pressure-dominated region of the supercritical disc as a part of the intrinsic spectrum of the accretion disc itself. This feature vanishes as the source transitions into the sub-Eddington state. The emissivity index of the accretion disc in the reflection component is significantly different before and after the transition, ∼3.0–5.0 and ∼7.0–9.0 in the super- and sub-Eddington states, respectively. Based on the reflection geometry of returning disc radiation, the geometrically thicker the accretion disc, the smaller the emissivity index. Therefore, we propose that the transition is primarily driven by the change of the accretion flow from a supercritical to a thin disc configuration.
Observational properties of active galactic nucleus obscuration during the peak of accretion growth
Authors: Vijarnwannaluk Bovornpratch , Akiyama Masayuki , Schramm Malte , Ueda Yoshihiro , Matsuoka Yoshiki , Toba Yoshiki , Matsumoto Naoki , Ruiz Angel , Georgantopoulos Ioannis , Pouliasis Ektoras , Koulouridis Elias , Ichikawa Kohei , Sawicki Marcin , Gwyn Stephen 
Published: March 2024

ABSTRACT
We investigated the gas obscuration and host galaxy properties of active galactic nuclei (AGNs) during the peak of cosmic accretion growth of supermassive black holes at redshift 0.8–1.8 using X-ray-detected AGNs with mid-infrared and far-infrared detection. The sample was classified as type-1 and type-2 AGNs using optical spectral and morphological classification while the host galaxy properties were estimated with multiwavelength spectral energy distribution fitting. For type-1 AGNs, the black hole mass was determined from MgII emission lines while the black hole mass of type-2 AGNs was inferred from the host galaxy’s stellar mass. Based on the derived parameters, the distribution of the sample in the absorption hydrogen column density (NH) versus Eddington ratio diagram is examined. Among the type-2 AGNs, 28 ± 5 per cent are in the forbidden zone, where the obscuration by dust torus cannot be maintained due to radiation pressure on dusty material. The fraction is higher than that observed in the local universe from the Burst Alert Telescope AGN Spectroscopic Survey data release 2 (BASS DR2) (11 ± 3 per cent). The higher fraction implies that the obscuration of the majority of AGNs is consistent with the radiation pressure regulated unified model but with an increased incidence of interstellar matter (ISM)-obscured AGNs. We discuss the possibility of dust-free absorption in type-1 AGNs and heavy ISM absorption in type-2 AGNs. We also find no statistical difference in the star-formation activity between type-1 and type-2 AGNs which may suggest that obscuration triggered by a gas-rich merging is not common among X-ray detected AGNs in this epoch.
Satellite quenching and morphological transformation of galaxies in groups and clusters
Authors: Oxland M , Parker L C , de Carvalho R R , Sampaio V M 
Published: March 2024

ABSTRACT
We investigate the role that dense environments have on the quenching of star formation and the transformation of morphology for a sample of galaxies selected from the Sloan Digital Sky Survey. We make a distinction between galaxies falling into groups [13 ≤ log(Mhalo/M⊙) &lt; 14] and clusters [log(Mhalo/M⊙) ≥ 14], and compare to a large sample of field galaxies. Using galaxy position in projected phase space as a proxy for time since infall, we study how galaxy specific star formation rate and morphology, parametrized by the bulge-to-total light ratio, change over time. After controlling for stellar mass, we find clear trends of increasing quenched and elliptical fractions as functions of infall time for galaxies falling into both groups and clusters. The trends are strongest for low-mass galaxies falling into clusters. By computing quenching and morphological transformation time-scales, we find evidence that star formation quenching occurs faster than morphological transformation in both environments. Comparing field galaxies to recently infalling galaxies, we determine that there is pre-processing of both star formation and morphology, with pre-processing affecting star formation rates more strongly. Our analysis favours quenching mechanisms that act quickly to suppress star formation, while other mechanisms that act on longer time-scales transform morphology through bulge growth and disc fading.
The fundamental plane of blazars based on the black hole spin-mass energy
Authors: Zhang Xu , Xiong Ding-rong , Gao Quan-gui , Yang Gui-qin , Lu Fang-wu , Na Wei-wei , Qin Long-hua 
Published: March 2024

ABSTRACT
We examine the fundamental plane of 91 blazars which include flat-spectrum radio quasars and BL Lacertae objects with known X-ray luminosity (LR), radio luminosity (LX), and black hole mass measurements (M) to reflect the relationship between jet and accretion for blazars. The fundamental plane of blazars are logLR = ${0.273}_{+0.059}^{-0.059}\log L_X$ + ${0.695}_{+0.191}^{-0.191}\log M$ + ${25.457}_{+2.728}^{-2.728}$ and logLR = ${0.190}_{+0.049}^{-0.049}\log L_X$ + ${0.475}_{+0.157}^{-0.157}\log M$ + ${28.568}_{+2.245}^{-2.245}$ after considering the effect of beam factor. Our results suggest that the jet of blazars has connection with accretion. We set the black hole spin energy as a new variable to correct the black hole mass and explore the effect of black hole spin on the fundamental relationship. We find that the fundamental plane of blazars is affected by the black hole spin, which is similar to the previous work for active galactic nuclei. We additionally examine a new fundamental plane which is based on the black hole spin-mass energy (Mspin). The new fundamental plane (logLR = ${0.332}_{+0.081}^{-0.081}\log L_X$ + ${0.502}_{+0.091}^{-0.091}\log M_{spin}$ + ${22.606}_{+3.346}^{-3.346}$ with R-Square = 0.575) shows that Mspin has a better correlation coefficient compared to the M for fundamental plane of blazars. These results suggest that the black hole spin should be considered as an important factor for the study of fundamental plane for blazars. And these may further our understanding of the Blandford–Znajek process in blazars.
Radio spectra of pulsars fitted with the spectral distribution function of the emission from their current sheet
Authors: Ardavan Houshang 
Published: March 2024

ABSTRACT
In their catalogue of pulsars’ radio spectra, Swainston et al. distinguish between five different forms of these spectra: those that can be fitted with (i) a simple power law, (ii) a broken power law, (iii) a low-frequency turn-over, (iv) a high-frequency turn-over or (v) a double turn-over spectrum. Here, we choose two examples from each of these categories and fit them with the spectral distribution function of the caustics that are generated by the superluminally moving current sheet in the magnetosphere of a non-aligned neutron star. In contrast to the prevailing view that the curved features of pulsars’ radio spectra arise from the absorption of the observed radiation in high-density environments, our results imply that these features are intrinsic to the emission mechanism. We find that all observed features of pulsar spectra (including those that are normally fitted with simple or broken power laws) can be described by a single spectral distribution function and regarded as manifestations of a single emission mechanism. From the results of an earlier analysis of the emission from a pulsar’s current sheet and the values of the fit parameters for each spectrum, we also determine the physical characteristics of the central neutron star of each considered example and its magnetosphere.
Photoabsorption spectra of solid O2 in ultraviolet and far-vacuum ultraviolet region at 9–30 K
Authors: Lo Jen-Iu , Lu Hsiao-Chi , Hung Wei-Hsiu , Sivaraman B , Mason N J , Cheng Bing-Ming 
Published: March 2024

Abstract
We report ultraviolet and far-vacuum ultraviolet (FUV) absorption spectra of solid molecular oxygen recorded over the wavelength region 110–365 nm for temperatures between 9 and 30 K, in which the light source was dispersed from a synchrotron. The UV/FUV spectra of solids O2 deposited at various temperatures appeared distinctly different profiles due to variation of compositions of α-O2, β-O2, and the imperfect crystal structure at the specific temperature; in addition, the icy sample exhibited its own scattering curve deposited at specific temperature. Resolved from the thermal ramping technique, the absorption spectra of solids α-O2 and β-O2 were established in the wavelength region 110–250 nm at 9 and 30 K, respectively, for the first time.
Magnetospheric flows in X-ray pulsars – I. Instability at super-Eddington regime of accretion
Authors: Mushtukov A A , Ingram A , Suleimanov V F , DiLullo N , Middleton M , Tsygankov S S , van der Klis M , Portegies Zwart S 
Published: March 2024

ABSTRACT
Within the magnetospheric radius, the geometry of accretion flow in X-ray pulsars is shaped by a strong magnetic field of a neutron star. Starting at the magnetospheric radius, accretion flow follows field lines and reaches the stellar surface in small regions located close to the magnetic poles of a star. At low mass accretion rates, the dynamics of the flow is determined by gravitational attraction and rotation of the magnetosphere due to the centrifugal force. At the luminosity range close to the Eddington limit and above it, the flow is additionally affected by the radiative force. We construct a model simulating accretion flow dynamics over the magnetosphere, assuming that the flow strictly follows field lines and is affected by gravity, radiative, and centrifugal forces only. The magnetic field of a neutron star is taken to be dominated by the dipole component of arbitrary inclination with respect to the accretion disc plane. We show that accretion flow becomes unstable at high mass accretion rates and tends to fluctuate quasi-periodically with a typical period comparable to the free-fall time from the inner disc radius. The inclination of a magnetic dipole with respect to the disc plane and strong anisotropy of X-ray radiation stabilize the mass accretion rate at the poles of a star, but the surface density of material covering the magnetosphere fluctuates even in this case.
Despite the odds: formation of the SARS-CoV-2 methylation complex
Authors: Matsuda Alex , Plewka Jacek , Rawski Michał , Mourão André , Zajko Weronika , Siebenmorgen Till , Kresik Leanid , Lis Kinga , Jones Alisha N , Pachota Magdalena , Karim Abdulkarim , Hartman Kinga , Nirwal Shivlee , Sonani Ravi , Chykunova Yuliya , Minia Igor , Mak Paweł , Landthaler Markus , Nowotny Marcin , Dubin Grzegorz , Sattler Michael , Suder Piotr , Popowicz Grzegorz M , Pyrć Krzysztof , Czarna Anna 
Published: March 2024

Abstract
Coronaviruses modify their single-stranded RNA genome with a methylated cap during replication to mimic the eukaryotic mRNAs. The capping process is initiated by several nonstructural proteins (nsp) encoded in the viral genome. The methylation is performed by two methyltransferases, nsp14 and nsp16, while nsp10 acts as a co-factor to both. Additionally, nsp14 carries an exonuclease domain which operates in the proofreading system during RNA replication of the viral genome. Both nsp14 and nsp16 were reported to independently bind nsp10, but the available structural information suggests that the concomitant interaction between these three proteins would be impossible due to steric clashes. Here, we show that nsp14, nsp10, and nsp16 can form a heterotrimer complex upon significant allosteric change. This interaction is expected to encourage the formation of mature capped viral mRNA, modulating nsp14’s exonuclease activity, and protecting the viral RNA. Our findings show that nsp14 is amenable to allosteric regulation and may serve as a novel target for therapeutic approaches.
Expanding the flexibility of base editing for high-throughput genetic screens in bacteria
Authors: Gawlitt Sandra , Collins Scott P , Yu Yanying , Blackman Samuel A , Barquist Lars , Beisel Chase L 
Published: March 2024

Abstract
Genome-wide screens have become powerful tools for elucidating genotype-to-phenotype relationships in bacteria. Of the varying techniques to achieve knockout and knockdown, CRISPR base editors are emerging as promising options. However, the limited number of available, efficient target sites hampers their use for high-throughput screening. Here, we make multiple advances to enable flexible base editing as part of high-throughput genetic screening in bacteria. We first co-opt the Streptococcus canis Cas9 that exhibits more flexible protospacer-adjacent motif recognition than the traditional Streptococcus pyogenes Cas9. We then expand beyond introducing premature stop codons by mutating start codons. Next, we derive guide design rules by applying machine learning to an essentiality screen conducted in Escherichia coli. Finally, we rescue poorly edited sites by combining base editing with Cas9-induced cleavage of unedited cells, thereby enriching for intended edits. The efficiency of this dual system was validated through a conditional essentiality screen based on growth in minimal media. Overall, expanding the scope of genome-wide knockout screens with base editors could further facilitate the investigation of new gene functions and interactions in bacteria.
Exhaustive identification of genome-wide binding events of transcriptional regulators
Authors: Nordin Anna , Pagella Pierfrancesco , Zambanini Gianluca , Cantù Claudio 
Published: March 2024

Abstract
Genome-wide binding assays aspire to map the complete binding pattern of gene regulators. Common practice relies on replication—duplicates or triplicates—and high stringency statistics to favor false negatives over false positives. Here we show that duplicates and triplicates of CUT&RUN are not sufficient to discover the entire activity of transcriptional regulators. We introduce ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation), a pipeline that harnesses large numbers of CUT&RUN replicates to discover the full set of binding events and chart the line between false positives and false negatives. We employed ICEBERG to map the full set of H3K4me3-marked regions, the targets of the co-factor β-catenin, and those of the transcription factor TBX3, in human colorectal cancer cells. The ICEBERG datasets allow benchmarking of individual replicates, comparing the performance of peak calling and replication approaches, and expose the arbitrary nature of strategies to identify reproducible peaks. Instead of a static view of genomic targets, ICEBERG establishes a spectrum of detection probabilities across the genome for a given factor, underlying the intrinsic dynamicity of its mechanism of action, and permitting to distinguish frequent from rare regulation events. Finally, ICEBERG discovered instances, undetectable with other approaches, that underlie novel mechanisms of colorectal cancer progression.
Biochemical characterization of the meiosis-essential yet evolutionarily divergent topoisomerase VIB-like protein MTOPVIB from Arabidopsis thaliana
Authors: Chen Hsin-Wen , Yeh Hsin-Yi , Chang Chih-Chiang , Kuo Wei-Chen , Lin Sheng-Wei , Vrielynck Nathalie , Grelon Mathilde , Chan Nei-Li , Chi Peter 
Published: March 2024

Abstract
Formation of programmed DNA double-strand breaks is essential for initiating meiotic recombination. Genetic studies on Arabidopsis thaliana and Mus musculus have revealed that assembly of a type IIB topoisomerase VI (Topo VI)-like complex, composed of SPO11 and MTOPVIB, is a prerequisite for generating DNA breaks. However, it remains enigmatic if MTOPVIB resembles its Topo VI subunit B (VIB) ortholog in possessing robust ATPase activity, ability to undergo ATP-dependent dimerization, and activation of SPO11-mediated DNA cleavage. Here, we successfully prepared highly pure A. thaliana MTOPVIB and MTOPVIB-SPO11 complex. Contrary to expectations, our findings highlight that MTOPVIB differs from orthologous Topo VIB by lacking ATP-binding activity and independently forming dimers without ATP. Most significantly, our study reveals that while MTOPVIB lacks the capability to stimulate SPO11-mediated DNA cleavage, it functions as a bona fide DNA-binding protein and plays a substantial role in facilitating the dsDNA binding capacity of the MOTOVIB-SPO11 complex. Thus, we illustrate mechanistic divergence between the MTOPVIB-SPO11 complex and classical type IIB topoisomerases.
FUS reads histone H3K36me3 to regulate alternative polyadenylation
Authors: Jia Junqi , Fan Haonan , Wan Xinyi , Fang Yuan , Li Zhuoning , Tang Yin , Zhang Yanjun , Huang Jun , Fang Dong 
Published: March 2024

Abstract
Complex organisms generate differential gene expression through the same set of DNA sequences in distinct cells. The communication between chromatin and RNA regulates cellular behavior in tissues. However, little is known about how chromatin, especially histone modifications, regulates RNA polyadenylation. In this study, we found that FUS was recruited to chromatin by H3K36me3 at gene bodies. The H3K36me3 recognition of FUS was mediated by the proline residues in the ZNF domain. After these proline residues were mutated or H3K36me3 was abolished, FUS dissociated from chromatin and bound more to RNA, resulting in an increase in polyadenylation sites far from stop codons genome-wide. A proline mutation corresponding to a mutation in amyotrophic lateral sclerosis contributed to the hyperactivation of mitochondria and hyperdifferentiation in mouse embryonic stem cells. These findings reveal that FUS is an H3K36me3 reader protein that links chromatin-mediated alternative polyadenylation to human disease.
Engineering an Escherichia coli strain for production of long single-stranded DNA
Authors: Shen Konlin , Flood Jake J , Zhang Zhihuizi , Ha Alvin , Shy Brian R , Dueber John E , Douglas Shawn M 
Published: March 2024

Abstract
Long single-stranded DNA (ssDNA) is a versatile molecular reagent with applications including RNA-guided genome engineering and DNA nanotechnology, yet its production is typically resource-intensive. We introduce a novel method utilizing an engineered Escherichia coli ‘helper’ strain and phagemid system that simplifies long ssDNA generation to a straightforward transformation and purification procedure. Our method obviates the need for helper plasmids and their associated contamination by integrating M13mp18 genes directly into the E. coli chromosome. We achieved ssDNA lengths ranging from 504 to 20 724 nt with titers up to 250 μg/l following alkaline lysis purification. The efficacy of our system was confirmed through its application in primary T-cell genome modifications and DNA origami folding. The reliability, scalability and ease of our approach promise to unlock new experimental applications requiring large quantities of long ssDNA.