bluuebunny/crossref_metadata_2025_split huggingface dataset:
MRI turbulence in vertically stratified accretion discs at large magnetic Prandtl numbers
Authors: Held Loren E , Mamatsashvili George , Pessah Martin E 
Published: April 2024

ABSTRACT
The discovery of the first binary neutron star merger, GW170817, has spawned a plethora of global numerical relativity simulations. These simulations are often ideal (with dissipation determined by the grid) and/or axisymmetric (invoking ad hoc mean-field dynamos). However, binary neutron star mergers (similar to X-ray binaries and active galactic nuclei inner discs) are characterized by large magnetic Prandtl numbers, $\rm Pm$, (the ratio of viscosity to resistivity). $\rm Pm$ is a key parameter determining dynamo action and dissipation but it is ill-defined (and likely of order unity) in ideal simulations. To bridge this gap, we investigate the magnetorotational instability (MRI) and associated dynamo at large magnetic Prandtl numbers using fully compressible, three-dimensional, vertically stratified, isothermal simulations of a local patch of a disc. We find that, within the bulk of the disc (z ≲ 2H, where H is the scale-height), the turbulent intensity (parametrized by the stress-to-thermal-pressure ratio α), and the saturated magnetic field energy density, Emag, produced by the MRI dynamo, both scale as a power with Pm at moderate Pm (4 ≲ Pm ≲ 32): Emag ∼ Pm0.74 and α ∼ Pm0.71, respectively. At larger Pm (≳ 32), we find deviations from power-law scaling and the onset of a plateau. Compared to our recent unstratified study, this scaling with Pm becomes weaker further away from the disc mid-plane, where the Parker instability dominates. We perform a thorough spectral analysis to understand the underlying dynamics of small-scale MRI-driven turbulence in the mid-plane and of large-scale Parker-unstable structures in the atmosphere.
General upper limit on the electric charge of Sgr A* in the Reissner–Nordström metric
Authors: Mishra Ruchi , Vieira Ronaldo S S , Kluźniak Włodek 
Published: April 2024

ABSTRACT
In general relativity, the gravitational field of an electrically charged, non-rotating, spherically symmetric body is described by the Reissner–Nordström (RN) metric. Depending on the charge to mass ratio, the solution describes a black hole or a naked singularity. In the naked-singularity regime, a general property of this metric is the existence of a radius, known as the zero-gravity radius, where a test particle would remain at rest. As a consequence of repulsive gravity there is no circular orbit inside this radius, and at least a part of any quasi-stable structure must necessarily lie outside of it. Assuming the iconic torus in the compact source Sgr A* at the Galactic centre observed by the Event Horizon Telescope (EHT) to be the image of a quasi-stationary fluid structure, we provide rigorous constraints in the RN metric on the electric charge-to-mass ratio Q/M of Sgr A*. A comparison between the EHT observations and the space–time zero-gravity radius provides the most conservative limit on the charge of Sgr A* to be |Q/M| &lt; 2.32 in geometrized units. A charged naked singularity respecting this charge-to-mass constraint is consistent with the current EHT observations, if the image is not interpreted as a photon ring.
xGASS: the scatter of the H i–halo mass relation of central galaxies
Authors: Saraf Manasvee , Cortese Luca , Wong O Ivy , Catinella Barbara , Janowiecki Steven , Hardwick Jennifer A 
Published: April 2024

ABSTRACT
Empirical studies of the relationship between baryonic matter in galaxies and the gravitational potential of their host haloes are important to constrain our theoretical framework for galaxy formation and evolution. One such relation, between the atomic hydrogen (H i) mass of central galaxies (MH i,c) and the total mass of their host haloes (Mhalo), has attracted significant interest in the last few years. In this work, we use the extended GALEX Arecibo SDSS Survey to examine the scatter of the H i–halo mass relation for a representative sample of central galaxies. Our findings reveal a flat median relation at $\mathrm{ log}_{10}(M_{\rm {H\,{\small I},c}}/\rm {M}_{\odot }) \approx 9.40$, across $11.1 \lt \mathrm{ log}_{10}(M_{\rm {halo}}/{{\rm M}_{\odot }}) \lt 14.1$. This flat relation stems from the statistical dominance of star-forming, disc galaxies at low Mhalo in combination with the increasing prevalence of passive, high stellar concentration systems at higher Mhalo. The scatter of this relation and the stellar specific angular momentum of centrals have a strong link (Spearman’s rank correlation coefficient ≥0.5). Comparisons with simulations suggest that the kinematic state of host haloes may be primarily driving this scatter. Our findings highlight that the H i–halo mass parameter space is too complex to be completely represented by simple median or average relations and we show that tensions with previous works are most likely due to selection biases. We recommend that future observational studies, and their comparisons with theoretical models, bin central galaxies also by their secondary properties to enable a statistically robust understanding of the processes regulating the cold gas content within central galaxies of dark matter haloes.
New Herbig–Haro objects associated with embedded sources
Authors: Movsessian T A , Magakian T Yu , Reipurth B , Andreasyan H R 
Published: April 2024

ABSTRACT
We continue to present the results of the Byurakan Narrow Band Imaging Survey (BNBIS). The main goal of this survey is to search for Herbig–Haro (HH) objects and jets in Galactic dark clouds. In this work we present the results of the search in the vicinity of infrared sources that are bright in the WISE survey and embedded in the dark clouds. The survey is performed with the 1-m Schmidt telescope of Byurakan Observatory, lately equipped with a new CCD detector, which allows to obtain one square degree images of the sky in various filters. Narrow-band filters were used to obtain H α and [S ii] images, and a medium-width filter was used for the continuum imaging. New HH flows and knots were found near six embedded IR sources, which constitutes a significant proportion of the objects observed. At least two of the newly found HH flows (HH 1226 and HH 1227) lie in isolated dark clouds, thus pointing to active star formation in these regions. Other flows are also located in detached and dense globules or filaments. The length of the HH 1228 flow is about 1 pc; it has also a molecular hydrogen counterpart of the same extension. Coordinates, charts, detailed descriptions and distance estimates are provided. The lower limits of bolometric luminosities of the source stars are typical for low-mass young stellar objects.
Particle-in-cell simulations of the magnetorotational instability in stratified shearing boxes
Authors: Sandoval Astor , Riquelme Mario , Spitkovsky Anatoly , Bacchini Fabio 
Published: April 2024

ABSTRACT
The magnetorotational instability (MRI) plays a crucial role in regulating the accretion efficiency in astrophysical accretion discs. In low-luminosity discs around black holes, such as Sgr A* and M87, Coulomb collisions are infrequent, making the MRI physics effectively collisionless. The collisionless MRI gives rise to kinetic plasma effects that can potentially affect its dynamic and thermodynamic properties. We present 2D and 3D particle-in-cell (PIC) plasma simulations of the collisionless MRI in stratified discs using shearing boxes with net vertical field. We use pair plasmas, with initial β = 100 and concentrate on subrelativistic plasma temperatures (kBT ≲ mc2). Our 2D and 3D runs show disc expansion, particle and magnetic field outflows, and a dynamo-like process. They also produce magnetic pressure dominated discs with (Maxwell stress dominated) viscosity parameter α ∼ 0.5–1. By the end of the simulations, the dynamo-like magnetic field tends to dominate the magnetic energy and the viscosity in the discs. Our 2D and 3D runs produce fairly similar results, and are also consistent with previous 3D MHD (magnetohydrodynamic) simulations. Our simulations also show non-thermal particle acceleration, approximately characterized by power-law tails with temperature-dependent spectral indices − p. For temperatures $k_\mathrm{ B}T \sim 0.05-0.3\, mc^2$, we find p ≈ 2.2–1.9. The maximum accelerated particle energy depends on the scale separation between MHD and Larmor-scale plasma phenomena in a way consistent with previous PIC results of magnetic reconnection-driven acceleration. Our study constitutes a first step towards modelling from first principles potentially observable stratified MRI effects in low-luminosity accretion discs around black holes.
Discovering DNA shape motifs with multiple DNA shape features: generalization, methods, and validation
Authors: Chen Nanjun , Yu Jixiang , Liu Zhe , Meng Lingkuan , Li Xiangtao , Wong Ka-Chun 
Published: April 2024

Abstract
DNA motifs are crucial patterns in gene regulation. DNA-binding proteins (DBPs), including transcription factors, can bind to specific DNA motifs to regulate gene expression and other cellular activities. Past studies suggest that DNA shape features could be subtly involved in DNA–DBP interactions. Therefore, the shape motif annotations based on intrinsic DNA topology can deepen the understanding of DNA–DBP binding. Nevertheless, high-throughput tools for DNA shape motif discovery that incorporate multiple features altogether remain insufficient. To address it, we propose a series of methods to discover non-redundant DNA shape motifs with the generalization to multiple motifs in multiple shape features. Specifically, an existing Gibbs sampling method is generalized to multiple DNA motif discovery with multiple shape features. Meanwhile, an expectation-maximization (EM) method and a hybrid method coupling EM with Gibbs sampling are proposed and developed with promising performance, convergence capability, and efficiency. The discovered DNA shape motif instances reveal insights into low-signal ChIP-seq peak summits, complementing the existing sequence motif discovery works. Additionally, our modelling captures the potential interplays across multiple DNA shape features. We provide a valuable platform of tools for DNA shape motif discovery. An R package is built for open accessibility and long-lasting impact: https://zenodo.org/doi/10.5281/zenodo.10558980.
Fine-tuning the tRNA anticodon arm for multiple/consecutive incorporations of β-amino acids and analogs
Authors: Katoh Takayuki , Suga Hiroaki 
Published: April 2024

Abstract
Ribosomal incorporation of β-amino acids into nascent peptides is much less efficient than that of the canonical α-amino acids. To overcome this, we have engineered a tRNA chimera bearing T-stem of tRNAGlu and D-arm of tRNAPro1, referred to as tRNAPro1E2, which efficiently recruits EF-Tu and EF-P. Using tRNAPro1E2 indeed improved β-amino acid incorporation. However, multiple/consecutive incorporations of β-amino acids are still detrimentally poor. Here, we attempted fine-tuning of the anticodon arm of tRNAPro1E2 aiming at further enhancement of β-amino acid incorporation. By screening various mutations introduced into tRNAPro1E2, C31G39/C28G42 mutation showed an approximately 3-fold enhancement of two consecutive incorporation of β-homophenylglycine (βPhg) at CCG codons. The use of this tRNA made it possible for the first time to elongate up to ten consecutive βPhg's. Since the enhancement effect of anticodon arm mutations differs depending on the codon used for β-amino acid incorporation, we optimized anticodon arm sequences for five codons (CCG, CAU, CAG, ACU and UGG). Combination of the five optimal tRNAs for these codons made it possible to introduce five different kinds of β-amino acids and analogs simultaneously into model peptides, including a macrocyclic scaffold. This strategy would enable ribosomal synthesis of libraries of macrocyclic peptides containing multiple β-amino acids.
Bridging DNA contacts allow Dps from E. coli to condense DNA
Authors: Shahu Sneha , Vtyurina Natalia , Das Moumita , Meyer Anne S , Ganji Mahipal , Abbondanzieri Elio A 
Published: April 2024

Abstract
The DNA-binding protein from starved cells (Dps) plays a crucial role in maintaining bacterial cell viability during periods of stress. Dps is a nucleoid-associated protein that interacts with DNA to create biomolecular condensates in live bacteria. Purified Dps protein can also rapidly form large complexes when combined with DNA in vitro. However, the mechanism that allows these complexes to nucleate on DNA remains unclear. Here, we examine how DNA topology influences the formation of Dps–DNA complexes. We find that DNA supercoils offer the most preferred template for the nucleation of condensed Dps structures. More generally, bridging contacts between different regions of DNA can facilitate the nucleation of condensed Dps structures. In contrast, Dps shows little affinity for stretched linear DNA before it is relaxed. Once DNA is condensed, Dps forms a stable complex that can form inter-strand contacts with nearby DNA, even without free Dps present in solution. Taken together, our results establish the important role played by bridging contacts between DNA strands in nucleating and stabilizing Dps complexes.
SingmiR: a single-cell miRNA alignment and analysis tool
Authors: Engel Annika , Rishik Shusruto , Hirsch Pascal , Keller Verena , Fehlmann Tobias , Kern Fabian , Keller Andreas 
Published: April 2024

Abstract
Single-cell RNA sequencing (RNA-seq) has revolutionized our understanding of cell biology, developmental and pathophysiological molecular processes, paving the way toward novel diagnostic and therapeutic approaches. However, most of the gene regulatory processes on the single-cell level are still unknown, including post-transcriptional control conferred by microRNAs (miRNAs). Like the established single-cell gene expression analysis, advanced computational expertise is required to comprehensively process newly emerging single-cell miRNA-seq datasets. A web server providing a workflow tailored for single-cell miRNA-seq data with a self-explanatory interface is currently not available. Here, we present SingmiR, enabling the rapid (pre-)processing and quantification of human miRNAs from noncoding single-cell samples. It performs read trimming for different library preparation protocols, generates automated quality control reports and provides feature-normalized count files. Numerous standard and advanced analyses such as dimension reduction, clustered feature heatmaps, sample correlation heatmaps and differential expression statistics are implemented. We aim to speed up the prototyping pipeline for biologists developing single-cell miRNA-seq protocols on small to medium-sized datasets. SingmiR is freely available to all users without the need for a login at https://www.ccb.uni-saarland.de/singmir.
ADMETlab 3.0: an updated comprehensive online ADMET prediction platform enhanced with broader coverage, improved performance, API functionality and decision support
Authors: Fu Li , Shi Shaohua , Yi Jiacai , Wang Ningning , He Yuanhang , Wu Zhenxing , Peng Jinfu , Deng Youchao , Wang Wenxuan , Wu Chengkun , Lyu Aiping , Zeng Xiangxiang , Zhao Wentao , Hou Tingjun , Cao Dongsheng 
Published: April 2024

Abstract
ADMETlab 3.0 is the second updated version of the web server that provides a comprehensive and efficient platform for evaluating ADMET-related parameters as well as physicochemical properties and medicinal chemistry characteristics involved in the drug discovery process. This new release addresses the limitations of the previous version and offers broader coverage, improved performance, API functionality, and decision support. For supporting data and endpoints, this version includes 119 features, an increase of 31 compared to the previous version. The updated number of entries is 1.5 times larger than the previous version with over 400 000 entries. ADMETlab 3.0 incorporates a multi-task DMPNN architecture coupled with molecular descriptors, a method that not only guaranteed calculation speed for each endpoint simultaneously, but also achieved a superior performance in terms of accuracy and robustness. In addition, an API has been introduced to meet the growing demand for programmatic access to large amounts of data in ADMETlab 3.0. Moreover, this version includes uncertainty estimates in the prediction results, aiding in the confident selection of candidate compounds for further studies and experiments. ADMETlab 3.0 is publicly for access without the need for registration at: https://admetlab3.scbdd.com.
Hypoxia-inducible factor prolyl hydroxylase inhibitors for anaemia in chronic kidney disease: a clinical practice document by the European Renal Best Practice board of the European Renal Association
Authors: Stoumpos Sokratis , Crowe Kirsty , Sarafidis Pantelis , Barratt Jonathan , Bolignano Davide , Del Vecchio Lucia , Małyszko Jolanta , Więcek Andrzej , Ortiz Alberto , Cozzolino Mario 
Published: April 2024

ABSTRACT
Anaemia is a common complication of chronic kidney disease (CKD) and is associated with poor long-term outcomes and quality of life. The use of supplemental iron, erythropoiesis-stimulating agents (ESAs) and blood transfusions has been the mainstay for treatment of anaemia in CKD for more than 3 decades. Despite available treatments, CKD patients with anaemia are undertreated and moderate–severe anaemia remains prevalent in the CKD population. Anaemia has consistently been associated with greater mortality, hospitalization, cardiovascular events and CKD progression in CKD patients, and the risk increases with anaemia severity.
Hypoxia-inducible factor (HIF) prolyl hydroxylase (PH) inhibitors have a novel mechanism of action by mimicking the body's response to hypoxia and have emerged as an alternative to ESAs for treatment of anaemia in CKD. Their efficacy in correcting and maintaining haemoglobin has been demonstrated in &gt;30 phase 3 clinical trials. Additionally, HIF activation results in various pleiotropic effects beyond erythropoiesis, with cholesterol reduction and improved iron homeostasis and potential anti-inflammatory effects. The long-term safety of these agents, particularly with respect to cardiovascular and thromboembolic events, and their possible effect on tumour growth needs to be fully elucidated. This article presents in detail the effects of HIF-PH inhibitors, describes their mechanisms of action and pharmacologic properties and discusses their place in the treatment of anaemia in CKD according to the available evidence.
Better kidney allograft survival despite higher-risk donor and recipient characteristics between 1995 and 2014
Authors: Ng Monica Suet Ying , Jones Andrew Thomas , Mallett Andrew John , O'Shaughnessy Michelle Marie 
Published: April 2024

ABSTRACT

Background and hypothesis
Advances in organ procurement, surgical techniques, immunosuppression regimens, and prophylactic antibiotic therapies have dramatically improved kidney transplant graft failure. It is unclear how these interventions have affected longer-term graft failure. It is hypothesized that graft failure has improved over the last 20 years.

Methods
Data on all first kidney transplants from 1995 to 2014 were extracted from the Australia and New Zealand Dialysis and Transplant Registry with follow-up as of 31 December 2021. Primary exposure was transplant era, classified into 5-year intervals. Primary outcome was all-cause 5-year graft failure. Secondary outcomes included all-cause 10-year graft failure and cause-specific graft failure. Kaplan–Meier curves and multivariable Cox proportional hazards regression models were used to assess trends in all-cause graft failure. Fine–Gray subdistribution hazard models verified that changes in death rates were not biasing the Cox proportional hazards regression models. Cumulative incidence functions were used to assess temporal trends in cause-specific graft failure.

Results
Across 10 871 kidney transplants, there was a shift towards transplanting more recipients aged &gt;45 years old, with more comorbidities, longer dialysis vintage, body mass index &gt;30 kg/m2, and greater human leukocyte antigen mismatches. Donor age has increased but no clear shift in donor source was observed. Compared to 1995–99 (reference), the adjusted hazard ratio for 5-year graft failure was 0.78 (95% CI 0.67–0.91), 0.70 (95% CI 0.59–0.83), and 0.60 (95% CI 0.50–0.73) for 2000–04, 2005–09, and 2010–14, respectively. Ten-year graft failure similarly reduced from 0.83 (95% CI 0.74–0.93) for 2000–04 to 0.78 (95% CI 0.68–0.89) for 2010–14, compared to 1995–99.

Conclusion
Medium- and long-term all-cause graft failure has improved steadily since 1995–99. Significant reductions in graft failure due to rejection and vascular causes were observed at 5 years, and due to rejection, vascular causes, death, and glomerular disease at 10 years.
The Relationship Between Time Spent on Social Media and Adolescent Cigarette, E-cigarette, and Dual Use: A Longitudinal Analysis of the UK Millennium Cohort Study
Authors: Purba Amrit Kaur , Henderson Marion , Baxter Andrew , Pearce Anna , Katikireddi S Vittal 
Published: April 2024

Abstract

Introduction
To estimate the effect of social media use in 14 year olds on risk of and inequalities in cigarette, e-cigarette, and dual use at 17 years, using the UK-representative Millennium Cohort Study (born 2000–2002).

Aims and Methods
The relationship of time spent on social media (using questionnaires [n = 8987] and time-use-diaries [n = 2520]) with cigarette, e-cigarette, and dual use was estimated using adjusted odds ratios (AORs) or relative risk ratios (ARRRs). Effect modification was examined (using parental education as an indicator for socioeconomic circumstances) by comparing adjusted risk differences within low and high-parental education groups. Analyses accounted for prespecified confounders (identified via directed acyclic graphs), baseline outcome measures (to address reverse causality), sample design, attrition, and item-missingness (through multiple imputation).

Results
Time spent on social media was associated with increased risk of cigarette, e-cigarette, and dual use in a dose–response manner. Social media use for ≥2 hours/day (vs. 1–&lt;30 minutes) was associated with increased cigarette (AOR 2.76 [95% confidence interval 2.19 to 3.48]), e-cigarette (3.24 [2.59 to 4.05]), and dual use (ARRR 4.11 [2.77 to 6.08]). The risk of cigarette use among 30 minutes–&lt;1 hour/day users (vs. non-users) were smaller in those with high versus low parental education (ARDs 1.4% vs. 12.4%). Similar findings were observed across the higher time categories. Analyses using time-use-diaries, in complete case samples, and with additional adjustment for baseline outcome measures generally revealed similar findings.

Conclusions
After accounting for observed confounders and potential reverse causality, findings suggest social media use increases the risk of cigarette, e-cigarette, and dual use in a dose–response manner. Guidance addressing adolescent online safety should be prioritized.

Implications
This study’s identification of a dose–response relationship and differential effects across socioeconomic groups, could assist in the development of guidance on time spent on social media. The adverse effects of social media use on adolescent cigarette, e-cigarette, and dual use supports legislation aimed at promoting adolescent online safety. Study findings strengthen calls to prohibit social media marketing of nicotine-related products and importantly highlight the need to increase awareness and understanding of the underlying algorithms which drive adolescent exposure to nicotine-related content on social media to ensure they are functioning in a way that best serves the adolescent population.