bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiwavelength photometric study of RR lyrae variables in the globular cluster NGC 5272 (Messier 3)
Authors: Kumar Nitesh , Bhardwaj Anupam , Singh Harinder P , Rejkuba Marina , Marconi Marcella , Prugniel Philippe 
Published: May 2024

ABSTRACT
We present a comprehensive photometric study of RR Lyrae stars in the M3 globular cluster, utilizing a vast data set of 3140 optical (UBVRI) CCD images spanning 35 yr from astronomical data archives. We have successfully identified previously known 238 RR Lyrae stars from the photometric data, comprising 178 RRab, 49 RRc, and 11 RRd stars. Multiband periodogram was used to significantly improve the long-term periods of 65 per cent of RR Lyrae stars in our sample, thanks to the unprecedentedly long temporal coverage of the observations. The light curve templates were used to obtain accurate and precise mean magnitudes and amplitudes of all RR Lyrae variables. We combined optical (UBVRI) and near-infrared (NIR, JHKs) photometry of RR Lyrae variables to investigate their location in the colour-magnitude diagrams as well as the pulsation properties such as period distributions, Bailey diagrams and amplitude ratios. The period–luminosity relations in R and I bands and Period–Wesenheit relations were derived after excluding outliers identified in CMDs. The Period–Wesenheit relations calibrated via the theoretically predicted relations were used to determine a distance modulus of $\mu = 15.04 \pm 0.04 \, {\rm (stats)} \pm 0.19 \, {\rm {(syst.)}}$ mag (using metal-independent WBV Wesenheit) and $\mu = 15.03 \pm 0.04 \, {\rm (stats)} \pm 0.17 \, {\rm {(syst.)}}$ mag (using metal-dependent WVI Wesenheit). Our distance measurements are in excellent agreement with published distances to M3 in the literature. We also employed an artificial neural network based comparison of theoretical and observed light curves to determine physical parameters (mass, luminosity, and effective temperature) for 79 non-Blazhko RRab stars that agree with limited literature measurements.
TOI-837 b is a young Saturn-sized exoplanet with a massive 70 M⊕ core
Authors: Barragán Oscar , Yu Haochuan , Freckelton Alix Violet , Meech Annabella , Cretignier Michael , Mortier Annelies , Aigrain Suzanne , Klein Baptiste , O’Sullivan Niamh K , Gillen Edward , Nielsen Louise Dyregaard , Mallorquín Manuel , Zicher Norbert 
Published: May 2024

ABSTRACT
We present an exhaustive photometric and spectroscopic analysis of TOI-837, a F9/G0 35 Myr young star, hosting a transiting exoplanet, TOI-837 b, with an orbital period of ∼8.32 d. Utilizing data from the Transiting Exoplanet Survey Satellite and ground-based observations, we determine a planetary radius of $0.818_{-0.024}^{+0.034}$ RJ for TOI-837 b. Through detailed High Accuracy Radial Velocity Planet Searcher spectroscopic time series analysis, we derive a Doppler semi-amplitude of $34.7_{-5.6}^{+5.3}$ ${\rm m\, s^{-1}}$, corresponding to a planetary mass of $0.379_{-0.061}^{+0.058}$ MJ. The derived planetary properties suggest a substantial core of approximately 70 M⊕, constituting about 60 per cent of the planet’s total mass. This finding poses a significant challenge to existing theoretical models of core formation. We propose that future atmospheric observations with JWST could provide insights into resolving ambiguities of TOI-837 b, offering new perspectives on its composition, formation, and evolution.
A semi-analytical model for the propagation of a relativistic jet in a magnetized medium
Authors: García-García Leonardo , López-Cámara Diego , Lazzati Davide 
Published: May 2024

ABSTRACT
The merger of two magnetized compact objects, such as neutron stars, forms a compact object which may launch a relativistic and collimated jet. Numerical simulations of the process show that a dense and highly magnetized medium surrounds the system. This study presents a semi-analytical model that models the effects that a static magnetized medium with a tangled field produces in relativistic, collimated, and non-magnetized jets. The model is a first approximation that addresses the magnetic field present in the medium and is based on pressure equilibrium principles between the jet, cocoon, and external medium. A fraction of the ambient medium field is allowed to be entrained in the cocoon. We find that the jet and cocoon properties may be affected by high magnetic fields (≳ 1015 G) and mixing. The evolution of the system may vary up to $\sim 10{{\ \rm per\ cent}}$ (compared to the non-magnetized case). Low-mixing may produce a slower broader jet with a broader and more energetic cocoon would be produced. On the other hand, high-mixing could produce a faster narrower jet with a narrow and less-energetic cocoon. Two-dimensional hydrodynamical simulations are used to validate the model and to constrain the mixing parameter. Although the magnetic field and mixing have a limited effect, our semi-analytic model captures the general trend consistent with numerical results. For high magnetization, the results were found to be more consistent with the low mixing case in our semi-analytic model.
H i galaxy signatures in the SARAO MeerKAT galactic plane survey − III. Unveiling the obscured part of the Vela Supercluster
Authors: Rajohnson Sambatriniaina H A , Kraan-Korteweg Renée C , Chen Hao , Frank Bradley S , Steyn Nadia , Kurapati Sushma , Pisano D J , Staveley-Smith Lister , Serra Paolo , Goedhart Sharmila , Camilo Fernando 
Published: May 2024

ABSTRACT
We conducted a search for $\textrm {H}\, \scriptstyle \mathrm{I}$ emission of the gas-rich galaxies in the Vela region (260° ≤ ℓ ≤ 290°, −2° ≤ b ≤ 1°) to explore the Vela Supercluster (VSCL) at Vhel ∼ 18 000 $\rm km\, s^{-1}$, largely obscured by Galactic dust. Within the mostly Radio Frequency Interference-free band (250 &lt; Vhel &lt; 25 000 $\rm km\, s^{-1}$) of MeerKAT, the analysis focuses on 157 hexagonally distributed pointings extracted from the South African Radio Astronomy Observatory MeerKAT Galactic Plane Survey located in the Vela region (Vela−SMGPS). These were combined into 10 contiguous mosaics, covering an ∼90 square degrees area. Among the 843 $\textrm {H}\, \scriptstyle \mathrm{I}$ detected sources, 39 were previously discovered in the H i Parkes Zone of Avoidance survey (Vhel &lt; 12 000 $\rm km\, s^{-1}$; rms ∼ 6 $\rm mJy\, beam^{-1}$). With the improved rms level of the Vela−SMGPS, i.e. 0.29–0.56 $\rm mJy\, beam^{-1}$, our study unveils nearly 12 times more detections (471 candidates) in that same velocity range. We furthermore could identify 187 galaxy candidates with an $\textrm {H}\, \scriptstyle \mathrm{I}$ mass limit reaching $\log (M_{\rm HI}/\rm {\rm M}_{\odot }) = 9.44$ in the VSCL velocity range Vhel ∼ 19 500 ± 3500 $\rm km\, s^{-1}$. We find indications of two wall-like overdensities that confirm the original suspicion that these walls intersect at low latitudes around longitudes of ℓ ∼ 272°–278°. We also find a strong signature most likely associated with the Hydra/Antlia extension and evidence of a previously unknown narrow filament at Vhel ∼ 12 000 $\rm km\, s^{-1}$. This paper demonstrates the efficiency of systematic $\textrm {H}\, \scriptstyle \mathrm{I}$ surveys with the Square Kilometre Array (SKA) precursor MeerKAT, even in the most obscured part of the Zone of Avoidance.
AlPaCas: allele-specific CRISPR gene editing through a protospacer-adjacent-motif (PAM) approach
Authors: Rosignoli Serena , Lustrino Elisa , Conci Alessio , Fabrizi Alessandra , Rinaldo Serena , Latella Maria Carmela , Enzo Elena , Prosseda Gianni , De Rosa Laura , De Luca Michele , Paiardini Alessandro 
Published: May 2024

Abstract
Gene therapy of dominantly inherited genetic diseases requires either the selective disruption of the mutant allele or the editing of the specific mutation. The CRISPR-Cas system holds great potential for the genetic correction of single nucleotide variants (SNVs), including dominant mutations. However, distinguishing between single-nucleotide variations in a pathogenic genomic context remains challenging. The presence of a PAM in the disease-causing allele can guide its precise targeting, preserving the functionality of the wild-type allele. The AlPaCas (Aligning Patients to Cas) webserver is an automated pipeline for sequence-based identification and structural analysis of SNV-derived PAMs that satisfy this demand. When provided with a gene/SNV input, AlPaCas can: (i) identify SNV-derived PAMs; (ii) provide a list of available Cas enzymes recognizing the SNV (s); (iii) propose mutational Cas-engineering to enhance the selectivity towards the SNV-derived PAM. With its ability to identify allele-specific genetic variants that can be targeted using already available or engineered Cas enzymes, AlPaCas is at the forefront of advancements in genome editing. AlPaCas is open to all users without a login requirement and is freely available at https://schubert.bio.uniroma1.it/alpacas.
ViralFlow v1.0—a computational workflow for streamlining viral genomic surveillance
Authors: da Silva Alexandre Freitas , da Silva Neto Antonio Marinho , Aksenen Cleber Furtado , Jeronimo Pedro Miguel Carneiro , Dezordi Filipe Zimmer , Almeida Suzana Porto , Costa Hudson Marques Paula , Salvato Richard Steiner , Campos Tulio de Lima , Wallau Gabriel da Luz , of the Fiocruz Genomic Network on behalf 
Published: May 2024

Abstract
ViralFlow v1.0 is a computational workflow developed for viral genomic surveillance. Several key changes turned ViralFlow into a general-purpose reference-based genome assembler for all viruses with an available reference genome. New virus-agnostic modules were implemented to further study nucleotide and amino acid mutations. ViralFlow v1.0 runs on a broad range of computational infrastructures, from laptop computers to high-performance computing (HPC) environments, and generates standard and well-formatted outputs suited for both public health reporting and scientific problem-solving. ViralFlow v1.0 is available at: https://viralflow.github.io/index-en.html.
A single-cell strategy for the identification of intronic variants related to mis-splicing in pancreatic cancer
Authors: Duman Emre Taylan , Sitte Maren , Conrads Karly , Mackay Adi , Ludewig Fabian , Ströbel Philipp , Ellenrieder Volker , Hessmann Elisabeth , Papantonis Argyris , Salinas Gabriela 
Published: May 2024

Abstract
Most clinical diagnostic and genomic research setups focus almost exclusively on coding regions and essential splice sites, thereby overlooking other non-coding variants. As a result, intronic variants that can promote mis-splicing events across a range of diseases, including cancer, are yet to be systematically investigated. Such investigations would require both genomic and transcriptomic data, but there currently exist very few datasets that satisfy these requirements. We address this by developing a single-nucleus full-length RNA-sequencing approach that allows for the detection of potentially pathogenic intronic variants. We exemplify the potency of our approach by applying pancreatic cancer tumor and tumor-derived specimens and linking intronic variants to splicing dysregulation. We specifically find that prominent intron retention and pseudo-exon activation events are shared by the tumors and affect genes encoding key transcriptional regulators. Our work paves the way for the assessment and exploitation of intronic mutations as powerful prognostic markers and potential therapeutic targets in cancer.
Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modifications
Authors: Carlesso Antonio , Hörberg Johanna , Deganutti Giuseppe , Reymer Anna , Matsson Pär 
Published: May 2024

Abstract
Antisense oligonucleotides (ASOs) offer ground-breaking possibilities for selective pharmacological intervention for any gene product-related disease. Therapeutic ASOs contain extensive chemical modifications that improve stability to enzymatic cleavage and modulate binding affinity relative to natural RNA/DNA. Molecular dynamics (MD) simulation can provide valuable insights into how such modifications affect ASO conformational sampling and target binding. However, force field parameters for chemically modified nucleic acids (NAs) are still underdeveloped. To bridge this gap, we developed parameters to allow simulations of ASOs with the widely applied phosphorothioate (PS) backbone modification, and validated these in extensive all-atom MD simulations of relevant PS-modified NA systems representing B-DNA, RNA, and DNA/RNA hybrid duplex structures. Compared to the corresponding natural NAs, single PS substitutions had marginal effects on the ordered DNA/RNA duplex, whereas substantial effects of phosphorothioation were observed in single-stranded RNA and B-DNA, corroborated by the experimentally derived structure data. We find that PS-modified NAs shift between high and low twist states, which could affect target recognition and protein interactions for phosphorothioated oligonucleotides. Furthermore, conformational sampling was markedly altered in the PS-modified ssRNA system compared to that of the natural oligonucleotide, indicating sequence-dependent effects on conformational preference that may in turn influence duplex formation.
PitViper: a software for comparative meta-analysis and annotation of functional screening data
Authors: Meslin Paul-Arthur , Kelly Lois M , Benbarche Salima , Lecourt Séverine , Lin Kevin H , Rutter Justine C , Bassil Christopher F , Itzykson Raphael , Wood Kris C , Puissant Alexandre , Lobry Camille 
Published: May 2024

Abstract
Recent advancements in shRNA and Cas protein technologies have enabled functional screening methods targeting genes or non-coding regions using single or pooled shRNA and sgRNA. CRISPR-based systems have also been developed for modulating DNA accessibility, resulting in CRISPR-mediated interference (CRISPRi) or activation (CRISPRa) of targeted genes or genomic DNA elements. However, there is still a lack of software tools for integrating diverse array of functional genomics screening outputs that could offer a cohesive framework for comprehensive data integration. Here, we developed PitViper, a flexible and interactive open-source software designed to fill this gap, providing reliable results for the type of elements being screened. It is an end-to-end automated and reproducible bioinformatics pipeline integrating gold-standard methods for functional screening analysis. Our sensitivity analyses demonstrate that PitViper is a useful tool for identifying potential super-enhancer liabilities in a leukemia cell line through genome-wide CRISPRi-based screening. It offers a robust, flexible, and interactive solution for integrating data analysis and reanalysis from functional screening methods, making it a valuable resource for researchers in the field.
Prophylactic treatment of FSGS recurrence in patients who relapsed on a previous kidney graft
Authors: Uro-Coste Charlotte , Lambert Céline , Audard Vincent , Couzi Lionel , Caillard Sophie , Büchler Matthias , Del Bello Arnaud , Malvezzi Paolo , Pernin Vincent , Colosio Charlotte , Mesnard Laurent , Bertrand Dominique , Martinez Frank , Ducloux Didier , Poulain Coralie , Thierry Antoine , Danthu Clément , Greze Clarisse , Lanaret Camille , Moal Valérie , Hertig Alexandre , Dantal Jacques , Legendre Christophe , Chatelet Valérie , Sicard Antoine , Gosset Clément , Maillard Nicolas , Duveau Agnès , Petit Clémence , Kamar Nassim , Heng Anne-Elisabeth , Anglicheau Dany , Garrouste Cyril 
Published: May 2024

ABSTRACT

Background
Recurrence of focal segmental glomerulosclerosis (FSGS) is common after kidney transplantation and is classically associated with a significant decrease in graft survival. A major risk factor is a prior history of FSGS recurrence on a previous graft. This analysis reports the impact of a prophylactic treatment of FSGS recurrence in very high-risk patients who experienced a recurrence on a previous graft.

Methods
We performed a retrospective multicentre observational study in 25 French transplantation centres. The inclusion criteria were patients aged more than 18 years who had undergone kidney transplant between 31 December 2004 and 31 December 2020, and who had a history of FSGS recurrence on a previous graft.

Results
We identified 66 patients: 40 received prophylactic treatment (PT+), including intravenous cyclosporine and/or rituximab and/or plasmapheresis, and 26 did not receive any prophylactic treatment (PT–). The time to progression to end-stage kidney disease was similar between groups. The PT+ group was younger at FSGS diagnosis and at the time of kidney retransplantation and lost their previous graft faster. The overall recurrence rate was 72.7% (76.9% in the PT– group and 70.0% in the PT+ group, P = .54). At least partial remission was achieved in 87.5% of patients. The 5-year graft survival was 67.7% [95% confidence interval (CI) 53.4%–78.4%]: 65.1% (95% CI 48.7%–77.4%) in patients with FSGS recurrence vs 77.3% (95% CI 43.8%–92.3%) in patients without recurrence (P = .48).

Conclusion
Our study suggests that prophylactic treatment should not be used routinely in patients receiving a second transplantation after recurrence of FSGS on a previous graft. The recurrence rate is high regardless of the use of prophylactic treatment. However, the 5-year graft survival remains satisfactory.
Propionate and butyrate counteract renal damage and progression to chronic kidney disease
Authors: Corte-Iglesias Viviana , Saiz Maria Laura , Andrade-Lopez Ana Cristina , Salazar Nuria , Bernet Cristian Ruiz , Martin-Martin Cristina , Borra Jesús Martinez , Lozano Juan-Jose , Aransay Ana M , Diaz-Corte Carmen , Lopez-Larrea Carlos , Suarez-Alvarez Beatriz 
Published: May 2024

ABSTRACT

Background
Short-chain fatty acids (SCFAs), mainly acetate, propionate and butyrate, are produced by gut microbiota through fermentation of complex carbohydrates that cannot be digested by the human host. They affect gut health and can contribute at the distal level to the pathophysiology of several diseases, including renal pathologies.

Methods
SCFA levels were measured in chronic kidney disease (CKD) patients (n = 54) at different stages of the disease, and associations with renal function and inflammation parameters were examined. The impact of propionate and butyrate in pathways triggered in tubular cells under inflammatory conditions was analysed using genome-wide expression assays. Finally, a pre-clinical mouse model of folic acid–induced transition from acute kidney injury to CKD was used to analyse the preventive and therapeutic potential of these microbial metabolites in the development of CKD.

Results
Faecal levels of propionate and butyrate in CKD patients gradually reduce as the disease progresses, and do so in close association with established clinical parameters for serum creatinine, blood urea nitrogen and the estimated glomerular filtration rate. Propionate and butyrate jointly downregulated the expression of 103 genes related to inflammatory processes and immune system activation triggered by tumour necrosis factor-α in tubular cells. In vivo, the administration of propionate and butyrate, either before or soon after injury, respectively, prevented and slowed the progression of damage. This was indicated by a decrease in renal injury markers, the expression of pro-inflammatory and pro-fibrotic markers, and recovery of renal function over the long term.

Conclusions
Propionate and butyrate levels are associated with a progressive loss of renal function in CKD patients. Early administration of these SCFAs prevents disease advancement in a pre-clinical model of acute renal damage, demonstrating their therapeutic potential independently of the gut microbiota.
Spillovers from tax shocks to the Euro area
Authors: Mierzwa Sascha 
Published: May 2024

Abstract
I study the spillover effects of legislated discretionary tax changes in the USA, Germany, and the UK to a panel of eleven Eurozone countries for the period 1980Q1–2018Q4 employing Local Projections. When considering aggregated tax shocks, I find little evidence for significant spillovers. When allowing for state-dependent effects, I find no effects of German or US tax cuts regardless of the state of the business cycle. When allowing for asymmetric effects, there is, in general, evidence for negative (positive) spillovers from US, German, and UK tax hikes (UK tax cuts). US tax hikes always cause adverse spillovers, whereas the effects for Germany and the UK are state dependent. When considering country-specific effects, the effects turn out as heterogeneous across the Eurozone countries. UK tax cuts are generally expansionary, whereas US (German) tax cuts cause positive spillovers mainly during recessionary (non-recessionary) times.
Who should decide how much information to collect?
Authors: Li Youping , Zhang Jianhu 
Published: May 2024

Abstract
This article examines the tradeoffs concerning the collection and disclosure of personal information and considers either the seller or the buyers choosing how much information to collect. We identify two channels through which having heterogeneous buyers make the decision increases social welfare: the full internalization of privacy costs and the customized choice of information levels. Perhaps surprisingly, the buyers voluntarily provide more information than what is mandatorily collected particularly when privacy is a significant concern, which often benefits the seller. Consumer and total welfare are increased with buyers choosing how much information to collect unless the external value of information is sufficiently large relative to the buyers’ privacy cost and heterogeneity in valuation. Given the growing privacy concerns surrounding personal data, our analysis supports offering consumers the autonomy, which can result in a Pareto improvement.
A self-consistent model for dust settling and the vertical shear instability in protoplanetary disks
Authors: Fukuhara Yuya , Okuzumi Satoshi 
Published: May 2024

Abstract
The spatial distribution of dust particles in protoplanetary disks affects dust evolution and planetesimal formation processes. The vertical shear instability (VSI) is one of the candidate hydrodynamic mechanisms that can generate turbulence in the outer disk region and affect dust diffusion. Turbulence driven by the VSI has a predominant vertical motion that can prevent dust settling. On the other hand, the dust distribution controls the spatial distribution of the gas cooling rate, thereby affecting the strength of VSI-driven turbulence. Here, we present a semi-analytic model that determines the vertical dust distribution and the strength of VSI-driven turbulence in a self-consistent manner. The model uses an empirical formula for the vertical diffusion coefficient in VSI-driven turbulence obtained from our recent hydrodynamical simulations. The formula returns the vertical diffusion coefficient as a function of the vertical profile of the cooling rate, which is determined by the vertical dust distribution. We use this model to search for an equilibrium vertical dust profile where settling balances with turbulent diffusion for a given maximum grain size. We find that if the grains are sufficiently small, there exists a stable equilibrium dust distribution where VSI-driven turbulence is sustained at a level of αz ∼ 10−3, where αz is the dimensionless vertical diffusion coefficient. However, as the maximum grain size increases, the equilibrium solution vanishes because the VSI can no longer stop the settling of the grains. This runaway settling may explain highly settled dust rings found in the outer part of some protoplanetary disks.