bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soft photon heating: a semi-analytic framework and applications to 21-cm cosmology
Authors: Cyr Bryce , Acharya Sandeep Kumar , Chluba Jens 
Published: September 2024

ABSTRACT
The presence of an abundant population of low-frequency photons at high redshifts (such as a radio background) can source leading order effects on the evolution of the matter and spin temperatures through rapid free–free absorptions. This effect, known as soft photon heating, can have a dramatic impact on the differential brightness temperature, $\Delta T_{\rm b}$, a central observable in 21-cm cosmology. Here, we introduce a semi-analytic framework to describe the dynamics of soft photon heating, providing a simplified set of evolution equations and a useful numerical scheme which can be used to study this generic effect. We also perform quasi-instantaneous and continuous soft photon injections to elucidate the different regimes in which soft photon heating is expected to impart a significant contribution to the global 21-cm signal and its fluctuations. We find that soft photon backgrounds produced after recombination with spectral index $\gamma \gt 3.0$ undergo significant free–free absorption, and therefore this heating effect cannot be neglected. The effect becomes stronger with steeper spectral index, and in some cases the injection of a synchrotron-like spectrum ($\gamma = 3.6$) can suppress the amplitude of $\Delta T_{\rm b}$ relative to the standard model prediction (where an additional radio background is absent), making the global 21-cm signal even more difficult to detect in these scenarios.
Modelling hydrogen-deficient carbon stars in mesa – the effects of total mass and mass ratio
Authors: Crawford Courtney L , Nikultsev Nikita , Clayton Geoffrey C , Tisserand Patrick , Soon Jamie , Pedersen May G 
Published: September 2024

ABSTRACT
Hydrogen-deficient carbon (HdC) stars are rare, low-mass, chemically peculiar, supergiant variables believed to be formed by a double white dwarf (DWD) merger, specifically of a carbon/oxygen- (CO-) and a helium-white dwarf (He-WD). They consist of two subclasses – the dust-producing R Coronae Borealis (RCB) variables and their dustless counterparts the dustless HdCs (dLHdCs). Additionally, there is another, slightly cooler set of potentially related carbon stars, the DY Persei type variables which have some, but not conclusive, evidence of hydrogen-deficiency. Recent works have begun to explore the relationship between these three classes of stars, theorizing that they share an evolutionary pathway (a DWD merger) but come from different binary populations, specifically different total masses ($M_\text{tot}$) and mass ratios (q). In this work, we use the mesa modelling framework that has previously been used to model RCB stars and vary the merger parameters, $M_\text{tot}$ and q, to explore how those parameters affect the abundances, temperatures, and luminosities of the resultant post-merger stars. We find that lower $M_\text{tot}$ and larger q’s both decrease the luminosity and temperatures of post-merger models to the region of the Hertzsprung–Russell diagram populated by the dLHdCs. These lower $M_\text{tot}$ and larger q models also have smaller oxygen isotopic ratios ($^{16}$O/$^{18}$O) which is consistent with recent observations of dLHdCs compared to RCBs. None of the models generated in this work can explain the existence of the DY Persei type variables, however this may arise from the assumed metallicity of the models.
Deep learning the intergalactic medium using Lyman-alpha forest at 4 ≤ z ≤ 5
Authors: Nasir Fahad , Gaikwad Prakash , Davies Frederick B , Bolton James S , Puchwein Ewald , Bosman Sarah E I 
Published: September 2024

ABSTRACT
Unveiling the thermal history of the intergalactic medium (IGM) at $4 \le z \le 5$ holds the potential to reveal early onset He ii reionization or lingering thermal fluctuations from H i reionization. We set out to reconstruct the IGM gas properties along simulated Lyman-alpha (Lyα) forest data on pixel-by-pixel basis, employing deep neural networks. Our approach leverages the Sherwood-Relics simulation suite, consisting of diverse thermal histories, to generate mock spectra. Our convolutional and residual networks with likelihood metric predict the Ly$\rm {\alpha }$ optical depth-weighted density or temperature for each pixel in the Ly$\rm {\alpha }$ forest skewer. We find that our network can successfully reproduce IGM conditions with high fidelity across range of instrumental signal-to-noise ratio. These predictions are subsequently translated into the temperature–density plane, facilitating the derivation of reliable constraints on thermal parameters. This allows us to estimate temperature at mean cosmic density, $T_{\rm 0}$, with 1σ confidence, $\delta {T_{\rm 0}} \lesssim 1000 \ {\rm K}$, using only one $20 \ h^{-1} \, {\rm cMpc}$ sightline ($\Delta z\simeq 0.04$) with a typical reionization history. Existing studies utilize redshift path-length comparable to $\Delta z\simeq 4$ for similar constraints. We can also provide more stringent constraints on the slope ($1\sigma$ confidence interval, $\delta {\rm \gamma } \lesssim 0.1$) of the IGM temperature–density relation as compared to other traditional approaches. We test the reconstruction on a single high signal-to-noise observed spectrum ($20 \ h^{-1}\,{\rm cMpc}$ segment) and recover thermal parameters consistent with current measurements. This machine learning approach has the potential to provide accurate yet robust measurements of IGM thermal history at the redshifts in question.
Towards solving the origin of circular polarization in FRB 20180301A
Authors: Uttarkar Pavan A , Shannon Ryan M , Lower Marcus E , Kumar Pravir , Price Danny C , Deller A T , Gourdji K 
Published: September 2024

ABSTRACT
Fast radio bursts (FRBs) are short-time-scale transients of extragalactic origin. The number of detected FRBs has grown dramatically since their serendipitous discovery from archival data. Some FRBs have also been seen to repeat. The polarimetric properties of repeating FRBs show diverse behaviour and, at times, extreme polarimetric morphology, suggesting a complex magneto-ionic circumburst environment for this class of FRB. The polarimetric properties such as circular polarization behaviour of FRBs are crucial for understanding their surrounding magnetic-ionic environment. The circular polarization previously observed in some of the repeating FRB sources has been attributed to propagation effects such as generalized Faraday rotation (GFR), where conversion from linear to circular polarization occurs due to the non-circular modes of transmission in relativistic plasma. The discovery burst from the repeating FRB 20180301A showed significant frequency-dependent circular polarization behaviour, which was initially speculated to be instrumental due to a sidelobe detection. Here, we revisit the properties given the subsequent interferometric localization of the burst, which indicates that the burst was detected in the primary beam of the Parkes/Murriyang 20-cm multibeam receiver. We develop a Bayesian Stokes-Q, U, and V fit method to model the GFR effect, which is independent of the total polarized flux parameter. Using the GFR model we show that the rotation measure (RM) estimated is two orders of magnitude smaller and opposite sign ($\sim$28 rad m$^{-2}$) than the previously reported value. We interpret the implication of the circular polarization on its local magnetic environment and reinterpret its long-term temporal evolution in RM.
X-ray polarization signatures in bombarded magnetar atmospheres
Authors: Kelly Ruth M E , González-Caniulef Denis , Zane Silvia , Turolla Roberto , Taverna Roberto 
Published: September 2024

ABSTRACT
Magnetars are neutron stars that host huge, complex magnetic fields which require supporting currents to flow along the closed field lines. This makes magnetar atmospheres different from those of passively cooling neutron stars because of the heat deposited by back-flowing charges impinging on the star surface layers. This particle bombardment is expected to imprint the spectral and, even more, the polarization properties of the emitted thermal radiation. We present solutions for the radiative transfer problem for bombarded plane-parallel atmospheres in the high magnetic field regime. The temperature profile is assumed a priori, and selected in such a way to reflect the varying rate of energy deposition in the slab (from the impinging currents and/or from the cooling crust). We find that thermal X-ray emission powered entirely by the energy released in the atmosphere by the magnetospheric back bombardment is linearly polarized and X-mode dominated, but its polarization degree is significantly reduced (down to 10 per cent–50 per cent) when compared with that expected from a standard atmosphere heated only from the cooling crust below. By increasing the fraction of heat flowing in from the crust the polarization degree of the emergent radiation increases, first at higher energies (${\sim} 10\ \mathrm{keV}$) and then in the entire soft X-ray band. We use our models inside a ray-tracing code to derive the expected emission properties as measured by a distant observer and compare our results with recent IXPE observations of magnetar sources.
Polyubiquitinated PCNA triggers SLX4-mediated break-induced replication in alternative lengthening of telomeres (ALT) cancer cells
Authors: Kim Sangin , Park Su Hyung , Kang Nalae , Ra Jae Sun , Myung Kyungjae , Lee Kyoo-young 
Published: September 2024

Abstract
Replication stresses are the major source of break-induced replication (BIR). Here, we show that in alternative lengthening of telomeres (ALT) cells, replication stress-induced polyubiquitinated proliferating cell nuclear antigen (PCNA) (polyUb-PCNA) triggers BIR at telomeres and the common fragile site (CFS). Consistently, depleting RAD18, a PCNA ubiquitinating enzyme, reduces the occurrence of ALT-associated promyelocytic leukemia (PML) bodies (APBs) and mitotic DNA synthesis at telomeres and CFS, both of which are mediated by BIR. In contrast, inhibiting ubiquitin-specific protease 1 (USP1), an Ub-PCNA deubiquitinating enzyme, results in an increase in the above phenotypes in a RAD18- and UBE2N (the PCNA polyubiquitinating enzyme)-dependent manner. Furthermore, deficiency of ATAD5, which facilitates USP1 activity and unloads PCNAs, augments recombination-associated phenotypes. Mechanistically, telomeric polyUb-PCNA accumulates SLX4, a nuclease scaffold, at telomeres through its ubiquitin-binding domain and increases telomere damage. Consistently, APB increase induced by Ub-PCNA depends on SLX4 and structure-specific endonucleases. Taken together, our results identified the polyUb-PCNA-SLX4 axis as a trigger for directing BIR.
DciA secures bidirectional replication initiation in Vibrio cholerae
Authors: Besombes Amelie , Adam Yazid , Possoz Christophe , Junier Ivan , Barre Francois-Xavier , Ferat Jean-Luc 
Published: September 2024

Abstract
Replication is initiated bidirectionally in the three domains of life by the assembly of two replication forks at an origin of replication. This is made possible by the recruitment of two replicative helicases to a nucleoprotein platform built at the origin of replication with the initiator protein. The reason why replication is initiated bidirectionally has never been experimentally addressed due to the lack of a suitable biological system. Using genetic and genomic approaches, we show that upon depletion of DciA, replication is no longer initiated bidirectionally at the origin of replication of Vibrio cholerae chromosome 1. We show that following unidirectional replication on the left replichore, nascent DNA strands at ori1 anneal to each other to form a double-stranded DNA end. While this DNA end can be efficiently resected in recB+ cells, only a few cells use it to trigger replication on the right replichore. In most DciA-depleted cells, chromosome 1 is degraded leading to cell death. Our results suggest that DciA is essential to ensuring bidirectional initiation of replication in bacteria, preventing a cascade of deleterious events following unidirectional replication initiation.
GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data
Authors: Garbulowski Mateusz , Hillerton Thomas , Morgan Daniel , Seçilmiş Deniz , Sonnhammer Lisbet , Tjärnberg Andreas , Nordling Torbjörn E M , Sonnhammer Erik L L 
Published: September 2024

Abstract
Single-cell data is increasingly used for gene regulatory network (GRN) inference, and benchmarks for this have been developed based on simulated data. However, existing single-cell simulators cannot model the effects of gene perturbations. A further challenge lies in generating large-scale GRNs that often struggle with computational and stability issues. We present GeneSPIDER2, an update of the GeneSPIDER MATLAB toolbox for GRN benchmarking, inference, and analysis. Several software modules have improved capabilities and performance, and new functionalities have been added. A major improvement is the ability to generate large GRNs with biologically realistic topological properties in terms of scale-free degree distribution and modularity. Another major addition is a simulation of single-cell data, which is becoming increasingly popular as input for GRN inference. Specifically, we introduced the unique feature to generate single-cell data based on genetic perturbations. Finally, the simulated single-cell data was compared to real single-cell Perturb-seq data from two cell lines, showing that the synthetic and real data exhibit similar properties.
Transformer model generated bacteriophage genomes are compositionally distinct from natural sequences
Authors: Ratcliff Jeremy 
Published: September 2024

AbstractNovel applications of language models in genomics promise to have a large impact on the field. The megaDNA model is the first publicly available generative model for creating synthetic viral genomes. To evaluate megaDNA’s ability to recapitulate the nonrandom genome composition of viruses and assess whether synthetic genomes can be algorithmically detected, compositional metrics for 4969 natural bacteriophage genomes and 1002 de novo synthetic bacteriophage genomes were compared. Transformer-generated sequences had varied but realistic genome lengths, and 58% were classified as viral by geNomad. However, the sequences demonstrated consistent differences in various compositional metrics when compared to natural bacteriophage genomes by rank-sum tests and principal component analyses. A simple neural network trained to detect transformer-generated sequences on global compositional metrics alone displayed a median sensitivity of 93.0% and specificity of 97.9% (n = 12 independent models). Overall, these results demonstrate that megaDNA does not yet generate bacteriophage genomes with realistic compositional biases and that genome composition is a reliable method for detecting sequences generated by this model. While the results are specific to the megaDNA model, the evaluated framework described here could be applied to any generative model for genomic sequences.
Quantum geometry in condensed matter
Authors: Liu Tianyu , Qiang Xiao-Bin , Lu Hai-Zhou , Xie X C 
Published: September 2024

ABSTRACT
One of the most celebrated accomplishments of modern physics is the description of fundamental principles of nature in the language of geometry. As the motion of celestial bodies is governed by the geometry of spacetime, the motion of electrons in condensed matter can be characterized by the geometry of the Hilbert space of their wave functions. Such quantum geometry, comprising Berry curvature and the quantum metric, can thus exert profound influences on various properties of materials. The dipoles of both Berry curvature and the quantum metric produce nonlinear transport. The quantum metric plays an important role in flat-band superconductors by enhancing the transition temperature. The uniformly distributed momentum-space quantum geometry stabilizes the fractional Chern insulators and results in the fractional quantum anomalous Hall effect. Here we review in detail quantum geometry in condensed matter, paying close attention to its effects on nonlinear transport, superconductivity and topological properties. Possible future research directions in this field are also envisaged.
Pulmonary and extra-pulmonary effects of lung transplantation in an Italian cohort of patients with systemic sclerosis
Authors: Iannone Claudia , Pellico Maria Rosa , Morlacchi Letizia Corinna , Rossetti Valeria , Vicenzi Marco , Beretta Lorenzo , Severino Adriana , Airò Paolo , Cacciapaglia Fabio , Codullo Veronica , Faggioli Paola , Iagnocco Annamaria , Meloni Federica , Mercante Lorena , Saracco Marta , Stano Stefano , Zaccara Eleonora , Minniti Antonina , Cavalli Silvia , Trignani Giorgia , Blasi Francesco , Nosotti Mario , Boffini Massimo , Caporali Roberto , Del Papa Nicoletta 
Published: September 2024

Abstract

Objectives
Lung transplantation (LuTx) is a life-saving intervention for SSc patients with end-stage lung disease. The aim of this study was to evaluate patients’ survival and LuTx outcomes on systemic disease manifestations.

Methods
A retrospective evaluation was conducted on SSc patients who underwent LuTx between 2010 and 2021. Outcomes assessed at baseline, 6, 12 and 24 months post-LuTx included skin involvement by modified Rodnan skin score (mRSS), and global disease activity using a modified EUSTAR index (0–9 scale). Lung function rescue was evaluated by forced vital capacity (FVC). Patient survival was assessed by Kaplan–Meier analysis.

Results
Thirteen SSc patients were included, with a male/female ratio 9/4 and a median age of 48.7 years. Nine patients were affected by diffuse cutaneous scleroderma (dcSSc) and four by limited cutaneous scleroderma (lcSSc). FVC significantly increased from 56% of the predicted value at baseline to 78% at 2 years (P = 0.003). mRSS decreased from 7.4 ± 3.8 to 3.3 ± 2.5 in patients with dcSSc (P = 0.02). The modified EUSTAR index score decreased from 2.54 ± 1.8 at baseline to 0.49 ± 0.5 at 2 years (P = 0.02). Survival rate was 92.3% at 2 years, and 76.9% at 5 years. No unexpected adverse events were observed.

Conclusions
In SSc patients undergoing LuTx, an excellent 2-year survival was observed, without any disease-related adverse events. Our study supports LuTx as a viable option in SSc patients with end-stage lung disease. Apart from expected recovery of lung function, LuTx was associated with improvement of mRSS and global systemic disease activity.
Melatonin facilitates oocyte growth in goats and mice through increased nutrient reserves and enhanced mitochondrial function
Authors: He Changjiu , Wu Hao , Liu Ruiyan , Liao Jianning , Wang Xiaodong , Shi Hongru , Hou Fuqin , Reiter Russel J. , Liu Guoshi , Li Xiang 
Published: September 2024

AbstractOogenesis involves two phases: initial volumetric growth driven by nutrient accumulation and subsequent nuclear maturation. While melatonin (MLT) has been employed as a supplement to enhance the quality of fully grown oocytes during nuclear maturation phase, its impact on oocyte growth remains poorly studied. Here, we provide in vivo evidence demonstrating that follicle‐stimulating hormone increases MLT content in ovary. Administration of MLT improves oocyte growth and quality in mice and goats by enhancing nutrient reserves and mitochondrial function. Conversely, MLT‐deficient mice have smaller oocytes and dysfunctional mitochondria. Exploring the clinical implications of MLT in promoting oocyte growth, we observe that a brief 2‐day MLT treatment enhances oocyte quality and reproductive performance in older mice. These findings highlight the role of MLT in regulating oocyte growth and provide a specific treatment window for optimizing oocyte quality and reproductive performance in female animals.
O02 SIMULTANEOUS BLOOD PRESSURE AND ATRIAL FIBRILLATION SCREENING IN MAY MEASUREMENT MONTH 2022
Authors: Beaney Thomas , Kerr Gabriele , Schlaich Markus , Schutte Aletta , Stergiou George , Poulter Neil , Freedman Ben 
Published: September 2024

Background and objective:
May Measurement Month (MMM) is a global campaign aiming to raise awareness of raised blood pressure (BP). In 2022, concurrent screening for BP and atrial fibrillation (AF) was conducted in ten countries, given that hypertension and AF are both major treatable risk factors for stroke. Here, we evaluate AF prevalence and treatment by BP status among opportunistic samples of adults.

Methods:
In MMM, adults (≥18 years) undergo opportunistic BP screening. In ten participating countries, concurrent AF screening was carried out using OMRON Complete or M7 devices, in addition to three standardized, sitting BP measurements. ‘Known’ AF was defined as having had a previous diagnosis of either AF or irregular heartbeat, or taking oral anticoagulants. To risk-stratify those with AF, we calculated the CHA2DS2-VASc score. Hypertension was defined as a BP ≥140 and/or ≥90 mmHg (average of the second and third readings) and/or taking BP-lowering medication.

Results:
80,751 adults (mean age 50.1 years; 58.2% female) underwent BP and AF screening. AF was detected in 1,526 (1.9%), of whom 1,014 (66.4%) had ‘known’ AF. Of those with ‘known’ AF, 214 (21.1%) were taking anticoagulants and 644 (63.5%) were taking neither anticoagulants nor aspirin. AF was detected more commonly among those aged ≥60 than <60 (3.2% vs 1.2%: p<0.001). Hypertension was detected more commonly among those with than without AF (63.6% vs 45.2%; age-sex-adjusted p<0.001).
There was a graded association in anticoagulant and aspirin treatment rates according to CHA2DS2-VASc score in participants with ‘known’ AF (Table). Amongst participants with ‘known’ AF, anticoagulant usage was reported by 35.7% of those with a class 1 indication for anticoagulation according to CHA2DS2-VASc score.

Conclusions
Opportunistic AF screening in the MMM 2022 campaign detected AF in 3.2% of participants aged ≥60, and hypertension was more common in those with AF. Over one third of detected cases were not ‘known’ cases. Only 35.7% of ‘known’ cases with a class 1 indication for anticoagulants were treated.