bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detailed spectrophotometric analysis of the superluminous and fast evolving SN 2019neq
Authors: Fiore Achille , Benetti Stefano , Tartaglia Leonardo , Jerkstrand Anders , Salmaso Irene , Tomasella Lina , Morales-Garoffolo Antonia , Geier Stefan , Elias-Rosa Nancy , Cappellaro Enrico , Wang Xiaofeng , Mo Jun , Chen Zhihao , Yan Shengyu , Pastorello Andrea , Mazzali Paolo A , Ciolfi Riccardo , Cai Yongzhi , Fraser Morgan , Gutiérrez Claudia P , Karamehmetoglu Emir , Kuncarayakti Hanindyo , Moran Shane , Ochner Paolo , Reguitti Andrea , Reynolds Thomas M , Valerin Giorgio 
Published: November 2023

ABSTRACT
SN 2019neq was a very fast evolving superluminous supernova. At a redshift z = 0.1059, its peak absolute magnitude was −21.5 ± 0.2 mag in g band. In this work, we present data and analysis from an extensive spectrophotometric follow-up campaign using multiple observational facilities. Thanks to a nebular spectrum of SN 2019neq, we investigated some of the properties of the host galaxy at the location of SN 2019neq and found that its metallicity and specific star formation rate are in a good agreement with those usually measured for SLSNe-I hosts. We then discuss the plausibility of the magnetar and the circumstellar interaction scenarios to explain the observed light curves, and interpret a nebular spectrum of SN 2019neq using published sumo radiative-transfer models. The results of our analysis suggest that the spin-down radiation of a millisecond magnetar with a magnetic field $B\simeq 6\times 10^{14}\, \mathrm{G}$ could boost the luminosity of SN 2019neq.
Disc tearing in a Be star: predicted 3D observations
Authors: Suffak M W , Jones C E , Carciofi A C 
Published: November 2023

ABSTRACT
We build on our previous work involving smoothed particle hydrodynamic simulations of Be stars, by using the model that exhibited disc tearing as input into the three-dimensional Monte Carlo radiative transfer code hdust to predict observables from a variety of viewing angles throughout the disc tearing process. We run one simulation at the start of each orbital period from 20 to 72 orbital periods, which covers two complete disc tearing events. The resulting trends in observables are found to be dependent on the relative position of the observer and the tearing disc. The H $\rm \alpha$ equivalent width, V magnitude, and polarization can all increase or decrease in any combination depending on the viewpoint of the observer. The H $\rm \alpha$ line profile also displays changes in strength and peak separation throughout the tearing process. We show how the outer disc of the torn system can have a large effect on the H $\rm \alpha$ line profile, and also contributes to a wavelength-dependent polarization position angle, resulting in a similar sawtooth shape to the polarization percentage. Finally, we compare our predictions to Pleione (28 Tau) where evidence has suggested that a disc tearing event has occurred in the past. We find that our tearing disc model can broadly match the trends seen in Pleione’s observables, as well as produce the two-component H $\rm \alpha$ lines observed in Pleione. This is the strongest evidence, thus far, of Pleione’s disc having indeed experienced a tearing event.
Machine learning applications in Jupiter-host star classification using stellar spectra
Authors: Zammit Miguel A , Zarb Adami Kristian 
Published: November 2023

ABSTRACT
The link between stellar host properties, be it chemical, physical, dynamical, or galactic in nature, with the presence of planetary companions, has been one that has been repeatedly tested in the literature. Several corroborated work has argued that the correlation between a stellar atmosphere’s chemistry and the presence of gas giant companions is primordial in nature, implying that the chemical budget in a protoplanetary disc, and by proxy the eventual stellar host, increases the likelihood of gas giant formation. In this work, we aim to use the power of computer vision to build and test a machine learning classifier capable of discriminating between gas giant host stars and a comparison sample, using spectral data of the host stars in the visible regime. High-resolution spectra are used to preserve any inherent information which may contribute to the classification, and are fed into a stacked ensemble design incorporating several convolutional neural networks. The spectral range is binned such that each is assigned to a first-level voter, with the meta-learner aggregating their votes into a final classification. We contextualize and elaborate on the model design and results presented in a prior proceedings publication, and present an amended architecture incorporating semisupervized learning. Both models achieve relatively strong performance metrics and generalize over the holdout sets well, yet still present signs of overfitting.
Unraveling blunt-end RNA binding and ATPase-driven translocation activities of the RIG-I family helicase LGP2
Authors: Lee Kuan-Ying , Craig Candice , Patel Smita S 
Published: November 2023

Abstract
The RIG-I family helicases, comprising RIG-I, MDA5 and LGP2, are cytoplasmic RNA sensors that trigger an antiviral immune response by specifically recognizing foreign RNAs. While LGP2 lacks the signaling domain necessary for immune activation, it plays a vital role in regulating the RIG-I/MDA5 signaling pathway. In this study, we investigate the mechanisms underlying this regulation by examining the oligomeric state, RNA binding specificity, and translocation activity of human LGP2 and the impact of ATPase activity. We show that LGP2, like RIG-I, prefers binding blunt-ended double-stranded (ds) RNAs over internal dsRNA regions or RNA overhangs and associates with blunt-ends faster than with overhangs. Unlike RIG-I, a 5′-triphosphate (5′ppp), Cap0, or Cap1 RNA-end does not influence LGP2’s RNA binding affinity. LGP2 hydrolyzes ATP in the presence of RNA but at a 5–10 fold slower rate than RIG-I. Nevertheless, LGP2 uses its ATPase activity to translocate and displace biotin-streptavidin interactions. This activity is significantly hindered by a methylated RNA patch, particularly on the 3′-strand, suggesting a 3′-strand tracking mechanism like RIG-I. The preference of LGP2 for blunt-end RNA binding, its insensitivity to Cap0/Cap1 modification, and its translocation/protein displacement ability have substantial implications for how LGP2 regulates the RNA sensing process by MDA5/RIG-I.
Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics
Authors: Li Zilong , Schlick Tamar 
Published: November 2023

Abstract
The structure and dynamics of the eukaryotic genome are intimately linked to gene regulation and transcriptional activity. Many chromosome conformation capture experiments like Hi-C have been developed to detect genome-wide contact frequencies and quantify loop/compartment structures for different cellular contexts and time-dependent processes. However, a full understanding of these events requires explicit descriptions of representative chromatin and chromosome configurations. With the exponentially growing amount of data from Hi-C experiments, many methods for deriving 3D structures from contact frequency data have been developed. Yet, most reconstruction methods use polymer models with low resolution to predict overall genome structure. Here we present a Brownian Dynamics (BD) approach termed Hi-BDiSCO for producing 3D genome structures from Hi-C and Micro-C data using our mesoscale-resolution chromatin model based on the Discrete Surface Charge Optimization (DiSCO) model. Our approach integrates reconstruction with chromatin simulations at nucleosome resolution with appropriate biophysical parameters. Following a description of our protocol, we present applications to the NXN, HOXC, HOXA and Fbn2 mouse genes ranging in size from 50 to 100 kb. Such nucleosome-resolution genome structures pave the way for pursuing many biomedical applications related to the epigenomic regulation of chromatin and control of human disease.
Internal RNA 2′-O-methylation on the HIV-1 genome impairs reverse transcription
Authors: Decombe Alice , Peersen Olve , Sutto-Ortiz Priscila , Chamontin Célia , Piorkowski Géraldine , Canard Bruno , Nisole Sébastien , Decroly Etienne 
Published: November 2023

Abstract
Viral RNA genomes are modified by epitranscriptomic marks, including 2′-O-methylation that is added by cellular or viral methyltransferases. 2′-O-Methylation modulates RNA structure, function and discrimination between self- and non-self-RNA by innate immune sensors such as RIG-I-like receptors. This is illustrated by human immunodeficiency virus type-1 (HIV-1) that decorates its RNA genome through hijacking the cellular FTSJ3 2′-O-methyltransferase, thereby limiting immune sensing and interferon production. However, the impact of such an RNA modification during viral genome replication is poorly understood. Here we show by performing endogenous reverse transcription on methylated or hypomethylated HIV-1 particles, that 2′-O-methylation negatively affects HIV-1 reverse transcriptase activity. Biochemical assays confirm that RNA 2′-O-methylation impedes reverse transcriptase activity, especially at low dNTP concentrations reflecting those in quiescent cells, by reducing nucleotide incorporation efficiency and impairing translocation. Mutagenesis highlights K70 as a critical amino acid for the reverse transcriptase to bypass 2′-O-methylation. Hence, the observed antiviral effect due to viral RNA 2′-O-methylation antagonizes the FTSJ3-mediated proviral effects, suggesting the fine-tuning of RNA methylation during viral replication.
ESRP1 controls biogenesis and function of a large abundant multiexon circRNA
Authors: Liu Dawei , Dredge B Kate , Bert Andrew G , Pillman Katherine A , Toubia John , Guo Wenting , Dyakov Boris J A , Migault Melodie M , Conn Vanessa M , Conn Simon J , Gregory Philip A , Gingras Anne-Claude , Patel Dinshaw , Wu Baixing , Goodall Gregory J 
Published: November 2023

Abstract
While the majority of circRNAs are formed from infrequent back-splicing of exons from protein coding genes, some can be produced at quite high level and in a regulated manner. We describe the regulation, biogenesis and function of circDOCK1(2–27), a large, abundant circular RNA that is highly regulated during epithelial-mesenchymal transition (EMT) and whose formation depends on the epithelial splicing regulator ESRP1. CircDOCK1(2–27) synthesis in epithelial cells represses cell motility both by diverting transcripts from DOCK1 mRNA production to circRNA formation and by direct inhibition of migration by the circRNA. HITS-CLIP analysis and CRISPR-mediated deletions indicate ESRP1 controls circDOCK1(2–27) biosynthesis by binding a GGU-containing repeat region in intron 1 and detaining its splicing until Pol II completes its 157 kb journey to exon 27. Proximity-dependent biotinylation (BioID) assay suggests ESRP1 may modify the RNP landscape of intron 1 in a way that disfavours communication of exon 1 with exon 2, rather than physically bridging exon 2 to exon 27. The X-ray crystal structure of RNA-bound ESRP1 qRRM2 domain reveals it binds to GGU motifs, with the guanines embedded in clamp-like aromatic pockets in the protein.
Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation DNA sequencing
Authors: Hijikata Atsushi , Suyama Mikita , Kikugawa Shingo , Matoba Ryo , Naruto Takuya , Enomoto Yumi , Kurosawa Kenji , Harada Naoki , Yanagi Kumiko , Kaname Tadashi , Miyako Keisuke , Takazawa Masaki , Sasai Hideo , Hosokawa Junichi , Itoga Sakae , Yamaguchi Tomomi , Kosho Tomoki , Matsubara Keiko , Kuroki Yoko , Fukami Maki , Adachi Kaori , Nanba Eiji , Tsuchida Naomi , Uchiyama Yuri , Matsumoto Naomichi , Nishimura Kunihiro , Ohara Osamu 
Published: November 2023

Abstract
Next-generation DNA sequencing (NGS) in short-read mode has recently been used for genetic testing in various clinical settings. NGS data accuracy is crucial in clinical settings, and several reports regarding quality control of NGS data, primarily focusing on establishing NGS sequence read accuracy, have been published thus far. Variant calling is another critical source of NGS errors that remains unexplored at the single-nucleotide level despite its established significance. In this study, we used a machine-learning-based method to establish an exome-wide benchmark of difficult-to-sequence regions at the nucleotide-residue resolution using 10 genome sequence features based on real-world NGS data accumulated in The Genome Aggregation Database (gnomAD) of the human reference genome sequence (GRCh38/hg38). The newly acquired metric, designated the ‘UNMET score,’ along with additional lines of structural information from the human genome, allowed us to assess the sequencing challenges within the exonic region of interest using conventional short-read NGS. Thus, the UNMET score could provide a basis for addressing potential sequential errors in protein-coding exons of the human reference genome sequence GRCh38/hg38 in clinical sequencing.
Anaemia in CKD—treatment standard
Authors: Macdougall Iain C 
Published: November 2023

ABSTRACT
Anaemia is one of the most common complications of chronic kidney disease (CKD), having a significant impact on quality of life, and is also associated with a number of adverse clinical outcomes. Its pathogenesis is multifactorial, caused largely by an inadequate production of erythropoietin from the diseased kidneys, with iron deficiency, inflammation, shortened red cell lifespan and enhanced blood loss also being contributory factors. The management of this condition was transformed in the late 1980s by the advent of recombinant human erythropoietin (epoetin), and treatment paradigms have developed over the last three decades, largely focusing on a combination of epoetin or its analogues (erythropoiesis-stimulating agents; ESAs) along with iron supplementation, often administered intravenously due to increased hepcidin levels limiting iron absorption from the gut. Indeed, in patients with early CKD and iron deficiency, iron per se may be sufficient to improve the anaemia, delaying the need for ESA therapy. Other causes of anaemia should be excluded and corrected (if possible) before resorting to treatment with ESAs and iron. More recently, the hypoxia-inducible factor–prolyl hydroxylase inhibitors have entered the therapeutic arena; these are orally active agents that upregulate endogenous erythropoietin production as well as a number of iron-regulatory genes which may also enhance erythropoiesis. The latter drugs are highly efficacious, and may have advantages in inflammatory conditions causing resistance to conventional ESA therapy, but concerns exist regarding their safety, particularly in the longer term. This article reviews the current standards of treatment, as well as recent novel developments in the management of anaemia in CKD.
Arteriovenous access creation and hazards of hospitalization and death in patients starting hemodialysis
Authors: Alencar de Pinho Natalia , Prezelin-Reydit Mathilde , Harambat Jerome , Couchoud Cécile , Glaudet Florence , Combe Christian , Rondeau Virginie , Leffondré Karen 
Published: November 2023

ABSTRACT

Background
Recent evidence suggests an overestimation of the benefits associated with arteriovenous (AV) fistula versus graft in certain populations. We assessed hazards of all-cause and cause-specific hospitalization and death associated with AV access type in patients who started hemodialysis with a catheter in France, overall and by subgroups of age, sex and comorbidities.

Methods
We performed a target trial emulation including patients who initiated hemodialysis with a catheter from 2010 through 2018 and were followed by the REIN Registry. We identified first-created fistula or graft through the French national health-administrative database. We used joint frailty models to deal with recurrent hospitalizations and potential informative censoring by death, and inverse probability weighting to account for confounding.

Results
From the 18 800 patients included (mean age 68 ± 15 years, 35% women), 5% underwent AV graft creation first. The weighted hazard ratio (wHR) of all-cause hospitalization associated with graft was 1.08 [95% confidence interval (CI) 1.02 to 1.15], that of vascular access–related hospitalization was 1.43 (95% CI 1.32 to 1.55), and those of cardiovascular- and infection-related hospitalizations were 1.14 (95% CI 1.03 to 1.26) and 1.11 (95% CI 0.97 to 1.28), respectively. Results were consistent for most subgroups, except that the highest hazard of all-cause, cardiovascular- and infection-related hospitalizations with graft was blunted in patients with comorbidities (i.e. diabetes, wHR 1.01, 95% CI 0.93 to 1.10; 1.10, 95% CI 0.96 to 1.26; and 0.94, 95% CI 0.78 to 1.12, respectively).

Conclusions
In patients starting hemodialysis with a catheter, AV graft creation is associated with increased hazard of vascular access–related hospitalizations compared with fistula. This may not be the case for death or other causes of hospitalization.
Machine-learned wearable sensors for real-time hand-motion recognition: toward practical applications
Authors: Pyun Kyung Rok , Kwon Kangkyu , Yoo Myung Jin , Kim Kyun Kyu , Gong Dohyeon , Yeo Woon-Hong , Han Seungyong , Ko Seung Hwan 
Published: November 2023

ABSTRACT
Soft electromechanical sensors have led to a new paradigm of electronic devices for novel motion-based wearable applications in our daily lives. However, the vast amount of random and unidentified signals generated by complex body motions has hindered the precise recognition and practical application of this technology. Recent advancements in artificial-intelligence technology have enabled significant strides in extracting features from massive and intricate data sets, thereby presenting a breakthrough in utilizing wearable sensors for practical applications. Beyond traditional machine-learning techniques for classifying simple gestures, advanced machine-learning algorithms have been developed to handle more complex and nuanced motion-based tasks with restricted training data sets. Machine-learning techniques have improved the ability to perceive, and thus machine-learned wearable soft sensors have enabled accurate and rapid human-gesture recognition, providing real-time feedback to users. This forms a crucial component of future wearable electronics, contributing to a robust human–machine interface. In this review, we provide a comprehensive summary covering materials, structures and machine-learning algorithms for hand-gesture recognition and possible practical applications through machine-learned wearable electromechanical sensors.
Non-cigarette Tobacco Use and Stroke Among West Africans: Evidence From the SIREN Study
Authors: Fakunle Adekunle Gregory , Okekunle Akinkunmi Paul , Asowata Osahon Jeffery , Akpa Onoja , Sarfo Fred S , Akpalu Albert , Wahab Kolawole , Obiako Reginald , Komolafe Morenikeji , Owolabi Lukman , Osaigbovo Godwin O , Adeoye Abiodun M , Tiwari Hemant K , Uvere Ezinne O , Akinyemi Joshua , Jenkins Carolyn , Arulogun Oyedunni , Ibinaiye Philip , Appiah Lambert T , Bello Temilade , Singh Arti , Yaria Joseph , Calys-Tagoe Benedict , Ogbole Godwin , Chukwuonye Ijezie , Melikam Chidinma , Adebayo Philip , Mensah Yaw , Adebayo Oladimeji , Adeniyi Sunday , Oguike Wisdom , Donna Arnett , Akinyemi Rufus , Ovbiagele Bruce , Owolabi Mayowa 
Published: November 2023

Abstract

Introduction
Non-cigarette tobacco (NCT) represents a form of tobacco use with a misperceived significance in chronic disease events. Whether NCT use is sufficient to promote stroke events, especially among Africans, is yet to be understood. This study assessed the relationship between NCT use and stroke among indigenous Africans.

Methods
A total of 7617 respondents (NCT users: 41 vs. non-NCT: 7576) from the Stroke Investigative Research and Educational Network (SIREN) study were included in the current analysis. NCT use was defined as self-reported use of smoked (cigars or piper) or smokeless (snuff or chewed) tobacco in the past year preceding stroke events. Stroke was defined based on clinical presentation and confirmed with a cranial computed tomography/magnetic resonance imaging. Multivariable-adjusted logistic regression was applied to estimate the odds ratio (OR) and 95% confidence interval (CI) for the relationship of NCT with stroke at a two-sided p &lt; .05.

Results
Out of the 41 (0.54%) who reported NCT use, 27 (65.9%) reported using smokeless NCT. NCT users were older than non-NCT users (62.8 ± 15.7 vs. 57.7 ± 14.8 years). Overall, NCT use was associated with first-ever stroke (OR: 2.08; 95% CI: 1.02, 4.23) in the entire sample. Notably, smokeless NCT use was independently associated with higher odds of stroke (OR: 2.74; 95% CI: 1.15, 6.54), but smoked NCT use (OR: 0.16; 95% CI: 0.02, 1.63) presented a statistically insignificant association after adjusting for hypertension and other covariates.

Conclusions
NCT use was associated with higher odds of stroke, and public health interventions targeting NCT use might be promising in reducing the burden of stroke among indigenous Africans.

Implications
A detailed understanding of the relationship between NCT use and stroke will likely inform well-articulated policy guidance and evidence-based recommendations for public health prevention and management of stroke on the African continent.
Detached from Sympathy, Unconscious of Trauma: The Impact of the Forensic Virtues of Impartiality and Detachment on Rape Examinations in Britain 1924–1978
Authors: Dirven Pauline 
Published: November 2023

Summary
This article asks why British mainstream forensic literature and practice did not acknowledge the long-term mental consequences of rape for victims and their need for a sympathetic approach before the 1970s. I argue that this was not simply out of ignorance, considering that in the period 1924–1978 there already were some medical practitioners—women doctors, psychiatrists and gynaecologists—who expressed concern for these matters. However, the forensic expert witnesses, who were influential in the field, considered the virtue of sympathy and the practices of care that women doctors promoted to be incompatible with the judicial virtue of impartiality. To avoid any suggestion of partiality, which would damage their authority in the adversarial courtroom, these men instead employed the epistemic virtue of emotional detachment. This led them to adopt a sceptical attitude towards rape victims and drew their attention away from the psychological care women and children might require.