bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring theex-situcomponents withinGaiaDR3
Authors: Li Zhuohan , Zhao Gang , Zhang Ruizhi , Xue Xiang-Xiang , Chen Yuqin , Amarante João A S 
Published: December 2023

ABSTRACTThe presence of Gaia DR3 provides a large sample of stars with complete 6D information, offering a fertile ground for the exploration of stellar objects that were accreted to the Milky Way through ancient merger events. In this study, we developed a deep learning methodology to identify ex-situ stars within the Gaia DR3 catalogue. After two phases of training, our neural network (NN) model was capable of performing binary classification of stars based on input data consisting of 3D position and velocity, as well as actions. From the target sample of 27 085 748 stars, our NN model managed to identify 160 146 ex-situ stars. The metallicity distribution suggests that this ex-situ sample comprises multiple components but appears to be predominated by the Gaia-Sausage-Enceladus (GSE). We identified member stars of the Magellanic Clouds, Sagittarius, and 20 globular clusters throughout our examination. Furthermore, an extensive group of member stars from GSE, Thamnos, Sequoia, Helmi streams, Wukong, and Pontus were meticulously selected, constituting an ideal sample for the comprehensive study of substructures. Finally, we conducted a preliminary estimation to determine the proportions of ex-situ stars in the thin disc, thick disc, and halo, which resulted in percentages of 0.1 per cent, 1.6 per cent, and 63.2 per cent, respectively. As the vertical height from the Galactic disc and distance from the Galactic centre increased, there was a corresponding upward trend in the ex-situ fraction of the target sample.
The true fraction of repeating fast radio bursts revealed through CHIME source count evolution
Authors: Yamasaki Shotaro , Goto Tomotsugu , Ling Chih-Teng , Hashimoto Tetsuya 
Published: December 2023

ABSTRACT
Fast Radio Bursts (FRBs) are classified into repeaters and non-repeaters, with only a few per cent of the observed FRB population from the Canadian Hydrogen Intensity Mapping Experiment (CHIME) confirmed as repeaters. However, this figure represents only a lower limit due to the observational biases, and the true fraction of repeaters remains unknown. Correcting for these biases uncovers a notable decline in apparently non-repeating FRB detection rate as the CHIME operational time increases. This finding suggests that a significant portion of apparently non-repeating FRBs could in fact exhibit repetition when observed over more extended periods. A simple population model infers that the true repeater fraction likely exceeds 50 per cent with 99 per cent confidence, a figure substantially larger than the observed face value, even consistent with 100 per cent. This greater prevalence of repeaters had previously gone unnoticed due to their very low repetition rates (∼10−3.5 h−1 on average). Hence, theoretical FRB models must incorporate these low-rate repeaters. Furthermore, our results indicate a significantly higher repeater volume number density, potentially exceeding observed values by up to 104 times, which in turn impacts comparisons with potential FRB progenitors.
Visualizing a two-state conformational ensemble in stem–loop 3 of the transcriptional regulator 7SK RNA
Authors: Camara Momodou B , Lange Bret , Yesselman Joseph D , Eichhorn Catherine D 
Published: December 2023

Abstract
Structural plasticity is integral to RNA function; however, there are currently few methods to quantitatively resolve RNAs that have multiple structural states. NMR spectroscopy is a powerful approach for resolving conformational ensembles but is size-limited. Chemical probing is well-suited for large RNAs but provides limited structural and kinetics information. Here, we integrate the two approaches to visualize a two-state conformational ensemble for the central stem–loop 3 (SL3) of 7SK RNA, a critical element for 7SK RNA function in transcription regulation. We find that the SL3 distal end exchanges between two equally populated yet structurally distinct states in both isolated SL3 constructs and full-length 7SK RNA. We rationally designed constructs that lock SL3 into a single state and demonstrate that both chemical probing and NMR data fit to a linear combination of the two states. Comparison of vertebrate 7SK RNA sequences shows either or both states are highly conserved. These results provide new insights into 7SK RNA structural dynamics and demonstrate the utility of integrating chemical probing with NMR spectroscopy to gain quantitative insights into RNA conformational ensembles.
Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression
Authors: Loza Martin , Vandenbon Alexis , Nakai Kenta 
Published: December 2023

Abstract
In this research, we elucidate the presence of around 11,000 housekeeping cis-regulatory elements (HK-CREs) and describe their main characteristics. Besides the trivial promoters of housekeeping genes, most HK-CREs reside in promoter regions and are involved in a broader role beyond housekeeping gene regulation. HK-CREs are conserved regions rich in unmethylated CpG sites. Their distribution highly correlates with that of protein-coding genes, and they interact with many genes over long distances. We observed reduced activity of a subset of HK-CREs in diverse cancer subtypes due to aberrant methylation, particularly those located in chromosome 19 and associated with zinc finger genes. Further analysis of samples from 17 cancer subtypes showed a significantly increased survival probability of patients with higher expression of these genes, suggesting them as housekeeping tumor suppressor genes. Overall, our work unravels the presence of housekeeping CREs indispensable for the maintenance and stability of cells.
Peak-agnostic high-resolution cis-regulatory circuitry mapping using single cell multiome data
Authors: Zhang Zidong , Ruf-Zamojski Frederique , Zamojski Michel , Bernard Daniel J , Chen Xi , Troyanskaya Olga G , Sealfon Stuart C 
Published: December 2023

Abstract
Single same cell RNAseq/ATACseq multiome data provide unparalleled potential to develop high resolution maps of the cell-type specific transcriptional regulatory circuitry underlying gene expression. We present CREMA, a framework that recovers the full cis-regulatory circuitry by modeling gene expression and chromatin activity in individual cells without peak-calling or cell type labeling constraints. We demonstrate that CREMA overcomes the limitations of existing methods that fail to identify about half of functional regulatory elements which are outside the called chromatin ‘peaks’. These circuit sites outside called peaks are shown to be important cell type specific functional regulatory loci, sufficient to distinguish individual cell types. Analysis of mouse pituitary data identifies a Gata2-circuit for the gonadotrope-enriched disease-associated Pcsk1 gene, which is experimentally validated by reduced gonadotrope expression in a gonadotrope conditional Gata2-knockout model. We present a web accessible human immune cell regulatory circuit resource, and provide CREMA as an R package.
The protein phosphatase EYA4 promotes homologous recombination (HR) through dephosphorylation of tyrosine 315 on RAD51
Authors: de la Peña Avalos Bárbara , Paquet Nicolas , Tropée Romain , Coulombe Yan , Palacios Hannah , Leung Justin W , Masson Jean-Yves , Duijf Pascal H G , Dray Eloïse 
Published: December 2023

Abstract
Efficient DNA repair and limitation of genome rearrangements rely on crosstalk between different DNA double-strand break (DSB) repair pathways, and their synchronization with the cell cycle. The selection, timing and efficacy of DSB repair pathways are influenced by post-translational modifications of histones and DNA damage repair (DDR) proteins, such as phosphorylation. While the importance of kinases and serine/threonine phosphatases in DDR have been extensively studied, the role of tyrosine phosphatases in DNA repair remains poorly understood. In this study, we have identified EYA4 as the protein phosphatase that dephosphorylates RAD51 on residue Tyr315. Through its Tyr phosphatase activity, EYA4 regulates RAD51 localization, presynaptic filament formation, foci formation, and activity. Thus, it is essential for homologous recombination (HR) at DSBs. DNA binding stimulates EYA4 phosphatase activity. Depletion of EYA4 decreases single-stranded DNA accumulation following DNA damage and impairs HR, while overexpression of EYA4 in cells promotes dephosphorylation and stabilization of RAD51, and thereby nucleoprotein filament formation. Our data have implications for a pathological version of RAD51 in EYA4-overexpressing cancers.
Enhancer–promoter interactions can form independently of genomic distance and be functional across TAD boundaries
Authors: Balasubramanian Deevitha , Borges Pinto Pedro , Grasso Alexia , Vincent Séverine , Tarayre Hélène , Lajoignie Damien , Ghavi-Helm Yad 
Published: December 2023

Abstract
Topologically Associating Domains (TADs) have been suggested to facilitate and constrain enhancer–promoter interactions. However, the role of TAD boundaries in effectively restricting these interactions remains unclear. Here, we show that a significant proportion of enhancer–promoter interactions are established across TAD boundaries in Drosophila embryos, but that developmental genes are strikingly enriched in intra- but not inter-TAD interactions. We pursued this observation using the twist locus, a master regulator of mesoderm development, and systematically relocated one of its enhancers to various genomic locations. While this developmental gene can establish inter-TAD interactions with its enhancer, the functionality of these interactions remains limited, highlighting the existence of topological constraints. Furthermore, contrary to intra-TAD interactions, the formation of inter-TAD enhancer–promoter interactions is not solely driven by genomic distance, with distal interactions sometimes favored over proximal ones. These observations suggest that other general mechanisms must exist to establish and maintain specific enhancer–promoter interactions across large distances.
Efficacy and toxicity of bimodal radiotherapy in WHO grade 2 meningiomas following subtotal resection with carbon ion boost: Prospective phase 2 MARCIE trial
Authors: Deng Maximilian Y , Maas Sybren L N , Hinz Felix , Karger Christian P , Sievers Philipp , Eichkorn Tanja , Meixner Eva , Hoegen-Sassmannshausen Philipp , Hörner-Rieber Juliane , Lischalk Jonathan W , Seidensaal Katharina , Bernhardt Denise , Jungk Christine , Unterberg Andreas , Wick Antje , Wick Wolfgang , von Deimling Andreas , Sahm Felix , Combs Stephanie , Herfarth Klaus , Debus Jürgen , König Laila 
Published: December 2023

Abstract

Background
Novel radiotherapeutic modalities using carbon ions provide an increased relative biological effectiveness (RBE) compared to photons, delivering a higher biological dose while reducing radiation exposure for adjacent organs. This prospective phase 2 trial investigated bimodal radiotherapy using photons with carbon-ion (C12)-boost in patients with WHO grade 2 meningiomas following subtotal resection (Simpson grade 4 or 5).

Methods
A total of 33 patients were enrolled from July 2012 until July 2020. The study treatment comprised a C12-boost (18 Gy [RBE] in 6 fractions) applied to the macroscopic tumor in combination with photon radiotherapy (50 Gy in 25 fractions). The primary endpoint was the 3-year progression-free survival (PFS), and the secondary endpoints included overall survival, safety and treatment toxicities.

Results
With a median follow-up of 42 months, the 3-year estimates of PFS, local PFS and overall survival were 80.3%, 86.7%, and 89.8%, respectively. Radiation-induced contrast enhancement (RICE) was encountered in 45%, particularly in patients with periventricularly located meningiomas. Patients exhibiting RICE were mostly either asymptomatic (40%) or presented immediate neurological and radiological improvement (47%) after the administration of corticosteroids or bevacizumab in case of radiation necrosis (3/33). Treatment-associated complications occurred in 1 patient with radiation necrosis who died due to postoperative complications after resection of radiation necrosis. The study was prematurely terminated after recruiting 33 of the planned 40 patients.

Conclusions
Our study demonstrates a bimodal approach utilizing photons with C12-boost may achieve a superior local PFS to conventional photon RT, but must be balanced against the potential risks of toxicities.
High-speed flexible near-infrared organic photodiode for optical communication
Authors: Zhu Yu , Chen Hongbin , Han Ruiman , Qin Hao , Yao Zhaoyang , Liu Hang , Ma Yanfeng , Wan Xiangjian , Li Guanghui , Chen Yongsheng 
Published: December 2023

ABSTRACT
Optical communication is a particularly compelling technology for tackling the speed and capacity bottlenecks in data communication in modern society. Currently, the silicon photodetector plays a dominant role in high-speed optical communication across the visible-near-infrared spectrum. However, its intrinsic rigid structure, high working bias and low responsivity essentially limit its application in next-generation flexible optoelectronic devices. Herein, we report a narrow-bandgap non-fullerene acceptor (NFA) with a remarkable π-extension in the direction of both central and end units (CH17) with respect to the Y6 series, which demonstrates a more effective and compact 3D molecular packing, leading to lower trap states and energetic disorders in the photoactive film. Consequently, the optimized solution-processed organic photodetector (OPD) with CH17 exhibits a remarkable response time of 91 ns (λ = 880 nm) due to the high charge mobility and low parasitic capacitance, exceeding the values of most commercial Si photodiodes and all NFA-based OPDs operating in self-powered mode. More significantly, the flexible OPD exhibits negligible performance attenuation (&lt;1%) after bending for 500 cycles, and maintains 96% of its initial performance even after 550 h of indoor exposure. Furthermore, the high-speed OPD demonstrates a high data transmission rate of 80 MHz with a bit error rate of 3.5 $ \times $ 10−4, meaning it has great potential in next-generation high-speed flexible optical communication systems.
Smoking Quit Attempts and Associated Factors Among Rural Adults Who Smoke Daily in the United States
Authors: Bittencourt Lorna , Rubenstein Dana , Noonan Devon , McClernon F Joseph , Carroll Dana Mowls 
Published: December 2023

Abstract

Introduction
Rural American communities are heavily affected by tobacco-related health disparities. This study aims to evaluate the prevalence of quit attempts (QAs) and factors that promote or impede QA among rural adults who smoke daily.

Methods
Data from Wave 5 of the Population Assessment of Tobacco and Health study were analyzed. Multivariable logistic regression was used to identify factors associated with QA. Backward selection was used to identify variables included in the final model with statistical significance set at p &lt; .05.

Results
Among 1610 rural adults who smoked daily, the prevalence of a QA in the past 12 months was 25.6% (95% confidence interval [CI]: 23.2, 28.2). Factors associated with greater QA odds: having greater education (adjusted odds ratio [aOR] = 1.35, 95% CI: 1.03, 1.77), e-cigarette use (aOR = 1.35 95% CI: 1.03, 1.80), disapproval of smoking from friends/family (aOR = 1.46, 95% CI: 1.09–1.94), greater frequency of thinking about the harm of tobacco (aOR = 1.48, 95% CI: 1.28, 1.71), fair/poor physical health (aOR = 1.31, 95% CI: 1.00, 1.70), and being advised to quit by a doctor (aOR = 1.63, 95% CI:1.25, 2.13). Smokeless tobacco use (aOR = 0.67, 95% CI: 0.47, 0.96) and greater cigarettes per day (aOR = 0.67, 95% CI: 0.47, 0.96) were associated with QA lower odds.

Conclusions
Only one in four rural adults who smoke made a past-year QA. Interventions that promote provider advice to quit smoking, tobacco health harms, and normative beliefs may increase QAs in rural communities.

Implications
Along with higher smoking rates and lower QAs, rural communities face limited access to programs, medication, and health care professionals as tools to help them quit smoking. Public Health initiatives should focus on developing cultural sensitivity training targeting health care professionals to advise patients to quit smoking and the role of multiple tobacco product use. Furthermore, given the low rates of smoking QAs, future mixed-methods research is needed to inform policies and interventions targeted at eliminating tobacco-related health disparities.
Health insurance status, lifestyle choices and the presence of non-communicable diseases: a systematic review
Authors: Folayan Adeola , Cheong Mark Wing Loong , Fatt Quek Kia , Su Tin Tin 
Published: December 2023

Abstract

Background
Although health insurance (HI) has effectively mitigated healthcare financial burdens, its contribution to healthy lifestyle choices and the presence of non-communicable diseases (NCDs) is not well established. We aimed to systematically review the existing evidence on the effect of HI on healthy lifestyle choices and NCDs.

Methods
A systematic review was conducted across PubMed, Medline, Embase, Cochrane Library and CINAHLComplet@EBSCOhost from inception until 30 September 2022, capturing studies that reported the effect of HI on healthy lifestyle and NCDs. A narrative synthesis of the studies was done. The review concluded both longitudinal and cross-sectional studies. A critical appraisal checklist for survey-based studies and the National Institutes of Health Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies were used for the quality assessment.

Result
Twenty-four studies met the inclusion criteria. HI was associated with the propensity to engage in physical activities (6/11 studies), consume healthy diets (4/7 studies), not to smoke (5/11 studies) or take alcohol (5/10 studies). Six (of nine) studies showed that HI coverage was associated with a lowered prevalence of NCDs.

Conclusion
This evidence suggests that HI is beneficial. More reports showed that it propitiated a healthy lifestyle and was associated with a reduced prevalence of NCDs.
Unveiling protein corona composition: predicting with resampling embedding and machine learning
Authors: Liao Rong , Zhuang Yan , Li Xiangfeng , Chen Ke , Wang Xingming , Feng Cong , Yin Guangfu , Zhu Xiangdong , Lin Jiangli , Zhang Xingdong 
Published: December 2023

Abstract
Biomaterials with surface nanostructures effectively enhance protein secretion and stimulate tissue regeneration. When nanoparticles (NPs) enter the living system, they quickly interact with proteins in the body fluid, forming the protein corona (PC). The accurate prediction of the PC composition is critical for analyzing the osteoinductivity of biomaterials and guiding the reverse design of NPs. However, achieving accurate predictions remains a significant challenge. Although several machine learning (ML) models like Random Forest (RF) have been used for PC prediction, they often fail to consider the extreme values in the abundance region of PC absorption and struggle to improve accuracy due to the imbalanced data distribution. In this study, resampling embedding was introduced to resolve the issue of imbalanced distribution in PC data. Various ML models were evaluated, and RF model was finally used for prediction, and good correlation coefficient (R2) and root-mean-square deviation (RMSE) values were obtained. Our ablation experiments demonstrated that the proposed method achieved an R2 of 0.68, indicating an improvement of approximately 10%, and an RMSE of 0.90, representing a reduction of approximately 10%. Furthermore, through the verification of label-free quantification of four NPs: hydroxyapatite (HA), titanium dioxide (TiO2), silicon dioxide (SiO2) and silver (Ag), and we achieved a prediction performance with an R2 value &gt;0.70 using Random Oversampling. Additionally, the feature analysis revealed that the composition of the PC is most significantly influenced by the incubation plasma concentration, PDI and surface modification.
The cost-effectiveness of adding an ultrasound corticosteroid and local anaesthetic injection to advice and education for hip osteoarthritis
Authors: Kigozi Jesse , Oppong Raymond , Paskins Zoe , Bromley Kieran , Lewis Martyn , Hughes Gemma , Hughes Emily , Hennings Susie , Cherrington Andrea , Hall Alison , Holden Melanie A , Stevenson Kay , Menon Ajit , Roberts Philip , Peat George , Jinks Clare , Foster Nadine E , Mallen Christian D , Roddy Edward 
Published: December 2023

Abstract

Objectives
Evidence for the comparative cost-effectiveness of intra-articular corticosteroid injection in people with hip osteoarthritis (OA) remains unclear. This study investigated the cost-effectiveness of best current treatment (BCT), comprising advice and education, with BCT plus a single ultrasound-guided intra-articular hip injection of 40 mg triamcinolone acetonide and 4 ml 1% lidocaine hydrochloride (BCT+US-T).

Methods
A trial-based cost–utility analysis of BCT+US-T compared with BCT was undertaken over 6 months. Patient-level cost data were obtained, and effectiveness was measured in terms of quality-adjusted life years (QALYs), allowing the calculation of cost per QALY gained from a UK National Health Service (NHS) perspective.

Results
BCT+US-T was associated with lower mean NHS costs (BCT+US-T minus BCT: −£161.6; 95% CI: −£583.95, £54.18) and small but significantly higher mean QALYs than BCT alone over 6 months (BCT+US-T minus BCT: 0.0487; 95% CI: 0.0091, 0.0886). In the base case, BCT+US-T was the most cost-effective and dominated BCT alone. Differences in total costs were driven by number of visits to NHS consultants, private physiotherapists and chiropractors, and hip surgery, which were more common with BCT alone than BCT+US-T.

Conclusion
Intra-articular corticosteroid injection plus BCT (BCT+US-T) for patients with hip OA results in lower costs and better outcomes, and is highly cost-effective, compared with BCT alone.

Trial registration
EudraCT: 2014-003412-37 (8 August 2015) and registered with Current Controlled Trials: ISRCTN 50550256 (28 July 2015).

Trial protocol
Full details of the trial protocol can be found in the Supplementary Appendix, available with the full text of this article at https://bmcmusculoskeletdisord.biomedcentral.com/articles/10.1186/s12891-018-2153-0, doi: doi.org/10.1186/s12891-018-2153-0.