bluuebunny/crossref_metadata_2025_split huggingface dataset:
The frequency and mass-ratio distribution of binaries in clusters II: radial segregation in the nearby dissolving open clusters Hyades and Praesepe
Authors: Albrow Michael D 
Published: February 2024

ABSTRACT
We have determined the mass functions, mass-ratio distribution functions, and fractions of binary stars with mass ratios above particular thresholds for radially separated populations of stars in the nearby open clusters Hyades and Praesepe. Radial mass segregation is detected, with the populations of stars within the tidal radii having much flatter mass functions than those outside the tidal radii. Within the tidal radii, the frequency of binary stars with mass ratio q &gt; 0.5 is 50–75 per cent higher for Hyades and 5–30 per cent higher for Praesepe. We also, for the first time, detect mass-ratio radial segregation. Of the binaries for which q &gt; 0.5, ∼80 per cent of the inner Hyades population also have q &gt; 0.75, while for the extra-tidal population, the ratio is ∼50 per cent. For Praesepe, ∼67 per cent of the inner sample have q &gt; 0.75, and 35–45 per cent of the outer sample.
A candidate for central tidal disruption event in the broad line AGN SDSS J1605 with double-peaked broad H β
Authors: Zhang Xue-Guang 
Published: February 2024

ABSTRACT
In this letter, motivated by double-peaked broad Balmer emission lines probably related to tidal disruption events (TDEs), a potential TDE candidate is reported in Sloan Digital Sky Survey (SDSS) J160536+134838 (=SDSS J1605) at z ∼ 0.44 having quasar-like spectrum but with double-peaked broad H β. The long-term Catalina Sky Survey (CSS) light curve can be naturally described by a main-sequence star of $2.82_{-0.19}^{+0.20}{\rm M_\odot }$ disrupted by the central black hole (BH) of $144_{-21}^{+26} \times 10^6{\rm M_\odot }$ in SDSS J1605. Meanwhile, the All-Sky Automated Survey for SuperNovae light curves afterwards show none apparent trend variability, indicating the bright CSS flare in SDSS J1605 unique and different enough from variability of normal active galactic nuclei (AGN). Furthermore, there is a consistency between the TDE model determined sizes of debris with the sizes of emission regions for the double-peaked broad H β described by the accretion disc model, supporting the disc-like broad emission line regions (BLRs) probably related to a central TDE in SDSS J1605. And the virial BH mass ∼7 times higher than the TDE model determined value can be naturally explained by R–L relation determined BLRs sizes very larger than the actual distance of emission regions related to TDEs debris in SDSS J1605. Although no clear conclusion on double-peaked broad lines absolutely related to TDEs, the results here provide clues to detect potential TDEs in AGN with double-peaked broad lines.
G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity
Authors: Liang Hui-ting , Yan Jiang-yu , Yao Hao-jun , Zhang Xue-nan , Xing Zhi-ming , Liu Lin , Chen Yao-qing , Li Guo-rui , Huang Jing , He Yi-de , Zheng Ke-wei 
Published: February 2024

Abstract
Human DNA topoisomerase 1 (Top1) is a crucial enzyme responsible for alleviating torsional stress on DNA during transcription and replication, thereby maintaining genome stability. Previous researches had found that non-working Top1 interacted extensively with chromosomal DNA in human cells. However, the reason for its retention on chromosomal DNA remained unclear. In this study, we discovered a close association between Top1 and chromosomal DNA, specifically linked to the presence of G-quadruplex (G4) structures. G4 structures, formed during transcription, trap Top1 and hinder its ability to relax neighboring DNAs. Disruption of the Top1–G4 interaction using G4 ligand relieved the inhibitory effect of G4 on Top1 activity, resulting in a further reduction of R-loop levels in cells. Additionally, the activation of Top1 through the use of a G4 ligand enhanced the toxicity of Top1 inhibitors towards cancer cells. Our study uncovers a negative regulation mechanism of human Top1 and highlights a novel pathway for activating Top1.
Molecular and thermodynamic determinants of self-assembly and hetero-oligomerization in the enterobacterial thermo-osmo-regulatory protein H-NS
Authors: Lukose Bincy , Maruno Takahiro , Faidh Mohammed A , Uchiyama Susumu , Naganathan Athi N 
Published: February 2024

Abstract
Environmentally regulated gene expression is critical for bacterial survival under stress conditions, including extremes in temperature, osmolarity and nutrient availability. Here, we dissect the thermo- and osmo-responsory behavior of the transcriptional repressor H-NS, an archetypal nucleoid-condensing sensory protein, ubiquitous in enterobacteria that infect the mammalian gut. Through experiments and thermodynamic modeling, we show that H-NS exhibits osmolarity, temperature and concentration dependent self-association, with a highly polydisperse native ensemble dominated by monomers, dimers, tetramers and octamers. The relative population of these oligomeric states is determined by an interplay between dimerization and higher-order oligomerization, which in turn drives a competition between weak homo- versus hetero-oligomerization of protein-protein and protein-DNA complexes. A phosphomimetic mutation, Y61E, fully eliminates higher-order self-assembly and preserves only dimerization while weakening DNA binding, highlighting that oligomerization is a prerequisite for strong DNA binding. We further demonstrate the presence of long-distance thermodynamic connectivity between dimerization and oligomerization sites on H-NS which influences the binding of the co-repressor Cnu, and switches the DNA binding mode of the hetero-oligomeric H-NS:Cnu complex. Our work thus uncovers important organizational principles in H-NS including a multi-layered thermodynamic control, and provides a molecular framework broadly applicable to other thermo-osmo sensory proteins that employ similar mechanisms to regulate gene expression.
Extending DeepTrio for sensitive detection of complex de novo mutation patterns
Authors: Brand Fabian , Guski Jannis , Krawitz Peter 
Published: February 2024

Abstract
De novo mutations (DNMs), and among them clustered DNMs within 20 bp of each other (cDNMs) are known to be a potential cause of genetic disorders. However, identifying DNM in whole genome sequencing (WGS) data is a process that often suffers from low specificity. We propose a deep learning framework for DNM and cDNM detection in WGS data based on Google's DeepTrio software for variant calling, which considers regions of 110 bp up- and downstream from possible variants to take information from the surrounding region into account. We trained a model each for the DNM and cDNM detection tasks and tested it on data generated on the HiSeq and NovaSeq platforms. In total, the model was trained on 82 WGS trios generated on the NovaSeq and 16 on the HiSeq. For the DNM detection task, our model achieves a sensitivity of 95.7% and a precision of 89.6%. The extended model adds confidence information for cDNMs, in addition to standard variant classes and DNMs. While this causes a slight drop in DNM sensitivity (91.96%) and precision (90.5%), on HG002 cDNMs can be isolated from other variant classes in all cases (5 out of 5) with a precision of 76.9%. Since the model emits confidence probabilities for each variant class, it is possible to fine-tune cutoff thresholds to allow users to select a desired trade-off between sensitivity and specificity. These results show that DeepTrio can be retrained to identify complex mutational signatures with only little modification effort.
Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates
Authors: Chen Yibi , Dougan Katherine E , Nguyen Quan , Bhattacharya Debashish , Chan Cheong Xin 
Published: February 2024

AbstractDinoflagellates are a diverse group of phytoplankton, ranging from harmful bloom-forming microalgae to photosymbionts of coral reefs. Genome-scale data from dinoflagellates reveal atypical genomic features, extensive genomic divergence, and lineage-specific innovation of gene functions. Long non-coding RNAs (lncRNAs), known to regulate gene expression in eukaryotes, are largely unexplored in dinoflagellates. Here, using high-quality genome and transcriptome data, we identified 48039 polyadenylated lncRNAs in three dinoflagellate species: the coral symbionts Cladocopium proliferum and Durusdinium trenchii, and the bloom-forming species, Prorocentrum cordatum. These lncRNAs have fewer introns and lower G+C content than protein-coding sequences; 37 768 (78.6%) are unique with respect to sequence similarity. We classified all lncRNAs based on conserved motifs (k-mers) into distinct clusters, following properties of protein-binding and/or subcellular localisation. Interestingly, 3708 (7.7%) lncRNAs are differentially expressed under heat stress, algal lifestyle, and/or growth phase, and share co-expression patterns with protein-coding genes. Based on inferred triplex interactions between lncRNA and putative promoter regions, we identified 19 460 putative gene targets for 3721 lncRNAs; 907 genes exhibit differential expression under heat stress. These results reveal, for the first time, the diversity of lncRNAs in dinoflagellates and how lncRNAs may regulate gene expression as a heat-stress response in these ecologically important microbes.
Proton Pump Inhibitors and Cyclin-Dependent Kinase 4/6 Inhibitors in Patients With Breast Cancer
Authors: Takahashi Kaori , Uozumi Ryuji , Mukohara Toru , Hayashida Tetsu , Iwabe Midori , Iihara Hirotoshi , Kusuhara-Mamishin Kanako , Kitagawa Yuko , Tsuchiya Masami , Kitahora Mika , Nagayama Aiko , Kosaka Shinkichi , Asano-Niwa Yoshimi , Seki Tomoko , Ohnuki Koji , Suzuki Akio , Ono Fumiko , Futamura Manabu , Kawazoe Hitoshi , Nakamura Tomonori 
Published: February 2024

Abstract

Background
Proton pump inhibitors (PPIs) reduce the bioavailability of several anticancer drugs. The impact of PPIs co-administered with cyclin-dependent kinase 4 and 6 inhibitors is controversial. We aimed to clarify whether the concomitant use of PPIs impacts palbociclib and abemaciclib effectiveness in breast cancer treatment.

Patients and Methods
This multicenter, retrospective, observational study, conducted across 4 medical institutions in Japan, consecutively included patients with endocrine-resistant metastatic breast cancer, receiving palbociclib or abemaciclib between December 2017 and August 2022. Propensity score-matched analyses were performed. Treatment efficacy and safety with and without PPIs were compared. Progression-free survival and overall survival were estimated using the Kaplan-Meier method and compared using a log-rank test. A Cox proportional hazards model was used to estimate the hazard ratio.

Results
The study included 240 patients. After 1:1 matching, 112 patients were treated with and without PPIs. The median progression-free survival period was 1.2 years in the PPI group and 1.3 years in the non-PPI group (hazard ratio, 1.19; 95% CI, 0.70-2.02). The median overall survival period was 3.6 years in the PPI group, whereas it was not reached in the non-PPI group (hazard ratio, 1.23; 95% CI, 0.61-2.47). Consistent results were obtained for subgroups receiving palbociclib (n = 177) and abemaciclib (n = 63) without propensity score matching. Adverse event incidence and severity were similar in both groups.

Conclusion
The effectiveness of cyclin-dependent kinase 4/6 inhibitors is unlikely to be affected by concomitant PPI use. Future prospective pharmacokinetic studies are warranted.
AI-related data ethics oversight in UK policing
Authors: Sorell Tom 
Published: February 2024

Abstract
This paper considers the question of how police-related AI projects and data projects in general are normatively assessed in the UK. After locating data ethics in relation to policing ethics, I shall consider the workings of perhaps the leading regional data ethics committee in the UK. I go on to consider the approach of another committee that might in the future provide national data ethics advice for the police. Finally, I summarize the normative ethics frameworks in use in the two committees and their heavy reliance on the concepts of necessity and proportionality. I suggest that these concepts may have to be supplemented by systematic thinking about varieties of harm and the way in which severe harm may generate obligations to prevent it, where prevention may be assisted by AI models.
Enhanced Classical Radiation Damping of Electronic Cyclotron Motion in the Vicinity of the Van Hove Singularity in a Waveguide
Authors: Goto Yuki , Garmon Savannah , Petrosky Tomio 
Published: February 2024

Abstract
We study the damping process of electron cyclotron motion and the resulting emission in a waveguide using the classical Friedrichs model without relying on perturbation analysis such as Fermi’s golden rule. A Van Hove singularity appears at the lower bound (or cutoff frequency) of the dispersion associated with each of the electromagnetic field modes in the waveguide. In the vicinity of the Van Hove singularity, we found that not only is the decay process associated with the resonance pole enhanced (amplification factor ∼104) but the branch-point effect is also comparably enhanced. As a result, the timescale on which most of the decay occurs is dramatically shortened. Further, this suggests that the non-Markovian branch-point effect should be experimentally observable in the vicinity of the Van Hove singularity. Our treatment yields a physically acceptable solution without the problematic runaway solution that is well known to appear in the traditional treatment of classical radiation damping based on the Abraham–Lorentz equation.
Prevalence and acceptability of psychological and/or economic intimate partner violence, and utilization of mental health services by its survivors in Lithuania
Authors: Grigaitė Ugnė , Azeredo-Lopes Sofia , Žeimė Eglė , Slotkus Paulius Yamin , Heitmayer Maxi , Aluh Deborah Oyine , Pedrosa Bárbara , Silva Manuela , Santos-Dias Margarida , Cardoso Graça , Caldas-de-Almeida José Miguel 
Published: February 2024

Abstract

Background
Lithuania has one of the highest averages in the European Union when it comes to psychological and/or economic intimate partner violence (PE-IPV). IPV survivors are several times more likely to have mental health conditions than those without IPV experiences. The aim of this article is to study the prevalence, characteristics and attitudes of PE-IPV survivors in Lithuania, and the predictors of them accessing mental health services.

Methods
A cross-sectional study based on a national survey representative of the adult population. The survey was implemented by a third-party independent market research company employing an online survey panel. Logistic regression models were used in the analysis.

Results
Almost 50% of women in Lithuania experience PE-IPV. Females are significantly more likely to experience it than males. The vast majority of women find PE-IPV unacceptable; however, only one-third of survivors seek any type of help. Only one-tenth approach mental health services, with divorcees being at higher odds of doing so.

Conclusions
Further research is needed to explore predictors and contextual factors of why IPV survivors seek mental healthcare, or not. Policy implications include the need to eliminate IPV and mental health stigma; develop accessible mental health services and effective treatment approaches.
Effectiveness and safety of treat-to-target strategy for methotrexate-naïve rheumatoid arthritis patients &gt;75 years of age
Authors: Matsumoto Takumi , Sugihara Takahiko , Hosoya Tadashi , Ishizaki Tatsuro , Kubo Kanae , Kamiya Mari , Baba Hiroyuki , Tsuchida Marina , Hirano Fumio , Kojima Masayo , Miyasaka Nobuyuki , Harigai Masayoshi 
Published: February 2024

Abstract

Objectives
To identify differences in effectiveness and safety of a treat-to-target (T2T) strategy comparing late-onset MTX-naïve RA patients (LORA) ≥75 or &lt;75 years of age.

Methods
Treatment was adjusted to target low disease activity with conventional synthetic DMARDs followed by biologic DMARDs (bDMARDs) in LORA ≥75 years (n = 98, mean age 80.0 years) and LORA &lt;75 years (n = 99) with moderate–high disease activity. Achievement of Simplified Disease Activity Index (SDAI) remission at week 156 by non-responder imputation analysis was evaluated as a primary outcome.

Results
LORA ≥75 years had more comorbidities than LORA &lt;75 years, but SDAI and ACPA positivity were similar at baseline. Of the LORA ≥75 years, 70.4% started MTX and 34.1% and 37.1% received a bDMARD at week 52 and 156, respectively (very similar to the LORA &lt;75 years). Glucocorticoid use was more frequent in the LORA ≥75 years than in the LORA &lt;75 years. Comorbidities/adverse events more frequently contributed to the reasons for non-adherence to T2T in the LORA ≥75 than in the LORA &lt;75. At week 156, 32.7% of the LORA ≥75 and 66.7% of the LORA &lt;75 achieved SDAI remission (P &lt; 0.001). The cumulative incidence of serious adverse events (SAEs) over 156 weeks was 42.8% in the LORA ≥75 and 22.1% in the LORA &lt;75. Multivariable analysis indicated an increased risk of SDAI non-remission at week 156 in the LORA ≥75 [odds ratio 2.82 (95% CI 1.29. 6.14)] after adjusting for comorbidities at baseline, non-adherence to T2T and SAEs.

Conclusions
It was more difficult to achieve remission in the LORA ≥75 patients than in the LORA &lt;75 patients due to both poor treatment response and safety issues.
Microbiome-friendly PS/PVP electrospun fibrous membrane with antibiofilm properties for dental engineering
Authors: Chen Jiamin , Guo Jia , Lu Xueyun , Yin Derong , Zhou Cuisong , Li Yuqing , Zhou Xuedong 
Published: February 2024

Abstract
Dental caries is one of the most prevalent and biofilm-associated oral diseases in humans. Streptococcus mutans, with a high ability to form biofilms by adhering to hard surfaces, has been established as an important etiological agent for dental caries. Therefore, it is crucial to find a way to prevent the formation of cariogenic biofilm. Here, we report an electrospun fibrous membrane that could inhibit the adhesion and biofilm formation of S. mutans. Also, the polystyrene (PS)/polyvinyl pyrrolidone (PVP) electrospun fibrous membrane altered the 3D biofilm architecture and decreased water-insoluble extracellular polysaccharide production. Notably, the anti-adhesion mechanism which laid in Coulomb repulsion between the negatively charged PS/PVP electrospun fibrous membrane and S. mutans was detected by zeta potential. Furthermore, metagenomics sequencing analysis and CCK-8 assay indicated that PS/PVP electrospun fibrous membrane was microbiome-friendly and displayed no influence on the cell viability of human gingival epithelial cells and human oral keratinocytes. Moreover, an in vitro simulation experiment demonstrated that PS/PVP electrospun fibrous membrane could decrease colony-forming unit counts of S. mutans effectively, and PS/PVP electrospun fibrous membrane carrying calcium fluoride displayed better anti-adhesion ability than that of PS/PVP electrospun fibrous membrane alone. Collectively, this research showed that the PS/PVP electrospun fibrous membrane has potential applications in controlling and preventing dental caries.
3D printing sequentially strengthening high-strength natural polymer hydrogel bilayer scaffold for cornea regeneration
Authors: Nie Xiongfeng , Tang Yong , Wu Tengling , Zhao Xinrui , Xu Ziyang , Yang Rong , Sun Yage , Wu Bin , Han Quanhong , Hui Jingwen , Liu Wenguang 
Published: February 2024

Abstract
3D printing of high-strength natural polymer biodegradable hydrogel scaffolds simultaneously resembling the biomechanics of corneal tissue and facilitating tissue regeneration remains a huge challenge due to the inherent brittleness of natural polymer hydrogels and the demanding requirements of printing. Herein, concentrated aqueous solutions of gelatin and carbohydrazide-modified alginate (Gel/Alg-CDH) are blended to form a natural polymer hydrogel ink, where the hydrazides in Alg-CDH are found to form strong hydrogen bonds with the gelatin. The hydrogen-bonding-strengthened Gel/Alg-CDH hydrogel demonstrates an appropriate thickened viscosity and shear thinning for extrusion printing. The strong hydrogen bonds contribute to remarkably increased mechanical properties of Gel/Alg-CDH hydrogel with a maximum elongation of over 400%. In addition, sequentially Ca2+-physical crosslinking and then moderately chemical crosslinking significantly enhance the mechanical properties of Gel/Alg-CDH hydrogels that ultimately exhibit an intriguing J-shaped stress–strain curve (tensile strength of 1.068 MPa and the toughness of 677.6 kJ/m2). The dually crosslinked Gel-Alg-CDH-Ca2+-EDC hydrogels demonstrate a high transparency, physiological swelling stability and rapid enzymatic degradability, as well as suturability. The growth factor and drug-loaded biomimetic bilayer hydrogel scaffold are customized via a multi-nozzle printing system. This bioactive bilayer hydrogel scaffold considerably promotes regeneration of corneal epithelium and stroma and inhibits cornea scarring in rabbit cornea keratoplasty.
Lung imaging patterns in connective tissue disease–associated interstitial lung disease impact prognosis and immunosuppression response
Authors: Zheng Boyang , Marinescu Daniel-Costin , Hague Cameron J , Muller Nestor L , Murphy Darra , Churg Andrew , Wright Joanne L , Al-Arnawoot Amna , Bilawich Ana-Maria , Bourgouin Patrick , Cox Gerard , Durand Celine , Elliot Tracy , Ellis Jennifer , Fisher Jolene H , Fladeland Derek , Grant-Orser Amanda , Goobie Gillian C , Guenther Zachary , Haider Ehsan , Hambly Nathan , Huynh James , Johannson Kerri A , Karjala Geoffrey , Khalil Nasreen , Kolb Martin , Leipsic Jonathon , Lok Stacey D , MacIsaac Sarah , McInnis Micheal , Manganas Helene , Marcoux Veronica , Mayo John , Morisset Julie , Scallan Ciaran , Sedlic Tony , Shapera Shane , Sun Kelly , Tan Victoria , Wong Alyson W , Ryerson Christopher J 
Published: February 2024

Abstract

Objectives
Interstitial lung disease (ILD) in CTDs has highly variable morphology. We aimed to identify imaging features and their impact on ILD progression, mortality, and immunosuppression response.

Methods
Patients with CTD-ILD had high-resolution chest CT (HRCT) reviewed by expert radiologists blinded to clinical data for overall imaging pattern [usual interstitial pneumonia (UIP); non-specific interstitial pneumonia (NSIP); organizing pneumonia (OP); fibrotic hypersensitivity pneumonitis (fHP); and other]. Transplant-free survival and change in percent-predicted forced vital capacity (FVC) were compared using Cox and linear mixed-effects models adjusted for age, sex, smoking, and baseline FVC. FVC decline after immunosuppression was compared with pre-treatment.

Results
Among 645 CTD-ILD patients, the most frequent CTDs were SSc (n = 215), RA (n = 127), and inflammatory myopathies (n = 100). NSIP was the most common pattern (54%), followed by UIP (20%), fHP (9%), and OP (5%). Compared with the case for patients with UIP, FVC decline was slower in patients with NSIP (by 1.1%/year, 95% CI 0.2, 1.9) or OP (by 3.5%/year, 95% CI 2.0, 4.9), and mortality was lower in patients with NSIP [hazard ratio (HR) 0.65, 95% CI 0.45, 0.93] or OP (HR 0.18, 95% CI 0.05, 0.57), but higher in fHP (HR 1.58, 95% CI 1.01, 2.40). The extent of fibrosis also predicted FVC decline and mortality. After immunosuppression, FVC decline was slower compared with pre-treatment in NSIP (by 2.1%/year, 95% CI 1.4, 2.8), with no change for UIP or fHP.

Conclusion
Multiple radiologic patterns are possible in CTD-ILD, including a fHP pattern. NSIP and OP were associated with better outcomes and response to immunosuppression, while fHP had worse survival compared with UIP.