bluuebunny/crossref_metadata_2025_split huggingface dataset:
Haplotype-resolved chromosomal-level genome assembly reveals regulatory variations in mulberry fruit anthocyanin content
Authors: Xia Zhongqiang , Fan Wei , Liu Duanyang , Chen Yuane , Lv Jing , Xu Mengxia , Zhang Meirong , Ren Zuzhao , Chen Xuefei , Wang Xiujuan , Li Liang , Zhu Panpan , Liu Changying , Song Zhiguang , Huang Chuanshu , Wang Xiling , Wang Shuchang , Zhao Aichun 
Published: April 2024

Abstract
Understanding the intricate regulatory mechanisms underlying the anthocyanin content (AC) in fruits and vegetables is crucial for advanced biotechnological customization. In this study, we generated high-quality haplotype-resolved genome assemblies for two mulberry cultivars: the high-AC ‘Zhongsang5801’ (ZS5801) and the low-AC ‘Zhenzhubai’ (ZZB). Additionally, we conducted a comprehensive analysis of genes associated with AC production. Through genome-wide association studies (GWAS) on 112 mulberry fruits, we identified MaVHAG3, which encodes a vacuolar-type H+-ATPase G3 subunit, as a key gene linked to purple pigmentation. To gain deeper insights into the genetic and molecular processes underlying high AC, we compared the genomes of ZS5801 and ZZB, along with fruit transcriptome data across five developmental stages, and quantified the accumulation of metabolic substances. Compared to ZZB, ZS5801 exhibited significantly more differentially expressed genes (DEGs) related to anthocyanin metabolism and higher levels of anthocyanins and flavonoids. Comparative analyses revealed expansions and contractions in the flavonol synthase (FLS) and dihydroflavonol 4-reductase (DFR) genes, resulting in altered carbon flow. Co-expression analysis demonstrated that ZS5801 displayed more significant alterations in genes involved in late-stage AC regulation compared to ZZB, particularly during the phase stage. In summary, our findings provide valuable insights into the regulation of mulberry fruit AC, offering genetic resources to enhance cultivars with higher AC traits.
Aligning United States Law with International Norms Would Remove Major Barriers to Protection in Gender Claims
Authors: Musalo Karen 
Published: April 2024

Abstract
The protection of women and girls fleeing gender-based harms has been controversial in the United States (US), with advances followed by setbacks. The US interpretation of particular social group and its nexus analysis, both of which diverge from guidance by the United Nations High Commissioner for Refugees (UNHCR), is the most significant barrier to protection. It has become almost impossible for women and girls to rely upon the particular social group ground because of current requirements that social groups not only be defined by immutable or fundamental characteristics, but also be socially distinct and have particularity. Establishing nexus is also a significant obstacle, with the US requirement of proof of the persecutor’s intent. In the first month of his administration, President Biden issued an executive order on migration, which raised hopes that these obstacles to protection would be removed. The order committed to protecting survivors of domestic violence and to issuing regulations that would make the US interpretation of particular social group consistent with international standards. The target date for the regulations was November 2021, but they have yet to issue. This article examines how the evolution of the US interpretation of particular social group and nexus has diverged from UNHCR recommendations. It shows how protection has been denied in gender cases involving the most egregious of harms. The article concludes by providing recommendations for realignment with international standards, which set a benchmark for evaluating the promised Biden administration regulations on the issue.
Log-Concavity of the Alexander Polynomial
Authors: Hafner Elena S , Mészáros Karola , Vidinas Alexander 
Published: April 2024

Abstract
The central question of knot theory is that of distinguishing links up to isotopy. The first polynomial invariant of links devised to help answer this question was the Alexander polynomial (1928). Almost a century after its introduction, it still presents us with tantalizing questions, such as Fox’s conjecture (1962) that the absolute values of the coefficients of the Alexander polynomial $\Delta _{L}(t)$ of an alternating link $L$ are unimodal. Fox’s conjecture remains open in general with special cases settled by Hartley (1979) for two-bridge knots, by Murasugi (1985) for a family of alternating algebraic links, and by Ozsváth and Szabó (2003) for the case of genus $2$ alternating knots, among others. We settle Fox’s conjecture for special alternating links. We do so by proving that a certain multivariate generalization of the Alexander polynomial of special alternating links is Lorentzian. As a consequence, we obtain that the absolute values of the coefficients of $\Delta _{L}(t)$, where $L$ is a special alternating link, form a log-concave sequence with no internal zeros. In particular, they are unimodal.
Multimatroids and Rational Curves with Cyclic Action
Authors: Clader Emily , Damiolini Chiara , Eur Christopher , Huang Daoji , Li Shiyue 
Published: April 2024

Abstract
We study the connection between multimatroids and moduli spaces of rational curves with cyclic action. Multimatroids are generalizations of matroids and delta-matroids that naturally arise in topological graph theory. The perspective of moduli of curves provides a tropical framework for studying multimatroids, generalizing the previous connection between type-$A$ permutohedral varieties (Losev–Manin moduli spaces) and matroids, and the connection between type-$B$ permutohedral varieties and delta-matroids. Specifically, we equate a combinatorial nef cone of the moduli space with the space of ${\mathbb {R}}$-multimatroids, a generalization of multimatroids, and we introduce the independence polytopal complex of a multimatroid, whose volume is identified with an intersection number on the moduli space. As an application, we give a combinatorial formula for a natural class of intersection numbers on the moduli space by relating to the volumes of independence polytopal complexes of multimatroids.
The Tension within Norms: Agency and Risks in Pursuit of Global Climate Justice
Authors: Minnella Carlotta , Pathak Swapna , Scauso Marcos Sebastian 
Published: April 2024

AbstractHow can IR theory capture both the possibilities of agency for historically underrepresented groups and the limitations that different social struggles present for them? This paper proposes a framework based on relational approaches, decolonial perspectives, and the concept of “tension” between possibilities and risks of agency to analyze the dynamics of norm emergence and circulation. It builds on, but moves beyond, constructivist analyses of the norm life cycle and adopts a relational and decolonial lens in order to probe normative agency and its consequences within the context of international negotiations. Focusing on constructivist theories of socialization with multiple feedback effects, the paper calls for a fourth agentic turn in the study of norms and their genealogy and offers an analytical and empirical roadmap to chart a more complex scenario of co-constitution for norms. The paper refers to the case of climate justice to illustrate, empirically, the importance of employing the concept of tension to unveil agentic moments in norm circulation, while also highlighting, theoretically, the risks and limitations that are present in meanings that continue to reinforce colonial legacies.
Corallococcus senghenyddensis sp. nov., a myxobacterium with potent antimicrobial activity
Authors: Arakal Benita S , Rowlands Richard S , McCarthy Michael , Whitworth David E , Maddocks Sarah E , James Philip E , Livingstone Paul G 
Published: April 2024

Abstract

Aim
Corallococcus species are diverse in the natural environment with 10 new Corallococcus species having been characterized in just the last 5 years. As well as being an abundant myxobacterial genus, they produce several secondary metabolites, including Corallopyronin, Corramycin, Coralmycin, and Corallorazine. We isolated a novel strain Corallococcus spp RDP092CA from soil in South Wales, UK, using Candida albicans as prey bait and characterized its predatory activities against pathogenic bacteria and yeast.

Methods and results
The size of the RDP092CA genome was 8.5 Mb with a G + C content of 71.4%. Phylogenetically, RDP092CA is closely related to Corallococcus interemptor, C. coralloides, and C. exiguus. However, genome average nucleotide identity and digital DNA–DNA hybridization values are lower than 95% and 70% when compared to those type strains, implying that it belongs to a novel species. The RDP092CA genome harbours seven types of biosynthetic gene clusters (BGCs) and 152 predicted antimicrobial peptides. In predation assays, RDP092CA showed good predatory activity against Escherichia coli, Pseudomonas aeruginosa, Citrobacter freundii, and Staphylococcus aureus but not against Enterococcus faecalis. It also showed good antibiofilm activity against all five bacteria in biofilm assays. Antifungal activity against eight Candida spp. was variable, with particularly good activity against Meyerozyma guillermondii DSM 6381. Antimicrobial peptide RDP092CA_120 exhibited potent antibiofilm activity with &gt;50% inhibition and &gt;60% dispersion of biofilms at concentrations down to 1 μg/ml.

Conclusions
We propose that strain RDP092CA represents a novel species with promising antimicrobial activities, Corallococcus senghenyddensis sp. nov. (=NBRC 116490T =CCOS 2109T), based on morphological, biochemical, and genomic features.
Twin support vector machines based on chaotic mapping dung beetle optimization algorithm
Authors: Huang Huajuan , Yao Zhenhua , Wei Xiuxi , Zhou Yongquan 
Published: April 2024

Abstract
Twin Support Vector Machine (TSVM) is a powerful machine learning method that is usually used to solve binary classification problems. But although the classification speed and performance of TSVM is better than that of primitive support vector machine, TSVM still faces the problem of difficult parameter selection; therefore, to overcome the problem of parameter selection of TSVM, this paper proposes a Chaotic Mapping Dung Beetle Optimization Algorithm-based Twin Support Vector Machine (CMDBO-TSVM) for automatic parameter selection. Due to the uncertainty of the random initialization population of the original Dung Beetle Optimization Algorithm, this paper additionally adds chaotic mapping initialization to improve the Dung Beetle Optimization Algorithm. Experiments on the dataset through this paper show that the classification accuracy of the CMDBO-TSVM has a better performance.
Three-dimensional inversion for short-offset transient electromagnetic data based on 3D U-Net
Authors: Zhao Yang , Wu Xin , Chen Weiying , Xue Junjie , Shi Jinjing 
Published: April 2024

Abstract
The short-offset transient electromagnetic (SOTEM) method carries out surveys in the near source region; the strong signal makes it suitable for deep detection with high precision. When the underground structure is complex, three-dimensional (3D) inversion of SOTEM data is necessary to meet the need of high-precision detection. Currently, difficulties faced by the conventional 3D inversion methods include high computational complexity, and the influence of the initial model. Deep learning (DL), as a completely nonlinear algorithm, can predict the underground structure from the measured data. DL is completely data-driven and does not use traditional misfit optimization methods. In this study, an efficient method is proposed to conduct 3D inversion for SOTEM data, which trains a 3D U-Net based on massive data to establish a mapping from SOTEM data to geoelectric models. After the training is completed, we input the new SOTEM data into the trained network, and the corresponding geoelectric model can be obtained. Although the training is a time-consuming process, prediction for new data can be completed in seconds. The inversion results for simulated data indicate that the 3D U-Net has good generalization performance and anti-noise ability. The inversion performance of 3D U-Net on the double-anomaly model improves by 51.1% compared to a 3D fully convolutional network (FCN). The inversion results of the 3D U-Net on the field data successfully delineated the aquiferous collapse column. The inversion results for simulated and field data demonstrate that the proposed method can achieve accurate 3D inversion for large volume of data while greatly saving computational time.
Predictive factors of nivolumab plus ipilimumab treatment efficacy in metastatic renal cell carcinoma patients
Authors: Ohba Kojiro , Nakanishi Hiromi , Kawada Ken , Nakamura Yuichiro , Mitsunari Kensuke , Matsuo Tomohiro , Mochizuki Yasushi , Imamura Ryoichi 
Published: April 2024

Abstract

Objective
Nivolumab plus ipilimumab is a recommended first-line therapy regimen for metastatic renal cell carcinoma. However, it is not clear which patient characteristics are associated with its effectiveness.

Methods
We retrospectively examined 67 metastatic renal cell carcinoma patients treated with nivolumab plus ipilimumab as a first-line therapy in multiple institutions from September 2018 to August 2022. We analyzed the relationships between survival outcomes and patient-related variables, including paraneoplastic symptoms. We also analyzed the relationships between changes in symptoms and parameters and outcomes.

Results
Of the 67 patients, 32 patients had paraneoplastic symptoms. The median progression-free survival was 14.9 months and median overall survival was 43.3 months. The objective response rate was 49.25% (33 patients), including two patients with complete response. Patients with cytoreductive nephrectomy, bone metastasis, high C-reactive protein levels and paraneoplastic symptoms were significantly correlated with short progression-free survival in the univariate analysis. Multivariate analysis of these factors showed that the presence of paraneoplastic symptoms at treatment initiation remained an independent predictor of progression-free survival. Of the 32 patients with paraneoplastic symptoms at treatment initiation, 12 patients had symptomatic improvement and 20 did not. The 1-year progression-free survival rates were significantly longer in improved patients compared with those with no improvement.

Conclusions
Patients without cytoreductive nephrectomy and with bone metastasis, liver metastasis, high C-reactive protein levels and paraneoplastic symptoms were significantly correlated with shorter progression-free survival. The presence of paraneoplastic symptoms was an independent predictor of progression-free survival. Improvement in paraneoplastic symptoms may reflect the treatment efficacy of nivolumab plus ipilimumab.
Molecular advances in bud dormancy in trees
Authors: Ding Jihua , Wang Kejing , Pandey Shashank , Perales Mariano , Allona Isabel , Khan Md Rezaul Islam , Busov Victor B , Bhalerao Rishikesh P 
Published: April 2024

Abstract
Seasonal bud dormancy in perennial woody plants is a crucial and intricate process that is vital for the survival and development of plants. Over the past few decades, significant advancements have been made in understanding many features of bud dormancy, particularly in model species, where certain molecular mechanisms underlying this process have been elucidated. We provide an overview of recent molecular progress in understanding bud dormancy in trees, with a specific emphasis on the integration of common signaling and molecular mechanisms identified across different tree species. Additionally, we address some challenges that have emerged from our current understanding of bud dormancy and offer insights for future studies.
Navigating Amaryllidaceae alkaloids: bridging gaps and charting biosynthetic territories
Authors: Liyanage Nuwan Sameera , Awwad Fatima , Gonçalves dos Santos Karen Cristine , Jayawardena Thilina U , Mérindol Natacha , Desgagné-Penix Isabel 
Published: April 2024

Abstract
Amaryllidaceae alkaloid (AA) biosynthesis has garnered significant attention in recent years, particularly with the commercialization of galanthamine as a treatment for the symptoms of Alzheimer’s disease. A significant amount of research work over the last eight decades has focused on the understanding of AA biosynthesis, starting from early radiolabelling studies to recent multi-omics analysis with modern biotechnological advancements. Those studies enabled the identification of hundreds of metabolites, the characterization of biochemical pathways, and an understanding of the environmental stimuli and of the molecular regulation of these pharmaceutically and agriculturally important metabolites. Despite numerous studies, there remain significant gaps in understanding the biosynthesis of AAs in Amaryllidaceae plants. As such, further research is needed to fully elucidate the metabolic pathways and facilitate their production. This review aims to provide a comprehensive summary of the current state of knowledge on AA biosynthesis, from elicitation of expression of transcription factors in the cell nucleus to alkaloid transport in the apoplast, and to highlight the challenges that need to be overcome for further advancement.
Modelling stochastic and quasi-periodic behaviour in stellar time-series: Gaussian process regression versus power-spectrum fitting
Authors: O’Sullivan Niamh K , Aigrain Suzanne 
Published: April 2024

ABSTRACT
As the hunt for an Earth-like exoplanets has intensified in recent years, so has the effort to characterize and model the stellar signals that can hide or mimic small planetary signals. Stellar variability arises from a number of sources, including granulation, supergranulation, oscillations, and activity, all of which result in quasi-periodic or stochastic behaviour in photometric and/or radial velocity observations. Traditionally, the characterization of these signals has mostly been done in the frequency domain. However, the recent development of scalable Gaussian process regression methods makes direct time-domain modelling of stochastic processes a feasible and arguably preferable alternative, obviating the need to estimate the power spectral density of the data before modelling it. In this paper, we compare the two approaches using a series of experiments on simulated data. We show that frequency-domain modelling can lead to inaccurate results, especially when the time-sampling is irregular. By contrast, Gaussian process regression results are often more precise, and systematically more accurate, in both the regular and irregular time-sampling regimes. While this work was motivated by the analysis of radial velocity and photometry observations of main-sequence stars in the context of planet searches, we note that our results may also have applications for the study of other types of astrophysical variability such as quasi-periodic oscillations in X-ray binaries and active galactic nuclei variability.
Evidence for a nearly orthogonal rotator in GX 301–2 with phase-resolved cyclotron resonant scattering features
Authors: Chen Xiao , Ding Yuanze , Wang Wei , Nishimura Osamu , Liu Qi , Zhang Shuang-Nan , Ge Mingyu , Lu Fangjun , Qu Jinlu , Song Liming , Zhang Shu 
Published: April 2024

ABSTRACT
Cyclotron resonant scattering features (CRSFs) are the absorption features in the X-ray spectra of strongly magnetized accretion neutron stars (NSs), which are probably the most reliable probe to the surface magnetic fields of NSs. The high-mass X-ray binary GX 301–2 exhibits a very wide, variable, and complicated CRSF in the average spectra, which should be two absorption lines based on Nuclear Spectroscopic Telescope Array (NuStar) and Hard X-ray Modulation Telescope (Insight-HXMT) observations. With the Insight-HXMT frequent observations, we performed the phase-resolved spectroscopy and confirmed two cyclotron absorption lines in the phase-resolved spectra, with their centroid energy ratio ∼1.6–1.7 in the supercritical luminosity case. A major hindrance in understanding those CRSFs is the very poorly constrained magnetic inclination angle, which is also a fundamental property of an NS and key to understanding the emission characteristics of a pulsar. Comparing the phase-resolved CRSF with simulated X-ray spectra, the magnetic inclination angle is found to be ≳70°, i.e. nearly orthogonal between the NS’s spin and magnetic axis. The implications of an orthogonal rotator and magnetic structure evolution in the accreting X-ray binary are also discussed.
The formation of transiting circumplanetary debris discs from the disruption of satellite systems during planet–planet scattering
Authors: Mustill Alexander J , Davies Melvyn B , Kenworthy Matthew A 
Published: April 2024

ABSTRACT
Several stars show deep transits consistent with discs of roughly $1\mathrm{\, R}_\odot$ seen at moderate inclinations, likely surrounding planets on eccentric orbits. We show that this configuration arises naturally as a result of planet–planet scattering when the planets possess satellite systems. Planet–planet scattering explains the orbital eccentricities of the discs’ host bodies, while the close encounters during scattering lead to the exchange of satellites between planets and/or their destabilization. This leads to collisions between satellites and their tidal disruption close to the planet. Both of these events lead to large quantities of debris being produced, which in time will settle into a disc such as those observed. The mass of debris required is comparable to a Ceres-sized satellite. Through N-body simulations of planets with clones of the Galilean satellite system undergoing scattering, we show that 90 per cent of planets undergoing scattering will possess debris from satellite destruction. Extrapolating to smaller numbers of satellites suggests that tens of per cent of such planets should still possess circumplanetary debris discs. The debris trails arising from these events are often tilted at tens of degrees to the planetary orbit, consistent with the inclinations of the observed discs. Disruption of satellite systems during scattering thus simultaneously explains the existence of debris, the tilt of the discs, and the eccentricity of the planets they orbit.