bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana
Authors: Xu Linhao , Zheng Shiwei , Witzel Katja , Van De Slijke Eveline , Baekelandt Alexandra , Mylle Evelien , Van Damme Daniel , Cheng Jinping , De Jaeger Geert , Inzé Dirk , Jiang Hua 
Published: February 2024

AbstractThe nuclear matrix is a nuclear compartment that has diverse functions in chromatin regulation and transcription. However, how this structure influences epigenetic modifications and gene expression in plants is largely unknown. In this study, we show that a nuclear matrix binding protein, AHL22, together with the two transcriptional repressors FRS7 and FRS12, regulates hypocotyl elongation by suppressing the expression of a group of genes known as SMALL AUXIN UP RNAs (SAURs) in Arabidopsis thaliana. The transcriptional repression of SAURs depends on their attachment to the nuclear matrix. The AHL22 complex not only brings these SAURs, which contain matrix attachment regions (MARs), to the nuclear matrix, but it also recruits the histone deacetylase HDA15 to the SAUR loci. This leads to the removal of H3 acetylation at the SAUR loci and the suppression of hypocotyl elongation. Taken together, our results indicate that MAR-binding proteins act as a hub for chromatin and epigenetic regulators. Moreover, we present a mechanism by which nuclear matrix attachment to chromatin regulates histone modifications, transcription, and hypocotyl elongation.
Palmitic acid in type 2 diabetes mellitus promotes atherosclerotic plaque vulnerability via macrophage Dll4 signaling
Authors: Wang Xiqiang , Zhu Ling , Liu Jing , Ma Yanpeng , Qiu Chuan , Liu Chengfeng , Gong Yangchao , Yuwen Ya , Guan Gongchang , Zhang Yong , Pan Shuo , Wang Junkui , Liu Zhongwei 
Published: February 2024

AbstractPatients with Type 2 Diabetes Mellitus are increasingly susceptible to atherosclerotic plaque vulnerability, leading to severe cardiovascular events. In this study, we demonstrate that elevated serum levels of palmitic acid, a type of saturated fatty acid, are significantly linked to this enhanced vulnerability in patients with Type 2 Diabetes Mellitus. Through a combination of human cohort studies and animal models, our research identifies a key mechanistic pathway: palmitic acid induces macrophage Delta-like ligand 4 signaling, which in turn triggers senescence in vascular smooth muscle cells. This process is critical for plaque instability due to reduced collagen synthesis and deposition. Importantly, our findings reveal that macrophage-specific knockout of Delta-like ligand 4 in atherosclerotic mice leads to reduced plaque burden and improved stability, highlighting the potential of targeting this pathway. These insights offer a promising direction for developing therapeutic strategies to mitigate cardiovascular risks in patients with Type 2 Diabetes Mellitus.
Electric control of optically-induced magnetization dynamics in a van der Waals ferromagnetic semiconductor
Authors: Hendriks Freddie , Rojas-Lopez Rafael R. , Koopmans Bert , Guimarães Marcos H. D. 
Published: February 2024

AbstractElectric control of magnetization dynamics in two-dimensional (2D) magnetic materials is an essential step for the development of novel spintronic nanodevices. Electrostatic gating has been shown to greatly affect the static magnetic properties of some van der Waals magnets, but the control over their magnetization dynamics is still largely unexplored. Here we show that the optically-induced magnetization dynamics in the van der Waals ferromagnet Cr2Ge2Te6 can be effectively controlled by electrostatic gates, with a one order of magnitude change in the precession amplitude and over 10% change in the internal effective field. In contrast to the purely thermally-induced mechanisms previously reported for 2D magnets, we find that coherent opto-magnetic phenomena play a major role in the excitation of magnetization dynamics in Cr2Ge2Te6. Our work sets the first steps towards electric control over the magnetization dynamics in 2D ferromagnetic semiconductors, demonstrating their potential for applications in ultrafast opto-magnonic devices.
Poly-γ-glutamylation of biomolecules
Authors: Bashiri Ghader , Bulloch Esther M. M. , Bramley William R. , Davidson Madison , Stuteley Stephanie M. , Young Paul G. , Harris Paul W. R. , Naqvi Muhammad S. H. , Middleditch Martin J. , Schmitz Michael , Chang Wei-Chen , Baker Edward N. , Squire Christopher J. 
Published: February 2024

AbstractPoly-γ-glutamate tails are a distinctive feature of archaeal, bacterial, and eukaryotic cofactors, including the folates and F420. Despite decades of research, key mechanistic questions remain as to how enzymes successively add glutamates to poly-γ-glutamate chains while maintaining cofactor specificity. Here, we show how poly-γ-glutamylation of folate and F420 by folylpolyglutamate synthases and γ-glutamyl ligases, non-homologous enzymes, occurs via processive addition of L-glutamate onto growing γ-glutamyl chain termini. We further reveal structural snapshots of the archaeal γ-glutamyl ligase (CofE) in action, crucially including a bulged-chain product that shows how the cofactor is retained while successive glutamates are added to the chain terminus. This bulging substrate model of processive poly-γ-glutamylation by terminal extension is arguably ubiquitous in such biopolymerisation reactions, including addition to folates, and demonstrates convergent evolution in diverse species from archaea to humans.
Liquid crystalline inverted lipid phases encapsulating siRNA enhance lipid nanoparticle mediated transfection
Authors: Pattipeiluhu Roy , Zeng Ye , Hendrix Marco M.R.M. , Voets Ilja K. , Kros Alexander , Sharp Thomas H. 
Published: February 2024

AbstractEfficient cytosolic delivery of RNA molecules remains a formidable barrier for RNA therapeutic strategies. Lipid nanoparticles (LNPs) serve as state-of-the-art carriers that can deliver RNA molecules intracellularly, as exemplified by the recent implementation of several vaccines against SARS-CoV-2. Using a bottom-up rational design approach, we assemble LNPs that contain programmable lipid phases encapsulating small interfering RNA (siRNA). A combination of cryogenic transmission electron microscopy, cryogenic electron tomography and small-angle X-ray scattering reveals that we can form inverse hexagonal structures, which are present in a liquid crystalline nature within the LNP core. Comparison with lamellar LNPs reveals that the presence of inverse hexagonal phases enhances the intracellular silencing efficiency over lamellar structures. We then demonstrate that lamellar LNPs exhibit an in situ transition from a lamellar to inverse hexagonal phase upon interaction with anionic membranes, whereas LNPs containing pre-programmed liquid crystalline hexagonal phases bypass this transition for a more efficient one-step delivery mechanism, explaining the increased silencing effect. This rational design of LNPs with defined lipid structures aids in the understanding of the nano-bio interface and adds substantial value for LNP design, optimization and use.
The transcriptional regulatory network modulating human trophoblast stem cells to extravillous trophoblast differentiation
Authors: Kim Mijeong , Jang Yu Jin , Lee Muyoung , Guo Qingqing , Son Albert J. , Kakkad Nikita A. , Roland Abigail B. , Lee Bum-Kyu , Kim Jonghwan 
Published: February 2024

AbstractDuring human pregnancy, extravillous trophoblasts play crucial roles in placental invasion into the maternal decidua and spiral artery remodeling. However, regulatory factors and their action mechanisms modulating human extravillous trophoblast specification have been unknown. By analyzing dynamic changes in transcriptome and enhancer profile during human trophoblast stem cell to extravillous trophoblast differentiation, we define stage-specific regulators, including an early-stage transcription factor, TFAP2C, and multiple late-stage transcription factors. Loss-of-function studies confirm the requirement of all transcription factors identified for adequate differentiation, and we reveal that the dynamic changes in the levels of TFAP2C are essential. Notably, TFAP2C pre-occupies the regulatory elements of the inactive extravillous trophoblast-active genes during the early stage of differentiation, and the late-stage transcription factors directly activate extravillous trophoblast-active genes, including themselves as differentiation further progresses, suggesting sequential actions of transcription factors assuring differentiation. Our results reveal stage-specific transcription factors and their inter-connected regulatory mechanisms modulating extravillous trophoblast differentiation, providing a framework for understanding early human placentation and placenta-related complications.
Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing
Authors: Ledru Nicolas , Wilson Parker C. , Muto Yoshiharu , Yoshimura Yasuhiro , Wu Haojia , Li Dian , Asthana Amish , Tullius Stefan G. , Waikar Sushrut S. , Orlando Giuseppe , Humphreys Benjamin D. 
Published: February 2024

AbstractRenal proximal tubule epithelial cells have considerable intrinsic repair capacity following injury. However, a fraction of injured proximal tubule cells fails to undergo normal repair and assumes a proinflammatory and profibrotic phenotype that may promote fibrosis and chronic kidney disease. The healthy to failed repair change is marked by cell state-specific transcriptomic and epigenomic changes. Single nucleus joint RNA- and ATAC-seq sequencing offers an opportunity to study the gene regulatory networks underpinning these changes in order to identify key regulatory drivers. We develop a regularized regression approach to construct genome-wide parametric gene regulatory networks using multiomic datasets. We generate a single nucleus multiomic dataset from seven adult human kidney samples and apply our method to study drivers of a failed injury response associated with kidney disease. We demonstrate that our approach is a highly effective tool for predicting key cis- and trans-regulatory elements underpinning the healthy to failed repair transition and use it to identify NFAT5 as a driver of the maladaptive proximal tubule state.
The secondary somatosensory cortex gates mechanical and heat sensitivity
Authors: Taub Daniel G. , Jiang Qiufen , Pietrafesa Francesca , Su Junfeng , Carroll Aloe , Greene Caitlin , Blanchard Michael R. , Jain Aakanksha , El-Rifai Mahmoud , Callen Alexis , Yager Katherine , Chung Clara , He Zhigang , Chen Chinfei , Woolf Clifford J. 
Published: February 2024

AbstractThe cerebral cortex is vital for the processing and perception of sensory stimuli. In the somatosensory axis, information is received primarily by two distinct regions, the primary (S1) and secondary (S2) somatosensory cortices. Top-down circuits stemming from S1 can modulate mechanical and cooling but not heat stimuli such that circuit inhibition causes blunted perception. This suggests that responsiveness to particular somatosensory stimuli occurs in a modality specific fashion and we sought to determine additional cortical substrates. In this work, we identify in a mouse model that inhibition of S2 output increases mechanical and heat, but not cooling sensitivity, in contrast to S1. Combining 2-photon anatomical reconstruction with chemogenetic inhibition of specific S2 circuits, we discover that S2 projections to the secondary motor cortex (M2) govern mechanical and heat sensitivity without affecting motor performance or anxiety. Taken together, we show that S2 is an essential cortical structure that governs mechanical and heat sensitivity.
Tomography-based digital twin of Nd-Fe-B permanent magnets
Authors: Bolyachkin Anton , Dengina Ekaterina , Kulesh Nikita , Tang Xin , Sepehri-Amin Hossein , Ohkubo Tadakatsu , Hono Kazuhiro 
Published: February 2024

AbstractMany functional materials have been designed at the multiscale level. To properly simulate their physical properties, large and sophisticated computer models that can replicate microstructural features with nanometer-scale accuracy are required. This is the case for permanent magnets, which exhibit a long-standing problem of a significant offset between the simulated and experimental coercivities. To overcome this problem and resolve the Brown paradox, we propose an approach to construct large-scale finite element models based on the tomographic data from scanning electron microscopy. Our approach reconstructs a polycrystalline microstructure with actual shape, size, and packing of the grains as well as the individual regions of thin intergranular phase separated by triple junctions. Such a micromagnetic model can reproduce the experimental coercivity of ultrafine-grained Nd-Fe-B magnets along with its mechanism according to the angular dependence of coercivity. Furthermore, a remarkable role of thin triple junctions as nucleation centers for magnetization reversal is revealed. The developed digital twins of Nd-Fe-B permanent magnets can assist their optimization toward the ultimate coercivity, while the proposed tomography-based approach can be applied to a wide range of polycrystalline materials.
Dysfunctional attributions of success as a distinct feature of amotivation
Authors: Schormann Alisa L. A. , Butschbach Katja , Lincoln Tania M. , Riehle Marcel 
Published: February 2024

AbstractWe examined the association between causal attributions and self-reported motivational negative symptoms (amotivation) in a German online community sample (n = 251). Bivariate correlations revealed significant associations between amotivation and attribution of success to external, variable, and specific causes. No associations between amotivation and failure attributions were found. Our data suggest that demotivational causal attributions of success could be a feature of amotivation and a promising target for research and intervention.
Crop-GPA: an integrated platform of crop gene-phenotype associations
Authors: Gao Yujia , Zhou Qian , Luo Jiaxin , Xia Chuan , Zhang Youhua , Yue Zhenyu 
Published: February 2024

AbstractWith the increasing availability of large-scale biology data in crop plants, there is an urgent demand for a versatile platform that fully mines and utilizes the data for modern molecular breeding. We present Crop-GPA (https://crop-gpa.aielab.net), a comprehensive and functional open-source platform for crop gene-phenotype association data. The current Crop-GPA provides well-curated information on genes, phenotypes, and their associations (GPAs) to researchers through an intuitive interface, dynamic graphical visualizations, and efficient online tools. Two computational tools, GPA-BERT and GPA-GCN, are specifically developed and integrated into Crop-GPA, facilitating the automatic extraction of gene-phenotype associations from bio-crop literature and predicting unknown relations based on known associations. Through usage examples, we demonstrate how our platform enables the exploration of complex correlations between genes and phenotypes in crop plants. In summary, Crop-GPA serves as a valuable multi-functional resource, empowering the crop research community to gain deeper insights into the biological mechanisms of interest.
Attosecond electron microscopy by free-electron homodyne detection
Authors: Gaida John H. , Lourenço-Martins Hugo , Sivis Murat , Rittmann Thomas , Feist Armin , García de Abajo F. Javier , Ropers Claus 
Published: February 2024

AbstractTime-resolved electron microscopy aims to track nanoscale excitations and dynamic states of matter at a temporal resolution ultimately reaching the attosecond regime. Periodically time-varying fields in an illuminated specimen cause free-electron inelastic scattering, which enables the spectroscopic imaging of near-field intensities. However, access to the evolution of nanoscale fields and structures within the cycle of light requires sensitivity to the optical phase. Here we introduce free-electron homodyne detection as a universally applicable approach to electron microscopy of phase-resolved optical responses at high spatiotemporal resolution. In this scheme, a phase-controlled reference interaction serves as the local oscillator to extract arbitrary sample-induced modulations of a free-electron wavefunction. We demonstrate this principle through the phase-resolved imaging of plasmonic fields with few-nanometre spatial and sub-cycle temporal resolutions. Due to its sensitivity to both phase- and amplitude-modulated electron beams, free-electron homodyne detection measurements will be able to detect and amplify weak signals stemming from a wide variety of microscopic origins, including linear and nonlinear optical polarizations, atomic and molecular resonances, and attosecond-modulated structure factors.
Nearshore wave buoy data from southeastern Australia for coastal research and management
Authors: Kinsela Michael A. , Morris Bradley D. , Ingleton Timothy C. , Doyle Thomas B. , Sutherland Michael D. , Doszpot Neil E. , Miller Jeff J. , Holtznagel Stephen F. , Harley Mitchell D. , Hanslow David J. 
Published: February 2024

AbstractWind wave observations in shallow coastal waters are essential for calibrating, validating, and improving numerical wave models to predict sediment transport, shoreline change, and coastal hazards such as beach erosion and oceanic inundation. Although ocean buoys and satellites provide near-global coverage of deep-water wave conditions, shallow-water wave observations remain sparse and often inaccessible. Nearshore wave conditions may vary considerably alongshore due to coastline orientation and shape, bathymetry and islands. We present a growing dataset of in-situ wave buoy observations from shallow waters (<35 m) in southeast Australia that comprises over 7,000 days of measurements at 20 locations. The moored buoys measured wave conditions continuously for several months to multiple years, capturing ambient and storm conditions in diverse settings, including coastal hazard risk sites. The dataset includes tabulated time series of spectral and time-domain parameters describing wave height, period and direction at half-hourly temporal resolution. Buoy displacement and wave spectra data are also available for advanced applications. Summary plots and tables describing wave conditions measured at each location are provided.
QUIN 2.0 - new release of the QUaternary fault strain INdicators database from the Southern Apennines of Italy
Authors: Lavecchia Giusy , Bello Simone , Andrenacci Carlo , Cirillo Daniele , Pietrolungo Federico , Talone Donato , Ferrarini Federica , de Nardis Rita , Galli Paolo , Faure Walker Joanna , Sgambato Claudia , Menichetti Marco , Monaco Carmelo , Gambino Salvatore , De Guidi Giorgio , Barreca Giovanni , Carnemolla Francesco , Brighenti Fabio , Giuffrida Salvatore , Pirrotta Claudia , Carboni Filippo , Ferranti Luigi , Valoroso Luisa , Toscani Giovanni , Barchi Massimiliano R. , Roberts Gerald , Brozzetti Francesco 
Published: February 2024

AbstractQUIN database integrates and organizes structural-geological information from published and unpublished sources to constrain deformation in seismotectonic studies. The initial release, QUIN1.0, comprised 3,339 Fault Striation Pairs, mapped on 445 sites exposed along the Quaternary faults of central Italy. The present Data Descriptor introduces the QUIN 2.0 release, which includes 4,297 Fault Striation Pairs on 738 Structural Sites from southern Italy. The newly investigated faults span ~500 km along the Apennines chain, with strikes transitioning from ~SE to ~SW and comprehensively details Fault Striation Pairs’ location, attitude, kinematics, and deformation axes. Additionally, it offers a shapefile of the fault traces hosting the data. The QUIN 2.0 release offers a significant geographic extension to the QUIN 1.0, with comprehensive description of local geometric-kinematic complexities of the regional pattern. The QUIN data may be especially relevant for constraining intra-Apennine potential seismogenic deformation patterns, where earthquake data only offer scattered or incomplete information. QUIN’s data will support studies aimed at enhancing geological understanding, hazard assessment and comprehension of fault rupture propagation and barriers.
Thermodynamic and kinetic analysis of the response surface method for phenol removal from aqueous solution using graphene oxide-polyacrylonitrile nanofiber mats
Authors: Eweida Basant Yousri , Abd El-Aziz Asmaa M. , El-Maghraby Azza , Serag Eman 
Published: February 2024

AbstractPhenolic compound even at low concentrations, are considered to be priority pollutants due to their significant toxicity. Electrospinning was used to create a polyacrylonitril (PAN) nanofiber, which was then impregnated with graphene oxide (GO). After a preliminary investigation into the electrospinning parameters (e.g., using various voltages and polymer concentrations), the electrospun nanofibres were tuned, this study evaluated the effectiveness of these materials in removing phenolic compounds from wastewater through adsorption. Scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) were used to analyze the synthesized nanofiber mats. The scanning electron microscopy (SEM) analysis revealed that the structure of nanofiber mats was altered by the addition of graphene oxide (GO) in different ratios. Specifically, the surface of the fibres exhibited increased roughness, and the diameter of the fibres also experienced an increase. The average diameter of the fibres was measured to be (134.9 ± 21.43 nm) for the PAN/2.5% GO composite and (198 ± 33.94 nm) for the PAN/5% GO composite. FTIR spectra of the PAN/GO nanocomposites nanofiber displayed distinct peaks associated with graphene oxide (GO). These included a wide peak at 3400 cm−1, related to the presence of hydroxyl (O–H) groups, as well as peaks on 1600 as well as 1000 cm−1, which indicated the existence of epoxy groups. In this study response surface methodology (RSM) was implemented. To enhance the efficiency of removing substances, it is necessary to optimise parameters such as pH, contact time, and dosage of the adsorbent. The optimum pH for removing phenol via all nanofiber mats was determined to be 7, while at a dose of 2 mg dose adsorbents maximum removals for pure PAN, PAN/2.5 GO, and PAN/5 GO were 61.3941, 77.2118, and 92.76139%, respectively. All the adsorbents obey Langmuir isotherm model, and the empirical adsorption findings were fitted with the second-order model kinetically, also non-linear Elovich model. The maximal monolayer adsorption capacities for PAN, PAN/2.5 GO, and PAN/5 GO were found to be 57.4, 66.18, and 69.7 mg/g, respectively. Thermodynamic studies discovered that the adsorption of phenol on all adsorbents nanofiber mats was exothermic, the adsorption of phenol on nanofiber mats decreases as the temperature increases. All the adsorbents exhibit negative enthalpy and entropy. The PAN/GO composite's superior phenol removal suggested that it could be used as a latent adsorbent for efficient phenol removal from water and wastewater streams.