bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advanced oxidation protein products attenuate the autophagy-lysosome pathway in ovarian granulosa cells by modulating the ROS-dependent mTOR-TFEB pathway
Authors: Zhou Xing-Yu , Lai Yun-Hui , Zhang Jun , Li Ying , Wu Xiao-Min , Yang Yi-Zhen , Zhang Xiao-Fei , Ma Lin-Zi , Zheng Ke-Ming , Liu Yu-Dong , Wang Zhe , Chen Shi-Ling 
Published: February 2024

AbstractOxidative stress dysfunction has recently been found to be involved in the pathogenesis of premature ovarian insufficiency (POI). Previously, we found that advanced oxidation protein products (AOPPs) in plasma were elevated in women with POI and had an adverse effect on granulosa cell proliferation. However, the mechanism underlying the effects of AOPPs on autophagy-lysosome pathway regulation in granulosa cells remains unclear. In this study, the effect of AOPPs on autophagy and lysosomal biogenesis and the underlying mechanisms were explored by a series of in vitro experiments in KGN and COV434 cell lines. AOPP-treated rat models were employed to determine the negative effect of AOPPs on the autophagy-lysosome systems in vivo. We found that increased AOPP levels activated the mammalian target of rapamycin (mTOR) pathway, and inhibited the autophagic response and lysosomal biogenesis in KGN and COV434 cells. Furthermore, scavenging of reactive oxygen species (ROS) with N-acetylcysteine and blockade of the mTOR pathway with rapamycin or via starvation alleviated the AOPP-induced inhibitory effects on autophagy and lysosomal biogenesis, suggesting that these effects of AOPPs are ROS-mTOR dependent. The protein expression and nuclear translocation of transcription factor EB (TFEB), the key regulator of lysosomal and autophagic function, were also impaired by the AOPP-activated ROS-mTOR pathway. In addition, TFEB overexpression attenuated the AOPP-induced impairment of autophagic flux and lysosomal biogenesis in KGN and COV434 cells. Chronic AOPP stimulation in vivo also impaired autophagy and lysosomal biogenesis in granulosa cells of rat ovaries. The results highlight that AOPPs lead to impairment of autophagic flux and lysosomal biogenesis via ROS-mTOR-TFEB signaling in granulosa cells and participate in the pathogenesis of POI.
Endothelial Robo4 suppresses endothelial-to-mesenchymal transition induced by irradiation and improves hematopoietic reconstitution
Authors: Adzraku Seyram Yao , Cao Can , Zhou Qi , Yuan Ke , Hao Xiaowen , Li Yue , Yuan Shengnan , Huang Yujin , Xu Kailin , Qiao Jianlin , Ju Wen , Zeng Lingyu 
Published: February 2024

AbstractBone marrow ablation is routinely performed before hematopoietic stem cell transplantation (HSCT). Hematopoietic stem and progenitor cells (HSPCs) require a stable bone marrow microenvironment to expand and refill the peripheral blood cell pool after ablation. Roundabout guidance receptor 4 (Robo4) is a transmembrane protein exclusive to endothelial cells and is vital in preserving vascular integrity. Hence, the hypothesis is that Robo4 maintains the integrity of bone marrow endothelial cells following radiotherapy. We created an endothelial cell injury model with γ-radiation before Robo4 gene manipulation using lentiviral-mediated RNAi and gene overexpression techniques. We demonstrate that Robo4 and specific mesenchymal proteins (Fibronectin, Vimentin, αSma, and S100A4) are upregulated in endothelial cells exposed to irradiation (IR). We found that Robo4 depletion increases the expression of endoglin (CD105), an auxiliary receptor for the transforming growth factor (TGF-β) family of proteins, and promotes endothelial-to-mesenchymal transition (End-MT) through activation of both the canonical (Smad) and non-canonical (AKT/NF-κB) signaling pathways to facilitate Snail1 activation and its nuclear translocation. Endothelial Robo4 overexpression stimulates the expression of immunoglobulin-like adhesion molecules (ICAM-1 and VCAM-1) and alleviates irradiation-induced End-MT. Our coculture model showed that transcriptional downregulation of endothelial Robo4 reduces HSPC proliferation and increases HSC quiescence and apoptosis. However, Robo4 overexpression mitigated the damaged endothelium’s suppressive effects on HSC proliferation and differentiation. These findings indicate that by controlling End-MT, Robo4 preserves microvascular integrity after radiation preconditioning, protects endothelial function, and lessens the inhibitory effect of damaged endothelium on hematopoietic reconstitution.
Emergence of slip-ideal-slip behavior in tip-links serve as force filters of sound in hearing
Authors: Arora Nisha , Hazra Jagadish P. , Roy Sandip , Bhati Gaurav K. , Gupta Sarika , Yogendran K. P. , Chaudhuri Abhishek , Sagar Amin , Rakshit Sabyasachi 
Published: February 2024

AbstractTip-links in the inner ear convey force from sound and trigger mechanotransduction. Here, we present evidence that tip-links (collectively as heterotetrameric complexes of cadherins) function as force filters during mechanotransduction. Our force-clamp experiments reveal that the tip-link complexes show slip-ideal-slip bond dynamics. At low forces, the lifetime of the tip-link complex drops monotonically, indicating slip-bond dynamics. The ideal bond, rare in nature, is seen in an intermediate force regime where the survival of the complex remains constant over a wide range. At large forces, tip-links follow a slip bond and dissociate entirely to cut-off force transmission. In contrast, the individual tip-links (heterodimers) display slip-catch-slip bonds to the applied forces. While with a phenotypic mutant, we showed the importance of the slip-catch-slip bonds in uninterrupted hearing, our coarse-grained Langevin dynamics simulations demonstrated that the slip-ideal-slip bonds emerge as a collective feature from the slip-catch-slip bonds of individual tip-links.
Porous borders at the wild-crop interface promote weed adaptation in Southeast Asia
Authors: Li Lin-Feng , Pusadee Tonapha , Wedger Marshall J. , Li Ya-Ling , Li Ming-Rui , Lau Yee-Ling , Yap Soo-Joo , Jamjod Sansanee , Rerkasem Benjavan , Hao Yan , Song Beng-Kah , Olsen Kenneth M. 
Published: February 2024

AbstractHigh reproductive compatibility between crops and their wild relatives can provide benefits for crop breeding but also poses risks for agricultural weed evolution. Weedy rice is a feral relative of rice that infests paddies and causes severe crop losses worldwide. In regions of tropical Asia where the wild progenitor of rice occurs, weedy rice could be influenced by hybridization with the wild species. Genomic analysis of this phenomenon has been very limited. Here we use whole genome sequence analyses of 217 wild, weedy and cultivated rice samples to show that wild rice hybridization has contributed substantially to the evolution of Southeast Asian weedy rice, with some strains acquiring weed-adaptive traits through introgression from the wild progenitor. Our study highlights how adaptive introgression from wild species can contribute to agricultural weed evolution, and it provides a case study of parallel evolution of weediness in independently-evolved strains of a weedy crop relative.
Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn
Authors: Liebhoff Anna-Maria , Venkataraman Thiagarajan , Morgenlander William R. , Na Miso , Kula Tomasz , Waugh Kathleen , Morrison Charles , Rewers Marian , Longman Randy , Round June , Elledge Stephen , Ruczinski Ingo , Langmead Ben , Larman H. Benjamin 
Published: February 2024

AbstractWe investigate a relatively underexplored component of the gut-immune axis by profiling the antibody response to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). To cover large antigenic spaces, we develop Dolphyn, a method that uses machine learning to select peptides from protein sets and compresses the proteome through epitope-stitching. Dolphyn compresses the size of a peptide library by 78% compared to traditional tiling, increasing the antibody-reactive peptides from 10% to 31%. We find that the immune system develops antibodies to human gut bacteria-infecting viruses, particularly E.coli-infecting Myoviridae. Cost-effective PhIP-Seq libraries designed with Dolphyn enable the assessment of a wider range of proteins in a single experiment, thus facilitating the study of the gut-immune axis.
Photocured room temperature phosphorescent materials from lignosulfonate
Authors: Guo Hongda , Cao Mengnan , Liu Ruixia , Tian Bing , Liu Shouxin , Li Jian , Li Shujun , Strehmel Bernd , James Tony D. , Chen Zhijun 
Published: February 2024

AbstractPhotocured room temperature phosphorescent (RTP) materials hold great potential for practical applications but are scarcely reported. Here, we develop photocured RTP materials (P-Lig) using a combination of lignosulfonate, acrylamide, and ionic liquid (1-ethyl-3-methylimidazolium bromide). With this design, lignosulfonate simultaneously serves as RTP chromophore and photoinitiator. Specifically, lignosulfonate in the ionic liquid generates radicals to polymerize the acrylamide upon UV irradiation. The resulting lignosulfonate is automatically confined in an as-formed crosslinked matrix to provide RTP. As such RTP with an emission lifetime of ~110 ms is observed from the confined lignosulfonate in P-Lig. Additionally, energy transfer occur between P-Lig and Rhodamine B (RhB), triggering red afterglow emission when P-Lig is in situ loaded with RhB (P-Lig/RhB). As a demonstration of potential applications, the P-Lig and P-Lig/RhB are used as photocured RTP coatings and RTP inks for fabricating 3D materials and for information encryption.
Large dynamics of a phase separating arginine-glycine-rich domain revealed via nuclear and electron spins
Authors: Sicoli Giuseppe , Sieme Daniel , Overkamp Kerstin , Khalil Mahdi , Backer Robin , Griesinger Christian , Willbold Dieter , Rezaei-Ghaleh Nasrollah 
Published: February 2024

AbstractLiquid-liquid phase separation is the key process underlying formation of membrane-less compartments in cells. A highly dynamic cellular body with rapid component exchange is Cajal body (CB), which supports the extensive compositional dynamics of the RNA splicing machinery, spliceosome. Here, we select an arginine-glycine (RG)-rich segment of coilin, the major component of CB, establish its RNA-induced phase separation, and through combined use of nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) probes, interrogate its dynamics within the crowded interior of formed droplets. Taking advantage of glycine-based singlet-states, we show that glycines retain a large level of sub-nanoseconds dynamics inside the coilin droplets. Furthermore, the continuous-wave (CW) and electron-electron dipolar (PELDOR) and electron-nucleus hyperfine coupling EPR data (HYSCORE) support the RNA-induced formation of dynamic coilin droplets with high coilin peptide concentrations. The combined NMR and EPR data reveal the high dynamics of the RG-rich coilin within droplets and suggest its potential role in the large dynamics of CBs.
Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking
Authors: Wong Daniel P. G. H. , Good Benjamin H. 
Published: February 2024

AbstractGut microbiota can adapt to their host environment by rapidly acquiring new mutations. However, the dynamics of this process are difficult to characterize in dominant gut species in their complex in vivo environment. Here we show that the fine-scale dynamics of genome-wide transposon libraries can enable quantitative inferences of these in vivo evolutionary forces. By analyzing >400,000 lineages across four human Bacteroides strains in gnotobiotic mice, we observed positive selection on thousands of cryptic variants — most of which were unrelated to their original gene knockouts. The spectrum of fitness benefits varied between species, and displayed diverse tradeoffs over time and in different dietary conditions, enabling inferences of their underlying function. These results suggest that within-host adaptations arise from an intense competition between numerous contending variants, which can strongly influence their emergent evolutionary tradeoffs.
Extracting accurate materials data from research papers with conversational language models and prompt engineering
Authors: Polak Maciej P. , Morgan Dane 
Published: February 2024

AbstractThere has been a growing effort to replace manual extraction of data from research papers with automated data extraction based on natural language processing, language models, and recently, large language models (LLMs). Although these methods enable efficient extraction of data from large sets of research papers, they require a significant amount of up-front effort, expertise, and coding. In this work, we propose the method that can fully automate very accurate data extraction with minimal initial effort and background, using an advanced conversational LLM. consists of a set of engineered prompts applied to a conversational LLM that both identify sentences with data, extract that data, and assure the data’s correctness through a series of follow-up questions. These follow-up questions largely overcome known issues with LLMs providing factually inaccurate responses. can be applied with any conversational LLMs and yields very high quality data extraction. In tests on materials data, we find precision and recall both close to 90% from the best conversational LLMs, like GPT-4. We demonstrate that the exceptional performance is enabled by the information retention in a conversational model combined with purposeful redundancy and introducing uncertainty through follow-up prompts. These results suggest that approaches similar to , due to their simplicity, transferability, and accuracy are likely to become powerful tools for data extraction in the near future. Finally, databases for critical cooling rates of metallic glasses and yield strengths of high entropy alloys are developed using .
Heterogeneity of synaptic connectivity in the fly visual system
Authors: Cornean Jacqueline , Molina-Obando Sebastian , Gür Burak , Bast Annika , Ramos-Traslosheros Giordano , Chojetzki Jonas , Lörsch Lena , Ioannidou Maria , Taneja Rachita , Schnaitmann Christopher , Silies Marion 
Published: February 2024

AbstractVisual systems are homogeneous structures, where repeating columnar units retinotopically cover the visual field. Each of these columns contain many of the same neuron types that are distinguished by anatomic, genetic and – generally – by functional properties. However, there are exceptions to this rule. In the 800 columns of the Drosophila eye, there is an anatomically and genetically identifiable cell type with variable functional properties, Tm9. Since anatomical connectivity shapes functional neuronal properties, we identified the presynaptic inputs of several hundred Tm9s across both optic lobes using the full adult female fly brain (FAFB) electron microscopic dataset and FlyWire connectome. Our work shows that Tm9 has three major and many sparsely distributed inputs. This differs from the presynaptic connectivity of other Tm neurons, which have only one major, and more stereotypic inputs than Tm9. Genetic synapse labeling showed that the heterogeneous wiring exists across individuals. Together, our data argue that the visual system uses heterogeneous, distributed circuit properties to achieve robust visual processing.
Smart touchless human–machine interaction based on crystalline porous cages
Authors: Wang Jinrong , Lin Weibin , Chen Zhuo , Nikolaeva Valeriia O. , Alimi Lukman O. , Khashab Niveen M. 
Published: February 2024

AbstractThe rise of touchless technology, driven by the recent pandemic, has transformed human-machine interaction (HMI). Projections indicate a substantial growth in the touchless technology market, nearly tripling from $13.6 billion in 2021 to an estimated $37.6 billion by 2026. In response to the pandemic-driven shift towards touchless technology, here we show an organic cage-based humidity sensor with remarkable humidity responsiveness, forming the basis for advanced touchless platforms in potential future HMI systems. This cage sensor boasts an ultrafast response/recovery time (1 s/3 s) and exceptional stability (over 800 cycles) across relative humidity (RH) changes from 11% to 95%. The crystal structure’s 3D pore network and luxuriant water-absorbing functional groups both inside and outside of the cage contribute synergistically to superior humidity sensing. Demonstrating versatility, we showcase this cage in smart touchless control screens and touchless password managers, presenting cost-effective and easily processable applications of molecularly porous materials in touchless HMI.
Directive giant upconversion by supercritical bound states in the continuum
Authors: Schiattarella Chiara , Romano Silvia , Sirleto Luigi , Mocella Vito , Rendina Ivo , Lanzio Vittorino , Riminucci Fabrizio , Schwartzberg Adam , Cabrini Stefano , Chen Jiaye , Liang Liangliang , Liu Xiaogang , Zito Gianluigi 
Published: February 2024

AbstractPhotonic bound states in the continuum (BICs), embedded in the spectrum of free-space waves1,2 with diverging radiative quality factor, are topologically non-trivial dark modes in open-cavity resonators that have enabled important advances in photonics3,4. However, it is particularly challenging to achieve maximum near-field enhancement, as this requires matching radiative and non-radiative losses. Here we propose the concept of supercritical coupling, drawing inspiration from electromagnetically induced transparency in near-field coupled resonances close to the Friedrich–Wintgen condition2. Supercritical coupling occurs when the near-field coupling between dark and bright modes compensates for the negligible direct far-field coupling with the dark mode. This enables a quasi-BIC field to reach maximum enhancement imposed by non-radiative loss, even when the radiative quality factor is divergent. Our experimental design consists of a photonic-crystal nanoslab covered with upconversion nanoparticles. Near-field coupling is finely tuned at the nanostructure edge, in which a coherent upconversion luminescence enhanced by eight orders of magnitude is observed. The emission shows negligible divergence, narrow width at the microscale and controllable directivity through input focusing and polarization. This approach is relevant to various physical processes, with potential applications for light-source development, energy harvesting and photochemical catalysis.
Twisted-layer boron nitride ceramic with high deformability and strength
Authors: Wu Yingju , Zhang Yang , Wang Xiaoyu , Hu Wentao , Zhao Song , Officer Timothy , Luo Kun , Tong Ke , Du Congcong , Zhang Liqiang , Li Baozhong , Zhuge Zewen , Liang Zitai , Ma Mengdong , Nie Anmin , Yu Dongli , He Julong , Liu Zhongyuan , Xu Bo , Wang Yanbin , Zhao Zhisheng , Tian Yongjun 
Published: February 2024

AbstractMoiré superlattices formed by twisted stacking in van der Waals materials have emerged as a new platform for exploring the physics of strongly correlated materials and other emergent phenomena1–5. However, there remains a lack of research on the mechanical properties of twisted-layer van der Waals materials, owing to a lack of suitable strategies for making three-dimensional bulk materials. Here we report the successful synthesis of a polycrystalline boron nitride bulk ceramic with high room-temperature deformability and strength. This ceramic, synthesized from an onion-like boron nitride nanoprecursor with conventional spark plasma sintering and hot-pressing sintering, consists of interlocked laminated nanoplates in which parallel laminae are stacked with varying twist angles. The compressive strain of this bulk ceramic can reach 14% before fracture, about one order of magnitude higher compared with traditional ceramics (less than 1% in general), whereas the compressive strength is about six times that of ordinary hexagonal boron nitride layered ceramics. The exceptional mechanical properties are due to a combination of the elevated intrinsic deformability of the twisted layering in the nanoplates and the three-dimensional interlocked architecture that restricts deformation from propagating across individual nanoplates. The advent of this twisted-layer boron nitride bulk ceramic opens a gate to the fabrication of highly deformable bulk ceramics.
Progressive unanchoring of Antarctic ice shelves since 1973
Authors: Miles Bertie W. J. , Bingham Robert G. 
Published: February 2024

AbstractMass loss of the Antarctic Ice Sheet has been driven primarily by the thinning of the floating ice shelves that fringe the ice sheet1, reducing their buttressing potential and causing land ice to accelerate into the ocean2. Observations of ice-shelf thickness change by satellite altimetry stretch back only to 1992 (refs. 1,3–5) and previous information about thinning remains unquantified. However, extending the record of ice-shelf thickness change is possible by proxy, by measuring the change in area of the surface expression of pinning points—local bathymetric highs on which ice shelves are anchored6. Here we measure pinning-point change over three epochs spanning the periods 1973–1989, 1989–2000 and 2000−2022, and thus by proxy infer changes to ice-shelf thickness back to 1973–1989. We show that only small localized pockets of ice shelves were thinning between 1973 and 1989, located primarily in the Amundsen Sea Embayment and the Wilkes Land coastline. Ice-shelf thinning spreads rapidly into the 1990s and 2000s and is best characterized by the proportion of pinning points reducing in extent. Only 15% of pinning points reduced from 1973 to 1989, before increasing to 25% from 1989 to 2000 and 37% from 2000 to 2022. A continuation of this trend would further reduce the buttressing potential of ice shelves, enhancing ice discharge and accelerating the contribution of Antarctica to sea-level rise.
B cells orchestrate tolerance to the neuromyelitis optica autoantigen AQP4
Authors: Afzali Ali Maisam , Nirschl Lucy , Sie Christopher , Pfaller Monika , Ulianov Oleksii , Hassler Tobias , Federle Christine , Petrozziello Elisabetta , Kalluri Sudhakar Reddy , Chen Hsin Hsiang , Tyystjärvi Sofia , Muschaweckh Andreas , Lammens Katja , Delbridge Claire , Büttner Andreas , Steiger Katja , Seyhan Gönül , Ottersen Ole Petter , Öllinger Rupert , Rad Roland , Jarosch Sebastian , Straub Adrian , Mühlbauer Anton , Grassmann Simon , Hemmer Bernhard , Böttcher Jan P. , Wagner Ingrid , Kreutzfeldt Mario , Merkler Doron , Pardàs Irene Bonafonte , Schmidt Supprian Marc , Buchholz Veit R. , Heink Sylvia , Busch Dirk H. , Klein Ludger , Korn Thomas 
Published: February 2024

AbstractNeuromyelitis optica is a paradigmatic autoimmune disease of the central nervous system, in which the water-channel protein AQP4 is the target antigen1. The immunopathology in neuromyelitis optica is largely driven by autoantibodies to AQP42. However, the T cell response that is required for the generation of these anti-AQP4 antibodies is not well understood. Here we show that B cells endogenously express AQP4 in response to activation with anti-CD40 and IL-21 and are able to present their endogenous AQP4 to T cells with an AQP4-specific T cell receptor (TCR). A population of thymic B cells emulates a CD40-stimulated B cell transcriptome, including AQP4 (in mice and humans), and efficiently purges the thymic TCR repertoire of AQP4-reactive clones. Genetic ablation of Aqp4 in B cells rescues AQP4-specific TCRs despite sufficient expression of AQP4 in medullary thymic epithelial cells, and B-cell-conditional AQP4-deficient mice are fully competent to raise AQP4-specific antibodies in productive germinal-centre responses. Thus, the negative selection of AQP4-specific thymocytes is dependent on the expression and presentation of AQP4 by thymic B cells. As AQP4 is expressed in B cells in a CD40-dependent (but not AIRE-dependent) manner, we propose that thymic B cells might tolerize against a group of germinal-centre-associated antigens, including disease-relevant autoantigens such as AQP4.