bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Cascadia Slab Model From Receiver Functions
Authors: Bloch Wasja , Bostock Michael G. , Audet Pascal 
Published: October 2023

AbstractWe map the characteristic signature of the subducting Juan de Fuca and Gorda plates along the entire Cascadia forearc from northern Vancouver Island, Canada, to Cape Mendocino in northern California, USA, using teleseismic receiver functions. The subducting oceanic crustal complex, possibly including subcreted material, is parameterized by three horizons capable of generating mode‐converted waves: a negative velocity contrast at the top of a low velocity zone underlain by two horizons representing positive contrasts. The amplitude of the conversions varies likely due to differences in composition and/or fluid content. We analyzed the slab signature for 298 long‐running land seismic stations, estimated the depth of the three interfaces through inverse modeling and fitted regularized spline surfaces through the station control points to construct a margin‐wide, double‐layered slab model. Crystalline terranes that act as the static backstop appear to form the major structural barrier that controls the slab morphology. Where the backstop recedes landward beneath the Olympic Peninsula and Cape Mendocino, the slab subducts sub‐horizontally, while the seaward‐protruding and thickened Siletz terrane beneath central Oregon causes steepening of the slab. A tight bend in slab morphology south of the Olympic Peninsula coincides with the location of recurring large intermediate depth earthquakes. The top‐to‐Moho thickness of the slab generally exceeds the thickness of the oceanic crust by 2–12 km, suggesting thickening of the slab or underplating of slab material to the overriding North American plate.
Updates on Model Hierarchies for Understanding and Simulating the Climate System: A Focus on Data‐Informed Methods and Climate Change Impacts
Authors: Mansfield Laura A. , Gupta Aman , Burnett Adam C. , Green Brian , Wilka Catherine , Sheshadri Aditi 
Published: October 2023

AbstractThe climate model hierarchy encompasses models of varying complexity along different axes, ranging from idealized models that elegantly describe isolated mechanisms to fully coupled Earth system models that aspire to provide useable climate projections. Based on the second Model Hierarchies Workshop, which took place in 2022, we present perspectives on how this field has evolved since the first Model Hierarchies Workshop in 2016. In this period, we have witnessed a dramatic increase in the use of (a) machine learning in climate modeling and (b) climate models to estimate risks and influence decision making under climate change. Here, we discuss the implications of these growing areas of research and how we expect them to become integrated into the model hierarchies framework.
Multi‐Site Transfer Function Approach for Real‐Time Modeling of the Ground Electric Field Induced by Laterally‐Nonuniform Ionospheric Source
Authors: Kruglyakov Mikhail , Marshalko Elena , Kuvshinov Alexey , Smirnov Maxim , Viljanen Ari 
Published: October 2023

AbstractWe propose a novel approach to model the ground electric field (GEF) induced by laterally‐nonuniform ionospheric sources in real time. The approach exploits the multi‐site transfer function concept, continuous magnetic field measurements at multiple sites in the region of interest, and spatial modes describing the ionospheric source. We compared the modeled GEFs with those measured at two locations in Fennoscandia and observed good agreement between modeled and measured GEF. Besides, we compared GEF‐based geomagnetically induced current (GIC) with that measured at the Mäntsälä natural gas pipeline recording point and again observed remarkable agreement between modeled and measured GIC.
Morpho‐Tectonics of Transpressional Systems: Insights From Analog Modeling
Authors: Conrad Ethan M. , Reitano Riccardo , Faccenna Claudio , Becker Thorsten W. 
Published: October 2023

AbstractTranspressional margins are widespread, and their dynamics are relevant for plate boundary evolution globally. Though transpressional orogen evolution involves a topographic response to deformation, many studies focus only on the structural development of the system ignoring surface processes. Here, we present a new set of analog models constructed to investigate how tectonic and surface processes interact at transpressive plate boundaries and shape topography. Experiments are conducted by deforming a previously benchmarked crustal analog material in a meter‐scale plexiglass box while controlling erosion through misting nozzles mounted along the transpressional wedge. To analyze the experiments, we generate digital elevation models from laser scans and conduct image correlation analysis on photos taken during experiments. We focus on three experiments that cover a range of erosional conditions and shortening stages (two end‐member erosion models and a dry reference). In all experiments, a bivergent wedge forms, and strain partitioning broadly evolves according to previously established models. Regarding drainage networks, we find that the streams in our models develop differently through feedback between fault development and drainage rearrangement processes. Differences between end‐member erosional models can be explained by the varying response of streams to structure modulated by rainfall. Additionally, erosion may influence the structural evolution of transpressional topography, leading to accelerated strike‐slip partitioning. From these results, we create a model for developing structures, streams, and topography where incision and valley formation along main structures localize exhumation. We apply insights from the models to natural transpressional systems, including the Transverse Ranges, CA, and the Venezuelan Andes.
Toward Street‐Level Nowcasting of Flash Floods Impacts Based on HPC Hydrodynamic Modeling at the Watershed Scale and High‐Resolution Weather Radar Data
Authors: Costabile Pierfranco , Costanzo Carmelina , Kalogiros John , Bellos Vasilis 
Published: October 2023

AbstractIn our era, the rapid increase of parallel programming coupled with high‐performance computing (HPC) facilities allows for the use of two‐dimensional shallow water equation (2D‐SWE) algorithms for simulating floods at the “hydrological” catchment scale, rather than just at the “hydraulic” fluvial scale. This approach paves the way for the development of new operational systems focused on impact‐based flash‐floods nowcasting, wherein hydrodynamic simulations directly model the spatial and temporal variability of measured or predicted rainfall on impacts even at a street scale. Specifically, the main goal of this research is to make a step to move toward the implementation of an effective flash flood nowcasting system in which timely and accurate impact warnings are provided by including weather radar products in the HPC 2D‐SWEs modelling framework able to integrate watershed hydrology, flow hydrodynamics, and river urban flooding in just one model. The timing, location, and intensity of the street‐level evolution of some key elements at risk (people, vehicles, and infrastructures) are also discussed considering both calibration issues and the role played by the spatial and temporal rainfall resolution. All these issues are analyzed and discussed having as a starting point the flood event which hit the Mandra town (Athens, Greece) on the 15 November 2017, highlighting the feasibility and the accuracy of the overall approach and providing new insights for the research in this field.
Polygenic predisposition, sleep duration, and depression: evidence from a prospective population-based cohort
Authors: Hamilton Odessa S. , Steptoe Andrew , Ajnakina Olesya 
Published: October 2023

AbstractSuboptimal sleep durations and depression frequently cooccur. Short-sleep and long-sleep are commonly thought of as symptoms of depression, but a growing literature suggests that they may be prodromal. While each represents a process of mutual influence, the directionality between them remains unclear. Using polygenic scores (PGS), we investigate the prospective direction involved in suboptimal sleep durations and depression. Male and female participants, aged ≥50, were recruited from the English Longitudinal Study of Ageing (ELSA). PGS for sleep duration, short-sleep, and long-sleep were calculated using summary statistics data from the UK Biobank cohort. Sleep duration, categorised into short-sleep (“≤5 h”), optimal-sleep (“>5 to <9 h”), and long-sleep (“≥9 h”), was measured at baseline and across an average 8-year follow-up. Subclinical depression (Centre for Epidemiological Studies Depression Scale [≥4 of 7]) was also ascertained at baseline and across an average 8-year follow-up. One standard deviation increase in PGS for short-sleep was associated with 14% higher odds of depression onset (95% CI = 1.03–1.25, p = 0.008). However, PGS for sleep duration (OR = 0.92, 95% CI = 0.84–1.00, p = 0.053) and long-sleep (OR = 0.97, 95% CI = 0.89–1.06, p = 0.544) were not associated with depression onset during follow-up. During the same period, PGS for depression was not associated with overall sleep duration, short-sleep, or long-sleep. Polygenic predisposition to short-sleep was associated with depression onset over an average 8-year period. However, polygenic predisposition to depression was not associated with overall sleep duration, short-sleep or long-sleep, suggesting different mechanisms underlie the relationship between depression and the subsequent onset of suboptimal sleep durations in older adults.
Lactylation of METTL16 promotes cuproptosis via m6A-modification on FDX1 mRNA in gastric cancer
Authors: Sun Lianhui , Zhang Yuan , Yang Boyu , Sun Sijun , Zhang Pengshan , Luo Zai , Feng Tingting , Cui Zelin , Zhu Ting , Li Yuming , Qiu Zhengjun , Fan Guangjian , Huang Chen 
Published: October 2023

AbstractCuproptosis, caused by excessively high copper concentrations, is urgently exploited as a potential cancer therapeutic. However, the mechanisms underlying the initiation, propagation, and ultimate execution of cuproptosis in tumors remain unknown. Here, we show that copper content is significantly elevated in gastric cancer (GC), especially in malignant tumors. Screening reveals that METTL16, an atypical methyltransferase, is a critical mediator of cuproptosis through the m6A modification on FDX1 mRNA. Furthermore, copper stress promotes METTL16 lactylation at site K229 followed by cuproptosis. The process of METTL16 lactylation is inhibited by SIRT2. Elevated METTL16 lactylation significantly improves the therapeutic efficacy of the copper ionophore– elesclomol. Combining elesclomol with AGK2, a SIRT2-specific inhibitor, induce cuproptosis in gastric tumors in vitro and in vivo. These results reveal the significance of non-histone protein METTL16 lactylation on cuproptosis in tumors. Given the high copper and lactate concentrations in GC, cuproptosis induction becomes a promising therapeutic strategy for GC.
Structural basis for recruitment of TASL by SLC15A4 in human endolysosomal TLR signaling
Authors: Chen Xudong , Xie Min , Zhang Sensen , Monguió-Tortajada Marta , Yin Jian , Liu Chang , Zhang Youqi , Delacrétaz Maeva , Song Mingyue , Wang Yixue , Dong Lin , Ding Qiang , Zhou Boda , Tian Xiaolin , Deng Haiteng , Xu Lina , Liu Xiaohui , Yang Zi , Chang Qing , Na Jie , Zeng Wenwen , Superti-Furga Giulio , Rebsamen Manuele , Yang Maojun 
Published: October 2023

AbstractToll-like receptors (TLRs) are a class of proteins that play critical roles in recognizing pathogens and initiating innate immune responses. TASL, a recently identified innate immune adaptor protein for endolysosomal TLR7/8/9 signaling, is recruited by the lysosomal proton-coupled amino-acid transporter SLC15A4, and then activates IRF5, which in turn triggers the transcription of type I interferons and cytokines. Here, we report three cryo-electron microscopy (cryo-EM) structures of human SLC15A4 in the apo monomeric and dimeric state and as a TASL-bound complex. The apo forms are in an outward-facing conformation, with the dimeric form showing an extensive interface involving four cholesterol molecules. The structure of the TASL-bound complex reveals an unprecedented interaction mode with solute carriers. During the recruitment of TASL, SLC15A4 undergoes a conformational change from an outward-facing, lysosomal lumen-exposed state to an inward-facing state to form a binding pocket, allowing the N-terminal helix of TASL to be inserted into. Our findings provide insights into the molecular basis of regulatory switch involving a human solute carrier and offers an important framework for structure-guided drug discovery targeting SLC15A4-TASL-related human autoimmune diseases.
Asymptotic dispersion engineering for ultra-broadband meta-optics
Authors: Hu Yueqiang , Jiang Yuting , Zhang Yi , Yang Xing , Ou Xiangnian , Li Ling , Kong Xianghong , Liu Xingsi , Qiu Cheng-Wei , Duan Huigao 
Published: October 2023

AbstractDispersion decomposes compound light into its monochromatic components, which is detrimental to broadband imaging but advantageous for spectroscopic applications. Metasurfaces provide a unique path to modulate the dispersion by adjusting structural parameters on a two-dimensional plane. However, conventional linear phase compensation does not adequately match the meta-unit’s dispersion characteristics with required complex dispersion, hindering at-will dispersion engineering over a very wide bandwidth particularly. Here, we propose an asymptotic phase compensation strategy for ultra-broadband dispersion-controlled metalenses. Metasurfaces with extraordinarily high aspect ratio nanostructures have been fabricated for arbitrary dispersion control in ultra-broad bandwidth, and we experimentally demonstrate the single-layer achromatic metalenses in the visible to infrared spectrum (400 nm~1000 nm, NA = 0.164). Our proposed scheme provides a comprehensive theoretical framework for single-layer meta-optics, allowing for arbitrary dispersion manipulation without bandwidth restrictions. This development is expected to have significant applications in ultra-broadband imaging and chromatography detection, among others.
Nanomechanical action opens endo-lysosomal compartments
Authors: Zhao Yu , Ye Zhongfeng , Song Donghui , Wich Douglas , Gao Shuliang , Khirallah Jennifer , Xu Qiaobing 
Published: October 2023

AbstractEndo-lysosomal escape is a highly inefficient process, which is a bottleneck for intracellular delivery of biologics, including proteins and nucleic acids. Herein, we demonstrate the design of a lipid-based nanoscale molecular machine, which achieves efficient cytosolic transport of biologics by destabilizing endo-lysosomal compartments through nanomechanical action upon light irradiation. We fabricate lipid-based nanoscale molecular machines, which are designed to perform mechanical movement by consuming photons, by co-assembling azobenzene lipidoids with helper lipids. We show that lipid-based nanoscale molecular machines adhere onto the endo-lysosomal membrane after entering cells. We demonstrate that continuous rotation-inversion movement of Azo lipidoids triggered by ultraviolet/visible irradiation results in the destabilization of the membranes, thereby transporting cargoes, such as mRNAs and Cre proteins, to the cytoplasm. We find that the efficiency of cytosolic transport is improved about 2.1-fold, compared to conventional intracellular delivery systems. Finally, we show that lipid-based nanoscale molecular machines are competent for cytosolic transport of tumour antigens into dendritic cells, which induce robust antitumour activity in a melanoma mouse model.
Insights into the missing apiosylation step in flavonoid apiosides biosynthesis of Leguminosae plants
Authors: Wang Hao-Tian , Wang Zi-Long , Chen Kuan , Yao Ming-Ju , Zhang Meng , Wang Rong-Shen , Zhang Jia-He , Ågren Hans , Li Fu-Dong , Li Junhao , Qiao Xue , Ye Min 
Published: October 2023

AbstractApiose is a natural pentose containing an unusual branched-chain structure. Apiosides are bioactive natural products widely present in the plant kingdom. However, little is known on the key apiosylation reaction in the biosynthetic pathways of apiosides. In this work, we discover an apiosyltransferase GuApiGT from Glycyrrhiza uralensis. GuApiGT could efficiently catalyze 2″-O-apiosylation of flavonoid glycosides, and exhibits strict selectivity towards UDP-apiose. We further solve the crystal structure of GuApiGT, determine a key sugar-binding motif (RLGSDH) through structural analysis and theoretical calculations, and obtain mutants with altered sugar selectivity through protein engineering. Moreover, we discover 121 candidate apiosyltransferase genes from Leguminosae plants, and identify the functions of 4 enzymes. Finally, we introduce GuApiGT and its upstream genes into Nicotiana benthamiana, and complete de novo biosynthesis of a series of flavonoid apiosides. This work reports an efficient phenolic apiosyltransferase, and reveals mechanisms for its sugar donor selectivity.
Realization and topological properties of third-order exceptional lines embedded in exceptional surfaces
Authors: Tang Weiyuan , Ding Kun , Ma Guancong 
Published: October 2023

AbstractAs the counterpart of Hermitian nodal structures, the geometry formed by exceptional points (EPs), such as exceptional lines (ELs), entails intriguing spectral topology. We report the experimental realization of order-3 exceptional lines (EL3) that are entirely embedded in order-2 exceptional surfaces (ES2) in a three-dimensional periodic synthetic momentum space. The EL3 and the concomitant ES2, together with the topology of the underlying space, prohibit the evaluation of their topology in the eigenvalue manifold by prevailing topological characterization methods. We use a winding number associated with the resultants of the Hamiltonian. This resultant winding number can be chosen to detect only the EL3 but ignores the ES2, allowing the diagnosis of the topological currents carried by the EL3, which enables the prediction of their evolution under perturbations. We further reveal the connection between the intersection multiplicity of the resultants and the winding of the resultant field around the EPs and generalize the approach for detecting and topologically characterizing higher-order EPs. Our work exemplifies the unprecedented topology of higher-order exceptional geometries and may inspire new non-Hermitian topological applications.
CD8+ T cells control SIV infection using both cytolytic effects and non-cytolytic suppression of virus production
Authors: Policicchio Benjamin B. , Cardozo-Ojeda Erwing Fabian , Xu Cuiling , Ma Dongzhu , He Tianyu , Raehtz Kevin D. , Sivanandham Ranjit , Kleinman Adam J. , Perelson Alan S. , Apetrei Cristian , Pandrea Ivona , Ribeiro Ruy M. 
Published: October 2023

AbstractWhether CD8+ T lymphocytes control human immunodeficiency virus infection by cytopathic or non-cytopathic mechanisms is not fully understood. Multiple studies highlighted non-cytopathic effects, but one hypothesis is that cytopathic effects of CD8+ T cells occur before viral production. Here, to examine the role of CD8+ T cells prior to virus production, we treated SIVmac251-infected macaques with an integrase inhibitor combined with a CD8-depleting antibody, or with either reagent alone. We analyzed the ensuing viral dynamics using a mathematical model that included infected cells pre- and post- viral DNA integration to compare different immune effector mechanisms. Macaques receiving the integrase inhibitor alone experienced greater viral load decays, reaching lower nadirs on treatment, than those treated also with the CD8-depleting antibody. Models including CD8+ cell-mediated reduction of viral production (non-cytolytic) were found to best explain the viral profiles across all macaques, in addition an effect in killing infected cells pre-integration (cytolytic) was supported in some of the best models. Our results suggest that CD8+ T cells have both a cytolytic effect on infected cells before viral integration, and a direct, non-cytolytic effect by suppressing viral production.
A random optical parametric oscillator
Authors: Tovar Pedro , von der Weid Jean Pierre , Wang Yuan , Chen Liang , Bao Xiaoyi 
Published: October 2023

AbstractSynchronously pumped optical parametric oscillators (OPOs) provide ultra-fast light pulses at tuneable wavelengths. Their primary drawback is the need for precise cavity control (temperature and length), with flexibility issues such as fixed repetition rates and marginally tuneable pulse widths. Targeting a simpler and versatile OPO, we explore the inherent disorder of the refractive index in single-mode fibres realising the first random OPO – the parametric analogous of random lasers. This novel approach uses modulation instability (χ(3)non-linearity) for parametric amplification and Rayleigh scattering for feedback. The pulsed system exhibits high inter-pulse coherence (coherence time of ~0.4 ms), offering adjustable repetition rates (16.6–2000 kHz) and pulse widths (0.69–47.9 ns). Moreover, it operates continuously without temperature control loops, resulting in a robust and flexible device, which would find direct application in LiDAR technology. This work sets the stage for future random OPOs using different parametric amplification mechanisms.
Microbiome and transcriptome analyses reveal the influence of calcined dolomite application on Eriocheir sinensis in a rice–crab co-culture system
Authors: Li Yingdong , Li Lishong , Miao Wei , Li Xiaodong 
Published: October 2023

AbstractCo-culture systems of rice and aquatic animals can contribute to the ecological intensification of agriculture by reducing nutrient loss and the need for N fertilizer application and by enhancing nutrient-use efficiency. However, the input of high-protein diets into paddy fields, to facilitate the growth of aquatic animals, has been found to increase N pollution and acidification of the soil. Although soil amendments have been widely used to ameliorate acidic soils, reduce N2O emissions, and improve agronomic production, the relationship between soil amendments and aquatic animal remains unclear. Therefore, this study investigated the effects of calcined dolomite (hereafter referred to as dolomite) as an acidic soil amendment and Ca–Mg supplement in rice–crab co-culture using Eriocheir sinensis crabs (Chinese mitten crabs). High-throughput sequencing was used to examine crab bacterial community composition and crab hepatopancreas biology. Although the water pH was significantly increased in the dolomite group, the number, composition, and diversity of bacteria identified in crab gut microbiome did not vary significantly between the dolomite and control groups. In the dolomite group, the probiotic agents Candidatus Hepatoplasma and Lactobacillus were highly abundant in the crab gut, and immune- and retinol metabolism-related genes were significantly upregulated in the crab hepatopancreas. Overall, dolomite application increased crab health and water pH. Dolomite is a low-cost amendment, with better stability, compared to other soil amendments, thus making it ideal for sustainable and clean rice–aquatic animal co-culture.