bluuebunny/crossref_metadata_2025_split huggingface dataset:
Saucers, Fingers, and Lobes: New Insights on Sill Emplacement From Scaled Laboratory Experiments
Authors: Arachchige Uchitha N. , Cruden Alexander R. , Weinberg Roberto , Slim Anja , Köpping Jonas 
Published: October 2022

AbstractWe investigate the conditions under which saucer‐shaped sills form and segment in the upper crust. We performed a series of scaled laboratory experiments that employ visco‐elastic‐plastic Laponite RD® (LRD) gels to model upper crustal rocks, and Newtonian paraffin oil as the magma analog. Saucer‐shaped sills always formed in experiments with a two‐layer upper crust. These experiments show sharp transitions from an inner flat sill to outer inclined sheets, which are characterized by non‐planar margins. The results show that: (a) the transition from an inner flat sill to an outer inclined sheet occurs when the sill radius to overburden depth ratio is between 0.5 and 2.5; (b) outer inclined sheets dip angles vary from 15° to 25°; (c) this transition is controlled by the ratio of the Young's modulus between the host material layers; (d) irregular finger‐like and/or lobate segment geometries form at the propagating tip of the experimental sills; and (e) the evolution and geometry of marginal segments and their connectors are different within the inner and outer sill. The results also suggest that there is no strict requirement for high horizontal stresses (>5 MPa) to form natural saucer‐shaped sill geometries. We conclude that analog experiments of magma emplacement into layered visco‐elastic‐plastic upper crustal analogs reproduce the complexity of natural saucer‐shaped sills and their marginal segmentation. The behavior of the experimental sills is compatible with brittle‐elastic fracture mechanisms operating at the intrusion scale, while marginal lobes and finger‐like segments are most likely linked to small‐scale visco‐plastic instabilities occurring at the crack tip scale, possibly aided by the low fracture surface energy of the host material.
The Influence of Bare Ground Thermal Roughness Length Parameterization on the Simulation of Near‐Surface Air and Skin Temperatures Over the Tibetan Plateau
Authors: Zhou Xu , Yang Kun , Jiang Yaozhi , Sun Jing , Chen Yingying , Li Xin , Li Jianhui , Shi Jiancheng 
Published: October 2022

AbstractAn observation‐based parameterization of thermal roughness length (TRP) for bare ground has been implemented in the Weather Research and Forecasting model. This scheme introduces a temperature scale to account for the impact of atmospheric stability. The effect of the TRP scheme is evaluated by comparing simulations with the default and with the implemented one for the Tibetan Plateau (TP) region. We find that the newly implemented scheme generally shows remarkable improvement in simulating the nighttime near‐surface 2m air temperature (T2) and daytime surface skin temperature (TSK), with a reduction in cold biases. The newly implemented scheme directly leads to weakened sensible heat release to the atmosphere in the daytime, thereby increasing energy storage in the land. These changes enhance snow melting in spring and reduce snow accumulation in autumn. Due to reduced snow cover and decreased albedo in the two transitional seasons, more solar radiation is absorbed by the land surface, leading to higher TSK and T2. In summer, the snow albedo feedback plays a minor role when there is minimal snow cover. In winter, the solar radiation is weak, and the atmosphere is relatively stable. Consequently, the warming effect due to the newly implemented scheme is more remarkable in the transitional seasons than in summer and winter. This work demonstrates the importance of the TRP in simulating T2 and TSK in the coupled atmosphere‐land model, and reveals that the influence of this scheme on T2 and TSK over the TP region is mainly associated with snow‐albedo‐shortwave radiation processes.
Potential Caves: Inventory of Subsurface Access Points on the Surface of Titan
Authors: Malaska Michael J. , Schoenfeld Ashley , Wynne J. Judson , Mitchell Karl L. , White Oliver , Howard Alan , Moore Jeffrey , Umurhan Orkan 
Published: October 2022

AbstractWe propose that cycling hydrocarbon rains on Saturn's moon Titan are likely to create subsurface conduits through dissolution geology of the extensive organic and largely‐soluble substrate. In this work we inventory different terrains and locations on Titan that could host potential subsurface access points or caves. Using Cassini data, we identified and enumerated a cryovolcanic construct, filled and empty lake basins that may have formed through karstic processes, estimates of closed valleys in organic plateaux, and enigmatic equatorial pits. Our preliminary survey identified over 21,000 estimated locations for future exploration to identify potential caves and cave forming processes on that world. We speculate that the exploration of these caves could teach us about the cave forming processes, as well as the past climate history and perhaps even chemical deposition history on Titan.
Convective Momentum Transport and Its Impact on the Madden‐Julian Oscillation in E3SM‐MMF
Authors: Yang Qiu , Hannah Walter M. , Leung L. Ruby 
Published: October 2022

AbstractConvective momentum transport (CMT) is the process of vertical redistribution of horizontal momentum by small‐scale turbulent flows from moist convection. Traditional general circulation models (GCMs) and their multiscale modeling framework (MMF) versions poorly represent CMT due to insufficient information of subgrid‐scale flows at each GCM grid. Here the explicit scalar momentum transport (ESMT) scheme for representing CMT is implemented in the Energy Exascale Earth System Model‐Multiscale Modeling Framework (E3SM‐MMF) with embedded 2‐D cloud‐resolving models (CRMs), and verified against E3SM‐MMF simulations with 3‐D CRMs and observations. The results show that representing CMT by ESMT helps reduce climatological mean precipitation model bias over the western Pacific and the ITCZ regions, which is attributed to the weakened mean easterlies over the Pacific. Also, CMT from simulations with 2‐D and 3‐D CRMs impose a similar impact on Kelvin waves by reducing their variability and slowing down their phase speed, but opposite impacts on the Madden‐Julian Oscillation (MJO) variability. The ESMT scheme readily captures the climatological mean spatial patterns of the zonal and meridional components of CMT and their variability across multiple time scales, but shows some differences in estimating its magnitude. CMT mainly affects the MJO by decelerating its winds in the free troposphere, but accelerates its near‐surface winds. This study serves as a prototype for implementing CMT scheme in the MMF simulations, highlighting its crucial role in reducing model bias in mean state and spatiotemporal variability.
Mutual Coupling Mitigation in Array Dense Regime by an Antenna Distribution Optimization in SKA1‐LOW
Authors: Di Ninni Paola , Bercigli Mirko , Bolli Pietro , Labate Maria Grazia , Wijnholds Stefan J. 
Published: October 2022

AbstractThe Aperture Array Verification System 2.0 is the latest technological demonstrator designed for the Square Kilometer Array radio telescope operating at low frequency (50–350 MHz). This is an aperture phased array, known as a “station” of the radio telescope, with a pseudo‐random distribution of 256 dual polarized log‐periodic antennas. Mutual coupling effects among the antennas are known to produce detrimental effects especially at the lower end of the operating frequency band. This paper presents a relationship between the antennas electromagnetic performance and their physical position inside the station, followed by an identification of the most critical distances and alignment‐angles between antennas. The calibration accuracy of the station and its directivity within the field of view of the radio telescope are recalculated after repositioning ∼20% of the 256 antennas showing clear improvements in dense regime with respect to the actual AAVS2.0 layout.
Harmonics-assisted optical phase amplifier
Authors: Li Wu-Zhen , Yang Chen , Zhou Zhi-Yuan , Li Yan , Li Yin-Hai , Niu Su-Jian , Ge Zheng , Chen Li , Guo Guang-Can , Shi Bao-Sen 
Published: October 2022

AbstractThe change in the relative phase between two light fields serves as a basic principle for the measurement of the physical quantity that guides this change. It would therefore be highly advantageous if the relative phase could be amplified to enhance the measurement resolution. One well-known method for phase amplification involves the use of the multi-photon number and path-entangled state known as the NOON state; however, a high-number NOON state is very difficult to prepare and is highly sensitive to optical losses. Here we propose and experimentally demonstrate in principle a phase amplifier scheme with the assistance of a harmonic generation process. The relative phase difference between two polarization modes in a polarized interferometer is amplified coherently four times with cascaded second-harmonic generation processes. We demonstrate that these amplification processes can be recycled and therefore have the potential to realize much higher numbers of multiple amplification steps. The phase amplification method presented here shows considerable advantages over the method based on NOON states and will be highly promising for use in precision optical measurements.
Two-dimensional Dirac plasmon-polaritons in graphene, 3D topological insulator and hybrid systems
Authors: In Chihun , Kim Un Jeong , Choi Hyunyong 
Published: October 2022

AbstractCollective oscillations of massless particles in two-dimensional (2D) Dirac materials offer an innovative route toward implementing atomically thin devices based on low-energy quasiparticle interactions. Strong confinement of near-field distribution on the 2D surface is essential to demonstrate extraordinary optoelectronic functions, providing means to shape the spectral response at the mid-infrared (IR) wavelength. Although the dynamic polarization from the linear response theory has successfully accounted for a range of experimental observations, a unified perspective was still elusive, connecting the state-of-the-art developments based on the 2D Dirac plasmon-polaritons. Here, we review recent works on graphene and three-dimensional (3D) topological insulator (TI) plasmon-polariton, where the mid-IR and terahertz (THz) radiation experiences prominent confinement into a deep-subwavelength scale in a novel optoelectronic structure. After presenting general light-matter interactions between 2D Dirac plasmon and subwavelength quasiparticle excitations, we introduce various experimental techniques to couple the plasmon-polaritons with electromagnetic radiations. Electrical and optical controls over the plasmonic excitations reveal the hybridized plasmon modes in graphene and 3D TI, demonstrating an intense near-field interaction of 2D Dirac plasmon within the highly-compressed volume. These findings can further be applied to invent optoelectronic bio-molecular sensors, atomically thin photodetectors, and laser-driven light sources.
Single cell transcriptomics reveals distinct transcriptional responses to oxycodone and buprenorphine by iPSC-derived brain organoids from patients with opioid use disorder
Authors: Ho Ming-Fen , Zhang Cheng , Moon Irene , Zhu Xiujuan , Coombes Brandon J. , Biernacka Joanna , Skime Michelle , Oesterle Tyler S. , Karpyak Victor M. , Schmidt Kristen , Gliske Kate , Ngo Quyen , Skillon Cedric , Seppala Marvin D. , Li Hu , Weinshilboum Richard M. 
Published: October 2022

AbstractThe opioid epidemic represents a national crisis. Oxycodone is one of the most prescribed opioid medications in the United States, whereas buprenorphine is currently the most prescribed medication for opioid use disorder (OUD) pharmacotherapy. Given the extensive use of prescription opioids and the global opioid epidemic, it is essential to understand how opioids modulate brain cell type function at the single-cell level. We performed single nucleus RNA-seq (snRNA-seq) using iPSC-derived forebrain organoids from three male OUD subjects in response to oxycodone, buprenorphine, or vehicle for seven days. We utilized the snRNA-seq data to identify differentially expressed genes following drug treatment using the Seurat integrative analysis pipeline. We utilized iPSC-derived forebrain organoids and single-cell sequencing technology as an unbiased tool to study cell-type-specific and drug-specific transcriptional responses. After quality control filtering, we analyzed 25787 cells and identified sixteen clusters using unsupervised clustering analysis. Our results reveal distinct transcriptional responses to oxycodone and buprenorphine by iPSC-derived brain organoids from patients with OUD. Specifically, buprenorphine displayed a significant influence on transcription regulation in glial cells. However, oxycodone induced type I interferon signaling in many cell types, including neural cells in brain organoids. Finally, we demonstrate that oxycodone, but not buprenorphine activated STAT1 and induced the type I interferon signaling in patients with OUD. These data suggest that elevation of STAT1 expression associated with OUD might play a role in transcriptional regulation in response to oxycodone. In summary, our results provide novel mechanistic insight into drug action at single-cell resolution.
The effect of oxytocin nasal spray on social interaction in young children with autism: a randomized clinical trial
Authors: Guastella Adam J. , Boulton Kelsie A. , Whitehouse Andrew J. O. , Song Yun Ju , Thapa Rinku , Gregory Simon G. , Pokorski Izabella , Granich Joanna , DeMayo Marilena M. , Ambarchi Zahava , Wray John , Thomas Emma E. , Hickie Ian B. 
Published: October 2022

AbstractEarly supports to enhance social development in children with autism are widely promoted. While oxytocin has a crucial role in mammalian social development, its potential role as a medication to enhance social development in humans remains unclear. We investigated the efficacy, tolerability, and safety of intranasal oxytocin in young children with autism using a double-blind, randomized, placebo-controlled, clinical trial, following a placebo lead-in phase. A total of 87 children (aged between 3 and 12 years) with autism received 16 International Units (IU) of oxytocin (n = 45) or placebo (n = 42) nasal spray, morning and night (32 IU per day) for twelve weeks, following a 3-week placebo lead-in phase. Overall, there was no effect of oxytocin treatment over time on the caregiver-rated Social Responsiveness Scale (SRS-2) (p = 0.686). However, a significant interaction with age (p = 0.028) showed that for younger children, aged 3–5 years, there was some indication of a treatment effect. Younger children who received oxytocin showed improvement on caregiver-rated social responsiveness ( SRS-2). There was no other evidence of benefit in the sample as a whole, or in the younger age group, on the clinician-rated Clinical Global Improvement Scale (CGI-S), or any secondary measure. Importantly, placebo effects in the lead-in phase were evident and there was support for washout of the placebo response in the randomised phase. Oxytocin was well tolerated, with more adverse side effects reported in the placebo group. This study suggests the need for further clinical trials to test the benefits of oxytocin treatment in younger populations with autism.Trial registration www.anzctr.org.au (ACTRN12617000441314).
Dynamic HIV-1 spike motion creates vulnerability for its membrane-bound tripod to antibody attack
Authors: Yang Shuang , Hiotis Giorgos , Wang Yi , Chen Junjian , Wang Jia-huai , Kim Mikyung , Reinherz Ellis L. , Walz Thomas 
Published: October 2022

AbstractVaccines targeting HIV-1’s gp160 spike protein are stymied by high viral mutation rates and structural chicanery. gp160’s membrane-proximal external region (MPER) is the target of naturally arising broadly neutralizing antibodies (bnAbs), yet MPER-based vaccines fail to generate bnAbs. Here, nanodisc-embedded spike protein was investigated by cryo-electron microscopy and molecular-dynamics simulations, revealing spontaneous ectodomain tilting that creates vulnerability for HIV-1. While each MPER protomer radiates centrally towards the three-fold axis contributing to a membrane-associated tripod structure that is occluded in the upright spike, tilting provides access to the opposing MPER. Structures of spike proteins with bound 4E10 bnAb Fabs reveal that the antibody binds exposed MPER, thereby altering MPER dynamics, modifying average ectodomain tilt, and imposing strain on the viral membrane and the spike’s transmembrane segments, resulting in the abrogation of membrane fusion and informing future vaccine development.
GPR97 triggers inflammatory processes in human neutrophils via a macromolecular complex upstream of PAR2 activation
Authors: Chu Tai-Ying , Zheng-Gérard Céline , Huang Kuan-Yeh , Chang Yu-Chi , Chen Ying-Wen , I Kuan-Yu , Lo Yu-Ling , Chiang Nien-Yi , Chen Hsin-Yi , Stacey Martin , Gordon Siamon , Tseng Wen-Yi , Sun Chiao-Yin , Wu Yen-Mu , Pan Yi-Shin , Huang Chien-Hao , Lin Chun-Yen , Chen Tse-Ching , El Omari Kamel , Antonelou Marilina , Henderson Scott R. , Salama Alan , Seiradake Elena , Lin Hsi-Hsien 
Published: October 2022

AbstractNeutrophils play essential anti-microbial and inflammatory roles in host defense, however, their activities require tight regulation as dysfunction often leads to detrimental inflammatory and autoimmune diseases. Here we show that the adhesion molecule GPR97 allosterically activates CD177-associated membrane proteinase 3 (mPR3), and in conjugation with several protein interaction partners leads to neutrophil activation in humans. Crystallographic and deletion analysis of the GPR97 extracellular region identified two independent mPR3-binding domains. Mechanistically, the efficient binding and activation of mPR3 by GPR97 requires the macromolecular CD177/GPR97/PAR2/CD16b complex and induces the activation of PAR2, a G protein-coupled receptor known for its function in inflammation. Triggering PAR2 by the upstream complex leads to strong inflammatory activation, prompting anti-microbial activities and endothelial dysfunction. The role of the complex in pathologic inflammation is underscored by the finding that both GPR97 and mPR3 are upregulated on the surface of disease-associated neutrophils. In summary, we identify a PAR2 activation mechanism that directs neutrophil activation, and thus inflammation. The PR3/CD177/GPR97/PAR2/CD16b protein complex, therefore, represents a potential therapeutic target for neutrophil-mediated inflammatory diseases.
A distinct mammalian disome collision interface harbors K63-linked polyubiquitination of uS10 to trigger hRQT-mediated subunit dissociation
Authors: Narita Momoko , Denk Timo , Matsuo Yoshitaka , Sugiyama Takato , Kikuguchi Chisato , Ito Sota , Sato Nichika , Suzuki Toru , Hashimoto Satoshi , Machová Iva , Tesina Petr , Beckmann Roland , Inada Toshifumi 
Published: October 2022

AbstractTranslational stalling events that result in ribosome collisions induce Ribosome-associated Quality Control (RQC) in order to degrade potentially toxic truncated nascent proteins. For RQC induction, the collided ribosomes are first marked by the Hel2/ZNF598 E3 ubiquitin ligase to recruit the RQT complex for subunit dissociation. In yeast, uS10 is polyubiquitinated by Hel2, whereas eS10 is preferentially monoubiquitinated by ZNF598 in human cells for an unknown reason. Here, we characterize the ubiquitination activity of ZNF598 and its importance for human RQT-mediated subunit dissociation using the endogenous XBP1u and poly(A) translation stallers. Cryo-EM analysis of a human collided disome reveals a distinct composite interface, with substantial differences to yeast collided disomes. Biochemical analysis of collided ribosomes shows that ZNF598 forms K63-linked polyubiquitin chains on uS10, which are decisive for mammalian RQC initiation. The human RQT (hRQT) complex composed only of ASCC3, ASCC2 and TRIP4 dissociates collided ribosomes dependent on the ATPase activity of ASCC3 and the ubiquitin-binding capacity of ASCC2. The hRQT-mediated subunit dissociation requires the K63-linked polyubiquitination of uS10, while monoubiquitination of eS10 or uS10 is not sufficient. Therefore, we conclude that ZNF598 functionally marks collided mammalian ribosomes by K63-linked polyubiquitination of uS10 for the trimeric hRQT complex-mediated subunit dissociation.
Sliding nanomechanical resonators
Authors: Ying Yue , Zhang Zhuo-Zhi , Moser Joel , Su Zi-Jia , Song Xiang-Xiang , Guo Guo-Ping 
Published: October 2022

AbstractThe motion of a vibrating object is determined by the way it is held. This simple observation has long inspired string instrument makers to create new sounds by devising elegant string clamping mechanisms, whereby the distance between the clamping points is modulated as the string vibrates. At the nanoscale, the simplest way to emulate this principle would be to controllably make nanoresonators slide across their clamping points, which would effectively modulate their vibrating length. Here, we report measurements of flexural vibrations in nanomechanical resonators that reveal such a sliding motion. Surprisingly, the resonant frequency of vibrations draws a loop as a tuning gate voltage is cycled. This behavior indicates that sliding is accompanied by a delayed frequency response of the resonators, making their dynamics richer than that of resonators with fixed clamping points. Our work elucidates the dynamics of nanomechanical resonators with unconventional boundary conditions, and offers opportunities for studying friction at the nanoscale from resonant frequency measurements.
Ubiquitin proteolysis of a CDK-related kinase regulates titan cell formation and virulence in the fungal pathogen Cryptococcus neoformans
Authors: Cao Chengjun , Wang Keyi , Wang Yina , Liu Tong-Bao , Rivera Amariliz , Xue Chaoyang 
Published: October 2022

AbstractFungal pathogens often undergo morphological switches, including cell size changes, to adapt to the host environment and cause disease. The pathogenic yeast Cryptococcus neoformans forms so-called ‘titan cells’ during infection. Titan cells are large, polyploid, display alterations in cell wall and capsule, and are more resistant to phagocytosis and various types of stress. Titan cell formation is regulated by the cAMP/PKA signal pathway, which is stimulated by the protein Gpa1. Here, we show that Gpa1 is activated through phosphorylation by a CDK-related kinase (Crk1), which is targeted for degradation by an E3 ubiquitin ligase (Fbp1). Strains overexpressing CRK1 or an allele lacking a PEST domain exhibit increased production of titan cells similarly to the fbp1∆ mutant. Conversely, CRK1 deletion results in reduced titan cell production, indicating that Crk1 stimulates titan cell formation. Crk1 phosphorylates Gpa1, which then localizes to the plasma membrane and activates the cAMP/PKA signal pathway to induce cell enlargement. Furthermore, titan cell-overproducing strains trigger increased Th1 and Th17 cytokine production in CD4+ T cells and show attenuated virulence in a mouse model of systemic cryptococcosis. Overall, our study provides insights into the regulation of titan cell formation and fungal virulence.