bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wave Generation by Fluidized Granular Flows: Experimental Insights Into the Maximum Near‐Field Wave Amplitude
Authors: Lipiejko Natalia , Whittaker Colin N. , Lane Emily M. , Power William L. 
Published: June 2023

AbstractTsunamis can be generated by an impulsive displacement of water resulting from the entrance of pyroclastic density currents (PDCs). The maximum wave amplitude is of primary interest regarding tsunami modeling and applications to hazard assessment. This study explores tsunami generation by fluidized granular flows and analyzes published relationships predicting maximum wave amplitudes from PDC characteristics. A fluidized column of glass beads is released from a reservoir, flows down an inclined plane and enters a water‐filled flume, generating waves. Fluidized flows of greater mass enter the flume with greater velocities; however, all the analyzed flows impact the water with a supercritical impact Froude number. Flows of greater mass generate a single, high‐amplitude wave, followed by a longer‐period trough. The solitary‐like leading wave propagates along the flume with a nearly constant amplitude. In contrast, the leading wave is followed by a low‐amplitude trough and a second low‐amplitude crest when generated by lower mass flows. Dispersive effects are stronger for waves produced by flows of lower masses, causing the decrease of the amplitudes with distance from the shore. Increased breaking and dissipation cause decreased amplitudes of the waves generated in shallow water depths. The predictive equations, determined based on the impact Froude number and the water depth in the constant‐depth section of the flume, provide relatively good predictions of the maximum wave amplitudes. A new approach is proposed, which calculates the impact Froude number considering the water depth value where the wave generation occurs, providing an improved understanding of the wave generation process.
Surf, Turf, and Above the Earth: Unmet Needs for Coastal Air Quality Science in the Planetary Boundary Layer (PBL)
Authors: Sullivan John T. , Stauffer Ryan M. , Thompson Anne M. , Tzortziou Maria A. , Loughner Christopher P. , Jordan Carolyn E. , Santanello Joseph A. 
Published: June 2023

AbstractCoastal areas are some of the most densely populated and economically important regions in the world. As such, protecting the health of the human population and ecosystems at the coastal interface and understanding the impacts of environmental stressors such as air pollutants provides wide‐ranging benefits. Air quality (AQ) processes within coastal regions have been studied using ground and space‐based platforms, with intensive field campaigns focused on addressing key science questions that are typically partitioned into either direct atmospheric effects (e.g., anthropogenic emissions creating air pollution) or indirect processes and feedback loops (e.g., terrestrial/marine biogenic processes modifying atmospheric properties). The atmospheric planetary boundary layer (PBL) and its depth (or height) connect land, air, and the water surface via many pathways, especially with transport and exchange processes tied to the complexities of the coastal interface. We still cannot accurately characterize—through field, aircraft, or space‐based observations—the spatial and temporal PBL variability and processes within the PBL that couple together coastal dynamics and air quality. Several upcoming geostationary and polar‐orbiting satellite missions are likely to make significant progress in characterizing these air/land/water interactions over the next decade. Here, we present a framework of the current understanding of the PBL's role in coastal regions, primarily regarding air quality and atmospheric deposition, to motivate future concerted efforts from ground‐ and space‐based platforms to achieve a holistic understanding of the coastal interface.
Filtering of Magnetosonic Waves by Mesoscale Plasmaspheric Density Interfaces
Authors: Wu Zhiyong , Su Zhenpeng , Zheng Huinan , Wang Yuming 
Published: June 2023

AbstractMagnetosonic waves inside and outside the plasmasphere differ statistically in occurrence rate, frequency, and intensity. How the density interface separates magnetosonic waves inside and outside the plasmasphere remains not fully understood. Here we report an experimental test made with the Van Allen Probes mission from the plasmaspheric plume through the low‐density channel to the plasmaspheric core. Our linear instability analysis and two‐dimensional full‐wave modeling support that the magnetosonic waves propagate from elsewhere to the channel, undergo reflection and transmission at the flanking plasmaspheric density interfaces and eventually exhibit drastic differences in intensity and frequency coverage between neighboring regions. Such a mesoscale (tens of wavelength wide) interface with a strong refractive index gradient allows the transformation of incident waves to surface waves and consequently filters waves in both frequency and orientation. This unexpected filtering pattern could commonly occur at the plasmaspheric boundary and eventually affect the global distribution of magnetosonic waves.
How Long Can the Postseismic and Interseismic Phases of Great Subduction Earthquake Sustain? Toward an Integrated Earthquake‐Cycle Perspective
Authors: Li Shaoyang , Chen Ling 
Published: June 2023

AbstractThe transition of subduction systems from postseismic to interseismic phase is an important indicator of their stress state and readiness for subsequent events. However, understanding the dynamics of this transition of megathrust earthquakes is hindered by the short instrumental time compared to the centuries‐long recurrence interval (T). Here, with an updated earthquake‐cycle perspective of global spatiotemporally limited geodetic observations, we use generic viscoelastic earthquake‐cycle models to explore the evolution of time‐varying surface deformation. Self‐consistently, our models reproduce key observed features of the deformation cycle, suggesting common processes activated at different margins. The relative postseismic and interseismic durations are found dependent mainly nonlinearly on the ratio of T to mantle viscosity, with a plausible range of ∼0.2–0.4T at representative margins and minimum >0.55T, respectively. Our results thus provide a useful tool for understanding the similarities and differences of earthquake‐cycle deformation and guiding monitoring of possible future signals at world‐wide subduction zones.
HNF4A-BAP31-VDAC1 axis synchronously regulates cell proliferation and ferroptosis in gastric cancer
Authors: Zhou Qingqing , Liu Tengfei , Qian Wenjing , Ji Jun , Cai Qu , Jin Yangbing , Jiang Jinling , Zhang Jun 
Published: June 2023

AbstractB cell receptor associated protein 31 (BAP31) is closely associated with tumor progression, while the role and mechanism of BAP31 in gastric cancer (GC) remains unknown. This study explored that BAP31 was upregulated in GC tissues and high expression indicated poor survival of GC patients. BAP31 knockdown inhibited cell growth and induced G1/S arrest. Moreover, BAP31 attenuation increased the lipid peroxidation level of the membrane and facilitated cellular ferroptosis. Mechanistically, BAP31 regulated cell proliferation and ferroptosis by directly binding to VDAC1 and affected VDAC1 oligomerization and polyubiquitination. HNF4A was bound to BAP31 at the promoter and increased its transcription. Furthermore, knockdown of BAP31 inclined to make GC cells vulnerable to 5-FU and ferroptosis inducer, erastin, in vivo and in vitro. Our work suggests that BAP31 may serve as prognostic factor for gastric cancer and act as potential therapeutic strategy for gastric cancer.
SLC35E1 promotes keratinocyte proliferation in psoriasis by regulating zinc homeostasis
Authors: Huang Tao , Chen Shijun , Ding Ke , Zheng Baoqing , Lv Weiqi , Wang Xiaobo , Zhong Yadan , Huang Hongxin , Zhang Xin , Ma Shufeng , Yang Bin , Wang Xiaohua , Rong Zhili 
Published: June 2023

AbstractKeratinocyte hyperproliferation is a key pathogenic factor in psoriasis. However, the mechanisms that regulate keratinocyte hyperproliferation in this condition remain unclear. Here, we found that SLC35E1 was highly expressed in keratinocytes of patients with psoriasis and that Slc35e1−/− mice displayed a less severe imiquimod (IMQ)-induced psoriasis-like phenotype than their wild-type siblings. In addition, SLC35E1 deficiency inhibited keratinocyte proliferation in both mice and cultured cells. On a molecular level, SLC35E1 was found to regulate zinc ion concentrations and subcellular localization, while zinc ion chelation reversed the IMQ-induced psoriatic phenotype in Slc35e1−/− mice. Meanwhile, epidermal zinc ion levels were decreased in patients with psoriasis and zinc ion supplementation alleviated the psoriatic phenotype in an IMQ-induced mouse model of psoriasis. Our results indicated that SLC35E1 can promote keratinocyte proliferation by regulating zinc ion homeostasis and zinc ion supplementation has potential as a therapy for psoriasis.
Xylosyltransferase I mediates the synthesis of proteoglycans with long glycosaminoglycan chains and controls chondrocyte hypertrophy and collagen fibers organization of in the growth plate
Authors: Taieb Mahdia , Ghannoum Dima , Barré Lydia , Ouzzine Mohamed 
Published: June 2023

AbstractGenetic mutations in the Xylt1 gene are associated with Desbuquois dysplasia type II syndrome characterized by sever prenatal and postnatal short stature. However, the specific role of XylT-I in the growth plate is not completely understood. Here, we show that XylT-I is expressed and critical for the synthesis of proteoglycans in resting and proliferative but not in hypertrophic chondrocytes in the growth plate. We found that loss of XylT-I induces hypertrophic phenotype-like of chondrocytes associated with reduced interterritorial matrix. Mechanistically, deletion of XylT-I impairs the synthesis of long glycosaminoglycan chains leading to the formation of proteoglycans with shorter glycosaminoglycan chains. Histological and Second Harmonic Generation microscopy analysis revealed that deletion of XylT-I accelerated chondrocyte maturation and prevents chondrocytes columnar organization and arrangement in parallel of collagen fibers in the growth plate, suggesting that XylT-I controls chondrocyte maturation and matrix organization. Intriguingly, loss of XylT-I induced at embryonic stage E18.5 the migration of progenitor cells from the perichondrium next to the groove of Ranvier into the central part of epiphysis of E18.5 embryos. These cells characterized by higher expression of glycosaminoglycans exhibit circular organization then undergo hypertrophy and death creating a circular structure at the secondary ossification center location. Our study revealed an uncovered role of XylT-I in the synthesis of proteoglycans and provides evidence that the structure of glycosaminoglycan chains of proteoglycans controls chondrocyte maturation and matrix organization.
A multicentric consortium study demonstrates that dimethylarginine dimethylaminohydrolase 2 is not a dimethylarginine dimethylaminohydrolase
Authors: Ragavan Vinitha N. , Nair Pramod C. , Jarzebska Natalia , Angom Ramcharan Singh , Ruta Luana , Bianconi Elisa , Grottelli Silvia , Tararova Natalia D. , Ryazanskiy Daniel , Lentz Steven R. , Tommasi Sara , Martens-Lobenhoffer Jens , Suzuki-Yamamoto Toshiko , Kimoto Masumi , Rubets Elena , Chau Sarah , Chen Yingjie , Hu Xinli , Bernhardt Nadine , Spieth Peter M. , Weiss Norbert , Bornstein Stefan R. , Mukhopadhyay Debabrata , Bode-Böger Stefanie M. , Maas Renke , Wang Ying , Macchiarulo Antonio , Mangoni Arduino A. , Cellini Barbara , Rodionov Roman N. 
Published: June 2023

AbstractDimethylarginine dimethylaminohydrolase 1 (DDAH1) protects against cardiovascular disease by metabolising the risk factor asymmetric dimethylarginine (ADMA). However, the question whether the second DDAH isoform, DDAH2, directly metabolises ADMA has remained unanswered. Consequently, it is still unclear if DDAH2 may be a potential target for ADMA-lowering therapies or if drug development efforts should focus on DDAH2’s known physiological functions in mitochondrial fission, angiogenesis, vascular remodelling, insulin secretion, and immune responses. Here, an international consortium of research groups set out to address this question using in silico, in vitro, cell culture, and murine models. The findings uniformly demonstrate that DDAH2 is incapable of metabolising ADMA, thus resolving a 20-year controversy and providing a starting point for the investigation of alternative, ADMA-independent functions of DDAH2.
Efflux pump gene amplifications bypass necessity of multiple target mutations for resistance against dual-targeting antibiotic
Authors: Silva Kalinga Pavan T. , Sundar Ganesh , Khare Anupama 
Published: June 2023

AbstractAntibiotics that have multiple cellular targets theoretically reduce the frequency of resistance evolution, but adaptive trajectories and resistance mechanisms against such antibiotics are understudied. Here we investigate these in methicillin resistant Staphylococcus aureus (MRSA) using experimental evolution upon exposure to delafloxacin (DLX), a novel fluoroquinolone that targets both DNA gyrase and topoisomerase IV. We show that selection for coding sequence mutations and genomic amplifications of the gene encoding a poorly characterized efflux pump, SdrM, leads to high DLX resistance, circumventing the requirement for mutations in both target enzymes. In the evolved populations, sdrM overexpression due to genomic amplifications containing sdrM and two adjacent genes encoding efflux pumps results in high DLX resistance, while the adjacent hitchhiking efflux pumps contribute to streptomycin cross-resistance. Further, lack of sdrM necessitates mutations in both target enzymes to evolve DLX resistance, and sdrM thus increases the frequency of resistance evolution. Finally, sdrM mutations and amplifications are similarly selected in two diverse clinical isolates, indicating the generality of this DLX resistance mechanism. Our study highlights that instead of reduced rates of resistance, evolution of resistance to multi-targeting antibiotics can involve alternate high-frequency evolutionary paths, that may cause unexpected alterations of the fitness landscape, including antibiotic cross-resistance.
Persistent serum protein signatures define an inflammatory subcategory of long COVID
Authors: Talla Aarthi , Vasaikar Suhas V. , Szeto Gregory Lee , Lemos Maria P. , Czartoski Julie L. , MacMillan Hugh , Moodie Zoe , Cohen Kristen W. , Fleming Lamar B. , Thomson Zachary , Okada Lauren , Becker Lynne A. , Coffey Ernest M. , De Rosa Stephen C. , Newell Evan W. , Skene Peter J. , Li Xiaojun , Bumol Thomas F. , Juliana McElrath M. , Torgerson Troy R. 
Published: June 2023

AbstractLong COVID or post-acute sequelae of SARS-CoV-2 (PASC) is a clinical syndrome featuring diverse symptoms that can persist for months following acute SARS-CoV-2 infection. The aetiologies may include persistent inflammation, unresolved tissue damage or delayed clearance of viral protein or RNA, but the biological differences they represent are not fully understood. Here we evaluate the serum proteome in samples, longitudinally collected from 55 PASC individuals with symptoms lasting ≥60 days after onset of acute infection, in comparison to samples from symptomatically recovered SARS-CoV-2 infected and uninfected individuals. Our analysis indicates heterogeneity in PASC and identified subsets with distinct signatures of persistent inflammation. Type II interferon signaling and canonical NF-κB signaling (particularly associated with TNF), appear to be the most differentially enriched signaling pathways, distinguishing a group of patients characterized also by a persistent neutrophil activation signature. These findings help to clarify biological diversity within PASC, identify participants with molecular evidence of persistent inflammation, and highlight dominant pathways that may have diagnostic or therapeutic relevance, including a protein panel that we propose as having diagnostic utility for differentiating inflammatory and non-inflammatory PASC.
A village in a dish model system for population-scale hiPSC studies
Authors: Neavin Drew R. , Steinmann Angela M. , Farbehi Nona , Chiu Han Sheng , Daniszewski Maciej S. , Arora Himanshi , Bermudez Yasmin , Moutinho Cátia , Chan Chia-Ling , Bax Monique , Tyebally Mubarika , Gnanasambandapillai Vikkitharan , Lam Chuan E. , Nguyen Uyen , Hernández Damián , Lidgerwood Grace E. , Graham Robert M. , Hewitt Alex W. , Pébay Alice , Palpant Nathan J. , Powell Joseph E. 
Published: June 2023

AbstractThe mechanisms by which DNA alleles contribute to disease risk, drug response, and other human phenotypes are highly context-specific, varying across cell types and different conditions. Human induced pluripotent stem cells are uniquely suited to study these context-dependent effects but cell lines from hundreds or thousands of individuals are required. Village cultures, where multiple induced pluripotent stem lines are cultured and differentiated in a single dish, provide an elegant solution for scaling induced pluripotent stem experiments to the necessary sample sizes required for population-scale studies. Here, we show the utility of village models, demonstrating how cells can be assigned to an induced pluripotent stem line using single-cell sequencing and illustrating that the genetic, epigenetic or induced pluripotent stem line-specific effects explain a large percentage of gene expression variation for many genes. We demonstrate that village methods can effectively detect induced pluripotent stem line-specific effects, including sensitive dynamics of cell states.
Breakdown of self-incompatibility due to genetic interaction between a specific S-allele and an unlinked modifier
Authors: Li Yan , Mamonova Ekaterina , Köhler Nadja , van Kleunen Mark , Stift Marc 
Published: June 2023

AbstractBreakdown of self-incompatibility has frequently been attributed to loss-of-function mutations of alleles at the locus responsible for recognition of self-pollen (i.e. the S-locus). However, other potential causes have rarely been tested. Here, we show that self-compatibility of S1S1-homozygotes in selfing populations of the otherwise self-incompatible Arabidopsis lyrata is not due to S-locus mutation. Between-breeding-system cross-progeny are self-compatible if they combine S1 from the self-compatible cross-partner with recessive S1 from the self-incompatible cross-partner, but self-incompatible with dominant S-alleles. Because S1S1 homozygotes in outcrossing populations are self-incompatible, mutation of S1 cannot explain self-compatibility in S1S1 cross-progeny. This supports the hypothesis that an S1-specific modifier unlinked to the S-locus causes self-compatibility by functionally disrupting S1. Self-compatibility in S19S19 homozygotes may also be caused by an S19-specific modifier, but we cannot rule out a loss-of-function mutation of S19. Taken together, our findings indicate that breakdown of self-incompatibility is possible without disruptive mutations at the S-locus.
An approach to MOFaxanes by threading ultralong polymers through metal–organic framework microcrystals
Authors: Iizuka Tomoya , Sano Hiroyuki , Le Ouay Benjamin , Hosono Nobuhiko , Uemura Takashi 
Published: June 2023

AbstractMechanically interlocked architecture has inspired the fabrication of numerous molecular systems, such as rotaxanes, catenanes, molecular knots, and their polymeric analogues. However, to date, the studies in this field have only focused on the molecular-scale integrity and topology of its unique penetrating structure. Thus, the topological material design of such architectures has not been fully explored from the nano- to the macroscopic scale. Here, we propose a supramolecular interlocked system, MOFaxane, comprised of long chain molecules penetrating a microcrystal of metal–organic framework (MOF). In this study, we describe the synthesis of polypseudoMOFaxane that is one of the MOFaxane family. This has a polythreaded structure in which multiple polymer chains thread a single MOF microcrystal, forming a topological network in the bulk state. The topological crosslinking architecture is obtained by simply mixing polymers and MOFs, and displays characteristics distinct from those of conventional polyrotaxane materials, including suppression of unthreading reactions.
Muscleblind-like proteins use modular domains to localize RNAs by riding kinesins and docking to membranes
Authors: Hildebrandt Ryan P. , Moss Kathryn R. , Janusz-Kaminska Aleksandra , Knudson Luke A. , Denes Lance T. , Saxena Tanvi , Boggupalli Devi Prasad , Li Zhuangyue , Lin Kun , Bassell Gary J. , Wang Eric T. 
Published: June 2023

AbstractRNA binding proteins (RBPs) act as critical facilitators of spatially regulated gene expression. Muscleblind-like (MBNL) proteins, implicated in myotonic dystrophy and cancer, localize RNAs to myoblast membranes and neurites through unknown mechanisms. We find that MBNL forms motile and anchored granules in neurons and myoblasts, and selectively associates with kinesins Kif1bα and Kif1c through its zinc finger (ZnF) domains. Other RBPs with similar ZnFs associate with these kinesins, implicating a motor-RBP specificity code. MBNL and kinesin perturbation leads to widespread mRNA mis-localization, including depletion of Nucleolin transcripts from neurites. Live cell imaging and fractionation reveal that the unstructured carboxy-terminal tail of MBNL1 allows for anchoring at membranes. An approach, termed RBP Module Recruitment and Imaging (RBP-MRI), reconstitutes kinesin- and membrane-recruitment functions using MBNL-MS2 coat protein fusions. Our findings decouple kinesin association, RNA binding, and membrane anchoring functions of MBNL while establishing general strategies for studying multi-functional, modular domains of RBPs.
Reversible conversion between skyrmions and skyrmioniums
Authors: Yang Sheng , Zhao Yuelei , Wu Kai , Chu Zhiqin , Xu Xiaohong , Li Xiaoguang , Åkerman Johan , Zhou Yan 
Published: June 2023

AbstractSkyrmions and skyrmioniums are topologically non-trivial spin textures found in chiral magnetic systems. Understanding the dynamics of these particle-like excitations is crucial for leveraging their diverse functionalities in spintronic devices. This study investigates the dynamics and evolution of chiral spin textures in [Pt/Co]3/Ru/[Co/Pt]3 multilayers with ferromagnetic interlayer exchange coupling. By precisely controlling the excitation and relaxation processes through combined magnetic field and electric current manipulation, reversible conversion between skyrmions and skyrmioniums is achieved. Additionally, we observe the topological conversion from a skyrmionium to a skyrmion, characterized by the sudden emergence of the skyrmion Hall effect. The experimental realization of reversible conversion between distinct magnetic topological spin textures represents a significant development that promises to expedite the advancement of the next generation of spintronic devices.