bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulating the Thermal Regime and Surface Energy Balance of a Permafrost‐Underlain Forest in Mongolia
Authors: Zweigel Robin B. , Dashtseren Avirmed , Temuujin Khurelbaatar , Aalstad Kristoffer , Webster Clare , Stuenzi Simone M. , Aas Kjetil S. , Lee Hanna , Westermann Sebastian
Published: June 2024

Forests overlap with large parts of the northern hemisphere permafrost area, and representing canopy processes is therefore crucial for simulating thermal and hydrological conditions in these regions. Forests impact permafrost through the modulation of radiative fluxes and exchange of turbulent fluxes, precipitation interception and regulation of transpiration. Forests also feature distinct soil layers of litter and organic matter, which play central roles for the infiltration and evaporation of water, while also providing thermal insulation for deeper ground layers. In this study, we present a new module within the CryoGrid community model to simulate forest ecosystems and their impact on the surface water and energy balance. The module includes a big‐leaf vegetation scheme with adaptations for canopy heat storage and transpiration. Furthermore, we account for the effect of surface litter layers on water and energy transfer. We show that the model is capable of simulating radiation, snow cover and ground temperatures below a deciduous needleleaf forest on a north‐facing slope in the Khentii Mountains in Central Mongolia. A sensitivity analysis of topographic aspect and ecosystem configuration confirms the important role of the litter layers for the energy and water balance of the ground. Furthermore, it suggests that the presence of permafrost is primarily linked to topographic aspect rather than the presence of forest at this site. The presented model scheme can be used to study the development of the ground thermal regime in forests, including the state of permafrost, under different climate, ecosystem, and land use scenarios.
Adaptive Covariance Hybridization for the Assimilation of SST Observations Within a Coupled Earth System Reanalysis
Authors: Barthélémy Sébastien , Counillon François , Wang Yiguo
Published: June 2024

Ensemble data assimilation methods, such as the Ensemble Kalman Filter (EnKF), are well suited for climate reanalysis because they feature flow‐dependent covariance. However, because Earth System Models are heavy computationally, the method uses a few tens of members. Sampling error in the covariance matrix can introduce biases in the deep ocean, which may cause a drift in the reanalysis and in the predictions. Here, we assess the potential of the hybrid covariance approach (EnKF‐OI) to counteract sampling error. The EnKF‐OI combines the flow‐dependent covariance computed from a dynamical ensemble with another covariance matrix that is static but less prone to sampling error. We test the method within the Norwegian Climate Prediction Model, which combines the Norwegian Earth System Model and the EnKF. We test the performance of the reanalyzes in an idealized twin experiment, where we assimilate synthetic sea surface temperature observations monthly over 1980–2010. The dynamical and static ensembles consist respectively of 30 members and 315 seasonal members sampled from a pre‐industrial run. We compare the performance of the EnKF to an EnKF‐OI with a global hybrid coefficient, referred to as standard hybrid, and an EnKF‐OI with adaptive hybrid coefficients estimated in space and time. Both hybrid covariance methods cure the bias introduced by the EnKF at intermediate and deep water. The adaptive EnKF‐OI performs best overall by addressing sampling noise and rank deficiencies issues and can sustain low analysis errors by doing smaller updates than the standard hybrid version.
RaFSIP: Parameterizing Ice Multiplication in Models Using a Machine Learning Approach
Authors: Georgakaki Paraskevi , Nenes Athanasios
Published: June 2024

Accurately representing mixed‐phase clouds (MPCs) in global climate models (GCMs) is critical for capturing climate sensitivity and Arctic amplification. Secondary ice production (SIP), can significantly increase ice crystal number concentration (ICNC) in MPCs, affecting cloud properties and processes. Here, we introduce a machine‐learning (ML) approach, called Random Forest SIP (RaFSIP), to parameterize SIP in stratiform MPCs. RaFSIP is trained on 16 grid points with 10‐km horizontal spacing derived from a 2‐year simulation with the Weather Research and Forecasting (WRF) model, including explicit SIP microphysics. Designed for a temperature range of 0 to −25°C, RaFSIP simplifies the description of rime splintering, ice‐ice collisional break‐up, and droplet‐shattering using only a limited set of inputs. RaFSIP was evaluated offline before being integrated into WRF, demonstrating its stable online performance in a 1‐year simulation keeping the same model setup as during training. Even when coupled with the 50‐km grid spacing domain of WRF, RaFSIP reproduces ICNC predictions within a factor of 3 when compared to simulations with explicit SIP microphysics. The coupled WRF‐RaFSIP scheme replicates regions of enhanced SIP and accurately maps ICNCs and liquid water content, particularly at temperatures above −10°C. Uncertainties in RaFSIP minimally impact surface cloud radiative forcing in the Arctic, resulting in radiative biases under 3 Wm−2 compared to simulations with detailed microphysics. Although the performance of RaFSIP in convective clouds remains untested, its adaptable nature allows for data set augmentation to address this aspect. This framework opens possibilities for GCM simplification and process description through physics‐guided ML algorithms.
Understanding Disturbance Regimes From Patterns in Modeled Forest Biomass
Authors: Wang Siyuan , Yang Hui , Koirala Sujan , Forkel Matthias , Reichstein Markus , Carvalhais Nuno
Published: June 2024

Natural and anthropogenic disturbances are important drivers of tree mortality, shaping the structure, composition, and biomass distribution of forest ecosystems. Differences in disturbance regimes, characterized by the frequency, extent, and intensity of disturbance events, result in structurally different landscapes. In this study, we design a model‐based experiment to investigate the links between disturbance regimes and spatial biomass patterns. First, the effects of disturbance events on biomass patterns are simulated using a simple dynamic carbon cycle model based on different disturbance regime attributes, which are characterized via three parameters: μ (probability scale), α (clustering degree), and β (intensity slope). 856,800 dynamically stable biomass patterns were then simulated using combined disturbance regime, primary productivity, and background mortality. As independent variables, we use biomass synthesis statistics from simulated biomass patterns to retrieve three disturbance regime parameters. Results show confident inversion of all three “true” disturbance parameters, with Nash‐Sutcliffe efficiency of 94.8% for μ, 94.9% for α, and 97.1% for β. Biomass histogram statistics primarily dominate the prediction of μ and β, while texture features have a more substantial influence on α. Overall, these results demonstrate the association between biomass patterns and disturbance regimes. Given the increasing availability of Earth observation of biomass, our findings open a new avenue to understand better and parameterize disturbance regimes and their links with vegetation dynamics under climate change. Ultimately, at a large scale, this approach would improve our current understanding of controls and feedback at the biosphere‐atmosphere interface in the present Earth system models.
Simulation of Microcapsule Transport in Fractured Media Using Coupled CFD‐DEM
Authors: Zhang Xiaoming , Newell Pania
Published: June 2024

Geothermal energy is sustainable and gaining momentum as a solution to energy crises and environmental issues. However, challenges like production temperature and thermal breakthrough can impact geothermal project efficiency. One innovative solution to alleviate the thermal breakthrough is to inject polymer‐based materials that are encapsulated in microcapsules into fractures to modify fracture permeability and prevent preferential flow. In our study, we utilized a coupled computational fluid dynamics and discrete element method to simulate the transport of microcapsules under various scenarios controlled by microcapsule size, microcapsule concentration, and fracture roughness. For a smooth fracture, the results indicate that small microcapsules can travel through a smooth fracture regardless of their concentrations. Large microcapsules can transport through a smooth fracture when present in lower concentrations. However, medium and mixed‐size microcapsules tend to cause the sealing of a smooth fracture, irrespective of their concentrations. For a rough fracture, the transport of microcapsules is complicated by their interactions with the rough fracture walls. The presence of two sealing positions in a rough fracture adds further complexity to this transport phenomenon. The size and concentration of microcapsules control one sealing location, while the rough fracture walls determine the other sealing location. The rough walls substantially affect microcapsule transport, rendering the role of microcapsule size and concentration less significant. The simulation results suggest that complex fracture surfaces significantly elevate the occurrence of sealing behavior. To mitigate sealing behavior within more complex fractures, it would be beneficial to use smaller and lower concentrations of microcapsules.
Toward Flash Flood Modeling Using Gradient Resolving Representative Hillslopes
Authors: Manoj J Ashish , Loritz Ralf , Villinger Franziska , Mälicke Mirko , Koopaeidar Mehdi , Göppert Hans , Zehe Erwin
Published: June 2024

It is increasingly acknowledged that the acceleration of the global water cycle, largely driven by anthropogenic climate change, has a disproportionate impact on sub‐daily and small‐scale hydrological extreme events such as flash floods. These events occur thereby at local scales within minutes to hours, typically in response to high‐intensity rainfall events associated with convective storms. In the present work, we show that by employing physically based representative hillslope models that resolve the main gradients controlling overland flow hydrology and hydraulics, we can get reliable simulations of flash flood response in small data‐scarce catchments. To this end, we use climate reanalysis products and transfer soil parameters previously obtained for hydrological predictions in an experimental catchment in the same landscape. The inverted mass balance of flood reservoirs downstream is employed for model evaluation in these nearly ungauged basins. We show that our approach using representative hillslopes and climate data sets can provide reasonable uncalibrated estimates of the overland runoff response (flood magnitude, storm volume, and event runoff coefficients) in three of the four catchments considered. Given that flash floods typically occur at scales of a few km2 and in ungauged places, our results have implications for operational flash flood forecasting and open new avenues for using gradient resolving physically based models for the design of small and medium flood retention basins around the world.
Plant Morphology Impacts Bedload Sediment Transport
Authors: Liu Chao , Shan Yuqi , He Li , Li Fujian , Liu Xingnian , Nepf Heidi
Published: June 2024

Bedload sediment transport plays an important role in the evolution of rivers, marshes and deltas. In these aquatic environments, vegetation is widespread, and plant species have unique morphology. However, the impact of real plant morphology on flow and sediment transport has not been quantified. This study used model plants with real plant morphology, based on the aquatic species Phragmites australis, Acorus calamus and Typha latifolia. The frontal area of these species increases away from the bed, which leads to higher near‐bed velocity than would be predicted from depth‐average frontal area. A plant morphology coefficient was defined to quantify the impact of vertically‐varied plant frontal area. Laboratory experiments confirmed that the plant morphology coefficient improved the prediction of near‐bed velocity, near‐bed turbulent kinetic energy and bedload transport rate in canopies with realistic morphology. Plant morphology can alter transport rates by up to an order of magnitude, relative to the assumption of uniform morphology.
Plate‐Scale Imaging of Eastern US Reveals Ancient and Ongoing Continental Deformation
Authors: Brunsvik Brennan , Eilon Zachary , Lynner Colton
Published: June 2024

Eastern North America was constructed over several Wilson cycles, culminating in the breakup of Pangea. Previous seismological imaging lacked the resolution to depict precisely how ancient tectonic boundaries manifest throughout the lithosphere, how continental breakup modified the plate, or how ongoing mantle dynamics shapes the continental margin. We present a high‐resolution, plate‐scale seismic tomography model of the eastern US by combining an unprecedented suite of complementary data sets in a Bayesian framework. These data provide detailed resolution from crust to asthenosphere, identifying the base of the lithosphere and mid‐lithospheric discontinuities. The plate thins in steps that align with ancient orogens. The lithospheric step at the Appalachian front is associated with cells of mantle upwellings, likely edge‐driven convection, that erode the base of the plate and shape modern Appalachian topography. Low‐velocity structures in the lithospheric‐mantle align with the Grenville front and may be remnants of Rodinia assembly.
Sinuous Aurora at Mars: A Link to the Tail Current Sheet?
Authors: Lillis Robert J. , Deighan Justin , Chirakkil Krishnaprasad , Jain Sonal , Fillingim Matthew , Chaffin Michael , Holsclaw Greg , Susarla Raghuram , Brain David , Al Matroushi Hessa , Lootah Fatma , Al Mazmi Hoor , Dong Yaxue , Schneider Nick , Azari Abigail , Ramstad Robin , Nauth Murti , Ma Yingjuan , Halekas Jasper , Espley Jared , Curry Shannon
Published: June 2024

We examine the newly discovered phenomena of sinuous aurora on the nightside of Mars, using images of 130.4 and 135.6 nm oxygen emission measured by the Emirates Mars Mission EMUS ultraviolet spectrograph, and upstream measurements from the MAVEN and Mars Express spacecraft. They are detected in ∼3% of observations, totaling 73 clear detections. These emissions are narrow, elongated (1,000–6,000 km), cross Mars' UV terminator, and are oriented generally toward the anti‐solar point, clustering into north, south, east, and west‐oriented groups. Diverse morphologies are observed, though some spatial features, such as broad curves, may in some cases be due to temporal aliasing of aurora motion as each image is built up over 15–20 min. Sinuous aurora form away from Mars' strongest crustal magnetic fields and can be interrupted by moderate crustal fields. Sinuous aurora occurrence increases strongly with solar wind pressure, though brightness shows only a weak positive dependence on pressure. Interplanetary magnetic field (IMF) clock angle affects their occurrence and orientation: sinuous aurora show a broad range of orientations centered on the solar wind convection electric field (Econv) direction and forming in the +Econv hemisphere, although with moderate clockwise and counterclockwise average “twists” for westward and eastward IMF, respectively. From these features we infer a link between sinuous aurora and electron energization in Mars' magnetotail current sheet, where field geometry on the +Econv side of the sheet is more organized and symmetric. Determination of specific triggering conditions for sinuous aurora requires further investigation.
Investigating the Hot Zone Developed Under Short‐Circuiting Conditions and the Coupled Magnetosphere‐Ionosphere (M‐I) System for the Subauroral Arc's Inner‐Magnetosphere Generation Environment
Authors: Horvath Ildiko , Lovell Brian C.
Published: June 2024

Based on correlated magnetosphere‐ionosphere (M‐I) conjugate observations of seven events, we study the hot zone developed under short‐circuiting conditions leading (a) to the development of outward Subauroral Polarization Streams (SAPS) or Subauroral Ion Drifts (SAID) electric (E) field and (b) to the various subauroral arcs' absence or presence. Results show (a) the close relations of the hot zone earthward extent and peak ion temperature (Ti) to the magnitude of outward SAPS/SAID E field and (b) the hot zone's high Ti (∼11,000 eV) developed under enhanced plasma turbulence that was (c) generated by the amplified narrow hot ion and electron plasma density peaks, (d) sometimes in plasmaspheric plumes, and that was (e) sometimes further enhanced by the strong auroral kilometric radiation (AKR) waves (f) leading to the development of enhanced SAPS/SAID E field. From these (a–f) findings we conclude for the seven events investigated that (a) the hot zone's development under short‐circuiting conditions was regulated by the kinetic energy of mesoscale plasma flows and that (b) the hot zone created the favorable inner‐magnetosphere conditions during short circuiting (c) for stable auroral red (SAR) arc development by plasma turbulence, which is the common source of heat/suprathermal particles accelerated downward, and (d) in the plasmaspheric plume scenario for SAR arc and Strong Thermal Emission Velocity Enhancement (STEVE) arc development by the plumes' enhanced cold plasma populations leading to strong shear flows and thus shear‐flow instabilities well‐known associated with the SAPS/SAR arc and recently regarded as a potential driver mechanism of the STEVE arc.
Advances in fetal and neonatal neuroimaging and everyday exposures
Authors: Lautarescu Alexandra , Bonthrone Alexandra F. , Bos Brendan , Barratt Ben , Counsell Serena J.
Published: June 2024

The complex, tightly regulated process of prenatal brain development may be adversely affected by “everyday exposures” such as stress and environmental pollutants. Researchers are only just beginning to understand the neural sequelae of such exposures, with advances in fetal and neonatal neuroimaging elucidating structural, microstructural, and functional correlates in the developing brain. This narrative review discusses the wide-ranging literature investigating the influence of parental stress on fetal and neonatal brain development as well as emerging literature assessing the impact of exposure to environmental toxicants such as lead and air pollution. These ‘everyday exposures’ can co-occur with other stressors such as social and financial deprivation, and therefore we include a brief discussion of neuroimaging studies assessing the effect of social disadvantage. Increased exposure to prenatal stressors is associated with alterations in the brain structure, microstructure and function, with some evidence these associations are moderated by factors such as infant sex. However, most studies examine only single exposures and the literature on the relationship between in utero exposure to pollutants and fetal or neonatal brain development is sparse. Large cohort studies are required that include evaluation of multiple co-occurring exposures in order to fully characterize their impact on early brain development.

Impact

Increased prenatal exposure to parental stress and is associated with altered functional, macro and microstructural fetal and neonatal brain development.

Exposure to air pollution and lead may also alter brain development in the fetal and neonatal period.

Further research is needed to investigate the effect of multiple co-occurring exposures, including stress, environmental toxicants, and socioeconomic deprivation on early brain development.
DUSP22 inhibits lung tumorigenesis by suppression of EGFR/c-Met signaling
Authors: Lin Hsiao-Han , Chang Cheng-Wei , Liao Yu-Ting , Yeh Shauh-Der , Lin Hsiu-Ping , Ho Hui-Min , Cheung Chantal Hoi-Yin , Juan Hsueh-Fen , Chen Yi-Rong , Su Yu-Wen , Chen Li-Mei , Tan Tse-Hua , Lin Wen-Jye
Published: June 2024

DUSP22, an atypical dual-specificity phosphatase enzyme, plays a significant role in regulating multiple kinase signaling pathways by dephosphorylation. Our study demonstrated that decreased DUSP22 expression is associated with shorter disease-free survival, advanced TNM (tumor, lymph nodes, and metastasis), cancer stage, and higher tumor grade in lung adenocarcinoma (LUAD) patients. Exogenous DUSP22 expression reduces the colony-forming capacity of lung cancer cells and inhibits xenograft tumor growth primarily by targeting EGFR and suppressing its activity through dephosphorylation. Knockdown of DUSP22 using shRNA enhances EGFR dependency in HCC827 lung cancer cells and increases sensitivity to gefitinib, an EGFR inhibitor. Consistently, genetic deletion of DUSP22 enhances EGFRdel (exon 19 deletion)-driven lung tumorigenesis and elevates EGFR activity. Pharmacological inhibition of DUSP22 activates EGFR, ERK1/2, and upregulates downstream PD-L1 expression. Additionally, lentiviral deletion of DUSP22 by shRNA enhances lung cancer cell migration through EGFR/c-Met and PD-L1-dependent pathways. Gefitinib, an EGFR inhibitor, mechanistically suppresses migration induced by DUSP22 deletion and inhibits c-Met activity. Furthermore, cabozantinib, a c-Met inhibitor, reduces migration and attenuates EGFR activation caused by DUSP22 deletion. Collectively, our findings support the hypothesis that loss of DUSP22 function in lung cancer cells confers a survival advantage by augmenting EGFR signaling, leading to increased activation of downstream c-Met, ERK1/2, and PD-L1 axis, ultimately contributing to the progression of advanced lung cancer.
Monitoring ocular disease via optical nanostructures potentially applicable to corneal contact lens products
Authors: AlQattan Bader , Elsherif Mohamed , Alam Fahad , Butt Haider
Published: June 2024

Ocular diseases can cause vision problems or even blindness if they are not detected early. Some ocular diseases generate irregular physical changes in the eye; therefore, reliable diagnostic technology for continuous monitoring of the eye is an unmet clinical need. In this study, a pulsed laser (Nd:YAG) was used to create optical nanostructures on a hydrogel-based commercial contact lens. Simulations were used to determine the spacing of the nanostructures, which were then produced and tested on the lens in ambient humidity and fully hydrated environments. The nanostructures produced a 4° diffraction angle difference in response to the environmental changes. Vision obstruction was considered while designing the nanostructure features on the lens. The curved nanostructures exhibited a series of visible rainbow colors with an average range of 8° under normal room light. A spherical surface was also used to simulate the human eye, and application of a force (curvature change) caused the nanostructure spacing to change, influencing the visible color of the contact lenses. A smartphone camera application was used to measure the progress of ocular diseases by analyzing the RGB color values of the visible color. The nanostructures were also responsive to K+ ion variations in artificial tear fluids, with a 12 mmol L−1 sensitivity, which may allow the detection of ocular ionic strength changes.
Proof of concept for a new sensor to monitor marine litter from space
Authors: Cózar Andrés , Arias Manuel , Suaria Giuseppe , Viejo Josué , Aliani Stefano , Koutroulis Aristeidis , Delaney James , Bonnery Guillaume , Macías Diego , de Vries Robin , Sumerot Romain , Morales-Caselles Carmen , Turiel Antonio , González-Fernández Daniel , Corradi Paolo
Published: June 2024

Worldwide, governments are implementing strategies to combat marine litter. However, their effectiveness is largely unknown because we lack tools to systematically monitor marine litter over broad spatio-temporal scales. Metre-sized aggregations of floating debris generated by sea-surface convergence lines have been reported as a reliable target for detection from satellites. Yet, the usefulness of such ephemeral, scattered aggregations as proxy for sustained, large-scale monitoring of marine litter remains an open question for a dedicated Earth-Observation mission. Here, we track this proxy over a series of 300,000 satellite images of the entire Mediterranean Sea. The proxy is mainly related to recent inputs from land-based litter sources. Despite the limitations of in-orbit technology, satellite detections are sufficient to map hot-spots and capture trends, providing an unprecedented source-to-sink view of the marine litter phenomenon. Torrential rains largely control marine litter inputs, while coastal boundary currents and wind-driven surface sweep arise as key drivers for its distribution over the ocean. Satellite-based monitoring proves to be a real game changer for marine litter research and management. Furthermore, the development of an ad-hoc sensor can lower the minimum detectable concentration by one order of magnitude, ensuring operational monitoring, at least for seasonal-to-interannual variability in the mesoscale.
A clade of receptor-like cytoplasmic kinases and 14-3-3 proteins coordinate inositol hexaphosphate accumulation
Authors: Xu Li Lin , Cui Meng Qi , Xu Chen , Zhang Miao Jing , Li Gui Xin , Xu Ji Ming , Wu Xiao Dan , Mao Chuan Zao , Ding Wo Na , Benhamed Moussa , Ding Zhong Jie , Zheng Shao Jian
Published: June 2024

Inositol hexaphosphate (InsP6) is the major storage form of phosphorus in seeds. Reducing seed InsP6 content is a breeding objective in agriculture, as InsP6 negatively impacts animal nutrition and the environment. Nevertheless, how InsP6 accumulation is regulated remains largely unknown. Here, we identify a clade of receptor-like cytoplasmic kinases (RLCKs), named Inositol Polyphosphate-related Cytoplasmic Kinases 1-6 (IPCK1-IPCK6), deeply involved in InsP6 accumulation. The InsP6 concentration is dramatically reduced in seeds of ipck quadruple (T-4m/C-4m) and quintuple (C-5m) mutants, accompanied with the obviously increase of phosphate (Pi) concentration. The plasma membrane-localized IPCKs recruit IPK1 involved in InsP6 synthesis, and facilitate its binding and activity via phosphorylation of GRF 14-3-3 proteins. IPCKs also recruit IPK2s and PI-PLCs required for InsP4/InsP5 and InsP3 biosynthesis respectively, to form a potential IPCK-GRF-PLC-IPK2-IPK1 complex. Our findings therefore uncover a regulatory mechanism of InsP6 accumulation governed by IPCKs, shedding light on the mechanisms of InsP biosynthesis in eukaryotes.
Brain-state mediated modulation of inter-laminar dependencies in visual cortex
Authors: Das Anirban , Sheffield Alec G. , Nandy Anirvan S. , Jadi Monika P.
Published: June 2024

Spatial attention is critical for recognizing behaviorally relevant objects in a cluttered environment. How the deployment of spatial attention aids the hierarchical computations of object recognition remains unclear. We investigated this in the laminar cortical network of visual area V4, an area strongly modulated by attention. We found that deployment of attention strengthened unique dependencies in neural activity across cortical layers. On the other hand, shared dependencies were reduced within the excitatory population of a layer. Surprisingly, attention strengthened unique dependencies within a laminar population. Crucially, these modulation patterns were also observed during successful behavioral outcomes that are thought to be mediated by internal brain state fluctuations. Successful behavioral outcomes were also associated with phases of reduced neural excitability, suggesting a mechanism for enhanced information transfer during optimal states. Our results suggest common computation goals of optimal sensory states that are attained by either task demands or internal fluctuations.
Strain-induced long-range charge-density wave order in the optimally doped Bi2Sr2−xLaxCuO6 superconductor
Authors: Kawasaki Shinji , Tsukuda Nao , Lin Chengtian , Zheng Guo-qing
Published: June 2024

The mechanism of high-temperature superconductivity in copper oxides (cuprate) remains elusive, with the pseudogap phase considered a potential factor. Recent attention has focused on a long-range symmetry-broken charge-density wave (CDW) order in the underdoped regime, induced by strong magnetic fields. Here by 63,65Cu-nuclear magnetic resonance, we report the discovery of a long-range CDW order in the optimally doped Bi2Sr2−xLaxCuO6 superconductor, induced by in-plane strain exceeding ∣ε∣ = 0.15 %, which deliberately breaks the crystal symmetry of the CuO2 plane. We find that compressive/tensile strains reduce superconductivity but enhance CDW, leaving superconductivity to coexist with CDW. The findings show that a long-range CDW order is an underlying hidden order in the pseudogap state, not limited to the underdoped regime, becoming apparent under strain. Our result sheds light on the intertwining of various orders in the cuprates.
Ligand-based design of [18F]OXD-2314 for PET imaging in non-Alzheimer’s disease tauopathies
Authors: Lindberg Anton , Murrell Emily , Tong Junchao , Mason N. Scott , Sohn Daniel , Sandell Johan , Ström Peter , Stehouwer Jeffrey S. , Lopresti Brian J. , Viklund Jenny , Svensson Samuel , Mathis Chester A. , Vasdev Neil
Published: June 2024

Positron emission tomography (PET) imaging of tau aggregation in Alzheimer’s disease (AD) is helping to map and quantify the in vivo progression of AD pathology. To date, no high-affinity tau-PET radiopharmaceutical has been optimized for imaging non-AD tauopathies. Here we show the properties of analogues of a first-in-class 4R-tau lead, [18F]OXD-2115, using ligand-based design. Over 150 analogues of OXD-2115 were synthesized and screened in post-mortem brain tissue for tau affinity against [3H]OXD-2115, and in silico models were used to predict brain uptake. [18F]OXD-2314 was identified as a selective, high-affinity non-AD tau PET radiotracer with favorable brain uptake, dosimetry, and radiometabolite profiles in rats and non-human primate and is being translated for first-in-human PET studies.
No evidence for ongoing replication on ART in SIV-infected macaques
Authors: Immonen Taina T. , Fennessey Christine M. , Lipkey Leslie , Newman Laura , Macairan Agatha , Bosche Marjorie , Waltz Nora , Del Prete Gregory Q. , Lifson Jeffrey D. , Keele Brandon F.
Published: June 2024

The capacity of HIV-1 to replicate during optimal antiretroviral therapy (ART) is challenging to assess directly. To gain greater sensitivity to detect evolution on ART, we used a nonhuman primate (NHP) model providing precise control over the level of pre-ART evolution and more comprehensive analyses than are possible with clinical samples. We infected 21 rhesus macaques (RMs) with the barcoded virus SIVmac239M and initiated ART early to minimize baseline genetic diversity. RMs were treated for 285–1200 days. We used several tests of molecular evolution to compare 1352 near-full-length (nFL) SIV DNA single genome sequences from PBMCs, lymph nodes, and spleen obtained near the time of ART initiation and those present after long-term ART, none of which showed significant changes to the SIV DNA population during ART in any animal. To investigate the possibility of ongoing replication in unsampled putative tissue sanctuaries during ART, we discontinued treatment in four animals and confirmed that none of the 336 nFL SIV RNA sequences obtained from rebound plasma viremia showed evidence of evolution. The rigorous nature of our analyses reinforced the emerging consensus of a lack of appreciable ongoing replication on effective ART and validates the relevance of this NHP model for cure studies.
Hydrogen peroxide is required for light-induced stomatal opening across different plant species
Authors: Shi Wen , Liu Yue , Zhao Na , Yao Lianmei , Li Jinge , Fan Min , Zhong Bojian , Bai Ming-Yi , Han Chao
Published: June 2024

Stomatal movement is vital for plants to exchange gases and adaption to terrestrial habitats, which is regulated by environmental and phytohormonal signals. Here, we demonstrate that hydrogen peroxide (H2O2) is required for light-induced stomatal opening. H2O2 accumulates specifically in guard cells even when plants are under unstressed conditions. Reducing H2O2 content through chemical treatments or genetic manipulations results in impaired stomatal opening in response to light. This phenomenon is observed across different plant species, including lycopodium, fern, and monocotyledonous wheat. Additionally, we show that H2O2 induces the nuclear localization of KIN10 protein, the catalytic subunit of plant energy sensor SnRK1. The nuclear-localized KIN10 interacts with and phosphorylates the bZIP transcription factor bZIP30, leading to the formation of a heterodimer between bZIP30 and BRASSINAZOLE-RESISTANT1 (BZR1), the master regulator of brassinosteroid signaling. This heterodimer complex activates the expression of amylase, which enables guard cell starch degradation and promotes stomatal opening. Overall, these findings suggest that H2O2 plays a critical role in light-induced stomatal opening across different plant species.
Atomic order of rare earth ions in a complex oxide: a path to magnetotaxial anisotropy
Authors: Kaczmarek Allison C. , Rosenberg Ethan R. , Song Yixuan , Ye Kevin , Winter Gavin A. , Penn Aubrey N. , Gomez-Bombarelli Rafael , Beach Geoffrey S. D. , Ross Caroline A.
Published: June 2024

Complex oxides offer rich magnetic and electronic behavior intimately tied to the composition and arrangement of cations within the structure. Rare earth iron garnet films exhibit an anisotropy along the growth direction which has long been theorized to originate from the ordering of different cations on the same crystallographic site. Here, we directly demonstrate the three-dimensional ordering of rare earth ions in pulsed laser deposited (EuxTm1-x)3Fe5O12garnet thin films using both atomically-resolved elemental mapping to visualize cation ordering and X-ray diffraction to detect the resulting order superlattice reflection. We quantify the resulting ordering-induced ‘magnetotaxial’ anisotropy as a function of Eu:Tm ratio using transport measurements, showing an overwhelmingly dominant contribution from magnetotaxial anisotropy that reaches 30 kJ m−3for garnets with x = 0.5. Control of cation ordering on inequivalent sites provides a strategy to control matter on the atomic level and to engineer the magnetic properties of complex oxides.
Learning nonlinear operators in latent spaces for real-time predictions of complex dynamics in physical systems
Authors: Kontolati Katiana , Goswami Somdatta , Em Karniadakis George , Shields Michael D.
Published: June 2024

Predicting complex dynamics in physical applications governed by partial differential equations in real-time is nearly impossible with traditional numerical simulations due to high computational cost. Neural operators offer a solution by approximating mappings between infinite-dimensional Banach spaces, yet their performance degrades with system size and complexity. We propose an approach for learning neural operators in latent spaces, facilitating real-time predictions for highly nonlinear and multiscale systems on high-dimensional domains. Our method utilizes the deep operator network architecture on a low-dimensional latent space to efficiently approximate underlying operators. Demonstrations on material fracture, fluid flow prediction, and climate modeling highlight superior prediction accuracy and computational efficiency compared to existing methods. Notably, our approach enables approximating large-scale atmospheric flows with millions of degrees, enhancing weather and climate forecasts. Here we show that the proposed approach enables real-time predictions that can facilitate decision-making for a wide range of applications in science and engineering.
The effector-triggered immunity landscape of tomato against Pseudomonas syringae
Authors: Lonjon Fabien , Lai Yan , Askari Nasrin , Aiyar Niharikaa , Bundalovic-Torma Cedoljub , Laflamme Bradley , Wang Pauline W. , Desveaux Darrell , Guttman David S.
Published: June 2024

Tomato (Solanum lycopersicum) is one of the world’s most important food crops, and as such, its production needs to be protected from infectious diseases that can significantly reduce yield and quality. Here, we survey the effector-triggered immunity (ETI) landscape of tomato against the bacterial pathogen Pseudomonas syringae. We perform comprehensive ETI screens in five cultivated tomato varieties and two wild relatives, as well as an immunodiversity screen on a collection of 149 tomato varieties that includes both wild and cultivated varieties. The screens reveal a tomato ETI landscape that is more limited than what was previously found in the model plant Arabidopsis thaliana. We also demonstrate that ETI eliciting effectors can protect tomato against P. syringae infection when the effector is delivered by a non-virulent strain either prior to or simultaneously with a virulent strain. Overall, our findings provide a snapshot of the ETI landscape of tomatoes and demonstrate that ETI can be used as a biocontrol treatment to protect crop plants.
High performance magnesium-based plastic semiconductors for flexible thermoelectrics
Authors: Li Airan , Wang Yuechu , Li Yuzheng , Yang Xinlei , Nan Pengfei , Liu Kai , Ge Binghui , Fu Chenguang , Zhu Tiejun
Published: June 2024

Low-cost thermoelectric materials with simultaneous high performance and superior plasticity at room temperature are urgently demanded due to the lack of ever-lasting power supply for flexible electronics. However, the inherent brittleness in conventional thermoelectric semiconductors and the inferior thermoelectric performance in plastic organics/inorganics severely limit such applications. Here, we report low-cost inorganic polycrystalline Mg3Sb0.5Bi1.498Te0.002, which demonstrates a remarkable combination of large strain (~ 43%) and high figure of merit zT (~ 0.72) at room temperature, surpassing both brittle Bi2(Te,Se)3 (strain ≤ 5%) and plastic Ag2(Te,Se,S) and organics (zT ≤ 0.4). By revealing the inherent high plasticity in Mg3Sb2 and Mg3Bi2, capable of sustaining over 30% compressive strain in polycrystalline form, and the remarkable deformability of single-crystalline Mg3Bi2 under bending, cutting, and twisting, we optimize the Bi contents in Mg3Sb2-xBix (x = 0 to 1) to simultaneously boost its room-temperature thermoelectric performance and plasticity. The exceptional plasticity of Mg3Sb2-xBix is further revealed to be brought by the presence of a dense dislocation network and the persistent Mg-Sb/Bi bonds during slipping. Leveraging its high plasticity and strength, polycrystalline Mg3Sb2-xBix can be easily processed into micro-scale dimensions. As a result, we successfully fabricate both in-plane and out-of-plane flexible Mg3Sb2-xBix thermoelectric modules, demonstrating promising power density. The inherent remarkable plasticity and high thermoelectric performance of Mg3Sb2-xBix hold the potential for significant advancements in flexible electronics and also inspire further exploration of plastic inorganic semiconductors.
High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants
Authors: Fan Tingting , Cheng Yanhao , Wu Yuechao , Liu Shishi , Tang Xu , He Yao , Liao Shanyue , Zheng Xuelian , Zhang Tao , Qi Yiping , Zhang Yong
Published: June 2024

Cytosine base editors (CBEs) and adenine base editors (ABEs) enable precise C-to-T and A-to-G edits. Recently, ABE8e, derived from TadA-8e, enhances A-to-G edits in mammalian cells and plants. Interestingly, TadA-8e can also be evolved to confer C-to-T editing. This study compares engineered CBEs derived from TadA-8e in rice and tomato cells, identifying TadCBEa, TadCBEd, and TadCBEd_V106W as efficient CBEs with high purity and a narrow editing window. A dual base editor, TadDE, promotes simultaneous C-to-T and A-to-G editing. Multiplexed base editing with TadCBEa and TadDE is demonstrated in transgenic rice, with no off-target effects detected by whole genome and transcriptome sequencing, indicating high specificity. Finally, two crop engineering applications using TadDE are shown: introducing herbicide resistance alleles in OsALS and creating synonymous mutations in OsSPL14 to resist OsMIR156-mediated degradation. Together, this study presents TadA-8e derived CBEs and a dual base editor as valuable additions to the plant editing toolbox.
Mechanistic patterns and clinical implications of oncogenic tyrosine kinase fusions in human cancers
Authors: Cheong Taek-Chin , Jang Ahram , Wang Qi , Leonardi Giulia C. , Ricciuti Biagio , Alessi Joao V. , Di Federico Alessandro , Awad Mark M. , Lehtinen Maria K. , Harris Marian H. , Chiarle Roberto
Published: June 2024

Tyrosine kinase (TK) fusions are frequently found in cancers, either as initiating events or as a mechanism of resistance to targeted therapy. Partner genes and exons in most TK fusions are followed typical recurrent patterns, but the underlying mechanisms and clinical implications of these patterns are poorly understood. By developing Functionally Active Chromosomal Translocation Sequencing (FACTS), we discover that typical TK fusions involving ALK, ROS1, RET and NTRK1 are selected from pools of chromosomal rearrangements by two major determinants: active transcription of the fusion partner genes and protein stability. In contrast, atypical TK fusions that are rarely seen in patients showed reduced protein stability, decreased downstream oncogenic signaling, and were less responsive to inhibition. Consistently, patients with atypical TK fusions were associated with a reduced response to TKI therapies. Our findings highlight the principles of oncogenic TK fusion formation and selection in cancers, with clinical implications for guiding targeted therapy.
Electrical detection of mobile skyrmions with 100% tunneling magnetoresistance in a racetrack-like device
Authors: Zhao Mengqi , Chen Aitian , Huang Pei-Yuan , Liu Chen , Shen Laichuan , Liu Jiahao , Zhao Le , Fang Bin , Yue Wen-Cheng , Zheng Dongxing , Wang Ledong , Bai Hao , Shen Ka , Zhou Yan , Wang Shasha , Liu Enlong , He Shikun , Wang Yong-Lei , Zhang Xixiang , Jiang Wanjun
Published: June 2024

Magnetic skyrmions are topological spin textures that are regarded as promising information carriers for next-generation spintronic memory and computing devices. For practical applications, their deterministic generation, manipulation, and efficient detection are the most critical aspects. Although the generation and manipulation of skyrmions have been extensively studied, efficient electrical detection of mobile skyrmions by using techniques that are compatible with modern magnetic memory technology, remains to be adequately addressed. Here, through integrating magnetic multilayers that host nanoscale skyrmions, together with the magnetic tunnel junctions (MTJ), we demonstrate the electrical detection of skyrmions by using the tunneling magnetoresistance (TMR) effect with a TMR ratio that reaches over 100% at room temperature. By building prototype three-terminal racetrack-like devices, we further show the electrical detection of mobile skyrmions by recording the time-dependent TMR ratios. Along with many recent developments, our results could advance the development of skyrmionic memory and logic devices.
Efficient removal of allicin from the stalk of Allium fistulosum for dietary fiber production
Authors: Li Ye , Ma Jiayin , Cao Yubin , Yang Dong
Published: June 2024

The stalk of Allium fistulosum contains dietary fibers with complicated monosaccharide composition and glycosidic bond linkages, which renders it a better dietary fiber supplement. However, the unfavorable odor, majorly contributed by allicin, limits its applications. Although many physical and chemical methods have been developed to remove allicin, there is currently no comparison between their efficiencies. Here, we comprehensively compare all these methods of eliminating allicin in the Allium stalk by starting with optimization of the allicin extraction method. Results indicate that incubation of the chopped Allium stalk with water for 20 min and extraction with 75% ethanol reached a maximal extraction yield. Different methods of allicin elimination are examined, and physical removal of allicin by blanching at 100 °C reaches a maximal clearance rate of 73.3%, rendering it the most efficient and effective method eliminating allicin from the stalk of Allium fistulosum for the preparation of a totally green dietary fiber.
Chromosomal integration of the pSOL1 megaplasmid of Clostridium acetobutylicum for continuous and stable advanced biofuels production
Authors: Ehsaan Muhammad , Yoo Minyeong , Kuit Wouter , Foulquier Céline , Soucaille Philippe , Minton Nigel P.
Published: June 2024

Biofuel production by Clostridium acetobutylicum is compromised by strain degeneration due to loss of its pSOL1 megaplasmid. Here we used engineering biology to stably integrate pSOL1 into the chromosome together with a synthetic isopropanol pathway. In a membrane bioreactor continuously fed with glucose mineral medium, the final strain produced advanced biofuels, n-butanol and isopropanol, at high yield (0.31 g g−1), titre (15.4 g l−1) and productivity (15.5 g l−1 h−1) without degeneration.
Recovering true FRET efficiencies from smFRET investigations requires triplet state mitigation
Authors: Pati Avik K. , Kilic Zeliha , Martin Maxwell I. , Terry Daniel S. , Borgia Alessandro , Bar Sukanta , Jockusch Steffen , Kiselev Roman , Altman Roger B. , Blanchard Scott C.
Published: June 2024

Single-molecule fluorescence resonance energy transfer (smFRET) methods employed to quantify time-dependent compositional and conformational changes within biomolecules require elevated illumination intensities to recover robust photon emission streams from individual fluorophores. Here we show that outside the weak-excitation limit, and in regimes where fluorophores must undergo many rapid cycles of excitation and relaxation, non-fluorescing, excitation-induced triplet states with lifetimes orders of magnitude longer lived than photon-emitting singlet states degrade photon emission streams from both donor and acceptor fluorophores resulting in illumination-intensity-dependent changes in FRET efficiency. These changes are not commonly taken into consideration; therefore, robust strategies to suppress excited state accumulations are required to recover accurate and precise FRET efficiency, and thus distance, estimates. We propose both robust triplet state suppression and data correction strategies that enable the recovery of FRET efficiencies more closely approximating true values, thereby extending the spatial and temporal resolution of smFRET.
Jujubae Fructus extract prolongs lifespan and improves stress tolerance in Caenorhabditis elegans dependent on DAF-16/SOD-3
Authors: Zhang Zhi , Li Jiajia , Li Feng , Wang Tao , Luo Xiaoyan , Li Bing , You Yilin , Wu Changjing , Liu Xiaomeng
Published: June 2024

Jujubae Fructus, the fruit of Ziziphus jujuba Mill has been used as one of the medicine food homology species for thousands of years in China. Studies have shown that the active ingredients of Jujubae Fructus have a variety of biological effects, but its role in the aging process still lacks knowledge. Here, we investigated the effect of Jujubae Fructus extract (JE) on Caenorhabditis elegans lifespan and its potential mechanism. The lifespan of C. elegans treated with JE was signifificantly increased in a dose-dependent manner. In addition, JE treatment prolonged the reproductive period and increased normal activity during aging in C. elegans. Similarly, JE supplementation also enhanced the resistance to heat and oxidative stress in C. elegans. Furthermore, the mutant worms' lifespan assays demonstrated that JE requires daf-16 to prolong lifespan. DAF-16::GFP analysis of TJ356 showed that JE treatment translocates DAF-16::GFP to nucleus in transgenic worms. By analyzing the downstream of daf-16, we identify that JE may regulate sod3 downstream of daf-16. Mutant worms' lifespan and transgenic reporter gene expression assays revealed that increasing SOD-3 expression was critical for extending longevity in C. elegans with JE therapy. Collectively, these data indicate that JE may have an important role in C. elegans longevity that is dependent on DAF-16 and SOD-3.