bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing Non‐Phase‐Locked Tidal Currents in the California Current System Using High‐Frequency Radar
Authors: Kachelein Luke , Gille Sarah T. , Mazloff Matthew R. , Cornuelle Bruce D. 
Published: July 2024

AbstractOver 9 years of hourly surface current data from high‐frequency radar (HFR) off the US West Coast are analyzed using a Bayesian least‐squares fit for tidal components. The spatial resolution and geographic extent of HFR data allow us to assess the spatial structure of the non‐phase‐locked component of the tide. In the frequency domain, the record length and sampling rate allow resolution of discrete tidal lines corresponding to well‐known constituents and the near‐tidal broadband elevated continuum resulting from amplitude and phase modulation of the tides, known as cusps. The FES2014 tide model is used to remove the barotropic component of tidal surface currents in order to evaluate its contribution to the phase‐locked variance and spatial structure. The mean time scale of modulation is 243 days for the M2 constituent and 181 days for S2, with overlap in their range of values. These constituents' modulated amplitudes are significantly correlated in several regions, suggesting shared forcing mechanisms. Within the frequency band M2 ± 5 cycles per year, an average of 48% of energy is not at the phase‐locked frequency. When we remove the barotropic model, this increases to 64%. In both cases there is substantial regional variability. This indicates that a large fraction of tidal energy is not easily predicted (e.g., for satellite altimeter applications). The spatial autocorrelation of the non‐phase‐locked variance fraction drops to zero over a distance of 150 km, a scale that is comparable to the swath width of the Surface Water and Ocean Topography altimeter.
A Community Ionosphere‐Thermosphere Observing System Simulation Experiment (OSSE) Tool: Geospace Dynamics Constellation Example
Authors: Hsu Chih‐Ting , Matsuo Tomoko , Kershaw Helen , Dietrich Nicholas , Smith Marlee , Anderson Jeffrey , Garcia‐Sage Katherine , Yue Jia , Hozumi Yuta , Chou Min‐Yang 
Published: July 2024

AbstractObserving System Simulation Experiments (OSSEs) provide an effective way to evaluate the impact of assimilating data from a specific observing system on hindcasting, nowcasting, and forecasting of environmental systems. The NSF NCAR's Data Assimilation (DA) Research Testbed/Thermosphere‐Ionosphere‐Electrodynamics General Circulation Model (DART/TIEGCM) tool, to be hosted at the NASA Community Coordinated Modeling Center, serves as a valuable and accessible community resource for quantitatively evaluating the impact of observations from both current and future ionosphere‐thermosphere (IT) observing systems. This study demonstrates the utility of DART/TIEGCM as an IT OSSE tool, using synthetic observations simulated using a currently planned NASA Geospace Dynamics Constellation (GDC) observing system design. Five sets of OSSEs are carried out to compare the effects of assimilating various combinations of prospective GDC observations (e.g., neutral temperature, neutral wind, neutral composition, atomic oxygen ion density, and ion and electron temperature) during a major geomagnetic storm period of the St Patrick's Day Storm on 17 March 2013. The maximum error reduction in neutral temperature and atomic ion oxygen density is 24.6% and 43.3% compared to the control experiment. These OSSEs indicate the benefits of coupled IT DA approaches implemented in DART/TIEGCM to maximize the impact of multi‐parameter IT observations, such as those expected from the GDC mission. Although more work is required to draw any definitive conclusion on the GDC data impact, the study provides an illustrative example of how the DART/TIEGCM community tool can be used to evaluate observational impacts of planned or existing missions for geospace research and applications.
Deep Argo Observations of Antarctic Bottom Water in the Deep Fracture Zones of the Southwest Indian Ridge
Authors: Menezes Viviane V. , Robbins Pelle , Furey Heather , Mazloff Matthew 
Published: July 2024

AbstractThe Madagascar Basin is the primary pathway for Antarctic Bottom Water to ventilate the entire western Indian Ocean as part of the Global Overturning Circulation. The only way for this water mass to reach this basin is by crossing the Southwest Indian Ridge through its deep fracture zones. However, due to the scarcity of observations, the Antarctic Bottom Water presence has only been well‐established in the Atlantis II fracture zone. In May 2023, the Deep Madagascar Basin Experiment deployed three Deep SOLO Argo floats in the exit of the fracture zones that were more likely to transport Antarctic Bottom Water: Atlantis II, Novara, and Melville. These floats have been collecting temperature and salinity profiles every 3–5 days with high vertical resolution in the deep ocean. In the present paper, we use the first 7 months of float data to characterize the Antarctic Bottom Water in the deep fracture zone area, revisiting a half‐century puzzle about the Melville contribution. We also collected shipboard‐based profiles to calibrate float salinity and show it is within the Deep Argo program target accuracy. We find Antarctic Bottom Water in both Melville and Novara fracture zones, not only in Atlantis II. This is the first time the Novara contribution has been revealed. The floats also uncover their distinct properties, which may result from the different mixing histories.
Modeling Riverbed Elevation and Bedload Tracer Transport Resting Times Using Fractional Laplace Motion
Authors: Wu Zi , Singh Arvind 
Published: July 2024

AbstractRiverbed elevations play a crucial role in sediment transport and flow resistance, making it essential to understand and quantify their effects. This knowledge is vital for various fields, including river engineering and stream ecology. Previous observations have revealed that fluctuations in the bed surface can exhibit both multifractal and monofractal behaviors. Specifically, the probability distribution function (PDF) of elevation increments may transition from Laplace (two‐sided exponential) to Gaussian with increasing scales or consistently remain Gaussian, respectively. These differences at the finest timescale lead to distinct patterns of bedload particle exchange with the bed surface, thereby influencing particle resting times and streamwise transport. In this paper, we utilize the fractional Laplace motion (FLM) model to analyze riverbed elevation series, demonstrating its capability to capture both mono‐ and multi‐fractal behaviors. Our focus is on studying the resting time distribution of bedload particles during downstream transport, with the FLM model primarily parameterized based on the Laplace distribution of increments PDF at the finest timescale. Resting times are extracted from the bed elevation series by identifying pairs of adjacent deposition and entrainment events at the same elevation. We demonstrate that in cases of insufficient data series length, the FLM model robustly estimates the tail exponent of the resting time distribution. Notably, the tail of the exceedance probability distribution of resting times is much heavier for experimental measurements displaying Laplace increments PDF at the finest scale, compared to previous studies observing Gaussian PDF for bed elevation.
Comparing Information Theory Analysis With Cross‐Correlation and Minimum Variance Analysis of the Solar Wind Structures
Authors: Holland K. M. , Nykyri H. K. , Ma X. , Wing S. 
Published: July 2024

AbstractThe space weather effects at the Earth's magnetosphere are mostly driven by the solar wind that carries the interplanetary magnetic field (IMF). In this paper, we use 2 years of data in the solar wind from lunar orbiting ARTEMIS and MMS spacecraft upstream of the Earth's bow shock to study the structure of the IMF. We determine the lag times of IMF structures and their dependence on spacecraft positions by conducting an information theory analysis and comparing it with two traditional analysis methods: cross‐correlation (CC) analysis and minimum variance of magnetic field analysis (MVAB). For the events with long time intervals (i.e., >4 hr) and with small‐spatial separation between the MMS and ARTEMIS along the yGSM‐direction (i.e., <40Re, where Re is the Earth's radius), the lag times based on the CC and the mutual information (MI) analyses statistically agree with each other, with p‐values of 1.675 × 10−7 and 4.833 × 10−9, with the confidence of 95%. Both the results based on MI and CC have a large deviation from the results from MVAB. For some of the events, such a deviation could be improved by taking the fast mode speed into account; however, p‐tests showed that they were not statistically significant to the 95% confidence level.
Using a Differential Magnetometer Technique to Measure Geomagnetically Induced Currents: An Augmented Approach
Authors: Parry H. G. , Mann I. R. , Kale A. , Milling D. K. , Clark C. , Cui R. , Cordell D. , Unsworth M. J. 
Published: July 2024

AbstractGeoelectric fields produced by time‐varying magnetic fields during geomagnetic storms can result in potentially damaging geomagnetically induced currents (GICs) in long conductors at the Earth's surface. GICs can pose a significant risk to the integrity of grounded electrical infrastructure, particularly high‐voltage transformers. In this study, an inferred GIC is calculated using an augmented differential magnetometer measurement (DMM) technique on a 500 kV transmission line in central Alberta and is validated using a proximal transformer neutral‐to‐ground (TNG) current measurement by AltaLink L.P. using a Hall probe at a transformer substation. This research outlines a custom‐built and innovative DMM design by which both DMM sensors deployed around a power line measure the background geomagnetic disturbance (GMD) field and the magnetic field generated locally by the GIC. We show how this modified approach provides two independent estimates for GIC derived using only ΔBy or ΔBz, the magnetic field components perpendicular to the line carrying GIC. Results for a geomagnetic storm on 12 Oct 2021 show contemporaneous peaks in the TNG current and the DMM‐inferred GIC. The two data sets have similar waveforms and are within the same order of magnitude. The background GMD is reconstructed using DMM and shows excellent correlation to the measured GMD at the permanent Canadian Array for Real‐time Investigations of Magnetic Activity magnetic station at Ministik Lake, approximately 48.5 km away. Based on the results presented here, we verify the added utility value of DMM for temporary deployments for assessing GIC risk in electrical power grids.
Fabrication and characterization of high-sensitivity, wide-range, and flexible MEMS thermal flow velocity sensors
Authors: Li Min , Qin Guangzhao , Jia Chen , Zhang Danyu , Li Zhikang , Han Xiangguang , Xu Shusheng , Zhao Libo , Luo Guoxi , Liu Cunlang , Yang Ping , Lin Qijing 
Published: July 2024

AbstractWith the rapid development of various fields, including aerospace, industrial measurement and control, and medical monitoring, the need to quantify flow velocity measurements is increasing. It is difficult for traditional flow velocity sensors to fulfill accuracy requirements for velocity measurements due to their small ranges, susceptibility to environmental impacts, and instability. Herein, to optimize sensor performance, a flexible microelectromechanical system (MEMS) thermal flow sensor is proposed that combines the working principles of thermal loss and thermal temperature difference and utilizes a flexible cavity substrate made of a low-thermal-conductivity polyimide/SiO2 (PI/SiO2) composite porous film to broaden the measurement range and improve the sensitivity. The measurement results show that the maximum measurable flow velocity can reach 30 m/s with a resolution of 5.4 mm/s. The average sensitivities of the sensor are 59.49 mV/(m s−1) in the medium-to-low wind velocity range of 0–2 m/s and 467.31 mV/(m s−1) in the wind velocity range of 2–30 m/s. The sensor proposed in this work can enable new applications of flexible flow sensors and wearable devices.
mtDNA release promotes cGAS-STING activation and accelerated aging of postmitotic muscle cells
Authors: Li Ying , Cui Jie , Liu Lei , Hambright William S. , Gan Yutai , Zhang Yajun , Ren Shifeng , Yue Xianlin , Shao Liwei , Cui Yan , Huard Johnny , Mu Yanling , Yao Qingqiang , Mu Xiaodong 
Published: July 2024

AbstractThe mechanism regulating cellular senescence of postmitotic muscle cells is still unknown. cGAS-STING innate immune signaling was found to mediate cellular senescence in various types of cells, including postmitotic neuron cells, which however has not been explored in postmitotic muscle cells. Here by studying the myofibers from Zmpste24−/− progeria aged mice [an established mice model for Hutchinson-Gilford progeria syndrome (HGPS)], we observed senescence-associated phenotypes in Zmpste24−/− myofibers, which is coupled with increased oxidative damage to mitochondrial DNA (mtDNA) and secretion of senescence-associated secretory phenotype (SASP) factors. Also, Zmpste24−/− myofibers feature increased release of mtDNA from damaged mitochondria, mitophagy dysfunction, and activation of cGAS-STING. Meanwhile, increased mtDNA release in Zmpste24−/− myofibers appeared to be related with increased VDAC1 oligomerization. Further, the inhibition of VDAC1 oligomerization in Zmpste24−/− myofibers with VBIT4 reduced mtDNA release, cGAS-STING activation, and the expression of SASP factors. Our results reveal a novel mechanism of innate immune activation-associated cellular senescence in postmitotic muscle cells in aged muscle, which may help identify novel sets of diagnostic markers and therapeutic targets for progeria aging and aging-associated muscle diseases.
Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses
Authors: Stothart Mason. R. , McLoughlin Philip. D. , Medill Sarah. A. , Greuel Ruth. J. , Wilson Alastair. J. , Poissant Jocelyn. 
Published: July 2024

AbstractGut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013–2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.
Fluid flow drives phenotypic heterogeneity in bacterial growth and adhesion on surfaces
Authors: Hubert Antoine , Tabuteau Hervé , Farasin Julien , Loncar Aleksandar , Dufresne Alexis , Méheust Yves , Le Borgne Tanguy 
Published: July 2024

AbstractBacteria often thrive in surface-attached communities, where they can form biofilms affording them multiple advantages. In this sessile form, fluid flow is a key component of their environments, renewing nutrients and transporting metabolic products and signaling molecules. It also controls colonization patterns and growth rates on surfaces, through bacteria transport, attachment and detachment. However, the current understanding of bacterial growth on surfaces neglects the possibility that bacteria may modulate their division behavior as a response to flow. Here, we employed single-cell imaging in microfluidic experiments to demonstrate that attached Escherichia coli cells can enter a growth arrest state while simultaneously enhancing their adhesion underflow. Despite utilizing clonal populations, we observed a non-uniform response characterized by bistable dynamics, with co-existing subpopulations of non-dividing and actively dividing bacteria. As the proportion of non-dividing bacteria increased with the applied flow rate, it resulted in a reduction in the average growth rate of bacterial populations on flow-exposed surfaces. Dividing bacteria exhibited asymmetric attachment, whereas non-dividing counterparts adhered to the surface via both cell poles. Hence, this phenotypic diversity allows bacterial colonies to combine enhanced attachment with sustained growth, although at a reduced rate, which may be a significant advantage in fluctuating flow conditions.
Gaze-centered gating, reactivation, and reevaluation of economic value in orbitofrontal cortex
Authors: Ferro Demetrio , Cash-Padgett Tyler , Wang Maya Zhe , Hayden Benjamin Y. , Moreno-Bote Rubén 
Published: July 2024

AbstractDuring economic choice, options are often considered in alternation, until commitment. Nonetheless, neuroeconomics typically ignores the dynamic aspects of deliberation. We trained two male macaques to perform a value-based decision-making task in which two risky offers were presented in sequence at the opposite sides of the visual field, each followed by a delay epoch where offers were invisible. Surprisingly, during the two delays, subjects tend to look at empty locations where the offers had previously appeared, with longer fixations increasing the probability of choosing the associated offer. Spiking activity in orbitofrontal cortex reflects the value of the gazed offer, or of the offer associated with the gazed empty spatial location, even if it is not the most recent. This reactivation reflects a reevaluation process, as fluctuations in neural spiking correlate with upcoming choice. Our results suggest that look-at-nothing gazing triggers the reactivation of a previously seen offer for further evaluation.
Enhancing radiation-resistance and peroxidase-like activity of single-atom copper nanozyme via local coordination manipulation
Authors: Wu Jiabin , Zhu Xianyu , Li Qun , Fu Qiang , Wang Bingxue , Li Beibei , Wang Shanshan , Chang Qingchao , Xiang Huandong , Ye Chengliang , Li Qiqiang , Huang Liang , Liang Yan , Wang Dingsheng , Zhao Yuliang , Li Yadong 
Published: July 2024

AbstractThe inactivation of natural enzymes by radiation poses a great challenge to their applications for radiotherapy. Single-atom nanozymes (SAzymes) with high structural stability under such extreme conditions become a promising candidate for replacing natural enzymes to shrink tumors. Here, we report a CuN3-centered SAzyme (CuN3-SAzyme) that exhibits higher peroxidase-like catalytic activity than a CuN4-centered counterpart, by locally regulating the coordination environment of single copper sites. Density functional theory calculations reveal that the CuN3 active moiety confers optimal H2O2 adsorption and dissociation properties, thus contributing to high enzymatic activity of CuN3-SAzyme. The introduction of X-ray can improve the kinetics of the decomposition of H2O2 by CuN3-SAzyme. Moreover, CuN3-SAzyme is very stable after a total radiation dose of 500 Gy, without significant changes in its geometrical structure or coordination environment, and simultaneously still retains comparable peroxidase-like activity relative to natural enzymes. Finally, this developed CuN3-SAzyme with remarkable radioresistance can be used as an external field-improved therapeutics for enhancing radio-enzymatic therapy in vitro and in vivo. Overall, this study provides a paradigm for developing SAzymes with improved enzymatic activity through local coordination manipulation and high radioresistance over natural enzymes, for example, as sensitizers for cancer therapy.
A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials
Authors: Wang Duo , Liu Yaqing , Zhang Yuanfeng , Chen Qingwang , Han Yanxi , Hou Wanwan , Liu Cong , Yu Ying , Li Ziyang , Li Ziqiang , Zhao Jiaxin , Shi Leming , Zheng Yuanting , Li Jinming , Zhang Rui 
Published: July 2024

Abstract
Translating RNA-seq into clinical diagnostics requires ensuring the reliability and cross-laboratory consistency of detecting clinically relevant subtle differential expressions, such as those between different disease subtypes or stages. As part of the Quartet project, we present an RNA-seq benchmarking study across 45 laboratories using the Quartet and MAQC reference samples spiked with ERCC controls. Based on multiple types of ‘ground truth’, we systematically assess the real-world RNA-seq performance and investigate the influencing factors involved in 26 experimental processes and 140 bioinformatics pipelines. Here we show greater inter-laboratory variations in detecting subtle differential expressions among the Quartet samples. Experimental factors including mRNA enrichment and strandedness, and each bioinformatics step, emerge as primary sources of variations in gene expression. We underscore the profound influence of experimental execution, and provide best practice recommendations for experimental designs, strategies for filtering low-expression genes, and the optimal gene annotation and analysis pipelines. In summary, this study lays the foundation for developing and quality control of RNA-seq for clinical diagnostic purposes.
Senescent cancer-associated fibroblasts in pancreatic adenocarcinoma restrict CD8+ T cell activation and limit responsiveness to immunotherapy in mice
Authors: Assouline Benjamin , Kahn Rachel , Hodali Lutfi , Condiotti Reba , Engel Yarden , Elyada Ela , Mordechai-Heyn Tzlil , Pitarresi Jason R. , Atias Dikla , Steinberg Eliana , Bidany-Mizrahi Tirza , Forkosh Esther , Katz Lior H. , Benny Ofra , Golan Talia , Hofree Matan , Stewart Sheila A. , Atlan Karine A. , Zamir Gideon , Stanger Ben Z. , Berger Michael , Ben-Porath Ittai 
Published: July 2024

AbstractSenescent cells within tumors and their stroma exert complex pro- and anti-tumorigenic functions. However, the identities and traits of these cells, and the potential for improving cancer therapy through their targeting, remain poorly characterized. Here, we identify a senescent subset within previously-defined cancer-associated fibroblasts (CAFs) in pancreatic ductal adenocarcinomas (PDAC) and in premalignant lesions in mice and humans. Senescent CAFs isolated from mouse and humans expressed elevated levels of immune-regulatory genes. Depletion of senescent CAFs, either genetically or using the Bcl-2 inhibitor ABT-199 (venetoclax), increased the proportion of activated CD8+ T cells in mouse pancreatic carcinomas, whereas induction of CAF senescence had the opposite effect. Combining ABT-199 with an immune checkpoint therapy regimen significantly reduced mouse tumor burden. These results indicate that senescent CAFs in PDAC stroma limit the numbers of activated cytotoxic CD8+ T cells, and suggest that their targeted elimination through senolytic treatment may enhance immunotherapy.