bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Two‐Dimensional Evolution of Thermospheric ∑O/N2 Response to Weak Geomagnetic Activity During Solar‐Minimum Observed by GOLD
Authors: Cai Xuguang , Burns Alan G. , Wang Wenbin , Qian Liying , Solomon Stanley C. , Eastes Richard W. , Pedatella Nicholas , Daniell Robert E. , McClintock William E. 
Published: September 2020

AbstractWe conduct observational and modeling studies of thermospheric composition responses to weak geomagnetic activity (nongeomagnetic storms). We found that the thermospheric O and N2 column density ratio (∑O/N2) in part of the Northern Hemisphere measured by Global‐scale Observations of the Limb and Disk (GOLD) exhibited large and long‐lived depletions during weak geomagnetic activity in May and June 2019. The depletions reached 30% of quiet time values, extended equatorward to 10°N and lasted more than 10 hr. Furthermore, numerical simulation results are similar to these observations and indicate that the ∑O/N2 depletions were pushed westward by zonal winds. The ∑O/N2 evolution during weak geomagnetic activity suggests that the formation mechanism of the ∑O/N2 depletions is similar to that during a geomagnetic storm. The effects of weak geomagnetic activity are often ignored but, in fact, are important for understanding thermosphere neutral composition variability and hence the state of the thermosphere‐ionosphere system.
Borehole Diameter Controls Thermal‐Induced Convection and Evaporation From a Shallow Water Table
Authors: Levintal Elad , Dragila Maria I. , Lensky Nadav G. , Weisbrod Noam 
Published: September 2020

AbstractUnderstanding air exchange via boreholes, shafts, and wells is important for Earth and environmental sciences because of their potential role for increased evaporation and greenhouse gas emissions. Here, we investigated the effect of atmospheric temperature variability on air transport via a borehole as a function of its diameter. Field experiment included five boreholes with diameters ranging from 0.10 to 0.38 m and a depth of 3 m with an artificial water table at −2.7 m. Temperature was recorded in each borehole at 1‐min intervals for 1 year. Diurnal and seasonal air temperature changes triggered thermal instability, mainly during winter nights, which initiated thermal‐induced convection within the boreholes. The thermal‐induced convection penetrated deeper into the borehole as the diameter increased, doubling the water table evaporation rate for the largest borehole relative to the smallest. Borehole diameter plays an important role in controlling air exchange rates between the subsurface and the atmosphere.
Automatic Detection of Volcanic Surface Deformation Using Deep Learning
Authors: Sun Jian , Wauthier Christelle , Stephens Kirsten , Gervais Melissa , Cervone Guido , La Femina Peter , Higgins Machel 
Published: September 2020

AbstractInterferometric Synthetic Aperture Radar (InSAR) provides subcentimetric measurements of surface displacements, which are key for characterizing and monitoring magmatic processes in volcanic regions. The abundant measurements of surface displacements in multitemporal InSAR data routinely acquired by SAR satellites can facilitate near real‐time volcano monitoring on a global basis. However, the presence of atmospheric signals in interferograms complicates the interpretation of those InSAR measurements, which can even lead to a misinterpretation of InSAR signals and volcanic unrest. Given the vast quantities of SAR data available, an automatic InSAR data processing and denoising approach is required to separate volcanic signals that are cause of concern from atmospheric signals and noise. In this study, we employ a deep learning strategy that directly removes atmospheric and other noise signals from time‐consecutive unwrapped surface displacements obtained through an InSAR time series approach using an end‐to‐end convolutional neural network (CNN) with an encoder‐decoder architecture, modified U‐net. The CNN is trained with simulated synthetic unwrapped surface displacement maps and is then applied to real InSAR data. Our proposed architecture is capable of detecting dynamic spatio‐temporal patterns of volcanic surface displacements. We find that an ensemble‐average strategy is recommended to stabilize detected results for varying deformation rates and signal‐to‐noise ratios (SNRs). A case study is also presented where this method is applied to InSAR data covering Masaya volcano, Nicaragua and the results are validated using continuous GPS data. The results confirm that our network can indeed efficiently suppress atmospheric and other noise to reveal the noise‐free surface deformation.
Does Low‐Viscosity Fracturing Fluid Always Create Complex Fractures?
Authors: Chen Zhiqiang , Elsworth Derek , Wang Moran 
Published: September 2020

AbstractLower viscosity fluids are commonly believed to be able to create more complex fractures in hydraulic fracturing; however, the mechanism remains stubbornly unclear. We use a new grain‐scale model with accurate coupling of hydrodynamic forces to simulate the propagation of fluid‐driven fracturing. The results clarify that fracturing fluid with a lower viscosity does not always create more complex fractures. The heterogeneity in the rock exerts the principal control on systematic evolution of fracture complexity. In homogeneous rock, low viscosity fluids result in low breakdown pressure, but viscosity exerts little influence on fracture complexity. However, in heterogeneous rock, lower viscosity can lead to more complex network of fracturing. A regime map shows the dependence of fracture complexity on the degree of rock heterogeneity where low viscosity fracturing fluid more readily permeates weak defects and creates complex fracture networks.
Cold Water Upwelling Near the Anadyr Strait: Observations and Simulations
Authors: Kawaguchi Yusuke , Nishioka Jun , Nishino Shigeto , Fujio Shinzou , Lee Keunjong , Fujiwara Amane , Yanagimoto Daigo , Mitsudera Humio , Yasuda Ichiro 
Published: September 2020

AbstractAnadyr Strait, located at the northernmost reaches of the Bering Sea, influences pan‐Arctic climate through processes occurring in the strait as the Siberian Coastal Current carries water from the subpolar North Pacific Ocean into the western Arctic Ocean. A sharp sea surface temperature front near the Anadyr Strait segregates a tongue‐shaped mass of warm water from areas of cold‐water upwelling proximate to the Siberian coast. To clarify dynamical processes in this region, we conducted shipboard observations through and near the Anadyr and Bering straits during the summers of 2017 and 2018. Microstructure measurements show enhanced turbulence near the sea floor as strong throughflow occurs in the narrow straits. Direct observations of ocean currents indicate that the semidiurnal barotropic tide partly contributes to the near‐bottom currents driving mixing. Frictional effects accompanying the barotropic current are examined using a three‐dimensional regional model. Bottom friction produces a westward Ekman current in the bottom boundary layer, which then causes upwelling of underlying cold water on the western (Siberian) side of the Anadyr Strait. Secondary circulation across the strait is also maintained by the near‐surface eastward velocity, which is established by the steep slope of the main thermocline.
Description of Chemical Transport in Laboratory Rock Cores Using the Continuous Random Walk Formalism
Authors: Kurotori Takeshi , Zahasky Christopher , Benson Sally M. , Pini Ronny 
Published: September 2020

AbstractWe investigate chemical transport in laboratory rock cores using unidirectional pulse tracer experiments. Breakthrough curves (BTCs) measured at various flow rates in one sandstone and two carbonate samples are interpreted using the one‐dimensional Continuous Time Random Walk (CTRW) formulation with a truncated power law (TPL) model. Within the same framework, we evaluate additional memory functions to consider the Advection‐Dispersion Equation (ADE) and its extension to describe mass exchange between mobile and immobile solute phases (Single‐Rate Mass Transfer model, SRMT). To provide physical constraints to the models, parameters are identified that do not depend on the flow rate. While the ADE fails systematically at describing the effluent profiles for the carbonates, the SRMT and TPL formulations provide excellent fits to the measurements. They both yield a linear correlation between the dispersion coefficient and the Péclet number (DL ∝ Pe for
), and the longitudinal dispersivity is found to be significantly larger than the equivalent grain diameter, De. The BTCs of the carbonate rocks show clear signs of nonequilibrium effects. While the SRMT model explicitly accounts for the presence of microporous regions (up to 30% of the total pore space), in the TPL formulation the time scales of both advective and diffusive processes (t1(Pe) and t2) are associated with two characteristic heterogeneity length scales (
and l, respectively). We observed that l ≈ 2.5 × De and that anomalous transport arises when
. In this context, the SRMT and TPL formulations provide consistent, yet complementary, insight into the nature of anomalous transport in laboratory rock cores.
Vector Field‐Based Simulation of Tree‐Like Nonstationary Geostatistical Models
Authors: Vargas V. L. , Pesco S. 
Published: September 2020

AbstractIn this work, a new nonstationary multiple‐point geostatistical methodology called vector field‐based simulation is presented. This method generates multiple realizations of the phenomena being modeled, whose spatial continuity is described by a training image. It can be applied in reservoir characterization and can be used to study the behavior of hydrogeological systems. The main novelty of this work is that nonstationarity is addressed through a vector field inferred from the training image. This field represents the directions in which the image develops and controls the multiple‐point statistics methods (MPS) simulation. Additionally, our simulation is adapted to support hard data conditioning. The method is tested, and the realizations exhibit a similar morphology as the training image but with substantial variability. Furthermore, in the results it can be seen that the connectivity presented in the training image is preserved.
Comparative genomics reveals insights into cyanobacterial evolution and habitat adaptation
Authors: Chen Meng-Yun , Teng Wen-Kai , Zhao Liang , Hu Chun-Xiang , Zhou Yang-Kai , Han Bo-Ping , Song Li-Rong , Shu Wen-Sheng 
Published: September 2020

AbstractCyanobacteria are photosynthetic prokaryotes that inhabit diverse aquatic and terrestrial environments. However, the evolutionary mechanisms involved in the cyanobacterial habitat adaptation remain poorly understood. Here, based on phylogenetic and comparative genomic analyses of 650 cyanobacterial genomes, we investigated the genetic basis of cyanobacterial habitat adaptation (marine, freshwater, and terrestrial). We show: (1) the expansion of gene families is a common strategy whereby terrestrial cyanobacteria cope with fluctuating environments, whereas the genomes of many marine strains have undergone contraction to adapt to nutrient-poor conditions. (2) Hundreds of genes are strongly associated with specific habitats. Genes that are differentially abundant in genomes of marine, freshwater, and terrestrial cyanobacteria were found to be involved in light sensing and absorption, chemotaxis, nutrient transporters, responses to osmotic stress, etc., indicating the importance of these genes in the survival and adaptation of organisms in specific habitats. (3) A substantial fraction of genes that facilitate the adaptation of Cyanobacteria to specific habitats are contributed by horizontal gene transfer, and such genetic exchanges are more frequent in terrestrial cyanobacteria. Collectively, our results further our understandings of the adaptations of Cyanobacteria to different environments, highlighting the importance of ecological constraints imposed by the environment in shaping the evolution of Cyanobacteria.
Reactive oxygen species mediate anlotinib-induced apoptosis via activation of endoplasmic reticulum stress in pancreatic cancer
Authors: Yang Liguo , Zhou Xiaoshu , Sun Jinrui , Lei Qianghui , Wang Qi , Pan Di , Ding Mingxing , Ding Yi 
Published: September 2020

AbstractAnlotinib (AL3818), a novel multi-targeted receptor tyrosine kinase inhibitor, has recently been proven to be an antitumour drug. This study aimed to explore the antitumour effect of anlotinib and its underlying molecular mechanisms in human pancreatic cancer (PC) cells. The anti-proliferative effect of anlotinib for three PC cell lines was validated using CCK-8, colony formation and EdU detection assays. Cell cycle, cell apoptosis, and reactive oxygen species (ROS) detection assays, a PC xenograft model and immunohistochemistry were performed to elucidate the mechanisms by which anlotinib induced tumour lethality in vitro and in vivo. These results demonstrated that anlotinib inhibited proliferation, induced G2/M phase arrest and triggered apoptosis in PC cell lines. Anlotinib induced PC’s apoptosis through the accumulation of ROS which activated the endoplasmic reticulum (ER) stress via PERK/p-eIF2α/ATF4 pathway. Furthermore, we demonstrated that the expression level of Nrf2, an antioxidant protein, increased with anlotinib treatment. Nrf2 knockdown enhanced the pro-apoptotic effect of anlotinib and the expression of the PERK/p-eIF2α/ATF4 pathway. The in vivo results suggested that suppressing Nrf2 improved the antitumour effect of anlotinib on PC cells. These data indicated that the apoptotic effect of anlotinib on PC cells was induced by ER stress via the accumulation of ROS. In the future, anlotinib combined with an Nrf2 inhibitor may provide a new therapeutic strategy for the treatment of human PC.
LncRNA MM2P-induced, exosome-mediated transfer of Sox9 from monocyte-derived cells modulates primary chondrocytes
Authors: Bai Jinyu , Zhang Yingzi , Zheng Xin , Huang Man , Cheng Weinan , Shan Huajian , Gao Xiang , Zhang Mingchao , Sheng Lei , Dai Jun , Deng Yekun , Zhang Hong , Zhou Xiaozhong 
Published: September 2020

AbstractMonocyte-derived cells were shown to promote cartilage repair in osteoarthritis. The role of the long non-coding RNA (lncRNA) MM2P in this function of monocyte-derived cells remained unexplored. Treatment of RAW264.7 murine macrophages and mouse bone marrow-derived macrophages with IL-4 or IL-13 upregulated MM2P expression, upstream of STAT3 and STAT6 phosphorylation. Specifically, MM2P blocked SHP2-mediated dephosphorylation of STAT3 at Try705 and interacted with the RNA-binding protein FUS. In turn, p-STAT3 increased the Sox9 gene expression. These cells released Sox9 mRNA and protein-containing exosomes, as demonstrated by a transmission electron microscope, nanoparticle tracking analysis, and detection of typical surface markers. Their culture supernatant promoted the differentiation of mouse primary chondrocytes, i.e., upregulated the expression of Col1a2 and Acan genes and promoted the secretion of extracellular matrix components proteoglycan and type II collagen. These effects were mediated by Sox9 mRNA and protein delivered to chondrocytes by exosomes. Together, ex vivo treatment of monocyte-derived cells with IL-4 or IL-13 promoted chondrocyte differentiation and functions through exosome-mediated delivery of Sox9 mRNA and protein.
ALG13 participates in epileptogenesis via regulation of GABAA receptors in mouse models
Authors: Huo Junming , Ren Shuanglai , Gao Peng , Wan Ding , Rong Shikuo , Li Xinxiao , Liu Shenhai , Xu Siying , Sun Kuisheng , Guo Baorui , Wang Peng , Yu Baoli , Wu Ji , Wang Feng , Sun Tao 
Published: September 2020

AbstractALG13 (asparagine-linked glycosylation 13) plays crucial roles in the process of N-linked glycosylation. Mutations of the ALG13 gene underlie congenital disorders of glycosylation type I (CDG-I), a rare human genetic disorder with defective glycosylation. Epilepsy is commonly observed in congenital disorders of glycosylation type I (CDG-I). In our study, we found that about 20% of adult ALG13KO knockout mice display spontaneous seizures, which were identified in a simultaneous video and intracranial EEG recording. However, the mechanisms of ALG13 by which deficiency leads to epilepsy are unknown. Whole-cell patch-clamp recordings demonstrated that ALG13KO mice show a marked decrease in gamma-aminobutyric acid A receptor (GABAAR)-mediated inhibitory synaptic transmission. Furthermore, treatment with low-dose diazepam (a positive allosteric modulator of GABAA receptors), which enhances GABAAR function, also markedly ameliorates severity of epileptic seizures in ALG13KO mice. Moreover, ALG13 may influenced the expression of GABAARα2 membrane and total protein by changing transcription level of GABAARα2. Furthermore, protein interactions between ALG13 and GABAARα2 were observed in the cortex of wild-type mice. Overall, these results reveal that ALG13 may be involved in the occurrence of epilepsy through the regulation of GABAAR function, and may provide new insight into epilepsy prevention and treatment.
EDIL3 promotes epithelial–mesenchymal transition and paclitaxel resistance through its interaction with integrin αVβ3 in cancer cells
Authors: Gasca J. , Flores M. L. , Jiménez-Guerrero R. , Sáez M. E. , Barragán I. , Ruíz-Borrego M. , Tortolero M. , Romero F. , Sáez C. , Japón M. A. 
Published: September 2020

AbstractEpithelial–mesenchymal transition (EMT) has recently been associated with tumor progression, metastasis, and chemotherapy resistance in several tumor types. We performed a differential gene expression analysis comparing paclitaxel-resistant vs. paclitaxel-sensitive breast cancer cells that showed the upregulation ofEDIL3(EGF Like Repeats and Discoidin I Like Domains Protein 3). This gene codifies an extracellular matrix protein that has been identified as a novel regulator of EMT, so we studied its role in tumor progression and paclitaxel response. Our results demonstrated that EDIL3 expression levels were increased in paclitaxel-resistant breast and prostate cancer cells, and in subsets of high-grade breast and prostate tumors. Moreover, we observed that EDIL3 modulated the expression of EMT markers and this was impaired by cilengitide, which blocks the EDIL3–integrin αVβ3interaction. EDIL3 knockdown reverted EMT and sensitized cells to paclitaxel. In contrast, EDIL3 overexpression or the culture of cells in the presence of EDIL3-enriched medium induced EMT and paclitaxel resistance. Adding cilengitide resensitized these cells to paclitaxel treatment. In summary, EDIL3 may contribute to EMT and paclitaxel resistance through autocrine or paracrine signaling in cancer cells. Blockade of EDIL3–integrin αVβ3interaction by cilengitide restores sensitivity to paclitaxel and reverts EMT in paclitaxel-resistant cancer cells. Combinations of cilengitide and taxanes could be beneficial in the treatment of subsets of breast and prostate cancers.
Reinforcing materials modelling by encoding the structures of defects in crystalline solids into distortion scores
Authors: Goryaeva Alexandra M. , Lapointe Clovis , Dai Chendi , Dérès Julien , Maillet Jean-Bernard , Marinica Mihai-Cosmin 
Published: September 2020

AbstractThis work revises the concept of defects in crystalline solids and proposes a universal strategy for their characterization at the atomic scale using outlier detection based on statistical distances. The proposed strategy provides a generic measure that describes the distortion score of local atomic environments. This score facilitates automatic defect localization and enables a stratified description of defects, which allows to distinguish the zones with different levels of distortion within the structure. This work proposes applications for advanced materials modelling ranging from the surrogate concept for the energy per atom to the relevant information selection for evaluation of energy barriers from the mean force. Moreover, this concept can serve for design of robust interatomic machine learning potentials and high-throughput analysis of their databases. The proposed definition of defects opens up many perspectives for materials design and characterization, promoting thereby the development of novel techniques in materials science.
Using synchronized oscillators to compute the maximum independent set
Authors: Mallick Antik , Bashar Mohammad Khairul , Truesdell Daniel S. , Calhoun Benton H. , Joshi Siddharth , Shukla Nikhil 
Published: September 2020

AbstractNot all computing problems are created equal. The inherent complexity of processing certain classes of problems using digital computers has inspired the exploration of alternate computing paradigms. Coupled oscillators exhibiting rich spatio-temporal dynamics have been proposed for solving hard optimization problems. However, the physical implementation of such systems has been constrained to small prototypes. Consequently, the computational properties of this paradigm remain inadequately explored. Here, we demonstrate an integrated circuit of thirty oscillators with highly reconfigurable coupling to compute optimal/near-optimal solutions to the archetypally hard Maximum Independent Set problem with over 90% accuracy. This platform uniquely enables us to characterize the dynamical and computational properties of this hardware approach. We show that the Maximum Independent Set is more challenging to compute in sparser graphs than in denser ones. Finally, using simulations we evaluate the scalability of the proposed approach. Our work marks an important step towards enabling application-specific analog computing platforms to solve computationally hard problems.
A systematic review of antibody mediated immunity to coronaviruses: kinetics, correlates of protection, and association with severity
Authors: Huang Angkana T. , Garcia-Carreras Bernardo , Hitchings Matt D. T. , Yang Bingyi , Katzelnick Leah C. , Rattigan Susan M. , Borgert Brooke A. , Moreno Carlos A. , Solomon Benjamin D. , Trimmer-Smith Luke , Etienne Veronique , Rodriguez-Barraquer Isabel , Lessler Justin , Salje Henrik , Burke Donald S. , Wesolowski Amy , Cummings Derek A. T. 
Published: September 2020

AbstractMany public health responses and modeled scenarios for COVID-19 outbreaks caused by SARS-CoV-2 assume that infection results in an immune response that protects individuals from future infections or illness for some amount of time. The presence or absence of protective immunity due to infection or vaccination (when available) will affect future transmission and illness severity. Here, we review the scientific literature on antibody immunity to coronaviruses, including SARS-CoV-2 as well as the related SARS-CoV, MERS-CoV and endemic human coronaviruses (HCoVs). We reviewed 2,452 abstracts and identified 491 manuscripts relevant to 5 areas of focus: 1) antibody kinetics, 2) correlates of protection, 3) immunopathogenesis, 4) antigenic diversity and cross-reactivity, and 5) population seroprevalence. While further studies of SARS-CoV-2 are necessary to determine immune responses, evidence from other coronaviruses can provide clues and guide future research.