bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intra‐ and Inter‐Annual Variability of North Brazil Current Rings Using Angular Momentum Eddy Detection and Tracking Algorithm: Observations From 1993 to 2016
Authors: Aroucha L. C. , Veleda D. , Lopes F. S. , Tyaquiçã P. , Lefèvre N. , Araujo M. 
Published: November 2020

AbstractIn order to investigate intra‐ and inter‐annual variability of North Brazil Current (NBC) rings, angular momentum eddy detection and tracking algorithm (AMEDA) was used for identification of their occurrence, trajectories, and parameters. Based on 24 years (1993–2016) of geopotential height and geostrophic current fields reanalysis data from ARMOR 3D (¼°), we identified an average rate of five NBC rings shed by year. The rings present an average lifetime of 15.3 (±5.4) weeks, average speed‐based radius (Rmax) of 139.8 (±23.6) km, and mean sea surface height anomaly (SSHa) of 9.4 (±4.0) cm. The mean observed maximum azimuthal velocity (Vmax) was 0.27 (±0.08) m/s, while the averaged Rossby number (Ro) value was 0.08 (±0.04) and averaged kinetic energy (KE) was of 255.3 (±154.8) cm2/s2. NBC rings have larger dimensions, rotate faster, live less, and transfer more energy in boreal winter months. In contrast, those shed during boreal summer and early fall last longer, have smaller diameters and carry less energy. Besides, the analysis of ring merging pointed that the interaction between NBC rings generated a significantly increase in ring energy (52%), and velocity (22%). Finally, we observed the vertical anomalies temperature and salinity profiles, which indicated a thermocline deepening and sinking of coastal and tropical waters due to NBC rings downwelling. This study emphasizes the robustness and efficiency of AMEDA for studying rings in the ocean and further theorizes possible impacts of NBC ring on ocean physical and biogeochemical features in the Western Tropical North Atlantic.
Tidal Geopotential Dependence on Earth Ellipticity and Seawater Density and Its Detection With the GRACE Follow‐On Laser Ranging Interferometer
Authors: Han Shin‐Chan , Ghobadi‐Far Khosro , Ray Richard D. , Papanikolaou Thomas 
Published: November 2020

AbstractOcean tides produce significant gravitational perturbations that affect near‐Earth orbiting spacecraft. The gravitational potential induced by tidal mass redistribution is routinely modeled for global gravity analysis and orbit determination, although generally by assuming a spherical Earth and a uniform seawater density. The inadequacy of these simplifications is here addressed. We have developed an accurate yet efficient algorithm to compute the ocean tidal geopotential, allowing for Earth's elliptical shape and variable seawater density. Using this new computation, we find that (1) the effect of ellipticity is several percent of the tide signal over mid to high‐latitude regions, which is comparable to elevation error in the state‐of‐the‐art ocean tide models; (2) the effect of seawater density variations on the potential is as large as 2–3 cm in water‐height equivalent, primarily in deep water where density increases 2%–3% from compressibility. Our analysis of new Gravity Recovery and Climate Experiment Follow‐On (GRACE‐FO) laser ranging interferometer measurements reveals evident errors when ellipticity and density variations are ignored. When accounted for, the GRACE‐FO residual tidal gravity perturbations are reduced by half, depending on the adopted tide model; only the remaining half likely represents actual model elevation error. The use of a spherical surface and a uniform seawater density is no longer tenable given the precision of gravity measurements from GRACE and GRACE‐FO satellites.
Gray Zone Partitioning Functions and Parameterization of Turbulence Fluxes in the Convective Atmospheric Boundary Layer
Authors: Senel Cem Berk , Temel Orkun , Muñoz‐Esparza Domingo , Parente Alessandro , van Beeck Jeroen 
Published: November 2020

AbstractHere, we present the first attempt to fully represent three‐dimensional turbulence fluxes in the “Terra Incognita” or the gray zone in other words. In order to derive partitioning functions, representing the partitioning between subgrid and total fluxes, we make use of high‐resolution large‐eddy simulations (LES), which are performed with the Weather Research and Forecasting (WRF) model. LES computations are performed for various levels of convective instability, ranging from pure buoyant to strongly sheared convection. Then, the resulting reference‐LES fields are successively coarse grained from its original microscale grid spacing (
m) up to typical mesoscale grid spacings (
km). The given process is applied by means of an advanced filter, that is, the Butterworth filter. It enables a clear scale‐specific filtering that results in a more controlled energy transition from lower to higher wavenumbers, unlike the drawbacks of current filters in use. Finally, we parameterize the subgrid scale (SGS) partitioning functions of 10 SGS turbulence quantities: momentum fluxes (τij, six terms), heat fluxes (qj, three terms), and turbulence kinetic energy (k). Turbulence partitioning relations are parameterized in a scale‐aware, stability‐dependent, and height‐dependent form, using the sigmoidal Gompertz function. Thus, the new gray zone model provides a framework that bridges the mesoscale and microscale limits and that is suitable for the development of next generation three‐dimensional, multiscale turbulence parameterization methods or planetary boundary layer schemes.
Scattering From a Strip With Mixed Boundary Conditions
Authors: Emets V. F. , Rogowski J. 
Published: November 2020

AbstractThis paper applies the collocation method to the modeling and simulation of scattering from a strip with the Dirichlet boundary condition on the upper interface and the Dirichlet and Neumann boundary conditions on the two subintervals along the lower interface. Green's theorem is used to reduce the mixed boundary value problem to the system of three coupled hypersingular and singular integral equations. The numerical results of the backscattering field characteristics are presented and compared with the high‐frequency approximations.
Semi‐Analytical Model of the Rician K‐Factor
Authors: Alayón Glazunov Andrés , Razavi Aidin , Maaskant Rob , Yang Jian 
Published: November 2020

AbstractThe analysis of the performance of 5G wireless communication systems employing Massive MIMO at millimeter‐wave frequencies is of great practical relevance. Of special relevance are the signal fluctuations. In the present paper, we introduce a semi‐analytical model for a generic scattering environment by using randomly distributed resonant scatterers to investigate the impact of the size of the scattering environment, the scatterer density, and the number of scatterers on the signal variability in terms of the Rician K‐factor as a function of frequency. We further present an investigation of the impact of scattering on the frequency dependence of the signal fading statistics in the 500 MHz–100 GHz band. The simplified model is also verified against full‐wave simulation using the Method of Moments (MoM).
Predicting Water and Sediment Partitioning in a Delta Channel Network Under Varying Discharge Conditions
Authors: Dong Tian Y. , Nittrouer Jeffrey A. , McElroy Brandon , Il'icheva Elena , Pavlov Maksim , Ma Hongbo , Moodie Andrew J. , Moreido Vsevolod M. 
Published: November 2020

AbstractChannel bifurcations control the distribution of water and sediment in deltas, and the routing of these materials facilitates land building in coastal regions. Yet few practical methods exist to provide accurate predictions of flow partitioning at multiple bifurcations within a distributary channel network. Herein, multiple nodal relations that predict flow partitioning at individual bifurcations, utilizing various hydraulic and channel planform parameters, are tested against field data collected from the Selenga River delta, Russia. The data set includes 2.5 months of time‐continuous, synoptic measurements of water and sediment discharge partitioning covering a flood hydrograph. Results show that width, sinuosity, and bifurcation angle are the best remotely sensed, while cross‐sectional area and flow depth are the best field measured nodal relation variables to predict flow partitioning. These nodal relations are incorporated into a graph model, thus developing a generalized framework that predicts partitioning of water discharge and total, suspended, and bedload sediment discharge in deltas. Results from the model tested well against field data produced for the Wax Lake, Selenga, and Lena River deltas. When solely using remotely sensed variables, the generalized framework is especially suitable for modeling applications in large‐scale delta systems, where data and field accessibility are limited.
TGR5 deficiency aggravates hepatic ischemic/reperfusion injury via inhibiting SIRT3/FOXO3/HIF-1ɑ pathway
Authors: Wang Qi , Wei Song , Li Lei , Qiu Jiannan , Zhou Shun , Shi Chengyu , Shi Yong , Zhou Haoming , Lu Ling 
Published: November 2020

AbstractIschemia/reperfusion (I/R) injury is responsible for liver injury during hepatic resection and liver transplantation. The plasma membrane-bound G protein-coupled bile acid receptor (TGR5) could regulate immune response in multiple liver diseases. Nevertheless, the underlying role of TGR5 in hepatic I/R injury remains largely unknown. This study aimed to investigate the potential mechanism of TGR5 in hepatic I/R injury. Wild-type (WT) and TGR5 knockout (TGR5KO) mice were used to perform hepatic I/R, and macrophages were isolated from mice for in vitro experiments. The results demonstrated that knockout of TGR5 in mice significantly exacerbated liver injury and inflammatory response. TGR5KO mice infused with WT macrophages showed relieved liver injury. Further study revealed that TGR5 knockout inhibited sirtuin 3 (SIRT3) and forkhead box O3 (FOXO3) expression. In vitro experiments indicated that SIRT3 inhibited acetylation, ubiquitination and degradation of FOXO3. FOXO3 inhibited HIF-1α transcription by binding to its promoter. TGR5 knockout inhibited SIRT3 expression, thus promoted the acetylation, ubiquitination, and degradation of FOXO3, which resulted in increased HIF-1α transcription and macrophages proinflammatory response. Collectively, TGR5 plays a critical protective role in hepatic I/R injury. FOXO3 deacetylation mediated by SIRT3 can attenuate hepatic I/R injury. TGR5 deficiency aggravates hepatic I/R injury via inhibiting SIRT3/FOXO3/HIF-1α pathway.
MiR396 is involved in plant response to vernalization and flower development in Agrostis stolonifera
Authors: Yuan Shuangrong , Li Zhigang , Yuan Ning , Hu Qian , Zhou Man , Zhao Junming , Li Dayong , Luo Hong 
Published: November 2020

Abstract
MicroRNA396 (miR396) has been demonstrated to regulate flower development by targeting growth-regulating factors (GRFs) in annual species. However, its role in perennial grasses and its potential involvement in flowering time control remain unexplored. Here we report that overexpression of miR396 in a perennial species, creeping bentgrass (Agrostis stolonifera L.), alters flower development. Most significantly, transgenic (TG) plants bypass the vernalization requirement for flowering. Gene expression analysis reveals that miR396 is induced by long-day (LD) photoperiod and vernalization. Further study identifies VRN1, VRN2, and VRN3 homologs whose expression patterns in wild-type (WT) plants are similar to those observed in wheat and barley during transition from short-day (SD) to LD, and SD to cold conditions. However, compared to WT controls, TG plants overexpressing miR396 exhibit significantly enhanced VRN1 and VRN3 expression, but repressed VRN2 expression under SD to LD conditions without vernalization, which might be associated with modified expression of methyltransferase genes. Collectively, our results unveil a potentially novel mechanism by which miR396 suppresses the vernalization requirement for flowering which might be related to the epigenetic regulation of VRN genes and provide important new insight into critical roles of a miRNA in regulating vernalization-mediated transition from vegetative to reproductive growth in monocots.
The role of arabinogalactan proteins (AGPs) in fruit ripening—a review
Authors: Leszczuk Agata , Kalaitzis Panagiotis , Blazakis Konstantinos N. , Zdunek Artur 
Published: November 2020

Abstract
Arabinogalactan proteins (AGPs) are proteoglycans challenging researchers for decades. However, despite the extremely interesting polydispersity of their structure and essential application potential, studies of AGPs in fruit are limited, and only a few groups deal with this scientific subject. Here, we summarise the results of pioneering studies on AGPs in fruit tissue with their structure, specific localization pattern, stress factors influencing their presence, and a focus on recent advances. We discuss the properties of AGPs, i.e., binding calcium ions, ability to aggregate, adhesive nature, and crosslinking with other cell wall components that may also be implicated in fruit metabolism. The aim of this review is an attempt to associate well-known features and properties of AGPs with their putative roles in fruit ripening. The putative physiological significance of AGPs might provide additional targets of regulation for fruit developmental programme. A comprehensive understanding of the AGP expression, structure, and untypical features may give new information for agronomic, horticulture, and renewable biomaterial applications.
RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops
Authors: Iezzoni Amy F. , McFerson Jim , Luby James , Gasic Ksenija , Whitaker Vance , Bassil Nahla , Yue Chengyan , Gallardo Karina , McCracken Vicki , Coe Michael , Hardner Craig , Zurn Jason D. , Hokanson Stan , van de Weg Eric , Jung Sook , Main Dorrie , da Silva Linge Cassia , Vanderzande Stijn , Davis Thomas M. , Mahoney Lise L. , Finn Chad , Peace Cameron 
Published: November 2020

AbstractThe Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality. However, rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding—a “chasm” existed between existing genomics and genetic information and the application of this knowledge in breeding. The RosBREED project (“Ros” signifying a Rosaceae genomics, genetics, and breeding community initiative, and “BREED”, indicating the core focus on breeding programs), addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative. RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S. rosaceous crop breeding programs, thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality. This review presents a synopsis of the approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. Enabling technologies and tools developed are described, including genome-wide scanning platforms and DNA diagnostic tests. Examples of DNA-informed breeding use by project participants are presented for all breeding stages, including pre-breeding for disease resistance, parental and seedling selection, and elite selection advancement. The chasm is now bridged, accelerating rosaceous crop genetic improvement.
The mutation of ent-kaurene synthase, a key enzyme involved in gibberellin biosynthesis, confers a non-heading phenotype to Chinese cabbage (Brassica rapa L. ssp. pekinensis)
Authors: Gao Yue , Huang Shengnan , Qu Gaoyang , Fu Wei , Zhang Meidi , Liu Zhiyong , Feng Hui 
Published: November 2020

Abstract
The presence of a leafy head is a vital agronomic trait that facilitates the evaluation of the yield and quality of Chinese cabbage. A non-heading mutant (nhm1) was identified in an ethyl methanesulfonate mutagenesis population of the heading Chinese cabbage double haploid line FT. Segregation analysis revealed that a single recessive gene, Brnhm1, controlled the mutant phenotype. Using MutMap, Kompetitive allele-specific PCR, and cloning analyses, we demonstrated that BraA07g042410.3C, which encodes an ent-kaurene synthase involved in the gibberellin biosynthesis pathway, is the nhm1 mutant candidate gene. A single-nucleotide mutation (C to T) in the fourth exon of BraA07g042410.3C caused an amino acid substitution from histidine to tyrosine. Compared to that of the wild-type FT, BraA07g042410.3C in the leaves of the nhm1 mutant had lower levels of expression. In addition, gibberellin contents were lower in the mutant than in the wild type, and the mutant plant phenotype could be restored to that of the wild type after exogenous GA3 treatment. These results indicate that BraA07g042410.3C caused the non-heading mutation. This is the first study to demonstrate a relationship between gibberellin content in the leaves and leafy head formation in Chinese cabbage. These findings facilitate the understanding of the mechanisms underlying leafy head development in Chinese cabbage.
The loss of function of HEL, which encodes a cellulose synthase interactive protein, causes helical and vine-like growth of tomato
Authors: Yang Qihong , Wan Xiaoshuai , Wang Jiaying , Zhang Yuyang , Zhang Junhong , Wang Taotao , Yang Changxian , Ye Zhibiao 
Published: November 2020

AbstractHelical growth is an economical way for plant to obtain resources. The classic microtubule–microfibril alignment model ofArabidopsishelical growth involves restriction of the appropriate orientation of cellulose microfibrils appropriately in the cell walls. However, the molecular mechanism underlying tomato helical growth remains unknown. Here, we identified a spontaneous tomatohelical(hel) mutant with right-handed helical cotyledons and petals but left-handed helical stems and true leaves. Genetic analysis revealed that thehelphenotype was controlled by a single recessive gene. Using map-based cloning, we cloned theHELgene, which encodes a cellulose interacting protein homologous to CSI1 ofArabidopsis. We identified a 27 bp fragment replacement that generated a premature stop codon. Transgenic experiments showed that the helical growth phenotype could be restored by the allele of this gene from wild-typePyriforme. In contrast, the knockout mutation ofHELinPyriformevia CRISPR/Cas9 resulted in helical growth. These findings shed light on the molecular control of the helical growth of tomato.
Brassica rapa orphan genes largely affect soluble sugar metabolism
Authors: Jiang Mingliang , Zhan Zongxiang , Li Haiyan , Dong Xiangshu , Cheng Feng , Piao Zhongyun 
Published: November 2020

Abstract
Orphan genes (OGs), which are genes unique to a specific taxon, play a vital role in primary metabolism. However, little is known about the functional significance of Brassica rapa OGs (BrOGs) that were identified in our previous study. To study their biological functions, we developed a BrOG overexpression (BrOGOE) mutant library of 43 genes in Arabidopsis thaliana and assessed the phenotypic variation of the plants. We found that 19 of the 43 BrOGOE mutants displayed a mutant phenotype and 42 showed a variable soluble sugar content. One mutant, BrOG1OE, with significantly elevated fructose, glucose, and total sugar contents but a reduced sucrose content, was selected for in-depth analysis. BrOG1OE showed reduced expression and activity of the Arabidopsis sucrose synthase gene (AtSUS); however, the activity of invertase was unchanged. In contrast, silencing of two copies of BrOG1 in B. rapa, BraA08002322 (BrOG1A) and BraSca000221 (BrOG1B), by the use of an efficient CRISPR/Cas9 system of Chinese cabbage (B. rapa ssp. campestris) resulted in decreased fructose, glucose, and total soluble sugar contents because of the upregulation of BrSUS1b, BrSUS3, and, specifically, the BrSUS5 gene in the edited BrOG1 transgenic line. In addition, we observed increased sucrose content and SUS activity in the BrOG1 mutants, with the activity of invertase remaining unchanged. Thus, BrOG1 probably affected soluble sugar metabolism in a SUS-dependent manner. This is the first report investigating the function of BrOGs with respect to soluble sugar metabolism and reinforced the idea that OGs are a valuable resource for nutrient metabolism.
WUSCHEL-related homeobox1 (WOX1) regulates vein patterning and leaf size in Cucumis sativus
Authors: Wang Hu , Niu Huanhuan , Li Chuang , Shen Guoyan , Liu Xiaofeng , Weng Yiqun , Wu Tao , Li Zheng 
Published: November 2020

AbstractIn plants,WUSCHEL-related homeobox1(WOX1) homologs promote lamina mediolateral outgrowth. However, the downstream components linking WOX1 and lamina development remain unclear. In this study, we revealed the roles of WOX1 in palmate leaf expansion in cucumber (Cucumis sativus). A cucumbermango fruit(mf) mutant, resulting from truncation of a WOX1-type protein (CsWOX1), displayed abnormal lamina growth and defects in the development of secondary and smaller veins.CsWOX1was expressed in the middle mesophyll and leaf margins and rescued defects of theArabidopsis wox1 prsdouble mutant. Transcriptomic analysis revealed that genes involved in auxin polar transport and auxin response were highly associated with leaf development. Analysis of the cucumbermf rl(round leaf) double mutant revealed that CsWOX1 functioned in vein development via PINOID (CsPID1)-controlled auxin transport. Overexpression ofCsWOX1in cucumber (CsWOX1-OE) affected vein patterning and produced ‘butterfly-shaped’ leaves. CsWOX1 physically interacted with CsTCP4a, which may account for the abnormal lamina development in themfmutant line and the smaller leaves in theCsWOX1-OE plants. Our findings demonstrated that CsWOX1 regulates cucumber leaf vein development by modulating auxin polar transport; moreover, CsWOX1 regulates leaf size by controllingCIN-TCPgenes.