bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observations of the Beam‐Driven Whistler Mode Waves in the Magnetic Reconnection Region at the Dayside Magnetopause
Authors: Zhao S. Q. , Xiao C. J. , Liu Terry Z. , Chen Huayue , Zhang H. , Shi M. J. , Teng Shangchun , Zhang H. S. , Wang X. G. , Pu Z. Y. , Liu M. Z. 
Published: January 2021

AbstractWe report observations of the whistler mode waves in the magnetic reconnection region at the dayside magnetopause using the magnetospheric multiscale (MMS) mission on January 11, 2016. In this event, whistlers mostly occur on the magnetospheric side of the reconnection central plane and are closely related to counter‐streaming electron beams in the medium energy range (200–300 eV). These counter‐streaming electron beams can be attributed to the accelerated magnetosheath electrons by the reconnection. Through quantitatively testing the Landau resonance condition and solving the kinetic dispersion relations, we present the evidence for whistler excitation by electron beams in the medium energy range. Additionally, the whistlers are observed simultaneously with the pitch‐angle scattering of electrons in the high‐energy range (300–3,000 eV). The calculation results show that this scattering is likely to occur through electron cyclotron wave‐particle interactions, which can isotropize electrons and exchange energy between plasmas and waves.
New Methods for Data Stacking and P‐ and S‐wave Arrival Time Determination Using the Deep Moonquake Apollo Recordings
Authors: Yuan Yuefeng , Garnero Edward J. , Zhu Peimin , Lin Pei‐ying , Weber Renee C. , Wang Fenghua 
Published: January 2021

AbstractA new method of simultaneous time domain cross‐correlation of multiple components of motion at multiple seismic stations is developed for P‐ and S‐wave identification for determination of arrival times of deep moonquakes using Apollo Passive Seismic Experiment (APSE) data. Deep moonquakes occur in selenographically isolated clusters, allowing the stacking of a large number of moonquakes in each cluster to improve signal‐to‐noise ratio. The method developed here seeks to improve upon multichannel cross‐correlation (MCCC) of a single component of motion and multiple events used in past work by incorporating all components and stations simultaneously. This multicomponent multichannel cross‐correlation (MCMCCC) method not only maximizes the inherent correlation between the 12 components (three components of motion at each of four stations) across all events in a given cluster, but also establishes representative stacked traces of moonquakes within each cluster. Additionally, the MCMCCC method utilizes components and events with the highest data quality to guide the inclusion of lower quality components and events (or events with fewer components). A closure difference residual time is introduced to identify moonquake events with better data and/or close source locations, to further improve the signal‐to‐noise ratio of stacked traces. A multicomponent short‐term to long‐term average algorithm is also developed to objectively determine P‐ and S‐wave arrivals that best align with their travel time curves based on lunar velocity models, simultaneously for all 12 components of motion. Newly computed deep moonquake cluster stacks and some updated deep moonquake cluster locations are presented, which improve upon past results.
An Instrument With Constant Volume Approach for In Situ Measurement of Surface Runoff and Suspended Sediment Concentration
Authors: Zhan Xiaoyun , Zhao Jun , Zhu‐Barker Xia , Shui Junfeng , Liu Baoyuan , Guo Minghang 
Published: January 2021

AbstractThere is an increasing demand for reliable methods to measure soil loss in order to get a better understanding of sediment movement and to develop process‐based sediment transport models. This study described the design, calibration, and practical application of an instrumented technique that automatically characterized surface flow in situ fields. The instrument consisted of a sampling assembly, a measuring assembly, and a management platform. The special design combined with a volume‐mass conversion relationship was used to determine the exact volume and mass of the sediment‐laden water, thereby allowing the implementation of real‐time measurement and synchronous calculation of runoff rate and sediment concentration. Calibration results showed that normal distributions and an average error of −3.67% were obtained for the target sediment concentrations of 2–1,000 g/L. Compared with the gravimetric method, the average error of the new technique for sediment concentration was 4.82%, and the highest precision was 98.50%. The high repeatability and accuracy of the technique suggest that it can be used with confidence to give satisfactory results in fields. A field experiment under natural rainfall showed that a grass‐covered plot had 18.94% less runoff rate and 42.92% lower sediment concentration than a bare soil plot, illustrating the impact of vegetation cover on reducing soil loss. This uniquely designed instrument provides a new approach to real‐time sediment detection in surface flow. It will be beneficial for rigorously evaluating runoff and sedimentation and for in‐depth research regarding water and soil loss processes.
Large and sensitive magnetostriction in ferromagnetic composites with nanodispersive precipitates
Authors: Gou Junming , Ma Tianyu , Liu Xiaolian , Zhang Changsheng , Sun Liangwei , Sun Guangai , Xia Weixing , Ren Xiaobing 
Published: January 2021

AbstractLarge and sensitive magnetostriction (large strain induced by small magnetic fields) is highly desired for applications of magnetostrictive materials. However, it is difficult to simultaneously improve magnetostriction and reduce the switching field because magnetostriction and the switching field are both proportional to the magnetocrystalline anisotropy. To solve this fundamental challenge, we report that introducing tetragonal nanoprecipitates into a cubic matrix can facilitate large and sensitive magnetostriction even in random polycrystals. As exhibited in a proof-of-principle reference, Fe–Ga alloys, the figure of merit—defined by the saturation magnetostriction over the magnetocrystalline anisotropy constant—can be enhanced by over 5-fold through optimum aging of the solution-treated precursor. On the one hand, the aging-induced nanodispersive face-centered tetragonal (FCT) precipitates create local tetragonal distortion of the body-centered cubic (BCC) matrix, substantially enhancing the saturation magnetostriction to be comparable to that of single crystal materials. On the other hand, these precipitates randomly couple with the matrix at the nanoscale, resulting in the collapse of net magnetocrystalline anisotropy. Our findings not only provide a simple and feasible approach to enhance the magnetostriction performance of random polycrystalline ferromagnets but also provide important insights toward understanding the mechanism of heterogeneous magnetostriction.
Enantioselective preparation of mechanically planar chiral rotaxanes by kinetic resolution strategy
Authors: Imayoshi Ayumi , Lakshmi Bhatraju Vasantha , Ueda Yoshihiro , Yoshimura Tomoyuki , Matayoshi Aki , Furuta Takumi , Kawabata Takeo 
Published: January 2021

AbstractAsymmetric synthesis of mechanically planar chiral rotaxanes and topologically chiral catenanes has been a long-standing challenge in organic synthesis. Recently, an excellent strategy was developed based on diastereomeric synthesis of rotaxanes and catenanes with mechanical chirality followed by removal of the chiral auxiliary. On the other hand, its enantioselective approach has been quite limited. Here, we report enantioselective preparation of mechanically planar chiral rotaxanes by kinetic resolution of the racemates via remote asymmetric acylation of a hydroxy group in the axis component, which provides an unreacted enantiomer in up to >99.9% ee in 29% yield (the theoretical maximum yield of kinetic resolution of racemate is 50%). While the rotaxane molecules are expected to have conformational complexity, our original catalysts enabled to discriminate the mechanical chirality of the rotaxanes efficiently with the selectivity factors in up to 16.
A fourth-generation high-dimensional neural network potential with accurate electrostatics including non-local charge transfer
Authors: Ko Tsz Wai , Finkler Jonas A. , Goedecker Stefan , Behler Jörg 
Published: January 2021

AbstractMachine learning potentials have become an important tool for atomistic simulations in many fields, from chemistry via molecular biology to materials science. Most of the established methods, however, rely on local properties and are thus unable to take global changes in the electronic structure into account, which result from long-range charge transfer or different charge states. In this work we overcome this limitation by introducing a fourth-generation high-dimensional neural network potential that combines a charge equilibration scheme employing environment-dependent atomic electronegativities with accurate atomic energies. The method, which is able to correctly describe global charge distributions in arbitrary systems, yields much improved energies and substantially extends the applicability of modern machine learning potentials. This is demonstrated for a series of systems representing typical scenarios in chemistry and materials science that are incorrectly described by current methods, while the fourth-generation neural network potential is in excellent agreement with electronic structure calculations.
Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis
Authors: Rai Amit , Hirakawa Hideki , Nakabayashi Ryo , Kikuchi Shinji , Hayashi Koki , Rai Megha , Tsugawa Hiroshi , Nakaya Taiki , Mori Tetsuya , Nagasaki Hideki , Fukushi Runa , Kusuya Yoko , Takahashi Hiroki , Uchiyama Hiroshi , Toyoda Atsushi , Hikosaka Shoko , Goto Eiji , Saito Kazuki , Yamazaki Mami 
Published: January 2021

AbstractPlant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly ofOphiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb,Ophiorrhizagenome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes’ evolution post γ whole-genome triplication, which occurred approximately 110 Mya inO. pumila, and before the whole-genome duplication inCamptotheca acuminataidentified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.
The circadian cryptochrome, CRY1, is a pro-tumorigenic factor that rhythmically modulates DNA repair
Authors: Shafi Ayesha A. , McNair Chris M. , McCann Jennifer J. , Alshalalfa Mohammed , Shostak Anton , Severson Tesa M. , Zhu Yanyun , Bergman Andre , Gordon Nicolas , Mandigo Amy C. , Chand Saswati N. , Gallagher Peter , Dylgjeri Emanuela , Laufer Talya S. , Vasilevskaya Irina A. , Schiewer Matthew J. , Brunner Michael , Feng Felix Y. , Zwart Wilbert , Knudsen Karen E. 
Published: January 2021

AbstractMechanisms regulating DNA repair processes remain incompletely defined. Here, the circadian factor CRY1, an evolutionally conserved transcriptional coregulator, is identified as a tumor specific regulator of DNA repair. Key findings demonstrate that CRY1 expression is androgen-responsive and associates with poor outcome in prostate cancer. Functional studies and first-in-field mapping of the CRY1 cistrome and transcriptome reveal that CRY1 regulates DNA repair and the G2/M transition. DNA damage stabilizes CRY1 in cancer (in vitro, in vivo, and human tumors ex vivo), which proves critical for efficient DNA repair. Further mechanistic investigation shows that stabilized CRY1 temporally regulates expression of genes required for homologous recombination. Collectively, these findings reveal that CRY1 is hormone-induced in tumors, is further stabilized by genomic insult, and promotes DNA repair and cell survival through temporal transcriptional regulation. These studies identify the circadian factor CRY1 as pro-tumorigenic and nominate CRY1 as a new therapeutic target.
Pore-forming Esx proteins mediate toxin secretion by Mycobacterium tuberculosis
Authors: Tak Uday , Dokland Terje , Niederweis Michael 
Published: January 2021

AbstractMycobacterium tuberculosis secretes the tuberculosis necrotizing toxin (TNT) to kill host cells. Here, we show that the WXG100 proteins EsxE and EsxF are essential for TNT secretion. EsxE and EsxF form a water-soluble heterodimer (EsxEF) that assembles into oligomers and long filaments, binds to membranes, and forms stable membrane-spanning channels. Electron microscopy of EsxEF reveals mainly pentameric structures with a central pore. Mutations of both WXG motifs and of a GXW motif do not affect dimerization, but abolish pore formation, membrane deformation and TNT secretion. The WXG/GXW mutants are locked in conformations with altered thermostability and solvent exposure, indicating that the WXG/GXW motifs are molecular switches controlling membrane interaction and pore formation. EsxF is accessible on the bacterial cell surface, suggesting that EsxEF form an outer membrane channel for toxin export. Thus, our study reveals a protein secretion mechanism in bacteria that relies on pore formation by small WXG proteins.
The nature of active sites for carbon dioxide electroreduction over oxide-derived copper catalysts
Authors: Cheng Dongfang , Zhao Zhi-Jian , Zhang Gong , Yang Piaoping , Li Lulu , Gao Hui , Liu Sihang , Chang Xin , Chen Sai , Wang Tuo , Ozin Geoffrey A. , Liu Zhipan , Gong Jinlong 
Published: January 2021

AbstractThe active sites for CO2 electroreduction (CO2R) to multi-carbon (C2+) products over oxide-derived copper (OD-Cu) catalysts are under long-term intense debate. This paper describes the atomic structure motifs for product-specific active sites on OD-Cu catalysts in CO2R. Herein, we describe realistic OD-Cu surface models by simulating the oxide-derived process via the molecular dynamic simulation with neural network (NN) potential. After the analysis of over 150 surface sites through NN potential based high-throughput testing, coupled with density functional theory calculations, three square-like sites for C–C coupling are identified. Among them, Σ3 grain boundary like planar-square sites and convex-square sites are responsible for ethylene production while step-square sites, i.e. n(111) × (100), favor alcohols generation, due to the geometric effect for stabilizing acetaldehyde intermediates and destabilizing Cu–O interactions, which are quantitatively demonstrated by combined theoretical and experimental results. This finding provides fundamental insights into the origin of activity and selectivity over Cu-based catalysts and illustrates the value of our research framework in identifying active sites for complex heterogeneous catalysts.
Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase
Authors: Gamiz-Arco Gloria , Gutierrez-Rus Luis I. , Risso Valeria A. , Ibarra-Molero Beatriz , Hoshino Yosuke , Petrović Dušan , Justicia Jose , Cuerva Juan Manuel , Romero-Rivera Adrian , Seelig Burckhard , Gavira Jose A. , Kamerlin Shina C. L. , Gaucher Eric A. , Sanchez-Ruiz Jose M. 
Published: January 2021

AbstractGlycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed.
Inositol pyrophosphates promote the interaction of SPX domains with the coiled-coil motif of PHR transcription factors to regulate plant phosphate homeostasis
Authors: Ried Martina K. , Wild Rebekka , Zhu Jinsheng , Pipercevic Joka , Sturm Kristina , Broger Larissa , Harmel Robert K. , Abriata Luciano A. , Hothorn Ludwig A. , Fiedler Dorothea , Hiller Sebastian , Hothorn Michael 
Published: January 2021

AbstractPhosphorus is an essential nutrient taken up by organisms in the form of inorganic phosphate (Pi). Eukaryotes have evolved sophisticated Pi sensing and signaling cascades, enabling them to stably maintain cellular Pi concentrations. Pi homeostasis is regulated by inositol pyrophosphate signaling molecules (PP-InsPs), which are sensed by SPX domain-containing proteins. In plants, PP-InsP-bound SPX receptors inactivate Myb coiled-coil (MYB-CC) Pi starvation response transcription factors (PHRs) by an unknown mechanism. Here we report that a InsP8–SPX complex targets the plant-unique CC domain of PHRs. Crystal structures of the CC domain reveal an unusual four-stranded anti-parallel arrangement. Interface mutations in the CC domain yield monomeric PHR1, which is no longer able to bind DNA with high affinity. Mutation of conserved basic residues located at the surface of the CC domain disrupt interaction with the SPX receptor in vitro and in planta, resulting in constitutive Pi starvation responses. Together, our findings suggest that InsP8regulates plant Pi homeostasis by controlling the oligomeric state and hence the promoter binding capability of PHRs via their SPX receptors.
Sensing the future of bio-informational engineering
Authors: Dixon Thomas A. , Williams Thomas C. , Pretorius Isak S. 
Published: January 2021

AbstractThe practices of synthetic biology are being integrated into ‘multiscale’ designs enabling two-way communication across organic and inorganic information substrates in biological, digital and cyber-physical system integrations. Novel applications of ‘bio-informational’ engineering will arise in environmental monitoring, precision agriculture, precision medicine and next-generation biomanufacturing. Potential developments include sentinel plants for environmental monitoring and autonomous bioreactors that respond to biosensor signaling. As bio-informational understanding progresses, both natural and engineered biological systems will need to be reimagined as cyber-physical architectures. We propose that a multiple length scale taxonomy will assist in rationalizing and enabling this transformative development in engineering biology.
TreeMap, a tree-level model of conterminous US forests circa 2014 produced by imputation of FIA plot data
Authors: Riley Karin L. , Grenfell Isaac C. , Finney Mark A. , Wiener Jason M. 
Published: January 2021

AbstractA 30 × 30m-resolution gridded dataset of forest plot identifiers was developed for the conterminous United States (CONUS) using a random forests machine-learning imputation approach. Forest plots from the US Forest Service Forest Inventory and Analysis program (FIA) were imputed to gridded c2014 landscape data provided by the LANDFIRE project using topographic, biophysical, and disturbance variables. The output consisted of a raster map of plot identifiers. From the plot identifiers, users of the dataset can link to a number of tree- and plot-level attributes stored in the accompanying tables and in the publicly available FIA DataMart, and then produce maps of any of these attributes, including number of trees per acre, tree species, and forest type. Of 67,141 FIA plots available, 62,758 of these (93.5%) were utilized at least once in imputation to 2,841,601,981 forested pixels in CONUS. Continuous high-resolution forest structure data at a national scale will be invaluable for analyzing carbon dynamics, habitat distributions, and fire effects.
The ISN/RPS 2016 classification predicts renal prognosis in patients with first-onset class III/IV lupus nephritis
Authors: Hachiya Asaka , Karasawa Munetoshi , Imaizumi Takahiro , Kato Noritoshi , Katsuno Takayuki , Ishimoto Takuji , Kosugi Tomoki , Tsuboi Naotake , Maruyama Shoichi 
Published: January 2021

AbstractLupus nephritis (LN) is a life-threatening complication of systemic lupus erythematosus. The 2003 pathological classification of LN was revised in 2016; it quantitatively evaluates the interstitium in addition to the glomeruli. We performed a retrospective multi-centre cohort study and investigated the utility of the 2016 classification—including the activity index (AI), chronicity index (CI), and each pathological component to predict complete remission or renal function decline, defined as 1.5-fold increase in serum creatinine levels—and compare with that of the 2003 classification. Ninety-one consecutive adult patients with first-onset class III/IV LN who were newly prescribed any immunosuppressants were enrolled and followed up for a median of 51 months from January 2004. Cox regression analysis demonstrated the subclasses based on the 2003 classification, which mainly evaluate glomerular lesions, were not associated with clinical outcomes. After adjustments for estimated glomerular filtration rate and urinary protein levels, higher CI and higher interstitial fibrosis and lower hyaline deposit scores were associated with renal functional decline. Similarly, higher CI and interstitial inflammation scores were associated with failure to achieve complete remission. Therefore, the 2016 classification can predict the clinical outcomes more precisely than the 2003 classification.
The effects of flooding and weather conditions on leptospirosis transmission in Thailand
Authors: Chadsuthi Sudarat , Chalvet-Monfray Karine , Wiratsudakul Anuwat , Modchang Charin 
Published: January 2021

AbstractThe epidemic of leptospirosis in humans occurs annually in Thailand. In this study, we have developed mathematical models to investigate transmission dynamics between humans, animals, and a contaminated environment. We compared different leptospire transmission models involving flooding and weather conditions, shedding and multiplication rate in a contaminated environment. We found that the model in which the transmission rate depends on both flooding and temperature, best-fits the reported human data on leptospirosis in Thailand. Our results indicate that flooding strongly contributes to disease transmission, where a high degree of flooding leads to a higher number of infected individuals. Sensitivity analysis showed that the transmission rate of leptospires from a contaminated environment was the most important parameter for the total number of human cases. Our results suggest that public education should target people who work in contaminated environments to preventLeptospirainfections.