bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling Joint Relationship and Design Scenarios Between Precipitation, Surface Temperature, and Atmospheric Precipitable Water Over Mainland China
Authors: Ayantobo Olusola Olaitan , Wei Jiahua , Wang Guangqian 
Published: February 2021

AbstractThis study employs copula model to discuss joint relationship and design scenarios between precipitation (P), surface temperature (T), and precipitable water (PW) in seven regions and mainland China over 1980–2016 within a bivariate framework. Markov Chain Monte Carlo modeling in a Bayesian framework was applied to calculate copula parameters while best fitted copulas were assessed using Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC), Root Mean Squared Error (RMSE), Nash‐Sutcliffe Efficiency (NSE), and maximum likelihood criteria. Results showed that the spatial variations of P decreased from South to Northwest, T decreased from South to North and from East to West. Distributions of P and T were similar, with higher values in regions c and d. PW was higher in the south, with more than 64.54 mm in the southwest, 25 mm in the north‐central. The correlation between PW and P as well as PW and T were higher than 0.74. Birnbaum Saunders distribution was considered appropriate to fit P in regions a and f while P and PW in other regions are good with Generalized Pareto. T performed better with generalized extreme in all regions. Moreover, Gumbel, Frank, and Joe copulas provided good fit for PW and P in regions b, f, and g, respectively while in regions a, c, d, and e, Nelson provided perfect fit. For PW and T, Nelson was a good fit in all regions. The bivariate probabilities and design scenarios in various regions suggest tremendous variations, with regions having high probabilities associated with low return periods. We showed that joint analysis of climate variables gives more robust design quantiles.
The Anthropocene: Comparing Its Meaning in Geology (Chronostratigraphy) with Conceptual Approaches Arising in Other Disciplines
Authors: Zalasiewicz Jan , Waters Colin N. , Ellis Erle C. , Head Martin J. , Vidas Davor , Steffen Will , Thomas Julia Adeney , Horn Eva , Summerhayes Colin P. , Leinfelder Reinhold , McNeill J. R. , Gałuszka Agnieszka , Williams Mark , Barnosky Anthony D. , Richter Daniel de B. , Gibbard Philip L. , Syvitski Jaia , Jeandel Catherine , Cearreta Alejandro , Cundy Andrew B. , Fairchild Ian J. , Rose Neil L. , Ivar do Sul Juliana A. , Shotyk William , Turner Simon , Wagreich Michael , Zinke Jens 
Published: February 2021

AbstractThe term Anthropocene initially emerged from the Earth System science community in the early 2000s, denoting a concept that the Holocene Epoch has terminated as a consequence of human activities. First associated with the onset of the Industrial Revolution, it was then more closely linked with the Great Acceleration in industrialization and globalization from the 1950s that fundamentally modified physical, chemical, and biological signals in geological archives. Since 2009, the Anthropocene has been evaluated by the Anthropocene Working Group, tasked with examining it for potential inclusion in the Geological Time Scale. Such inclusion requires a precisely defined chronostratigraphic and geochronological unit with a globally synchronous base and inception, with the mid‐twentieth century being geologically optimal. This reflects an Earth System state in which human activities have become predominant drivers of modifications to the stratigraphic record, making it clearly distinct from the Holocene. However, more recently, the term Anthropocene has also become used for different conceptual interpretations in diverse scholarly fields, including the environmental and social sciences and humanities. These are often flexibly interpreted, commonly without reference to the geological record, and diachronous in time; they often extend much further back in time than the mid‐twentieth century. These broader conceptualizations encompass wide ranges and levels of human impacts and interactions with the environment. Here, we clarify what the Anthropocene is in geological terms and compare the proposed geological (chronostratigraphic) definition with some of these broader interpretations and applications of the term “Anthropocene,” showing both their overlaps and differences.
Field‐Based Evidence for Intra‐Slab High‐Permeability Channel Formation at Eclogite‐Facies Conditions During Subduction
Authors: Piccoli Francesca , Ague Jay J. , Chu Xu , Tian Meng , Vitale Brovarone Alberto 
Published: February 2021

AbstractFluid release from subducting oceanic lithosphere is a key process for subduction zone geodynamics, from controlling arc volcanism to seismicity and tectonic exhumation. However, many fundamental details of fluid composition, flow pathways, and reactivity with slab‐forming rocks remain to be thoroughly understood. In this study we investigate a multi‐kilometer‐long, high‐pressure metasomatic system preserved in the lawsonite‐eclogite metamorphic unit of Alpine Corsica, France. The fluid‐mediated process was localized along a major intra‐slab interface, which is the contact between basement and cover unit. Two distinct metasomatic stages are identified and discussed. We show that these two stages resulted from the infiltration of deep fluids that were derived from the same source and had the same slab‐parallel, updip flow direction. By mass balance analysis, we quantify metasomatic mass changes along this fluid pathway and the time‐integrated fluid fluxes responsible for them. In addition, we also assess carbon fluxes associated with these metasomatic events. The magnitude of the estimated fluid fluxes (104–105) indicates that major intra‐slab interfaces such as lithological boundaries acted as fluid channels facilitating episodic pulses of fluid flow. We also show that when fluids are channelized, high time‐integrated fluid fluxes lead to carbon fluxes several orders of magnitude higher than carbon fluxes generated by local dehydration reactions. Given the size and geologic features of the investigated metasomatic system, we propose that it represents the first reported natural analogue of the so‐called high permeability channels predicted by numerical simulations.
Quasiperiodic 1‐Hour Alfvén Wave Resonances in Saturn's Magnetosphere: Theory for a Realistic Plasma/Field Model
Authors: Rusaitis L. , Khurana K. K. , Kivelson M. G. , Walker R. J. 
Published: February 2021

AbstractWe model the omnipresent quasiperiodic 60 min waves in Saturn's outer magnetosphere as field line resonances adopting a realistic magnetic field model and a measurement‐based plasma density distribution using Alfvén wave resonance theory for arbitrary field geometries (Singer et al., 1981). The modeled eigenfrequencies for the second and higher modes are roughly independent of invariant latitude, mapping into large regions of the magnetosphere up to at least 20 RS, and the third and fourth harmonic modes having close to 1 h eigenperiod. The model predicts the normalized amplitudes of these higher modes of the magnetic field perturbations at high latitudes to exceed the amplitudes at the plasma sheet, in agreement with the observations of more frequent occurrences at mid‐to‐high latitudes. The periods of the higher order field line resonances in the outer magnetosphere differ considerably from those in a dipole model, illustrating the importance of a realistic field model.
Morphology of Jupiter's Polar Auroral Bright Spot Emissions via Juno‐UVS Observations
Authors: Haewsantati K. , Bonfond B. , Wannawichian S. , Gladstone G. R. , Hue V. , Versteeg M. H. , Greathouse T. K. , Grodent D. , Yao Z. , Dunn W. , Gérard J.‐C. , Giles R. , Kammer J. , Guo R. , Vogt M. F. 
Published: February 2021

AbstractSince 2016, the Juno‐UVS (Ultraviolet Spectrograph) instrument has been taking spectral images of Jupiter's auroras in their full extent, including the nightside, which cannot be viewed from Earth. We present a systematic analysis of features in Jupiter's polar auroras called auroral bright spots, which were observed by Juno‐UVS during the first 25 orbits of the spacecraft. An auroral bright spot is an isolated localized and transient brightening in the polar region. Bright spots were identified in 16 perijoves (PJ) out of 24, mostly in either the northern or the southern hemisphere but rarely in both during the same PJ. The emitted power of the bright spots is time variable with peak power ranging from a few tens to a hundred of gigawatts. Moreover, we found that, for some PJs, bright spots exhibit quasiperiodic behavior. The spots, within PJ4 and PJ16, each reappeared within <2,000 km from the previous position in System III with periods of 28 and 22 min, respectively. This period is similar to periods previously identified in X‐rays and various other observations. The bright spot positions are in a specific region in the northern hemisphere in System III, but are scattered around the magnetic pole in the southern hemisphere, near the edge of the swirl region. Furthermore, the bright spots can be seen at any local time, rather than being confined to the noon sector as previously thought from Earth‐based observations. This suggests that the bright spots might not be firmly connected to the noon facing magnetospheric cusp processes.
Nighttime Magnetic Perturbation Events Observed in Arctic Canada: 3. Occurrence and Amplitude as Functions of Magnetic Latitude, Local Time, and Magnetic Disturbance Indices
Authors: Engebretson Mark J. , Pilipenko Viacheslav A. , Steinmetz Erik S. , Moldwin Mark B. , Connors Martin G. , Boteler David H. , Singer Howard J. , Opgenoorth Hermann , Schillings Audrey , Ohtani Shin , Gjerloev Jesper , Russell Christopher T. 
Published: February 2021

AbstractRapid changes of magnetic fields associated with nighttime magnetic perturbation events (MPEs) with amplitudes |ΔB| of hundreds of nT and 5–10 min duration can induce geomagnetically induced currents (GICs) that can harm technological systems. This study compares the occurrence and amplitude of nighttime MPEs with |dB/dt| ≥ 6 nT/s observed during 2015 and 2017 at five stations in Arctic Canada ranging from 64.7° to 75.2° in corrected geomagnetic latitude (MLAT) as functions of magnetic local time (MLT), the SME (SuperMAG version of AE) and SYM/H magnetic indices, and time delay after substorm onsets. Although most MPEs occurred within 30 min after a substorm onset, ∼10% of those observed at the four lower latitude stations occurred over two hours after the most recent onset. A broad distribution in local time appeared at all five stations between 1700 and 0100 MLT, and a narrower distribution appeared at the lower latitude stations between 0200 and 0700 MLT. There was little or no correlation between MPE amplitude and the SYM/H index; most MPEs at all stations occurred for SYM/H values between −40 and 0 nT. SME index values for MPEs observed >1 h after the most recent substorm onset fell in the lower half of the range of SME values for events during substorms, and dipolarizations in synchronous orbit at GOES 13 during these events were weaker or more often nonexistent. These observations suggest that substorms are neither necessary nor sufficient to cause MPEs, and hence predictions of GICs cannot focus solely on substorms.
Integrative analysis of physiological responses to high fat feeding with diffusion tensor images and neurochemical profiles of the mouse brain
Authors: Guadilla Irene , Lizarbe Blanca , Barrios Laura , Cerdán Sebastián , López-Larrubia Pilar 
Published: February 2021

Abstract
Background
Obesity proceeds with important physiological and microstructural alterations in the brain, but the precise relationships between the diet and feeding status, its physiological responses, and the observed neuroimaging repercussions, remain elusive. Here, we implemented a mouse model of high fat diet (HFD) feeding to explore specific associations between diet, feeding status, phenotypic and endocrine repercussions, and the resulting microstructural and metabolic alterations in the brain, as detected by diffusion tensor imaging (DTI) and neurochemical metabolic profiling.

Methods
Brain DTI images were acquired from adult male C57BL6/J mice after 6 weeks of HFD, or standard diet (SD) administrations, both under the fed, and overnight fasted conditions. Metabolomic profiles of the cortex (Ctx), hippocampus (Hipc), and hypothalamus (Hyp) were determined by 1H high-resolution magic angle spinning (HRMAS) spectroscopy, in cerebral biopsies dissected after microwave fixation. Mean diffusivity (MD), fractional anisotropy (FA) maps, and HRMAS profiles were complemented with determinations of phenotypic alterations and plasma levels of appetite-related hormones, measured by indirect calorimetry and multiplex assays, respectively. We used Z-score and alternating least squares scaling (ALSCAL) analysis to investigate specific associations between diet and feeding status, physiological, and imaging parameters.

Results
HFD induced significant increases in body weight and the plasma levels of glucose and fatty acids in the fed and fasted conditions, as well as higher cerebral MD (Ctx, Hipc, Hyp), FA (Hipc), and mobile saturated fatty acids resonances (Ctx, Hipc, Hyp). Z-score and ASLCAL analysis identified the precise associations between physiological and imaging variables.

Conclusions
The present study reveals that diet and feeding conditions elicit prominent effects on specific imaging and spectroscopic parameters of the mouse brain that can be associated to the alterations in phenotypic and endocrine variables. Together, present results disclose a neuro-inflammatory response to HFD, characterized primarily by vasogenic edema and compensatory responses in osmolyte concentrations.
A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat
Authors: Kolodziej Markus C. , Singla Jyoti , Sánchez-Martín Javier , Zbinden Helen , Šimková Hana , Karafiátová Miroslava , Doležel Jaroslav , Gronnier Julien , Poretti Manuel , Glauser Gaétan , Zhu Wangsheng , Köster Philipp , Zipfel Cyril , Wicker Thomas , Krattinger Simon G. , Keller Beat 
Published: February 2021

AbstractPlasma membrane-associated and intracellular proteins and protein complexes play a pivotal role in pathogen recognition and disease resistance signaling in plants and animals. The two predominant protein families perceiving plant pathogens are receptor-like kinases and nucleotide binding-leucine-rich repeat receptors (NLR), which often confer race-specific resistance. Leaf rust is one of the most prevalent and most devastating wheat diseases. Here, we clone the race-specific leaf rust resistance gene Lr14a from hexaploid wheat. The cloning of Lr14a is aided by the recently published genome assembly of ArinaLrFor, an Lr14a-containing wheat line. Lr14a encodes a membrane-localized protein containing twelve ankyrin (ANK) repeats and structural similarities to Ca2+-permeable non-selective cation channels. Transcriptome analyses reveal an induction of genes associated with calcium ion binding in the presence of Lr14a. Haplotype analyses indicate that Lr14a-containing chromosome segments were introgressed multiple times into the bread wheat gene pool, but we find no variation in the Lr14a coding sequence itself. Our work demonstrates the involvement of an ANK-transmembrane (TM)-like type of gene family in race-specific disease resistance in wheat. This forms the basis to explore ANK-TM-like genes in disease resistance breeding.
High resolution ensemble description of metamorphic and intrinsically disordered proteins using an efficient hybrid parallel tempering scheme
Authors: Appadurai Rajeswari , Nagesh Jayashree , Srivastava Anand 
Published: February 2021

AbstractMapping free energy landscapes of complex multi-funneled metamorphic proteins and weakly-funneled intrinsically disordered proteins (IDPs) remains challenging. While rare-event sampling molecular dynamics simulations can be useful, they often need to either impose restraints or reweigh the generated data to match experiments. Here, we present a parallel-tempering method that takes advantage of accelerated water dynamics and allows efficient and accurate conformational sampling across a wide variety of proteins. We demonstrate the improved sampling efficiency by benchmarking against standard model systems such as alanine di-peptide, TRP-cage and β-hairpin. The method successfully scales to large metamorphic proteins such as RFA-H and to highly disordered IDPs such as Histatin-5. Across the diverse proteins, the calculated ensemble averages match well with the NMR, SAXS and other biophysical experiments without the need to reweigh. By allowing accurate sampling across different landscapes, the method opens doors for sampling free energy landscape of complex uncharted proteins.
Self-assembly and regulation of protein cages from pre-organised coiled-coil modules
Authors: Lapenta Fabio , Aupič Jana , Vezzoli Marco , Strmšek Žiga , Da Vela Stefano , Svergun Dmitri I. , Carazo José María , Melero Roberto , Jerala Roman 
Published: February 2021

AbstractCoiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. CCPO folds are defined by the sequential order of concatenated orthogonal coiled-coil (CC) dimer-forming peptides, where a single-chain protein is programmed to fold into a polyhedral cage. Self-assembly of CC-based nanostructures from several chains, similarly as in DNA nanotechnology, could facilitate the design of more complex assemblies and the introduction of functionalities. Here, we show the design of a de novo triangular bipyramid fold comprising 18 CC-forming segments and define the strategy for the two-chain self-assembly of the bipyramidal cage from asymmetric and pseudo-symmetric pre-organised structural modules. In addition, by introducing a protease cleavage site and masking the interfacial CC-forming segments in the two-chain bipyramidal cage, we devise a proteolysis-mediated conformational switch. This strategy could be extended to other modular protein folds, facilitating the construction of dynamic multi-chain CC-based complexes.
Designed folding pathway of modular coiled-coil-based proteins
Authors: Aupič Jana , Strmšek Žiga , Lapenta Fabio , Pahovnik David , Pisanski Tomaž , Drobnak Igor , Ljubetič Ajasja , Jerala Roman 
Published: February 2021

AbstractNatural proteins are characterised by a complex folding pathway defined uniquely for each fold. Designed coiled-coil protein origami (CCPO) cages are distinct from natural compact proteins, since their fold is prescribed by discrete long-range interactions between orthogonal pairwise-interacting coiled-coil (CC) modules within a single polypeptide chain. Here, we demonstrate that CCPO proteins fold in a stepwise sequential pathway. Molecular dynamics simulations and stopped-flow Förster resonance energy transfer (FRET) measurements reveal that CCPO folding is dominated by the effective intra-chain distance between CC modules in the primary sequence and subsequent folding intermediates, allowing identical CC modules to be employed for multiple cage edges and thus relaxing CCPO cage design requirements. The number of orthogonal modules required for constructing a CCPO tetrahedron can be reduced from six to as little as three different CC modules. The stepwise modular nature of the folding pathway offers insights into the folding of tandem repeat proteins and can be exploited for the design of modular protein structures based on a given set of orthogonal modules.
Facilitation of molecular motion to develop turn-on photoacoustic bioprobe for detecting nitric oxide in encephalitis
Authors: Qi Ji , Feng Leyan , Zhang Xiaoyan , Zhang Haoke , Huang Liwen , Zhou Yutong , Zhao Zheng , Duan Xingchen , Xu Fei , Kwok Ryan T. K. , Lam Jacky W. Y. , Ding Dan , Xue Xue , Tang Ben Zhong 
Published: February 2021

AbstractNitric oxide (NO) is an important signaling molecule overexpressed in many diseases, thus the development of NO-activatable probes is of vital significance for monitoring related diseases. However, sensitive photoacoustic (PA) probes for detecting NO-associated complicated diseases (e.g., encephalitis), have yet to be developed. Herein, we report a NO-activated PA probe for in vivo detection of encephalitis by tuning the molecular geometry and energy transformation processes. A strong donor-acceptor structure with increased conjugation can be obtained after NO treatment, along with the active intramolecular motion, significantly boosting “turn-on” near-infrared PA property. The molecular probe exhibits high specificity and sensitivity towards NO over interfering reactive species. The probe is capable of detecting and differentiating encephalitis in different severities with high spatiotemporal resolution. This work will inspire more insights into the development of high-performing activatable PA probes for advanced diagnosis by making full use of intramolecular motion and energy transformation processes.
Mapping of susceptible variants for cold medicine-related Stevens–Johnson syndrome by whole-genome resequencing
Authors: Kawai Yosuke , Hitomi Yuki , Ueta Mayumi , Khor Seik-Soon , Nakatani Ken , Sotozono Chie , Kinoshita Shigeru , Nagasaki Masao , Tokunaga Katsushi 
Published: February 2021

AbstractStevens–Johnson syndrome (SJS) and its severe condition with extensive skin detachment and a poor prognosis, toxic epidermal necrolysis (TEN), are immunologically mediated severe cutaneous reactions of the skin and mucous membranes such as the ocular surface. Genetic variations on the HLA-A and other autosomal genes have been identified as risk factors for cold medicine-related SJS/TEN with severe ocular complications (CM-SJS/TEN with SOC). Using a whole-genome sequencing (WGS) approach, we explored other susceptible variants of CM-SJS/TEN with SOC, especially among rare variants and structural variants (SVs). WGS was performed on samples from 133 patients with CM-SJS/TEN with SOC and 418 healthy controls to obtain single nucleotide polymorphisms (SNPs) and SVs. Genome-wide association tests were performed with these variants. Our genome-wide association test reproduced the associations of the common variants of HLA-A and loci on chromosome 16q12.1. We also identified novel associations of SVs on these loci and an aggregation of rare coding variants on the TPRM8 gene. In silico gene expression analysis on the HLA-A locus revealed that the SNP (rs12202296), which was significantly associated with susceptibility to CM-SJS/TEN with SOC, was correlated to an increase in HLA-A expression levels in the whole blood (P = 2.9 × 10−17), from the GTEx database. The majority of variants that were significantly associated with CM-SJS/TEN with SOC were found in non-coding regions, indicating the regulatory role of genetic variations in the pathogenesis of CM-SJS/TEN with SOC.