bluuebunny/crossref_metadata_2025_split huggingface dataset:
Delineating the Role of Calcium in the Large‐Scale Distribution of Metal‐Bound Organic Carbon in Soils
Authors: Wang Simin , Jia Yufu , Liu Ting , Wang Yiyun , Liu Zongguang , Feng Xiaojuan 
Published: May 2021

AbstractMetal‐bound organic carbon (OC) is vital for the persistence of soil organic carbon (SOC). However, its relative importance in different land types (e.g., upland vs. wetland) remains unclear. Here by analyzing metal‐bound OC by the classic citrate‐bicarbonate‐dithionite method (OCCBD) from 62 soils from contrasting environments, we find that OCCBD constitutes an equally important proportion of SOC (OCCBD%) in wetlands as in uplands. Land‐use type and calcium (Ca) content are the best predictors of OCCBD%, likely owing to the contribution of OC directly associated with sulfate‐extractable Ca (OCNa2SO4) and Ca's bridging and aggregating effect on OCCBD. By further separating OCNa2SO4, we find that OCNa2SO4 accounts for ∼24% of OCCBD in Tibetan‐Mongolian grasslands and its relative contribution to OCCBD shift in an S‐shaped mode along the pH gradient (6–9). These findings highlight Ca's important effect on the distribution of metal‐bound OC at regional scales.
Diversity in Vertical Structures of Internal Tide Dissipation Rate Around the Indonesian Throughflow Exits Simulated by a High‐Resolution Nonhydrostatic Model
Authors: Wen Xixi , Peng Shiqiu , Qian Yu‐Kun , Li Yineng 
Published: May 2021

AbstractThe vertical structure of internal tide dissipation rate ϵ is essential to the parameterization of the internal tide‐induced mixing, yet its diversity has always been oversimplified in ocean circulation models. Based on a high‐vertical‐resolution (10 m) simulation around the exits of the Indonesian throughflow, the diversity in ϵ profiles near both the bottom and the thermocline was investigated by a hierarchical clustering classification. Five typical near‐bottom vertical structures of ϵ were found, of which the bottom‐intensified structure is dominant. From the maximum dissipation depths to the shallower water, all five profiles obey the same decaying function. There are three typical near‐thermocline structures of ϵ: one menifests the thermocline‐intensified pattern and the other two feature a surface‐intensified pattern characterized by a monotonic increase from 500‐m depth to the surface. All three vertical structures near thermocline could be scaled by the reciprocal of the Richardson number.
On the Optimal Design of Field Significance Tests for Changes in Climate Extremes
Authors: Wang Jianyu , Li Chao , Zwiers Francis , Zhang Xuebin , Li Guilong , Jiang Zhihong , Zhai Panmao , Sun Ying , Li Zhen , Yue Qun 
Published: May 2021

AbstractField significance tests have been widely used to detect climate change. In most cases, a local test is used to identify significant changes at individual locations, which is then followed by a field significance test that considers the number of locations in a region with locally significant changes. The choice of local test can affect the result, potentially leading to conflicting assessments of the impact of climate change on a region. We demonstrate that when considering changes in the annual extremes of daily precipitation, the simple Mann‐Kendall trend test is preferred as the local test over more complex likelihood ratio tests that compare the fits of stationary and nonstationary generalized extreme value distributions. This lesson allows us to report, with enhanced confidence, that the intensification of annual extremes of daily precipitation in China since 1961 became field significant much earlier than previously reported.
Deep Crustal Contact Between the Pamir and Tarim Basin Deduced From Receiver Functions
Authors: Xu Qiang , Zhao Junmeng , Yuan Xiaohui , Liu Hongbing , Ju Changhui , Schurr Bernd , Bloch Wasja 
Published: May 2021

AbstractThe deep crustal deformation in the east Pamir in response to the Cenozoic collision with the Tien Shan and the Tarim Basin is so far poorly constrained. We present new insights into the crustal structure of the east Pamir and its surrounding regions using P receiver functions from 40 temporary and permanent seismic stations. The crustal thickness reaches a maximum of 88 km beneath the central and southern east Pamir and decreases sharply to 50–60 km along the southern Tien Shan and to 41–50 km below the Tarim Basin. The most prominent crustal structures involve a double Moho, suggesting eastward underthrusting of the Pamir lower crust beneath southern east Pamir, and two Moho offsets, supporting delamination of Asian lower crust below the central east Pamir and pure shear shortening along the northeastern margin between the Pamir and Tarim Basin.
Infrared Spectral Evidence for K‐Metasomatism of Volcanic Rocks on Mars
Authors: Michalski Joseph R. , Niles Paul B. , Glotch Timothy D. , Cuadros Javier 
Published: May 2021

AbstractPotassium metasomatism is a common geologic process occurring in a range of environments on Earth. K‐metasomatism can dramatically change the chemistry of large volumes of crust resulting in formation of abundant K‐rich feldspar while preserving original rock textures. Remote sensing of Mars has revealed the presence of rare but striking felspar‐rich terrains as well as K‐rich phyllosilicates such as illite or muscovite. Furthermore, the Curiosity Rover has detected evidence for K‐enrichment in rocks at Gale Crater. In this study, we use spectroscopic and remote sensing analyses of K‐metasomatized rocks on Earth as a comparison to K‐rich and/or possible granitic rocks on Mars. The results suggest that evidence for K‐feldspar rich, quartz‐bearing, and illite‐bearing rocks on Mars is consistent with K‐metasomatism. K‐rich rocks in Gale Crater have themselves likely not been metasomatized, but the abundant feldspar within them might have been derived from metasomatized crust.
Seasonal Prediction of Bottom Temperature on the Northeast U.S. Continental Shelf
Authors: Chen Zhuomin , Kwon Young‐Oh , Chen Ke , Fratantoni Paula , Gawarkiewicz Glen , Joyce Terrence M. , Miller Timothy J. , Nye Janet A. , Saba Vincent S. , Stock Brian C. 
Published: May 2021

AbstractThe Northeast U.S. shelf (NES) is an oceanographically dynamic marine ecosystem and supports some of the most valuable demersal fisheries in the world. A reliable prediction of NES environmental variables, particularly ocean bottom temperature, could lead to a significant improvement in demersal fisheries management. However, the current generation of climate model‐based seasonal‐to‐interannual predictions exhibits limited prediction skill in this continental shelf environment. Here, we have developed a hierarchy of statistical seasonal predictions for NES bottom temperatures using an eddy‐resolving ocean reanalysis data set. A simple, damped local persistence prediction model produces significant skill for lead times up to ∼5 months in the Mid‐Atlantic Bight and up to ∼10 months in the Gulf of Maine, although the prediction skill varies notably by season. Considering temperature from a nearby or upstream (i.e., more poleward) region as an additional predictor generally improves prediction skill, presumably as a result of advective processes. Large‐scale atmospheric and oceanic indices, such as Gulf Stream path indices (GSIs) and the North Atlantic Oscillation Index, are also tested as predictors for NES bottom temperatures. Only the GSI constructed from temperature observed at 200 m depth significantly improves the prediction skill relative to local persistence. However, the prediction skill from this GSI is not larger than that gained using models incorporating nearby or upstream shelf/slope temperatures. Based on these results, a simplified statistical model has been developed, which can be tailored to fisheries management for the NES.
The SARS-CoV-2 protein ORF3a inhibits fusion of autophagosomes with lysosomes
Authors: Zhang Yabin , Sun Hao , Pei Rongjuan , Mao Binli , Zhao Zhenyu , Li Huihui , Lin Yong , Lu Kefeng 
Published: May 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the ongoing coronavirus disease 2019 pandemic. How SARS-CoV-2 regulates cellular responses to escape clearance by host cells is unknown. Autophagy is an intracellular lysosomal degradation pathway for the clearance of various cargoes, including viruses. Here, we systematically screened 28 viral proteins of SARS-CoV-2 and identified that ORF3a strongly inhibited autophagic flux by blocking the fusion of autophagosomes with lysosomes. ORF3a colocalized with lysosomes and interacted with VPS39, a component of the homotypic fusion and protein sorting (HOPS) complex. The ORF3a–VPS39 interaction prohibited the binding of HOPS with RAB7, which prevented the assembly of fusion machinery, leading to the accumulation of unfused autophagosomes. These results indicated the potential mechanism by which SARS-CoV-2 escapes degradation; that is, the virus interferes with autophagosome–lysosome fusion. Furthermore, our findings will facilitate strategies targeting autophagy for conferring potential protection against the spread of SARS-CoV-2.
Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity
Authors: Izoré Thierry , Candace Ho Y. T. , Kaczmarski Joe A. , Gavriilidou Athina , Chow Ka Ho , Steer David L. , Goode Robert J. A. , Schittenhelm Ralf B. , Tailhades Julien , Tosin Manuela , Challis Gregory L. , Krenske Elizabeth H. , Ziemert Nadine , Jackson Colin J. , Cryle Max J. 
Published: May 2021

AbstractNon-ribosomal peptide synthetases are important enzymes for the assembly of complex peptide natural products. Within these multi-modular assembly lines, condensation domains perform the central function of chain assembly, typically by forming a peptide bond between two peptidyl carrier protein (PCP)-bound substrates. In this work, we report structural snapshots of a condensation domain in complex with an aminoacyl-PCP acceptor substrate. These structures allow the identification of a mechanism that controls access of acceptor substrates to the active site in condensation domains. The structures of this complex also allow us to demonstrate that condensation domain active sites do not contain a distinct pocket to select the side chain of the acceptor substrate during peptide assembly but that residues within the active site motif can instead serve to tune the selectivity of these central biosynthetic domains.
Kinetic resolution of indolines by asymmetric hydroxylamine formation
Authors: Wang Gang , Lu Ran , He Chuangchuang , Liu Lei 
Published: May 2021

AbstractCatalytic kinetic resolution of amines represents a longstanding challenge in chemical synthesis. Here, we described a kinetic resolution of secondary amines through oxygenation to produce enantiopure hydroxylamines involving N–O bond formation. The economic and practical titanium-catalyzed asymmetric oxygenation with environmentally benign hydrogen peroxide as oxidant is applicable to a range of racemic indolines with multiple stereocenters and diverse substituent patterns in high efficiency with efficient chemoselectivity and enantio-discrimination. Late-stage asymmetric oxygenation of bioactive molecules that are otherwise difficult to synthesize was also explored.
An Arabidopsis AT-hook motif nuclear protein mediates somatic embryogenesis and coinciding genome duplication
Authors: Karami Omid , Rahimi Arezoo , Mak Patrick , Horstman Anneke , Boutilier Kim , Compier Monique , van der Zaal Bert , Offringa Remko 
Published: May 2021

AbstractPlant somatic cells can be reprogrammed into totipotent embryonic cells that are able to form differentiated embryos in a process called somatic embryogenesis (SE), by hormone treatment or through overexpression of certain transcription factor genes, such as BABY BOOM (BBM). Here we show that overexpression of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED 15 (AHL15) gene induces formation of somatic embryos on Arabidopsis thaliana seedlings in the absence of hormone treatment. During zygotic embryogenesis, AHL15 expression starts early in embryo development, and AH15 and other AHL genes are required for proper embryo patterning and development beyond the globular stage. Moreover, AHL15 and several of its homologs are upregulated and required for SE induction upon hormone treatment, and they are required for efficient BBM-induced SE as downstream targets of BBM. A significant number of plants derived from AHL15 overexpression-induced somatic embryos are polyploid. Polyploidisation occurs by endomitosis specifically during the initiation of SE, and is caused by strong heterochromatin decondensation induced by AHL15 overexpression.
The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics
Authors: Salminen Seppo , Collado Maria Carmen , Endo Akihito , Hill Colin , Lebeer Sarah , Quigley Eamonn M. M. , Sanders Mary Ellen , Shamir Raanan , Swann Jonathan R. , Szajewska Hania , Vinderola Gabriel 
Published: May 2021

AbstractIn 2019, the International Scientific Association for Probiotics and Prebiotics (ISAPP) convened a panel of experts specializing in nutrition, microbial physiology, gastroenterology, paediatrics, food science and microbiology to review the definition and scope of postbiotics. The term ‘postbiotics’ is increasingly found in the scientific literature and on commercial products, yet is inconsistently used and lacks a clear definition. The purpose of this panel was to consider the scientific, commercial and regulatory parameters encompassing this emerging term, propose a useful definition and thereby establish a foundation for future developments. The panel defined a postbiotic as a “preparation of inanimate microorganisms and/or their components that confers a health benefit on the host”. Effective postbiotics must contain inactivated microbial cells or cell components, with or without metabolites, that contribute to observed health benefits. The panel also discussed existing evidence of health-promoting effects of postbiotics, potential mechanisms of action, levels of evidence required to meet the stated definition, safety and implications for stakeholders. The panel determined that a definition of postbiotics is useful so that scientists, clinical triallists, industry, regulators and consumers have common ground for future activity in this area. A generally accepted definition will hopefully lead to regulatory clarity and promote innovation and the development of new postbiotic products.
Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution
Authors: Zhou Jiawei , Zhang Shuo , Wang Jie , Shen Hongmei , Ai Bin , Gao Wei , Zhang Cuijun , Fei Qili , Yuan Daojun , Wu Zhiqiang , Tembrock Luke R. , Li Sen , Gu Cuihua , Liao Xuezhu 
Published: May 2021

AbstractThe chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.
Experimental and computational evaluation of cyclic solvent injection in fractured tight hydrocarbon reservoirs
Authors: Ghanizadeh Amin , Song Chengyao , Hamdi Hamidreza , Clarkson Christopher R. 
Published: May 2021

AbstractMulti-fractured horizontal wells have enabled commercial production from low-permeability (‘tight’) hydrocarbon reservoirs but recoveries remain exceedingly small (< 5–10%). As a result, operators have investigated the use of solvent (gas) injection schemes, such as huff-n-puff (HNP), to improve oil recovery. Previous HNP laboratory approaches, classified primary as ‘flow-through-matrix’ and ‘flow-around-matrix’ typically (1) are not fully representative of field conditions at near-fracture regions and (2) require long test times, even when performed on fractured cores. The objectives of this proof-of-concept study are to (1) design and implement a new experimental procedure that better reproduces HNP schemes in near-fracture regions and (2) use the results, simulated with a compositional lab-calibrated model, to explore the controls on enhanced hydrocarbon recovery in depleted tight oil plays. Performing multiple CO2 and (simplified) lean gas HNP cycles, the integrated experimental and simulation approach proposed herein achieves the ultimate recovery factors in a significantly shorter time frame (25–50%) compared to previous studies. The integrated experimental and computational approach proposed herein is valuable for core-based evaluation of cyclic solvent (CO2, CH4) injection in tight hydrocarbon reservoirs for (1) hydrocarbon recovery and (2) subsurface greenhouse (CO2, CH4) gas disposal/storage applications.
Identification of potential plasma protein biomarkers for bipolar II disorder: a preliminary/exploratory study
Authors: Lee Sheng-Yu , Wang Tzu-Yun , Lu Ru-Band , Wang Liang-Jen , Li Sung-Chou , Tu Chi-Ying , Chang Cheng-Ho , Chiang Yung-Chih , Tsai Kuo-Wang 
Published: May 2021

AbstractThe diagnostic peripheral biomarkers are still lacking for the bipolar II disorder (BD-II). We used isobaric tags for relative and absolute quantification technology to identify five upregulated candidate proteins [matrix metallopeptidase 9 (MMP9), phenylalanyl-tRNA synthetase subunit beta (FARSB), peroxiredoxin 2 (PRDX2), carbonic anhydrase 1 (CA-1), and proprotein convertase subtilisin/kexin type 9 (PCSK9)] for the diagnosis of BD-II. We analysed the differences in the plasma levels of these candidate proteins between BD-II patients and controls (BD-II, n = 185; Controls, n = 186) using ELISA. To establish a diagnostic model for the prediction of BD-II, the participants were divided randomly into a training group (BD-II, n = 149; Controls, n = 150) and a testing group (BD-II, n = 36; Controls, n = 36). Significant increases were found in all five protein levels between BD-II and controls in the training group. Logistic regression was analysed to form the composite probability score of the five proteins in the training group. Receiver-operating characteristic curve analysis revealed the diagnostic validity of the probability score [area under curve (AUC) = 0.89, P < 0.001]. The composite probability score of the testing group also showed good diagnostic validity (AUC = 0.86, P < 0.001). We propose that plasma levels of PRDX2, CA-1, FARSB, MMP9, and PCSK9 may be associated with BD-II as potential biomarkers.
Exploring exchange and direct procurement strategies for Natufian food processing tools of el-Wad Terrace, Israel
Authors: Rosenberg Danny , Gluhak Tatjana M. , Kaufman Daniel , Yeshurun Reuven , Weinstein-Evron Mina 
Published: May 2021

AbstractWe present the results of a detailed geochemical provenance study of 54 Natufian (ca. 15,000–11,700 cal. BP) basalt pestles from the site of el-Wad Terrace (EWT), Israel. It is the first time precise locations from where basalt raw materials were derived are provided. The results indicate that the Natufian hunter-gatherers used multiple sources of basaltic rocks, distributed over a large area surrounding the Sea of Galilee. This area is located at a considerable distance from EWT, ca. 60–120 km away, in a region where contemporaneous Natufian basecamps are few. We consider two possible models that suggest vehicles for the transportation of these artifacts to EWT, namely the exchange obtaining model (EOM) and the direct procurement model (DPM). We argue that these mechanisms are not mutually exclusive and may have operated together. We also suggest that at a time of increasing Natufian territoriality, a large area around the Sea of Galilee remained unclaimed. The paper concludes with a brief discussion of the implications for the two models. In particular, we note that the DPM implies that technological know-how for pestle production was maintained within the EWT community.
Machine learning-based mortality prediction model for heat-related illness
Authors: Hirano Yohei , Kondo Yutaka , Hifumi Toru , Yokobori Shoji , Kanda Jun , Shimazaki Junya , Hayashida Kei , Moriya Takashi , Yagi Masaharu , Takauji Shuhei , Yamaguchi Junko , Okada Yohei , Okano Yuichi , Kaneko Hitoshi , Kobayashi Tatsuho , Fujita Motoki , Yokota Hiroyuki , Okamoto Ken , Tanaka Hiroshi , Yaguchi Arino 
Published: May 2021

AbstractIn this study, we aimed to develop and validate a machine learning-based mortality prediction model for hospitalized heat-related illness patients. After 2393 hospitalized patients were extracted from a multicentered heat-related illness registry in Japan, subjects were divided into the training set for development (n = 1516, data from 2014, 2017–2019) and the test set (n = 877, data from 2020) for validation. Twenty-four variables including characteristics of patients, vital signs, and laboratory test data at hospital arrival were trained as predictor features for machine learning. The outcome was death during hospital stay. In validation, the developed machine learning models (logistic regression, support vector machine, random forest, XGBoost) demonstrated favorable performance for outcome prediction with significantly increased values of the area under the precision-recall curve (AUPR) of 0.415 [95% confidence interval (CI) 0.336–0.494], 0.395 [CI 0.318–0.472], 0.426 [CI 0.346–0.506], and 0.528 [CI 0.442–0.614], respectively, compared to that of the conventional acute physiology and chronic health evaluation (APACHE)-II score of 0.287 [CI 0.222–0.351] as a reference standard. The area under the receiver operating characteristic curve (AUROC) values were also high over 0.92 in all models, although there were no statistical differences compared to APACHE-II. This is the first demonstration of the potential of machine learning-based mortality prediction models for heat-related illnesses.