bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial Activity and Root Carbon Inputs Are More Important than Soil Carbon Diffusion in Simulating Soil Carbon Profiles
Authors: Wang Ying‐Ping , Zhang Haicheng , Ciais Philippe , Goll Daniel , Huang Yuanyuan , Wood Jeffrey D. , Ollinger Scott V. , Tang Xuli , Prescher Anne‐Katrin 
Published: March 2021

AbstractIt is well‐known that soil carbon composition and turnover rate vary with soil depth, and the responses of soil carbon to global change in deeper soil layers may differ from those near the surface. Therefore, vertically resolved soil carbon models are needed for accurately predicting future soil carbon under global warming. In this study, we developed a vertically resolved soil carbon model by including vertical transport of soil carbon and using Michaelis‐Menten kinetics for soil carbon decomposition by microbes. The model was calibrated against six sites with the observed profiles of both soil carbon concentration and 14C measurements, and against 91 forest sites with soil carbon concentrations across a wide range of climate and soil conditions for four forest types in Europe and China. Results of independent model validation at another 93 sites showed that the calibrated model explained 40%–94% of the observed variance of soil carbon concentrations at different depths. Model sensitivity analysis showed that microbial activity and root carbon inputs are more important than soil carbon diffusion in simulating soil carbon profile. Results from our study highlight the need for detailed measurements of soil microbial activities and root carbon input at different soil depths in the field.
Natural products: potential treatments for cisplatin-induced nephrotoxicity
Authors: Fang Chun-yan , Lou Da-yong , Zhou Li-qin , Wang Jin-cheng , Yang Bo , He Qiao-jun , Wang Jia-jia , Weng Qin-jie 
Published: March 2021

AbstractCisplatin is a clinically advanced and highly effective anticancer drug used in the treatment of a wide variety of malignancies, such as head and neck, lung, testis, ovary, breast cancer, etc. However, it has only a limited use in clinical practice due to its severe adverse effects, particularly nephrotoxicity; 20%–35% of patients develop acute kidney injury (AKI) after cisplatin administration. The nephrotoxic effect of cisplatin is cumulative and dose dependent and often necessitates dose reduction or withdrawal. Recurrent episodes of AKI result in impaired renal tubular function and acute renal failure, chronic kidney disease, uremia, and hypertensive nephropathy. The pathophysiology of cisplatin-induced AKI involves proximal tubular injury, apoptosis, oxidative stress, inflammation, and vascular injury in the kidneys. At present, there are no effective drugs or methods for cisplatin-induced kidney injury. Recent in vitro and in vivo studies show that numerous natural products (flavonoids, saponins, alkaloids, polysaccharide, phenylpropanoids, etc.) have specific antioxidant, anti-inflammatory, and anti-apoptotic properties that regulate the pathways associated with cisplatin-induced kidney damage. In this review we describe the molecular mechanisms of cisplatin-induced nephrotoxicity and summarize recent findings in the field of natural products that undermine these mechanisms to protect against cisplatin-induced kidney damage and provide potential strategies for AKI treatment.
Substrate-engaged type III secretion system structures reveal gating mechanism for unfolded protein translocation
Authors: Miletic Sean , Fahrenkamp Dirk , Goessweiner-Mohr Nikolaus , Wald Jiri , Pantel Maurice , Vesper Oliver , Kotov Vadim , Marlovits Thomas C. 
Published: March 2021

AbstractMany bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome is the needle complex which assembles a continuous conduit crossing the bacterial envelope and the host cell membrane to mediate effector protein translocation. However, the molecular principles underlying type III secretion remain elusive. Here, we report a structure of an active Salmonella enterica serovar Typhimurium needle complex engaged with the effector protein SptP in two functional states, revealing the complete 800Å-long secretion conduit and unraveling the critical role of the export apparatus (EA) subcomplex in type III secretion. Unfolded substrates enter the EA through a hydrophilic constriction formed by SpaQ proteins, which enables side chain-independent substrate transport. Above, a methionine gasket formed by SpaP proteins functions as a gate that dilates to accommodate substrates while preventing leaky pore formation. Following gate penetration, a moveable SpaR loop first folds up to then support substrate transport. Together, these findings establish the molecular basis for substrate translocation through T3SSs and improve our understanding of bacterial pathogenicity and motility.
Shallow distance-dependent triplet energy migration mediated by endothermic charge-transfer
Authors: Lai Runchen , Liu Yangyi , Luo Xiao , Chen Lan , Han Yaoyao , Lv Meng , Liang Guijie , Chen Jinquan , Zhang Chunfeng , Di Dawei , Scholes Gregory D. , Castellano Felix N. , Wu Kaifeng 
Published: March 2021

AbstractConventional wisdom posits that spin-triplet energy transfer (TET) is only operative over short distances because Dexter-type electronic coupling for TET rapidly decreases with increasing donor acceptor separation. While coherent mechanisms such as super-exchange can enhance the magnitude of electronic coupling, they are equally attenuated with distance. Here, we report endothermic charge-transfer-mediated TET as an alternative mechanism featuring shallow distance-dependence and experimentally demonstrated it using a linked nanocrystal-polyacene donor acceptor pair. Donor-acceptor electronic coupling is quantitatively controlled through wavefunction leakage out of the core/shell semiconductor nanocrystals, while the charge/energy transfer driving force is conserved. Attenuation of the TET rate as a function of shell thickness clearly follows the trend of hole probability density on nanocrystal surfaces rather than the product of electron and hole densities, consistent with endothermic hole-transfer-mediated TET. The shallow distance-dependence afforded by this mechanism enables efficient TET across distances well beyond the nominal range of Dexter or super-exchange paradigms.
Loss of Quaking RNA binding protein disrupts the expression of genes associated with astrocyte maturation in mouse brain
Authors: Sakers Kristina , Liu Yating , Llaci Lorida , Lee Scott M. , Vasek Michael J. , Rieger Michael A. , Brophy Sean , Tycksen Eric , Lewis Renate , Maloney Susan E. , Dougherty Joseph D. 
Published: March 2021

AbstractQuaking RNA binding protein (QKI) is essential for oligodendrocyte development as myelination requires myelin basic protein mRNA regulation and localization by the cytoplasmic isoforms (e.g., QKI-6). QKI-6 is also highly expressed in astrocytes, which were recently demonstrated to have regulated mRNA localization. Here, we define the targets of QKI in the mouse brain via CLIPseq and we show that QKI-6 binds 3′UTRs of a subset of astrocytic mRNAs. Binding is also enriched near stop codons, mediated partially by QKI-binding motifs (QBMs), yet spreads to adjacent sequences. Using a viral approach for mosaic, astrocyte-specific gene mutation with simultaneous translating RNA sequencing (CRISPR-TRAPseq), we profile ribosome associated mRNA from QKI-null astrocytes in the mouse brain. This demonstrates a role for QKI in stabilizing CLIP-defined direct targets in astrocytes in vivo and further shows that QKI mutation disrupts the transcriptional changes for a discrete subset of genes associated with astrocyte maturation.
High-fidelity single-shot readout of single electron spin in diamond with spin-to-charge conversion
Authors: Zhang Qi , Guo Yuhang , Ji Wentao , Wang Mengqi , Yin Jun , Kong Fei , Lin Yiheng , Yin Chunming , Shi Fazhan , Wang Ya , Du Jiangfeng 
Published: March 2021

AbstractHigh fidelity single-shot readout of qubits is a crucial component for fault-tolerant quantum computing and scalable quantum networks. In recent years, the nitrogen-vacancy (NV) center in diamond has risen as a leading platform for the above applications. The current single-shot readout of the NV electron spin relies on resonance fluorescence method at cryogenic temperature. However, the spin-flip process interrupts the optical cycling transition, therefore, limits the readout fidelity. Here, we introduce a spin-to-charge conversion method assisted by near-infrared (NIR) light to suppress the spin-flip error. This method leverages high spin-selectivity of cryogenic resonance excitation and flexibility of photoionization. We achieve an overall fidelity > 95% for the single-shot readout of an NV center electron spin in the presence of high strain and fast spin-flip process. With further improvements, this technique has the potential to achieve spin readout fidelity exceeding the fault-tolerant threshold, and may also find applications on integrated optoelectronic devices.
Crystallization of CsPbBr3 single crystals in water for X-ray detection
Authors: Peng Jiali , Xia Chelsea Q. , Xu Yalun , Li Ruiming , Cui Lihao , Clegg Jack K. , Herz Laura M. , Johnston Michael B. , Lin Qianqian 
Published: March 2021

AbstractMetal halide perovskites have fascinated the research community over the past decade, and demonstrated unprecedented success in optoelectronics. In particular, perovskite single crystals have emerged as promising candidates for ionization radiation detection, due to the excellent opto-electronic properties. However, most of the reported crystals are grown in organic solvents and require high temperature. In this work, we develop a low-temperature crystallization strategy to grow CsPbBr3 perovskite single crystals in water. Then, we carefully investigate the structure and optoelectronic properties of the crystals obtained, and compare them with CsPbBr3 crystals grown in dimethyl sulfoxide. Interestingly, the water grown crystals exhibit a distinct crystal habit, superior charge transport properties and better stability in air. We also fabricate X-ray detectors based on the CsPbBr3 crystals, and systematically characterize their device performance. The crystals grown in water demonstrate great potential for X-ray imaging with enhanced performance metrics.
Disrupting upstream translation in mRNAs is associated with human disease
Authors: Lee David S. M. , Park Joseph , Kromer Andrew , Baras Aris , Rader Daniel J. , Ritchie Marylyn D. , Ghanem Louis R. , Barash Yoseph 
Published: March 2021

AbstractRibosome-profiling has uncovered pervasive translation in non-canonical open reading frames, however the biological significance of this phenomenon remains unclear. Using genetic variation from 71,702 human genomes, we assess patterns of selection in translated upstream open reading frames (uORFs) in 5’UTRs. We show that uORF variants introducing new stop codons, or strengthening existing stop codons, are under strong negative selection comparable to protein-coding missense variants. Using these variants, we map and validate gene-disease associations in two independent biobanks containing exome sequencing from 10,900 and 32,268 individuals, respectively, and elucidate their impact on protein expression in human cells. Our results suggest translation disrupting mechanisms relating uORF variation to reduced protein expression, and demonstrate that translation at uORFs is genetically constrained in 50% of human genes.
Metabolic responses to mild cold acclimation in type 2 diabetes patients
Authors: Remie Carlijn M. E. , Moonen Michiel P. B. , Roumans Kay H. M. , Nascimento Emmani B. M. , Gemmink Anne , Havekes Bas , Schaart Gert , Kornips Esther , Joris Peter J. , Schrauwen-Hinderling Vera B. , Hoeks Joris , Kersten Sander , Hesselink Matthijs K. C. , Phielix Esther , Lichtenbelt Wouter D. van Marken , Schrauwen Patrick 
Published: March 2021

AbstractMild cold acclimation for 10 days has been previously shown to markedly improve insulin sensitivity in patients with type 2 diabetes. Here we show in a single-arm intervention study (Trialregister.nl ID: NL4469/NTR5711) in nine patients with type 2 diabetes that ten days of mild cold acclimation (16–17 °C) in which observable, overt shivering was prevented, does not result in improved insulin sensitivity, postprandial glucose and lipid metabolism or intrahepatic lipid content and only results in mild effects on overnight fasted fat oxidation, postprandial energy expenditure and aortic augmentation index. The lack of marked metabolic effects in this study is associated with a lack of self-reported shivering and a lack of upregulation of gene expression of muscle activation or muscle contraction pathways in skeletal muscle and suggests that some form of muscle contraction is needed for beneficial effects of mild cold acclimation.
Molecular structure retrieval directly from laboratory-frame photoelectron spectra in laser-induced electron diffraction
Authors: Sanchez A. , Amini K. , Wang S.-J. , Steinle T. , Belsa B. , Danek J. , Le A. T. , Liu X. , Moshammer R. , Pfeifer T. , Richter M. , Ullrich J. , Gräfe S. , Lin C. D. , Biegert J. 
Published: March 2021

AbstractUbiquitous to most molecular scattering methods is the challenge to retrieve bond distance and angle from the scattering signals since this requires convergence of pattern matching algorithms or fitting methods. This problem is typically exacerbated when imaging larger molecules or for dynamic systems with little a priori knowledge. Here, we employ laser-induced electron diffraction (LIED) which is a powerful means to determine the precise atomic configuration of an isolated gas-phase molecule with picometre spatial and attosecond temporal precision. We introduce a simple molecular retrieval method, which is based only on the identification of critical points in the oscillating molecular interference scattering signal that is extracted directly from the laboratory-frame photoelectron spectrum. The method is compared with a Fourier-based retrieval method, and we show that both methods correctly retrieve the asymmetrically stretched and bent field-dressed configuration of the asymmetric top molecule carbonyl sulfide (OCS), which is confirmed by our quantum-classical calculations.
Near-ideal van der Waals rectifiers based on all-two-dimensional Schottky junctions
Authors: Zhang Xiankun , Liu Baishan , Gao Li , Yu Huihui , Liu Xiaozhi , Du Junli , Xiao Jiankun , Liu Yihe , Gu Lin , Liao Qingliang , Kang Zhuo , Zhang Zheng , Zhang Yue 
Published: March 2021

AbstractThe applications of any two-dimensional (2D) semiconductor devices cannot bypass the control of metal-semiconductor interfaces, which can be severely affected by complex Fermi pinning effects and defect states. Here, we report a near-ideal rectifier in the all-2D Schottky junctions composed of the 2D metal 1 T′-MoTe2 and the semiconducting monolayer MoS2. We show that the van der Waals integration of the two 2D materials can efficiently address the severe Fermi pinning effect generated by conventional metals, leading to increased Schottky barrier height. Furthermore, by healing original atom-vacancies and reducing the intrinsic defect doping in MoS2, the Schottky barrier width can be effectively enlarged by 59%. The 1 T′-MoTe2/healed-MoS2 rectifier exhibits a near-unity ideality factor of ~1.6, a rectifying ratio of >5 × 105, and high external quantum efficiency exceeding 20%. Finally, we generalize the barrier optimization strategy to other Schottky junctions, defining an alternative solution to enhance the performance of 2D-material-based electronic devices.
Lasso-grafting of macrocyclic peptide pharmacophores yields multi-functional proteins
Authors: Mihara Emiko , Watanabe Satoshi , Bashiruddin Nasir K. , Nakamura Nozomi , Matoba Kyoko , Sano Yumi , Maini Rumit , Yin Yizhen , Sakai Katsuya , Arimori Takao , Matsumoto Kunio , Suga Hiroaki , Takagi Junichi 
Published: March 2021

AbstractProtein engineering has great potential for devising multifunctional recombinant proteins to serve as next-generation protein therapeutics, but it often requires drastic modifications of the parental protein scaffolds e.g., additional domains at the N/C-terminus or replacement of a domain by another. A discovery platform system, called RaPID (Random non-standard Peptides Integrated Discovery) system, has enabled rapid discovery of small de novo macrocyclic peptides that bind a target protein with high binding specificity and affinity. Capitalizing on the optimized binding properties of the RaPID-derived peptides, here we show that RaPID-derived pharmacophore sequences can be readily implanted into surface-exposed loops on recombinant proteins and maintain both the parental peptide binding function(s) and the host protein function. We refer to this protein engineering method as lasso-grafting and demonstrate that it can endow specific binding capacity toward various receptors into a diverse set of scaffolds that includes IgG, serum albumin, and even capsid proteins of adeno-associated virus, enabling us to rapidly formulate and produce bi-, tri-, and even tetra-specific binder molecules.
Datasets of seed mucilage traits for Arabidopsis thaliana natural accessions with atypical outer mucilage
Authors: Cambert Mireille , Berger Adeline , Sallé Christine , Esling Stéphanie , Charif Delphine , Cadoret Tudel , Ralet Marie-Christine , North Helen M. , Rondeau-Mouro Corinne 
Published: March 2021

AbstractThe seeds of Arabidopsis thaliana become encapsulated by a layer of mucilage when imbibed. This polysaccharide-rich hydrogel is constituted of two layers, an outer layer that can be easily extracted with water and an inner layer that must be examined in situ in order to study its properties and structure in a non-destructive manner or disintegrated through hydrolysis or physical means in order to analyze its constituents. Mucilage production is an adaptive trait and we have exploited 19 natural accessions previously found to have atypical and varied outer mucilage characteristics. A detailed study using biochemical, histological and Time-Domain NMR analyses has been used to generate three related datasets covering 33 traits measured in four biological replicates. This data will be a rich resource for genetic, biochemical, structural and functional analyses investigating mucilage constituent polysaccharides or their role as adaptive traits.
Exchange-bias and magnetic anisotropy fields in core–shell ferrite nanoparticles
Authors: Silva F. G. , Depeyrot J. , Raikher Yu. L. , Stepanov V. I. , Poperechny I. S. , Aquino R. , Ballon G. , Geshev J. , Dubois E. , Perzynski R. 
Published: March 2021

AbstractExchange bias properties of MnFe$$_2$$

2

O$$_4$$

4

@$$\gamma$$
γ
–Fe$$_2$$

2

O$$_3$$

3

core–shell nanoparticles are investigated. The measured field and temperature dependencies of the magnetization point out a well-ordered ferrimagnetic core surrounded by a layer with spin glass-like arrangement. Quasi-static SQUID magnetization measurements are presented along with high-amplitude pulse ones and are cross-analyzed by comparison against ferromagnetic resonance experiments at 9 GHz. These measurements allow one to discern three types of magnetic anisotropies affecting the dynamics of the magnetic moment of the well-ordered ferrimagnetic NP’s core viz. the easy-axis (uniaxial) anisotropy, the unidirectional exchange-bias anisotropy and the rotatable anisotropy. The uniaxial anisotropy originates from the structural core–shell interface. The unidirectional exchange-bias anisotropy is associated with the spin-coupling at the ferrimagnetic/spin glass-like interface; it is observable only at low temperatures after a field-cooling process. The rotatable anisotropy is caused by partially-pinned spins at the core/shell interface; it manifests itself as an intrinsic field always parallel to the external applied magnetic field. The whole set of experimental results is interpreted in the framework of superparamagnetic theory, i.e., essentially taking into account the effect of thermal fluctuations on the magnetic moment of the particle core. In particular, it is found that the rotatable anisotropy of our system is of a uniaxial type.
ROCK inhibitors enhance the production of large lipid-enriched 3D organoids of 3T3-L1 cells
Authors: Ida Yosuke , Hikage Fumihito , Ohguro Hiroshi 
Published: March 2021

AbstractSince the recent discovery of prostaglandin-associated peri-orbitopathy, a great deal of interest has developed concerning the side effects of anti-glaucoma medications toward periocular fatty tissue, especially their adipogenesis. Two- or three-dimension (2D or 3D) cultures of the 3T3-L1 cells were employed to elucidate the effects of the Rho-associated coiled-coil containing protein kinase inhibitor (ROCK-i) the anti-glaucoma drug, Ripasudil, and other ROCK-i, such as Y27632 on adipogenesis. Ultrastructure by electron microscopy and physical stiffness measurements by a micro-squeezer demonstrated the 3D organoids had essentially matured during the 7-day culture. The effects of ROCK-i on 3D organoid sizes, lipid staining, the mRNA expression of adipogenesis related genes, Pparγ, Cebpa and Leptin, and extracellular matrix (ECM) including collagen (COL) 1, 4 and 6, and fibronectin, and physical stiffness were then conducted. Upon adipogenesis, the sizes, lipid staining and mRNA expressions of adipogenesis related genes, Col 4 and Col 6 were dramatically increased, and were further enhanced by ROCK-i. Micro-squeezer analysis demonstrated that adipogenesis resulted in a marked less stiffed 3D organoid and this was further enhanced by ROCK-i. Our present study indicates that ROCK-i significantly enhanced the production of large lipid-enriched 3T3-L1 3D organoids.
Effects of work organization on the occurrence and resolution of sleep disturbances among night shift workers: a longitudinal observational study
Authors: Lee Seungho , Park Jae Bum , Lee Kyung-Jong , Ham Seunghon , Jeong Inchul 
Published: March 2021

AbstractThis study aimed to investigate the association between work organization and the trajectories of insomnia patterns among night shift workers in a hospital. The health examination data of hospital workers, recorded from January 2014 to December 2018, were collected; 6765 records of 2615 night shift workers were included. Insomnia was defined as a score of ≥ 15 on the Insomnia Severity Index (ISI). Participants were categorized into five groups according to insomnia patterns derived from the analysis of their ISI scores. Work organization and socio-demographic characteristics were also investigated. Generalized estimating equation models and linear mixed models were constructed to analyze the longitudinal data. Of the total participants, 53.0% reported insomnia at least once during the follow-up period. The lack of nap opportunities and work-time control was associated with the occurrence of insomnia, whereas more than 5 years of shift work experience was related to the resolution of insomnia. All work-related factors were significantly related to insomnia risk; however, the effects were not significant in the sustained insomnia group. Although sleep problems are inevitable in night shift workers, well-designed work schedules and better work organization can help reduce the occurrence of insomnia among them.