bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subglacial Discharge and Its Down‐Fjord Transformation in West Greenland Fjords With an Ice Mélange
Authors: Mortensen John , Rysgaard Søren , Bendtsen Jørgen , Lennert Kunuk , Kanzow Torsten , Lund Henrik , Meire Lorenz 
Published: August 2020

AbstractBuoyant freshwater released at depth from under Greenland's marine‐terminating glaciers gives rise to vigorous buoyant discharge plumes adjacent to the termini. The water mass found down fjord formed by mixing of buoyant subglacial freshwater and ambient fjord water and subsequent modification by glacial ice melt in the ice mélange is referred to as subglacial water. It substantially affects both the physical and chemical properties of the fjords' marine environment. Despite the importance of this freshwater source, many uncertainties remain regarding its transformation and detection. Here we present observations close to a marine‐terminating glacier in a fjord with substantial ice mélange and follow the down‐fjord changes of the subglacial discharge plume. Heat brought to the surface by entrainment of warm ambient fjord water into the rising plume causes intense melting of the ice mélange close to the plume pool. This results in an increase of glacial ice melt fraction to total glacial meltwater from 1–2% in the plume pool to ~18% eleven kilometers down‐fjord, with the largest increase being observed within the first few kilometers. Down‐fjord of the ice mélange two temperature minima bound the layer containing subglacial water. The upper bound is linked to the adjacent ice mélange and down‐fjord runoff sources, whereas the lower bound is linked to the stratification of the ambient water. We show that similar bounds can be observed in other marine‐terminating glacier fjords along West Greenland that contain an ice mélange, suggesting that similar processes work in other fjords.
A New Approach for Estimating Salinity in the Southwest Atlantic and Its Application in a Data Assimilation Evaluation Experiment
Authors: Dorfschäfer G. S. , Tanajura C. A. S. , Costa F. B. , Santana R. C. 
Published: August 2020

AbstractA new method for generating synthetic salinity (SS) profiles in the Southwest Atlantic was developed and applied in data assimilation experiments. This method was based on the smallest integrated values of root mean square deviation (RMSD)—with respect to observations—to infer salinity through climatological data and by regressive methods on temperature (T) using a five‐order polynomial function (P5). In the 14 delimited subregions, the averaged RMSD of P5 was 45% smaller than interpolated climatological data. However, climatological salinity presented better results in the first top layers while P5 presented smaller errors in higher depths. Therefore, by joining the best that P5 and climatology may offer, a new hybrid approach was used to generate SS based on T from XBT profiles. The SS would allow more T profiles to be employed in the Oceanographic Modeling and Observation Network (REMO) data assimilation system, called RODAS, into the Hybrid Coordinate Ocean Model (HYCOM). The use of SS estimates has potential to improve model outputs, in which the presence of the T‐S pair is quite necessary. Three integrations were performed: one run without assimilation (FREE), one assimilating sea surface temperature, Argo profilers, and sea level anomaly (RODAS) and one similar to RODAS, but with added XBTs with SS (RODAS_XBT). The inclusion of XBT data in the HYCOM + RODAS system improved the position and magnitude of the Brazil Current (BC). It was shown that SS is feasible for producing ocean reanalysis and initial conditions for ocean forecast systems requiring very low computational cost.
Temporal and Vertical Oxygen Gradients Modulate Nitrous Oxide Production in a Seasonally Anoxic Fjord: Saanich Inlet, British Columbia
Authors: Ji Qixing , Jameson Brett D. , Juniper S. Kim , Grundle Damian S. 
Published: August 2020

AbstractNitrous oxide (N2O) is a strong greenhouse gas and an ozone depleting agent. In marine environments, N2O is produced biologically via ammonium oxidation, nitrite, and nitrate reduction. The relative importance of these principle production pathways is strongly influenced by oxygen availability. We conducted 15N tracer experiments of N2O production in parallel with measurements of N2O concentration and natural abundance isotopes/isotopomers in Saanich Inlet, a seasonally anoxic fjord, to investigate how temporal and vertical oxygen gradients regulate N2O production pathways and rates. In April, June, and August 2018, the depth of the oxic‐anoxic interface (dissolved oxygen = 2.5 μmol L−1 isoline) progressively deepened from 110 to 160 m. Within the oxygenated and suboxic water column, N2O supersaturation coincided with peak ammonium oxidation activity. Conditions in the anoxic deep water were potentially favorable to N2O production from nitrate and nitrite reduction, but N2O undersaturation was observed indicating that N2O consumption exceeded rates of production. In October, tidal mixing introduced oxygenated water from outside the inlet, displacing the suboxic and anoxic deep water. This oxygenation event stimulated N2O production from ammonium oxidation and increased water column N2O supersaturation while inhibiting nitrate and nitrite reduction to N2O. Results from 15N tracer incubation experiments and natural abundance isotopomer measurements both implicated ammonium oxidation as the dominant N2O production pathway in Saanich Inlet, fueled by high ammonium fluxes (0.6–3.5 nmol m−2 s−1) from the anoxic depths. Partial denitrification contributed little to water column N2O production because of low availability of nitrate and nitrite.
Paleogeothermal Gradients Across an Inverted Hyperextended Rift System: Example of the Mauléon Fossil Rift (Western Pyrenees)
Authors: Saspiturry N. , Lahfid A. , Baudin T. , Guillou‐Frottier L. , Razin P. , Issautier B. , Le Bayon B. , Serrano O. , Lagabrielle Y. , Corre B. 
Published: August 2020

AbstractThe fossil rift in the North Pyrenean Zone, which underwent high temperature‐low pressure metamorphism and alkaline magmatism during Early Cretaceous hyperextension, was studied to explore the geothermal regime at the time of rifting. In this work, we combined Raman lab analysis and thermal numerical modelling to shed light on the distribution of geothermal gradients across the inverted hyperextended Mauléon rift basin during Albian and Cenomanian time, its period of active extension. Data were acquired from a set of 155 samples from densely spaced outcrops and boreholes, analyzed using Raman spectroscopy of carbonaceous material. The estimated paleogeothermal gradient is strongly related to the structural position along the Albian‐Cenomanian rift, increasing along a proximal‐distal margin transect from ~34°C/km in the European proximal margin to ~37–47°C/km in the two necking zones and 57–60°C/km in the hyperextended domain. This pattern of the paleogeothermal gradient induced a complex interaction between brittle and ductile deformation during crustal extension. A numerical model reproducing the thermal evolution of the North Pyrenees since 120 Ma suggests that mantle heat flow values may have reached 100 mW/m2 during the rifting event. This model reveals that above the thermal pulse, the temperature gradient varied within a small range of 55 to 62°C/km, as inferred from RSCM peak temperatures. We demonstrate that the style of reactivation during subsequent convergence influenced the thermal structure of the inverted rift system.
A Numerical Study of Slug Tests in a Three‐Dimensional Heterogeneous Porous Aquifer Considering Well Inertial Effects
Authors: Liu Quan , Hu Linwei , Bayer Peter , Xing Yixuan , Qiu Pengxiang , Ptak Thomas , Hu Rui 
Published: August 2020

AbstractThe slug test is a common field technique for obtaining local hydraulic parameters near wells, applied, for example, for the hydrogeological investigation at contaminated sites. Although many slug test models have been developed for interpretation of measurements, only a few of them have considered heterogeneous conditions, and water column inertial effects are usually neglected. In this paper, we propose a novel three‐dimensional slug test model (3DHIM) for application in heterogeneous aquifers, considering inertial effects associated with skin effects and linear friction forces. After comparison with existing analytical and numerical solutions of slug tests, the model is applied to an aquifer analog to simulate a series of slug tests. The results from single‐well slug tests show that the well geometry (i.e., the well radius, well depth, and screen length) has an impact on the water level response. For cross‐well slug tests, the results indicate that the water level fluctuations not only include information on the hydraulic signal propagation process in the aquifer but also on well characteristics, such as wellbore storage and inertial effects. These effects cause a phase shift and amplitude change of the water level fluctuation. As the observation and test wells have a good hydraulic connection and similar well geometry, the water level amplitude could be amplified relative to aquifer pressure at the measured position. Therefore, we suggest considering wellbore storage and in‐well inertial effects in slug test‐based subsurface investigations, otherwise the parameter estimates based on well water levels may include errors, particularly in highly permeable layers.
Global transcriptional downregulation of TREX and nuclear trafficking machinery as pan-senescence phenomena: evidence from human cells and tissues
Authors: Kim Sung Young , Yang Eun Jae , Lee Sung Bae , Lee Young-Sam , Cho Kyoung A. , Park Sang Chul 
Published: August 2020

AbstractNucleocytoplasmic trafficking (NCT) of macromolecules is a fundamental process in eukaryotes that requires tight controls to maintain proper cell functions. Downregulation of the classical NCT pathway in senescent cells has been reported. However, whether this is a hallmark that exists across all types of cellular senescence remains unknown, and whether the mRNA export machinery is altered during senescence has not been demonstrated. Here, we show that the global transcriptomic downregulation of both the TREX (transcription-export) machinery and classical NLS-dependent protein transport machinery is a hallmark of varying types of senescence. A gene set-based approach using 25 different studies showed that the TREX-NCT gene set displays distinct common downregulated patterns in senescent cells versus its expression in their nonsenescent counterparts regardless of the senescence type, such as replicative senescence (RS), tumor cell senescence (TCS), oncogene-induced senescence (OIS), stem cell senescence (SCS), progeria and endothelial cell senescence (ECS). Similar patterns of TREX-NCT gene downregulation were also shown in two large human tissue genomic databases, the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) databases. We also found that early-stage cancer tissues show consistent age-related patterns of TREX-NCT enrichment, suggesting the potential significance of TREX-NCT genes in determining cell fate in the early stage of tumorigenesis. Moreover, human cancer tissues exhibit an opposite TREX-NCT enrichment pattern with aging, indicating that deviation from age-related changes in TREX-NCT genes may provide a novel but critical clue for the age-dependent pathogenesis of cancer and increase in cancer incidence with aging.
Evaluation-oriented exploration of photo energy conversion systems: from fundamental optoelectronics and material screening to the combination with data science
Authors: Saeki Akinori 
Published: August 2020

AbstractLight is a form of energy that can be converted to electric and chemical energies. Thus, organic photovoltaics (OPVs), perovskite solar cells (PSCs), photocatalysts, and photodetectors have evolved as scientific and commercial enterprises. However, the complex photochemical reactions and multicomponent materials involved in these systems have hampered rapid progress in their fundamental understanding and material design. This review showcases the evaluation-oriented exploration of photo energy conversion materials by using electrodeless time-resolved microwave conductivity (TRMC) and materials informatics (MI). TRMC with its unique options (excitation sources, environmental control, frequency modulation, etc.) provides not only accelerated experimental screening of OPV and PSC materials but also a versatile route toward shedding light on their charge carrier dynamics. Furthermore, MI powered by machine learning is shown to allow extremely high-throughput exploration in the large molecular space, which is compatible with experimental screening and combinatorial synthesis.
Cell-surface receptors enable perception of extracellular cytokinins
Authors: Antoniadi Ioanna , Novák Ondřej , Gelová Zuzana , Johnson Alexander , Plíhal Ondřej , Simerský Radim , Mik Václav , Vain Thomas , Mateo-Bonmatí Eduardo , Karady Michal , Pernisová Markéta , Plačková Lenka , Opassathian Korawit , Hejátko Jan , Robert Stéphanie , Friml Jiří , Doležal Karel , Ljung Karin , Turnbull Colin 
Published: August 2020

AbstractCytokinins are mobile multifunctional plant hormones with roles in development and stress resilience. Although their Histidine Kinase receptors are substantially localised to the endoplasmic reticulum, cellular sites of cytokinin perception and importance of spatially heterogeneous cytokinin distribution continue to be debated. Here we show that cytokinin perception by plasma membrane receptors is an effective additional path for cytokinin response. Readout from a Two Component Signalling cytokinin-specific reporter (TCSn::GFP) closely matches intracellular cytokinin content in roots, yet we also find cytokinins in extracellular fluid, potentially enabling action at the cell surface. Cytokinins covalently linked to beads that could not pass the plasma membrane increased expression of both TCSn::GFP and Cytokinin Response Factors. Super-resolution microscopy of GFP-labelled receptors and diminished TCSn::GFP response to immobilised cytokinins in cytokinin receptor mutants, further indicate that receptors can function at the cell surface. We argue that dual intracellular and surface locations may augment flexibility of cytokinin responses.
Excess-entropy scaling in supercooled binary mixtures
Authors: Bell Ian H. , Dyre Jeppe C. , Ingebrigtsen Trond S. 
Published: August 2020

AbstractTransport coefficients, such as viscosity or diffusion coefficient, show significant dependence on density or temperature near the glass transition. Although several theories have been proposed for explaining this dynamical slowdown, the origin remains to date elusive. We apply here an excess-entropy scaling strategy using molecular dynamics computer simulations and find a quasiuniversal, almost composition-independent, relation for binary mixtures, extending eight orders of magnitude in viscosity or diffusion coefficient. Metallic alloys are also well captured by this relation. The excess-entropy scaling predicts a quasiuniversal breakdown of the Stokes-Einstein relation between viscosity and diffusion coefficient in the supercooled regime. Additionally, we find evidence that quasiuniversality extends beyond binary mixtures, and that the origin is difficult to explain using existing arguments for single-component quasiuniversality.
High-performance p-channel transistors with transparent Zn doped-CuI
Authors: Liu Ao , Zhu Huihui , Park Won-Tae , Kim Se-Jun , Kim Hyungjun , Kim Myung-Gil , Noh Yong-Young 
Published: August 2020

Abstract‘Ideal’ transparent p-type semiconductors are required for the integration of high-performance thin-film transistors (TFTs) and circuits. Although CuI has recently attracted attention owing to its excellent opto-electrical properties, solution processability, and low-temperature synthesis, the uncontrolled copper vacancy generation and subsequent excessive hole doping hinder its use as a semiconductor material in TFT devices. In this study, we propose a doping approach through soft chemical solution process and transparent p-type Zn-doped CuI semiconductor for high-performance TFTs and circuits. The optimised TFTs annealed at 80 °C exhibit a high hole mobility of over 5 cm2 V−1 s−1 and high on/off current ratio of ~107 with good operational stability and reproducibility. The CuI:Zn semiconductors show intrinsic advantages for next-generation TFT applications and wider applications in optoelectronics and energy conversion/storage devices. This study paves the way for the realisation of transparent, flexible, and large-area integrated circuits combined with n-type metal-oxide semiconductor.
Multi-site clonality analysis uncovers pervasive heterogeneity across melanoma metastases
Authors: Rabbie Roy , Ansari-Pour Naser , Cast Oliver , Lau Doreen , Scott Francis , Welsh Sarah J. , Parkinson Christine , Khoja Leila , Moore Luiza , Tullett Mark , Wong Kim , Ferreira Ingrid , Gómez Julia M. Martínez , Levesque Mitchell , Gallagher Ferdia A. , Jiménez-Sánchez Alejandro , Riva Laura , Miller Martin L. , Allinson Kieren , Campbell Peter J. , Corrie Pippa , Wedge David C. , Adams David J. 
Published: August 2020

AbstractMetastatic melanoma carries a poor prognosis despite modern systemic therapies. Understanding the evolution of the disease could help inform patient management. Through whole-genome sequencing of 13 melanoma metastases sampled at autopsy from a treatment naïve patient and by leveraging the analytical power of multi-sample analyses, we reveal evidence of diversification among metastatic lineages. UV-induced mutations dominate the trunk, whereas APOBEC-associated mutations are found in the branches of the evolutionary tree. Multi-sample analyses from a further seven patients confirmed that lineage diversification was pervasive, representing an important mode of melanoma dissemination. Our analyses demonstrate that joint analysis of cancer cell fraction estimates across multiple metastases can uncover previously unrecognised levels of tumour heterogeneity and highlight the limitations of inferring heterogeneity from a single biopsy.
Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication
Authors: Vuong Wayne , Khan Muhammad Bashir , Fischer Conrad , Arutyunova Elena , Lamer Tess , Shields Justin , Saffran Holly A. , McKay Ryan T. , van Belkum Marco J. , Joyce Michael A. , Young Howard S. , Tyrrell D. Lorne , Vederas John C. , Lemieux M. Joanne 
Published: August 2020

AbstractThe main protease, Mpro(or 3CLpro) in SARS-CoV-2 is a viable drug target because of its essential role in the cleavage of the virus polypeptide. Feline infectious peritonitis, a fatal coronavirus infection in cats, was successfully treated previously with a prodrug GC376, a dipeptide-based protease inhibitor. Here, we show the prodrug and its parent GC373, are effective inhibitors of the Mprofrom both SARS-CoV and SARS-CoV-2 with IC50values in the nanomolar range. Crystal structures of SARS-CoV-2 Mprowith these inhibitors have a covalent modification of the nucleophilic Cys145. NMR analysis reveals that inhibition proceeds via reversible formation of a hemithioacetal. GC373 and GC376 are potent inhibitors of SARS-CoV-2 replication in cell culture. They are strong drug candidates for the treatment of human coronavirus infections because they have already been successful in animals. The work here lays the framework for their use in human trials for the treatment of COVID-19.
Copper(I)-catalyzed diastereo- and enantio-selective construction of optically pure exocyclic allenes
Authors: He Cheng-Yu , Tan Yun-Xuan , Wang Xin , Ding Rui , Wang Yi-Fan , Wang Feng , Gao Dingding , Tian Ping , Lin Guo-Qiang 
Published: August 2020

AbstractAmong about 150 identified allenic natural products, the exocyclic allenes constitute a major subclass. Substantial efforts are devoted to the construction of axially chiral allenes, however, the strategies to prepare chiral exocyclic allenes are still rare. Herein, we show an efficient strategy for the asymmetric synthesis of chiral exocyclic allenes with the simultaneous control of axial and central chirality through copper(I)-catalyzed asymmetric intramolecular reductive coupling of 1,3-enynes to cyclohexadienones. This tandem reaction exhibits good functional group compatibility and the corresponding optically pure exocyclic allenes bearing cis-hydrobenzofuran, cis-hydroindole, and cis-hydroindene frameworks, are obtained with high yields (up to 99% yield), excellent diastereoselectivities (generally >20:1 dr) and enantioselectivities (mostly >99% ee). Furthermore, a gram-scale experiment and several synthetic transformations of the chiral exocyclic allenes are also presented.
Single-molecule photoreaction quantitation through intraparticle-surface energy transfer (i-SET) spectroscopy
Authors: Zhou Jian , Li Changyu , Li Denghao , Liu Xiaofeng , Mu Zhao , Gao Weibo , Qiu Jianrong , Deng Renren 
Published: August 2020

AbstractQuantification of nanoparticle-molecule interaction at a single-molecule level remains a daunting challenge, mainly due to ultra-weak emission from single molecules and the perturbation of the local environment. Here we report the rational design of an intraparticle-surface energy transfer (i-SET) process, analogous to high doping concentration-induced surface quenching effects, to realize single-molecule sensing by nanoparticle probes. This design, based on a Tb3+-activator-rich core-shell upconversion nanoparticle, enables a much-improved spectral response to fluorescent molecules at single-molecule levels through enhanced non-radiative energy transfer with a rate over an order of magnitude faster than conventional counterparts. We demonstrate a quantitative analysis of spectral changes of one to four fluorophores tethered on a single nanoparticle through i-SET spectroscopy. Our results provide opportunities to identify photoreaction kinetics at single-molecule levels and provide direct information for understanding behaviors of individual molecules with unprecedented sensitivity.
Complete reversal of the atomic unquenched orbital moment by a single electron
Authors: Rejali Rasa , Coffey David , Gobeil Jeremie , González Jhon W. , Delgado Fernando , Otte Alexander F. 
Published: August 2020

AbstractThe orbital angular moment of magnetic atoms adsorbed on surfaces is often quenched as a result of an anisotropic crystal field. Due to spin-orbit coupling, what remains of the orbital moment typically delineates the orientation of the electron spin. These two effects limit the scope of information processing based on these atoms to essentially only one magnetic degree of freedom: the spin. In this work, we gain independent access to both the spin and orbital degrees of freedom of a single atom, inciting and probing excitations of each moment. By coordinating a single Fe atom atop the nitrogen site of the Cu2N lattice, we realize a single-atom system with a large zero-field splitting—the largest reported for Fe atoms on surfaces—and an unquenched uniaxial orbital moment that closely approaches the free-atom value. We demonstrate a full reversal of the orbital moment through a single-electron tunneling event between the tip and Fe atom, a process that is mediated by a charged virtual state and leaves the spin unchanged. These results, which we corroborate using density functional theory and first-principles multiplet calculations, demonstrate independent control over the spin and orbital degrees of freedom in a single-atom system.