bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in Sedimentary Phosphorus Burial Following Artificial Eutrophication of Lake 227, Experimental Lakes Area, Ontario, Canada
Authors: O'Connell D. W. , Ansems N. , Kukkadapu R. K. , Jaisi D. , Orihel D. M. , Cade‐Menun B. J. , Hu Y. , Wiklund J. , Hall R. I. , Chessell H. , Behrends T. , Van Cappellen P. 
Published: June 2020

AbstractLake 227 of the Experimental Lakes Area (ELA) in Ontario, Canada, has been fertilized with phosphorus (P) since 1969, which resulted in a rapid transition from oligotrophic to eutrophic conditions. Sediment cores collected from the oxygenated epilimnion, and the mostly anoxic hypolimnion of this unique lake contain a historical record of the changes in sediment P speciation and burial rates across the trophic transition. To elucidate these changes, results of chemical extractions were combined with 210Pb sediment dating, and with 31P NMR, Mössbauer, and XANES spectroscopies. Prior to 1969, organic P (POrg) was the major sedimentary P sink in Lake 227. Eutrophication of the lake coincided with marked increases in the burial rate of total P (TP), as well as in the relative contribution of the NaHCO3‐extractable P pool (humic‐bound P, PHum). Together, PHum and POrg account for ≥70% of total P burial in the sediments deposited since artificial fertilization started. The PHum fraction likely comprises phosphate complexes with humic substances. The strong linear correlation between P and iron (Fe) extracted by NaHCO3 implies a close association of the two elements in the humic fraction. Mössbauer and XANES spectra further indicate that most Fe in the post‐1969 sediments remained in the Fe (III) oxidation state, which is attributed to the stabilization of reducible Fe by organic matter, in part via the formation of phosphate‐Fe (III)‐humic complexes. Importantly, our results show that the eutrophication experimentation of Lake 227 caused the accumulation of a large reservoir of reactive sediment P, which may continue to fuel internal P loading to the water column once artificial fertilization is terminated.
Ice Particle Properties Inferred From Aggregation Modelling
Authors: Karrer M. , Seifert A. , Siewert C. , Ori D. , von Lerber A. , Kneifel S. 
Published: June 2020

AbstractWe generated a large number 105,000 of aggregates composed of various monomer types and sizes using an aggregation model. Combined with hydrodynamic theory, we derived ice particle properties such as mass, projected area, and terminal velocity as a function of monomer number and size. This particle ensemble allows us to study the relation of particle properties with a high level of detail which is often not provided by in situ measurements. The ice particle properties change rather smoothly with monomer number. We find very little differences in all particle properties between monomers and aggregates at sizes below 1 mm which is in contrast to many microphysics schemes. The impact of the monomer type on the particle properties decreases with increasing monomer number. Whether, for example, the terminal velocity of an aggregate is larger or smaller than an equal‐size monomer depends mostly on the monomer type. We fitted commonly used power laws as well as Atlas‐type relations, which represent the saturation of the terminal velocity at large sizes (terminal velocity asymptotically approaching a limiting value) to the data set and tested the impact of incorporating different levels of complexity with idealized simulations using a 1D Lagrangian super particle model. These simulations indicate that it is sufficient to represent the monomer number dependency of ice particle properties with only two categories (monomers and aggregates). The incorporation of the saturation velocity at larger sizes is found to be important to avoid an overestimation of self‐aggregation of larger snowflakes.
Quantifying the Effect of the Drake Passage Opening on the Eocene Ocean
Authors: Toumoulin A. , Donnadieu Y. , Ladant J.‐B. , Batenburg S. J. , Poblete F. , Dupont‐Nivet G. 
Published: June 2020

AbstractThe opening of the Drake Passage (DP) during the Cenozoic is a tectonic event of paramount importance for the development of modern ocean characteristics. Notably, it has been suggested that it exerts a primary role in the onset of the Antarctic Circumpolar Current (ACC) formation, in the cooling of high‐latitude South Atlantic waters and in the initiation of North Atlantic Deep Water (NADW) formation. Several model studies have aimed to assess the impacts of DP opening on climate, but most of them focused on surface climate, and only few used realistic Eocene boundary conditions. Here, we revisit the impact of the DP opening on ocean circulation with the IPSL‐CM5A2 Earth System Model. Using appropriate middle Eocene (40 Ma) boundary conditions, we perform and analyze simulations with different depths of the DP (0, 100, 1,000, and 2,500 m) and compare results to existing geochemical data. Our experiments show that DP opening has a strong effect on Eocene ocean structure and dynamics even for shallow depths. The DP opening notably allows the formation of a proto‐ACC and induces deep ocean cooling of 1.5°C to 2.5°C in most of the Southern Hemisphere. There is no NADW formation in our simulations regardless of the depth of the DP, suggesting that the DP on its own is not a primary control of deepwater formation in the North Atlantic. This study elucidates how and to what extent the opening of the DP contributed to the establishment of the modern global thermohaline circulation.
Mixed-state electron ptychography enables sub-angstrom resolution imaging with picometer precision at low dose
Authors: Chen Zhen , Odstrcil Michal , Jiang Yi , Han Yimo , Chiu Ming-Hui , Li Lain-Jong , Muller David A. 
Published: June 2020

AbstractBoth high resolution and high precision are required to quantitatively determine the atomic structure of complex nanostructured materials. However, for conventional imaging methods in scanning transmission electron microscopy (STEM), atomic resolution with picometer precision cannot usually be achieved for weakly-scattering samples or radiation-sensitive materials, such as 2D materials. Here, we demonstrate low-dose, sub-angstrom resolution imaging with picometer precision using mixed-state electron ptychography. We show that correctly accounting for the partial coherence of the electron beam is a prerequisite for high-quality structural reconstructions due to the intrinsic partial coherence of the electron beam. The mixed-state reconstruction gains importance especially when simultaneously pursuing high resolution, high precision and large field-of-view imaging. Compared with conventional atomic-resolution STEM imaging techniques, the mixed-state ptychographic approach simultaneously provides a four-times-faster acquisition, with double the information limit at the same dose, or up to a fifty-fold reduction in dose at the same resolution.
TECPR1 promotes aggrephagy by direct recruitment of LC3C autophagosomes to lysosomes
Authors: Wetzel Lisa , Blanchard Stéphane , Rama Sowmya , Beier Viola , Kaufmann Anna , Wollert Thomas 
Published: June 2020

AbstractThe accumulation of protein aggregates is involved in the onset of many neurodegenerative diseases. Aggrephagy is a selective type of autophagy that counteracts neurodegeneration by degrading such aggregates. In this study, we found that LC3C cooperates with lysosomal TECPR1 to promote the degradation of disease-related protein aggregates in neural stem cells. The N-terminal WD-repeat domain of TECPR1 selectively binds LC3C which decorates matured autophagosomes. The interaction of LC3C and TECPR1 promotes the recruitment of autophagosomes to lysosomes for degradation. Augmented expression of TECPR1 in neural stem cells reduces the number of protein aggregates by promoting their autophagic clearance, whereas knockdown of LC3C inhibits aggrephagy. The PH domain of TECPR1 selectively interacts with PtdIns(4)P to target TECPR1 to PtdIns(4)P containing lysosomes. Exchanging the PH against a tandem-FYVE domain targets TECPR1 ectopically to endosomes. This leads to an accumulation of LC3C autophagosomes at endosomes and prevents their delivery to lysosomes.
Sub-nanowatt resolution direct calorimetry for probing real-time metabolic activity of individual C. elegans worms
Authors: Hur Sunghoon , Mittapally Rohith , Yadlapalli Swathi , Reddy Pramod , Meyhofer Edgar 
Published: June 2020

AbstractCalorimetry has been widely used in metabolic studies, but direct measurements from individual small biological model organisms such as C. elegans or isolated single cells have been limited by poor sensitivity of existing techniques and difficulties in resolving very small heat outputs. Here, by careful thermal engineering, we developed a robust, highly sensitive and bio-compatible calorimetric platform that features a resolution of ~270 pW—more than a 500-fold improvement over the most sensitive calorimeter previously used for measuring the metabolic heat output of C. elegans. Using this calorimeter, we demonstrate time-resolved metabolic measurements of single C. elegans worms from larval to adult stages. Further, we show that the metabolic output is significantly lower in long-lived C. elegans daf-2 mutants. These demonstrations clearly highlight the broad potential of this tool for studying the role of metabolism in disease, development and aging of small model organisms and single cells.
Targeted inhibition of activated protein C by a non-active-site inhibitory antibody to treat hemophilia
Authors: Zhao Xiao-Yan , Wilmen Andreas , Wang Dongli , Wang Xinquan , Bauzon Maxine , Kim Ji-Yun , Linden Lars , Li Liang , Egner Ursula , Marquardt Tobias , Moosmayer Dieter , Tebbe Jan , Glück Julian Marius , Ellinger Philipp , McLean Kirk , Yuan Shujun , Yegneswaran Subramanian , Jiang Xiaoqiao , Evans Vince , Gu Jian-Ming , Schneider Doug , Zhu Ying , Xu Yifan , Mallari Cornell , Hesslein Ashley , Wang Yan , Schmidt Nicole , Gutberlet Katrin , Ruehl-Fehlert Christine , Freyberger Alexius , Hermiston Terry , Patel Chandra , Sim Derek , Mosnier Laurent O. , Laux Volker 
Published: June 2020

AbstractActivated protein C (APC) is a plasma serine protease with antithrombotic and cytoprotective functions. Based on the hypothesis that specific inhibition of APC’s anticoagulant but not its cytoprotective activity can be beneficial for hemophilia therapy, 2 types of inhibitory monoclonal antibodies (mAbs) are tested: A type I active-site binding mAb and a type II mAb binding to an exosite on APC (required for anticoagulant activity) as shown by X-ray crystallography. Both mAbs increase thrombin generation and promote plasma clotting. Type I blocks all APC activities, whereas type II preserves APC’s cytoprotective function. In normal monkeys, type I causes many adverse effects including animal death. In contrast, type II is well-tolerated in normal monkeys and shows both acute and prophylactic dose-dependent efficacy in hemophilic monkeys. Our data show that the type II mAb can specifically inhibit APC’s anticoagulant function without compromising its cytoprotective function and offers superior therapeutic opportunities for hemophilia.
Structural basis for divergent C–H hydroxylation selectivity in two Rieske oxygenases
Authors: Lukowski April L. , Liu Jianxin , Bridwell-Rabb Jennifer , Narayan Alison R. H. 
Published: June 2020

AbstractBiocatalysts that perform C–H hydroxylation exhibit exceptional substrate specificity and site-selectivity, often through the use of high valent oxidants to activate these inert bonds. Rieske oxygenases are examples of enzymes with the ability to perform precise mono- or dioxygenation reactions on a variety of substrates. Understanding the structural features of Rieske oxygenases responsible for control over selectivity is essential to enable the development of this class of enzymes for biocatalytic applications. Decades of research has illuminated the critical features common to Rieske oxygenases, however, structural information for enzymes that functionalize diverse scaffolds is limited. Here, we report the structures of two Rieske monooxygenases involved in the biosynthesis of paralytic shellfish toxins (PSTs), SxtT and GxtA, adding to the short list of structurally characterized Rieske oxygenases. Based on these structures, substrate-bound structures, and mutagenesis experiments, we implicate specific residues in substrate positioning and the divergent reaction selectivity observed in these two enzymes.
Coupling of melanocyte signaling and mechanics by caveolae is required for human skin pigmentation
Authors: Domingues Lia , Hurbain Ilse , Gilles-Marsens Floriane , Sirés-Campos Julia , André Nathalie , Dewulf Melissa , Romao Maryse , Viaris de Lesegno Christine , Macé Anne-Sophie , Blouin Cédric , Guéré Christelle , Vié Katell , Raposo Graça , Lamaze Christophe , Delevoye Cédric 
Published: June 2020

AbstractTissue homeostasis requires regulation of cell–cell communication, which relies on signaling molecules and cell contacts. In skin epidermis, keratinocytes secrete factors transduced by melanocytes into signaling cues promoting their pigmentation and dendrite outgrowth, while melanocytes transfer melanin pigments to keratinocytes to convey skin photoprotection. How epidermal cells integrate these functions remains poorly characterized. Here, we show that caveolae are asymmetrically distributed in melanocytes and particularly abundant at the melanocyte–keratinocyte interface in epidermis. Caveolae in melanocytes are modulated by ultraviolet radiations and keratinocytes-released factors, like miRNAs. Preventing caveolae formation in melanocytes increases melanin pigment synthesis through upregulation of cAMP signaling and decreases cell protrusions, cell–cell contacts, pigment transfer and epidermis pigmentation. Altogether, we identify that caveolae serve as molecular hubs that couple signaling outputs from keratinocytes to mechanical plasticity of pigment cells. The coordination of intercellular communication and contacts by caveolae is thus crucial to skin pigmentation and tissue homeostasis.
Transient lensing from a photoemitted electron gas imaged by ultrafast electron microscopy
Authors: Zandi Omid , Sykes Allan E. , Cornelius Ryan D. , Alcorn Francis M. , Zerbe Brandon S. , Duxbury Phillip M. , Reed Bryan W. , van der Veen Renske M. 
Published: June 2020

AbstractUnderstanding and controlling ultrafast charge carrier dynamics is of fundamental importance in diverse fields of (quantum) science and technology. Here, we create a three-dimensional hot electron gas through two-photon photoemission from a copper surface in vacuum. We employ an ultrafast electron microscope to record movies of the subsequent electron dynamics on the picosecond-nanosecond time scale. After a prompt Coulomb explosion, the subsequent dynamics is characterized by a rapid oblate-to-prolate shape transformation of the electron gas, and periodic and long-lived electron cyclotron oscillations inside the magnetic field of the objective lens. In this regime, the collective behavior of the oscillating electrons causes a transient, mean-field lensing effect and pronounced distortions in the images. We derive an analytical expression for the time-dependent focal length of the electron-gas lens, and perform numerical electron dynamics and probe image simulations to determine the role of Coulomb self-fields and image charges. This work inspires the visualization of cyclotron dynamics inside two-dimensional electron-gas materials and enables the elucidation of electron/plasma dynamics and properties that could benefit the development of high-brightness electron and X-ray sources.
Anomalous electrical magnetochiral effect by chiral spin-cluster scattering
Authors: Ishizuka Hiroaki , Nagaosa Naoto 
Published: June 2020

AbstractThe non-collinear spin configurations give rise to many nontrivial phenomena related to the Berry phase. They are often related to the vector and scalar spin chiralities. The scalar spin chirality leads to the topological Hall effect in metals, while the vector spin chirality to the ferroelectricity of spin origin, i.e., multiferroics in insulators. However, the role of the vector spin chirality in conducting systems has not yet been elucidated. Here we show theoretically that the spin correlation with vector spin chirality in chiral magnets scatters electrons asymmetrically, resulting in nonreciprocal transport phenomena, i.e., electrical magnetochiral effect (eMCE). This asymmetric scattering appears in the leading-order scattering term, implying a large nonreciprocity in the charge and spin currents. We find that the temperature and magnetic field dependence of the eMCE reproduces that observed in MnSi. Our results reveal the microscopic mechanism of eMCE and its potential in producing a large nonreciprocal response.
Modular self-assembly of gamma-modified peptide nucleic acids in organic solvent mixtures
Authors: Kumar Sriram , Pearse Alexander , Liu Ying , Taylor Rebecca E. 
Published: June 2020

AbstractNucleic acid-based materials enable sub-nanometer precision in self-assembly for fields including biophysics, diagnostics, therapeutics, photonics, and nanofabrication. However, structural DNA nanotechnology has been limited to substantially hydrated media. Transfer to organic solvents commonly used in polymer and peptide synthesis results in the alteration of DNA helical structure or reduced thermal stabilities. Here we demonstrate that gamma-modified peptide nucleic acids (γPNA) can be used to enable formation of complex, self-assembling nanostructures in select polar aprotic organic solvent mixtures. However, unlike the diameter-monodisperse populations of nanofibers formed using analogous DNA approaches, γPNA structures appear to form bundles of nanofibers. A tight distribution of the nanofiber diameters could, however, be achieved in the presence of the surfactant SDS during self-assembly. We further demonstrate nanostructure morphology can be tuned by means of solvent solution and by strand substitution with DNA and unmodified PNA. This work thereby introduces a science of γPNA nanotechnology.
Oxidation-boosted charge trapping in ultra-sensitive van der Waals materials for artificial synaptic features
Authors: Yang Feng-Shou , Li Mengjiao , Lee Mu-Pai , Ho I-Ying , Chen Jiann-Yeu , Ling Haifeng , Li Yuanzhe , Chang Jen-Kuei , Yang Shih-Hsien , Chang Yuan-Ming , Lee Ko-Chun , Chou Yi-Chia , Ho Ching-Hwa , Li Wenwu , Lien Chen-Hsin , Lin Yen-Fu 
Published: June 2020

AbstractExploitation of the oxidation behaviour in an environmentally sensitive semiconductor is significant to modulate its electronic properties and develop unique applications. Here, we demonstrate a native oxidation-inspired InSe field-effect transistor as an artificial synapse in device level that benefits from the boosted charge trapping under ambient conditions. A thin InOx layer is confirmed under the InSe channel, which can serve as an effective charge trapping layer for information storage. The dynamic characteristic measurement is further performed to reveal the corresponding uniform charge trapping and releasing process, which coincides with its surface-effect-governed carrier fluctuations. As a result, the oxide-decorated InSe device exhibits nonvolatile memory characteristics with flexible programming/erasing operations. Furthermore, an InSe-based artificial synapse is implemented to emulate the essential synaptic functions. The pattern recognition capability of the designed artificial neural network is believed to provide an excellent paradigm for ultra-sensitive van der Waals materials to develop electric-modulated neuromorphic computation architectures.
Strongly correlated Fermions strongly coupled to light
Authors: Roux Kevin , Konishi Hideki , Helson Victor , Brantut Jean-Philippe 
Published: June 2020

AbstractStrong quantum correlations in matter are responsible for some of the most extraordinary properties of materials, from magnetism to high-temperature superconductivity, but their integration in quantum devices requires a strong, coherent coupling with photons, which still represents a formidable technical challenge in solid state systems. In cavity quantum electrodynamics, quantum gases such as Bose-Einstein condensates or lattice gases have been strongly coupled with light. However, neither Fermionic quantum matter, comparable to electrons in solids, nor atomic systems with controlled interactions, have thus far been strongly coupled with photons. Here we report on the strong coupling of a quantum-degenerate unitary Fermi gas with light in a high finesse cavity. We map out the spectrum of the coupled system and observe well resolved dressed states, resulting from the strong coupling of cavity photons with each spin component of the gas. We investigate spin-balanced and spin-polarized gases and find quantitative agreement with ab initio calculation describing light-matter interaction. Our system offers complete and simultaneous control of atom-atom and atom-photon interactions in the quantum degenerate regime, opening a wide range of perspectives for quantum simulation.
Diagnostic evaluation of a deep learning model for optical diagnosis of colorectal cancer
Authors: Zhou Dejun , Tian Fei , Tian Xiangdong , Sun Lin , Huang Xianghui , Zhao Feng , Zhou Nan , Chen Zuoyu , Zhang Qiang , Yang Meng , Yang Yichen , Guo Xuexi , Li Zhibin , Liu Jia , Wang Jiefu , Wang Junfeng , Wang Bangmao , Zhang Guoliang , Sun Baocun , Zhang Wei , Kong Dalu , Chen Kexin , Li Xiangchun 
Published: June 2020

AbstractColonoscopy is commonly used to screen for colorectal cancer (CRC). We develop a deep learning model called CRCNet for optical diagnosis of CRC by training on 464,105 images from 12,179 patients and test its performance on 2263 patients from three independent datasets. At the patient-level, CRCNet achieves an area under the precision-recall curve (AUPRC) of 0.882 (95% CI: 0.828–0.931), 0.874 (0.820–0.926) and 0.867 (0.795–0.923). CRCNet exceeds average endoscopists performance on recall rate across two test sets (91.3% versus 83.8%; two-sided t-test, p < 0.001 and 96.5% versus 90.3%; p = 0.006) and precision for one test set (93.7% versus 83.8%; p = 0.02), while obtains comparable recall rate on one test set and precision on the other two. At the image-level, CRCNet achieves an AUPRC of 0.990 (0.987–0.993), 0.991 (0.987–0.995), and 0.997 (0.995–0.999). Our study warrants further investigation of CRCNet by prospective clinical trials.
Geometry and evolution of the ecological niche in plant-associated microbes
Authors: Chaloner Thomas M. , Gurr Sarah J. , Bebber Daniel P. 
Published: June 2020

AbstractThe ecological niche can be thought of as a volume in multidimensional space, where each dimension describes an abiotic condition or biotic resource required by a species. The shape, size, and evolution of this volume strongly determine interactions among species and influence their current and potential geographical distributions, but the geometry of niches is poorly understood. Here, we analyse temperature response functions and host plant ranges for hundreds of potentially destructive plant-associated fungi and oomycetes. We demonstrate that niche specialization is uncorrelated on abiotic (i.e. temperature response) and biotic (i.e. host range) axes, that host interactions restrict fundamental niche breadth to form the realized niche, and that both abiotic and biotic niches show limited phylogenetic constraint. The ecological terms ‘generalist’ and ‘specialist’ therefore do not apply to these microbes, as specialization evolves independently on different niche axes. This adaptability makes plant pathogens a formidable threat to agriculture and forestry.