Showing papers by "Academia Sinica published in 2018"
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TL;DR: An updated database containing 422 517 curated MTIs from 4076 miRNAs and 23 054 target genes collected from over 8500 articles is described, which serves as more comprehensively annotated, experimentally validated miRNA-target interactions databases in the field of miRNA related research.
Abstract: MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 22 nucleotides that are involved in negative regulation of mRNA at the post-transcriptional level. Previously, we developed miRTarBase which provides information about experimentally validated miRNA-target interactions (MTIs). Here, we describe an updated database containing 422 517 curated MTIs from 4076 miRNAs and 23 054 target genes collected from over 8500 articles. The number of MTIs curated by strong evidence has increased ∼1.4-fold since the last update in 2016. In this updated version, target sites validated by reporter assay that are available in the literature can be downloaded. The target site sequence can extract new features for analysis via a machine learning approach which can help to evaluate the performance of miRNA-target prediction tools. Furthermore, different ways of browsing enhance user browsing specific MTIs. With these improvements, miRTarBase serves as more comprehensively annotated, experimentally validated miRNA-target interactions databases in the field of miRNA related research. miRTarBase is available at http://miRTarBase.mbc.nctu.edu.tw/.
1,394 citations
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TL;DR: Molten-salt-assisted chemical vapour deposition is used to synthesize a wide variety of two-dimensional transition-metal chalcogenides and elaborate how the salt decreases the melting point of the reactants and facilitates the formation of intermediate products, increasing the overall reaction rate.
Abstract: Investigations of two-dimensional transition-metal chalcogenides (TMCs) have recently revealed interesting physical phenomena, including the quantum spin Hall effect1,2, valley polarization3,4 and two-dimensional superconductivity
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, suggesting potential applications for functional devices6–10. However, of the numerous compounds available, only a handful, such as Mo- and W-based TMCs, have been synthesized, typically via sulfurization11–15, selenization16,17 and tellurization
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of metals and metal compounds. Many TMCs are difficult to produce because of the high melting points of their metal and metal oxide precursors. Molten-salt-assisted methods have been used to produce ceramic powders at relatively low temperature
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and this approach
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was recently employed to facilitate the growth of monolayer WS2 and WSe2. Here we demonstrate that molten-salt-assisted chemical vapour deposition can be broadly applied for the synthesis of a wide variety of two-dimensional (atomically thin) TMCs. We synthesized 47 compounds, including 32 binary compounds (based on the transition metals Ti, Zr, Hf, V, Nb, Ta, Mo, W, Re, Pt, Pd and Fe), 13 alloys (including 11 ternary, one quaternary and one quinary), and two heterostructured compounds. We elaborate how the salt decreases the melting point of the reactants and facilitates the formation of intermediate products, increasing the overall reaction rate. Most of the synthesized materials in our library are useful, as supported by evidence of superconductivity in our monolayer NbSe2 and MoTe2 samples21,22 and of high mobilities in MoS2 and ReS2. Although the quality of some of the materials still requires development, our work opens up opportunities for studying the properties and potential application of a wide variety of two-dimensional TMCs.
1,174 citations
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TL;DR: Integrating the Pancharatnam–Berry phase with integrated resonant nanoantennas in a metalens design produces an achromatic device capable of full-colour imaging in the visible range in transmission mode.
Abstract: Metalenses consist of an array of optical nanoantennas on a surface capable of manipulating the properties of an incoming light wavefront. Various flat optical components, such as polarizers, optical imaging encoders, tunable phase modulators and a retroreflector, have been demonstrated using a metalens design. An open issue, especially problematic for colour imaging and display applications, is the correction of chromatic aberration, an intrinsic effect originating from the specific resonance and limited working bandwidth of each nanoantenna. As a result, no metalens has demonstrated full-colour imaging in the visible wavelength. Here, we show a design and fabrication that consists of GaN-based integrated-resonant unit elements to achieve an achromatic metalens operating in the entire visible region in transmission mode. The focal length of our metalenses remains unchanged as the incident wavelength is varied from 400 to 660 nm, demonstrating complete elimination of chromatic aberration at about 49% bandwidth of the central working wavelength. The average efficiency of a metalens with a numerical aperture of 0.106 is about 40% over the whole visible spectrum. We also show some examples of full-colour imaging based on this design. Integrating the Pancharatnam–Berry phase with integrated resonant nanoantennas in a metalens design produces an achromatic device capable of full-colour imaging in the visible range in transmission mode.
1,063 citations
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TL;DR: It is shown that metformin increases CTL activity by reducing the stability and membrane localization of programmed death ligand-1 (PD-L1), and it is discovered that AMP-activated protein kinase (AMPK) activated by met formin directly phosphorylates S195 of PD-L 1.
433 citations
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07 Jun 2018
TL;DR: This Primer addresses several aspects of HBV infection, including epidemiology, immune pathophysiology, diagnosis, prevention and management, including antiviral agents that directly act on viral replication and immunomodulators, such as interferon therapy.
Abstract: Hepatitis B virus (HBV) is a hepatotropic virus that can establish a persistent and chronic infection in humans through immune anergy. Currently, 3.5% of the global population is chronically infected with HBV, although the incidence of HBV infections is decreasing owing to vaccination and, to a lesser extent, the use of antiviral therapy to reduce the viral load of chronically infected individuals. The course of chronic HBV infection typically comprises different clinical phases, each of which potentially lasts for decades. Well-defined and verified serum and liver biopsy diagnostic markers enable the assessment of disease severity, viral replication status, patient risk stratification and treatment decisions. Current therapy includes antiviral agents that directly act on viral replication and immunomodulators, such as interferon therapy. Antiviral agents for HBV include reverse transcriptase inhibitors, which are nucleoside or nucleotide analogues that can profoundly suppress HBV replication but require long-term maintenance therapy. Novel compounds are being actively investigated to achieve the goal of HBV surface antigen seroclearance (functional cure), a serological state that is associated with a higher remission rate (thus, no viral rebound) after treatment cessation and a lower rate of cirrhosis and hepatocellular carcinoma. This Primer addresses several aspects of HBV infection, including epidemiology, immune pathophysiology, diagnosis, prevention and management. Hepatitis B virus is a human hepatotropic DNA virus that can cause a lifelong chronic infection and progressive liver disease. This Primer discusses the epidemiology, mechanisms, diagnosis, prevention and management of chronic hepatitis B virus infection.
425 citations
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Cold Spring Harbor Laboratory1, University of Arizona2, International Rice Research Institute3, University of Chicago4, University of Georgia5, Wayne State University6, Chinese Academy of Sciences7, Max Planck Society8, University of Hohenheim9, Rice University10, Sant'Anna School of Advanced Studies11, DuPont Pioneer12, National Taiwan University13, Academia Sinica14, Ghent University15, University of Perpignan16, Universidade Federal de Pelotas17, University of Maryland, College Park18, University of Zurich19, University of Queensland20, National Institute of Genetics21, United States Department of Agriculture22
TL;DR: This study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young ‘AA’ subclade containing the two domesticated species and announcing many new haplotypes of potential use for future crop protection.
Abstract: The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.
365 citations
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TL;DR: In this paper, a search for new phenomena in final states with an energetic jet and large missing transverse momentum is reported, and the results are translated into exclusion limits in models with pair-produced weakly interacting dark-matter candidates, large extra spatial dimensions, and supersymmetric particles in several compressed scenarios.
Abstract: Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses proton-proton collision data corresponding to an integrated luminosity of 36.1 fb−1 at a centre-of-mass energy of 13 TeV collected in 2015 and 2016 with the ATLAS detector at the Large Hadron Collider. Events are required to have at least one jet with a transverse momentum above 250 GeV and no leptons (e or μ). Several signal regions are considered with increasing requirements on the missing transverse momentum above 250 GeV. Good agreement is observed between the number of events in data and Standard Model predictions. The results are translated into exclusion limits in models with pair-produced weakly interacting dark-matter candidates, large extra spatial dimensions, and supersymmetric particles in several compressed scenarios.
358 citations
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European Centre for Medium-Range Weather Forecasts1, University of Bristol2, National Space Institute3, Goddard Space Flight Center4, European Space Agency5, National Oceanic and Atmospheric Administration6, Goethe University Frankfurt7, University of South Florida8, University of Bremen9, Academia Sinica10, University of Texas at Austin11, Chinese Academy of Sciences12, University of New South Wales13, Trent University14, University of Siegen15, IFREMER16, Commonwealth Scientific and Industrial Research Organisation17, California Institute of Technology18, University of Bonn19, University of Urbino20, Dresden University of Technology21, Old Dominion University22, University of Leeds23, ETH Zurich24, University of Grenoble25, University of Bern26, Northern Oklahoma College27, Australian National University28, University of Oslo29, University of Rennes30, University of the Balearic Islands31, University of Reading32, University of California, San Diego33, University of Ottawa34, University of California, Irvine35, University of Colorado Boulder36, University of Zurich37, Woods Hole Oceanographic Institution38, Delft University of Technology39, Alfred Wegener Institute for Polar and Marine Research40, Ohio State University41, University of Hamburg42, Utrecht University43, University of California44, Bjerknes Centre for Climate Research45, University of Tasmania46, University of La Rochelle47
TL;DR: In this paper, the authors present estimates of the altimetry-based global mean sea level (average variance of 3.1 +/- 0.3 mm/yr and acceleration of 0.1 mm/r2 over 1993-present), as well as of the different components of the sea level budget over 2005-present, using GRACE-based ocean mass estimates.
Abstract: Global mean sea level is an integral of changes occurring in the climate system in response to
unforced climate variability as well as natural and anthropogenic forcing factors. Its temporal
evolution allows detecting changes (e.g., acceleration) in one or more components. Study of
the sea level budget provides constraints on missing or poorly known contributions, such as
the unsurveyed deep ocean or the still uncertain land water component. In the context of the
World Climate Research Programme Grand Challenge entitled “Regional Sea Level and
Coastal Impacts”, an international effort involving the sea level community worldwide has
been recently initiated with the objective of assessing the various data sets used to estimate
components of the sea level budget during the altimetry era (1993 to present). These data sets
are based on the combination of a broad range of space-based and in situ observations, model
estimates and algorithms. Evaluating their quality, quantifying uncertainties and identifying
sources of discrepancies between component estimates is extremely useful for various
applications in climate research. This effort involves several tens of scientists from about fifty
research teams/institutions worldwide (www.wcrp-climate.org/grand-challenges/gc-sea-
level). The results presented in this paper are a synthesis of the first assessment performed
during 2017-2018. We present estimates of the altimetry-based global mean sea level (average
rate of 3.1 +/- 0.3 mm/yr and acceleration of 0.1 mm/yr2 over 1993-present), as well as of the
different components of the sea level budget (http://doi.org/10.17882/54854). We further
examine closure of the sea level budget, comparing the observed global mean sea level with
the sum of components. Ocean thermal expansion, glaciers, Greenland and Antarctica
contribute by 42%, 21%, 15% and 8% to the global mean sea level over the 1993-present. We
also study the sea level budget over 2005-present, using GRACE-based ocean mass estimates
instead of sum of individual mass components. Results show closure of the sea level budget
within 0.3 mm/yr. Substantial uncertainty remains for the land water storage component, as
shown in examining individual mass contributions to sea level.
338 citations
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TL;DR: Targeting protein glycosylation as a potential strategy to enhance immune checkpoint therapy is suggested, as it remains largely unknown whether the sugar moiety contributes to immunosuppression.
335 citations
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TL;DR: This review focuses on the roles of NRT1 and NRT2 in nitrate uptake and nitrate allocation among different tissues; the functions of the transceptor N RT1.1, transcription factors, and small signaling peptides in nitrates signaling and tissue communication are described; and the new strategies for improving nitrogen-use efficiency are compiled.
Abstract: Nitrogen accounts for approximately 60% of the fertilizer consumed each year; thus, it represents one of the major input costs for most nonlegume crops. Nitrate is one of the two major forms of nitrogen that plants acquire from the soil. Mechanistic insights into nitrate transport and signaling have enabled new strategies for enhancing nitrogen utilization efficiency, for lowering input costs for farming, and, more importantly, for alleviating environmental impacts (e.g., eutrophication and production of the greenhouse gas N2O). Over the past decade, significant progress has been made in understanding how nitrate is acquired from the surroundings, how it is efficiently distributed into different plant tissues in response to environmental changes, how nitrate signaling is perceived and transmitted, and how shoot and root nitrogen status is communicated. Several key components of these processes have proven to be novel tools for enhancing nitrate- and nitrogen-use efficiency. In this review, we focus on the...
330 citations
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TL;DR: The motivation for this new pixel layer, the Insertable B-Layer (IBL), was to maintain or improve the robustness and performance of the ATLAS tracking system, given the higher instantaneous and integrated luminosities realised following the shutdown.
Abstract: During the shutdown of the CERN Large Hadron Collider in 2013-2014, an additional pixel layer was installed between the existing Pixel detector of the ATLAS experiment and a new, smaller radius beam pipe. The motivation for this new pixel layer, the Insertable B-Layer (IBL), was to maintain or improve the robustness and performance of the ATLAS tracking system, given the higher instantaneous and integrated luminosities realised following the shutdown. Because of the extreme radiation and collision rate environment, several new radiation-tolerant sensor and electronic technologies were utilised for this layer. This paper reports on the IBL construction and integration prior to its operation in the ATLAS detector.
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TL;DR: A carbon-doped SnS2 (SnS2-C) metal dichalcogenide nanostructure is synthesized, which exhibits a highly active and selective photocatalytic conversion of CO2 to hydrocarbons under visible-light, and represents an important contribution towards high quantum efficiency artificial photosynthesis based on gas phase photoc atalytic CO2 reduction under visible light.
Abstract: Photocatalytic formation of hydrocarbons using solar energy via artificial photosynthesis is a highly desirable renewable-energy source for replacing conventional fossil fuels. Using an l-cysteine-based hydrothermal process, here we synthesize a carbon-doped SnS2 (SnS2-C) metal dichalcogenide nanostructure, which exhibits a highly active and selective photocatalytic conversion of CO2 to hydrocarbons under visible-light. The interstitial carbon doping induced microstrain in the SnS2 lattice, resulting in different photophysical properties as compared with undoped SnS2. This SnS2-C photocatalyst significantly enhances the CO2 reduction activity under visible light, attaining a photochemical quantum efficiency of above 0.7%. The SnS2-C photocatalyst represents an important contribution towards high quantum efficiency artificial photosynthesis based on gas phase photocatalytic CO2 reduction under visible light, where the in situ carbon-doped SnS2 nanostructure improves the stability and the light harvesting and charge separation efficiency, and significantly enhances the photocatalytic activity. Photocatalytic reduction of CO2 to hydrocarbons is a promising route to both CO2 utilization and renewable fuel production. Here the authors identify that carbon-doped SnS2 possesses a high catalytic efficiency towards CO2 reduction owing to low photogenerated charge recombination rates.
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TL;DR: An algorithm is proposed that acquires general-purpose skills by combining unsupervised representation learning and reinforcement learning of goal-conditioned policies, efficient enough to learn policies that operate on raw image observations and goals for a real-world robotic system, and substantially outperforms prior techniques.
Abstract: For an autonomous agent to fulfill a wide range of user-specified goals at test time, it must be able to learn broadly applicable and general-purpose skill repertoires. Furthermore, to provide the requisite level of generality, these skills must handle raw sensory input such as images. In this paper, we propose an algorithm that acquires such general-purpose skills by combining unsupervised representation learning and reinforcement learning of goal-conditioned policies. Since the particular goals that might be required at test-time are not known in advance, the agent performs a self-supervised "practice" phase where it imagines goals and attempts to achieve them. We learn a visual representation with three distinct purposes: sampling goals for self-supervised practice, providing a structured transformation of raw sensory inputs, and computing a reward signal for goal reaching. We also propose a retroactive goal relabeling scheme to further improve the sample-efficiency of our method. Our off-policy algorithm is efficient enough to learn policies that operate on raw image observations and goals for a real-world robotic system, and substantially outperforms prior techniques.
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TL;DR: While a cross-correlation underlines the high similarity of many variables, a more detailed view in four mountain regions reveals local differences, as well as scale variations in the aggregated variables at different spatial grains.
Abstract: A suite of global, cross-scale topographic variables for environmental and biodiversity modeling
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TL;DR: In this paper, the authors used mid-infrared optoelectronic microscopy to investigate the Berry curvature in monolayer WTe2 and observed an in-plane circular photogalvanic current even under normal incidence.
Abstract: Recent experimental evidence for the quantum spin Hall (QSH) state in monolayer WTe2 has linked the fields of two-dimensional materials and topological physics1–7. This two-dimensional topological crystal also displays unconventional spin–torque8 and gate-tunable superconductivity7. Whereas the realization of the QSH has demonstrated the nontrivial topology of the electron wavefunctions of monolayer WTe2, the geometrical properties of the wavefunction, such as the Berry curvature9, remain unstudied. Here we utilize mid-infrared optoelectronic microscopy to investigate the Berry curvature in monolayer WTe2. By optically exciting electrons across the inverted QSH gap, we observe an in-plane circular photogalvanic current even under normal incidence. The application of an out-of-plane displacement field allows further control of the direction and magnitude of the photocurrent. The observed photocurrent reveals a Berry curvature dipole that arises from the nontrivial wavefunctions near the inverted gap edge. The Berry curvature dipole and strong electric field effect are enabled by the inverted band structure and tilted crystal lattice of monolayer WTe2. Such an electrically switchable Berry curvature dipole may facilitate the observation of a wide range of quantum geometrical phenomena such as the quantum nonlinear Hall10,11, orbital-Edelstein12 and chiral polaritonic effects13,14.
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TL;DR: Compared with state-of-the-art approaches, SSDH achieves higher retrieval accuracy, while the classification performance is not sacrificed; yet it is effective and outperforms other hashing approaches on several benchmarks and large datasets.
Abstract: This paper presents a simple yet effective supervised deep hash approach that constructs binary hash codes from labeled data for large-scale image search. We assume that the semantic labels are governed by several latent attributes with each attribute on or off , and classification relies on these attributes. Based on this assumption, our approach, dubbed supervised semantics-preserving deep hashing (SSDH), constructs hash functions as a latent layer in a deep network and the binary codes are learned by minimizing an objective function defined over classification error and other desirable hash codes properties. With this design, SSDH has a nice characteristic that classification and retrieval are unified in a single learning model. Moreover, SSDH performs joint learning of image representations, hash codes, and classification in a point-wised manner, and thus is scalable to large-scale datasets. SSDH is simple and can be realized by a slight enhancement of an existing deep architecture for classification; yet it is effective and outperforms other hashing approaches on several benchmarks and large datasets. Compared with state-of-the-art approaches, SSDH achieves higher retrieval accuracy, while the classification performance is not sacrificed.
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TL;DR: In this article, it was shown that Kramers-Weyl fermions are a universal topological property of all non-magnetic chiral crystals with spin-orbit coupling and are guaranteed by structural chirality, lattice translation and time-reversal symmetry.
Abstract: Chiral crystals are materials with a lattice structure that has a well-defined handedness due to the lack of inversion, mirror or other roto-inversion symmetries. Although it has been shown that the presence of crystalline symmetries can protect topological band crossings, the topological electronic properties of chiral crystals remain largely uncharacterized. Here we show that Kramers-Weyl fermions are a universal topological electronic property of all non-magnetic chiral crystals with spin-orbit coupling and are guaranteed by structural chirality, lattice translation and time-reversal symmetry. Unlike conventional Weyl fermions, they appear at time-reversal-invariant momenta. We identify representative chiral materials in 33 of the 65 chiral space groups in which Kramers-Weyl fermions are relevant to the low-energy physics. We determine that all point-like nodal degeneracies in non-magnetic chiral crystals with relevant spin-orbit coupling carry non-trivial Chern numbers. Kramers-Weyl materials can exhibit a monopole-like electron spin texture and topologically non-trivial bulk Fermi surfaces over an unusually large energy window.
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TL;DR: The authors show that epithelial-mesenchymal transition induces glycosylation and stabilisation of PD-L1; antagonising this process renders cancer cells sensitive to anti-Tim3-therapy, revealing it as a potential strategy to enhance cancer immunotherapy efficacy.
Abstract: Enriched PD-L1 expression in cancer stem-like cells (CSCs) contributes to CSC immune evasion. However, the mechanisms underlying PD-L1 enrichment in CSCs remain unclear. Here, we demonstrate that epithelial-mesenchymal transition (EMT) enriches PD-L1 in CSCs by the EMT/β-catenin/STT3/PD-L1 signaling axis, in which EMT transcriptionally induces N-glycosyltransferase STT3 through β-catenin, and subsequent STT3-dependent PD-L1 N-glycosylation stabilizes and upregulates PD-L1. The axis is also utilized by the general cancer cell population, but it has much more profound effect on CSCs as EMT induces more STT3 in CSCs than in non-CSCs. We further identify a non-canonical mesenchymal-epithelial transition (MET) activity of etoposide, which suppresses the EMT/β-catenin/STT3/PD-L1 axis through TOP2B degradation-dependent nuclear β-catenin reduction, leading to PD-L1 downregulation of CSCs and non-CSCs and sensitization of cancer cells to anti-Tim-3 therapy. Together, our results link MET to PD-L1 stabilization through glycosylation regulation and reveal it as a potential strategy to enhance cancer immunotherapy efficacy.
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TL;DR: The tunability of this kagome magnet reveals a strong interplay between an externally applied field, electronic excitations and nematicity, providing new ways of controlling spin–orbit properties and exploring emergent phenomena in topological or quantum materials10–12.
Abstract: Owing to the unusual geometry of kagome lattices—lattices made of corner-sharing triangles—their electrons are useful for studying the physics of frustrated, correlated and topological quantum electronic states1–9. In the presence of strong spin–orbit coupling, the magnetic and electronic structures of kagome lattices are further entangled, which can lead to hitherto unknown spin–orbit phenomena. Here we use a combination of vector-magnetic-field capability and scanning tunnelling microscopy to elucidate the spin–orbit nature of the kagome ferromagnet Fe3Sn2 and explore the associated exotic correlated phenomena. We discover that a many-body electronic state from the kagome lattice couples strongly to the vector field with three-dimensional anisotropy, exhibiting a magnetization-driven giant nematic (two-fold-symmetric) energy shift. Probing the fermionic quasi-particle interference reveals consistent spontaneous nematicity—a clear indication of electron correlation—and vector magnetization is capable of altering this state, thus controlling the many-body electronic symmetry. These spin-driven giant electronic responses go well beyond Zeeman physics and point to the realization of an underlying correlated magnetic topological phase. The tunability of this kagome magnet reveals a strong interplay between an externally applied field, electronic excitations and nematicity, providing new ways of controlling spin–orbit properties and exploring emergent phenomena in topological or quantum materials10–12. The topological magnet Fe3Sn2 exhibits a giant nematic energy shift of a many-body electronic state, demonstrating anisotropic spin–orbit tunability.
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TL;DR: The working mechanisms of the direct electroluminescence from the donor/acceptor interface and the exciplex-forming systems as cohost for the realization of high efficiency OLEDs are reviewed and discussed.
Abstract: Organic materials that display thermally activated delayed fluorescence (TADF) are a striking class of functional materials that have witnessed a booming progress in recent years. In addition to pure TADF emitters achieved by the subtle manipulations of intramolecular charge transfer processes with sophisticated molecular structures, a new class of efficient TADF-based OLEDs with emitting layer formed by blending electron donor and acceptor molecules that involve intermolecular charge transfer have also been fabricated. In contrast to pure TADF materials, the exciplex-based systems can realize small ΔEST (0–0.05 eV) much more easily since the electron and hole are positioned on two different molecules, thereby giving small exchange energy. Consequently, exciplex-based OLEDs have the prospective to maximize the TADF contribution and achieve theoretical 100% internal quantum efficiency. Therefore, the challenging issue of achieving small ΔEST in organic systems could be solved. In this article, we summarize...
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Reiner Schlitzer1, Robert F. Anderson2, Elena Masferrer Dodas3, Maeve C. Lohan4 +310 more•Institutions (98)
TL;DR: The GEOTRACES Intermediate Data Product 2017 (IDP2017) as discussed by the authors is the second publicly available data product of the international GEOTrACES programme, and contains data measured and quality controlled before the end of 2016.
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TL;DR: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time to enable users to calculate temporal trends in biodiversity within and amongst assemblage using a broad range of metrics.
Abstract: Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables included: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km(2) (158 cm(2)) to 100 km(2) (1,000,000,000,000 cm(2)).Time period and grainBio: TIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurement: BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.
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TL;DR: The physiological attributes of E. coli that are most relevant for metabolic engineering are discussed, as well as emerging techniques that enable efficient phenotype construction that address some of the future challenges in broadening substrate range and fighting phage infection.
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TL;DR: A sensitive analytical microfluidic platform for rapid and sensitive isolation of tumor-specific extracellular vesicles and identifies genes specific to GBM as well as transcripts that are hallmarks for the four genetic subtypes of the disease.
Abstract: Extracellular vesicles (EVs) carry RNA, DNA, proteins, and lipids. Specifically, tumor-derived EVs have the potential to be utilized as disease-specific biomarkers. However, a lack of methods to isolate tumor-specific EVs has limited their use in clinical settings. Here we report a sensitive analytical microfluidic platform (EVHB-Chip) that enables tumor-specific EV-RNA isolation within 3 h. Using the EVHB-Chip, we achieve 94% tumor-EV specificity, a limit of detection of 100 EVs per μL, and a 10-fold increase in tumor RNA enrichment in comparison to other methods. Our approach allows for the subsequent release of captured tumor EVs, enabling downstream characterization and functional studies. Processing serum and plasma samples from glioblastoma multiforme (GBM) patients, we can detect the mutant EGFRvIII mRNA. Moreover, using next-generation RNA sequencing, we identify genes specific to GBM as well as transcripts that are hallmarks for the four genetic subtypes of the disease.
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TL;DR: The observation of new properties of secondary cosmic rays Li, Be, and B measured in the rigidity range 1.9 GV to 3.3 TV with a total of 5.4×10^{6} nuclei collected by AMS during the first five years of operation aboard the International Space Station is reported.
Abstract: We report on the observation of new properties of secondary cosmic rays Li, Be, and B measured in the rigidity (momentum per unit charge) range 1.9 GV to 3.3 TV with a total of 5.4×10^{6} nuclei collected by AMS during the first five years of operation aboard the International Space Station. The Li and B fluxes have an identical rigidity dependence above 7 GV and all three fluxes have an identical rigidity dependence above 30 GV with the Li/Be flux ratio of 2.0±0.1. The three fluxes deviate from a single power law above 200 GV in an identical way. This behavior of secondary cosmic rays has also been observed in the AMS measurement of primary cosmic rays He, C, and O but the rigidity dependences of primary cosmic rays and of secondary cosmic rays are distinctly different. In particular, above 200 GV, the secondary cosmic rays harden more than the primary cosmic rays.
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TL;DR: Current and emerging strategies for EV imaging for prospective studies are reviewed, covering current and emerging methods to visualize and study their spatiotemporal properties.
Abstract: Extracellular vesicles (EVs) are lipid bilayer-enclosed nanoparticles released by cells. They range from 30 nm to several micrometers in diameter, and ferry biological cargos such as proteins, lipids, RNAs and DNAs for local and distant intercellular communications. EVs have since been found to play a role in development, as well as in diseases including cancers. To elucidate the roles of EVs, researchers have established different methods to visualize and study their spatiotemporal properties. However, since EV are nanometer-sized, imaging them demands a full understanding of each labeling strategy to ensure accurate monitoring. This review covers current and emerging strategies for EV imaging for prospective studies.
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TL;DR: The state-of-the-art fabrication methods and surveying their cutting-edge applications of the metasurfaces are reviewed.
Abstract: The research and development of optical metasurfaces has been primarily driven by the curiosity for novel optical phenomena that are unattainable from materials that exist in nature and by the desire for miniaturization of optical devices. Metasurfaces constructed of artificial patterns of subwavelength depth make it possible to achieve flat, ultrathin optical devices of high performance. A wide variety of fabrication techniques have been developed to explore their unconventional functionalities which in many ways have revolutionized the means with which we control and manipulate electromagnetic waves. The relevant research community could benefit from an overview on recent progress in the fabrication and applications of the metasurfaces. This review article is intended to serve that purpose by reviewing the state-of-the-art fabrication methods and surveying their cutting-edge applications.
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01 Jan 2018TL;DR: In this paper, an algorithm that combines unsupervised representation learning and reinforcement learning of goal-conditioned policies is proposed to acquire general-purpose skills by combining self-supervised training with reinforcement learning.
Abstract: For an autonomous agent to fulfill a wide range of user-specified goals at test time, it must be able to learn broadly applicable and general-purpose skill repertoires. Furthermore, to provide the requisite level of generality, these skills must handle raw sensory input such as images. In this paper, we propose an algorithm that acquires such general-purpose skills by combining unsupervised representation learning and reinforcement learning of goal-conditioned policies. Since the particular goals that might be required at test-time are not known in advance, the agent performs a self-supervised "practice" phase where it imagines goals and attempts to achieve them. We learn a visual representation with three distinct purposes: sampling goals for self-supervised practice, providing a structured transformation of raw sensory inputs, and computing a reward signal for goal reaching. We also propose a retroactive goal relabeling scheme to further improve the sample-efficiency of our method. Our off-policy algorithm is efficient enough to learn policies that operate on raw image observations and goals in a real-world physical system, and substantially outperforms prior techniques.
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TL;DR: The sampled-data feedback control, which is assumed to allow norm-bounded uncertainty and involves a constant signal transmission delay, is constructed for the first time in this paper, and a sufficient condition is developed, such that the nonfragile exponential stability of the error system is guaranteed.
Abstract: This paper considers nonfragile exponential synchronization for complex dynamical networks (CDNs) with time-varying coupling delay. The sampled-data feedback control, which is assumed to allow norm-bounded uncertainty and involves a constant signal transmission delay, is constructed for the first time in this paper. By constructing a suitable augmented Lyapunov function, and with the help of introduced integral inequalities and employing the convex combination technique, a sufficient condition is developed, such that the nonfragile exponential stability of the error system is guaranteed. As a result, for the case of sampled-data control free of norm-bound uncertainties, some sufficient conditions of sampled-data synchronization criteria for the CDNs with time-varying coupling delay are presented. As the formulations are in the framework of linear matrix inequality, these conditions can be easily solved and implemented. Two illustrative examples are presented to demonstrate the effectiveness and merits of the proposed feedback control.
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University of Oxford1, Okinawa Institute of Science and Technology2, Spanish National Research Council3, University of New South Wales4, Garvan Institute of Medical Research5, University of Western Australia6, Imperial College London7, Pompeu Fabra University8, University of Paris9, University of Barcelona10, Radboud University Nijmegen11, Academy of Sciences of the Czech Republic12, École Normale Supérieure13, French Institute of Health and Medical Research14, Centre national de la recherche scientifique15, French Alternative Energies and Atomic Energy Commission16, University of Cambridge17, University of Porto18, Stazione Zoologica Anton Dohrn19, University of St Andrews20, Sun Yat-sen University21, University of Lyon22, Aix-Marseille University23, University of Montpellier24, University of Manchester25, PSL Research University26, Beijing University of Chinese Medicine27, Academia Sinica28, Cincinnati Children's Hospital Medical Center29, University of Cincinnati Academic Health Center30, Harry Perkins Institute of Medical Research31, University of Bergen32
TL;DR: Genomic, epigenomic and transcriptomic data derived from the Mediterranean amphioxus provide insights into the evolution of the genomic regulatory landscape of chordates, and pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations.
Abstract: Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that-in vertebrates-over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations.