Showing papers by "Tsinghua University published in 2012"

Guidelines for the use and interpretation of assays for monitoring autophagy

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

Observation of Electron-Antineutrino Disappearance at Daya Bay

Abstract: The Daya Bay Reactor Neutrino Experiment has measured a nonzero value for the neutrino mixing angle θ13 with a significance of 5.2 standard deviations. Antineutrinos from six 2.9 GW_(th) reactors were detected in six antineutrino detectors deployed in two near (flux-weighted baseline 470 m and 576 m) and one far (1648 m) underground experimental halls. With a 43 000 ton–GW_(th)–day live-time exposure in 55 days, 10 416 (80 376) electron-antineutrino candidates were detected at the far hall (near halls). The ratio of the observed to expected number of antineutrinos at the far hall is R=0.940± 0.011(stat.)±0.004(syst.). A rate-only analysis finds sin^22θ_(13)=0.092±0.016(stat.)±0.005(syst.) in a three-neutrino framework.

Advanced Asymmetric Supercapacitors Based on Ni(OH)2/Graphene and Porous Graphene Electrodes with High Energy Density

Abstract: Hierarchical flowerlike nickel hydroxide decorated on graphene sheets has been prepared by a facile and cost-effective microwave-assisted method. In order to achieve high energy and power densities, a high-voltage asymmetric supercapacitor is successfully fabricated using Ni(OH)2/graphene and porous graphene as the positive and negative electrodes, respectively. Because of their unique structure, both of these materials exhibit excellent electrochemical performances. The optimized asymmetric supercapacitor could be cycled reversibly in the high-voltage region of 0–1.6 V and displays intriguing performances with a maximum specific capacitance of 218.4 F g−1 and high energy density of 77.8 Wh kg−1. Furthermore, the Ni(OH)2/graphene//porous graphene supercapacitor device exhibits an excellent long cycle life along with 94.3% specific capacitance retained after 3000 cycles. These fascinating performances can be attributed to the high capacitance and the positive synergistic effects of the two electrodes. The impressive results presented here may pave the way for promising applications in high energy density storage systems.

Nitrogen-Doped Graphene Quantum Dots with Oxygen-Rich Functional Groups

Abstract: Graphene quantum dots (GQDs) represent a new class of quantum dots with unique properties. Doping GQDs with heteroatoms provides an attractive means of effectively tuning their intrinsic properties and exploiting new phenomena for advanced device applications. Herein we report a simple electrochemical approach to luminescent and electrocatalytically active nitrogen-doped GQDs (N-GQDs) with oxygen-rich functional groups. Unlike their N-free counterparts, the newly produced N-GQDs with a N/C atomic ratio of ca. 4.3% emit blue luminescence and possess an electrocatalytic activity comparable to that of a commercially available Pt/C catalyst for the oxygen reduction reaction (ORR) in an alkaline medium. In addition to their use as metal-free ORR catalysts in fuel cells, the superior luminescence characteristic of N-GQDs allows them to be used for biomedical imaging and other optoelectronic applications.

Molecular ecological network analyses

Abstract: Background: Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Results: Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with highthroughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open-accessible now (http://ieg2.ou.edu/MENA). Conclusions: The RMT-based molecular ecological network analysis provides powerful tools to elucidate network interactions in microbial communities and their responses to environmental changes, which are fundamentally important for research in microbial ecology and environmental microbiology.

An oxygen reduction electrocatalyst based on carbon nanotube–graphene complexes

Abstract: Oxygen reduction reaction catalysts based on precious metals such as platinum or its alloys are routinely used in fuel cells because of their high activity. Carbon-supported materials containing metals such as iron or cobalt as well as nitrogen impurities have been proposed to increase scalability and reduce costs, but these alternatives usually suffer from low activity and/or gradual deactivation during use. Here, we show that few-walled carbon nanotubes, following outer wall exfoliation via oxidation and high-temperature reaction with ammonia, can act as an oxygen reduction reaction electrocatalyst in both acidic and alkaline solutions. Under a unique oxidation condition, the outer walls of the few-walled carbon nanotubes are partially unzipped, creating nanoscale sheets of graphene attached to the inner tubes. The graphene sheets contain extremely small amounts of irons originated from nanotube growth seeds, and nitrogen impurities, which facilitate the formation of catalytic sites and boost the activity of the catalyst, as revealed by atomic-scale microscopy and electron energy loss spectroscopy. Whereas the graphene sheets formed from the unzipped part of the outer wall of the nanotubes are responsible for the catalytic activity, the inner walls remain intact and retain their electrical conductivity, which facilitates charge transport during electrocatalysis.

Topological crystalline insulators in the SnTe material class

Abstract: Topologically protected states of matter are receiving widespread attention owing to their unusual electronic properties Using numerical simulations, this study predicts that tin telluride is a physical realization of a new class of materials termed topological crystalline insulators

Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells

Abstract: Accumulating evidence has shown that dysfunctional mitochondria can be selectively removed by mitophagy. Dysregulation of mitophagy is implicated in the development of neurodegenerative disease and metabolic disorders. How individual mitochondria are recognized for removal and how this process is regulated remain poorly understood. Here we report that FUNDC1, an integral mitochondrial outer-membrane protein, is a receptor for hypoxia-induced mitophagy. FUNDC1 interacted with LC3 through its typical LC3-binding motif Y(18)xxL(21), and mutation of the LC3-interaction region impaired its interaction with LC3 and the subsequent induction of mitophagy. Knockdown of endogenous FUNDC1 significantly prevented hypoxia-induced mitophagy, which could be reversed by the expression of wild-type FUNDC1, but not LC3-interaction-deficient FUNDC1 mutants. Mechanistic studies further revealed that hypoxia induced dephosphorylation of FUNDC1 and enhanced its interaction with LC3 for selective mitophagy. Our findings thus offer insights into mitochondrial quality control in mammalian cells.

Process Mining Manifesto

Abstract: Process mining techniques are able to extract knowledge from event logs commonly available in today’s information systems. These techniques provide new means to discover, monitor, and improve processes in a variety of application domains. There are two main drivers for the growing interest in process mining. On the one hand, more and more events are being recorded, thus, providing detailed information about the history of processes. On the other hand, there is a need to improve and support business processes in competitive and rapidly changing environments. This manifesto is created by the IEEE Task Force on Process Mining and aims to promote the topic of process mining. Moreover, by defining a set of guiding principles and listing important challenges, this manifesto hopes to serve as a guide for software developers, scientists, consultants, business managers, and end-users. The goal is to increase the maturity of process mining as a new tool to improve the (re)design, control, and support of operational business processes.

Interface-Induced High-Temperature Superconductivity in Single Unit-Cell FeSe Films on SrTiO3

Abstract: We report high transition temperature superconductivity in one unit-cell (UC) thick FeSe films grown on a Se-etched SrTiO3 (001) substrate by molecular beam epitaxy (MBE). A superconducting gap as large as 20 meV and the magnetic field induced vortex state revealed by in situ scanning tunneling microscopy (STM) suggest that the superconductivity of the 1 UC FeSe films could occur around 77 K. The control transport measurement shows that the onset superconductivity temperature is well above 50 K. Our work not only demonstrates a powerful way for finding new superconductors and for raising TC, but also provides a well-defined platform for systematic studies of the mechanism of unconventional superconductivity by using different superconducting materials and substrates.

Advanced Oxidation Processes for Wastewater Treatment: Formation of Hydroxyl Radical and Application

Abstract: Advanced oxidation processes (AOPs), defined as those technologies that utilize the hydroxyl radical (·OH) for oxidation, have received increasing attention in the research and development of wastewater treatment technologies in the last decades. These processes have been applied successfully for the removal or degradation of toxic pollutants or used as pretreatment to convert recalcitrant pollutants into biodegradable compounds that can then be treated by conventional biological methods. The efficacy of AOPs depends on the generation of reactive free radicals, the most important of which is the hydroxyl radical (·OH). The authors summarize the formation reactions of ·OH and the mechanisms of pollutants degradation. They cover six types of advanced oxidation processes, including radiation, photolysis and photocatalysis, sonolysis, electrochemical oxidation technologies, Fenton-based reactions, and ozone-based processes. Controversial issues in pollutants degradation mechanism were discussed. They review t...

Dual-polarity plasmonic metalens for visible light

Abstract: Surface topography and refractive index profile dictate the deterministic functionality of a lens. The polarity of most lenses reported so far, that is, either positive (convex) or negative (concave), depends on the curvatures of the interfaces. Here we experimentally demonstrate a counter-intuitive dual-polarity flat lens based on helicity-dependent phase discontinuities for circularly polarized light. Specifically, by controlling the helicity of the input light, the positive and negative polarity are interchangeable in one identical flat lens. Helicity-controllable real and virtual focal planes, as well as magnified and demagnified imaging, are observed on the same plasmonic lens at visible and near-infrared wavelengths. The plasmonic metalens with dual polarity may empower advanced research and applications in helicity-dependent focusing and imaging devices, angular-momentum-based quantum information processing and integrated nano-optoelectronics.

Magnetic Nanoscaled Fe3O4/CeO2 Composite as an Efficient Fenton-Like Heterogeneous Catalyst for Degradation of 4-Chlorophenol

Abstract: Magnetic nanoscaled Fe3O4/CeO2 composite was prepared by the impregnation method and characterized as a heterogeneous Fenton-like catalyst for 4-chlorophenol (4-CP) degradation. The catalytic activity was evaluated in view of the effects of various processes, pH value, catalyst addition, hydrogen peroxide (H2O2) concentration, and temperature, and the pseudo-first-order kinetic constant of 0.11 min–1 was obtained for 4-CP degradation at 30 °C and pH 3.0 with 30 mM H2O2, 2.0 g L–1 Fe3O4/CeO2, and 0.78 mM 4-CP. The high utilization efficiency of H2O2, calculated as 79.2%, showed a promising application of the catalyst in the oxidative degradation of organic pollutants. The reusability of Fe3O4/CeO2 composite was also investigated after six successive runs. On the basis of the results of metal leaching, the effects of radical scavengers, intermediates determination, and X-ray photoelectron spectroscopic (XPS) analysis, the dissolution of Fe3O4 facilitated by CeO2 played a significant role, and 4-CP was decom...

Protein-inorganic hybrid nanoflowers

Abstract: Flower-shaped inorganic nanocrystals(1-3) have been used for applications in catalysis(4,5) and analytical science(6,7), but so far there have been no reports of 'nanoflowers' made of organic components(8). Here, we report a method for creating hybrid organic-inorganic nanoflowers using copper (II) ions as the inorganic component and various proteins as the organic component. The protein molecules form complexes with the copper ions, and these complexes become nucleation sites for primary crystals of copper phosphate. Interaction between the protein and copper ions then leads to the growth of micrometre-sized particles that have nanoscale features and that are shaped like flower petals. When an enzyme is used as the protein component of the hybrid nanoflower, it exhibits enhanced enzymatic activity and stability compared with the free enzyme. This is attributed to the high surface area and confinement of the enzymes in the nanoflowers.

RASL: Robust Alignment by Sparse and Low-Rank Decomposition for Linearly Correlated Images

Abstract: This paper studies the problem of simultaneously aligning a batch of linearly correlated images despite gross corruption (such as occlusion). Our method seeks an optimal set of image domain transformations such that the matrix of transformed images can be decomposed as the sum of a sparse matrix of errors and a low-rank matrix of recovered aligned images. We reduce this extremely challenging optimization problem to a sequence of convex programs that minimize the sum of l1-norm and nuclear norm of the two component matrices, which can be efficiently solved by scalable convex optimization techniques. We verify the efficacy of the proposed robust alignment algorithm with extensive experiments on both controlled and uncontrolled real data, demonstrating higher accuracy and efficiency than existing methods over a wide range of realistic misalignments and corruptions.

Dispersionless Phase Discontinuities for Controlling Light Propagation

Abstract: Ultrathin metasurfaces consisting of a monolayer of subwavelength plasmonic resonators are capable of generating local abrupt phase changes and can be used for controlling the wavefront of electromagnetic waves. The phase change occurs for transmitted or reflected wave components whose polarization is orthogonal to that of a linearly polarized (LP) incident wave. As the phase shift relies on the resonant features of the plasmonic structures, it is in general wavelength-dependent. Here, we investigate the interaction of circularly polarized (CP) light at an interface composed of a dipole antenna array to create spatially varying abrupt phase discontinuities. The phase discontinuity is dispersionless, that is, it solely depends on the orientation of dipole antennas, but not their spectral response and the wavelength of incident light. By arranging the antennas in an array with a constant phase gradient along the interface, the phenomenon of broadband anomalous refraction is observed ranging from visible to ...

Dramatic Activity of C3N4/BiPO4 Photocatalyst with Core/Shell Structure Formed by Self-Assembly

Abstract: Core/shell structured C3N4/BiPO4 photocatalyst is fabricated via a facile ultrasonic dispersion method. The thickness of the shell may be controlled by tuning the amount of C3N4 in the dispersion, which determines the enhanced level of photocatalytic activity. The optimum photocatalytic activity of C3N4/BiPO4 at a weight ratio of 4% (C3N4/BiPO4) under UV irradiation is almost 4.5 times as high as that of reference P25 (TiO2) and 2.5 times of BiPO4. More attractively, the dramatic visible light photocatalytic activity is generated due to the C3N4 loaded. The enhancement in performance is demonstrated to be the match of lattice and energy level between the C3N4 and BiPO4. This match facilitates the separation and transfer of photogenerated electron–hole pairs at the heterojunction interfaces and may be important for other core/shell structured materials. In addition, this method is expected to be extended for other C3N4 loaded materials.

A Versatile, Ultralight, Nitrogen‐Doped Graphene Framework

Abstract: Graphene lite: a density of (2.1 ± 0.3) mg cm(-3), the lowest to date for a graphene framework architecture, is achieved by preparing an ultralight, N-doped, 3D graphene framework (see photo of a block of the material balancing on a dandelion). Its adsorption capacity for oils and organic solvents is much higher than that of the best carbonaceous sorbents, and it is a promising electrode material for supercapacitors (484 F g(-1)) and as a metal-free catalyst for the oxygen reduction reaction.

Biomass recalcitrance. Part I: the chemical compositions and physical structures affecting the enzymatic hydrolysis of lignocellulose

Abstract: Lignocellulosic biomass is recalcitrant to biodegradation due to the rigid and compact structure of plant cell wall The recalcitrance of biomass is mainly constructed by its chemical compositions that build a spatial network as a protective bulwark Generally, the factors affecting the accessibility of biomass cellulose can be divided into direct and indirect factors The direct factors refer to the accessible surface area, and the indirect factors include biomass structure-relevant factors (pore size and volume, particle size, and specific surface area), chemical compositions (lignin, hemicelluloses, and acetyl group), and cellulose structure-relevant factors (cellulose crystallinity and degree of polymerization) Pre-treatment is actually the process to alter indirect factors and improve direct factors thus enhancing the accessibility of cellulose In this review, we summarize the effects of chemical compositions and physical structures on the enzymatic digestibility of lignocellulosic biomass We suggest that future work should be focused on but not limited to the molecular mechanisms of biomass recalcitrance by investigating the microscale and nanoscale features as well as hydrogen bonds network of lignocellulosic biomass © 2012 Society of Chemical Industry and John Wiley & Sons, Ltd

Locating in fingerprint space: wireless indoor localization with little human intervention

Abstract: Indoor localization is of great importance for a range of pervasive applications, attracting many research efforts in the past decades. Most radio-based solutions require a process of site survey, in which radio signatures of an interested area are annotated with their real recorded locations. Site survey involves intensive costs on manpower and time, limiting the applicable buildings of wireless localization worldwide. In this study, we investigate novel sensors integrated in modern mobile phones and leverage user motions to construct the radio map of a floor plan, which is previously obtained only by site survey. On this basis, we design LiFS, an indoor localization system based on off-the-shelf WiFi infrastructure and mobile phones. LiFS is deployed in an office building covering over 1600m2, and its deployment is easy and rapid since little human intervention is needed. In LiFS, the calibration of fingerprints is crowdsourced and automatic. Experiment results show that LiFS achieves comparable location accuracy to previous approaches even without site survey.

Plastics derived from biological sources: present and future: a technical and environmental review.

Abstract: In the time period 2010 2015, the worldwide annual production of plastics is very likely to surpass 300 million tons,1,2 requiring multiple amounts of petroleum and leading to hundreds of millions of tons ofCO2 in addition to health risks for the public due to the release of other types of emissions.1,3 A large amount of plastics (at least 40% of the total consumption) is used in short-term applications, and the resulting waste can quickly lead to additional environmental damage unless adequate waste management systems are in place. For example, conventional petrochemical plastics are harmful for terrestrial and sea animals as well as birds that tend to eat plastic residues;4 these impacts could be reduced by plastics that are biodegradable by microorganisms. In short, petrochemical plastics are not sustainable and bio-based sustainable plastics should be developed to avoid problems caused by the petrochemical plastics.

Three-dimensional graphene architectures

Abstract: Graphene has been widely explored for applications in electronics, sensors, actuators, catalysis and bio- or energy related systems. For these purposes, graphene materials usually have to be fabricated or assembled into desired micro-/nano-architectures for tuning and/or controlling their electrical, optical, mechanical, chemical or electrochemical properties. In this feature article, we review recent achievements in the studies of three-dimensional (3D) graphene architectures. The methodology for preparing these 3D graphene micro-/nano-architectures and their potential applications have been summarized.

Oxygen Reduction Electrocatalyst Based on Strongly Coupled Cobalt Oxide Nanocrystals and Carbon Nanotubes

Abstract: Electrocatalyst for oxygen reduction reaction (ORR) is crucial for a variety of renewable energy applications and energy-intensive industries. The design and synthesis of highly active ORR catalysts with strong durability at low cost is extremely desirable but remains challenging. Here, we used a simple two-step method to synthesize cobalt oxide/carbon nanotube (CNT) strongly coupled hybrid as efficient ORR catalyst by directly growing nanocrystals on oxidized multiwalled CNTs. The mildly oxidized CNTs provided functional groups on the outer walls to nucleate and anchor nanocrystals, while retaining intact inner walls for highly conducting network. Cobalt oxide was in the form of CoO due to a gas-phase annealing step in NH3. The resulting CoO/nitrogen-doped CNT (NCNT) hybrid showed high ORR current density that outperformed Co3O4/graphene hybrid and commercial Pt/C catalyst at medium overpotential, mainly through a 4e reduction pathway. The metal oxide/carbon nanotube hybrid was found to be advantageous o...