Showing papers by "National Tsing Hua 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.

Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages

Abstract: Aims In ecology and conservation biology, the number of species counted in a biodiversity study is a key metric but is usually a biased underestimate of total species richness because many rare species are not detected. Moreover, comparing species richness among sites or samples is a statistical challenge because the observed number of species is sensitive to the number of individuals counted or the area sampled. For individual-based data, we treat a single, empirical sample of species abundances from an investigator-defined species assemblage or community as a reference point for two estimation objectives under two sampling models: estimating the expected number of species (and its unconditional variance) in a random sample of (i) a smaller number of individuals (multinomial model) or a smaller area sampled (Poisson model) and (ii) a larger number of individuals or a larger area sampled. For sample-based incidence (presence–absence) data, under a Bernoulli product model, we treat a single set of species incidence frequencies as the reference point to estimate richness for smaller and larger numbers of sampling units. Methods The first objective is a problem in interpolation that we address with classical rarefaction (multinomial model) and Coleman rarefaction (Poisson model) for individual-based data and with sample-based rarefaction (Bernoulli product model) for incidence frequencies. The second is a problem in extrapolation that we address with sampling-theoretic predictors for the number of species in a larger sample (multinomial model), a larger area (Poisson model) or a larger number of sampling units (Bernoulli product model), based on an estimate of asymptotic species richness. Although published methods exist for many of these objectives, we bring them together here with some new estimators under a unified statistical and notational framework. This novel integration of mathematically distinct approaches allowed us to link interpolated (rarefaction) curves and extrapolated curves to plot a unified species accumulation curve for empirical examples. We provide new, unconditional variance estimators for classical, individual-based rarefaction and for Coleman rarefaction, long missing from the toolkit of biodiversity measurement. We illustrate these methods with datasets for tropical beetles, tropical trees and tropical ants.

Coverage‐based rarefaction and extrapolation: standardizing samples by completeness rather than size

Abstract: We propose an integrated sampling, rarefaction, and extrapolation methodology to compare species richness of a set of communities based on samples of equal completeness (as measured by sample coverage) instead of equal size. Traditional rarefaction or extrapolation to equal-sized samples can misrepresent the relationships between the richnesses of the communities being compared because a sample of a given size may be sufficient to fully characterize the lower diversity community, but insufficient to characterize the richer community. Thus, the traditional method systematically biases the degree of differences between community richnesses. We derived a new analytic method for seamless coverage-based rarefaction and extrapolation. We show that this method yields less biased comparisons of richness between communities, and manages this with less total sampling effort. When this approach is integrated with an adaptive coverage-based stopping rule during sampling, samples may be compared directly without rarefaction, so no extra data is taken and none is thrown away. Even if this stopping rule is not used during data collection, coverage-based rarefaction throws away less data than traditional size-based rarefaction, and more efficiently finds the correct ranking of communities according to their true richnesses. Several hypothetical and real examples demonstrate these advantages.

A Review of CO2 Capture by Absorption and Adsorption

Abstract: Global warming resulting from the emission of greenhouse gases, especially CO2, has become a widespread concern in the recent years. Though various CO2 capture technologies have been proposed, chemical absorption and adsorption are currently believed to be the most suitable ones for post-combustion power plants. The operation of the chemical absorption process is reviewed in this work, together with the use of absorbents, such as the ionic liquid, alkanolamines and their blended aqueous solutions. The major concerns for this technology, including CO2 capture efficiency, absorption rate, energy required in regeneration, and volume of absorber, are addressed. For adsorption, in addition to physical adsorbents, various mesoporous solid adsorbents impregnated with polyamines and grafted with aminosilanes are reviewed in this work. The major concerns for selection of adsorbent, including cost, adsorption rate, CO2 adsorption capacity, and thermal stability, are compared and discussed. More effective and less energy-consuming regeneration techniques for CO2-loaded adsorbents are also proposed. Future works for both absorption and adsorption are suggested.

Nanoantennas for visible and infrared radiation.

Abstract: Nanoantennas for visible and infrared radiation can strongly enhance the interaction of light with nanoscale matter by their ability to efficiently link propagating and spatially localized optical fields. This ability unlocks an enormous potential for applications ranging from nanoscale optical microscopy and spectroscopy over solar energy conversion, integrated optical nanocircuitry, opto-electronics and density-of-states engineering to ultra-sensing as well as enhancement of optical nonlinearities. Here we review the current understanding of metallic optical antennas based on the background of both well-developed radiowave antenna engineering and plasmonics. In particular, we discuss the role of plasmonic resonances on the performance of nanoantennas and address the influence of geometrical parameters imposed by nanofabrication. Finally, we give a brief account of the current status of the field and the major established and emerging lines of investigation in this vivid area of research.

Graphene Annealing: How Clean Can It Be?

Abstract: Surface contamination by polymer residues has long been a critical problem in probing graphene’s intrinsic properties and in using graphene for unique applications in surface chemistry, biotechnology, and ultrahigh speed electronics. Poly(methyl methacrylate) (PMMA) is a macromolecule commonly used for graphene transfer and device processing, leaving a thin layer of residue to be empirically cleaned by annealing. Here we report on a systematic study of PMMA decomposition on graphene and of its impact on graphene’s intrinsic properties using transmission electron microscopy (TEM) in combination with Raman spectroscopy. TEM images revealed that the physisorbed PMMA proceeds in two steps of weight loss in annealing and cannot be removed entirely at a graphene susceptible temperature before breaking. Raman analysis shows a remarkable blue-shift of the 2D mode after annealing, implying an anneal-induced band structure modulation in graphene with defects. Calculations using density functional theory show that l...

Superhydrophobic and superoleophilic properties of graphene-based sponges fabricated using a facile dip coating method

Abstract: Superhydrophobic and superoleophilic graphene-based sponges are demonstrated as efficient absorbents for a broad range of oils and organic solvents with high selectivity, good recyclability, and excellent absorption capacities up to 165 times their own weight. The findings show promise for large-scale removal of organic contaminants, especially in the field of oil spillage cleanup.

Highly conductive PEDOT:PSS electrode by simple film treatment with methanol for ITO-free polymer solar cells

Abstract: We proposed a simple yet robust film treatment method with methanol having only one hydroxyl group to enhance the conductivity of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) by four orders of magnitude. Different methods of film treatment: immersing PEDOT:PSS film in the methanol solution; dropping methanol on the film; and a combination of these are employed and the results are compared. The conductivity of PEDOT:PSS films was enhanced from 0.3 S cm−1 to 1362 S cm−1 after film treatment with methanol. Other alcohols like ethanol and propanol were also used to treat the PEDOT:PSS film and showed inferior conductivity enhancement compared to methanol. The conductivity enhancement was greatly affected by the hydrophilicity and dielectric constant of the alcohols used. The mechanism of conductivity enhancement was investigated through various characterization techniques including FTIR, XPS and AFM. Removal of the insulator PSS from the film, and morphology and conformational changes are the mechanisms for the conductivity enhancement. The treated films also showed high transmittance and low sheet resistance desirable for a standalone electrode. ITO-free polymer solar cells were fabricated using PEDOT:PSS electrodes treated with methanol and showed almost equal performance to ITO electrodes.

Plasmonic Nanolaser Using Epitaxially Grown Silver Film

Abstract: A nanolaser is a key component for on-chip optical communications and computing systems. Here, we report on the low-threshold, continuous-wave operation of a subdiffraction nanolaser based on surface plasmon amplification by stimulated emission of radiation. The plasmonic nanocavity is formed between an atomically smooth epitaxial silver film and a single optically pumped nanorod consisting of an epitaxial gallium nitride shell and an indium gallium nitride core acting as gain medium. The atomic smoothness of the metallic film is crucial for reducing the modal volume and plasmonic losses. Bimodal lasing with similar pumping thresholds was experimentally observed, and polarization properties of the two modes were used to unambiguously identify them with theoretically predicted modes. The all-epitaxial approach opens a scalable platform for low-loss, active nanoplasmonics.

Synthesis of Cu2O nanocrystals from cubic to rhombic dodecahedral structures and their comparative photocatalytic activity.

Abstract: In this study, a new series of Cu2O nanocrystals with systematic shape evolution from cubic to face-raised cubic, edge- and corner-truncated octahedral, all-corner-truncated rhombic dodecahedral, {100}-truncated rhombic dodecahedral, and rhombic dodecahedral structures have been synthesized. The average sizes for the cubes, edge- and corner-truncated octahedra, {100}-truncated rhombic dodecahedra, and rhombic dodecahedra are approximately 200, 140, 270, and 290 nm, respectively. An aqueous mixture of CuCl2, sodium dodecyl sulfate, NaOH, and NH2OH·HCl was prepared to produce these nanocrystals at room temperature. Simple adjustment of the amounts of NH2OH·HCl introduced enables this particle shape evolution. These novel particle morphologies have been carefully analyzed by transmission electron microscopy (TEM). The solution color changes quickly from blue to green, yellow, and then orange within 1 min of reaction in the formation of nanocubes, while such color change takes 10–20 min in the growth of rhomb...

Automatic Single-Image-Based Rain Streaks Removal via Image Decomposition

Abstract: Rain removal from a video is a challenging problem and has been recently investigated extensively. Nevertheless, the problem of rain removal from a single image was rarely studied in the literature, where no temporal information among successive images can be exploited, making the problem very challenging. In this paper, we propose a single-image-based rain removal framework via properly formulating rain removal as an image decomposition problem based on morphological component analysis. Instead of directly applying a conventional image decomposition technique, the proposed method first decomposes an image into the low- and high-frequency (HF) parts using a bilateral filter. The HF part is then decomposed into a “rain component” and a “nonrain component” by performing dictionary learning and sparse coding. As a result, the rain component can be successfully removed from the image while preserving most original image details. Experimental results demonstrate the efficacy of the proposed algorithm.

Wafer-Scale MoS2 Thin Layers Prepared by MoO3 Sulfurization

Abstract: Atomically thin molybdenum disulfide (MoS2) layers have attracted great interest due to their direct-gap property and potential applications in optoelectronics and energy harvesting. Meanwhile, they are extremely bendable, promising for applications in flexible electronics. However, the synthetic approach to obtain large-area MoS2 atomic thin layers is still lacking. Here we report that wafer-scale MoS2 thin layers can be obtained using MoO3 thin films as a starting material followed by a two-step thermal process, reduction of MoO3 at 500 °C in hydrogen and sulfurization at 1000 °C in the presence of sulfur. Spectroscopic, optical and electrical characterizations reveal that these films are polycrystalline and with semiconductor properties. The obtained MoS2 films are uniform in thickness and easily transferable to arbitrary substrates, which make such films suitable for flexible electronics or optoelectronics.

A Hybrid Piezoelectric Structure for Wearable Nanogenerators

Abstract: A hybrid-fiber nanogenerator comprising a ZnO nanowire array, PVDF polymer and two electrodes is presented. Depending on the bending or spreading action of the human arm, at an angle of ∼90°, the hybrid fiber reaches electrical outputs of ∼0.1 V and ∼10 nA cm(-2) . The unique structure of the hybrid fiber may inspire future research in wearable energy-harvesting technology.

Metal sulfide nanostructures: synthesis, properties and applications in energy conversion and storage

Abstract: Metal sulfide nanomaterials have attracted great attention because of their excellent properties and promising applications in electronic, optical and optoelectronic devices. Well-aligned nanostructure arrays on substrates are highly attractive for their enhanced properties and novel applications. The general solution route and thermal evaporation under controlled conditions have been utilized for oriented growth of various metal sulfide nanostructure arrays and demonstrated their applications in energy conversion and storage. The article provides an overview of recent research and significant advances reported in the literature, covering from synthesis to properties and to applications especially in energy conversion and storage, such as lithium-ion batteries, solar cells, fuel cells and piezoelectric nanogenerators.

Innovative Efficiency and Stock Returns

Abstract: We find that innovative efficiency (IE), patents or citations scaled by R&D, is a strong positive predictor of future returns after controlling for firm characteristics and risk. The IE-return relation is associated with the loading on a mispricing factor, and the high Sharpe ratio of the Efficient Minus Inefficient (EMI) portfolio suggests that mispricing plays an important role. Further tests based upon attention and uncertainty proxies suggest that limited attention contributes to the effect. The high weight of the EMI portfolio return in the tangency portfolio suggests that IE captures incremental pricing effects relative to well-known factors.

Mitochondrial fission contributes to mitochondrial dysfunction and insulin resistance in skeletal muscle.

Abstract: Mitochondrial dysfunction in skeletal muscle has been implicated in the development of insulin resistance and type 2 diabetes. Considering the importance of mitochondrial dynamics in mitochondrial and cellular functions, we hypothesized that obesity and excess energy intake shift the balance of mitochondrial dynamics, further contributing to mitochondrial dysfunction and metabolic deterioration in skeletal muscle. First, we revealed that excess palmitate (PA), but not hyperglycemia, hyperinsulinemia, or elevated tumor necrosis factor alpha, induced mitochondrial fragmentation and increased mitochondrion-associated Drp1 and Fis1 in differentiated C2C12 muscle cells. This fragmentation was associated with increased oxidative stress, mitochondrial depolarization, loss of ATP production, and reduced insulin-stimulated glucose uptake. Both genetic and pharmacological inhibition of Drp1 attenuated PA-induced mitochondrial fragmentation, mitochondrial depolarization, and insulin resistance in C2C12 cells. Furthermore, we found smaller and shorter mitochondria and increased mitochondrial fission machinery in the skeletal muscle of mice with genetic obesity and those with diet-induced obesity. Inhibition of mitochondrial fission improved the muscle insulin signaling and systemic insulin sensitivity of obese mice. Our findings indicated that aberrant mitochondrial fission is causally associated with mitochondrial dysfunction and insulin resistance in skeletal muscle. Thus, disruption of mitochondrial dynamics may underlie the pathogenesis of muscle insulin resistance in obesity and type 2 diabetes.

Transport magnetic proximity effects in platinum.

Abstract: Platinum (Pt) metal, being nonmagnetic and with a strong spin-orbit coupling interaction, has been central in detecting the pure spin current and establishing most of the recent spin-based phenomena. Magnetotransport measurements, both electrical and thermal, conclusively show strong ferromagnetic characteristics in thin Pt films on the ferromagnetic insulator due to the magnetic proximity effects. The pure spin current phenomena measured by Pt, including the inverse spin Hall and the spin Seebeck effects, are thus contaminated and not exclusively established.

Hedgehog spin texture and Berry's phase tuning in a magnetic topological insulator

Abstract: Understanding and control of spin degrees of freedom on the surfaces of topological materials are key to future applications as well as for realizing novel physics such as the axion electrodynamics associated with time-reversal (TR) symmetry breaking on the surface. We experimentally demonstrate magnetically induced spin reorientation phenomena simultaneous with a Dirac-metal to gapped-insulator transition on the surfaces of manganese-doped Bi2Se3 thin films. The resulting electronic groundstate exhibits unique hedgehog-like spin textures at low energies, which directly demonstrate the mechanics of TR symmetry breaking on the surface. We further show that an insulating gap induced by quantum tunnelling between surfaces exhibits spin texture modulation at low energies but respects TR invariance. These spin phenomena and the control of their Fermi surface geometrical phase first demonstrated in our experiments pave the way for the future realization of many predicted exotic magnetic phenomena of topological origin.

Saliency Detection in the Compressed Domain for Adaptive Image Retargeting

Abstract: Saliency detection plays important roles in many image processing applications, such as regions of interest extraction and image resizing. Existing saliency detection models are built in the uncompressed domain. Since most images over Internet are typically stored in the compressed domain such as joint photographic experts group (JPEG), we propose a novel saliency detection model in the compressed domain in this paper. The intensity, color, and texture features of the image are extracted from discrete cosine transform (DCT) coefficients in the JPEG bit-stream. Saliency value of each DCT block is obtained based on the Hausdorff distance calculation and feature map fusion. Based on the proposed saliency detection model, we further design an adaptive image retargeting algorithm in the compressed domain. The proposed image retargeting algorithm utilizes multioperator operation comprised of the block-based seam carving and the image scaling to resize images. A new definition of texture homogeneity is given to determine the amount of removal block-based seams. Thanks to the directly derived accurate saliency information from the compressed domain, the proposed image retargeting algorithm effectively preserves the visually important regions for images, efficiently removes the less crucial regions, and therefore significantly outperforms the relevant state-of-the-art algorithms, as demonstrated with the in-depth analysis in the extensive experiments.

A review of sensor-based methods for monitoring hydrogen sulfide

Abstract: We review sensor-based methods commonly employed for monitoring hydrogen sulfide (H2S), and recent developments in H2S-sensing instrumentation. We evaluate the basic quality-assurance parameters of different sensor types for quantifying H2S in terms of major operational criteria (e.g., response time, limit of detection, common operating range of concentrations, and stability). We also describe the applicability of these sensor-based methods with respect to practicality in various environmental settings. Finally, we highlight the limitations and the future prospects of these sensor-based methods. a 2011 Elsevier Ltd. All rights reserved.

Proposing a resolution to debates on diversity partitioning

Abstract: There have been intense debates about the decomposition of regional diversity (gamma) into its within-community component (alpha) and between-community component (beta). Although a recent Ecology Forum achieved consensus in the use of "numbers equivalents" (Hill numbers) as the proper choice of diversity measure, three related major issues were still left unresolved. (1) What is the precise meaning of the "independence" or "statistical independence" of alpha diversity and beta diversity? (2) Which partitioning (additive vs. multiplicative) should be used for a given application? (3) What is the proper formula for alpha diversity, as there are two formulas in the literature? This paper proposes a possible resolution to each of these issues. For the first issue, we clarify the definitions of "independence" and "statistical independence" from two perspectives so that confusion about this issue can be cleared up. We also discuss the causes of dependence, so that the dependence relationship between any two diversity components in both partitioning schemes can be rigorously justified by theory and also intuitively understood by simulation. For the second issue, both multiplicative and additive beta diversities based on Hill numbers are useful measures and quantify different aspects of communities. However, neither can be directly applied to compare relative compositional similarity or differentiation across multiple regions with different numbers of communities because multiplicative beta diversity depends on the number of communities, and additive beta diversity additionally depends on alpha (equivalently, on gamma). Such dependences should be removed. We propose transformations to remove these dependences, and we show that the transformed multiplicative beta and additive beta both lead to the same classes of measures, which are always in a range of [0, 1] and thus can be used to compare relative similarity or differentiation among communities across multiple regions. These similarity measures include multiple-community generalizations of the Sorenson, Jaccard, Horn, and Morisita-Horn measures. For the third issue, we present some observations including a finding about which alpha formula produces independent alpha and beta components. These may help to resolve the choice of a proper formula for alpha diversity. Some related issues are also briefly discussed.

Distributed Robust Multicell Coordinated Beamforming With Imperfect CSI: An ADMM Approach

Abstract: Multicell coordinated beamforming (MCBF), where multiple base stations (BSs) collaborate with each other in the beamforming design for mitigating the intercell interference (ICI), has been a subject drawing great attention recently. Most MCBF designs assume perfect channel state information (CSI) of mobile stations (MSs); however CSI errors are inevitable at the BSs in practice. Assuming elliptically bounded CSI errors, this paper studies the robust MCBF design problem that minimizes the weighted sum power of BSs subject to worst-case signal-to-interference-plus-noise ratio (SINR) constraints on the MSs. Our goal is to devise a distributed optimization method to obtain the worst-case robust beamforming solutions in a decentralized fashion with only local CSI used at each BS and limited backhaul information exchange between BSs. However, the considered problem is difficult to handle even in the centralized form. We first propose an efficient approximation method for solving the nonconvex centralized problem, using semidefinite relaxation (SDR), an approximation technique based on convex optimization. Then a distributed robust MCBF algorithm is further proposed, using a distributed convex optimization technique known as alternating direction method of multipliers (ADMM). We analytically show the convergence of the proposed distributed robust MCBF algorithm to the optimal centralized solution. We also extend the worst-case robust beamforming design as well as its decentralized implementation method to a fully coordinated scenario. Simulation results are presented to examine the effectiveness of the proposed SDR method and the distributed robust MCBF algorithm.

DOPA-mediated reduction allows the facile synthesis of fluorescent gold nanoclusters for use as sensing probes for ferric ions.

Abstract: In this paper, we describe a simple one-pot method, employing l-3,4-dihydroxyphenylalanine (l-DOPA) as a reducing/capping reagent, for the synthesis of fluorescent gold nanoclusters (AuNCs). Within a short reaction time of 15 min (excluding the time required for purification), this strategy allows the fabrication of homogeneous AuNCs having the capability to sense ferric ions (Fe3+). The as-prepared AuNCs exhibited a fluorescence emission at 525 nm and a quantum yield of 1.7%. On the basis of an aggregation-induced fluorescence quenching mechanism, these fluorescent AuNCs offer acceptable sensitivity, high selectivity, and a limit of detection of 3.5 μM for the determination of Fe3+ ions, which is lower than the maximum level (0.3 mg L–1, equivalent to 5.4 μM) of Fe3+ permitted in drinking water by the U.S. Environmental Protection Agency.