Taipei, Taiwan
Taipei, Taiwan

Time filter

Source Type

Huang Y.-T.,Academia Sinica, Taiwan
Epidemiology | Year: 2017

BACKGROUND.: Mediation analyses have been a popular approach to investigate the effect of an exposure on an outcome through a mediator. Mediation models with multiple mediators have been proposed for continuous and dichotomous outcomes. However, development of multi-mediator models for survival outcomes is still limited. METHODS.: We present methods for multi-mediator analyses using three survival models: Aalen additive hazard models, Cox proportional hazard models, and semiparametric probit models. Effects through mediators can be characterized by path-specific effects, for which definitions and identifiability assumptions are provided. We derive closed form expressions for path-specific effects for the three models, which are intuitively interpreted using a causal diagram. RESULTS.: Mediation analyses using Cox models under the rare outcome assumption and Aalen additive hazard models consider effects on log hazard ratio and hazard difference, respectively; analyses using semiparametric probit models consider effects on difference in transformed survival time as well as survival probability. The three models were applied to a hepatitis study where we investigated effects of hepatitis C on liver cancer incidence mediated through baseline and/or follow-up hepatitis B viral load. The three methods show consistent results on respective effect scales, which suggest an adverse estimated effect of hepatitis C on liver cancer not mediated through hepatitis B, and a protective estimated effect mediated through the baseline (and possibly follow-up) of hepatitis B viral load. CONCLUSIONS.: Causal mediation analyses of survival outcome with multiple mediators are developed for additive hazard and proportional hazard and probit models with utility demonstrated in a hepatitis study. Copyright © 2017 Wolters Kluwer Health, Inc. All rights reserved.

Chang C.-C.,Academia Sinica, Taiwan
East Asian Science, Technology, and Medicine | Year: 2015

This paper is intended to explain the changes in the activities of the Imperial Academy of Medicine during the Qing dynasty (1644-1911). By tracing its precedents and comparing their functions, I will explain its role during the Qing dynasty. Furthermore, the seemingly hidebound institutional codes in fact reveal interesting information about the dynamics of the Academy. Through examining the impacts of the regulations on personnel and their careers, we are able to explain the very different requirements of the Qing rulers for their medical service. Up until the Ming period (1368-1644) there was an institutional boundary between medical services for the palace and those for the state, even though they shared the same personnel. The Qing was the first dynasty in which even this unclear line disappeared. In this sense, the Qing Academy did not simply copy the tradition of its predecessors. Instead, the services for the emperor's individual needs became more and more central to its mission. Thus, the common people's rather critical perceptions of the bureau were largely true. In spite of its increased emphasis on serving the imperial household, the Qing Academy retained its connections with the government. As an alien regime, the Manchu court's concern for the security of its rulers was much higher than during the previous dynasty. To meet the needs of the new regime, the device of the Qing Academy emphasized fostering elites rather than selecting them. Now the Academy not only provided medical education to the junior members as in earlier periods, but also shaped them in behavior. This affected both the organization of the Imperial Medical Academy, and the strategies of the physicians employed in it.

Lin T.-C.,Chang Gung Memorial Hospital | Hsiao M.,Academia Sinica, Taiwan | Hsiao M.,Kaohsiung Medical University
Biochimica et Biophysica Acta - Reviews on Cancer | Year: 2017

Ghrelin is a small peptide with 28 amino acids, and has been characterized as the ligand of the growth hormone secretagogue receptor (GHSR). In addition to its original function in stimulating pituitary growth hormone release, ghrelin is multifunctional and plays a role in the regulation of energy balance, gastric acid release, appetite, insulin secretion, gastric motility and the turnover of gastric and intestinal mucosa. The discovery of ghrelin and GHSR expression beyond normal tissues suggests its role other than physiological function. Emerging evidences have revealed ghrelin's function in regulating several processes related to cancer progression, especially in metastasis and proliferation. We further show the relative GHRL and GHSR expression in pan-cancers from The Cancer Genome Atlas (TCGA), suggesting the potential pathological role of the axis in cancers. This review focuses on ghrelin's biological function in cancer progression, and reveals its clinical significance especially the impact on cancer patient outcome. © 2017 The Authors

Lambing C.,University of Cambridge | Franklin F.C.H.,University of Birmingham | Wang C.-J.R.,Academia Sinica, Taiwan
Plant Physiology | Year: 2017

Meiosis is a specialized cell division, essential in most reproducing organisms to halve the number of chromosomes, thereby enabling the restoration of ploidy levels during fertilization. A key step of meiosis is homologous recombination, which promotes homologous pairing and generates crossovers (COs) to connect homologous chromosomes until their separation at anaphase I. These CO sites, seen cytologically as chiasmata, represent a reciprocal exchange of genetic information between two homologous nonsister chromatids. This gene reshuffling during meiosis has a significant influence on evolution and also plays an essential role in plant breeding, because a successful breeding program depends on the ability to bring the desired combinations of alleles on chromosomes. However, the number and distribution of COs during meiosis is highly constrained. There is at least one CO per chromosome pair to ensure accurate segregation of homologs, but in most organisms, the CO number rarely exceeds three regardless of chromosome size. Moreover, their positions are not random on chromosomes but exhibit regional preference. Thus, genes in recombination-poor regions tend to be inherited together, hindering the generation of novel allelic combinations that could be exploited by breeding programs. Recently, much progress has been made in understanding meiotic recombination. In particular, many genes involved in the process in Arabidopsis (Arabidopsis thaliana) have been identified and analyzed. With the coming challenges of food security and climate change, and our enhanced knowledge of how COs are formed, the interest and needs in manipulating CO formation are greater than ever before. In this review, we focus on advances in understanding meiotic recombination and then summarize the attempts to manipulate CO formation. Last, we pay special attention to the meiotic recombination in polyploidy, which is a common genomic feature for many crop plants. © 2017 American Society of Plant Biologists. All rights reserved.

Chan T.-S.T.,Academia Sinica, Taiwan | Yang Y.-H.,Academia Sinica, Taiwan
IEEE Signal Processing Letters | Year: 2017

Singing voice separation attempts to separate the vocal and instrumental parts of a music recording, which is a fundamental problem in music information retrieval. Recent work on singing voice separation has shown that the low-rank representation and informed separation approaches are both able to improve separation quality. However, low-rank optimizations are computationally inefficient due to the use of singular value decompositions. Therefore, in this letter, we propose a new linear-time algorithm called informed group-sparse representation, and use it to separate the vocals from music using pitch annotations as side information. Experimental results on the iKala dataset confirm the efficacy of our approach, suggesting that the music accompaniment follows a group-sparse structure given a pretrained instrumental dictionary. We also show how our work can be easily extended to accommodate multiple dictionaries using the DSD100 dataset. © 1994-2012 IEEE.

Chou H.-J.,Academia Sinica, Taiwan | Chang R.Y.,Academia Sinica, Taiwan
IEEE Transactions on Wireless Communications | Year: 2017

This paper considers a device-to-device (D2D) communications underlaid multiple-input multiple-output cellular network and studies D2D mode selection from a previously unexamined perspective. Since D2D mode selection affects the network interference profile and vice versa, a joint D2D mode selection and interference management is desired but challenging. In this paper, we propose a holistic approach to this problem with interference-free considerations. We adopt the degrees-of-freedom (DoFs) as the mode-selection criterion and exploit the linear interference alignment technique for interference management. We analyze the achievable sum DoF of the potential D2D users according to their mode selections, and derive the probabilistic sum-rate relations between the proposed DoF-based mode selection scheme and the common received-signal-strength-index-based mode selection scheme in Poisson point process networks. Simulation illustrates the theoretical insights and shows the advantages of the proposed DoF-based mode selection scheme over conventional mode selection schemes from various perspectives. The proposed scheme presents a promising proposal for D2D mode selection in 5G communications. © 2016 IEEE.

Chen Y.-C.,Academia Sinica, Taiwan | Chen Y.-C.,Yuan Ze University
IEEE Transactions on Information Forensics and Security | Year: 2017

Visual cryptography (VC) is a variant form of secret sharing. In general threshold setting, the k-out-of-n VC allows that, in a set of n participants, any k can recover and reconstruct the secret by stacking their shares. Recently, the notion of multiple-secret VC has been introduced to embed multiple secrets. Region incrementing visual cryptography (RIVC) is referred to as a new type of multi-secret VC. RIVC defines s layers and takes s secrets, and then embeds each secret into each layer. The layers are defined by the number of participants; for example, let two secrets and two layers be S2,S3 and L2,L3 in two-out-of-three RIVC, where any two participants in L2 can recover S2 and three in L3 can recover S2,S3. However, there is another multi-secret VC, called fully incrementing visual cryptography (FIVC), which also has the layers, but only one secret Si will reveal in one layer Li. In this paper, our stating point is to propose a new notion of non-monotonic visual cryptography (NVC) for human vision system as a primitive to construct FIVC. We first present an ideal construction of simple NVC, which relies on a slightly unreasonable assumption. Based on the simple NVC, we show a few methods to extend the functionality for complicated cases of NVC. Then, the generic construction is presented as a systematic manner to eliminate the above-mentioned assumption. Finally, we formally introduce a transformation NVC-to-FIVC algorithm, which takes NVC as input and then produce a construction of FIVC. Also, show a demonstration the NVC-to-RIVC algorithm, and analyze some properties regarding NVC. We believe that the notion of NVC can potentially find other applications and is of independent interest. © 2005-2012 IEEE.

Allaerts W.,Erasmus University Rotterdam | Chang T.W.,Academia Sinica, Taiwan
Acta Biotheoretica | Year: 2017

The Hygiene Hypothesis has been recognized as an important cornerstone to explain the sudden increase in the prevalence of asthma and allergic diseases in modernized culture. The recent epidemic of allergic diseases is in contrast with the gradual implementation of Homo sapiens sapiens to the present-day forms of civilization. This civilization forms a gradual process with cumulative effects on the human immune system, which co-developed with parasitic and commensal Helminths. The clinical manifestation of this epidemic, however, became only visible in the second half of the twentieth century. In order to explain these clinical effects in terms of the underlying IgE-mediated reactions to innocuous environmental antigens, the low biodiversity of antigens in the domestic environment plays a pivotal role. The skewing of antigen exposure as a cumulative effect of reducing biodiversity in the immediate human environment as well as in changing food habits, provides a sufficient and parsimonious explanation for the rise in allergic diseases in a highly developed and helminth-free modernized culture. Socio-economic tendencies that incline towards a further reduction of environmental biodiversity may provide serious concern for future health. This article explains that the “Hygiene Hypothesis”, the “Old Friends Hypothesis”, and the “Skewed Antigen Exposure Hypothesis” are required to more fully explain the rise of allergy in modern societies. © 2017 The Author(s)

Chen Y.-t.,Academia Sinica, Taiwan | Tai C.-Y.,Academia Sinica, Taiwan
Traffic | Year: 2017

Circuit formation in the brain requires neurite outgrowth throughout development to establish synaptic contacts with target cells. Active endocytosis of several adhesion molecules facilitates the dynamic exchange of these molecules at the surface and promotes neurite outgrowth in developing neurons. The endocytosis of N-cadherin, a calcium-dependent adhesion molecule, has been implicated in the regulation of neurite outgrowth, but the mechanism remains unclear. Here, we identified that a fraction of N-cadherin internalizes through clathrin-mediated endocytosis (CME). Two tyrosine-based motifs in the cytoplasmic domain of N-cadherin recognized by the μ2 subunit of the AP-2 adaptor complex are responsible for CME of N-cadherin. Moreover, β-catenin, a core component of the N-cadherin adhesion complex, inhibits N-cadherin endocytosis by masking the 2 tyrosine-based motifs. Removal of β-catenin facilitates μ2 binding to N-cadherin, thereby increasing clathrin-mediated N-cadherin endocytosis and neurite outgrowth without affecting the steady-state level of surface N-cadherin. These results identify and characterize the mechanism controlling N-cadherin endocytosis through β-catenin-regulated μ2 binding to modulate neurite outgrowth. © 2017 John Wiley & Sons A/S.

Sheu S.-Y.,National Yang Ming University | Liu Y.-C.,National Yang Ming University | Yang D.-Y.,Academia Sinica, Taiwan
Physical Chemistry Chemical Physics | Year: 2017

Cooperativity is important in controlling the biological functions of allosteric proteins. Understanding the detailed mechanisms of cooperativity and allosteric regulation in such proteins is essential to understanding their function; however, the mechanism by which allosteric proteins undergo conformational transitions to aid the ligand escape process and its relevance to interfacial water molecules is not well understood. Here, we perform molecular dynamics simulations to examine these issues in Scapharca dimeric hemoglobin. The effects of interfacial water on dimeric motion, ligand escape probability, gate function, and cross-correlation are considered. The results reveal that interfacial water exhibits an unbalanced stress distribution in the interface region, leading to a bias helix bundle motion that not only can expedite the escape of the first ligand but also can increase the interval between the escape of both ligands. Correspondingly, the gate function follows the same time scale as the F-helix movement, and the gate opening is non-stochastic; moreover, the inconsistent motion between the gate parts resembles cooperative behavior. An explicit analysis of the intersubunit communication map provides at least 14 signal transduction pathways. Our results significantly aid in understanding the role of interfacial water in manipulating cooperativity and will lead to further applications involving molecular machines. © the Owner Societies 2017.

Hsu C.-Y.,National Taiwan University | Wu C.-S.,Academia Sinica, Taiwan | Chaw S.-M.,Academia Sinica, Taiwan
Genome biology and evolution | Year: 2016

Many genes in the plastid genomes (plastomes) of plants are organized as gene clusters, in which genes are co-transcribed, resembling bacterial operons. These plastid operons are highly conserved, even among conifers, whose plastomes are highly rearranged relative to other seed plants. We have determined the complete plastome sequence of Sciadopitys verticillata (Japanese umbrella pine), the sole member of Sciadopityaceae. The Sciadopitys plastome is characterized by extensive inversions, pseudogenization of four tRNA genes after tandem duplications, and a unique pair of 370-bp inverted repeats involved in the formation of isomeric plastomes. We showed that plastomic inversions in Sciadopitys have led to shuffling of the remote conserved operons, resulting in the birth of four chimeric gene clusters. Our data also demonstrated that the relocated genes can be co-transcribed in these chimeric gene clusters. The plastome of Sciadopitys advances our current understanding of how the conifer plastomes have evolved toward increased diversity and complexity. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Wu C.-S.,Academia Sinica, Taiwan | Chaw S.-M.,Academia Sinica, Taiwan
Genome Biology and Evolution | Year: 2016

Conifers II (cupressophytes), comprising about 400 tree species in five families, are the most diverse group of living gymnosperms. Their plastid genomes (plastomes) are highly variable in size and organization, but such variation has never been systematically studied. In this study, we assessed the potentialmechanisms underlying the evolution of cupressophyte plastomes.Weanalyzed the plastomes of 24 representative genera in all of the five cupressophyte families, focusing on their variation in size, noncoding DNA content, and nucleotide substitution rates. Using a tree-basedmethod, we further inferred the ancestral plastomic organizations of internal nodes and evaluated the inversions across the evolutionary history of cupressophytes. Our data showed that variation in plastome size is statistically associated with the dynamics of noncoding DNA content, which results in different degrees of plastomic compactness among the cupressophyte families. The degrees of plastomic inversions also vary among the families, with the number of inversions per genus ranging from 0 in Araucariaceae to 1.27 in Cupressaceae. In addition, we demonstrated that synonymous substitution rates are significantly correlated with plastome size aswell as degree of inversions. These data suggest that in cupressophytes, mutation rates play a critical role in driving the evolution of plastomic size while plastomic inversions evolve in a neutral manner. © The Author 2016.

Baldrich P.,Center for Research in Agricultural Genomics | Hsing Y.-I.C.,Academia Sinica, Taiwan | San Segundo B.,Center for Research in Agricultural Genomics
Genome biology and evolution | Year: 2016

MicroRNAs (miRNAs) are small noncoding RNAs that direct posttranscriptional gene silencing in eukaryotes. They are frequently clustered in the genomes of animals and can be independently transcribed or simultaneously transcribed into single polycistronic transcripts. Only a few miRNA clusters have been described in plants, and most of them are generated from independent transcriptional units. Here, we used a combination of bioinformatic tools and experimental analyses to discover new polycistronic miRNAs in rice. A genome-wide analysis of clustering patterns of MIRNA loci in the rice genome was carried out using a criterion of 3 kb as the maximal distance between two miRNAs. This analysis revealed 28 loci with the ability to form the typical hairpin structure of miRNA precursors in which 2 or more mature miRNAs mapped along the same structure. RT-PCR provided evidence for the polycistronic nature of seven miRNA precursors containing homologous or nonhomologous miRNA species. Polycistronic miRNAs and candidate polycistronic miRNAs are located across different rice chromosomes, except chromosome 12, and resided in both duplicated and nonduplicated chromosomal regions. Finally, most polycistronic and candidate polycistronic miRNAs showed a pattern of conservation in the genome of rice species with an AA genome. The diversity in the organization of MIR genes that are transcribed as polycistrons suggests a versatile mechanism for the control of gene expression in different biological processes and supports additional levels of complexity in miRNA functioning in plants. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Wu W.-N.,Academia Sinica, Taiwan
Acta Geodaetica et Geophysica | Year: 2016

Kavitha and Raghukanth (Acta Geod Geophys 1–33, 2015) proposed an algorithm to forecast the earthquake energy release for the global seismogenic zones. They concluded that “the developed model is efficient in forecasting the annual earthquake energy release of most of the seismogenic zone”. However, for several representative case studies their predictions not only are significantly smaller than the observations but also have unreasonable uncertainty. This commentary discusses some of the problems associated with the earthquake data selection for the input of modeling, which may improve the accuracy of the earthquake energy prediction. © 2015, Akadémiai Kiadó.

Tomassetti N.,University of Perugia | Feng J.,Sun Yat Sen University | Feng J.,Academia Sinica, Taiwan
Astrophysical Journal Letters | Year: 2017

A new analysis of cosmic ray (CR) data collected by the SOKOL experiment in space found that the deuteron-to-helium ratio at energies between 500 and 2000 GeV/nucleon takes the value d/He ∼ 1.5. As we will show, this result cannot be explained by standard models of secondary CR production in the interstellar medium and points to the existence of a high-energy source of CR deuterons. To account for the deuteron excess in CRs, we argue that the only viable solution is hadronic interaction processes of accelerated particles inside old supernova remnants (SNRs). From this mechanism, however, the B/C ratio is also expected to increase at energies above ∼50 of GeV/nucleon, in conflict with new precision data just released by the AMS-02 experiment. Hence, if this phenomenon is a real physical effect, hadronic production of CR deuterons must occur in SNRs characterized by low metal abundance. In such a scenario, the sources accelerating C - O nuclei are not the same as those accelerating helium or protons, so that the connection between d/He ratio and B/C ratio is broken, and the latter cannot be used to place constraints on the production of light isotopes or antiparticles. © 2017. The American Astronomical Society. All rights reserved.

Inoue K.T.,Osaka University | Matsushita S.,Academia Sinica, Taiwan | Minezaki T.,University of Tokyo | Chiba M.,Tohoku University
Astrophysical Journal Letters | Year: 2017

We report the 4s detection of a faint object with a flux of ∼0.3 mJy, in the vicinity of the quadruply lensed QSO MG 0414+0534 using the Atacama Large Millimeter/submillimeter array (ALMA) Band 7. The object is most probably a dusty dark dwarf galaxy, which has not been detected in either the optical, near-infrared, or radio (centimeter) bands. An anomaly in the flux ratio of the lensed images observed in Band 7 and the mid-infrared band and the reddening of the QSO light color can be simultaneously explained if we consider the object as a lensing substructure with an ellipticity of ∼0.7 at a redshift of 0.5 ≲ z ≲ 1. Using the best-fit lens models with three lenses, we find that the dark matter plus baryon mass associated with the object is ∼109 Mo, the dust mass is ∼107 Mo, and the linear size is ≳5 kpc. Thus, our findings suggest that the object is a dusty dark dwarf galaxy. A substantial portion of faint submillimeter galaxies (SMGs) in the universe may be attributed to such dark objects. © 2017. The American Astronomical Society. All rights reserved.

Umetsu K.,Academia Sinica, Taiwan | Diemer B.,Harvard - Smithsonian Center for Astrophysics
Astrophysical Journal | Year: 2017

The lensing signal around galaxy clusters can, in principle, be used to test detailed predictions for their average mass profile from numerical simulations. However, the intrinsic shape of the profiles can be smeared out when a sample that spans a wide range of cluster masses is averaged in physical length units. This effect especially conceals rapid changes in gradient such as the steep drop associated with the splashback radius, a sharp edge corresponding to the outermost caustic in accreting halos. We optimize the extraction of such local features by scaling individual halo profiles to a number of spherical overdensity radii, and apply this method to 16 X-rayselected, high-mass clusters targeted in the Cluster Lensing And Supernova survey with Hubble. By forwardmodeling the weak- and strong-lensing data presented by Umetsu et al., we show that, regardless of the scaling overdensity, the projected ensemble density profile is remarkably well described by a Navarro-Frenk-White (NFW) or Einasto profile out to R ∼ 2.5 h-1 Mpc, beyond which the profiles flatten. We constrain the NFW concentration to c200c = 3.66 ± 0.11 at M200c ≃ 1.0 × 1015 h-1 M⊙, consistent with and improved from previous work that used conventionally stacked lensing profiles, and in excellent agreement with theoretical expectations. Assuming the profile form of Diemer & Kravtsov and generic priors calibrated from numerical simulations, we place a lower limit on the splashback radius of the cluster halos, if it exists, of Rsp 3D/r200m > 0.89 (Rsp 3D > 1.83 h-1 Mpc) at 68% confidence. The corresponding density feature is most pronounced when the cluster profiles are scaled by r200m, and smeared out when scaled to higher overdensities. © 2017. The American Astronomical Society. All rights reserved.

Geballe T.R.,Gemini Observatory | Burton M.G.,Armagh Observatory and Planetarium | Pike R.E.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2017

Vibration-rotation lines of H2 from highly excited levels approaching the dissociation limit have been detected at a number of locations in the shocked gas of the Orion Molecular Cloud (OMC-1), including in a Herbig-Haro object near the tip of one of the OMC-1 "fingers." Population diagrams show that, while the excited H2 is almost entirely at a kinetic temperature of ∼1800 K (typical for vibrationally shock-excited H2), as in the previously reported case of Herbig-Haro object HH 7 up to a few percent of the H2 is at a kinetic temperature of ∼5000 K. The location with the largest fraction of hot H2 is the Herbig-Haro object, where the outflowing material is moving at a higher speed than at the other locations. Although theoretical work is required for a better understanding of the 5000 K H2 (including how it cools), its existence and the apparent dependence of its abundance relative to that of the cooler component on the relative velocities of the outflow and the surrounding ambient gas appear broadly consistent with it having recently reformed. The existence of this high-temperature H2 appears to be a common characteristic of shock-excited molecular gas. © 2017. The American Astronomical Society. All rights reserved..

Liu G.-C.,Tamkang University | Ng K.-W.,Academia Sinica, Taiwan
Physics of the Dark Universe | Year: 2017

It was known that isocurvature perturbation of a nearly massless cosmological axion field can lead to rotation of E-mode polarization into B-mode polarization in the cosmic microwave background (CMB) by the presence of a parity violating coupling of the field to the topological density of electromagnetism, resulting in a phenomenon known as anisotropic cosmic birefringence. In this Letter, we propose a new source of anisotropic cosmic birefringence induced by dark matter adiabatic density perturbation. If dark matter is ultralight axions that carry a coupling to photon, its adiabatic density fluctuations will induce anisotropic cosmic birefringence with a blue-tilted rotation power spectrum, thus generating CMB B-mode polarization on sub-degree angular scales. Using current POLARBEAR and SPTPol B-mode polarization data, we derive a constraint on the axion–photon coupling strength (β) and the axion mass (m), β2(10−22eV∕m)2<8×1015. It is shown that the birefringence B modes can dominate over CMB lensing B modes at high l, manifesting as an excess power for l<1500 in future CMB lensing B-mode searches. In addition, we derive the lensing–rotation cross correlation that can be a potential test to the present model. © 2017 Elsevier B.V.

Vilella K.,CNRS Paris Institute of Global Physics | Vilella K.,Academia Sinica, Taiwan | Kaminski E.,CNRS Paris Institute of Global Physics
Physics of the Earth and Planetary Interiors | Year: 2017

The long-term habitability of a planet rises from its ability to generate and maintain an atmosphere through partial melting and volcanism. This question has been mainly addressed in the framework of plate tectonics, which may be too specific to apply to the wide range of internal dynamics expected for exoplanets, and even to the thermal evolution of the early Earth. Here we propose a more general theoretical approach of convection to build a regime diagram giving the conditions for partial melting to occur, in planetary bodies, as a function of key parameters that can be estimated for exoplanets, their size and internal heating rate. To that aim, we introduce a refined view of the Thermal Boundary Layer (TBL) in a convective system heated from within, that focuses on the temperature and thickness of the TBL at the top of the hottest temperature profiles, along which partial melting shall first occur. This “Hottest Thermal Boundary Layer” (HotTBL) is first characterized using fully theoretical scaling laws based on the dynamics of thermal boundary layers. These laws are the first ones proposed in the literature that do not rely on empirical determinations of dimensionless constants and that apply to both low Rayleigh and high Rayleigh convective regimes. We show that the scaling laws can be successfully applied to planetary bodies by comparing their predictions to full numerical simulations of the Moon. We then use the scaling laws to build a regime diagram for exoplanets. Combined with estimates of internal heating in exoplanets, the regime diagram predicts that in the habitable zone partial melting occurs in planets younger than the Earth. © 2017 Elsevier B.V.

Ghoshal A.,University of Burdwan | Ho Y.K.,Academia Sinica, Taiwan
Journal of Physics B: Atomic, Molecular and Optical Physics | Year: 2017

We have investigated the resonances in the e+-He(1s2s 3Se) system interacting with screened potentials by using the stabilization method. Two types of screened potential have been considered: static screened Coulomb potential and exponential cosine-screened Coulomb potential. A model potential has been used to describe the interaction between the outer electron and the He+ ionic core. We have found two resonances below the Ps(n = 2) He+ threshold. For the unscreened case, our results are in nice agreement with some of the most accurate results available in the literature. © 2017 IOP Publishing Ltd Printed in the UK.

Wu H.-K.,Academia Sinica, Taiwan | Wu H.-K.,National Taiwan University | Lee T.-K.,Academia Sinica, Taiwan
Physical Review B - Condensed Matter and Materials Physics | Year: 2017

Since the discovery of half-filled cuprate to be a Mott insulator, the excitation spectra above the chemical potential for the unoccupied states has attracted much research attention. There were many theoretical works using different numerical techniques to study this problem, but many have reached different conclusions. One of the reasons is the lack of very detailed high-resolution experimental results for the theories to be compared with. Recently, the scanning tunneling spectroscopy [P. Cai, Nat. Phys. 12, 1047 (2016)1745-247310.1038/nphys3840; C. Ye, Nat. Commun. 4, 1365 (2013)2041-172310.1038/ncomms2369] on lightly doped Mott insulator with an antiferromagnetic order found the presence of in-gap states with energy of order half an eV above the chemical potential. The measured spectral properties with doping are not quite consistent with earlier theoretical works. Although the experiment has disorder and localization effect, but for the energy scale we will study here, a model without disorder is sufficed to illustrate the underlying physics. We perform a diagonalization method on top of the variational Monte Carlo calculation to study the evolution of antiferromagnetic Mott state with doped hole concentration in the Hubbard model. Our results found in-gap states that behave similarly with ones reported by STS. These in-gap states acquire a substantial amount of dynamical spectral weight transferred from the upper Hubbard band. The in-gap states move toward chemical potential with increasing spectral weight as doping increases. Our result also provides information about the energy scale of these in-gap states in relation with the Coulomb coupling strength U. © 2017 American Physical Society.

Cheng C.-H.,National Changhua University of Education | Yip S.-K.,Academia Sinica, Taiwan
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2017

We consider the thermodynamic potential Ω of an N component Fermi gas with a short-range interaction obeying SU(N) symmetry. We analyze especially the nonanalytic part of Ω in the temperature T at low T. We examine the temperature range where one can observe this T4lnT contribution and discuss how it can be extracted experimentally. © 2017 American Physical Society.

Chao Y.-T.,Academia Sinica, Taiwan | Yen S.-H.,Academia Sinica, Taiwan | Yeh J.-H.,Academia Sinica, Taiwan | Chen W.-C.,Academia Sinica, Taiwan | Shih M.-C.,Academia Sinica, Taiwan
Plant and Cell Physiology | Year: 2017

Orchidaceae, the orchid family, encompasses more than 25,000 species and five subfamilies. Due to their beautiful and exotic flowers, distinct biological and ecological features, orchids have aroused wide interest among both researchers and the general public. We constructed the Orchidstra database, a resource for orchid transcriptome assembly and gene annotations. The Orchistra database has been under active development since 2013. To accommodate the increasing amount of orchid transcriptome data and house more comprehensive information, Orchidstra 2.0 has been built with a new database system to store the annotations of 510,947 protein-coding genes and 161,826 noncoding transcripts, covering 18 orchid species belonging to 12 genera in five subfamilies of Orchidaceae. We have improved the N50 size of proteincoding genes, provided new functional annotations (including protein-coding gene annotations, protein domain/family information, pathways analysis, Gene Ontology term assignments, orthologous genes across orchid species, cross-links to the database of model species, and miRNA information), and improved the user interface with better website performance. We also provide new database functionalities for database searching and sequence retrieval. Moreover, the Orchidstra 2.0 database incorporates detailed RNA-Seq gene expression data from various tissues and developmental stages in different orchid species. The database will be useful for gene prediction and gene family studies, and for exploring gene expression in orchid species. The Orchidstra 2.0 database is freely accessible at © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

A portion of the mitochondrial cytochrome c oxidase I gene was sequenced using both genomic DNA and complement DNA from three planktonic copepod Neocalanus species (N. cristatus, N. plumchrus, and N. flemingeri). Small but critical sequence differences in CO1 were observed between gDNA and cDNA from N. plumchrus. Furthermore, careful observation revealed the presence of recombination between sequences in gDNA from N. plumchrus. Moreover, a chimera of the N. cristatus and N. plumchrus sequences was obtained from N. plumchrus gDNA. The observed phenomena can be best explained by the preferential amplification of the nuclear mitochondrial pseudogenes from gDNA of N. plumchrus. Two conclusions can be drawn from the observations. First, nuclear mitochondrial pseudogenes are pervasive in N. plumchrus. Second, a mating between a female N. cristatus and a male N. plumchrus produced viable offspring, which further backcrossed to a N. plumchrus individual. These observations not only demonstrate intriguing mating behavior in these species, but also emphasize the importance of careful interpretation of species marker sequences amplified from gDNA. © 2017 Machida, Lin.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Yakushkina T.,National Research University Higher School of Economics | Saakian D.B.,Academia Sinica, Taiwan
Journal of the Physical Society of Japan | Year: 2017

Lethal mutations are very common in asexual evolution, both in RNA viruses and in the clonal evolution of cancer cells. In a special case of lethal mutations (truncated selection), after a critical total number of mutations the replicator (the virus or the cell) has no offspring. We consider the Eigen and Crow-Kimura models with truncated fitness landscapes, and calculate the fraction of viable replicators (that do have offspring) in the population. We derive a formula for the fraction of the population with nonlethal replicators for the case of a uniform distribution of lethal sequences in the sequence space. We assume that our results can be applied to the origin of life and cancer biology. ©2017 The Physical Society of Japan.

Hirashita H.,Academia Sinica, Taiwan | Nozawa T.,Japan National Astronomical Observatory
Planetary and Space Science | Year: 2017

We have recently suggested that dust growth in the cold gas phase dominates the dust abundance in elliptical galaxies while dust is efficiently destroyed in the hot X-ray emitting plasma (hot gas). In order to understand the dust evolution in elliptical galaxies, we construct a simple model that includes dust growth in the cold gas and dust destruction in the hot gas. We also take into account the effect of mass exchange between these two gas components induced by active galactic nucleus (AGN) feedback. We survey reasonable ranges of the relevant parameters in the model and find that AGN feedback cycles actually produce a variety in cold gas mass and dust-to-gas ratio. By comparing with an observational sample of nearby elliptical galaxies, we find that, although the dust-to-gas ratio varies by an order of magnitude in our model, the entire range of the observed dust-to-gas ratios is difficult to be reproduced under a single parameter set. Variation of the dust growth efficiency is the most probable solution to explain the large variety in dust-to-gas ratio of the observational sample. Therefore, dust growth can play a central role in creating the variation in dust-to-gas ratio through the AGN feedback cycle and through the variation in dust growth efficiency. © 2017 Elsevier Ltd.

Konishi K.,Academia Sinica, Taiwan | Fuji N.,CNRS Paris Institute of Global Physics | Deschamps F.,Academia Sinica, Taiwan
Geophysical Journal International | Year: 2017

We investigate the elastic and anelastic structure of the lowermost mantle at the western edge of the Pacific large low shear velocity province (LLSVP) by inverting a collection of S and ScS waveforms. The transverse component data were obtained from F-net for 31 deep earthquakes beneath Tonga and Fiji, filtered between 12.5 and 200 s. We observe a regional variation of S and ScS arrival times and amplitude ratios, according to which we divide our region of interest into three subregions. For each of these subregions, we then perform 1- D (depth-dependent) waveform inversions simultaneously for radial profiles of shear wave velocity (VS) and seismic quality factor (Q). Models for all three subregions show low VS and low Q structures from 2000 km depth down to the core-mantle boundary.We further find that VS and Q in the central subregion, sampling the Caroline plume, are substantially lower than in the surrounding regions, whatever the depth. In the central subregion, VS-anomalies with respect to PREM (dVS) and Q are about -2.5 per cent and 216 at a depth of 2850 km, and -0.6 per cent and 263 at a depth of 2000 km. By contrast, in the two other regions, dVS and Q are -2.2 per cent and 261 at a depth of 2850 km, and -0.3 per cent and 291 at a depth of 2000 km. At depths greater than ~2500 km, these differences may indicate lateral variations in temperature of ~100 K within the Pacific LLSVP. At shallower depths, they may be due to the temperature difference between the Caroline plume and its surroundings, and possibly to a small fraction of iron-rich material entrained by the plume. © The Authors 2016. Published by Oxford University Press on behalf of The Royal Astronomical Society.

Zhang G.,Hefei University of Technology | Zhang G.,Academia Sinica, Taiwan
EPJ Web of Conferences | Year: 2017

If the Higgs boson discovered at the Large Hadron Collider (LHC) is not exactly the one in the Standard Model, an alternative mechanism is needed to restore unitarity in the scattering amplitude of longitudinal gauge bosons, and new resonances may appear. This paper presents a search for new heavy neutral resonances (R) produced through vector boson fusion process qq → Rqq → ℓ+νℓ qq (ℓ = e; μ) using 3.2 fb-1 of data at p s = 13 TeV recorded by the ATLAS detector at the LHC. No excess above the Standard Model background expectation is observed. Limits are set on the production of five types of neutral resonances with different spin and isospin quantum numbers using a K-matrix unitarization of the vector boson scattering process. © The Authors, published by EDP Sciences, 2017.

Chen D.-P.,Academia Sinica, Taiwan | Lin Y.-C.,Academia Sinica, Taiwan | Fann C.S.J.,Academia Sinica, Taiwan
Briefings in Functional Genomics | Year: 2016

DNA methylation is one of the most important epigenetic mechanisms, and participates in the pathogenic processes of many diseases. Differentially methylated regions (DMRs) in the genome have been reported and implicated in a number of different diseases, tissues and cell types, and are associated with gene expression levels. Therefore, identification of DMRs is one of the most critical and fundamental issues in dissecting the disease etiologies. Based on bisulfite conversion, advances in sequence- and array-based technologies have helped investigators study genome-wide DNA methylation. Many methods have been developed to detect DMRs, and they have revolutionized our understanding of DNA methylation and provided new insights into its role in diverse biological functions. According to data and region types, we discuss various methods in detecting DMRs, their utility and limitations comprehensively. We recommend using a few of the methods in the same data and region type to detect DMRs because they could be complementary to one another. © The Author 2016. Published by Oxford University Press.

Liang W.-J.,National Cheng Kung University | Lin G.-X.,National Cheng Kung University | Lu C.-S.,Academia Sinica, Taiwan
IEEE Transactions on Image Processing | Year: 2017

Cost-efficient compressive sensing of large-scale images with quickly reconstructed high-quality results is very challenging. In this paper, we present an algorithm to solve convex optimization via the tree structure sparsity pattern, which can be run in the operator to reduce computation cost and maintain good quality, especially for large-scale images. We also provide convergence analysis and convergence rate analysis for the proposed method. The feasibility of our method is verified through simulations and comparison with the state-of-the-art algorithms. © 1992-2012 IEEE.

Yang H.-C.,Academia Sinica, Taiwan | Lin Y.-T.,Academia Sinica, Taiwan
BMC Proceedings | Year: 2016

Homozygosity disequilibrium (HD) describes a nonrandom pattern of sizable runs of homozygosity (ROH) that deviated from a random distribution of homozygotes and heterozygotes in the genome. In this study, we developed a double-weight local polynomial model for estimating homozygosity intensity. This new estimation method enables considering the local property and genetic information of homozygosity in the human genome when detecting regions of HD. By using this new method, we estimated whole-genome homozygosity intensities by analyzing real whole-genome sequencing data of 959 related individuals from 20 large pedigrees provided by Genetic Analysis Workshop 19 (GAW19). Through the analysis, we derived the distribution of HD in the human genome and provided evidence for the genetic component of natural variation in HD. Generalized estimating equation analysis for 855 related individuals was performed to identify regions of HD associated with diastolic blood pressure (DBP), systolic blood pressure, and hypertension (HTN), with concomitant adjustment for age and sex. We identified one DBP-associated and 2 HTN-associated regions of HD. We also studied the gene regulation of HD by analyzing the real whole-genome transcription data of 647 individuals. A set of gene expressions regulated by the DBP-and HTN-associated regions of HD was identified. Finally, we conducted simulation studies to evaluate the performance of our homozygosity association test. The results showed that the association test had a high power and that type 1 error was controlled. The methods have been integrated into our developed Loss-of-Heterozygosity Analysis Suite software, which can be downloaded at © 2016 The Author(s).

Fan H.-F.,National Yang Ming University | Hsieh T.-S.,Academia Sinica, Taiwan | Ma C.-H.,University of Texas at Austin | Jayaram M.,University of Texas at Austin
Nucleic Acids Research | Year: 2016

Serine and tyrosine site-specific recombinases (SRs and YRs, respectively) provide templates for understanding the chemical mechanisms and conformational dynamics of strand cleavage/exchange between DNA partners. Current evidence suggests a rather intriguing mechanism for serine recombination, in which one half of the cleaved synaptic complex undergoes a 180° rotation relative to the other. The 'small' and 'large' SRs contain a compact aminoterminal catalytic domain, but differ conspicuously in their carboxyl-Terminal domains. So far, only one serine recombinase has been analyzed using single substrate molecules. We now utilized singlemolecule tethered particle motion (TPM) to follow step-by-step recombination catalyzed by a large SR, phage πC31 integrase. The integrase promotes unidirectional DNA exchange between attB and attP sites to integrate the phage genome into the host chromosome. The recombination directionality factor (RDF; πC31 gp3) activates the excision reaction (attL x attR). From integrase-induced changes in TPM in the presence or absence of gp3, we delineated the individual steps of recombination and their kinetic features. The gp3 protein appears to regulate recombination directionality by selectively promoting or excluding active conformations of the synapse formed by specific att site partners. Our results support a 'gated rotation' of the synaptic complex between DNA cleavage and joining. © The Author(s) 2016.

Kao M.-J.,Academia Sinica, Taiwan
Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms | Year: 2017

We provide a simple and novel algorithmic design technique, for which we call iterative partial rounding, that gives a tight rounding-based approximation for vertex cover with hard capacities (VC-HC). In particular, we obtain an f- Approximation for VC-HC on hypergraphs, improving over a previous results of Cheung et al. (SODA 2014) to the tight extent. This also closes the gap of approximation since it was posted by Chuzhoy and Naor in (FOCS 2002). Our main technical tool for establishing the approximation guarantee is a separation lemma that certifies the existence of a strong partition for solutions that are basic feasible in an extended version of the natural LP. We believe that our rounding technique is of independent interest when hard constraints are considered. Copyright © by SIAM.

Sharma B.S.,Academia Sinica, Taiwan
Gene Reports | Year: 2017

B-cell translocation gene 3 (BTG3), recognized as a member of an antiproliferative B-cell translocation gene/Transducer of ErbB2 (BTG/Tob) gene family, is a downstream target of p53 and is induced upon genotoxic stress in a p53 and Checkpoint kinase 1 (CHK1), a vital checkpoint kinase which contributes significantly in cell survival and cell cycle checkpoints, dependent manner. Post-translational modifications of CHK1 (phosphorylation and ubiquitination) facilitated by interaction with BTG3 have been observed suggesting their possible role in tumorigenesis, although the underlying mechanisms are unclear. Methylation, as one of the types of post-translational modifications, is a critical event during cell cycle checkpoint controls and DNA damage repair. Here, for the first time, it is reported that overexpression of BTG3 vividly enhances the methylation of CHK1. Expression of CHK1 was detected in a cancer cell line in this study. This work also reveals the significant role of the kinase domain of CHK1 for BTG3 facilitated methylation as BTG3 overexpression only promoted the methylation of wild type CHK1 but failed to promote the methylation of CHK1 mutants which were impaired for their kinase domain. This novel finding would therefore greatly enhance our understanding of the mechanisms underlying interactions between important cancer biomarkers. © 2017 Elsevier Inc.

Huang M.-D.,Academia Sinica, Taiwan | Chen T.-L.L.,Academia Sinica, Taiwan | Huang A.H.C.,Academia Sinica, Taiwan | Huang A.H.C.,University of California at Riverside
Plant Physiology | Year: 2013

Lipid transfer proteins (LTPs) are small secretory proteins in plants with defined lipid-binding structures for possible lipid exocytosis. Special groups of LTPs unique to the anther tapetum are abundant, but their functions are unclear. We studied a special group of LTPs, type III LTPs, in Arabidopsis (Arabidopsis thaliana). Their transcripts were restricted to the anther tapetum, with levels peaking at the developmental stage of maximal pollen-wall exine synthesis. We constructed an LTP-Green Fluorescent Protein (LTP-GFP) plasmid, transformed it into wild-type plants, and monitored LTP-GFP in developing anthers with confocal laser scanning microscopy. LTP-GFP appeared in the tapetum and was secreted via the endoplasmic reticulum-trans-Golgi network machinery into the locule. It then moved to the microspore surface and remained as a component of exine. Immunotransmission electron microscopy of native LTP in anthers confirmed the LTP-GFP observations. The in vivo association of LTP-GFP and exine in anthers was not observed with non-type III or structurally modified type III LTPs or in transformed exine-defective mutant plants. RNA interference knockdown of individual type III LTPs produced no observable mutant phenotypes. RNA interference knockdown of two type III LTPs produced microscopy-observable morphologic changes in the intine underneath the exine (presumably as a consequence of changes in the exine not observed by transmission electron microscopy) and pollen susceptible to dehydration damage. Overall, we reveal a novel transfer pathway of LTPs in which LTPs bound or nonbound to exine precursors are secreted from the tapetum to become microspore exine constituents; this pathway explains the need for plentiful LTPs to incorporate into the abundant exine. © 2013 American Society of Plant Biologists. All Rights Reserved.

Liu F.-T.,University of California at Davis | Liu F.-T.,Academia Sinica, Taiwan | Yang R.-Y.,University of California at Davis | Hsu D.K.,University of California at Davis | Hsu D.K.,Academia Sinica, Taiwan
Annals of the New York Academy of Sciences | Year: 2012

Galectins are animal lectins that bind to β-galactosides, such as lactose and N-acetyllactosamine, in free form or contained in glycoproteins or glycolipids. They are located intracellularly or extracellularly. In the latter they exhibit bivalent or multivalent interactions with glycans on cell surfaces and induce various cellular responses, including production of cytokines and other inflammatory mediators, cell adhesion, migration, and apoptosis. Furthermore, they can form lattices with membrane glycoprotein receptors and modulate receptor properties. Intracellular galectins can participate in signaling pathways and alter biological responses, including apoptosis, cell differentiation, and cell motility. Current evidence indicates that galectins play important roles in acute and chronic inflammatory responses, as well as other diverse pathological processes. Galectin involvement in some processes in vivo has been discovered, or confirmed, through studies of genetically engineered mouse strains, each deficient in a given galectin. Current evidence also suggests that galectins may be therapeutic targets or employed as therapeutic agents for these inflammatory responses. © 2012 New York Academy of Sciences.

Chen Y.-F.,Taipei Veterans General Hospital | Chen Y.-F.,National Yang Ming University | Tseng C.-Y.,National Yang Ming University | Wang H.-W.,National Yang Ming University | And 3 more authors.
Hepatology | Year: 2012

Liver transplantation is the only definitive treatment for end-stage cirrhosis and fulminant liver failure, but the lack of available donor livers is a major obstacle to liver transplantation. Recently, induced pluripotent stem cells (iPSCs) derived from the reprogramming of somatic fibroblasts, have been shown to resemble embryonic stem (ES) cells in that they have pluripotent properties and the potential to differentiate into all cell lineages in vitro, including hepatocytes. Thus, iPSCs could serve as a favorable cell source for a wide range of applications, including drug toxicity testing, cell transplantation, and patient-specific disease modeling. Here, we describe an efficient and rapid three-step protocol that is able to rapidly generate hepatocyte-like cells from human iPSCs. This occurs because the endodermal induction step allows for more efficient and definitive endoderm cell formation. We show that hepatocyte growth factor (HGF), which synergizes with activin A and Wnt3a, elevates the expression of the endodermal marker Foxa2 (forkhead box a2) by 39.3% compared to when HGF is absent (14.2%) during the endodermal induction step. In addition, iPSC-derived hepatocytes had a similar gene expression profile to mature hepatocytes. Importantly, the hepatocyte-like cells exhibited cytochrome P450 3A4 (CYP3A4) enzyme activity, secreted urea, uptake of low-density lipoprotein (LDL), and possessed the ability to store glycogen. Moreover, the hepatocyte-like cells rescued lethal fulminant hepatic failure in a nonobese diabetic severe combined immunodeficient mouse model. Conclusion: We have established a rapid and efficient differentiation protocol that is able to generate functional hepatocyte-like cells from human iPSCs. This may offer an alternative option for treatment of liver diseases. © 2011 American Association for the Study of Liver Diseases.

Chiou J.-M.,Academia Sinica, Taiwan | Muller H.-G.,University of California at Davis
Biometrika | Year: 2016

Functional data vectors consisting of samples of multivariate data where each component is a random function are encountered increasingly often but have not yet been comprehensively investigated. We introduce a simple pairwise interaction model that leads to an interpretable and straightforward decomposition of multivariate functional data and of their variation into component-specific processes and pairwise interaction processes. The latter quantify the degree of pairwise interactions between the components of the functional data vectors, while the component-specific processes reflect the functional variation of a particular functional vector component that cannot be explained by the other components. Thus the proposed model provides an extension of the usual notion of a covariance or correlation matrix for multivariate vector data to functional data vectors and generates an interpretable functional interaction map. The decomposition provided by the model can also serve as a basis for subsequent analysis, such as study of the network structure of functional data vectors. The decomposition of the total variance into componentwise and interaction contributions can be quantified by an $R2$-like decomposition. We provide consistency results for the proposed methods and illustrate the model by applying it to sparsely sampled longitudinal data from the Baltimore Longitudinal Study of Aging, examining the relationships between body mass index and blood fats. © 2016 Biometrika Trust.

Kuo D.M.-T.,National Central University | Chang Y.-C.,Academia Sinica, Taiwan
Physical Review B - Condensed Matter and Materials Physics | Year: 2010

The electrical conductance, thermal conductance, thermal power, and figure of merit (ZT) of semiconductor quantum dots (QDs) embedded into an insulator matrix connected with metallic electrodes are theoretically investigated in the Coulomb blockade regime. The multilevel Anderson model is used to simulate the multiple QDs junction system. The charge and heat currents in the sequential tunneling process are calculated by the Keldysh Green's function technique. In the linear-response regime the ZT values are still very impressive in the small tunneling rates case, although the effect of electron Coulomb interaction on ZT is significant. In the nonlinear-response regime, we have demonstrated that the thermal rectification behavior can be observed for the coupled QDs system, where the very strong asymmetrical coupling between the dots and electrodes, large energy-level separation between dots and strong interdot Coulomb interactions are required. © 2010 The American Physical Society.

Chang C.-S.J.,Academia Sinica, Taiwan | Chang C.-S.J.,National Chung Hsing University | Maloof J.N.,University of California at Davis | Wu S.-H.,Academia Sinica, Taiwan | Wu S.-H.,National Chung Hsing University
Plant Physiology | Year: 2011

Light regulates multiple aspects of growth and development in plants. Transcriptomic changes govern the expression of signaling molecules with the perception of light. Also, the 26S proteasome regulates the accumulation of positive and negative regulators for optimal growth of Arabidopsis (Arabidopsis thaliana) in the dark, light, or light/dark cycles. BBX22, whose induction is both light regulated and HY5 dependent, is a positive regulator of deetiolation in Arabidopsis. We found that during skotomorphogenesis, the expression of BBX22 needs to be tightly regulated at both transcriptional and posttranslational levels. During photomorphogenesis, the expression of BBX22 transiently accumulates to execute its roles as a positive regulator. BBX22 protein accumulates to a higher level under short-day conditions and functions to inhibit hypocotyl elongation. The proteasome-dependent degradation of BBX22 protein is tightly controlled even in plants overexpressing BBX22. An analysis of BBX22 degradation kinetics shows that the protein has a short half-life under both dark and light conditions. COP1 mediates the degradation of BBX22 in the dark. Although dispensable in the dark, HY5 contributes to the degradation of BBX22 in the light. The constitutive photomorphogenic development of the cop1 mutant is enhanced in cop1BBX22ox plants, which show a short hypocotyl, high anthocyanin accumulation, and expression of light-responsive genes. Exaggerated light responsiveness is also observed in cop1BBX22ox seedlings grown under short-day conditions. Therefore, the proper accumulation of BBX22 is crucial for plants to maintain optimal growth when grown in the dark as well as to respond to seasonal changes in daylength. © 2011 American Society of Plant Biologists.

Omura Y.,Nagoya University | Yu C.,Academia Sinica, Taiwan
Journal of High Energy Physics | Year: 2016

We discuss the 750 GeV diphoton excess at the LHC@13TeV in the framework of leptophobic U(1)′ model inspired by E6 grand unified theory (GUT). In this model, the Standard Model (SM) chiral fermions carry charges under extra U(1)′ gauge symmetry which is spontaneously broken by a U(1)′-charged singlet scalar (Φ). In addition, extra quarks and leptons are introduced to achieve the anomaly-free conditions, which is a natural consequence of the assumed E6 GUT. These new fermions are vectorlike under the SM gauge group but chiral under new U(1)′, and their masses come entirely from the nonzero vacuum expectation value of Φ through the Yukawa interactions. Then, the CP-even scalar hΦ from Φ can be produced at the LHC by the gluon fusion and decay to the diphoton via the one-loop diagram involving the extra quarks and leptons, and can be identified as the origin of diphoton excess at 750 GeV. In this model, hΦ can decay into a pair of dark matter particles as well as a pair of scalar bosons, thereby a few tens of the decay width may be possible. © 2016, The Author(s).

Zulueta M.M.L.,Academia Sinica, Taiwan | Lin S.-Y.,Academia Sinica, Taiwan | Hu Y.-P.,Academia Sinica, Taiwan | Hung S.-C.,Academia Sinica, Taiwan | Hung S.-C.,National Chiao Tung University
Current Opinion in Chemical Biology | Year: 2013

Heparin and heparan sulfate bind a host of basic proteins that take advantage of the sugar's dense structural information. The significance of these interactions in various aspects of development, physiology, and disease stimulated keen interest in evaluating structure-activity relationships. The well-defined heparin and heparan sulfate oligosaccharides needed for these studies can be mainly accessed by chemical synthesis and, more recently by chemoenzymatic means. The various synthetic strategies available to chemical synthesis have recently enabled the acquisition of several regular and irregular sequences, including a number of dodecasaccharides, through improved coupling methods and judicial protecting group manipulations. Controlled chain elongation and critical application of modification enzymes allowed the generation of well-defined constructs via chemoenzymatic synthesis. Investigations of various protein interactions with the synthetic constructs delivered valuable information that could aid future drug development endeavors. © 2013 Elsevier Ltd.

Huang C.-H.,National Chiao Tung University | Luo L.,Academia Sinica, Taiwan | Chen T.-M.,National Chiao Tung University
Journal of the Electrochemical Society | Year: 2011

A series of Ce3- and Eu2-coactivated Ca 9Y(PO4)7 phosphors were synthesized by high temperature solid-state reactions. The Ca9Y(PO4) 7:Ce3,Eu2 phosphor showed two emission bands under 292 nm excitation: the one observed at 342 nm was attributed to the 4f 05d1 → 4f 1 transition of Ce3 ion emission, and the other found at 492 nm was assigned to the 4 65d1 → 4f 7 transition of Eu2 ions. Through an effective resonance-type energy transfer, the Ca 9Y(PO4)7:Ce3,Eu2 phosphors exhibit a systematically varied hues from ultraviolet to blue-greenish and the relative intensity of ultraviolet and blue-greenish emissions can be tuned by properly tuning the relative dopant composition of Ce 3Eu2. The energy transfer from a sensitizer Ce3 to an activator Eu2 in Ca9Y(PO4)7 host matrix was studied and demonstrated to be a resonant type via a dipole-dipole mechanism based on the decay lifetime analysis. Furthermore, we have calculated the critical distance for Ce3 → Eu2 energy transfer to be about 30.7 by both concentration quenching and spectral overlap methods. © 2011 The Electrochemical Society.

Oh S.,Academia Sinica, Taiwan | Oh S.,National Taiwan University | Tandean J.,National Central University | Tandean J.,National Taiwan University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2011

The recent measurement of the like-sign dimuon charge asymmetry in semileptonic b-hadron decays by the D0 Collaboration is about three sigmas away from the standard-model prediction, hinting at the presence of CP-violating new physics in the mixing of Bs mesons. We consider the possibility that this anomalous result arises from the contribution of a light spin-1 particle. Taking into account various experimental constraints, we find that the effect of such a particle with mass below the b-quark mass can yield a prediction consistent with the anomalous D0 measurement within its one-sigma range. © 2011 Elsevier B.V.

Huang K.Y.,Yuan Ze University | Huang K.Y.,Academia Sinica, Taiwan | Huang K.Y.,National Chiao Tung University
Database : the journal of biological databases and curation | Year: 2014

Protein phosphorylation catalyzed by kinases plays crucial roles in regulating a variety of intracellular processes. Owing to an increasing number of in vivo phosphorylation sites that have been identified by mass spectrometry (MS)-based proteomics, the RegPhos, available online at, was developed to explore protein phosphorylation networks in human. In this update, we not only enhance the data content in human but also investigate kinase-substrate phosphorylation networks in mouse and rat. The experimentally validated phosphorylation sites as well as their catalytic kinases were extracted from public resources, and MS/MS phosphopeptides were manually curated from research articles. RegPhos 2.0 aims to provide a more comprehensive view of intracellular signaling networks by integrating the information of metabolic pathways and protein-protein interactions. A case study shows that analyzing the phosphoproteome profile of time-dependent cell activation obtained from Liquid chromatography-mass spectrometry (LC-MS/MS) analysis, the RegPhos deciphered not only the consistent scheme in B cell receptor (BCR) signaling pathway but also novel regulatory molecules that may involve in it. With an attempt to help users efficiently identify the candidate biomarkers in cancers, 30 microarray experiments, including 39 cancerous versus normal cells, were analyzed for detecting cancer-specific expressed genes coding for kinases and their substrates. Furthermore, this update features an improved web interface to facilitate convenient access to the exploration of phosphorylation networks for a group of genes/proteins. Database URL:

Wu H.-M.,Tamkang University | Tien Y.-J.,National Central University | Chen C.-h.,Academia Sinica, Taiwan
Computational Statistics and Data Analysis | Year: 2010

GAP is a Java-designed exploratory data analysis (EDA) software for matrix visualization (MV) and clustering of high-dimensional data sets. It provides direct visual perception for exploring structures of a given data matrix and its corresponding proximity matrices, for variables and subjects. Various matrix permutation algorithms and clustering methods with validation indices are implemented for extracting embedded information. GAP has a friendly graphical user interface for easy handling of data and proximity matrices. It is more powerful and effective than conventional graphical methods when dimension reduction techniques fail or when data is of ordinal, binary, and nominal type. © 2008 Elsevier B.V. All rights reserved.

Chang L.J.,National Chiao Tung University | Lin P.,National Chiao Tung University | Lee S.F.,Academia Sinica, Taiwan
Applied Physics Letters | Year: 2012

We experimentally demonstrate domain wall (DW) oscillators excited by in-plane ac current through permalloy based pseudo-spin valve wires, which contain one pair of artificial protrusions. By measuring the spin-transfer-torque induced resonance of a pinned antiparallel transverse DW, under transverse external fields, we show that the antiparallel transverse DW oscillates with a resonance frequency as high as 2.92GHz, depending on the widths of protrusions. For DW oscillations induced by injection of dc currents, the observed peaks in dV/dI associated with the reversible change of magnetoresistance are attributed to the reversible motions of the DW. © 2012 American Institute of Physics.

Sharma S.,Academia Sinica, Taiwan | Villamor J.G.,Max Planck Institute for Plant Breeding Research | Verslues P.E.,Academia Sinica, Taiwan
Plant Physiology | Year: 2011

To better define the still unclear role of proline (Pro) metabolism in drought resistance, we analyzed Arabidopsis (Arabidopsis thaliana) Δ 1-pyrroline-5-carboxylate synthetase1 (p5cs1) mutants deficient in stress-induced Pro synthesis as well as praline dehydrogenase (pdh1) mutants blocked in Pro catabolism and found that both Pro synthesis and catabolism were required for optimal growth at low water potential (Ψ w). The abscisic acid (ABA)-deficient mutant aba2-1 had similar reduction in root elongation as p5cs1 and p5cs1/aba2-1 double mutants. However, the reduced growth of aba2-1 but not p5cs1/aba2-1 could be complemented by exogenous ABA, indicating that Pro metabolism was required for ABA-mediated growth protection at low Ψ w. PDH1 maintained high expression in the root apex and shoot meristem at low Ψ w rather than being repressed, as in the bulk of the shoot tissue. This, plus a reduced oxygen consumption and buildup of Pro in the root apex of pdh1-2, indicated that active Pro catabolism was needed to sustain growth at low Ψ w. Conversely, P5CS1 expression was most highly induced in shoot tissue. Both p5cs1-4 and pdh1-2 had a more reduced NADP/NADPH ratio than the wild type at low Ψ w. These results indicate a new model of Pro metabolism at low Ψ w whereby Pro synthesis in the photosynthetic tissue regenerates NADP while Pro catabolism in meristematic and expanding cells is needed to sustain growth. Tissue-specific differences in Pro metabolism and function in maintaining a favorable NADP/NADPH ratio are relevant to understanding metabolic adaptations to drought and efforts to enhance drought resistance.© 2011 American Society of Plant Biologists. All Rights Reserved.

Zhong Y.-L.,Chung Yuan Christian University | Sergeev A.,State University of New York at Buffalo | Chen C.-D.,Academia Sinica, Taiwan | Lin J.-J.,National Chiao Tung University
Physical Review Letters | Year: 2010

To identify and investigate the mechanisms of electron-phonon (e-ph) relaxation in weakly disordered metallic conductors, we measure the electron dephasing rate in a series of suspended and supported 15-nm thick AuPd wires. In a wide temperature range, from ∼8K to above 20 K, the e-ph interaction dominates in the dephasing processes. The corresponding relaxation rate reveals a quadratic temperature dependence, τe-ph-1=AepT2, where Aep 5×109K-2s-1 is essentially the same for all samples studied. Our observations are shown to be in good agreement with the theory which predicts that, even in weakly disordered metallic structures at moderately low temperatures, the major mechanism of the e-ph relaxation is the electron scattering from vibrating defects and impurities. © 2010 The American Physical Society.

Shih C.-F.,Georgia Institute of Technology | Liao W.,National Taiwan University | Liao W.,Academia Sinica, Taiwan | Chao H.-L.,National Chiao Tung University
IEEE Transactions on Wireless Communications | Year: 2011

In this paper, we introduce the concept of "route robustness" for path selection in multi-hop cognitive radio networks. We demonstrate that the aggregate throughput and the robustness of routes determined by the proposed route selection strategy are superior to existing rate-based selection strategies. The rationale behind our approach is to guarantee a basic level of robustness for a set of routes (referred to as skeletons in this paper). Then, we select some routes from this robust route set and determine the spectrum to be allocated on each link along these routes such that the system throughput is maximized. We also design a polynomial time algorithm for this problem, and evaluate our proposed mechanism via simulations. The results show that our proposed algorithm indeed achieves a near optimal solution of this problem for multi-hop overlay CR networks. © 2006 IEEE.

Chang Y.-H.,Academia Sinica, Taiwan | Lin C.-T.,Academia Sinica, Taiwan | Chen T.-Y.,Academia Sinica, Taiwan | Hsu C.-L.,National Chiao Tung University | And 5 more authors.
Advanced Materials | Year: 2013

A three-dimensional Ni foam deposited with graphene layers on surfaces is used as a conducting solid support to load MoSx catalysts for electrocatalytic hydrogen evolution. The graphene sheets grown on Ni foams provide robust protection and efficiently increase the stability in acid. The superior performance of hydrogen evolution is attributed to the relatively high catalyst loading weight as well as its relatively low resistance. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Zulueta M.M.L.,Academia Sinica, Taiwan | Zhong Y.-Q.,Academia Sinica, Taiwan | Zhong Y.-Q.,National Tsing Hua University | Hung S.-C.,Academia Sinica, Taiwan | Hung S.-C.,National Chiao Tung University
Chemical Communications | Year: 2013

Carbohydrates either conjugated or as free entities are major players in numerous biological processes. The desire to comprehend the nature of their functions and further develop therapeutic and diagnostic applications has fuelled the recent upsurge in the glycoscience field. Mainly accessed through chemical synthesis, homogeneous and well-defined sugar constructs are on high demand for structure-activity evaluation. Although the d-sugars, particularly the d-hexoses, have dominated the carbohydrate landscape, l-hexoses also attracted attention because they are known components of important polysaccharides, antibiotics, and other natural products. Nonetheless, the l-hexose-based materials needed for making building blocks for sugar assemblies are rare and are usually expensive if commercially available. Thus, intense efforts were focused on the development of innovative and reliable methods for the acquisition of l-hexoses and their derivatives. This review outlines several efficient and cost-effective routes for the chemical syntheses of l-hexoses, particularly focusing on approaches that utilize commercially abundant sugars as starting materials. A sampling of the applications of the generated l-hexoses in preparing biologically relevant compounds is also provided. © The Royal Society of Chemistry 2013.

Chang C.-F.,National Taiwan Normal University | Ma E.,University of California at Riverside | Yuan T.-C.,Academia Sinica, Taiwan
Journal of High Energy Physics | Year: 2014

The U(1) D gauge sector containing one dark Higgs boson h D and one dark photon γ D may be explored through the decays of the 126 GeV particle discovered at the Large Hadron Collider (LHC), assumed here as the heavier mass eigenstate h 1 in the mixing of the standard model h with h D. The various decays of h 1 to γ D γ D, h 2 h 2, h 2 γ D γ D and h 2 h 2 h 2 would yield multilepton final states through the mixing of γ D with the photon and the decay h 2 → γ D γ D, where h 2 is the lighter dark Higgs. Future searches for signals of multilepton jets at the LHC may reveal the existence of this possible dark sector governed simply by the original Abelian Higgs model. © 2014 The Author(s).

Kuo D.M.-T.,National Central University | Chang Y.-C.,Academia Sinica, Taiwan
Nanotechnology | Year: 2013

The thermoelectric properties of a quantum dot array (QDA) embedded in a nanowire connected to metallic electrodes are investigated theoretically via the extended Hubbard model in the Coulomb blockade regime. Coupled quantum dots (QDs) with dot number N = 2-5 are considered. It is found that the thermoelectric properties converge to almost the same results when N approaches 5, indicating that our results are applicable for a QDA with a large number of QDs. Our studies indicate that in order to achieve the optimal figure of merit (ZT), it is preferable to have the QD energy levels above the Fermi energy (EF) of the electrodes of the QDA junction. The effects of QD energy level and interdot coupling variations (due to the QD size and position fluctuation) on the thermoelectric properties are also examined. We find that the QD size fluctuation significantly suppresses the maximum ZT in the weak interdot hopping strength (tℓ,j). We also find that the Seebeck coefficient is insensitive to tℓ,j and the tunneling rates when the QD energy levels are far above EF. For a given tℓ,j and large on-site Coulomb interactions, increasing the QD number N in the QDA would suppress the maximum ZT value. It is possible to achieve an optimal ZT larger than 3 by tailoring the physical parameters of the QDA junction system. © 2013 IOP Publishing Ltd.

Yin J.-F.,Academia Sinica, Taiwan | Yin J.-F.,National Chiao Tung University | Velayudham M.,Academia Sinica, Taiwan | Bhattacharya D.,Academia Sinica, Taiwan | And 2 more authors.
Coordination Chemistry Reviews | Year: 2012

Research on dye-sensitized solar cells (DSC) is progressing at a rapid pace. The structural and electronic factors associated with ruthenium photosensitizers can have a significant effect on the performance of DSCs. This review emphasizes the recent developments and strategies employed in the structural design of ruthenium photosensitizers. The influence of molecular engineering on photophysical and electrochemical properties along with photovoltaic parameters and the efficiency of DSCs are also reviewed. Hence, drawing a correlation between the structure of photosensitizers, the properties and photovoltaic parameters of corresponding DSCs will be helpful in terms of optimizing new dyes for the generation of efficient solar cells. © 2012 Elsevier B.V.

Alemu Mengistie D.,Academia Sinica, Taiwan | Alemu Mengistie D.,National Tsing Hua University | Wang P.-C.,National Tsing Hua University | Chu C.-W.,Academia Sinica, Taiwan | Chu C.-W.,National Chiao Tung University
Journal of Materials Chemistry A | Year: 2013

We systematically investigated the effect of the molecular weight of additives on the conductivity of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) by using different concentrations and molecular weights of polyethylene glycol (PEG) and ethylene glycol (EG). The conductivity enhancement depends on both the molecular weight and concentration of PEG used. The conductivity of PEDOT:PSS was enhanced from 0.3 S cm-1 to 805 S cm-1 with 2% PEG but to only 640 S cm-1 with 6% EG. PEGs with molecular weight higher than 400 have too low mobility to impart the required screening effect, and hence, the conductivity enhancement is less. Through FTIR, XPS and AFM investigations, the mechanism for the conductivity enhancement is found to be charge screening between PEDOT and PSS followed by phase separation and reorientation of PEDOT chains leading to bigger and better connected particles. The molecular weight and concentration of PEG also affect solar cell performances even though the conductivities are the same. Due to their high conductivity and high transmittance, ITO-free organic solar cell devices fabricated using PEDOT:PSS treated with 2% PEG anodes exhibited performance almost equal to that of the ITO counterparts. © 2013 The Royal Society of Chemistry.

Lee T.-Y.,Yuan Ze University | Chen Y.-J.,Academia Sinica, Taiwan | Lu C.-T.,Yuan Ze University | Ching W.-C.,Academia Sinica, Taiwan | And 2 more authors.
Bioinformatics | Year: 2012

S-nitrosylation (SNO), a selective and reversible protein post-translational modification that involves the covalent attachment of nitric oxide (NO) to the sulfur atom of cysteine, critically regulates protein activity, localization and stability. Due to its importance in regulating protein functions and cell signaling, a mass spectrometry-based proteomics method rapidly evolved to increase the dataset of experimentally determined SNO sites. However, there is currently no database dedicated to the integration of all experimentally verified S-nitrosylation sites with their structural or functional information. Thus, the dbSNO database is created to integrate all available datasets and to provide their structural analysis. Up to April 15, 2012, the dbSNO has manually accumulated >3000 experimentally verified S-nitrosylated peptides from 219 research articles using a text mining approach. To solve the heterogeneity among the data collected from different sources, the sequence identity of these reported S-nitrosylated peptides are mapped to the UniProtKB protein entries. To delineate the structural correlation and consensus motif of these SNO sites, the dbSNO database also provides structural and functional analyses, including the motifs of substrate sites, solvent accessibility, protein secondary and tertiary structures, protein domains and gene ontology. © The Author 2012. Published by Oxford University Press. All rights reserved.

Wu J.-Y.,National Chi Nan University | Huang S.-M.,National Chi Nan University | Huang S.-M.,Academia Sinica, Taiwan
CrystEngComm | Year: 2011

A total of five homochiral metal-organic coordination polymers (MOCPs) showing high thermal stability have been assembled from the reaction of divalent transition-metal ions (Co2+, Zn2+, and Cd2+), rigid enantiopure d-camphoric acid (d-H2Cam), and achiral neutral N,N′-bis(pyrid-4-yl)piperazine (bpypip) ligand under hydro(solvo)thermal conditions. Compound [Co2(d-Cam)2(bpypip)] (1) features a chiral-layered cobalt-camphorate coordination (4,4)-net, which is pillared by auxiliary linear N-tethering bpypip linkers to yield a homochiral three-dimensional coordination framework with Schläfli symbol of 4 4·610·8. Compounds [M(d-HCam) 2(bpypip)] (2, M = Cd; 3, M = Zn) have nearly identical one-dimensional M-bpypip zigzag coordination-chain structures, in which each metal ion further attaches to two partially deprotonated monoanionic d-HCam terminals, which exhibit two types of partially deprotonating manner in 2 but only one type in 3. Through chain-to-chain C(O)OH⋯O(carboxylate) hydrogen bonds, the zigzag coordination-chain becomes extended to a three-dimensional uninodal 6-connected supramolecular network, which can be considered as a result of a M-d-HCam-based 4-connected supramolecular 65·8-net intersected by M-bpypip-based zigzag coordination-chains. Of particular interest, the supramolecular assembly contains a couple of single-stranded right- (SRH) and left-handed (SLH) supramolecular helices and a couple of double-stranded right- (DRH) and left-handed (DLH) supramolecular helices, and therefore exists as a meso-net in topology, i.e., there is no spatial chirality. Compounds [M2(OH)(OAc)(d-Cam)(bpypip)] (4, M = Co; 5, M = Zn) have identically homochiral ladder-like chain structures having meso-M2 units and presenting three kinds of different anions, i.e., hydroxyl, acetate, and d-Cam. The obtained acetate anion may be generated from the hydrolyzation of dimethylacetamide (DMAc) under hydro(solvo)thermal conditions. © 2011 The Royal Society of Chemistry.

Su Y.-T.,National Chiao Tung University | Lin H.-Y.,National Chiao Tung University | Putikam R.,National Chiao Tung University | Matsui H.,National Chiao Tung University | And 3 more authors.
Nature Chemistry | Year: 2014

Criegee intermediates, which are carbonyl oxides produced when ozone reacts with unsaturated hydrocarbons, play an important role in the formation of OH and organic acids in the atmosphere, but they have eluded direct detection until recently. Reactions that involve Criegee intermediates are not understood fully because data based on their direct observation are limited. We used transient infrared absorption spectroscopy to probe directly the decay kinetics of formaldehyde oxide (CH 2 OO) and found that it reacts with itself extremely rapidly. This fast self-reaction is a result of its zwitterionic character. According to our quantum-chemical calculations, a cyclic dimeric intermediate that has the terminal O atom of one CH 2 OO bonded to the C atom of the other CH 2 OO is formed with large exothermicity before further decomposition to 2H 2 CO + O 2 (1 Δ g). We suggest that the inclusion of this previously overlooked rapid reaction in models may affect the interpretation of previous laboratory experiments that involve Criegee intermediates. © 2014 Macmillan Publishers Limited.

Thanasekaran P.,Academia Sinica, Taiwan | Luo T.-T.,Academia Sinica, Taiwan | Wu J.-Y.,National Chi Nan University | Lu K.-L.,Academia Sinica, Taiwan
Dalton Transactions | Year: 2012

New concepts on the design and synthesis of crystalline metal-organic frameworks (MOFs) have made them a subject of considerable interest in the growing field of materials science. By creating larger cavity sizes by a nearly infinite combination of metal nodes and organic linkers, many innovative characteristics of microporous MOFs have been revealed. The primary goal of this perspective article is to highlight the frontiers in the development of giant MOFs that are deliberately constructed from metallated or metal-free bulky scaffolds. Incorporating these types of distinct bulky ligands into giant MOFs may lead to MOFs with a large cavity size, intriguing properties and new framework topology. Emerging applications of these materials in catalysis, adsorption, and sensors are also discussed. © 2012 The Royal Society of Chemistry.

Chiang C.-W.,National Central University | Chiang C.-W.,Academia Sinica, Taiwan | Chiang C.-W.,National Center for Theoretical science | Yagyu K.,National Central University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

The decays of a Higgs boson to the γγ and Zγ final states are purely quantum mechanical phenomena that are closely related to each other. We study the effects of an extended Higgs sector on the decay rates of the two modes. We propose that a simultaneous determination of them and the ZZ mode is a useful way to see whether the Higgs boson recently observed by the LHC experiments is of the standard model type or could be a member of a larger Higgs sector. © 2013 American Physical Society.

Ko K.-C.,National Kaohsiung Normal University | Hsu H.-H.,Academia Sinica, Taiwan | Chou C.,Academia Sinica, Taiwan
Journal of Climate | Year: 2012

Propagation and maintenance mechanisms of the tropical cyclone/submonthly wave pattern in the western North Pacific are explored. The wave pattern exhibited an equivalent barotropic structure with maximum vorticity and kinetic energy in the lower troposphere and propagated northwestward in the Philippine Sea in the intraseasonal oscillation (ISO) westerly phase and north-northeastward near the East Asian coast in the easterly phase. The mean flow advection played a dominant role in the propagation in both phases. Barotropic energy conversion is the dominant process in maintaining the kinetic energy of the pattern. The wave pattern tended to occur in the confluent zone between the monsoon trough and the anticyclonic ridge, where the kinetic energy could be efficiently extracted from the westerly mean flow associated with the monsoon trough. The individual circulation circuit embedded in the pattern was oriented northeast- southwest (east-west) to have optimal growth and propagation during the ISO westerly (easterly) phase. When tropical cyclones (TCs) developed in a development-favorable background flow provided by the submonthly wave pattern, they in turn enhanced the amplitudes of the vorticity and kinetic energy of the submonthly wave pattern by more than 50% and helped extract significantly more energy from the background ISO circulation. This TC feedback was much more significant in the ISO westerly phase because of the stronger clustering effect on TCs by the enhanced monsoon trough. © 2012 American Meteorological Society.

Wang K.-Y.,National Central University | Liu C.-H.,Academia Sinica, Taiwan
Geophysical Research Letters | Year: 2010

Due to the difficulty in making reliable and timely four-dimensional observations of atmospheric temperature in the vicinity of the path of the total solar eclipse, direct measurements of temperature changes from the troposphere to the stratosphere during a total solar eclipse still haven't been reported before. In this work we use profiles of temperature measurements from a constellation of the FORMOSAT-3/COSMIC (FS3/C) LEO satellites to estimate temperature changes during the 22 July 2009 total solar eclipse. The FS3/C data reveals a very important temperature response structure in the vertical. The cooling in the troposphere can be attributed to the reduction in solar heating, which is thermally driven. The warming in the stratosphere, especially for those that occurred between 13 and 23 km altitudes could be dynamically driven, which can be induced by the thermal contraction of the troposphere. Copyright 2010 by the American Geophysical Union.

Shin L.-J.,Academia Sinica, Taiwan | Lo J.-C.,Academia Sinica, Taiwan | Lo J.-C.,National Taiwan University | Chen G.-H.,Academia Sinica, Taiwan | And 3 more authors.
Plant Cell | Year: 2013

Fe is an essential micronutrient for plant growth and development; plants have developed sophisticated strategies to acquire ferric Fe from the soil. Nongraminaceous plants acquire Fe by a reduction-based mechanism, and graminaceous plants use a chelation-based mechanism. In Arabidopsis thaliana, which uses the reduction-based method, IRON-REGULATED TRANSPORTER1 (IRT1) functions as the most important transporter for ferrous Fe uptake. Rapid and constitutive degradation of IRT1 allows plants to quickly respond to changing conditions to maintain Fe homeostasis. IRT1 degradation involves ubiquitination. To identify the specific E3 ubiquitin ligases involved in IRT1 degradation, we screened a set of insertional mutants in RING-type E3 ligases and identified a mutant that showed delayed degradation of IRT1 and loss of IRT1-ubiquitin complexes. The corresponding gene was designated IRT1 DEGRADATION FACTOR1 (IDF1). Evidence of direct interaction between IDF1 and IRT1 in the plasma membrane supported the role of IDF1 in IRT1 degradation. IRT1 accumulation was reduced when coexpressed with IDF1 in yeast or Xenopus laevis oocytes. IDF1 function was RING domain dependent. The idf1 mutants showed increased tolerance to Fe deficiency, resulting from increased IRT1 levels. This evidence indicates that IDF1 directly regulates IRT1 degradation through its RING-type E3 ligase activity. © American Society of Plant Biologists. All rights reserved.

Chhowalla M.,Rutgers University | Shin H.S.,Ulsan National Institute of Science and Technology | Eda G.,National University of Singapore | Li L.-J.,Academia Sinica, Taiwan | And 2 more authors.
Nature Chemistry | Year: 2013

Ultrathin two-dimensional nanosheets of layered transition metal dichalcogenides (TMDs) are fundamentally and technologically intriguing. In contrast to the graphene sheet, they are chemically versatile. Mono- or few-layered TMDs-obtained either through exfoliation of bulk materials or bottom-up syntheses-are direct-gap semiconductors whose bandgap energy, as well as carrier type (n- or p-type), varies between compounds depending on their composition, structure and dimensionality. In this Review, we describe how the tunable electronic structure of TMDs makes them attractive for a variety of applications. They have been investigated as chemically active electrocatalysts for hydrogen evolution and hydrosulfurization, as well as electrically active materials in opto-electronics. Their morphologies and properties are also useful for energy storage applications such as electrodes for Li-ion batteries and supercapacitors. © 2013 Macmillan Publishers Limited. All rights reserved.

Tseng C.-W.,Academia Sinica, Taiwan | Chen Y.-L.,National Central University | Tao Y.-T.,Academia Sinica, Taiwan
Organic Electronics: physics, materials, applications | Year: 2012

Hybrid films of pentacene and aluminum nanoparticles were prepared by depositing pentacene on a SiO 2 surface decorated with aluminum nanoparticles and used as the active channel materials in a thin film transistor. Surface pre-treatment of the aluminum nanoparticles with oxygen plasma and/or organophosphonic acids render the particles surface with different coatings and work functions, which affect the charge trapping/storing ability of the nanoparticles. This in turn results in an electric bistability of the pentacene film-based transistor/memory devices. Correlations of memory window, switching response, and memory retention characteristics with the aluminum nanoparticle surface treatment are provided. © 2012 Elsevier B.V. All rights reserved.

Ho Y.K.,Academia Sinica, Taiwan
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2011

We investigate the lowest-lying S-wave resonant states of two-electron atoms confined by a spherical quantum cavity under the framework of the stabilization method. Hylleraas-type wave functions (basis length N = 444) taking the correlation effects between all the charged particles into account are used in the present paper. The finite oscillator potential is used to represent the confinement potential. We present the resonant parameters (energies and widths) of the quantum-confined two-electron atoms with different depths and various ranges of the potentials. © 2011 American Physical Society.

Liu H.-K.,National Central University | Lii K.-H.,National Central University | Lii K.-H.,Academia Sinica, Taiwan
Inorganic Chemistry | Year: 2011

A uranium(IV) silicate has been synthesized under high-temperature, high-pressure hydrothermal conditions. The structure consists of unbranched dreier single layers with the composition [Si2O5] that are connected by UO6 octahedra to form a 3D framework with 7-ring channels where the Cs+ cations are located. Each UO6 octahedron spans four neighboring dreier single chains and, therefore, introduces a high degree of corrugation in the silicate layers. The U 4f X-ray photoelectron spectroscopy spectrum was measured to confirm the valence state of the uranium. A comparison of related metal silicate structures is made. After the synthesis of this compound, all members in the family of uranium silicates and germanates with oxidation states of uranium from 4+ to 6+ have been observed. © 2011 American Chemical Society.

Cheung C.-Y.,Academia Sinica, Taiwan | Hwang C.-W.,National Kaohsiung Normal University
Journal of High Energy Physics | Year: 2014

In this paper, we investigate symmetry breaking effects in strong and radiative decays of heavy mesons. We study 1/mQ corrections within the heavy quark effective theory. These effects are studied in a covariant model for heavy mesons. The numerical results are consistent with the experimental data and some other theoretical calculations. These provide a vote of confidence for the validity of this covariant model. © The Authors.

Nguyen Q.B.,National Central University | Lii K.-H.,National Central University | Lii K.-H.,Academia Sinica, Taiwan
Inorganic Chemistry | Year: 2011

A very rare tetravalent uranium germanate has been synthesized under hydrothermal conditions at 585 °C and 160 MPa. Its structure contains layers of single-ring Ge3O9 6- germanate anions that are connected by UO6 octahedra and dimers of edge-sharing GeO 5 trigonal bipyramids to form a three-dimensional framework with intersecting 6- and 7-ring channels. UV-visible, photoluminescence, and U 4f X-ray photoelectron spectroscopy were used to confirm the valence state of uranium. © 2011 American Chemical Society.

Tsai W.-S.,National Chi Nan University | Ting S.-Y.,National Chi Nan University | Wei P.-K.,Academia Sinica, Taiwan | Wei P.-K.,National Taiwan Ocean University
Optics Express | Year: 2012

The evanescent tails of a guiding mode as well as its first and second derivatives were measured by a modified end-fire coupling method. The effective index of the waveguide can be obtained by simultaneously fitting these three fields using single parameter. Combined with an inverse calculation algorithm, the fields with fitted evanescent tails showed great improvement in the refractive index profiling of the optical waveguide, especially at the substrate region. Single-mode optical fibers and planar waveguides of proton-exchanged (PE) and titanium-indiffusion (Ti:LiNbO3) on lithium niobate substrates with different refractive index profiles were measured for the demonstration. © 2012 Optical Society of America.

Chang S.-W.,Academia Sinica, Taiwan | Chang S.-W.,National Chiao Tung University
IEEE Journal on Selected Topics in Quantum Electronics | Year: 2012

We present a convenient and self-consistent approach to calculate confinement factors and modal volumes of micro- and nanocavities, which are important for ultrasmall lasers and cavity quantum electrodynamics. This scheme does not rely on the numerical integrations related to optical fields and can avoid the indefinite dependence of physical quantities on integration regions. As a result of this built-in invariance to integration regions, the field representation of the confinement factor, in additional to its conventional expression, contains counter terms of volume and surface integrals, which cancel the effect of arbitrary integration volumes. This procedure is useful for small open cavities or those without sharp boundaries that distinguish cavity regions from free spaces. The uncertainty from different choices of integration regions can be thus eliminated. © 1995-2012 IEEE.

Line M.R.,California Institute of Technology | Liang M.C.,Academia Sinica, Taiwan | Liang M.C.,National Central University | Yung Y.L.,California Institute of Technology
Astrophysical Journal | Year: 2010

Recent infrared spectroscopy of hot exoplanets is beginning to reveal their atmospheric composition. Deep within the planetary atmosphere, the composition is controlled by thermochemical equilibrium. Photochemistry becomes important higher in the atmosphere, at levels above ∼1 bar. These two chemistries compete between 1 and 10 bars in hot-Jupiter-like atmospheres, depending on the strength of the eddy mixing and temperature. HD189733b provides an excellent laboratory in which to study the consequences of chemistry of hot atmospheres. The recent spectra of HD189733b contain signatures of CH4, CO 2, CO, and H2O. Here we identify the primary chemical pathways that govern the abundances of CH4, CO2, CO, and H2O in the cases of thermochemical equilibrium chemistry, photochemistry, and their combination. Our results suggest that the disequilibrium mechanisms can significantly enhance the abundances of these species above their thermochemical equilibrium value, so some caution must be taken when assuming that an atmosphere is in strict thermochemical equilibrium. © 2010. The American Astronomical Society. All rights reserved..

Cheng H.-Y.,Academia Sinica, Taiwan | Chiang C.-W.,Academia Sinica, Taiwan | Chiang C.-W.,National Central University | Chiang C.-W.,National Center for Theoretical science | Kuo A.-L.,National Central University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

Current data of charmless B meson decays to two pseudoscalar mesons (PP) and one vector and one pseudoscalar mesons (VP) are analyzed within the framework of flavor SU(3) symmetry, a working principle that we have tested by allowing symmetry breaking factors in the decay amplitudes and found to be a good approximate symmetry. In the PP sector, the color-suppressed tree amplitude is found to be larger than previously known and has a strong phase of ∼-70° relative to the color-favored tree amplitude. We have extracted for the first time the W-exchange and penguin-annihilation amplitudes. The former has a size of about the QCD-penguin amplitude and a phase opposite to that of the color-favored tree amplitude, while the latter is suppressed in magnitude but gives the dominant contribution to the Bs0→π+π- and π0π0 decays. In the VP sector, one striking feature is that the color-suppressed tree amplitude with the spectator quark ending up in the vector meson has a large size and a strong phase of ∼-90° relative to the color-favored tree amplitudes. The associated electroweak penguin amplitude also has a similar strong phase and a magnitude comparable to the corresponding QCD penguin amplitude. This leads to a large branching fraction of order 10-6 for Bs0→φπ0. In contrast, the color-suppressed tree, QCD penguin, and electroweak penguin amplitudes with the spectator quark ending up in the pseudoscalar meson have magnitudes more consistent with naive expectations. Besides, current data are not sufficiently precise for us to fix the W-exchange amplitudes. For both the PP and VP sectors, predictions of all the decay modes are made based upon our preferred fit results and compared with data and those made by perturbative approaches. We have identified a few observables to be determined experimentally in order to discriminate among theory calculations. © 2015 American Physical Society.

Kuo D.M.T.,National Central University | Chang Y.-C.,Academia Sinica, Taiwan
Nanoscale Research Letters | Year: 2012

We have theoretically studied the thermoelectric properties of serially coupled quantum dots (SCQDs) embedded in an insulator connected to metallic electrodes. In the framework of Keldysh Green's function technique, the Landauer formula of transmission factor is obtained using the equation of motion method. Based on such analytical expressions of charge and heat currents, we calculate the electrical conductance, Seebeck coefficient, electron thermal conductance, and figure of merit (ZT) of SCQDs in the linear response regime. The effects of interdot hopping and electron Coulomb interactions on ZT are analyzed. We demonstrate that ZT is not a monotonic increasing function of interdot electron hopping strength (tc). We also show that in the absence of phonon thermal conductance, SCQD can reach the Carnot efficiency as tc approaches zero. © 2012 Kuo and Chang.

Chang S.-W.,Academia Sinica, Taiwan | Chang S.-W.,National Chiao Tung University
Optics Express | Year: 2011

We develop a frequency-domain formulation in the form of generalized eigenvalue problems for reciprocal microlasers and nanolasers. While the goal is to explore the resonance properties of dispersive cavities, the starting point of our approach is the mode expansion of arbitrary current sources inside the active regions of lasers. Due to the Lorentz reciprocity, a mode orthogonality relation is present and serves as the basis to distinguish various cavity modes. This scheme can also incorporate the asymmetric Fano lineshape into the emission spectra of cavities. We show how to obtain the important parameters of laser cavities based on this formulation. The proposed approach could be an alternative to other computation schemes such as the finite-difference-time- domain method for reciprocal cavities. © 2011 Optical Society of America.

Bahou M.,National Chiao Tung University | Wu Y.-J.,National Synchrotron Radiation Research Center | Lee Y.-P.,National Chiao Tung University | Lee Y.-P.,Academia Sinica, Taiwan
Physical Chemistry Chemical Physics | Year: 2013

Protonated naphthalene (C10H9 +) and its neutral counterparts (hydronaphthyl radicals, C10H9) are important intermediates in the reactions of aromatic compounds and in understanding the unidentified infrared (IR) emissions from interstellar media. We report the IR spectra of 1-C10H9 +, 2-C 10H9 +, 1-C10H9, and 2-C10H9 trapped in solid para-hydrogen (p-H2); the latter three are new. These species were produced upon electron bombardment of a mixture of naphthalene (C10H8) and p-H2 during matrix deposition. The intensities of IR features of 1-C 10H9 + decreased after the matrix was maintained in darkness for 19 h, whereas those of 1-C10H9 and 2-C10H9 increased. Irradiation of this matrix sample with light at 365 nm diminished lines of 1-C10H9 + and 2-C10H9 and enhanced lines of 1-C10H 9 and 2-C10H9 +; the latter species was unstable and converted to 1-C10H9 + in less than 30 min and 2-C10H9 was converted to 1-C 10H9 at 365 nm. Observed wavenumbers and relative intensities of these species agree satisfactorily with the anharmonic vibrational wavenumbers and IR intensities predicted with the B3PW91/6-311++G(2d,2p) method. Compared with spectra recorded previously with IR photodissociation of Ar-tagged C10H9 + or IR multiphoton dissociation of C10H9 +, our method has the advantages of producing high-resolution IR spectra with a wide spectral coverage, true IR intensity and excellent ratio of signal to noise; both protonated species and their neutral counterparts are produced with little interference from other fragments. With these advantages, the IR spectra of 1-C10H9 +, 2-C10H9 +, 1-C10H9, and 2-C10H9 are here clearly characterized. © 2013 The Owner Societies.

Chiang P.-J.,National Kaohsiung University of Applied Sciences | Chang S.-W.,Academia Sinica, Taiwan | Chang S.-W.,National Chiao Tung University
Optics Express | Year: 2013

We present a formulation to analyze photonic periodic structures from viewpoints of sources and gain. The approach is based on a generalized eigenvalue problem and mode expansions of sources which sustain optical fields with phase boundary conditions. Using this scheme, we calculate power spectra, dispersion relations, and quality factors of Bloch modes in one-dimensional periodic structures consisting of dielectrics or metals. We also compare the results calculated from this scheme with those from the complex-frequency method. The outcomes of these two approaches generally agree well and only deviate slightly in the regime of low quality factors. © 2013 Optical Society of America.

Cheng H.-Y.,Academia Sinica, Taiwan | Chiang C.-W.,Academia Sinica, Taiwan | Chiang C.-W.,National Central University | Chiang C.-W.,National Center for Theoretical science
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

Evidence of CP violation in the charm sector has been observed recently by the LHCb and CDF collaborations. Adopting the topological diagram approach, we study flavor SU(3) symmetry breaking effects in the weak decay tree amplitudes of singly Cabibbo-suppressed D→PP decays. The symmetry breaking in the color-allowed and color-suppressed amplitudes is estimated with the help of the factorization ansatz, while that in the W-exchange amplitude is done by fitting to related branching fraction data. We find that the W-exchange amplitudes stay in the second quadrant relative to the color-allowed tree amplitude, albeit there are two possibilities for one type of W-exchange amplitude. The weak decay penguin amplitudes, on the other hand, are evaluated within the framework of QCD factorization. Using the input of topological tree amplitudes extracted from the Cabibbo-favored decay modes and the perturbative results for QCD-penguin amplitudes, we make predictions for the branching fractions and CP asymmetries of singly Cabibbo-suppressed modes. The predictions of branching fractions are generally improved from those in the SU(3) limit. We conclude that the direct CP asymmetry difference between D0→K +K - and D0→π +π - is about -(0.139±0.004)% and -(0.151±0.004)% for the two solutions of W-exchange amplitudes, respectively. We also find that the CP asymmetry of D0→K0K ̄0 dominated by the interference between W-exchange amplitudes ranges from -0.62×10 -3 to -1.82×10 -3. We study phenomenological implications of two new physics scenarios for explaining the observed CP asymmetry in the charm sector, one with large penguin amplitudes and the other with a large chromomagnetic dipole operator. We find that the two scenarios can be discriminated by the measurements of CP asymmetries of a set of decay modes. © 2012 American Physical Society.

Kuo D.M.-T.,National Central University | Shiau S.-Y.,Academia Sinica, Taiwan | Chang Y.-C.,Academia Sinica, Taiwan
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

The charge transport of serially coupled quantum dots (SCQD) connected to the metallic electrodes is theoretically investigated in the Coulomb blockade regime. A closed-form expression for the tunneling current of SCQD in the weak interdot hopping limit is obtained by solving an extended two-site Hubbard model via the Green's function method. We use this expression to investigate spin current rectification, negative differential conductance, and coherent tunneling in the nonlinear response regime. The current rectification arising from the space symmetry breaking of SCQD is suppressed by increasing temperature. The calculation of SCQD is extended to the case of multiple parallel SCQDs for studying the charge ratchet effect and SCQD with multiple levels. In the linear response regime, the functionalities of spin filter and low-temperature current filter are demonstrated to coexist in this system. It is further demonstrated that two-electron spin-singlet and -triplet states can be readily resolved from the measurement of the Seebeck coefficient rather than that of electrical conductance. © 2011 American Physical Society.

Tsai D.-S.,National Taiwan University | Liu K.-K.,Academia Sinica, Taiwan | Lien D.-H.,National Taiwan University | Tsai M.-L.,National Taiwan University | And 5 more authors.
ACS Nano | Year: 2013

Few-layered MoS2 as Schottky metal-semiconductor-metal photodetectors (MSM PDs) for use in harsh environments makes its debut as two-dimensional (2D) optoelectronics with high broadband gain (up to 13.3), high detectivity (up to ∼1010 cm Hz1/2/W), fast photoresponse (rise time of ∼70 μs and fall time of ∼110 μs), and high thermal stability (at a working temperature of up to 200 °C). Ultrahigh responsivity (0.57 A/W) of few-layer MoS2 at 532 nm is due to the high optical absorption (∼10% despite being less than 2 nm in thickness) and a high photogain, which sets up a new record that was not achievable in 2D nanomaterials previously. This study opens avenues to develop 2D nanomaterial-based optoelectronics for harsh environments in imaging techniques and light-wave communications as well as in future memory storage and optoelectronic circuits. © 2013 American Chemical Society.

Chiang C.-W.,National Central University | Chiang C.-W.,Academia Sinica, Taiwan | Chiang C.-W.,National Center for Theoretical science | Nomura T.,National Central University | Tsumura K.,National Taiwan University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

Doubly charged Higgs bosons are predicted in many new physics models with an extended Higgs sector that contains a Higgs triplet field. Current experimental searches have been focusing mainly on the scenario in which the same-sign dilepton decay modes are the dominant ones. We study the scenario where the vacuum expectation value of the triplet field is sufficiently large so that the associated charged Higgs bosons decay dominantly to a pair of weak gauge bosons instead. A detailed simulation of the signal and the backgrounds is performed for the CERN Large Hadron Collider (LHC) at the collision energy of 8 TeV and 14 TeV. We find that different cuts should be imposed for the events, depending on whether the doubly charged Higgs boson mass is greater than about 200 GeV. In the higher mass region, the forward jet tagging proves to be useful in enhancing the signal significance. We show the discovery reach of the LHC running at 8 and 14 TeV, with two benchmark triplet vacuum expectation values. With an integrated luminosity of 10fb -1 at 8 TeV, the doubly charged Higgs boson with a mass of ∼180GeV can be tested at 5σ level in such a scenario. © 2012 American Physical Society.

Cheng H.-Y.,Academia Sinica, Taiwan | Cheng H.-Y.,National Center for Theoretical science | Chiang C.-W.,National Central University | Chiang C.-W.,National Center for Theoretical science
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

Motivated by the recent observation of CP violation in the charm sector by LHCb, we study direct CP asymmetries in the standard model (SM) for the singly Cabibbo-suppressed two-body hadronic decays of charmed mesons using the topological-diagram approach. In this approach, the magnitude and the phase of topological weak annihilation amplitudes, which arise mainly from final-state rescattering, can be extracted from the data. Consequently, direct CP asymmetry adir(tree) at tree level can be reliably estimated. In general, it lies in the range 10 -4

Li H.-N.,Academia Sinica, Taiwan | Li Z.,Michigan State University | Yuan C.-P.,Michigan State University | Yuan C.-P.,Peking University
Physical Review Letters | Year: 2011

We provide a novel development in jet physics by predicting the energy profiles of light-quark and gluon jets in the framework of perturbative QCD. Resumming large logarithmic contributions to all orders in the coupling constant, our predictions are shown to agree well with Tevatron CDF and Large Hadron Collider CMS data. We also extend our resummation formalism to the invariant mass distributions of light-quark and gluon jets produced in hadron collisions. The predicted peak positions and heights in jet mass distributions are consistent with CDF data within uncertainties induced by parton distribution functions. © 2011 American Physical Society.

Wu J.-L.,National Chiao Tung University | Chen F.-C.,National Chiao Tung University | Hsiao Y.-S.,Academia Sinica, Taiwan | Chien F.-C.,Academia Sinica, Taiwan | And 4 more authors.
ACS Nano | Year: 2011

We have systematically explored how plasmonic effects influence the characteristics of polymer photovoltaic devices (OPVs) incorporating a blend of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). We blended gold nanoparticles (Au NPs) into the anodic buffer layer to trigger localized surface plasmon resonance (LSPR), which enhanced the performance of the OPVs without dramatically sacrificing their electrical properties. Steady state photoluminescence (PL) measurements revealed a significant increase in fluorescence intensity, which we attribute to the increased light absorption in P3HT induced by the LSPR. As a result, the rate of generation of excitons was enhanced significantly. Furthermore, dynamic PL measurements revealed that the LSPR notably reduced the lifetime of photogenerated excitons in the active blend, suggesting that interplay between the surface plasmons and excitons facilitated the charge transfer process. This phenomenon reduced the recombination level of geminate excitons and, thereby, increased the probability of exciton dissociation. Accordingly, both the photocurrents and fill factors of the OPV devices were enhanced significantly. The primary origin of this improved performance was local enhancement of the electromagnetic field surrounding the Au NPs. The power conversion efficiency of the OPV device incorporating the Au NPs improved to 4.24% from a value of 3.57% for the device fabricated without Au NPs. © 2011 American Chemical Society.

Huang J.-H.,Academia Sinica, Taiwan | Fang J.-H.,Academia Sinica, Taiwan | Liu C.-C.,Academia Sinica, Taiwan | Chu C.-W.,Academia Sinica, Taiwan | Chu C.-W.,National Chiao Tung University
ACS Nano | Year: 2011

In this study, we found that the work functions (Φw) of solution-processable, functional graphene/carbon nanotube-based transparent conductors were readily manipulated, varying between 5.1 and 3.4 eV, depending on the nature of the doping alkali carbonate salt. We used the graphene-based electrodes possessing lower values of Φw as cathodes in inverted-architecture polymer photovoltaic devices to effectively collect electrons, giving rise to an optimal power conversion efficiency of 1.27%. © 2011 American Chemical Society.

Lee T.-Y.,Yuan Ze University | Chen Y.-J.,Academia Sinica, Taiwan | Lu T.-C.,Yuan Ze University | Huang H.-D.,National Chiao Tung University
PLoS ONE | Year: 2011

S-nitrosylation, the covalent attachment of a nitric oxide to (NO) the sulfur atom of cysteine, is a selective and reversible protein post-translational modification (PTM) that regulates protein activity, localization, and stability. Despite its implication in the regulation of protein functions and cell signaling, the substrate specificity of cysteine S-nitrosylation remains unknown. Based on a total of 586 experimentally identified S-nitrosylation sites from SNAP/L-cysteine-stimulated mouse endothelial cells, this work presents an informatics investigation on S-nitrosylation sites including structural factors such as the flanking amino acids composition, the accessible surface area (ASA) and physicochemical properties, i.e. positive charge and side chain interaction parameter. Due to the difficulty to obtain the conserved motifs by conventional motif analysis, maximal dependence decomposition (MDD) has been applied to obtain statistically significant conserved motifs. Support vector machine (SVM) is applied to generate predictive model for each MDD-clustered motif. According to five-fold cross-validation, the MDD-clustered SVMs could achieve an accuracy of 0.902, and provides a promising performance in an independent test set. The effectiveness of the model was demonstrated on the correct identification of previously reported S-nitrosylation sites of Bos taurus dimethylarginine dimethylaminohydrolase 1 (DDAH1) and human hemoglobin subunit beta (HBB). Finally, the MDD-clustered model was adopted to construct an effective web-based tool, named SNOSite (, for identifying S-nitrosylation sites on the uncharacterized protein sequences. © 2011 Lee et al.

Bahou M.,National Chiao Tung University | Wu Y.-J.,National Synchrotron Radiation Research Center | Lee Y.-P.,National Chiao Tung University | Lee Y.-P.,Academia Sinica, Taiwan
Journal of Physical Chemistry Letters | Year: 2013

Protonated polycyclic aromatic hydrocarbons (H+PAHs) have been reported to have infrared (IR) bands at wavenumbers near those of unidentified infrared (UIR) emission bands from interstellar objects. We produced 1-C 16H11 + and 1-C16H11 upon electron bombardment during matrix deposition of p-H2 containing pyrene (C16H10) in a small proportion. Intensities of absorption features of 1-C16H11 + decreased after the matrix was maintained in darkness or irradiated with light at 365 nm, whereas those of 1-C16H11 increased. The observed line wavenumbers and relative intensities of 1-C16H11 + and 1-C16H11 agree satisfactorily with the scaled vibrational wavenumbers and IR intensities predicted with the B3PW91/6-311++G(2d,2p) method. Our method, being relatively clean with negligible fragmentation, is applicable to larger H+PAH; it has the advantages of producing excellent IR spectra covering a broad spectral range with narrow lines and accurate intensities, so that structural identification among various isomers is feasible. © 2013 American Chemical Society.

McDonald M.J.,Academia Sinica, Taiwan | Wang W.-C.,National Chiao Tung University | Huang H.-D.,National Chiao Tung University | Leu J.-Y.,Academia Sinica, Taiwan
PLoS Biology | Year: 2011

The genome-sequencing gold rush has facilitated the use of comparative genomics to uncover patterns of genome evolution, although their causal mechanisms remain elusive. One such trend, ubiquitous to prokarya and eukarya, is the association of insertion/deletion mutations (indels) with increases in the nucleotide substitution rate extending over hundreds of base pairs. The prevailing hypothesis is that indels are themselves mutagenic agents. Here, we employ population genomics data from Escherichia coli, Saccharomyces paradoxus, and Drosophila to provide evidence suggesting that it is not the indels per se but the sequence in which indels occur that causes the accumulation of nucleotide substitutions. We found that about two-thirds of indels are closely associated with repeat sequences and that repeat sequence abundance could be used to identify regions of elevated sequence diversity, independently of indels. Moreover, the mutational signature of indel-proximal nucleotide substitutions matches that of error-prone DNA polymerases. We propose that repeat sequences promote an increased probability of replication fork arrest, causing the persistent recruitment of error-prone DNA polymerases to specific sequence regions over evolutionary time scales. Experimental measures of the mutation rates of engineered DNA sequences and analyses of experimentally obtained collections of spontaneous mutations provide molecular evidence supporting our hypothesis. This study uncovers a new role for repeat sequences in genome evolution and provides an explanation of how fine-scale sequence contextual effects influence mutation rates and thereby evolution. © 2011 McDonald et al.

Cheng H.-Y.,Academia Sinica, Taiwan | Chiang C.-W.,Academia Sinica, Taiwan | Chiang C.-W.,National Central University | Chiang C.-W.,National Center for Theoretical science
Journal of High Energy Physics | Year: 2012

Certain dark matter interactions with nuclei are mediated possibly by a scalar or pseudoscalar Higgs boson. The estimation of the corresponding cross sections requires a correct evaluation of the couplings between the scalar or pseudoscalar Higgs boson and the nucleons. Progress has been made in two aspects relevant to this study in the past few years. First, recent lattice calculations show that the strange-quark sigma term σ s and the strange-quark content in the nucleon are much smaller than what are expected previously. Second, lattice and model analyses imply sizable SU(3) breaking effects in the determination on the axial-vector coupling constant g 8 A that in turn affect the extraction of the isosinglet coupling g 0 A and the strange quark spin component Δs from polarized deep inelastic scattering experiments. Based on these new developments, we re-evaluate the relevant nucleon matrix elements and compute the scalar and pseudoscalar couplings of the proton and neutron. We also find that the strange quark contribution in both types of couplings is smaller than previously thought. © SISSA 2012.

Liu K.-K.,Academia Sinica, Taiwan | Zhang W.,Academia Sinica, Taiwan | Lee Y.-H.,Academia Sinica, Taiwan | Lin Y.-C.,Academia Sinica, Taiwan | And 9 more authors.
Nano Letters | Year: 2012

The two-dimensional layer of molybdenum disulfide (MoS 2) has recently attracted much interest due to its direct-gap property and potential applications in optoelectronics and energy harvesting. However, the synthetic approach to obtain high-quality and large-area MoS 2 atomic thin layers is still rare. Here we report that the high-temperature annealing of a thermally decomposed ammonium thiomolybdate layer in the presence of sulfur can produce large-area MoS 2 thin layers with superior electrical performance on insulating substrates. Spectroscopic and microscopic results reveal that the synthesized MoS 2 sheets are highly crystalline. The electron mobility of the bottom-gate transistor devices made of the synthesized MoS 2 layer is comparable with those of the micromechanically exfoliated thin sheets from MoS 2 crystals. This synthetic approach is simple, scalable, and applicable to other transition metal dichalcogenides. Meanwhile, the obtained MoS 2 films are transferable to arbitrary substrates, providing great opportunities to make layered composites by stacking various atomically thin layers. © 2012 American Chemical Society.

Der-Huang M.,Academia Sinica, Taiwan | Huang A.H.C.,University of California at Riverside
Plant Physiology | Year: 2016

Subcellular lipid droplets (LDs) in diverse plant cells and species are coated with stabilizing oleosins of at least five phylogenic lineages and perform different functions. We examined two types of inadequately studied LDs for coated oleosins and their characteristics. The epidermis but not mesophyll of leaves of vanilla (Vanilla planifolia) and most other Asparagales species contained solitary and clustered LDs (<0.5 μm), some previously studied by electron microscopy and speculated to be for cuticle formation. In vanilla leaves, transcripts of oleosins of the U lineage were present in both epidermis and mesophyll, but oleosin occurred only in epidermis. Immuno-confocal laser scanning microscopy revealed that the LDs were coated with oleosins. LDs in isolated fractions did not coalesce, and the fractions contained heterogeneous proteins including oleosins and diverse lipids. These findings reflect the in situ structure and possible functions of the LDs. Fruit mesocarp of avocado (Persea americana) and other Lauraceae species possessed large LDs, which likely function in attracting animals for seed dispersal. They contained transcripts of oleosin of a novel M phylogenic lineage. Each avocado mesocarp fatty cell possessed one to several large LDs (5 to 20 μm) and at their periphery, numerous small LDs (<0.5 μm). Immuno-confocal laser scanning microscopy revealed that oleosin was present mostly on the small LDs. LDs in isolated fractions coalesced rapidly, and the fraction contained oleosin and several other proteins and triacylglycerols as the main lipids. These two new types of oleosin-LDs exemplify the evolutionary plasticity of oleosins-LDs in generating novel functions in diverse cell types and species. © 2016 American Society of Plant Biologists. All rights reserved.

Lee C.-S.,National Tsing Hua University | Lin C.-H.,National Central University | Wang S.-L.,National Tsing Hua University | Lii K.-H.,National Central University | Lii K.-H.,Academia Sinica, Taiwan
Angewandte Chemie - International Edition | Year: 2010

Figure Presented For U'r eyes only: A mixed-valence uranium silicate containing three different valence states of uranium has been synthesized under high-temperature, high-pressure hydrothermal conditions. The structure contains uranium silicate sheets with uranophane anion topology that are connected by UO6 octahedra to form a 2D layered structure with Na+ ions within and between the layers. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Huang K.-J.,National Chiao Tung University | Hsiao Y.-S.,Academia Sinica, Taiwan | Whang W.-T.,National Chiao Tung University
Organic Electronics: physics, materials, applications | Year: 2011

In this study, we used thermal evaporation with a low sublimation temperature (42 °C) to deposit 1,5-diaminoanthraquinone (DAAQ) in various morphologies - including nanorods, nanocornerstones, and nanofibers - onto various substrates. Three major factors influenced the growth of vertically aligned DAAQ nanofibers on the electrodes: a low water contact angle (WCA) for the substrate and intermolecular hydrogen bonding and π-π interactions between the DAAQ molecules. On Au and Ti substrates (low-WCA), the DAAQ nanofibers DAAQ-Au and DAAQ-Ti, respectively, possessed great verticality and high aspect ratios; they also exhibited field emission characteristics, with maximum emission current densities of 0.31 and 0.65 mA/cm 2, respectively, at an applied electric field of 12 V/μm. The turn-on electric fields for producing a current density of 10 μA/cm 2 were 8.5 V/μm for DAAQ-Au and 8.25 V/μm for DAAQ-Ti. From the slopes of Fowler-Nordheim plots, we calculated the field enhancement factors (β) of DAAQ-Au and DAAQ-Ti to be 447 and 831, respectively. Field emission stability studies revealed that the DAAQ nanofibers possessed outstanding anti-degrading capability. The emission current did not decrease, but rather increased slightly, after 3000 s. Given the advantages of this simple low-temperature process and the impressive anti-degrading field emission characteristics, such DAAQ nanofibers have great potential for use in various electronics applications (e.g., as organic field emitters). © 2011 Elsevier B.V. All rights reserved.

Liu T.-P.,Academia Sinica, Taiwan | Liu T.-P.,Stanford University | Yu S.-H.,National University of Singapore
Archive for Rational Mechanics and Analysis | Year: 2013

We develop a theory of invariant manifolds for the steady Boltzmann equation and apply it to the study of boundary layers and nonlinear waves. The steady Boltzmann equation is an infinite dimensional differential equation, so the standard center manifold theory for differential equations based on spectral information does not apply here. Instead, we employ a time-asymptotic approach using the pointwise information of Green's function for the construction of the linear invariant manifolds. At the resonance cases when the Mach number at the far field is around one of the critical values of -1, 0 or 1, the truly nonlinear theory arises. In such a case, there are wave patterns combining the fast decaying Knudsen-type and slow varying fluid-like waves. The key Knudsen manifolds consisting of only Knudsentype layers are constructed through delicate analysis of identifying the singular behavior around the critical Mach numbers. Around Mach number ± 1, the fluidlike waves are compressive and expansive waves; and around the Mach number 0, they are linear thermal layers. The quantitative analysis of the fluid-like waves is done using the reduction of dimensions to the center manifolds.Two-scale nonlinear dynamics based on those on the Knudsen and center manifolds are formulated for the study of the global dynamics of the combined wave patterns. There are striking bifurcations in the transition of evaporation to condensation and in the transition of the Milne's problem with a subsonic far field to one with a supersonic far field. The analysis of these wave patterns allows us to understand the Sone Diagram for the study of the complete condensation boundary value problem. The monotonicity of the Boltzmann shock profiles, a problem that initially motivated the present study, is shown as a consequence of the quantitative analysis of the nonlinear fluid-like waves. © 2013 Springer-Verlag Berlin Heidelberg.

Huang C.-J.,National Central University | Chang Y.-C.,Academia Sinica, Taiwan
Materials | Year: 2014

A novel biointerface bearing zwitterionic carboxybetaine moieties was developed for effective resistance to nonspecific adsorption of proteins and blood cells. Self-assembled thin films (SAFs) of (N, N-dimethylaminopropyl) trimethoxysilane were formed as mattress layers by either vapor or solution deposition. Subsequently, the tertiary amine head groups on SAFs were reacted with β-propiolactone to give zwitterionic carboxybetaine moieties via in situ synthesis. The optimal reaction time of 8 h for both preparation methods was verified by static contact angle measurements. According to the X-ray photoelectron spectroscopy, 67.3% of amine groups on SAFs prepared from the vapor deposition was converted to the zwitterionic structures after reaction of β-propiolactone. The antifouling properties of the zwitterionic biointerfaces were quantitatively evaluated in the presence of protein solutions using a quartz crystal microbalance with dissipation, showing a great improvement by factors of 6.5 and 20.2 from tertiary amine SAFs and bare SiO2 surfaces, respectively. More importantly, the zwitterionic SAFs were brought to contact with undiluted human blood in chaotic-mixer microfluidic systems; the results present their capability to effectively repel blood cell adhesion. Accordingly, in this work, development of carboxybetaine SAFs offers a facile yet effective strategy to fabricate biocompatible biointerfaces for a variety of potential applications in surface coatings for medical devices. © 2013 by the authors.

Chuang M.-K.,National Chiao Tung University | Lin S.-W.,National Chiao Tung University | Chen F.-C.,National Chiao Tung University | Chu C.-W.,Academia Sinica, Taiwan | Hsu C.-S.,National Chiao Tung University
Nanoscale | Year: 2014

In this work, gold nanoparticle/graphene oxide (AuNP/GO) nanocomposites are synthesized and used as anodic buffer layers in organic photovoltaic devices (OPVs). The application of thiol-terminated polyethylene glycol as a capping agent prevents the aggregation of AuNPs on the GO surface and further improves the solubility and stability of these nanomaterials in solutions. When AuNP/GO nanomaterials served as the buffer layers, they introduced localized surface plasmon resonance (LSPR) in the OPVs, leading to noticeable enhancements in the photocurrent and the efficiencies of the OPVs. We attribute the primary origin of the improvement in device performance to local field enhancement induced by the LSPR. We anticipate that this study might open up new avenues for constructing plasmon-enhancing layers on the nanoscale to improve the performance of solar cells. © 2013 The Royal Society of Chemistry.

Fan T.-F.,National Penghu University of Science and Technology | Liau C.-J.,Academia Sinica, Taiwan | Liu D.-R.,National Chiao Tung University
International Journal of Approximate Reasoning | Year: 2011

In this paper, we propose a dominance-based fuzzy rough set approach for the decision analysis of a preference-ordered uncertain or possibilistic data table, which is comprised of a finite set of objects described by a finite set of criteria. The domains of the criteria may have ordinal properties that express preference scales. In the proposed approach, we first compute the degree of dominance between any two objects based on their imprecise evaluations with respect to each criterion. This results in a valued dominance relation on the universe. Then, we define the degree of adherence to the dominance principle by every pair of objects and the degree of consistency of each object. The consistency degrees of all objects are aggregated to derive the quality of the classification, which we use to define the reducts of a data table. In addition, the upward and downward unions of decision classes are fuzzy subsets of the universe. Thus, the lower and upper approximations of the decision classes based on the valued dominance relation are fuzzy rough sets. By using the lower approximations of the decision classes, we can derive two types of decision rules that can be applied to new decision cases. © 2011 Elsevier Ltd. All rights reserved.

Huang J.-K.,Academia Sinica, Taiwan | Pu J.,Waseda University | Hsu C.-L.,Academia Sinica, Taiwan | Chiu M.-H.,Academia Sinica, Taiwan | And 7 more authors.
ACS Nano | Year: 2014

The monolayer transition metal dichalcogenides have recently attracted much attention owing to their potential in valleytronics, flexible and low-power electronics, and optoelectronic devices. Recent reports have demonstrated the growth of large-size two-dimensional MoS2 layers by the sulfurization of molybdenum oxides. However, the growth of a transition metal selenide monolayer has still been a challenge. Here we report that the introduction of hydrogen in the reaction chamber helps to activate the selenization of WO 3, where large-size WSe2 monolayer flakes or thin films can be successfully grown. The top-gated field-effect transistors based on WSe2 monolayers using ionic gels as the dielectrics exhibit ambipolar characteristics, where the hole and electron mobility values are up to 90 and 7 cm2/Vs, respectively. These films can be transferred onto arbitrary substrates, which may inspire research efforts to explore their properties and applications. The resistor-loaded inverter based on a WSe2 film, with a gain of ∼13, further demonstrates its applicability for logic-circuit integrations. © 2013 American Chemical Society.

Hsu W.-T.,National Chiao Tung University | Zhao Z.-A.,National Chiao Tung University | Li L.-J.,Academia Sinica, Taiwan | Li L.-J.,China Medical University at Taichung | And 5 more authors.
ACS Nano | Year: 2014

Optical second harmonic generation (SHG) is known as a sensitive probe to the crystalline symmetry of few-layer transition metal dichalcogenides (TMDs). Layer-number dependent and polarization resolved SHG have been observed for the special case of Bernal stacked few-layer TMDs, but it remains largely unexplored for structures deviated from this ideal stacking order. Here we report on the SHG from homo- and heterostructural TMD bilayers formed by artificial stacking with an arbitrary stacking angle. The SHG from the twisted bilayers is a coherent superposition of the SH fields from the individual layers, with a phase difference depending on the stacking angle. Such an interference effect is insensitive to the constituent layered materials and thus applicable to hetero-stacked bilayers. A proof-of-concept demonstration of using the SHG to probe the domain boundary and crystal polarity of mirror twins formed in chemically grown TMDs is also presented. We show here that the SHG is an efficient, sensitive, and nondestructive characterization for the stacking orientation, crystal polarity, and domain boundary of van der Waals heterostructures made of noncentrosymmetric layered materials. © 2014 American Chemical Society.

Lu C.-T.,Yuan Ze University | Huang K.-Y.,Yuan Ze University | Su M.-G.,Yuan Ze University | Lee T.-Y.,Yuan Ze University | And 4 more authors.
Nucleic Acids Research | Year: 2013

Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM ( is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource. © The Author(s) 2012.

Huang Y.,Nanyang Technological University | Dong X.,Nanjing University of Posts and Telecommunications | Liu Y.,Nanyang Technological University | Li L.-J.,Academia Sinica, Taiwan | Chen P.,Nanyang Technological University
Journal of Materials Chemistry | Year: 2011

Graphene, which is a recently discovered single-atom-thick planar sheet of carbon atoms perfectly arranged in a honeycomb lattice, has great potential in biosensing owing to its extraordinary electrical, physical, and optical properties. In this work, we demonstrate a graphene based biosensor to electrically detect E. coli bacteria with high sensitivity and specificity. The large-sized graphene film was grown by chemical vapor deposition and functionalized with anti-E. coli antibodies and passivation layer. Significant conductance increase of the graphene device was observed after exposure to E. coli bacteria at a concentration as low as 10 cfu/mL, while no significant response was triggered by high concentration of the another bacterial strain. In addition, this biosensor was employed to detect the glucose induced metabolic activities of the bound E. coli bacteria in real time. This simple, fast, sensitive, and label-free nanoelectronic biosensor, in principle, could serve as a high throughput platform for detection of any pathogenic bacteria, and for functional studies or screening of antibacterial drugs. © 2011 The Royal Society of Chemistry.

Algaba J.C.,Academia Sinica, Taiwan | Gabuzda D.C.,University College Cork | Smith P.S.,University of Arizona
Monthly Notices of the Royal Astronomical Society | Year: 2012

Previous research showed that most BL Lac objects and some quasars have aligned very long baseline interferometry (VLBI) core and optical polarizations, although some of the active galactic nuclei (AGNs) also showed no obvious relationship between their VLBI core and optical polarization angles. This may indicate that some AGNs have cospatial regions of optical and radio emission, while others do not. However, another possibility is that some of the VLBI cores had Faraday rotations of the order of several tens of thousands of rad m -2, which were not properly fitted using the three-frequency data due to nπ ambiguities in the observed polarization angles, leading to incorrect subtraction of the effects of the core Faraday rotation, and so incorrect intrinsic radio polarization angles χ 0. With this is mind, we obtained additional 12+15+22+24+43 GHz plus optical observations for eight of 40 AGNs previously considered, enabling improved sampling of Faraday effects. Our results indicate that, although some VLBI radio cores have comparatively high rotation measures, this alone cannot explain the misalignments found between the radio core and optical VLBI polarization angles, Δχ= |χ opt-χ 0|. Comparisons between Δχ and (i) the orientation of χ 0 relative to the jet direction, (ii) the degree of polarization of the core, (iii) a depolarization factor, (iv) the core rotation measures and (v) the core magnetic fields 1pc from the jet base do not yield evidence for any correlations between these properties. There is, however, some evidence that the maximum observed Δχ tends to decrease as the core-region magnetic field increases, suggesting that large misalignments in Δχ could be associated in part with relatively low core magnetic fields. Thus, although the overall distribution of Δχ for all 40 sources in our sample does show a significant peak at Δχ∼ 0, it remains unclear what distinguishes these AGN cores from those showing appreciable misalignment between optical and VLBI core polarization position angles. © 2011 The Authors Monthly Notices of the Royal Astronomical Society © 2011 RAS.

Chattopadhyay S.,National Yang Ming University | Huang Y.F.,Academia Sinica, Taiwan | Huang Y.F.,National Taiwan University | Jen Y.J.,National Taipei University of Technology | And 4 more authors.
Materials Science and Engineering R: Reports | Year: 2010

Abstract Optical reflection, or in other words the loss of reflection, from a surface becomes increasingly crucial in determining the extent of the light-matter interaction. The simplest example of using an anti-reflecting (AR) surface is possibly the solar cell that incorporates an AR coating to harvest sunlightmore effectively. Researchers have now found ways to mimic biological structures, such as moth eyes or cicada wings, which have been used for the AR purpose by nature herself. These nanoscopic biomimetic structures lend valuable clues in fabricating and designing gradient refractive index materials that are efficient AR structures. The reflectance from a selected sub-wavelength or gradient index structures have come down to below 1% in the visible region of the spectrum and efforts are on to achieve broader bands of such enhanced AR regime. In addition to the challenge of broader bands, the performance of AR structures is also limited by factors such as omnidirectional properties and polarization of incident light. This review presents selected state-of-the-art AR techniques, reported over the last half a century, and their guiding principles to predict a logical trend for future research in this field. © 2010 Elsevier B.V. All rights reserved.

Wu C.-J.,National Cheng Kung University | Chen Y.-W.,National Central University | Tai J.-H.,Academia Sinica, Taiwan | Chen S.-H.,National Cheng Kung University
Journal of Proteome Research | Year: 2011

17β-Estradiol (E2) regulates transcriptional activity partly by inducing protein-kinase cascades, leading to the phosphorylation of estrogen receptors (ERs) and other functional proteins. Many of these phosphorylation events are also modulated by growth factors. To gain an insight into E2-modulated protein phosphorylation, we applied quantitative phosphoproteomics to investigate global changes in protein phosphorylation induced by E2 in MCF-7 cells. Proteomic analyses using stable isotope dimethyl labeling coupled with immobilized metal affinity chromatography-hydrophilic interaction liquid chromatography (IMAC-HILIC) fractionation and nanoLC-MS/MS identified and quantified 2857 unique phosphorylation sites in 1338 phosphoproteins from 1 mg of total cellular protein. In addition to S118 of ERα, a 30-min E2 treatment significantly altered the status of 403 phosphorylation sites, including 112 novel sites. Interestingly, the substrate motifs for ERK1/2 were largely enriched in both the up-regulated and down-regulated phosphorylation sites. An increase in the phosphorylation on either the T202 or Y204 sites of ERK1 was observed after E2 treatment, while dual phosphorylation on both sites were not detected, implying that a feedback loop to deactivate MAPK signaling was achieved during a 30-min E2 treatment. In contrast, the PKA and CKII substrate motifs were majorly enriched among the up-regulated phosphorylation sites. Western blot analysis confirmed that E2 increased the phosphorylation level of S226 within a CKII motif of HSP90β by a factor of 2- to 3-fold without changing the total protein expression level. E2 also up-regulated phosphorylations of S255 in HSP90β and S353 within a CKII motif of HSP90α. These results indicated that E2 may modulate gene transcription by affecting the stability, function, and activity of many regulators through a HSP90 phosphorylation-mediated chaperoning process. This study, using a quantitative, multidimensional separation phosphoproteomic approach that required a relatively low amount of cells, provides new insights into the diversity, variability, and dynamic nature of the protein phosphorylation/ dephosphorylation elicited by E2. © 2011 American Chemical Society.

Lee H.-Y.,National Taiwan University | Hwang J.-S.,Academia Sinica, Taiwan | Jeng J.-S.,National Taiwan University Hospital | Wang J.-D.,National Taiwan University Hospital
Stroke | Year: 2010

BACKGROUND AND PURPOSE-: Few studies have evaluated the long-term health impact of stroke as categorized into different subtypes. The aim of this study is to quantify the loss of quality-adjusted life expectancy related to ischemic stroke and intracerebral hemorrhage. METHODS-: The hospital-based cohort, which consisted of 13 194 patients with first-ever stroke onset dates between 1995 and 2007, was classified into lacunar and nonlacunar infarctions and intracerebral hemorrhages. After linking with the National Mortality Registry, survival functions were determined and extrapolated over a 50-year period based on the survival ratio between the patients' survival and age-and sex-matched reference population's as calculated from the vital statistics of Taiwan. The survival functions were then multiplied by the quality of life assessed under the EuroQol 5-dimension (EQ-5D) questionnaire based on a sample of 486 patients with stroke. RESULTS-: The quality-adjusted life expectancy for a patient with ischemic stroke was 8.7 quality-adjusted life-years with an average loss of 8.3 quality-adjusted life-years, and there appeared to be no difference between lacunar and nonlacunar infarctions. Patients with intracerebral hemorrhage had a similar quality-adjusted life expectancy as those with ischemic stroke but with a significantly greater loss relative to the reference population (14.1 quality-adjusted life-years) because of younger ages. CONCLUSION-: The lifelong health burden due to stroke was approximately 9.5 quality-adjusted life-years and should be considered in future cost-effectiveness analyses for prevention. © 2010 American Heart Association, Inc.

Lin H.-H.,National Chiao Tung University | Lin H.-H.,QNAP Inc | Chuang J.-H.,National Chiao Tung University | Liu T.-L.,Academia Sinica, Taiwan
IEEE Transactions on Image Processing | Year: 2011

To model a scene for background subtraction, Gaussian mixture modeling (GMM) is a popular choice for its capability of adaptation to background variations. However, GMM often suffers from a tradeoff between robustness to background changes and sensitivity to foreground abnormalities and is inefficient in managing the tradeoff for various surveillance scenarios. By reviewing the formulations of GMM, we identify that such a tradeoff can be easily controlled by adaptive adjustments of the GMM's learning rates for image pixels at different locations and of distinct properties. A new rate control scheme based on high-level feedback is then developed to provide better regularization of background adaptation for GMM and to help resolving the tradeoff. Additionally, to handle lighting variations that change too fast to be caught by GMM, a heuristic rooting in frame difference is proposed to assist the proposed rate control scheme for reducing false foreground alarms. Experiments show the proposed learning rate control scheme, together with the heuristic for adaptation of over-quick lighting change, gives better performance than conventional GMM approaches. © 2011 IEEE.

Grillet L.,Academia Sinica, Taiwan | Mari S.,French National Institute for Agricultural Research | Schmidt W.,Academia Sinica, Taiwan
Frontiers in Plant Science | Year: 2014

Iron (Fe) is one of the most abundant elements on earth, but its limited bioavailability poses a major constraint for agriculture and constitutes a serious problem in human health. Due to an improved understanding of the mechanisms that control Fe homeostasis in plants, major advances toward engineering biofortified crops have been made during the past decade. Examples of successful biofortification strategies are, however, still scarce and the process of Fe loading into seeds is far from being well understood in most crop species. In particular in grains where the embryo represents the main storage compartment such as legumes, increasing the seed Fe content remains a challenging task. This review aims at placing the recently identified actors in Fe transport into the unsolved puzzle of grain filling, taking the differences of Fe distribution between various species into consideration. We summarize the current knowledge on Fe transport between symplasmic and apoplasmic compartments, and provide models for Fe trafficking and localization in different seed types that may help to develop high seed Fe germplasms. © 2014 Grillet, Mari and Schmidt.

Cheng H.-Y.,Academia Sinica, Taiwan | Oh S.,Yonsei University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2012

In light of the recent neutrino experimental results from the Daya Bay and RENO Collaborations, we construct a realistic tribimaximal-like Pontecorvo-Maki-Nakagawa-Sakata (PMNS) leptonic mixing matrix. Motivated by the Qin-Ma (QM) parametrization for the quark mixing matrix in which the CP-odd phase is approximately maximal, we propose a simple ansatz for the charged lepton mixing matrix, namely, it has the QM-like parametrization, and assume the tribimaximal mixing (TBM) pattern for the neutrino mixing matrix. The deviation of the leptonic mixing matrix from the TBM one is then systematically studied. While the deviation of the solar and atmospheric neutrino mixing angles from the corresponding TBM values, i.e. sin 2θ 12=1/3 and sin 2θ 23=1/2, is fairly small, we find a non-vanishing reactor mixing angle given by sinθ13≈λ/2 (λ≈0.22 being the Cabibbo angle). Specifically, we obtain θ 13≃9.2° and δCP≃δQM≃O(90°). Furthermore, we show that the leptonic CP violation characterized by the Jarlskog invariant is |JCPℓ|≃λ/6, which could be tested in the future experiments such as the upcoming long baseline neutrino oscillation ones. © 2012 Elsevier B.V.

Cheng H.-Y.,Academia Sinica, Taiwan | Cheng H.-Y.,Brookhaven National Laboratory | Chiang C.-W.,Academia Sinica, Taiwan | Chiang C.-W.,National Central University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2010

In this work we study the two-body hadronic charmed meson decays, including both the PP and VP modes. The latest experimental data are first analyzed in the diagrammatic approach. The magnitudes and strong phases of the flavor amplitudes are extracted from the Cabibbo-favored decay modes using χ2 minimization. The best-fitted values are then used to predict the branching fractions of the singly Cabibbo-suppressed and doubly Cabibbo-suppressed decay modes in the flavor SU(3) symmetry limit. We observe significant SU(3) breaking effects in some of the singly Cabibbo-suppressed channels. In the case of VP modes, we point out that the AP and AV amplitudes cannot be completely determined based on currently available data. We conjecture that the quoted experimental results for both Ds+→K̄0K *+ and Ds+→ρ+η ′ are overestimated. We compare the sizes of color-allowed and color-suppressed tree amplitudes extracted from the diagrammatical approach with the effective parameters a1 and a2 defined in the factorization approach. The ratio |a2/a1| is more or less universal among the D→K̄π, K ̄*π, and K̄ρ modes. This feature allows us to discriminate between different solutions of topological amplitudes. For the long-standing puzzle about the ratio Γ(D0→K +K-)/Γ(D0→π+π-), we argue that, in addition to the SU(3) breaking effect in the spectator amplitudes, the long-distance resonant contribution through the nearby resonance f0(1710) can naturally explain why D0 decays more copiously to K +K- than π+π- through the W-exchange topology. This has to do with the dominance of the scalar glueball content of f0(1710) and the chiral-suppression effect in the decay of a scalar glueball into two pseudoscalar mesons. The same final-state interaction also explains the occurrence of D0→K0K̄0 and its vanishing amplitude when SU(3) flavor symmetry is exact. Owing to the G-parity selection rule, Ds+→π+ω does not receive contributions from the short-distance W-annihilation and resonant final-state interactions, but it can proceed through the weak decays Ds+→ρ+η( 1′) followed by the final-state rescattering of ρ+η(′) into π+ω through quark exchange. © 2010 The American Physical Society.

Akeroyd A.G.,National Central University | Chiang C.-W.,Academia Sinica, Taiwan
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2010

The Higgs triplet model contains two CP-even neutral scalar eigenstates, each having components from an isospin doublet and an isospin triplet scalar field. The mixing angle can be maximal if the masses of the scalar eigenstates are close to degeneracy. We quantify the dependence of the mixing angle on the mass splitting and on the vacuum expectation value of the neutral triplet scalar. We determine the parameter space for maximal mixing, and study the observability of both CP-even Higgs bosons at the CERN LHC. © 2010 The American Physical Society.

Oh S.,Academia Sinica, Taiwan | Tandean J.,National Central University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2011

The anomalously large like-sign dimuon charge asymmetry in semileptonic b-hadron decays recently measured by the D0 Collaboration may be hinting at the presence of CP-violating new physics in the mixing of Bs mesons. It has been suggested that the effect of a nonstandard spin-1 particle lighter than the b quark with flavor-changing couplings to b and s quarks can reproduce the D0 result within its one-sigma range. Here we explore the possibility that the new particle also couples to charged leptons =e,μ and thus contributes to rare b→s processes involving the leptons. We consider in particular constraints on its couplings from existing experimental data on the inclusive B→Xs +- and exclusive B→K( *)+- decays, as well as the anomalous magnetic moments of the leptons. We find that there is parameter space of the particle that is allowed by the current data. We discuss how future measurements of these B transitions and the rare decays of the Bs meson, such as Bs→(·,η,η′)+ - and Bs→+-, at LHCb and next-generation B factories may probe its presence or couplings more stringently. © 2011 American Physical Society.

Wu C.-H.,A-Life Medical | Wu C.-H.,Academia Sinica, Taiwan | Kuo Y.-H.,Academia Sinica, Taiwan | Hong R.-L.,National Taiwan University Hospital | And 2 more authors.
Science Translational Medicine | Year: 2015

Colorectal cancer is one of the most commonly diagnosed cancers and a leading cause of cancer mortality worldwide. Current treatment for colorectal cancer results in only limited success, and more effective therapeutic approaches are thus urgently needed. The development of new methods for early detection and effective treatments for cancer is contingent on the identification of biomarkers on the surface of cancer cells, as well as isolation of tumor-specific ligands with high binding affinity to such biomarkers. In vitro biopanning of a phage-displayed peptide library was used to identify specific peptides binding to human colorectal carcinoma cells. The targeting peptide pHCT74 showed the greatest potential for drug delivery in both in vitro and in vivo studies. The use of biotinylated peptides combined with an affinity trapping method and liquid chromatography-tandem mass spectrometry identified the target protein for the pHCT74 peptide as α-enolase. In animal model studies, combined pHCT74-conjugated liposomal doxorubicin (pHCT74-LD) and pHCT74-conjugated liposomal vinorelbine (pHCT74-sLV) therapy exhibited an enhanced antitumor effect and markedly extended the survival of mice with human colorectal cancer in subcutaneous and orthotopic models. Our findings indicate that α-enolase-targeted lipid nanoparticles have great potential for application in targeted drug delivery systems for colorectal cancer therapy. © 2015, American Association for the Advancement of Science. All rights reserved.

Davis R.A.,University of California at Davis | Lin C.-H.,Academia Sinica, Taiwan | Gervay-Hague J.,University of California at Davis
Chemical Communications | Year: 2012

In a three-step protocol involving regioselective enzymatic acylation, per-O-trimethylsilylation, and a one-pot α-glycosidation-deprotection sequence, cholesteryl-6-O-tetradecanoyl-α-d-glucopyranoside (α-CAG) of Helicobacter pylori is afforded starting from glucose in an overall yield of 45%. The production of CAG can be scaled to make purified quantities available to the biological community for the first time. © 2012 The Royal Society of Chemistry.

Chang S.-W.,Academia Sinica, Taiwan | Chang S.-W.,National Chiao Tung University
Journal of Lightwave Technology | Year: 2014

We show that the bidirectionality of optical modes exists in general bianisotropic but reciprocal photonic crystals and related structures. Using this property, we obtain an alternative bidirectionality of modes with sources (gain) in active photonic crystals. In the former, we conclude that degeneracies of modes with complex anti-parallel wave vectors are always identical as long as the structure is reciprocal. With the latter, we setup an associated biorthogonality relation in the Rayleigh-Carson form for modes in active photonic crystals. © 1983-2012 IEEE.

Yalcin A.D.,Academia Sinica, Taiwan | Gumuslu S.,Akdeniz University
Expert Opinion on Biological Therapy | Year: 2014

Background: D-dimer (DD), a fibrin degradation product formed during the lysis of a thrombus, is also detected in high levels in patients with active chronic urticaria (CU). Severe persistent allergic asthma (SPA) is associated with a procoagulant state in the bronchoalveolar space, further aggravated by impaired local activities of the anticoagulant protein C/protein S, antithrombin III system and fibrinolysis. This was demonstrated as massive fibrin depositions found in the alveoli of a SPA patient who died from a SPA attack and who did not respond to treatment. Objectives: For this reason, we investigated the effect of omalizumab both in bronchial and systemic vascular areas and evaluated SPA (group I) and CU (group II) patients before and after therapy period. Methods: Blood samples were taken before treatment (A), on 4th month (B), on 8th month (C) and on 12th month (D) post treatment in both groups. Results: We compared DD levels between groups: the significant DD difference was observed between group-IA and group-IC (p = 0.031); between group-IA and group-ID (p = 0.003); between group-IB and group-ID (p = 0.049) and between group IIA-1 and group-IID (p = 0.015). In the IIA-1 group, there was a significant positive correlation between DD and age (p = 0.008, r = 0.848). Conclusion: In conclusion, mediators and cells classically involved in procoagulant and anticoagulant pathways together play a role in SPA and CU pathophysiology, where omalizumab has its effect. ©2014 Informa UK, Ltd.

Chiang C.-W.,National Central University | Chiang C.-W.,Academia Sinica, Taiwan | Chiang C.-W.,National Center for Theoretical science | Yamada T.,National Central University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2014

The Georgi-Machacek model extends the standard model Higgs sector by adding two isospin triplet scalar fields and imposing global SU(2)R symmetry on them. A feature of the model is that the triplets can acquire a large vacuum expectation value without conflicting with the current experimental bound on the ρ parameter. We investigate the electroweak phase transition in the Georgi-Machacek model by evaluating the finite-temperature effective potential of the Higgs sector. The electroweak phase transition can be sufficiently strong in a large parameter space when the triplets acquire a vacuum expectation value of O(10)GeV, opening a possibility to realize successful electroweak baryogenesis. © 2014 Elsevier B.V.

Chiang C.-W.,National Central University | Chiang C.-W.,Academia Sinica, Taiwan | Chiang C.-W.,National Center for Theoretical science | Yagyu K.,National Central University
Journal of High Energy Physics | Year: 2013

Based on current data of the Higgs boson search at the Large Hadron Collider, we constrain the parameter space of the two-Higgs doublet models where a softly broken Z 2 symmetry is employed to avoid flavor-changing neutral currents at tree level. There are four types of Yukawa interactions under the Z 2 charge assignments of the standard model fermions. We find that the model with Type-II Yukawa interactions can better explain the experimental data among all. In this scenario, the couplings of the light CP-even Higgs boson h with weak gauge bosons are almost standard model-like or only slightly different in a small range of tan β. In particular, we scrutinize a well-constrained region previously ignored by other analyses and study the phenomenology of the extra Higgs bosons at the Large Hadron Collider. © 2013 SISSA, Trieste, Italy.

Chang S.-W.,Academia Sinica, Taiwan | Chang S.-W.,National Chiao Tung University
Optics Express | Year: 2012

We propose a chiral Fabry-Perot cavity in which only the cavity modes in almost pure spin (circular polarization) states lase in the presence of gain. In absence of imposed nonreciprocal environments and time-reversal symmetry breaking of emitter states to favor the emission of circularly-polarized photons, only the resonance of modes with a specific spin orientation remains in the cavity. We demonstrate a prototype of the cavity using distributed Bragg reflectors and cholesteric liquid crystals. This reciprocal cavity may provide a method to control the angular momentum state of emitters based on stimulated emissions. © 2012 Optical Society of America.

Chan Y.-H.,Academia Sinica, Taiwan | Chiu C.-K.,University of British Columbia | Sun K.,University of Texas at Dallas
Physical Review B - Condensed Matter and Materials Physics | Year: 2015

We study one-component fermions in chain lattices with proximity-induced superconducting gap and interparticle short-range interaction, capable of hosting Majorana fermions. By systematically tracking various physical quantities, we show that topological states and topological phase transitions in the system can be identified by multiple signatures in thermodynamic quantities and pair-condensate properties, in good agreement with the known signatures in the ground-state energy and entanglement spectrum. We find the disappearance of the topological phase in a largely attractive regime, in which the system undergoes a first-order transition between two topologically trivial states. In addition, the stability of the signatures against finite size, disorder, and inhomogeneity is analyzed. Our results provide additional degrees of freedom for the characterization of topological states with interaction and for the experimental detection of emergent Majorana fermions. © 2015 American Physical Society.

Huang N.-L.,Academia Sinica, Taiwan | Huang M.-D.,Academia Sinica, Taiwan | Chen T.-L.L.,Academia Sinica, Taiwan | Huang A.H.C.,Academia Sinica, Taiwan | Huang A.H.C.,University of California at Riverside
Plant Physiology | Year: 2013

In primitive and higher plants, intracellular storage lipid droplets (LDs) of triacylglycerols are stabilized with a surface layer of phospholipids and oleosin. In chlorophytes (green algae), a protein termed major lipid-droplet protein (MLDP) rather than oleosin on LDs was recently reported. We explored whether MLDP was present directly on algal LDs and whether algae had oleosin genes and oleosins. Immunofluorescence microscopy revealed that MLDP in the chlorophyte Chlamydomonas reinhardtii was associated with endoplasmic reticulum subdomains adjacent to but not directly on LDs. In C. reinhardtii, low levels of a transcript encoding an oleosin-like protein (oleolike) in zygotes-tetrads and a transcript encoding oleosin in vegetative cells transferred to an acetate-enriched medium were found in transcriptomes and by reverse transcription-polymerase chain reaction. The C. reinhardtii LD fraction contained minimal proteins with no detectable oleolike or oleosin. Several charophytes (advanced green algae) possessed low levels of transcripts encoding oleosin but not oleolike. In the charophyte Spirogyra grevilleana, levels of oleosin transcripts increased greatly in cells undergoing conjugation for zygote formation, and the LD fraction from these cells contained minimal proteins, two of which were oleosins identified via proteomics. Because the minimal oleolike and oleosins in algae were difficult to detect, we tested their subcellular locations in Physcomitrella patens transformed with the respective algal genes tagged with a Green Fluorescent Protein gene and localized the algal proteins on P. patens LDs. Overall, oleosin genes having weak and cell/development-specific expression were present in green algae. We present a hypothesis for the evolution of oleosins from algae to plants. © 2013 American Society of Plant Biologists. All Rights Reserved.

Tsai W.-S.,National Chi Nan University | Piao S.-C.,National Chi Nan University | Wei P.-K.,Academia Sinica, Taiwan
Optics Letters | Year: 2011

We present a modified end-fire coupling method to reconstruct two-dimensional index profiles of optical waveguides. The reconstruction is based on the measured differential optical fields and an inverse algorithm for the Helmholtz equation. The differential fields are obtained from spatially perturbed images recorded by a CCD camera. A closed-loop piezoelectric stage given a sinusoidal wave and an oil-immersion objective lens for high-resolution images are used in the measurement. A single-mode fiber and a Ti:LiNbO3 waveguide with known index profile at 632:8nm are measured for demonstration. The measured index profiles agree quite well with core regions of known index profiles. © 2011 Optical Society of America.

Alemu D.,Academia Sinica, Taiwan | Alemu D.,National Tsing Hua University | Wei H.-Y.,National Taiwan University | Ho K.-C.,National Taiwan University | And 2 more authors.
Energy and Environmental Science | Year: 2012

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. © 2012 The Royal Society of Chemistry.

Lin C.-T.,Academia Sinica, Taiwan | Loan P.T.K.,National Chiao Tung University | Chen T.-Y.,Academia Sinica, Taiwan | Liu K.-K.,Academia Sinica, Taiwan | And 3 more authors.
Advanced Functional Materials | Year: 2013

There is broad interest in using graphene or graphene oxide sheets as a transducer for label-free and selective electrical detection of biomolecules such as DNA. However, it is still not well explored how the DNA molecules interact with and influence the properties of graphene during the detection. Here, Hall effect measurements based on the Van der Pauw method are used to perform single-base sequence selective detection of DNA on graphene sheets, which are prepared by chemical vapor deposition. The sheet resistance increases and the mobility decreases with the addition of either complementary or one-base mismatched DNA to the graphene device. The hole carrier concentration of the graphene devices increases significantly with the addition of complementary DNA but it is less affected by the one-base mismatched DNA. It is concluded that the increase in hole carrier density, indicating p-doping to graphene, is better correlated with the DNA hybridization compared to the commonly used parameters such as conductivity change. The different electrical observations of p-doping from Hall effect measurements and n-doping from electrolyte-gated transistors can be explained by the characteristic morphology of partially hybridized DNA on graphene and the mismatch between DNA chain length and Debye length in electrolytes. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Huang J.-H.,Academia Sinica, Taiwan | Chu C.-W.,Academia Sinica, Taiwan | Chu C.-W.,National Chiao Tung University
Electrochimica Acta | Year: 2011

In this study, we have prepared a series of poly(3,4- ethylenedioxythiophene) (PEDOT) with various molecular weight by using an inhibitor, imidazole (Im). The X-ray diffraction (XRD) results show that the PEDOT with larger molecular weight enhances the polymer chain ordering and stacking which leads to higher conductivity. With increasing the amount of Im, the conductivity of PEDOT can be increased from 4.01 S cm-1 (Im = 0.0 M) to 153.6 S cm-1 (Im = 1.8 M). Comparisons of the cyclic voltammetry (CV), it enables correlation between the conductivity and specific capacitance, which is important for understanding the electrochemical capacitive behavior of conjugated polymer for pseudo-capacitor application. The PEDOT prepared with 1.8 M Im shows a specific capacitance of 124 F g-1, which is 2.2 times larger than the one without Im (57 F g-1). © 2011 Elsevier Ltd. All rights reserved.

Wu J.-Y.,National Chi Nan University | Liu Y.-C.,Academia Sinica, Taiwan | Chao T.-C.,National Chi Nan University
Inorganic Chemistry | Year: 2014

An infinite Ag(I) coordination 41-helical chain, [Ag(Hdpma)](NO3)2·H2O (1), was synthesized by the self-assembly of AgNO3 and di(3-pyridylmethyl) amine (dpma). Helix 1 is 5-fold interweaved and has a topological diamondoid-like net that is extended by ligand-unsupported helix-to-helix argentophilic interactions. Two identical diamondoid-like nets with opposite chiralities interpenetrate to form the whole 3D framework as a meso compound. Typical anion-exchange reactions cause a remarkable single-crystal-to-single- crystal (SCSC) structural transformation from the 1D helix 1 to the 0D molecular loop [Ag(dpma-NO)(NO2)]2 (2) (induced by the nitrite anion, NO2 -) and a 1D molecular ladder [Ag(dpma)(H 2O)](NO3) (induced by the fluoride anion, F-). Molecular loop 2 is an N-nitroso compound. This work is the first to present observations of nitrite-dominated in situ N-nitrosation of an amine ligand which accompanies SCSC structural transformation via an anion-exchange reaction. © 2014 American Chemical Society.

Hsu C.-L.,National Chiao Tung University | Lin C.-T.,Academia Sinica, Taiwan | Huang J.-H.,Academia Sinica, Taiwan | Chu C.-W.,Academia Sinica, Taiwan | And 2 more authors.
ACS Nano | Year: 2012

Figure Persented: Large-area graphene grown by chemical vapor deposition (CVD) is a promising candidate for transparent conducting electrode applications in flexible optoelectronic devices such as light-emitting diodes or organic solar cells. However, the power conversion efficiency (PCE) of the polymer photovoltaic devices using a pristine CVD graphene anode is still not appealing due to its much lower conductivity than that of conventional indium tin oxide. We report a layer-by-layer molecular doping process on graphene for forming sandwiched graphene/tetracyanoquinodimethane (TCNQ)/graphene stacked films for polymer solar cell anodes, where the TCNQ molecules (as p-dopants) were securely embedded between two graphene layers. Poly(3-hexylthiophene)/phenyl-C61-butyric acid methyl ester (P3HT/PCBM) bulk heterojunction polymer solar cells based on these multilayered graphene/TCNQ anodes are fabricated and characterized. The P3HT/PCBM device with an anode structure composed of two TCNQ layers sandwiched by three CVD graphene layers shows optimum PCE (∼2.58%), which makes the proposed anode film quite attractive for next-generation flexible devices demanding high conductivity and transparency. © 2012 American Chemical Society.

Pan X.,Academia Sinica, Taiwan | Wong G.T.F.,Academia Sinica, Taiwan | Wong G.T.F.,National Central University
Deep-Sea Research Part II: Topical Studies in Oceanography | Year: 2015

By using field in situ observations, data from the NOMAD database, and remotely sensed data from MODIS-Aqua, an improved algorithm has been developed for estimating the surface concentrations of dissolved organic carbon (DOC) in the Northern South China Sea Shelf-sea (NoSoCS) and adjacent waters through a combination of the remotely sensed sea-surface temperature (SST) and the absorption coefficient of colored dissolved organic matter (CDOM). Unlike previously reported algorithms, which were based on only one of these two parameters, this algorithm does not require seasonal tuning and is applicable to both coastal and pelagic waters. The uncertainty in the remotely sensed concentrations of DOC is about ±4-10. μM. The climatological distributions of the satellite-derived surface DOC in the NoSoCS and adjacent waters between 2002 and 2012 followed a general trend of increasing concentrations landward, from about 58 and 73. μM in the open South China Sea (SCS) in January and July, respectively, to >100. μM at the mouth of the Pearl River. The intra-annual changes in the monthly average concentration of DOC in the NoSoCS follow a distinct seasonal cycle, with the lowest and highest concentrations, 56. μM and 75. μM, in February and July, respectively. The seasonal cycle of DOC was in phase with that of SST but out of phase with that of primary production, suggesting that biological activity was not likely its primary control. Instead, it was consistent with the entrainment of the cold and less DOC-rich sub-surface water in the surface water by enhanced vertical mixing during winter, and the high inflow of organic-rich river water to the NoSoCS in summer. Sub-regionally, lower concentrations of DOC were found in the known upwelling zones in the NoSoCS, where vertical mixing was enhanced. In the inner shelf, the effect of riverine input was indicated by higher concentrations of DOC in the plume of water at the mouth of the Pearl River. This work represents the first attempt to characterize the regional distribution of surface concentration of DOC in the NoSoCS and adjacent waters. © 2015 Elsevier Ltd.

Chen C.-H.,National Cheng Kung University | Chiang C.-W.,National Central University | Chiang C.-W.,Academia Sinica, Taiwan | Chiang C.-W.,National Center for Theoretical science | And 2 more authors.
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2015

We propose a dark matter explanation to simultaneously account for the excess of antiproton-to-proton and positron power spectra observed in the AMS-02 experiment while having the right dark matter relic abundance and satisfying the current direct search bounds. We extend the Higgs triplet model with a hidden gauge symmetry of SU(2)X that is broken to Z3 by a quadruplet scalar field, rendering the associated gauge bosons stable weakly-interacting massive particle dark matter candidates. By coupling the complex Higgs triplet and the SU(2)X quadruplet, the dark matter candidates can annihilate into triplet Higgs bosons each of which in turn decays into lepton or gauge boson final states. Such a mechanism gives rise to correct excess of positrons and antiprotons with an appropriate choice of the triplet vacuum expectation value. Besides, the model provides a link between neutrino mass and dark matter phenomenology. © 2015 The Authors.

News Article | November 21, 2016

An international team led by researchers from Tohoku University has found an extremely faint dwarf satellite galaxy of the Milky Way. The team's discovery is part of the ongoing Subaru Strategic Survey using Hyper Suprime-Cam. The satellite, named Virgo I, lies in the direction of the constellation Virgo. At the absolute magnitude of -0.8 in the optical waveband, it may well be the faintest satellite galaxy yet found. Its discovery suggests the presence of a large number of yet-undetected dwarf satellites in the halo of the Milky Way and provides important insights into galaxy formation through hierarchical assembly of dark matter. Currently, some 50 satellite galaxies to the Milky Way have been identified. About 40 of them are faint and diffuse and belong to the category of so-called "dwarf spheroidal galaxies". Many recently discovered dwarf galaxies, especially those seen in systematic photometric surveys such as the Sloan Digital Sky Survey (SDSS) and the Dark Energy Survey (DES) are very faint with absolute luminosity in the optical waveband below -8 magnitude. These are so-called "ultra-faint dwarf galaxies". However, previous searches made use of telescopes with a diameter of 2.5 to 4 meters, so only satellites relatively close to the Sun or those with higher magnitudes were identified. Those that are more distant or faint ones in the halo of the Milky Way are yet to be detected. The combination of the large aperture of 8.2-meter Subaru Telescope and the large field-of-view Hyper Suprime-Cam (HSC) instrument is very powerful in this study. It enables an efficient search for very faint dwarf satellites over large areas of the sky. The first step in searching out a new dwarf galaxy is to identify an over density of stars in the sky, using photometric data. Next is to assess that the over dense appearance is not due to line-of-sight or accidental juxtapositions of unrelated dense fields, but is really a stellar system. The standard method for doing this is to look for a characteristic distribution of stars in the color-magnitude diagram (comparable to the Hertzsprung-Russell diagram). Stars in a general field shows no particular patterns in this diagram. Daisuke Homma, a graduate student at Tohoku University, found Virgo I under the guidance of his advisor, Masashi Chiba, and their international collaborators. "We have carefully examined the early data of the Subaru Strategic Survey with HSC and found an apparent over density of stars in Virgo with very high statistical significance, showing a characteristic pattern of an ancient stellar system in the color-magnitude diagram," he said. "Surprisingly, this is one of the faintest satellites, with absolute magnitude of -0.8 in the optical waveband. This is indeed a galaxy, because it is spatially extended with a radius of 124 light years - systematically larger than a globular cluster with comparable luminosity." The faintest dwarf satellites identified so far was Segue I, discovered by SDSS (-1.5 mag) and Cetus II in DES (0.0 mag). Cetus II is yet to be confirmed, as it is too compact as a galaxy. Virgo I may ultimately turn out to be the faintest one ever discovered. It lies at a distance of 280,000 light years from the Sun, and such a remote galaxy with faint brightness has not been identified in previous surveys. It is beyond the reach of SDSS, which has previously surveyed the same area in the direction of the constellation Virgo. According to Chiba, the leader of this search project, the discovery has profound implications. "This discovery implies hundreds of faint dwarf satellites waiting to be discovered in the halo of the Milky Way," he said. "How many satellites are indeed there and what properties they have, will give us an important clue of understanding how the Milky Way formed and how dark matter contributed to it." Formation of galaxies like the Milky Way is thought to proceed through the hierarchical assembly of dark matter, forming dark halos, and through the subsequent infall of gas and star formation affected by gravity. Standard models of galaxy formation in the context of the so-called cold dark matter (CDM) theory predict the presence of hundreds of small dark halos orbiting in a Milky Way-sized dark halo and a comparable number of luminous satellite companions. However, only tens of satellites have ever been identified. This falls well short of a theoretical predicted number, which is part of the so-called "missing satellite problem". Astronomers may need to consider other types of dark matter than CDM or to invoke baryonic physics suppressing galaxy formation to explain the shortfall in the number of satellites. Another possibility is that they have seen only a fraction of all the satellites associated with the Milky Way due to various observational biases. The issue remains unsolved. One of the motivations for the Subaru Strategic Survey using HSC is to do increase observations in the search for Milky Way satellites. The early data from this survey is what led to the discovery of Virgo I. This program will continue to explore much wider areas of the sky and is expected to find more satellites like Virgo I. These tiny companions to be discovered in the near future may tell us much more about history of the Milky Way's formation. Daisuke Homma (Tohoku University, Japan), Masashi Chiba (Tohoku University, Japan), Sakurako Okamoto (Shanghai Astronomical Observatory, China), Yutaka Komiyama (National Astronomical Observatory of Japan (NAOJ), Japan), Masayuki Tanaka (NAOJ, Japan), Mikito Tanaka (Tohoku University, Japan), Miho N. Ishigaki (Kavli Institute for the Physics and Mathematics of the Universe (Kavli IPMU, WPI), University of Tokyo, Japan), Masayuki Akiyama (Tohoku University, Japan), Nobuo Arimoto (Subaru Telescope, NAOJ, USA), Jose A, Garmilla (Princeton University, USA), Robert H. Lupton (Princeton University, USA), Michael A. Strauss (Princeton University, USA), Hisanori Furusawa (NAOJ, Japan), Satoshi Miyazaki (NAOJ, Japan), Hitoshi Murayama (Kavli IPMU, WPI, University of Tokyo, Japan), Atsushi J. Nishizawa (Nagoya University, Japan), Masahiro Takada (Kavli IPMU, WPI, University of Tokyo, Japan), Tomonori Usuda (NAOJ, Japan), Shiang-Yu Wang (Institute of Astronomy and Astrophysics, Academia Sinica, Taiwan) Leo II: An Old Dwarf Galaxy with Juvenescent Heart http://subarutelescope.

Peng S.,CAS Institute of Automation | Hwang W.-L.,Academia Sinica, Taiwan | Hwang W.-L.,Kainan University
IEEE Transactions on Signal Processing | Year: 2010

The operator-based signal separation approach uses an adaptive operator to separate a signal into additive subcomponents. The approach can be formulated as an optimization problem whose optimal solution can be derived analytically. However, the following issues must still be resolved: estimating the robustness of the operator's parameters and the Lagrangian multipliers, and determining how much of the information in the null space of the operator should be retained in the residual signal. To address these problems, we propose a novel optimization formula for operator-based signal separation and show that the parameters of the problem can be estimated adaptively. We demonstrate the effectiveness of the proposed method by processing several signals, including real-life signals. © 2006 IEEE.

Griest K.,University of California at San Diego | Cieplak A.M.,University of California at San Diego | Cieplak A.M.,Brookhaven National Laboratory | Lehner M.J.,Academia Sinica, Taiwan | Lehner M.J.,University of Pennsylvania
Physical Review Letters | Year: 2013

We present new limits on the allowed masses of a dark matter (DM) halo consisting of primordial black holes (PBH) (or any other massive compact halo object). We analyze two years of data from the Kepler satellite, searching for short-duration bumps caused by gravitational microlensing. After removing background events consisting of variable stars, flare events, and comets or asteroids moving through the Kepler field, we find no microlensing candidates. We measure the efficiency of our selection criteria by adding millions of simulated microlensing lensing events into the Kepler light curves. We find that PBH DM with masses in the range 2×10-9M to 10-7M cannot make up the entirety of the DM in the Milky Way. At the low-mass end, this decreases the allowed mass range by more than an order of magnititude. © 2013 American Physical Society.

Hu X.,CAS Institute of Automation | Peng S.,CAS Institute of Automation | Hwang W.-L.,Academia Sinica, Taiwan | Hwang W.-L.,Kainan University
IEEE Transactions on Signal Processing | Year: 2012

Empirical mode decomposition (EMD) is an adaptive and data-driven approach for analyzing multicomponent nonlinear and nonstationary signals. The stop criterion, envelope technique, and mode-mixing problem are the most important topics that need to be addressed in order to improve the EMD algorithm. In this paper, we study the envelope technique and the mode-mixing problem caused by separating multicomponent AM-FM signals with the EMD algorithm. We present a new necessary condition on the envelope that questions the current assumption that the envelope passes through the extreme points of an intrinsic mode function (IMF). Then, we present a solution to the mode-mixing problem that occurs when multicomponent AM-FM signals are separated. We experiment on several signals, including simulated signals and real-life signals, to demonstrate the efficacy of the proposed method in resolving the mode-mixing problem. © 2011 IEEE.

Chang W.-C.,Academia Sinica, Taiwan | Peng J.-C.,Academia Sinica, Taiwan | Peng J.-C.,University of Illinois at Urbana - Champaign
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2011

We have generalized the approach of Brodsky et al. for the intrinsic charm quark distribution in the nucleons to the light-quark sector involving intrinsic u-,d-,s and s- sea quarks. We compare the calculations with the existing d--u-, s+s-, and u-+d--s-s- data. The good agreement between the theory and the data allows the extraction of the probabilities for the |uuduu-〉, |uuddd-〉, and |uudss-〉 five-quark Fock states in the proton. We also calculate the x-dependence of the intrinsic charm after taking into consideration the QCD evolution of the intrinsic quark distribution. © 2011 Elsevier B.V.

Chao K.-C.,Academia Sinica, Taiwan | Yang H.-T.,Taipei Medical University Hospital | Chen M.-W.,National Taiwan University
Journal of Cellular and Molecular Medicine | Year: 2012

The purpose of this study was to investigate how human umbilical cord mesenchymal stem cells (HUMSCs) affect breast cancer tumourigenesis. To observe the influence of HUMSCs on tumourigenesis in vitro, we performed a co-culture of MDA MB-231 breast cancer cells with HUMSCs, and a result of HUMSCs on tumourigenesis in vivo was achieved by injection of HUMSCs into nonobese diabetic/severe combined immunodeficient mice following tumour establishment with MDA-MB231. During the co-culture, apoptosis of MDA-MB231 was noted, which was driven either by binding with HUMSC through direct cell-cell contact or by formation of a novel cell-in-cell phenomenon after internalization of HUMSC. Also, treatment with HUMSC injection was efficacious in both in situ and metastatic breast cancers in the animal models. Since HUMSCs were proved to efficaciously suppress breast cancer tumourigenesis both in vitro and in vivo, it is our expectation that treatment with HUMSCs can be a viable therapy for breast cancer in the near future. In addition, we share a new point of view on the role of HUMSCs in foetal development during pregnancy. © 2012 The Authors. Journal of Cellular and Molecular Medicine © 2012 Foundation for Cellular and Molecular Medicine/Blackwell Publishing Ltd.

Lee K.-W.,Academia Sinica, Taiwan | Chen P.W.,National Chiayi University | Yu S.-M.,Academia Sinica, Taiwan | Yu S.-M.,National Chung Hsing University
Plant, Cell and Environment | Year: 2014

Rice is characterized by a broad range of metabolic and morphological adaptations to flooding, such as germination and mobilization of stored nutrients under submergence until seedlings reach the water surface to carry out photosynthesis, and sustainable growth of mature plants for long durations under partial submergence. The underlying mechanisms of the molecular basis of adaptation to anaerobic germination and seedling growth in rice are being uncovered. Induction of an ensemble of hydrolases to mobilize endosperm nutrient reserves is one of the key factors for successful germination and coleoptile elongation in rice under submergence. To compensate for reduced efficiency of Tricarboxylic Acid cycle and oxidative respiration in mitochondria under O2 deficient conditions, α-amylases play a central role in the hydrolysis of starch to provide sugar substrates for glycolysis and alcohol fermentation for generating ATP. We review the progress on the molecular mechanism regulating α-amylase expression that involves the integration of signals generated by the hormone gibberellin (GA), sugar starvation and O2 deprivation that results in germination and sustainable seedling growth in rice under anaerobic conditions. Comparisons are also made between dicots and monocots for the molecular mechanism of induction of genes involved in alcohol fermentation and sugar/O2 deficiency sensing system. © 2014 John Wiley & Sons Ltd.

Liu K.-F.,University of Kentucky | Chang W.-C.,Academia Sinica, Taiwan | Cheng H.-Y.,Academia Sinica, Taiwan | Peng J.-C.,University of Illinois at Urbana - Champaign
Physical Review Letters | Year: 2012

According to the path-integral formalism of the hadronic tensor, the nucleon sea contains two distinct components called the connected sea (CS) and the disconnected sea (DS). We discuss how the CS and DS are accessed in the lattice QCD calculation of the moments of the parton distributions. We show that the CS and DS components of ū(x)+d̄(x) can be extracted by using recent data on the strangeness parton distribution, the CT10 global fit, and the lattice result of the ratio of the strange to u(d) moments in the disconnected insertion. The extracted CS and DS for ū(x)+d̄(x) have a distinct Bjorken x dependence in qualitative agreement with expectation. The analysis also shows that the momentum fraction of ū(x)+d̄(x) is about equally divided between the CS and DS at Q2=2.5 GeV2. Implications for the future global analysis of parton distributions are presented. © 2012 American Physical Society.

Pun I.-F.,Woods Hole Oceanographic Institution | Lin I.-I.,National Taiwan University | Lin I.-I.,Academia Sinica, Taiwan | Lo M.-H.,National Taiwan University
Geophysical Research Letters | Year: 2013

The Main Development Region (MDR) for tropical cyclones (TCs) in the western North Pacific Ocean is the most active TC region in the world. Based on synergetic analyses of satellite altimetry and gravity observations, we found that the subsurface ocean conditions in the western North Pacific MDR has become even more favorable for the intensification of typhoons and supertyphoons. Compared to the early 1990s, a 10% increase in both the depth of the 26°C isotherm (D26) and Tropical Cyclone Heat Potential (TCHP) has occurred in the MDR. In addition, the areas of high TCHP (≥ 110 kJ cm-2) and large D26 (≥ 110 m) have 13% and 17% increases, respectively. Because these high TCHP and large D26 regions are often associated with intensification of the most intense TCs (i.e. supertyphoons), this recent warming requires close attention and monitoring. Key Points Ocean conditions in the MDR are becoming even more favorable for typhoons Averaged D26 and TCHP over MDR have increased by 10% as compared to the 90's There is a 13% increase in high TCHP (>= 110kj/cm2) area coverage ©2013. American Geophysical Union. All Rights Reserved.

Tseng C.M.,National Taiwan University | Lamborg C.H.,Woods Hole Oceanographic Institution | Hsu S.C.,Academia Sinica, Taiwan
Geophysical Research Letters | Year: 2013

A unique seasonal pattern in dissolved elemental mercury (DEM) was observed in the tropical monsoon-dominated South China Sea (SCS). The DEM concentration varied seasonally, with a high in summer of 160 ± 40 fM (net evasion 580 ± 120 pmol m-2 d-1, n = 4) and a low in winter of 60 ± 30 fM (net invasion -180 ± 110, n = 4) and showed a positive correlation with sea surface temperature (SST). The elevated DEM concentration in summer appears mainly abiologically driven. In winter, the SCS acts as a sink of atmosphere Hg0 as a result of low SST and high wind of the year, enhanced vertical mixing, and elevated atmospheric gaseous elemental mercury. Annually, the SCS serves as a source of Hg0 to the atmosphere of 300 ± 50 pmol m-2 d-1 (385 ± 64kmol Hg yr -1, ~2.6% of global emission in ~1% of global ocean area), suggesting high regional Hg pollution impacts from the surrounding Mainland (mostly China). © 2013. American Geophysical Union. All Rights Reserved.

Pan K.-C.,University of Basel | Ricker P.M.,University of Illinois at Urbana - Champaign | Taam R.E.,Northwestern University | Taam R.E.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2014

The nature of the progenitor systems of type Ia supernovae (SNe Ia) is still unclear. One way to distinguish between the single-degenerate scenario and double-degenerate scenario for their progenitors is to search for the surviving companions (SCs). Using a technique that couples the results from multi-dimensional hydrodynamics simulations with calculations of the structure and evolution of main-sequence- (MS-) and helium-rich SCs, the color and magnitude of MS- and helium-rich SCs are predicted as functions of time. The SC candidates in Galactic type Ia supernova remnants (Ia SNR) and nearby extragalactic Ia SNRs are discussed. We find that the maximum detectable distance of MS SCs (helium-rich SCs) is 0.6-4 Mpc (0.4-16 Mpc), if the apparent magnitude limit is 27 in the absence of extinction, suggesting that the Large and Small Magellanic Clouds and the Andromeda Galaxy are excellent environments in which to search for SCs. However, only five Ia SNRs have been searched for SCs, showing little support for the standard channels in the singe-degenerate scenario. To better understand the progenitors of SNe Ia, we encourage the search for SCs in other nearby Ia SNRs. © 2014. The American Astronomical Society. All rights reserved..

Yu S.,Harvard University | Kim H.Y.,Seoul National University | Chang Y.-J.,Academia Sinica, Taiwan | Dekruyff R.H.,Harvard University | Umetsu D.T.,Genentech
Journal of Allergy and Clinical Immunology | Year: 2014

Asthma is a complex and heterogeneous disease with several phenotypes, including an allergic asthma phenotype characterized by TH2 cytokine production and associated with allergen sensitization and adaptive immunity. Asthma also includes nonallergic asthma phenotypes, such as asthma associated with exposure to air pollution, infection, or obesity, that require innate rather than adaptive immunity. These innate pathways that lead to asthma involve macrophages, neutrophils, natural killer T cells, and innate lymphoid cells, newly described cell types that produce a variety of cytokines, including IL-5 and IL-13. We review the recent data regarding innate lymphoid cells and their role in asthma. © 2013 American Academy of Allergy, Asthma & Immunology.

Pan K.-C.,University of Illinois at Urbana - Champaign | Ricker P.M.,University of Illinois at Urbana - Champaign | Taam R.E.,Northwestern University | Taam R.E.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2010

The impact of Type Ia supernova (SN) ejecta on a helium-star companion is investigated via high-resolution, two-dimensional hydrodynamic simulations. For a range of helium-star models and initial binary separations, it is found that the mass unbound in the interaction, δM ub, is related to the initial binary separation, a, by a power law of the form δ M ub ∝ am . This power-law index is found to vary from -3.1 to -4.0, depending on the mass of the helium star. The small range of this index brackets values found previously for hydrogen-rich companions, suggesting that the dependence of the unbound mass on orbital separation is not strongly sensitive to the nature of the binary companion. The kick velocity is also related to the initial binary separation by a power law with an index in a range from -2.7 to -3.3, but the power-law index differs from those found in previous studies for hydrogen-rich companions. The space motion of the companion after the SN is dominated by its orbital velocity in the pre-SN binary system. The level of Ni/Fe contamination of the companion resulting from the passage of the SN ejecta is difficult to estimate, but an upper limit on the mass of bound nickel is found to be ∼ 5 × 10-4 M ⊙. © 2010. The American Astronomical Society. All rights reserved.

Huang K.-F.,Woods Hole Oceanographic Institution | Huang K.-F.,Academia Sinica, Taiwan | Oppo D.W.,Woods Hole Oceanographic Institution | Curry W.B.,Woods Hole Oceanographic Institution | Curry W.B.,Bermuda Institute of Ocean Sciences
Earth and Planetary Science Letters | Year: 2014

Antarctic Intermediate Water (AAIW) is a key player in the global ocean circulation, contributing to the upper limb of the Atlantic Meridional Overturning Circulation (AMOC), and influencing interhemispheric heat exchange and the distribution of salinity, nutrients and carbon. However, the deglacial history of AAIW flow into the North Atlantic is controversial. Here we present a multicore-top neodymium isotope calibration, which confirms the ability of unclean foraminifera to faithfully record bottom water neodymium isotopic composition (εNd) values in their authigenic coatings. We then present the first foraminifera-based reconstruction of εNd from three sediment cores retrieved from within modern AAIW, in the western tropical North Atlantic. Our records reveal similar glacial and interglacial contributions of AAIW, and a pronounced decrease in the AAIW fraction during North Atlantic deglacial cold episodes, Heinrich Stadial 1 (HS1) and Younger Dryas (YD). Our results suggest two separate phases of reduced fraction of AAIW in the tropical Atlantic during HS1, with a greater reduction during early HS1. If a reduction in AAIW fraction also reflects reduced AMOC strength, this finding may explain why, in many regions, there are two phases of hydrologic change within HS1, and why atmospheric CO2 rose more rapidly during early than late HS1. Our result suggesting less flow of AAIW into the Atlantic during North Atlantic cold events contrasts with evidence from the Pacific, where intermediate-depth εNd records may indicate increased flow of AAIW into the Pacific during the these same events. Antiphased εNd behavior between intermediate depths of the North Atlantic and Pacific implies that the flow of AAIW into Atlantic and Pacific seesawed during the last deglaciation. © 2014 Elsevier B.V.

Chang W.-C.,Academia Sinica, Taiwan | Peng J.-C.,University of Illinois at Urbana - Champaign
Progress in Particle and Nuclear Physics | Year: 2014

We review the current status and future prospects on the subject of flavor structure of the nucleon sea. The flavor structure of the nucleon sea provides unique information on the non-perturbative aspects of strong interactions allowing stringent tests of various models on the partonic structures of the nucleons as well as lattice QCD calculations. The scope of this review covers the unpolarized, polarized, and the transverse-momentum dependent sea-quark distributions of the nucleons. While the main focus of this review is on the physics motivation and recent progress on the subject of the nucleon sea, we also discuss future prospects of addressing some outstanding issues on the flavor structure of the nucleon sea. © 2014 Elsevier Ltd. All rights reserved.

Engling G.,Academia Sinica, Taiwan | Gelencser A.,University of Pannonia
Elements | Year: 2010

Atmospheric brown clouds are atmospheric accumulations of carbonaceous aerosol particles spanning vast areas of the globe. They have recently gained much attention, from the scientific community and from the general population, as they severely impact several aspects of everyday life. Aside from affecting regional air quality and negatively impacting human health, these clouds affect biogeochemical cycles and profoundly influence the radiation budget of the Earth, resulting in severe climatic and economic consequences. Carbonaceous aerosol particles are generated primarily by combustion processes, including biomass and fossil fuel burning. Natural emissions and transformations of volatile organic species in the atmosphere also contribute to the development of atmospheric brown clouds.

Chiu C.-Y.,National Chiayi University | Wang H.-M.,Academia Sinica, Taiwan
IEEE Transactions on Circuits and Systems for Video Technology | Year: 2010

This paper presents a novel time-series linear search (TLS) method for detecting video copies. The method utilizes a sliding window to locate window sequences that are near-duplicates of a given query sequence. We address two issues of the conventional TLS method in order to strengthen its video copy detection capability. First, to accelerate the TLS process, we use a sequence-level signature as a compact representation of a video sequence based on the min-hash theory, and develop an efficient heap manipulation technique for fast generation of each window sequence's signature. Second, to improve the robustness of the TLS method, we use two techniques, namely, window length estimation and threshold transform, to resolve the containment relation problem caused by various types of video transformation and editing, such as frame cropping and speed change. The results of experiments on the MUSCLE-VCD-2007 dataset demonstrate that the proposed method is efficient and robust against different types of video transformation and editing. © 2006 IEEE.

Pan K.-C.,University of Illinois at Urbana - Champaign | Ricker P.M.,University of Illinois at Urbana - Champaign | Taam R.E.,Northwestern University | Taam R.E.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2012

The nature of the progenitor systems of Type Ia supernovae is still uncertain. One way to distinguish between the single-degenerate scenario and double-degenerate scenario is to search for the post-impact remnant star. To examine the characteristics of the post-impact remnant star, we have carried out three-dimensional hydrodynamic simulations of supernova impacts on main-sequence-like stars. We explore the evolution of the post-impact remnants using the stellar evolution code MESA. We find that the luminosity and radius of the remnant star dramatically increase just after the impact. After the explosion, post-impact companions continue to expand on a progenitor-dependent timescale of 102.5-103years before contracting. It is found that the time evolution of the remnant star is dependent not only on the amount of energy absorbed but also on the depth of the energy deposition. We examine the viability of the candidate star Tycho G as the possible remnant companion in Tycho's supernova by comparing it to the evolved post-impact remnant stars in our simulations. The closest model in our simulations has a similar effective temperature, but the luminosity and radius are twice as large. By examining the angular momentum distribution in our simulations, we find that the surface rotational speed could drop to 10 km s-1 if the specific angular momentum is conserved during the post-impact evolution, implying that Tycho G cannot be completely ruled out because of its low surface rotation speed. © 2012. The American Astronomical Society. All rights reserved.

Chang W.-C.,Academia Sinica, Taiwan | Peng J.-C.,Academia Sinica, Taiwan | Peng J.-C.,University of Illinois at Urbana - Champaign
Physical Review Letters | Year: 2011

The existence of the five-quark Fock states for the intrinsic charm quark in the nucleons was suggested some time ago, but conclusive evidence is still lacking. We generalize the previous theoretical approach to the light-quark sector and study possible experimental signatures for such five-quark states. In particular, we compare the d̄-ū and ū+d̄-s-s̄ data with the calculations based on the five-quark Fock states. The qualitative agreement between the data and the calculations is interpreted as evidence for the existence of the intrinsic light-quark sea in the nucleons. The probabilities for the and Fock states are also extracted. © 2011 American Physical Society.

Pan K.-C.,University of Illinois at Urbana - Champaign | Ricker P.M.,University of Illinois at Urbana - Champaign | Taam R.E.,Northwestern University | Taam R.E.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2012

Type Ia supernovae are thought to be caused by thermonuclear explosions of a carbon-oxygen white dwarf in close binary systems. In the single-degenerate scenario (SDS), the companion star is non-degenerate and can be significantly affected by the explosion. We explore this interaction by means of multi-dimensional adaptive mesh refinement simulations using the FLASH code. We consider several different companion types, including main-sequence-like stars (MS), red giants (RG), and helium stars (He). In addition, we include the symmetry-breaking effects of orbital motion, rotation of the non-degenerate star, and Roche-lobe overflow. A detailed study of a sub-grid model for Type Ia supernovae is also presented. We find that the dependence of the unbound stellar mass and kick velocity on the initial binary separation can be fitted by power-law relations. By using the tracer particles in FLASH, the process leading to the unbinding of matter is dominated by ablation, which has usually been neglected in past analytical studies. The level of Ni/Fe contamination of the companion that results from the passage of the supernova ejecta is found to be 10-5 M ⊙ for the MS star, 10-4 M ⊙ for the He star, and 10-8 M ⊙ for the RG. The spinning MS companion star loses about half of its initial angular momentum during the impact, causing the rotational velocity to drop to a quarter of the original rotational velocity, suggesting that the Tycho G star is a promising progenitor candidate in the SDS. © 2012. The American Astronomical Society. All rights reserved..

Pan K.-C.,University of Illinois at Urbana - Champaign | Ricker P.M.,University of Illinois at Urbana - Champaign | Taam R.E.,Northwestern University | Taam R.E.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2013

The progenitor systems of Type Ia supernovae (SNe Ia) are still under debate. Based on recent hydrodynamics simulations, non-degenerate companions in the single-degenerate scenario (SDS) should survive the supernova (SN) impact. One way to distinguish between the SDS and the double-degenerate scenario is to search for the post-impact remnant stars (PIRSs) in SN Ia remnants. Using a technique that combines multi-dimensional hydrodynamics simulations with one-dimensional stellar evolution simulations, we have examined the post-impact evolution of helium-rich binary companions in the SDS. It is found that these helium-rich PIRSs (He PIRSs) dramatically expand and evolve to a luminous phase (L ∼ 104 L ⊙) about 10 yr after an SN explosion. Subsequently, they contract and evolve to become hot blue-subdwarf-like (sdO-like) stars by releasing gravitational energy, persisting as sdO-like stars for several million years before evolving to the helium red-giant phase. We therefore predict that a luminous OB-like star should be detectable within ∼30 yr after the SN explosion. Thereafter, it will shrink and become an sdO-like star in the central regions of SN Ia remnants within star-forming regions for SN Ia progenitors evolved via the helium-star channel in the SDS. These He PIRSs are predicted to be rapidly rotating (v rot ≳ 50 km s-1) and to have high spatial velocities (v linear ≳ 500 km s-1). Furthermore, if SN remnants have diffused away and are not recognizable at a later stage, He PIRSs could be an additional source of single sdO stars and/or hypervelocity stars. © 2013. The American Astronomical Society. All rights reserved.

Cheng T.-L.,Kaohsiung Medical University | Chuang K.-H.,Kaohsiung Medical University | Chen B.-M.,Academia Sinica, Taiwan | Roffler S.R.,Academia Sinica, Taiwan
Bioconjugate Chemistry | Year: 2012

Attachment of poly(ethylene glycol) (PEG) to proteins, peptides, liposomes, drugs, and nanoparticles can improve pharmaceutical pharmacokinetic properties and enhance in vivo biological efficacy. Since the first PEGylated product was approved by the Food and Drug Administration in 1990, increasing numbers of PEGylated compounds have entered clinical use. Successful clinical development of PEGylated pharmaceuticals requires accurate methods for the qualitative and quantitative analysis of intact PEG conjugates in biological fluids. In this article, we review assay methods that can be utilized for the detection and measurement of PEGylated pharmaceuticals in complex biological samples for determination of biodistribution and pharmacokinetic properties. In particular, we describe relevant colorimetric, chromatographic, radiolabeled, biological, and enzyme-linked immunosorbent assays for the pharmacokinetic study of PEGylated molecules. © 2012 American Chemical Society.

Chen Y.C.,National Taiwan University | Chen Y.C.,Taipei Medical University Hospital | Dong G.H.,Shenyang University | Lin K.C.,National Taipei University of Nursing and Health Sciences | And 2 more authors.
Obesity Reviews | Year: 2013

The aims of our meta-analysis were (i) to quantify the predictability of childhood overweight and obesity on the risk of incident asthma; and (ii) to evaluate the gender difference on this relationship. The selection criteria included prospective cohort paediatric studies which use age- and sex-specific body mass index (BMI) as a measure of childhood overweight and the primary outcome of incident asthma. A total of 1,027 studies were initially identified through online database searches, and finally 6 studies met the inclusion criteria. The combined result of reported relative risk from the 6 included studies revealed that overweight children conferred increased risks of incident asthma as compared with non-overweight children (relative risk, 1.19; 95% confidence interval [CI], 1.03-1.37). The relationship was further elevated for obesity vs. non-obesity (relative risk, 2.02; 95% CI, 1.16-3.50). A dose-responsiveness of elevated BMI on asthma incidence was observed (P for trend, 0.004). Obese boys had a significantly larger effect than obese girls (relative risk, boys: 2.47; 95% CI, 1.57-3.87; girls: 1.25; 95% CI, 0.51-3.03), with significant dose-dependent effect. Proposed mechanisms of gender difference could be through pulmonary mechanics, sleep disordered breathing and leptin. Further research might be needed to better understand the exact mechanism of gender difference on the obesity-asthma relationship. © 2012 The Authors. obesity reviews © 2012 International Association for the Study of Obesity.

Ho J.,Academia Sinica, Taiwan | Hwang W.-L.,Kainan University
IEEE Transactions on Image Processing | Year: 2013

From the perspective of the Bayesian approach, the denoising problem is essentially a prior probability modeling and estimation task. In this paper, we propose an approach that exploits a hidden Bayesian network, constructed from wavelet coefficients, to model the prior probability of the original image. Then, we use the belief propagation (BP) algorithm, which estimates a coefficient based on all the coefficients of an image, as the maximum-a-posterior (MAP) estimator to derive the denoised wavelet coefficients. We show that if the network is a spanning tree, the standard BP algorithm can perform MAP estimation efficiently. Our experiment results demonstrate that, in terms of the peak-signal-to-noise-ratio and perceptual quality, the proposed approach outperforms state-of-the-art algorithms on several images, particularly in the textured regions, with various amounts of white Gaussian noise. © 2012 IEEE.

Wong M.-T.,Academia Sinica, Taiwan | Chen S.S.-L.,Academia Sinica, Taiwan | Chen S.S.-L.,Kaohsiung Medical University
Cellular and Molecular Immunology | Year: 2016

Infection with hepatitis C virus (HCV), a major viral cause of chronic liver disease, frequently progresses to steatosis and cirrhosis, which can lead to hepatocellular carcinoma. HCV infection strongly induces host responses, such as the activation of the unfolded protein response, autophagy and the innate immune response. Upon HCV infection, the host induces the interferon (IFN)-mediated frontline defense to limit virus replication. Conversely, HCV employs diverse strategies to escape host innate immune surveillance. Type I IFN elicits its antiviral actions by inducing a wide array of IFN-stimulated genes (ISGs). Nevertheless, the mechanisms by which these ISGs participate in IFN-mediated anti-HCV actions remain largely unknown. In this review, we first outline the signaling pathways known to be involved in the production of type I IFN and ISGs and the tactics that HCV uses to subvert innate immunity. Then, we summarize the effector mechanisms of scaffold ISGs known to modulate IFN function in HCV replication. We also highlight the potential functions of emerging ISGs, which were identified from genome-wide siRNA screens, in HCV replication. Finally, we discuss the functions of several cellular determinants critical for regulating host immunity in HCV replication. This review will provide a basis for understanding the complexity and functionality of the pleiotropic IFN system in HCV infection. Elucidation of the specificity and the mode of action of these emerging ISGs will also help to identify novel cellular targets against which effective HCV therapeutics can be developed. © 2015 CSI and USTC. All rights reserved.

Lee C.-H.,Academia Sinica, Taiwan | Haenggi M.,University of Notre Dame
IEEE Transactions on Wireless Communications | Year: 2012

Consider a cognitive radio network with two types of users: primary users (PUs) and cognitive users (CUs), whose locations follow two independent Poisson point processes. The cognitive users follow the policy that a cognitive transmitter is active only when it is outside the primary user exclusion regions. We found that under this setup the active cognitive users form a point process called the Poisson hole process. Due to the interaction between the primary users and the cognitive users through exclusion regions, an exact calculation of the interference and the outage probability seems unfeasible. Instead, two different approaches are taken to tackle this problem. First, bounds for the interference (in the form of Laplace transforms) and the outage probability are derived, and second, it is shown how to use a Poisson cluster process to model the interference in this kind of network. Furthermore, the bipolar network model with different exclusion region settings is analyzed. © 2012 IEEE.

Lin Y.-C.,Academia Sinica, Taiwan | Ho Y.K.,Fu Jen Catholic University
Canadian Journal of Physics | Year: 2014

Quantum entanglement for two electrons in the excited states of helium-like atom or ions is investigated using two-electron wave functions constructed in the B-spline basis. As a measure of spatial (electron-electron orbital) entanglement, the von Neumann entropy and linear entropy of the reduced density matrix are calculated for the 1s2s 1,3S excited states for systems with some selected Z values from Z = 2 to 100. Results for the helium atom are compared with other available calculations. We have also investigated the entropies for these excited states when the nucleus charge is reduced from Z = 2 continuously to Z = 1. At such a critical charge, all the singly excited states of this system become unbound, and the linear entropies and the von Neumann entropies for the excited states approach 1/2 and 1, respectively; the limits for the entropies when one electron is bound to the nucleus, and the other is free. © 2015 Published by NRC Research Press.

Fu T.S.-T.,Academia Sinica, Taiwan | Fu T.S.-T.,University of Taipei | Lee C.-S.,Memorial Hospital | Lee C.-S.,Kainan University | And 3 more authors.
The Lancet | Year: 2013

Background Macrosocial changes might affect mental health. We investigated whether the prevalence of common mental disorders (CMDs) changed over a 20-year period of industrialisation in Taiwan. Methods We used the 12-item Chinese Health Questionnaire to assess mental status of Taiwanese adults in 1990, 1995, 2000, 2005, and 2010. Respondents with scores of 3 or higher were classified as having probable CMDs. We assessed trends of probable CMDs with the Cochran-Armitage test and their risk factors (sex, age, marital status, educational level, employment status, and physical health) with multivariable logistic regression. The trends were compared with national rates of unemployment, divorce, and suicide. Findings Of 10 548 respondents, 9079 (86•1%) completed questionnaires. The prevalence of probable CMDs doubled from 11•5% in 1990 to 23•8% in 2010 (time trend p<0•001). Increases paralleled rises in national rates of unemployment, divorce, and suicide at all five timepoints. Significant risk factors for probable CMDs were female sex (adjusted odds ratio 1•6, 95% CI 1•4-1•8), 6 or fewer years of education (1•3, 1•1-1•5), unemployment (1•4, 1•1-1•7), and poor physical health that limited daily activities (6•5, 5•4-8•0). When we controlled for these factors in multivariable models, the time trends remained significant (p<0•0001). Interpretation National rates of unemployment, divorce, and suicide increased in parallel with prevalence of probable CMDs in Taiwan. Therefore, clinical and social preventive measures both seem important during times of change to the economy and labour market. Funding Taiwan National Science Council.

Cheung K.,National Center for Theoretical science | Cheung K.,National Tsing Hua University | Cheung K.,Konkuk University | Keung W.-Y.,National Center for Theoretical science | And 4 more authors.
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2015

Recently, the ATLAS Collaboration recorded an interesting anomaly in diboson production with excesses at the diboson invariant mass around 2 TeV in boosted jets of all the WZ, W+W-, and ZZ channels. We offer a theoretical interpretation of the anomaly using a phenomenological right-handed model with extra W' and Z' bosons. Constraints from narrow total decay widths, dijet cross sections, and W/Z+H production are taken into account. We also comment on a few other possibilities. © 2015 Published by Elsevier B.V.

Chen Y.-H.,National Tsing Hua University | Lee M.-J.,National Tsing Hua University | Wang I.-C.,National Tsing Hua University | Du S.,Hong Kong University of Science and Technology | And 4 more authors.
Physical Review Letters | Year: 2013

A high-storage efficiency and long-lived quantum memory for photons is an essential component in long-distance quantum communication and optical quantum computation. Here, we report a 78% storage efficiency of light pulses in a cold atomic medium based on the effect of electromagnetically induced transparency. At 50% storage efficiency, we obtain a fractional delay of 74, which is the best up-to-date record. The classical fidelity of the recalled pulse is better than 90% and nearly independent of the storage time, as confirmed by the direct measurement of phase evolution of the output light pulse with a beat-note interferometer. Such excellent phase coherence between the stored and recalled light pulses suggests that the current result may be readily applied to single photon wave packets. Our work significantly advances the technology of electromagnetically induced transparency-based optical memory and may find practical applications in long-distance quantum communication and optical quantum computation. © 2013 American Physical Society.

Griest K.,University of California at San Diego | Lehner M.J.,Academia Sinica, Taiwan | Lehner M.J.,University of Pennsylvania | Cieplak A.M.,University of California at San Diego | Jain B.,University of Pennsylvania
Physical Review Letters | Year: 2011

If the dark matter consists of primordial black holes (PBHs), we show that gravitational lensing of stars being monitored by NASA's Kepler search for extrasolar planets can cause significant numbers of detectable microlensing events. A search through the roughly 150000 light curves would result in large numbers of detectable events for PBHs in the mass range 5×10 -10Ma to 10-4Ma. Nondetection of these events would close almost 2 orders of magnitude of the mass window for PBH dark matter. The microlensing rate is higher than previously noticed due to a combination of the exceptional photometric precision of the Kepler mission and the increase in cross section due to the large angular sizes of the relatively nearby Kepler field stars. We also present a new formalism for calculating optical depth and microlensing rates in the presence of large finite-source effects. © 2011 American Physical Society.

Liu H.,California Institute of Technology | Kwon O.-H.,California Institute of Technology | Kwon O.-H.,Ulsan National Institute of Science and Technology | Tang J.,Academia Sinica, Taiwan | Zewail A.H.,California Institute of Technology
Nano Letters | Year: 2014

In this Letter, we introduce conical-scanning dark-field imaging in four-dimensional (4D) ultrafast electron microscopy to visualize single-particle dynamics of a polycrystalline ensemble undergoing phase transitions. Specifically, the ultrafast metal-insulator phase transition of vanadium dioxide is induced using laser excitation and followed by taking electron-pulsed, time-resolved images and diffraction patterns. The single-particle selectivity is achieved by identifying the origin of all constituent Bragg spots on Debye-Scherrer rings from the ensemble. Orientation mapping and dynamic scattering simulation of the electron diffraction patterns in the monoclinic and tetragonal phase during the transition confirm the observed behavior of Bragg spots change with time. We found that the threshold temperature for phase recovery increases with increasing particle sizes and we quantified the observation through a theoretical model developed for single-particle phase transitions. The reported methodology of conical scanning, orientation mapping in 4D imaging promises to be powerful for heterogeneous ensemble, as it enables imaging and diffraction at a given time with a full archive of structural information for each particle, for example, size, morphology, and orientation while minimizing radiation damage to the specimen. © 2014 American Chemical Society.

Voshchinnikov N.V.,Saint Petersburg State University | Hirashita H.,Academia Sinica, Taiwan
Monthly Notices of the Royal Astronomical Society | Year: 2014

We apply the time evolution of grain size distributions through accretion and coagulation found in our previous work to the modelling of the wavelength dependence of interstellar linear polarization. We focus in particular on the parameters of the Serkowski curve K and λmax, characterizing the width and maximum wavelength of this curve, respectively. We use aligned silicate and non-aligned carbonaceous spheroidal particles with different aspect ratios a/b. The imperfect alignment of grains with sizes larger than a cut-off size rV,cut is considered. We find that the evolutionary effects on the polarization curve are negligible in the original model with commonly used material parameters (hydrogen number density nH =103 cm-3, gas temperature Tgas =10 K and sticking probability for accretion Sacc =0.3). Therefore, we apply the tuned model, where the coagulation threshold of silicate is removed. In this model, λmax displaces to longerwavelengths and the polarization curve becomes wider (K reduces) on timescales ~(30-50)(nH/103cm-3)-1 Myr. The tuned models at T ≲ 30(nH/103cm-3)-1 Myr and different values of the parameters rV,cut can also explain the observed trend between K and λmax. It is significant that the evolutionary effect appears in the perpendicular direction to the effect of rV,cut on the K - λmax diagram. Very narrow polarization curves can be reproduced if we change the type of particles (prolate/oblate) and/or vary a/b. © 2014 The Authors.

Tang H.,Hong Kong University of Science and Technology | Dou K.,Academia Sinica, Taiwan | Kaun C.-C.,Academia Sinica, Taiwan | Kuang Q.,Hong Kong University of Science and Technology | Yang S.,Hong Kong University of Science and Technology
Journal of Materials Chemistry A | Year: 2014

MoSe2 nanosheets and MoSe2/graphene hybrids have been prepared by a facile hydrothermal method. The number of layers of the MoSe 2 nanosheets is typically <10 as confirmed directly by transmission electron microscopy and indirectly by a red shift of the characteristic A1g Raman peak. The hydrogen evolution reaction (HER) studies show that the onset potentials of MoSe2 and MoSe 2/RGO hybrids are only ∼0.15 V vs. RHE and ∼0.05 V vs. RHE, respectively, about 20-30 mV lower than those of MoS2 and its graphene hybrids reported previously. Density functional theory calculations reveal that the Gibbs free energy for atomic hydrogen adsorption (ΔG0H) on MoSe2 edges is closer to thermoneutral than that on MoS2, with an H coverage of about 75% on the edge under operating conditions, which is also higher than that of MoS2 reported in the literature. The consistency between the experimental and computational results indicates that MoSe2 nanosheets have potential to be a better HER catalyst than their MoS2 counterpart. © 2013 The Royal Society of Chemistry.

Lin P.,Hong Kong University of Science and Technology | Engling G.,Academia Sinica, Taiwan | Yu J.Z.,Hong Kong University of Science and Technology | Yu J.Z.,U.S. National Center for Atmospheric Research
Atmospheric Chemistry and Physics | Year: 2010

HUmic-LIke Substances (HULIS) are an abundant unresolved mixture of organic compounds present in atmospheric samples. Biomass burning (BB) has been recognized as an important primary source of HULIS, but measurements of HULIS in various fresh BB particles are lacking. In this work, HULIS in emissions of rice straw burning was measured in a number of field and chamber experiments. The average HULIS/OC ratio was 0.34±0.05 in μg/μgC, showing small variance among emissions under different burning conditions. The influence of BB on ambient HULIS levels was investigated by examining the spatial and temporal variation of HULIS and other aerosol constituents and interspecies relations in ambient PM2.5. The PM2.5 samples were collected at an urban and a suburban location in the Pearl River Delta (PRD), China over a period of one year. The HULIS concentrations in the ambient PM2.5 were significantly higher in air masses originating from regions influenced by BB. Significant correlations between HULIS and water-soluble K+ concentrations at both sites further support that BB was an important source of HULIS. Ambient concentrations of HULIS also correlated well with those of sulfate, oxalate, and oxidant (the sum of O3 and NO2). The HULIS/OC ratios in BB-influenced ambient aerosols (∼0.6) were much higher than those in the fresh BB emissions (0.34), implying that secondary formation was also an important source of HULIS in the atmosphere. The annual average HULIS concentrations were 4.9 μg m-3 at the urban site and 7.1 μg m-3 at the suburban site while the annual average concentrations of elemental carbon were 3.3 μg m-3 and 2.4 μg m-3, respectively. The urban-suburban spatial gradient of HULIS was opposite to that of elemental carbon, negating vehicular exhaust as a significant primary emission source of HULIS. © 2010 Author(s).

Schroeder J.I.,University of California at San Diego | Delhaize E.,CSIRO | Frommer W.B.,Carnegie Institution for Science | Guerinot M.L.,Dartmouth College | And 9 more authors.
Nature | Year: 2013

With the global population predicted to grow by at least 25 per cent by 2050, the need for sustainable production of nutritious foods is critical for human and environmental health. Recent advances show that specialized plant membrane transporters can be used to enhance yields of staple crops, increase nutrient content and increase resistance to key stresses, including salinity, pathogens and aluminium toxicity, which in turn could expand available arable land. © 2013 Macmillan Publishers Limited. All rights reserved.

Ahn Y.H.,Academia Sinica, Taiwan | Chen C.-S.,Academia Sinica, Taiwan | Chen C.-S.,National Center for Theoretical science South
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2010

We consider an effective theory with an SU(2)×U(1) ×A4×Z2×Z4 symmetry and investigate the possibility of a linking TeV-leptogenesis with a reactor angle |Ue3| through A4 symmetry breaking which is at a scale higher than electroweak scale under the framework of radiative seesaw. It has been shown that tribimaximal (TBM) mixing can be obtained by forging vacuum expectation value alignment of the A4. Especially, one A4 triplet scalar field with cutoff scale Λ is added in neutrino Yukawa sector, which is responsible for the deviation of the exact TBM, to explain leptogenesis as well as a nonzero |Ue3|. Above the scale of Λ the leptonic Yukawa sectors will lead to the exact TBM. We analyze possible spectrums of light neutrinos and their flavor mixing angles corresponding to heavy Majorana neutrino mass ordering, and show that nonresonance leptogenesis at TeV scale constrained by low energy data is achievable, both analytically as well as numerically. We show that only normal hierarchical spectrum of light neutrino would be strongly favored by the current Wilkinson Microwave Anisotropy Probe data, and also show that a relatively large |Ue3| corresponds to the value of baryon asymmetry 6.2×10-10. © 2010 The American Physical Society.

Ohyama Y.,Academia Sinica, Taiwan | Hota A.,Academia Sinica, Taiwan | Hota A.,Center for Excellence in Basic science
Astrophysical Journal Letters | Year: 2013

IC 3418 is a dwarf irregular galaxy falling into the Virgo cluster, and a 17 kpc long trail is seen behind the galaxy, which is considered to have formed due to ram pressure stripping. The trail contains compact knots and diffuse blobs of ultraviolet and blue optical emission and, thus, it is a clear site of recent star formation but in an unusual environment, surrounded by a million degree intra-cluster medium. We report on our optical spectroscopy of a compact source in the trail, SDSS J122952.66+112227.8, and show that the optical spectrum is dominated by emission from a massive blue supergiant star. If confirmed, our report would mark the farthest star with spectroscopic observation. We interpret that a massive O-type star formed in situ in the trail has evolved recently out of the main sequence into this blue supergiant phase, and now lacks any detectable spectral sign of its associated H II region. We argue that turbulence within the ram pressure striped gaseous trail may play a dominant role for the star formation within such trails. © 2013. The American Astronomical Society. All rights reserved..

Chung K.-M.,Academia Sinica, Taiwan | Ostrovsky R.,University of California at Los Angeles | Pass R.,Cornell University | Visconti I.,University of Salerno
Proceedings - Annual IEEE Symposium on Foundations of Computer Science, FOCS | Year: 2013

Resettable-security, introduced by Canetti, Goldreich, Goldwasser and Micali (STOC'00), considers the security of cryptographic two-party protocols (in particular zero-knowledge arguments) in a setting where the attacker may "reset" or "rewind" one of the players. The strongest notion of resettable security, simultaneous resettability, introduced by Barak, Goldreich, Goldwasser and Lindell (FOCS'01), requires resettable security to hold for both parties: in the context of zero-knowledge, both the soundness and the zero-knowledge conditions remain robust to resetting attacks. To date, all known constructions of protocols satisfying simultaneous resettable security rely on the existence of ZAPs; constructions of ZAPs are only known based on the existence of trapdoor permutations or number-theoretic assumptions. In this paper, we provide a new method for constructing protocols satisfying simultaneous resettable security while relying only on the minimal assumption of one-way functions. Our key results establish, assuming only one-way functions: • Every language in NP has an ω(1)-round simultaneously resettable witness indistinguishable argument system. • Every language in NP has a (polynomial-round) simultaneously resettable zero-knowledge argument system. The key conceptual insight in our technique is relying on black-box impossibility results for concurrent zeroknowledge to achieve resettable-security. Copyright © 2013 by The Institute of Electrical and Electronics Engineers, Inc.

Kang L.-W.,Academia Sinica, Taiwan | Lin C.-W.,National Tsing Hua University | Fu Y.-H.,MStar Semiconductor Inc.
IEEE Transactions on Image Processing | Year: 2012

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. © 2011 IEEE.

Liu H.-C.,National Taiwan University | Liu H.-C.,Academia Sinica, Taiwan | Liao H.-T.,Academia Sinica, Taiwan | Liao H.-T.,XING | Charng Y.-Y.,Academia Sinica, Taiwan
Plant, Cell and Environment | Year: 2011

In Arabidopsis, there are four homologs of class A1 heat shock factor (HSFA1) genes, which likely encode the master regulators of heat shock response (HSR). However, previous studies with double knockout (KO) mutants were unable to confirm this point probably due to functional redundancy. Here, we generated a quadruple KO (QK) and four triple KO mutants to dissect their functions. Our data show that members of the HSFA1 group not only play a pivotal role in HSR but also are involved in growth and development. Alterations in morphology and retardation in growth were observed in the quadruple but not in triple KO mutants. The basal and acquired thermotolerance capacity was dramatically decreased in the QK mutant but varied in triple KO mutants at different developmental stages. The transcriptomics profiles suggested that more than 65% of the heat stress (HS)-up-regulated genes were HSFA1 dependent. HSFA1s were also involved in the expression of several HS genes induced by H2O2, salt and mannitol, which is consistent with the increased sensitive phenotype of the QK mutant to the stress factors. In conclusion, the Arabidopsis HSFA1s function as the master regulators of HSR and participate as important components in other abiotic stress responses as well. © 2011 Blackwell Publishing Ltd.

Wu H.-Y.,National Taiwan University | Liu M.-S.,Academia Sinica, Taiwan | Lin T.-P.,National Taiwan University | Cheng Y.-S.,National Taiwan University
Plant Physiology | Year: 2011

The membrane protein AtTLP18.3 of Arabidopsis (Arabidopsis thaliana) contains a domain of unknown function, DUF477; it forms a polysome with photosynthetic apparatuses in the thylakoid lumen. To explore the molecular function of AtTLP18.3, we resolved its crystal structures with residues 83 to 260, the DUF477 only, and performed a series of biochemical analyses to discover its function. The gene expression of AtTLP18.3 followed a circadian rhythm. X-ray crystallography revealed the folding of AtTLP18.3 as a three-layer sandwich with three a-helices in the upper layer, four β-sheets in the middle layer, and two a-helices in the lower layer, which resembles a Rossmann fold. Structural comparison suggested that AtTLP18.3 might be a phosphatase. The enzymatic activity of AtTLP18.3 was further confirmed by phosphatase assay with various substrates (e.g. p-nitrophenyl phosphate, 6,8-difluoro-4-methylumbelliferyl phosphate, O-phospho-L-serine, and several synthetic phosphopeptides). Furthermore, we obtained the structure of AtTLP18.3 in complex with O-phospho-L-serine to identify the binding site of AtTLP18.3. Our structural and biochemical studies revealed that AtTLP18.3 has the molecular function of a novel acid phosphatase in the thylakoid lumen. DUF477 is accordingly renamed the thylakoid acid phosphatase domain. © 2011 American Society of Plant Biologists. All Rights Reserved.

Asada K.,Academia Sinica, Taiwan | Nakamura M.,Academia Sinica, Taiwan | Doi A.,Japan Aerospace Exploration Agency | Nagai H.,Japan National Astronomical Observatory | Inoue M.,Academia Sinica, Taiwan
Astrophysical Journal Letters | Year: 2014

The velocity field of the M87 jet from milli-arcsecond (mas) to arcsecond scales is extensively investigated together with new radio images taken from European VLBI Network (EVN) observations. We detected proper motions of components located at between 160 mas from the core and the HST-1 complex for the first time. Newly derived velocity fields exhibit a systematic increase from sub- to superluminal speeds in the upstream of HST-1. If we assume that the observed velocities reflect the bulk flow, here we suggest that the M87 jet may be gradually accelerated through a distance of 106 times the Schwarzschild radius of the supermassive black hole. The acceleration zone is co-spatial with the jet parabolic region, which is interpreted as the collimation zone of the jet. The acceleration and collimation take place simultaneously, which we suggest is characteristic of magnetohydrodynamic flows. The distribution of the velocity field has a peak at HST-1, which is considered as the site of over-collimation, and shows a deceleration downstream of HST-1 where the jet is conical. Our interpretation of the velocity map in the M87 jet provides a hypothesis for active galactic nuclei which suggests that the acceleration and collimation zone of relativistic jets extends over the whole scale within the sphere of influence of the supermassive black hole. © 2014. The American Astronomical Society. All rights reserved..

Gkountela S.,University of California at Los Angeles | Zhang K.X.,University of California at Los Angeles | Shafiq T.A.,University of California at Los Angeles | Liao W.-W.,Academia Sinica, Taiwan | And 3 more authors.
Cell | Year: 2015

Global DNA demethylation in humans is a fundamental process that occurs in pre-implantation embryos and reversion to naive ground state pluripotent stem cells (PSCs). However, the extent of DNA methylation reprogramming in human germline cells is unknown. Here, we performed whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq) of human prenatal germline cells from 53 to 137 days of development. We discovered that the transcriptome and methylome of human germline is distinct from both human PSCs and the inner cell mass (ICM) of human blastocysts. Using this resource to monitor the outcome of global DNA demethylation with reversion of primed PSCs to the naive ground state, we uncovered hotspots of ultralow methylation at transposons that are protected from demethylation in the germline and ICM. Taken together, the human germline serves as a valuable in vivo tool for monitoring the epigenome of cells that have emerged from a global DNA demethylation event. © 2015 Elsevier Inc.

Lin Y.-P.,National Taiwan University | Zhao L.,Academia Sinica, Taiwan | Hung S.-H.,National Taiwan University
Geophysical Research Letters | Year: 2014

Seismic anisotropy in the mantle plays an important role in our understanding of the Earth's internal dynamics, and shear wave splitting has always been a key observable in the investigation of seismic anisotropy. To date the interpretation of shear wave splitting in terms of anisotropy has been largely based on ray-theoretical modeling of a single vertically incident plane SKS or SKKS wave. In this study, we use sensitivity kernels of shear wave splitting to anisotropic parameters calculated by the normal-mode theory to demonstrate that the interference of SKS with other phases of similar arrival times, near-field effect, and multiple reflections in the crust lead to significant variations of SKS splitting with epicentral distance. The full-wave kernels not only widen the possibilities in the source-receiver geometry in making shear wave splitting measurements but also provide the capability for tomographic inversion to resolve vertical and lateral variations in the anisotropic structures. Key Points Full-wave effects lead to complexities in splitting intensity Our method widens the range of source-receiver geometry in splitting analysis Full-wave kernels enable 3-D imaging of anisotropy structures ©2014. American Geophysical Union. All Rights Reserved.

Lee C.-K.,Academia Sinica, Taiwan | Pao C.-W.,Academia Sinica, Taiwan | Chen C.-W.,National Taiwan University
Energy and Environmental Science | Year: 2013

A comprehensive insight into the correlations of the nanoscale organizations of polymer and nanocrystals in polymer/inorganic nanocrystal bulk heterojunction (BHJ) hybrid solar cells is the key toward nanomorphology control for improving device performance. In this study, we investigated the organizations of both the polymer and nanocrystals in polymer/inorganic nanocrystal hybrid solar cells by performing multiscale molecular simulations of P3HT:TiO2 nanocrystal BHJs incorporating nanocrystals with two different dimensionalities, namely, zero-dimensional nanoparticles (NPs), and one-dimensional nanorods (NRs). We reveal that nanocrystal dimensionality has significant impacts on the polymer/nanocrystal organizations for polymer/inorganic nanocrystal hybrid blends. One-dimensional nanocrystals, such as TiO2 NRs, can effectively enhance the polymer degree of crystallinity as a result of preferential polymer chain alignment along the axial dimension of the NRs, thereby promoting hole transport; in addition, the elongated, anisotropic NRs significantly reduce the probability of electron hopping, and maintain a high specific interfacial area for efficient exciton dissociation. Therefore, the present study demonstrates the possibility of the nanoscale morphology control of polymer/inorganic nanocrystal BHJ hybrid blends via tuning the nanocrystal shapes, which is potentially helpful for developing next-generation polymer/inorganic nanocrystal hybrid electronic devices such as solar cells or thin film transistors. © The Royal Society of Chemistry 2013.

Lin K.C.-J.,Academia Sinica, Taiwan | Chen C.-W.,Academia Sinica, Taiwan | Chou C.-F.,National Taiwan University
Proceedings - IEEE INFOCOM | Year: 2012

As mobile devices have become more ubiquitous, mobile users increasingly expect to utilize proximity-based connectivity, e.g., WiFi and Bluetooth, to opportunistically share multimedia content based on their personal preferences. However, many previous studies investigate content dissemination protocols that distribute a single object to as many users in an opportunistic mobile social network as possible without considering user preference. In this paper, we propose PrefCast, a preference-aware content dissemination protocol that targets on maximally satisfying user preference for content objects. Due to non-persistent connectivity between users in a mobile social network, when a user meets neighboring users for a limited contact duration, it needs to efficiently disseminate a suitable set of objects that can bring possible future contacts a high utility (the quantitative metric of preference satisfaction). We formulate such a problem as a maximum-utility forwarding model, and propose an algorithm that enables each user to predict how much utility it can contribute to future contacts and solve its optimal forwarding schedule in a distributed manner. Our trace-based evaluation shows that PrefCast can produce a 18.5% and 25.2% higher average utility than the protocols that only consider contact frequency or preference of local contacts, respectively. © 2012 IEEE.

Mizuse K.,Tohoku University | Kuo J.-L.,Academia Sinica, Taiwan | Fujii A.,Tohoku University
Chemical Science | Year: 2011

The nature of water networks exposed to ionizing radiation is important in various radiation-related chemistry and biology. To understand structural evolution of ionized water networks at the molecular level, we report here infrared spectra of water cluster radical cations (H2O)n+ (n = 3 - 11) in the gas phase. Spectral features of free OH stretch modes are quite similar to those of protonated water clusters H+(H2O)n, of which the hydrogen-bond network structures have been revealed. In addition, we observed an extra band attributed to the stretch of an OH radical in (H2O)n+. These results indicate that nominal (H2O)n+ should be regarded as H+(H2O)n-1(OH) motifs having similar network shapes to those of H+(H2O)n. We also analyzed hydrogen-bonded OH stretch bands and found that hydrogenbond strength is a key factor to determine the position of the OH radical relative to the protonated site (H3O+/H5O2+). Because an OH radical is a weaker hydrogen bond acceptor than water, the first solvation shell of the protonated site is preferentially filled with water. As a result, the OH radical is separated from the protonated (charged) site by at least one water molecule in n≥ 5 clusters. This result shows the instability of the H3O+-OH ion-radical contact pair in water networks, and implies the higher mobility of the OH radical due to its release from the charged site. Observed structural preferences are confirmed both in cold and warm cluster ion sources. © The Royal Society of Chemistry 2011.

Fan X.,Jilin University | Zheng W.T.,Jilin University | Kuo J.-L.,Academia Sinica, Taiwan | Singh D.J.,Oak Ridge National Laboratory | Singh D.J.,Jilin University
ACS Applied Materials and Interfaces | Year: 2013

We analyzed the adsorption of Li on graphene in the context of anodes for lithium-ion batteries (LIBs) using first-principles methods including van der Waals interactions. We found that although Li can reside on the surface of defect-free graphene under favorable conditions, the binding is much weaker than to graphite and the concentration on a graphene surface is not higher than in graphite. At low concentration, Li ions spread out on graphene because of Coulomb repulsion. With increased Li content, we found that small Li clusters can be formed on graphene. Although this result suggests that graphene nanosheets can conceivably have a higher ultimate Li capacity than graphite, it should be noted that such nanoclusters can potentially nucleate Li dendrites, leading to failure. The implications for nanostructured carbon anodes in batteries are discussed. © 2013 American Chemical Society.

Lu H.-C.,National Taiwan University | Liao W.,National Taiwan University | Liao W.,King Saud University | Liao W.,Academia Sinica, Taiwan
IEEE Journal on Selected Areas in Communications | Year: 2012

In this paper, we study the cooperative strategies of relay stations in wireless relay networks. In such networks, relay stations distributed across the network and centrally controlled by the base station can be exploited to form cooperative antenna arrays. We show that via relay station cooperation, the achievable downstream rate of mobile stations can be enhanced. Thus, we determine which relay stations should cooperate with one another and which mobile stations should receive data from the cooperative relays such that the performance of the entire network can be optimized. The utility maximization relay station cooperation problem is formulated with the goal of maximizing system capacity and balancing user traffic demand. We analyze the complexity of this problem and show that it can be decomposed into two NP-hard sub-problems. To tackle this problem, we propose two algorithms with different degrees of efficiency and complexity. The simulation results show that relay station cooperation can not only enhance the throughput of the network, but also improve fairness among users. More importantly, we find that proper relay station placement can further enhance the throughput gain. © 2006 IEEE.

Iloeje U.H.,Bristol Myers Squibb | Yang H.-I.,China Medical University at Taichung | Chen C.-J.,Academia Sinica, Taiwan | Chen C.-J.,National Taiwan University
Liver International | Year: 2012

Chronic hepatitis B virus (HBV) infection is a serious public health problem because of its worldwide prevalence and potential to cause adverse consequences. The Risk Evaluation of Viral Load Elevation and Associated Liver Disease/Cancer-Hepatitis B Virus (REVEAL-HBV) study carried out in Taiwan was used to investigate the natural history of chronic hepatitis B. The REVEAL-HBV study has established an HBV viral load paradigm in the natural history of chronic hepatitis B (CHB). Serum HBV DNA level has been shown to be significantly and independently associated with incidence of hepatocellular carcinoma (HCC) and cirrhosis and liver-related mortality across a biological gradient. It is also a major predictor of HBsAg seroclearance. Genetic features including HBV genotype and basal core promoter A1762T/G1764A mutant, and precore G1896A mutant were documented as predictors of HCC risk. Inactive HBV carriers still had an increased risk on HCC development and liver-related mortality compared with HBsAg -seronegatives. Nomograms focusing on facilitating risk communication between patients and clinicians were developed incorporating non-invasive clinical parameters to predict long-term HCC risk. These will hopefully contribute to evidence-based decisions in the clinical management of CHB patients. A somewhat provocative and novel finding from the REVEAL-HBV study is the association of chronic HBV infection in active replication with an increased pancreatic cancer risk especially in women less than 50 years old. This finding will hopefully spur further research in this area seeking confirmatory evidence. Finally, we hope that the REVEAL-HBV study will continue to be a source of data to answer other important questions in chronic hepatitis B research going forward. © 2012 John Wiley & Sons A/S.

Chang F.-P.,National Taiwan University | Chen Y.-P.,Academia Sinica, Taiwan | Mou C.-Y.,National Taiwan University
Small | Year: 2014

An approach for enzyme therapeutics is elaborated with cell-implanted nanoreactors that are based on multiple enzymes encapsulated in hollow silica nanospheres (HSNs). The synthesis of HSNs is carried out by silica sol-gel templating of water-in-oil microemulsions so that polyethyleneimine (PEI) modifi ed enzymes in aqueous phase are encapsulated inside the HSNs. PEI-grafted superoxide dismutase (PEI-SOD) and catalase (PEI-CAT) encapsulated in HSNs are prepared with quantitative control of the enzyme loadings. Excellent activities of superoxide dismutation by PEI-SOD@HSN are found and transformation of H 2 O 2 to water by PEI-CAT@ HSN. When PEI-SOD and PEI-CAT are co-encapsulated, cascade transformation of superoxide through hydrogen peroxide to water was facile. Substantial fractions of HSNs exhibit endosome escape to cytosol after their delivery to cells. The production of downstream reactive oxygen species (ROS) and COX-2/p-p38 expression show that co-encapsulated SOD/CAT inside the HSNs renders the highest cell protection against the toxicant N , N '-dimethyl-4,4'-bipyridinium dichloride (paraquat). The rapid cell uptake and strong detoxifi cation effect on superoxide radicals by the SOD/CATencapsulated hollow mesoporous silica nanoparticles demonstrate the general concept of implanting catalytic nanoreactors in biological cells with designed functions. © 2014 Wiley-VCH Verlag GmbH &Co. KGaA, Weinheim.

Tang H.-W.,Academia Sinica, Taiwan | Tang H.-W.,National Taiwan University | Wang Y.-B.,Academia Sinica, Taiwan | Wang S.-L.,Academia Sinica, Taiwan | And 4 more authors.
EMBO Journal | Year: 2011

Autophagy is a membrane-mediated degradation process of macromolecule recycling. Although the formation of double-membrane degradation vesicles (autophagosomes) is known to have a central role in autophagy, the mechanism underlying this process remains elusive. The serine/threonine kinase Atg1 has a key role in the induction of autophagy. In this study, we show that overexpression of Drosophila Atg1 promotes the phosphorylation-dependent activation of the actin-associated motor protein myosin II. A novel myosin light chain kinase (MLCK)-like protein, Spaghetti-squash activator (Sqa), was identified as a link between Atg1 and actomyosin activation. Sqa interacts with Atg1 through its kinase domain and is a substrate of Atg1. Significantly, myosin II inhibition or depletion of Sqa compromised the formation of autophagosomes under starvation conditions. In mammalian cells, we found that the Sqa mammalian homologue zipper-interacting protein kinase (ZIPK) and myosin II had a critical role in the regulation of starvation-induced autophagy and mammalian Atg9 (mAtg9) trafficking when cells were deprived of nutrients. Our findings provide evidence of a link between Atg1 and the control of Atg9-mediated autophagosome formation through the myosin II motor protein. © 2011 European Molecular Biology Organization | All Rights Reserved.

Allahverdyan A.E.,Yerevan Physics Institute | Hovhannisyan K.V.,Yerevan Physics Institute | Hovhannisyan K.V.,ICFO - Institute of Photonic Sciences | Melkikh A.V.,Ural Federal University | Gevorkian S.G.,Academia Sinica, Taiwan
Physical Review Letters | Year: 2013

We want to understand whether and to what extent the maximal (Carnot) efficiency for heat engines can be reached at a finite power. To this end we generalize the Carnot cycle so that it is not restricted to slow processes. We show that for realistic (i.e., not purposefully designed) engine-bath interactions, the work-optimal engine performing the generalized cycle close to the maximal efficiency has a long cycle time and hence vanishing power. This aspect is shown to relate to the theory of computational complexity. A physical manifestation of the same effect is Levinthal's paradox in the protein folding problem. The resolution of this paradox for realistic proteins allows to construct engines that can extract at a finite power 40% of the maximally possible work reaching 90% of the maximal efficiency. For purposefully designed engine-bath interactions, the Carnot efficiency is achievable at a large power. © 2013 American Physical Society.

Wang F.,Academia Sinica, Taiwan | Liu K.,Academia Sinica, Taiwan | Liu K.,National Tsing Hua University | Liu K.,National Taiwan University | And 2 more authors.
Nature Chemistry | Year: 2012

The concept of geometrical constraints and steric hindrance in reactions is implanted deeply in a chemist's 'chemical intuition'. However, until now a true three-dimensional view of these steric effects has not been realized experimentally for any chemical reaction in full. Here we report the complete three-dimensional characterization of the sterics of a benchmark polyatomic reaction by measuring the dependence of the product state-resolved angular distributions on the spatial alignment of the reactive bond in a crossed molecular beam experiment. The results prove the existence of two distinct microscopic reaction mechanisms. Detailed analysis reveals that the origin of the stereodynamics in the HCl(ν = 0) + CD 3(0 0) product channel can be captured by a textbook line-of-centres collision model. In contrast, a time-delay pathway, which includes a sharp switch from in-plane to out-of-plane scattering in the forwards direction, appears to be operative in forming the excited HCl(ν = 1) + CD 3(0 0) product pair. © 2012 Macmillan Publishers Limited. All rights reserved.

You J.-J.,Academia Sinica, Taiwan | Lin-Chao S.,Academia Sinica, Taiwan | Lin-Chao S.,National Taiwan University
Journal of Biological Chemistry | Year: 2010

Neuritogenesis, or neurite outgrowth, is a critical process for neuronal differentiation and maturation in which growth cones are formed from highly dynamic actin structures. Gas7 (growth arrest-specific gene 7), a new member of the PCH(Pombe Cdc15 homology) protein family, is predominantly expressed in neurons and is required for the maturation of primary cultured Purkinje neurons as well as the neuron-like differentiation of PC12 cells upon nerve growth factor stimulation.Wereport that Gas7 co-localizes and physically interacts with N-WASP, a key regulator of Arp2/3 complex-mediated actin polymerization, in the cortical region of Gas7-transfected Neuro-2a cells and growth cones of hippocampal neurons. The interaction between Gas7 and N-WASP is mediated by WW-Prodomains, which is unique in the PCH protein family, where most interactions are of the SH3-Pro kind. The interaction contributes to the formation of membrane protrusions and processes by recruiting the Arp2/3 complex in a Cdc42-independent manner. Importantly, specific interaction between Gas7 and N-WASP is required for regular neurite outgrowth of hippocampal neurons. The data demonstrate an essential role of Gas7 through its interaction with N-WASP during neuronal maturation/differentiation. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

Sanghavi B.J.,University of Virginia | Varhue W.,University of Virginia | Chavez J.L.,Air Force Research Lab | Chou C.-F.,Academia Sinica, Taiwan | Swami N.S.,University of Virginia
Analytical Chemistry | Year: 2014

Neuropeptides are vital to the transmission and modulation of neurological signals, with Neuropeptide Y (NPY) and Orexin A (OXA) offering diagnostic information on stress, depression, and neurotrauma. NPY is an especially significant biomarker, since it can be noninvasively collected from sweat, but its detection has been limited by poor sensitivity, long assay times, and the inability to scale-down sample volumes. Herein, we apply electrokinetic preconcentration of the neuropeptide onto patterned graphene-modified electrodes in a nanochannel by frequency-selective dielectrophoresis for 10 s or by electrochemical adsorptive accumulation for 300 s, to enable the electrochemical detection of NPY and OXA at picomolar levels from subnanoliter samples, with sufficient signal sensitivity to avoid interferences from high levels of dopamine and ascorbic acid within biological matrices. Given the high sensitivity of the methodology within small volume samples, we envision its utility toward off-line detection from droplets collected by microdialysis for the eventual measurement of neuropeptides at high spatial and temporal resolutions. © 2014 American Chemical Society.

You Z.-Q.,Academia Sinica, Taiwan | Hsu C.-P.,Academia Sinica, Taiwan | Hsu C.-P.,National Taiwan University
International Journal of Quantum Chemistry | Year: 2014

Excitation energy transfer (EET) is a process where the electronically excitation is transferred from a donor to an acceptor. EET is widely seen in both natural and in artificial systems, such as light-harvesting in photosynthesis, the fluorescence resonance energy transfer technique, and the design of light-emitting molecular devices. In this work, we outline the theories describing both singlet and triplet EET (SEET and TEET) rates, with a focus on the physical nature and computational methods for the electronic coupling factor, an important parameter in predicting EET rates. The SEET coupling is dominated by the Coulomb coupling, and the remaining short-range coupling is very similar to the TEET coupling. The magnitude of the Coulomb coupling in SEET can vary much, but the contribution of short-range coupling has been found to be similar across different excited states in naphthalene. The exchange coupling has been believed to be the major physical contribution to the short-range coupling, but it has been pointed out that other contribution, such as the orbital overlap effect is similar or even larger in strength. The computational aspects and the subsequent physical implication for both SEET and TEET coupling values are summarized in this work. © 2013 The Authors. International Journal of Quantum Chemistry Published by Wiley Periodicals, Inc. Electronic coupling is an important factor in predicting excitation energy transfer rates. For the singlet case, there is a dominating Coulomb coupling, which eventually becomes dipole-dipole coupling. A shortrange coupling is important for both the triplet case and the short distance in the singlet case. This article reviews the theory and physics behind the coupling for both singlet and triplet cases, and discusses computational aspects for calculating the coupling using first-principle methods. © 2013 The Authors. International Journal of Quantum Chemistry Published by Wiley Periodicals, Inc.

Cheng L.-C.,National Taiwan University | Jiang X.,CAS National Center for Nanoscience and Technology | Wang J.,CAS National Center for Nanoscience and Technology | Chen C.,CAS National Center for Nanoscience and Technology | And 2 more authors.
Nanoscale | Year: 2013

With the advancements in nanotechnology, studies on the synthesis, modification, application, and toxicology evaluation of nanomaterials are gaining increased attention. In particular, the applications of nanomaterials in biological systems are attracting considerable interest because of their unique, tunable, and versatile physicochemical properties. Artificially engineered nanomaterials can be well controlled for appropriate usage, and the tuned physicochemical properties directly influence the interactions between nanomaterials and cells. This review summarizes recently synthesized major nanomaterials that have potential biomedical applications. Focus is given on the interactions, including cellular uptake, intracellular trafficking, and toxic response, while changing the physicochemical properties of versatile materials. The importance of physicochemical properties such as the size, shape, and surface modifications of the nanomaterials in their biological effects is also highlighted in detail. The challenges of recent studies and future prospects are presented as well. This review benefits relatively new researchers in this area and gives them a systematic overview of nano-bio interaction, hopefully for further experimental design. © 2013 The Royal Society of Chemistry.

Brasser R.,Academia Sinica, Taiwan | Ida S.,Tokyo Institute of Technology | Kokubo E.,Japan National Astronomical Observatory
Monthly Notices of the Royal Astronomical Society | Year: 2013

We investigate the obliquity and spin period of Earth-Moon-like systems after 4.5 Gyr of tidal evolution with various satellite masses (ms = 0.0025mp - 0.05mp, where mp is the planet mass) and initial planetary obliquity (ε0 = 0{ring operator}-175{ring operator}), and discuss their relations to the habitability of the planet. The satellite initially orbits in the planet's equatorial plane at ~4 planetary radii and the planet's initial rotation period is 5 h. The other tidal parameters are modelled after the Earth and Moon and we keep the satellite on a circular orbit. We find three possible outcomes: either (i) the system is still evolving, such as our own, (ii) the system is in the double synchronous state, with the planet's obliquity at either 0{ring operator} or 180{ring operator}, or (iii) the satellite has collided with the planet. The case (iii) occurs for initial planetary spins in the range ε0 ~ 60{ring operator}-120{ring operator}. For other ε0, the satellite survives. The transition between case (i) and (ii) is abrupt and occurs at slightly larger satellite mass (ms ~ 0.02mp) than the lunar mass. For higher masses the system is in the double synchronous state and the final planetary spin periods (Pp) are longer than 96 h. We also discuss the habitability of the planet in each case. We suggest that cases (ii) and (iii) are less habitable than case (i). Using results from models of giant impacts and satellite accretion, we found that the systems that mimic our own, i.e. with rotation period 12 < Pp < 48 h and current planetary obliquity εp < 40{ring operator} or εp > 140{ring operator} only represent 14 per cent of the possible outcomes. This estimate may only be reliable to within factors of a few, depending on how the probability is evaluated. Elser et al. conclude that the probability of a terrestrial planet having a heavy satellite is 13 per cent. Combining these results suggests that the probability of ending up with a system such as our own is of the order of 2 per cent. © 2012 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

Liu H.-C.,National Taiwan University | Charng Y.-Y.,National Taiwan University | Charng Y.-Y.,Academia Sinica, Taiwan
Plant Physiology | Year: 2013

There are 21 heat shock factor (HSF) homologs in Arabidopsis (Arabidopsis thaliana), of which members of class A1 (HSFA1a/HSFA1b/HSFA1d/HSFA1e) play the major role in activating the transcription of heat-induced genes, including HSFA2. Once induced, HSFA2 becomes the dominant HSF and is able to form heterooligomeric complexes with HSFA1. However, whether HSFA2 could function independently as a transcription regulator in the absence of the HSFA1s was undetermined. To address this question, we introduced a Cauliflower mosaic virus 35S promoter:HSFA2 construct into hsfa1a/hsfa1b/hsfa1d/hsfa1e quadruple knockout (QK) and wild-type (Wt) backgrounds to yield transgenic lines A2QK and A2Wt, respectively. Constitutive expression of HSFA2 rescued the developmental defects of the QK mutant and promoted callus formation in A2QK, but not in A2Wt, after heat treatment. Transcriptome analysis showed that heat stress response genes are differentially regulated by the HSFA1s and HSFA2; the genes involved in metabolism and redox homeostasis are preferentially regulated by HSFA2, while HSFA1-preferring genes are enriched in transcription function. Ectopic expression of HSFA2 complemented the defects of QK in tolerance to different heat stress regimes, and to hydrogen peroxide, but not to salt and osmotic stresses. Furthermore, we showed that HSFA1a/HSFA1b/HSFA1d are involved in thermotolerance to mild heat stress at temperatures as low as 27°C. We also noticed subfunctionalization of the four Arabidopsis A1-type HSFs in diverse abiotic stress responses. Overall, this study reveals the overlapping and distinct functions of class A1 and A2 HSFs and may enable more precise use of HSFs in engineering stress tolerance in the future. © 2013 American Society of Plant Biologists. All Rights Reserved.

Jana D.,University of Calcutta | Sun C.-L.,Chang Gung University | Chen L.-C.,National Taiwan University | Chen K.-H.,National Taiwan University | Chen K.-H.,Academia Sinica, Taiwan
Progress in Materials Science | Year: 2013

This review covers the electronic, optical and electrochemical properties along with electronic behaviors of boron (B) and nitrogen (N) substituted Single Wall Carbon Nanotubes (SWCNTs) underlying density functional theory (DFT) simulations. It is intended to be of interest for both experimentalists and theorists to expand application in the fields of SWCNTs. In particular, this article will focus on the electronically driven optical properties of C xNy nanotubes as a function of N concentration and B xCy nanotubes as a function of B under the action of a uniform electric field with various polarization directions through relaxed C-C bond length ab initio DFT. The link between the electronic band structure and the peak of the loss function will be highlighted. Within the formalism of DFT, we also consider the aspects of vacancy-defected SWCNTs. The effect of nitrogen incorporation is quite pronounced in enhancing the electrochemical properties of CNTs. In fact, this is a growing field due to the need of developing next-generation H-based energies. Finally, an attempt will be made for a comparative study of these theoretical results with experimental ones. Although there are ample experimental reports of N incorporation, at least less than 10%, in the nanostructured carbon, the experimental results on B-alloyed and N-alloyed SWCNTs are scarce. The review concludes with an outlook on the technological potential of these nano-composite systems as optical devices and nano-sensors. © 2013 Elsevier Ltd. All rights reserved.

Lu Y.-H.,Academia Sinica, Taiwan | Lu Y.-H.,National Taiwan University | Yang C.-W.,Academia Sinica, Taiwan | Hwang I.-S.,Academia Sinica, Taiwan
Langmuir | Year: 2012

It was numerically predicted that dissolved gas particles could enrich and adsorb at hydrophobic liquid interfaces. Here we observe nucleation and growth of bright patches of ∼0.45 nm high on the graphite surface in pure water with frequency-modulation atomic force microscopy when the dissolved gas concentration is below the saturation level. The bright patches, suspected to be caused by adsorption of nitrogen molecules at the graphite water interface, are composed of domains of a rowlike structure with the row separation of 4.2 ± 0.3 nm. The observation of this ordered adlayer might underline the gas segregation at various water interfaces. © 2012 American Chemical Society.

Li Z.-Y.,University of Virginia | Li Z.-Y.,Academia Sinica, Taiwan | Krasnopolsky R.,Academia Sinica, Taiwan | Shang H.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2011

Dense, star-forming cores of molecular clouds are observed to be significantly magnetized. A realistic magnetic field of moderate strength has been shown to suppress, through catastrophic magnetic braking, the formation of a rotationally supported disk (RSD) during the protostellar accretion phase of low-mass star formation in the ideal MHD limit. We address, through two-dimensional (axisymmetric) simulations, the question of whether realistic levels of non-ideal effects, computed with a simplified chemical network including dust grains, can weaken the magnetic braking enough to enable an RSD to form. We find that ambipolar diffusion (AD), the dominant non-ideal MHD effect over most of the density range relevant to disk formation, does not enable disk formation, at least in two dimensions. The reason is that AD allows the magnetic flux that would be dragged into the central stellar object in the ideal MHD limit to pile up instead in a small circumstellar region, where the magnetic field strength (and thus the braking efficiency) is greatly enhanced. We also find that, on the scale of tens of AU or more, a realistic level of Ohmic dissipation does not weaken the magnetic braking enough for an RSD to form, either by itself or in combination with AD. The Hall effect, the least explored of these three non-ideal MHD effects, can spin up the material close to the central object to a significant, supersonic rotation speed, even when the core is initially non-rotating, although the spun-up material remains too sub-Keplerian to form an RSD. The problem of catastrophic magnetic braking that prevents disk formation in dense cores magnetized to realistic levels remains unresolved. Possible resolutions of this problem are discussed. © 2011. The American Astronomical Society. All rights reserved.

Kuo T.-M.,Academia Sinica, Taiwan | Kuo T.-M.,National Taiwan University | Hirashita H.,Academia Sinica, Taiwan
Monthly Notices of the Royal Astronomical Society: Letters | Year: 2012

In high-redshift (z>5) quasars, a large amount of dust (~10 8M ⊙) has been observed. In order to explain the large dust content, we focus on a possibility that grain growth by the accretion of heavy elements is the dominant dust source. We adopt a chemical evolution model applicable to nearby galaxies, but utilize parameters adequate to high-z quasars. It is assumed that metals and dust are predominantly ejected by Type II supernovae (SNe). We have found that grain growth strongly depends on the grain size distribution. If we simply use the size distribution of grains ejected from SNe, grain growth is inefficient because of the lack of small grains (i.e.small surface-to-volume ratio of the dust grains). However, if we take small grain production by interstellar shattering into consideration, grain growth is efficient enough to account for the rich dust abundance in high-z quasars. Our results not only confirm that grain growth is necessary to explain the large amount of dust in high-z quasars, but also demonstrate that grain size distributions have a critical impact on grain growth. © 2012 The Authors, MNRAS 424, L34-L38 Monthly Notices of the Royal Astronomical Society. © 2012 RAS.

Wang Z.-F.,National Taiwan University | Wang Z.-F.,Academia Sinica, Taiwan | Chang T.-C.,National Taiwan University | Chang T.-C.,Academia Sinica, Taiwan
Nucleic Acids Research | Year: 2012

Because various non-parallel G-quadruplexes of human telomeric sequences in K+ solution can be converted to a parallel G-quadruplex by adding polyethylene glycol (PEG) as a co-solvent, we have taken advantage of this property of PEG to study the covalent attachment of a PEG unit to a G-quadruplex ligand, 3,6-bis(1-methyl-4-vinylpyridinium) carbazole diiodide (BMVC). The hybrid ligand with the PEG unit, BMVC-8C3O or BMVC-6C2O by substituting either the tetraethylene glycol or the triethylene glycol terminated with a methyl-piperidinium cation in N-9 position of BMVC, not only induces structural change from different non-parallel G-quadruplexes to a parallel G-quadruplex but also increases the melting temperature of human telomeres in K+ solution by more than 45°C. In addition, our ligand work provides further confidence that the local water structure plays the key to induce conformational change of human telomere. © 2012 The Author(s).

Topsakal M.,Bilkent University | Bagci V.M.K.,Academia Sinica, Taiwan | Ciraci S.,Bilkent University
Physical Review B - Condensed Matter and Materials Physics | Year: 2010

The current-voltage characteristics of armchair graphene nanoribbons under a local uniaxial tension are investigated by using first-principles quantum transport calculations. It is shown that for a given value of bias voltage, the resulting current depends strongly on the applied tension. The observed trends are explained by means of changes in the band gaps of the nanoribbons due to the applied uniaxial tension. In the course of plastic deformation, the irreversible structural changes and derivation of carbon monatomic chains from graphene pieces can be monitored by two-probe transport measurements. © 2010 The American Physical Society.

Chiu T.-W.,National Taiwan University | Hsieh T.-H.,Academia Sinica, Taiwan | Mao Y.-Y.,National Taiwan University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2011

We determine the topological susceptibility of the gauge configurations generated by lattice simulations using two flavors of optimal domain-wall fermion on the 163×32 lattice with length 16 in the fifth dimension, at the lattice spacing a≃0.1 fm. Using the adaptive thick-restart Lanczos algorithm, we project the low-lying eigenmodes of the overlap Dirac operator, and obtain the topological charge of each configuration, for eight ensembles with pion masses in the range 220-550 MeV. From the topological charge, we compute the topological susceptibility and the second normalized cumulant. Our result of the topological susceptibility agrees with the sea-quark mass dependence predicted by the chiral perturbation theory and provides a determination of the chiral condensate, ΣMŜ(2 GeV)=[259(6)(7) MeV]3, and the pion decay constant Fπ=92(12)(2) MeV. © 2011 Elsevier B.V.

Chen H.-Y.,Academia Sinica, Taiwan | Chen H.-Y.,National Taiwan University | Yeh S.-C.,Academia Sinica, Taiwan | Chen C.-T.,National Taiwan University | Chen C.-T.,Academia Sinica, Taiwan
Journal of Materials Chemistry | Year: 2012

We report a detailed comparison of absorption spectroscopy, electrochemistry, DFT calculations, field-effect charge mobility, as well as organic photovoltaic characteristics between thiophene- and selenophene-bridged donor-acceptor low-band-gap copolymers. In these copolymers, a significant reduction of the band-gap energy was observed for selenophene-bridged copolymers by UV-visible absorption spectroscopy and cyclic voltammetry. Field-effect charge mobility studies reveal that the enhanced hole mobility of the selenophene-bridged copolymers hinges on the solubilising alkyl side chain of the copolymers. Both cyclic voltammetry experiments and theoretical calculations showed that the decreased band-gap energy is mainly due to the lowering of the LUMO energy level, and the raising of the HOMO energy level is just a secondary cause. These results are reflected in a significant increase of the short circuit current density (J SC) but a slight decrease of the open circuit voltage (V OC) of their bulk-heterojunction organic photovoltaics (BHJ OPVs), of which the electron donor materials are a selenophene-bridged donor-acceptor copolymer: poly{9-dodecyl-9H-carbazole-alt-5, 6-bis(dodecyloxy)-4,7-di(selenophen-2-yl) benzo[c][1,2,5]-thiadiazole} (pCzSe) or poly{4,8-bis(2-ethylhexyloxy)benzo[1,2-b;4,5-b′]dithiophene-alt-5,6- bis(dodecyloxy)-4,7-di(selenophen-2-yl)benzo[c][1,2,5]-thiadiazole} (pBDTSe), or a thiophene-bridged donor-acceptor copolymer: poly{9-dodecyl-9H-carbazole-alt- 5,6-bis(dodecyloxy)-4,7-di(thiophen-2-yl)benzo[c][1,2,5]-thiadiazole} (pCzS) or poly{4,8-bis(2-ethylhexyloxy)benzo[1,2-b;4,5-b′]dithiophene-alt-5, 6-bis(dodecyloxy)-4,7-di(thiophen-2-yl)benzo[c][1,2,5]-thiadiazole} (pBDTS); the electron acceptor material is [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). Judging from our device data, the potential Se-Se interactions of the selenophene-bridged donor-acceptor copolymers, which is presumably beneficial for the fill factor (FF) of BHJ OPVs, is rather susceptible to the device fabrication conditions. © 2012 The Royal Society of Chemistry.

Liao H.-C.,National Taiwan University | Jao M.-H.,National Taiwan University | Shyue J.-J.,Academia Sinica, Taiwan | Chen Y.-F.,National Taiwan University | Su W.-F.,National Taiwan University
Journal of Materials Chemistry A | Year: 2013

The present research demonstrates a facile one-pot heating process without injection to synthesize an important light harvesting quaternary nanocrystal: wurtzite copper-zinc-tin sulfide (w-CZTS). High quality w-CZTS nanocrystals can be easily obtained by mixing all the precursors and simply heating to the reaction temperature. The nano-crystal formation mechanism is thoroughly investigated and resolved by X-ray diffraction spectroscopy (XRD), transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS). It starts with the nucleation of plasmonic djurleite Cu1.94S, subsequent growth of CZTS-Cu1.94S heterostructures and inter-diffusion of cations and then finally leads to single phase and single crystal w-CZTS nanocrystals. The mechanism of nanocrystal formation can be applied universally regardless of the type of zinc and tin precursor for high quality w-CZTS nanocrystals. The in-depth interpretations of the reaction mechanism of this process significantly advance the current knowledge of multi-component nanocrystal formation. The developed method is scalable for high throughput and low cost w-CZTS suspensions which await practical photovoltaic applications. © 2013 The Royal Society of Chemistry.

Hsu S.-H.,Academia Sinica, Taiwan | Hsu S.-H.,National Taiwan University | Hung S.-F.,Academia Sinica, Taiwan | Chien S.-H.,Academia Sinica, Taiwan | Chien S.-H.,National Taiwan University
Journal of Power Sources | Year: 2013

Photoanodes consisting of CdS sensitized titania nanorods with ZnS passivation layer are applied for solar cells. Single crystal TiO2 nanorods have been directly grown vertically on transparent conducting glass by a facile hydrothermal method and deposited with CdS and then a ZnS layer on the TiO2 surface via a successive ionic layer adsorption and reaction (SILAR) method. The properties of ZnS/CdS/TiNR are characterized by XRD, SEM, TEM, UV-Vis, XPS, and electrochemical analysis. The effect of ZnS amount is studied in this system. Electrochemical results indicate the photocurrent density (Jsc) is greatly improved by increasing amount of ZnS. The incident photo-to-current conversion efficiency (IPCE), open-circuit voltage-decay (OCVD) method, and electrochemical impedance spectra (EIS) obviously substantiate these results. By optimizing the length of titania nanorods and the amount of CdS and ZnS, the best efficiency of 1.8% was achieved for solar cell under AM 1.5 G illumination with Jsc = 4.19 mA cm-2, Voc = 0.82 V and FF = 54%. © 2013 Elsevier B.V. All rights reserved.

Chen L.-L.,Academia Sinica, Taiwan | Chung W.-C.,Academia Sinica, Taiwan | Lin C.-P.,National Taiwan University | Kuo C.-H.,Academia Sinica, Taiwan
PLoS ONE | Year: 2012

Phytoplasmas and mycoplasmas are two groups of important pathogens in the bacterial class Mollicutes. Because of their economical and clinical importance, these obligate pathogens have attracted much research attention. However, difficulties involved in the empirical study of these bacteria, particularly the fact that phytoplasmas have not yet been successfully cultivated outside of their hosts despite decades of attempts, have greatly hampered research progress. With the rapid advancements in genome sequencing, comparative genome analysis provides a new approach to facilitate our understanding of these bacteria. In this study, our main focus is to investigate the evolution of gene content in phytoplasmas, mycoplasmas, and their common ancestor. By using a phylogenetic framework for comparative analysis of 12 complete genome sequences, we characterized the putative gains and losses of genes in these obligate parasites. Our results demonstrated that the degradation of metabolic capacities in these bacteria has occurred predominantly in the common ancestor of Mollicutes, prior to the evolutionary split of phytoplasmas and mycoplasmas. Furthermore, we identified a list of genes that are acquired by the common ancestor of phytoplasmas and are conserved across all strains with complete genome sequences available. These genes include several putative effectors for the interactions with hosts and may be good candidates for future functional characterization. © 2012 Chen et al.

Chen C.K.-M.,Academia Sinica, Taiwan | Chan N.-L.,National Taiwan University | Wang A.H.-J.,Academia Sinica, Taiwan
Trends in Biochemical Sciences | Year: 2011

The β-propeller is a highly symmetrical structure with 4-10 repeats of a four-stranded antiparallel β-sheet motif. Although β-propeller proteins with different blade numbers all adopt disc-like shapes, they are involved in a diverse set of functions, and defects in this family of proteins have been associated with human diseases. However, it has remained ambiguous how variations in blade number could alter the function of β-propellers. In addition to the regularly arranged β-propeller topology, a recently discovered β-pinwheel propeller has been found. Here, we review the structural and functional diversity of β-propeller proteins, including β-pinwheels, as well as recent advances in the typical and atypical propeller structures. © 2011 Elsevier Ltd.

Lee S.,Academia Sinica, Taiwan | Lee S.,National Taiwan University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2010

We investigate a spherical collapse model with and without the spatial curvature. We obtain the exact solutions of dynamical quantities such as the ratio of the scale factor to its value at the turnaround epoch and the ratio of the overdensity radius to its value at the turnaround time with general cosmological parameters. The exact solutions of the overdensity at the turnaround epoch for the different models are also obtained. Thus, we are able to obtain the nonlinear overdensity at any epoch for the given model. We obtain that the nonlinear overdensity of the Einstein de Sitter (EdS) universe at the virial epoch is 18 π2 (frac(1, 2 π) + frac(3, 4))2 ≃ 147 instead of the well-known value 18 π2 ≃ 178. In the open universe, perturbations are virialized earlier than in the flat one and thus clusters are denser at the virial epoch. Also the critical density threshold of EdS universe from the linear theory at the virialized epoch is obtained as frac(3, 20) (9 π + 6)frac(2, 3) ≃ 1.58 instead of frac(3, 20) (12 π)frac(2, 3) ≃ 1.69. This value is same for the close and the open universes. We find that the observed quantities at high redshifts are less sensitive between different models. Even though the low redshift cluster shows the stronger model dependence than high redshift one, the differences between models might be still too small to be distinguished by observations if the curvature is small. From these analytic forms of dynamical quantities, we are able to estimate the abundances of both virialized and non-virialized clusters and the temperature and luminosity functions at any epoch. The current concordance model prefers the almost flat universe and thus the above results might be restricted by the academic interests only. However, the mathematical structure of the evolution equations of physical quantities for the curved space is identical with that for the flat universe including the dark energy with the equation of state ωde = - frac(1, 3). Thus, we might be able to extend these analytic solutions to the general dark energy model and they will provide the useful tools for probing the properties of dark energy. © 2010 Elsevier B.V. All rights reserved.

Chen C.-Y.,National Taiwan University | Chen C.-Y.,Academia Sinica, Taiwan | Chen S.-T.,Academia Sinica, Taiwan | Juan H.-F.,National Taiwan University | Huang H.-C.,National Yang Ming University
Bioinformatics | Year: 2012

Motivation: Evolutionary expansion of gene regulatory circuits seems to boost morphological complexity. However, the expansion patterns and the quantification relationships have not yet been identified. In this study, we focus on the regulatory circuits at the post-transcriptional level, investigating whether and how this principle may apply. Results: By analysing the structure of mRNA transcripts in multiple metazoan species, we observed a striking exponential correlation between the length of 30 untranslated regions (30UTR) and morphological complexity as measured by the number of cell types in each organism. Cellular diversity was similarly associated with the accumulation of microRNA genes and their putative targets. We propose that the lengthening of 30UTRs together with a commensurate exponential expansion in post-transcriptional regulatory circuits can contribute to the emergence of new cell types during animal evolution. © 2012 The Author.

Krasnopolsky R.,Academia Sinica, Taiwan | Li Z.-Y.,University of Virginia | Shang H.,Academia Sinica, Taiwan | Zhao B.,University of Virginia
Astrophysical Journal | Year: 2012

Magnetic flux redistribution lies at the heart of the problem of star formation in dense cores of molecular clouds that are magnetized to a realistic level. If all of the magnetic flux of a typical core were to be dragged into the central star, the stellar field strength would be orders of magnitude higher than the observed values. This well-known magnetic flux problem can in principle be resolved through non-ideal MHD effects. Two-dimensional (axisymmetric) calculations have shown that ambipolar diffusion, in particular, can transport magnetic flux outward relative to matter, allowing material to enter the central object without dragging the field lines along. We show through simulations that such axisymmetric protostellar accretion flows are unstable in three dimensions to magnetic interchange instability in the azimuthal direction. The instability is driven by the magnetic flux redistributed from the matter that enters the central object. It typically starts to develop during the transition from the prestellar phase of star formation to the protostellar mass accretion phase. In the latter phase, the magnetic flux is transported outward mainly through advection by strongly magnetized low-density regions that expand against the collapsing inflow. The tussle between the gravity-driven infall and magnetically driven expansion leads to a highly filamentary inner accretion flow that is more disordered than previously envisioned. The efficient outward transport of magnetic flux by advection lowers the field strength at small radii, making the magnetic braking less efficient and the formation of rotationally supported disks easier in principle. However, we find no evidence for such disks in any of our rotating collapse simulations. We conclude that the inner protostellar accretion flow is shaped to a large extent by the flux redistribution-driven magnetic interchange instability. How disks form in such an environment is unclear. © 2012. The American Astronomical Society. All rights reserved.

Jian H.-Y.,National Taiwan University | Lin L.,Academia Sinica, Taiwan | Chiueh T.,National Taiwan University
Astrophysical Journal | Year: 2012

We make use of four galaxy catalogs based on four different semi-analytical models (SAMs) implemented in the Millennium Simulation to study the environmental effects and the model dependence of the galaxy merger rate. We begin the analyses by finding that the galaxy merger rate in SAMs has a mild redshift evolution with luminosity-selected samples in the evolution-corrected B-band magnitude range,-21 ≤ Me B ≤ -19, consistent with the results of previous works. To study the environmental dependence of the galaxy merger rate, we adopt two estimators, the local overdensity (1 + δn), defined as the surface density from the nth nearest neighbor (n = 6 is chosen in this study), and the host halo mass Mh . We find that the galaxy merger rate F mg shows a strong dependence on the local overdensity (1 + δn) and the dependence is similar at all redshifts. For the overdensity estimator, the merger rate F mg is found to be about twenty times larger in the densest regions than in underdense ones in two of the four SAMs, while it is roughly four times higher in the other two. In other words, the discrepancies of the merger rate difference between the two extremes can differ by a factor of ∼5 depending on the SAMs adopted. On the other hand, for the halo mass estimator, F mg does not monotonically increase with the host halo mass M h but peaks in the Mh range between 1012 and 1013 h -1 M⊙, which corresponds to group environments. The high merger rate in high local density regions corresponds primarily to the high merger rate in group environments. In addition, we also study the merger probability of "close pairs" identified using the projected separation and the line-of-sight velocity difference C mg and the merger timescale T mg; these are two important quantities for observations to convert the pair fraction Nc into the galaxy merger rate. We discover that T mg has a weak dependence on environment and different SAMs, and is about 2Gyr old at z ∼ 1. In contrast, C mg depends on both environment (declining with density) and different SAMs; its environmental dependence is primarily due to the projection effect. At z ∼ 1, it is found that only ∼ 31% of projected close pairs will eventually merge by z = 0. We find that the projection effect is the dominant factor in accounting for the low merger probability of projected close pairs. © 2012. The American Astronomical Society. All rights reserved.

Fan X.,Jilin University | Zheng W.T.,Jilin University | Kuo J.-L.,Academia Sinica, Taiwan
RSC Advances | Year: 2013

With first-principle DFT calculations, the catalytic activity of heteroatom-doped carbon nanostructures in oxygen reduction reaction is investigated by exploring the active site of B-doped, N-doped and (B, N)-codoped and analyzing the kinetic pathways of oxygen reduction with the participation of protons. It is found that the heteroatom-doped graphene can become the effective catalysis materials for ORR with four-electron pathway. Especially, the formation of epoxide groups may be important for the four-electron processes on B-doped and (B, N)-codoped graphene. By the analysis of charge redistribution, the formation of active catalytic sites is attributed to the localized positive charge and electronic dipole induced by the dopant. © 2013 The Royal Society of Chemistry.

Chou C.,Academia Sinica, Taiwan | Chou C.,National Taiwan University | Chiang J.C.H.,University of California at Berkeley | Lan C.-W.,Civil Aeronautics Administration | And 3 more authors.
Nature Geoscience | Year: 2013

Global temperatures have risen over the past few decades. The water vapour content of the atmosphere has increased as a result, strengthening the global hydrological cycle. This, in turn, has led to wet regions getting wetter, and dry regions drier. Climate model simulations suggest that a similar intensification of existing patterns may also apply to the seasonal cycle of rainfall. Here, we analyse regional and global trends in seasonal precipitation extremes over the past three decades, using a number of global and land-alone observational data sets. We show that globally the annual range of precipitation has increased, largely because wet seasons have become wetter. Although the magnitude of the shift is uncertain, largely owing to limitations inherent in the data sets used, the sign of the tendency is robust. On a regional scale, the tendency for wet seasons to get wetter occurs over climatologically rainier regions. Similarly, the tendency for dry season to get drier is seen in drier regions. Even if the total amount of annual rainfall does not change significantly, the enhancement in the seasonal precipitation cycle could have marked consequences for the frequency of droughts and floods. © 2013 Macmillan Publishers Limited. All rights reserved.

Liu M.-C.,Academia Sinica, Taiwan | Chaussidon M.,French National Center for Scientific Research | Srinivasan G.,Indian Institute of Science | McKeegan K.D.,University of California at Los Angeles
Astrophysical Journal | Year: 2012

The short-lived radionuclide 41Ca plays an important role in constraining the immediate astrophysical environment and the formation timescale of the nascent solar system due to its extremely short half-life (0.1 Myr). Nearly 20 years ago, the initial ratio of 41Ca/40Ca in the solar system was determined to be (1.41 ± 0.14) × 10-8, primarily based on two Ca-Al-rich Inclusions (CAIs) from the CV chondrite Efremovka. With an advanced analytical technique for isotopic measurements, we reanalyzed the potassium isotopic compositions of the two Efremovka CAIs and inferred the initial ratios of 41Ca/40Ca to be (2.6 ± 0.9) × 10-9 and (1.4 ± 0.6) × 10 -9 (2σ), a factor of 7-10 lower than the previously inferred value. Considering possible thermal processing that led to lower 26Al/27Al ratios in the two CAIs, we propose that the true solar system initial value of 41Ca/40Ca should have been ∼4.2 × 10-9. Synchronicity could have existed between 26Al and 41Ca, indicating a uniform distribution of the two radionuclides at the time of CAI formation. The new initial 41Ca abundance is 4-16 times lower than the calculated value for steady-state galactic nucleosynthesis. Therefore, 41Ca could have originated as part of molecular cloud materials with a free decay time of 0.2-0.4 Myr. Alternative possibilities, such as a last-minute input from a stellar source and early solar system irradiation, could not be definitively ruled out. This underscores the need for more data from diverse CAIs to determine the true astrophysical origin of 41Ca. © 2012. The American Astronomical Society. All rights reserved..

Tu J.-Y.,Chinese Culture University | Chou C.,Academia Sinica, Taiwan | Chou C.,National Taiwan University
Environmental Research Letters | Year: 2013

The hourly rainfall at 21 ground stations in Taiwan is used to investigate changes in the frequency, intensity, and duration of rainfall, which can be divided into typhoon and non-typhoon rainfall, in the period of 1970-2010. As a whole, the frequency of rainfall shows a decreasing trend for lighter rain and an increasing trend for heavier rain. Also, the typhoon rainfall shows a significant increase for all intensities, while the non-typhoon rainfall exhibits a general trend of decreasing, particularly for lighter rain. In rainfall intensity, both typhoon and non-typhoon rainfall extremes become more intense, with an increased rate much greater than the Clausius-Clapeyron thermal scaling. Moreover, rainfall extremes associated with typhoons have tended to affect Taiwan rainfall for longer in recent decades. The more frequent, intense and long-lasting typhoon rainfall is mainly induced by the slower translation speed of the typhoons over the neighborhood of Taiwan, which could be associated with a weakening of steering flow in the western North Pacific and the northern South China Sea. © 2013 IOP Publishing Ltd.

Chen J.-M.,National Taiwan University | Chen M.-C.,Academia Sinica, Taiwan | Sun Y.S.,National Taiwan University
Computers and Education | Year: 2010

For students of English as a Foreign Language (EFL), reading exercises are critical not only for developing strong reading comprehension, but also for developing listening, speaking, and writing skills. Prior research suggests that social, collaborative learning environments are best suited for improving language ability. However, opportunities for English learners to collaboratively practice reading comprehension are minimal, and due to resource constraints and a lack of accurate evaluation methods, English instructors rarely assess student literacy effectively. In response to these problems, we propose a Tag-based Collaborative reading learning System (TACO) that makes use of Web 2.0 Internet social tagging techniques to provide a collaborative environment for reading English. We test our system's ability to both improve reading comprehension and aid teachers in accurately assessing literacy by conducting a three-month trial with 56 participating Taiwanese high school students from February to May 2009. During this period, post-testing results show a significant improvement in reading scores among participants in our tag-based system, and survey feedback from teachers suggests an improved capacity for literacy assessment. © 2010 Elsevier Ltd. All rights reserved.

Fan X.,Jilin University | Fan X.,Nanyang Technological University | Shen Z.,Nanyang Technological University | Liu A.Q.,Nanyang Technological University | Kuo J.-L.,Academia Sinica, Taiwan
Nanoscale | Year: 2012

Boron nitride (BN) domains are easily formed in the basal plane of graphene due to phase separation. With first-principles calculations, it is demonstrated theoretically that the band gap of graphene can be opened effectively around K (or K′) points by introducing small BN domains. It is also found that random doping with boron or nitrogen is possible to open a small gap in the Dirac points, except for the modulation of the Fermi level. The surface charges which belong to the π states near Dirac points are found to be redistributed locally. The charge redistribution is attributed to the change of localized potential due to doping effects. The band opening induced by the doped BN domain is found to be due to the breaking of localized symmetry of the potential. Therefore, doping graphene with BN domains is an effective method to open a band gap for carbon-based next-generation microelectronic devices. This journal is © The Royal Society of Chemistry 2012.

Chou C.,National Taiwan University | Hsueh Y.-C.,Academia Sinica, Taiwan
Journal of Climate | Year: 2010

Mechanisms of northward-propagating intraseasonal oscillations (ISOs) over the Indian Ocean (IO) and the western North Pacific (WNP) are examined for the possibility of their existence in observations. They include the following: 1) the vorticity advection effect, which is associated with the advection of anomalous baroclinic vorticity by mean baroclinic meridional winds; 2) the vertical wind shear effect, which is the vertical advection associated with the meridional gradient of baroclinic divergence and mean easterly vertical wind shear; 3) the moisture advection effect induced by mean flow; and 4) the air-sea interaction via surface latent heat flux. Because of differences in mean state, the influence of each mechanism on the northward-propagating ISOs is different between the IO and the WNP. The vorticity advection effect is consistently found over both the IO and the WNP, while the air-sea interaction has different impacts on the northward-propagating ISOs over the IO and the WNP. The vertical wind shear effect and the moisture advection effect are relatively important over the IO but not over the WNP. Processes to determine changes in SST are also different between the IO and the WNP. Over the IO, SST is mainly associated with surface solar radiation. Wind-stirring effects, surface latent heat flux, and subsurface water entrainment are secondary. Over the WNP, wind-stirring effects become important, but surface solar radiation is secondary. © 2010 American Meteorological Society.

Lee K.-L.,Academia Sinica, Taiwan | Chen P.-W.,National Taiwan Ocean University | Wu S.-H.,National Yang Ming University | Huang J.-B.,National Taiwan Ocean University | And 4 more authors.
ACS Nano | Year: 2012

Nanostructure-based sensors are capable of sensitive and label-free detection for biomedical applications. However, high-throughput and low-cost fabrication techniques are the main issues which should be addressed. In this study, chip-based nanostructures for intensity-sensitive detection were fabricated and tested using a thermal-annealing-assisted template-stripping method. Large-area uniform nanoslit arrays with a 500 nm period and various slit widths, from 30 to 165 nm, were made on plastic films. A transverse magnetic-polarized wave in these gold nanostructures generated sharp and asymmetric Fano resonances in transmission spectra. The full width at half-maximum bandwidth decreased with the decrease of the slit width. The narrowest bandwidth was smaller than 10 nm. Compared to nanoslit arrays on glass substrates using electron-beam lithography, the proposed chip has a higher intensity sensitivity up to 10367%/RIU (refractive index unit) and reaches a figure of merit up to 55. The higher intensity sensitivity for the template-stripped nanostructure is attributed to a smoother gold surface and larger grain sizes on the plastic film, which reduces the surface plasmon propagation loss. © 2012 American Chemical Society.

Chen S.H.,Duke University | Chan N.-L.,National Taiwan University | Hsieh T.-S.,Duke University | Hsieh T.-S.,Academia Sinica, Taiwan
Annual Review of Biochemistry | Year: 2013

DNA topoisomerases are nature's tools for resolving the unique problems of DNA entanglement that occur owing to unwinding and rewinding of the DNA helix during replication, transcription, recombination, repair, and chromatin remodeling. These enzymes perform topological transformations by providing a transient DNA break, formed by a covalent adduct with the enzyme, through which strand passage can occur. The active site tyrosine is responsible for initiating two transesterifications to cleave and then religate the DNA backbone. The cleavage reaction intermediate is exploited by cytotoxic agents, which have important applications as antibiotics and anticancer drugs. The reactions mediated by these enzymes can also be regulated by their binding partners; one example is a DNA helicase capable of modulating the directionality of strand passage, enabling important functions like reannealing denatured DNA and resolving recombination intermediates. In this review, we cover recent advances in mechanistic insights into topoisomerases and their various cellular functions. © 2013 by Annual Reviews. All rights reserved.

Fong C.S.,Sloan Kettering Cancer Center | Kim M.,Sloan Kettering Cancer Center | Kim M.,Cornell University | Yang T.T.,Academia Sinica, Taiwan | And 3 more authors.
Developmental Cell | Year: 2014

Centrioles are 9-fold symmetric structures duplicating once per cell cycle. Duplication involves self-oligomerization of the centriolar protein SAS-6, but how the 9-fold symmetry is invariantly established remains unclear. Here, we found that SAS-6 assembly can be shaped by preexisting (or mother) centrioles. During S phase, SAS-6 molecules are first recruited to the proximal lumen of the mother centriole, adopting a cartwheel-like organization through interactions with the luminal wall, rather than via their self-oligomerization activity. The removal or release of luminal SAS-6 requires Plk4 and the cartwheel protein STIL. Abolishing either the recruitment or the removal of luminal SAS-6 hinders SAS-6 (or centriole) assembly at the outside wall of mother centrioles. After duplication, the lumen of engaged mother centrioles becomes inaccessible to SAS-6, correlating with a block for reduplication. These results lead to a proposed model that centrioles may duplicate via a template-based process to preserve their geometry and copy number. © 2014 Elsevier Inc.

Wang J.-C.,National Taiwan University | Chu P.-Y.,Academia Sinica, Taiwan | Chen C.-M.,National Taiwan University | Lin J.-H.,Academia Sinica, Taiwan | Lin J.-H.,National Taiwan University
Nucleic Acids Research | Year: 2012

Identification of possible protein targets of small chemical molecules is an important step for unravelling their underlying causes of actions at the molecular level. To this end, we construct a web server, idTarget, which can predict possible binding targets of a small chemical molecule via a divide-and-conquer docking approach, in combination with our recently developed scoring functions based on robust regression analysis and quantum chemical charge models. Affinity profiles of the protein targets are used to provide the confidence levels of prediction. The divide-and-conquer docking approach uses adaptively constructed small overlapping grids to constrain the searching space, thereby achieving better docking efficiency. Unlike previous approaches that screen against a specific class of targets or a limited number of targets, idTarget screen against nearly all protein structures deposited in the Protein Data Bank (PDB). We show that idTarget is able to reproduce known off-targets of drugs or drug-like compounds, and the suggested new targets could be prioritized for further investigation. idTarget is freely available as a web-based server at © 2012 The Author(s).

Wei X.,University of California at Los Angeles | Li K.-C.,University of California at Los Angeles | Li K.-C.,Academia Sinica, Taiwan
Proceedings of the National Academy of Sciences of the United States of America | Year: 2010

To many biomedical researchers, effective tumor classification methods such as the support vector machine often appear like a black box not only because the procedures are complex but also because the required specifications, such as the choice of a kernel function, suffer from a clear guidance either mathematically or biologically. As commonly observed, samples within the same tumor class tend to be more similar in gene expression than samples from different tumor classes. But can this well-received observation lead to a useful procedure of classification and prediction? To address this issue, we first conceived a statistical framework and derived general conditions to serve as the theoretical foundation that supported the aforementioned empirical observation. Then we constructed a classification procedure that fully utilized the information obtained by comparing the distributions of within-class correlations with between-class correlations via Kullback-Leibler divergence. We compared our approach with many machine-learning techniques by applying to 22 binary- and multiclass gene-expression datasets involving human cancers. The results showed that our method performed as efficiently as support vector machine and Naïve Bayesian and outperformed other learning methods (decision trees, linear discriminate analysis, and k-nearest neighbor). In addition, we conducted a simulation study and showed that our method would be more effective if the arriving new samples are subject to the often-encountered baseline shift or increased noise level problems. Our method can be extended for general classification problems when only the similarity scores between samples are available.

Boyle E.,Cornell University | Chung K.-M.,Academia Sinica, Taiwan | Pass R.,Cornell University
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2014

We initiate the study of extractability obfuscation, a notion first suggested by Barak et al. (JACM 2012): An extractability obfuscator for a class of algorithms guarantees that if an efficient attacker can distinguish between obfuscations of two algorithms, then can efficiently recover (given M 1 and M 2) an input on which M 1 and M 2 provide different outputs. We rely on the recent candidate virtual black-box obfuscation constructions to provide candidate constructions of extractability obfuscators for NC 1; next, following the blueprint of Garg et al. (FOCS 2013), we show how to bootstrap the obfuscator for NC 1 to an obfuscator for all non-uniform polynomial-time Turing machines. In contrast to the construction of Garg et al., which relies on indistinguishability obfuscation for NC 1, our construction enables succinctly obfuscating non-uniform Turing machines (as opposed to circuits), without turning running-time into description size. We introduce a new notion of functional witness encryption, which enables encrypting a message m with respect to an instance x, language L, and function f, such that anyone (and only those) who holds a witness w for x â̂̂ L can compute f(m,w) on the message and particular known witness. We show that functional witness encryption is, in fact, equivalent to extractability obfuscation. We demonstrate other applications of extractability extraction, including the first construction of fully (adaptive-message) indistinguishability-secure functional encryption for an unbounded number of key queries and unbounded message spaces. We finally relate indistinguishability obfuscation and extractability obfuscation and show special cases when indistinguishability obfuscation can be turned into extractability obfuscation. © 2014 International Association for Cryptologic Research.

Lin Y.-C.,National Taiwan University | Huang D.-Y.,National Taiwan University | Chu C.-L.,National Taiwan University | Lin Y.-L.,Academia Sinica, Taiwan | And 2 more authors.
Science Signaling | Year: 2013

Toll-like receptors (TLRs) are a major family of pattern recognition receptors, and they play a crucial role in innate immune responses. Activation of TLR4 signaling at the plasma membrane by its ligand lipopolysaccharide (LPS) stimulates a proinflammatory pathway dependent on the E3 ubiquitin ligase TRAF6 (tumor necrosis factor receptor-associated factor 6) and the kinase TAK1 (transforming growth factor β-activated kinase 1), whereas TLR4 signaling at endosomes stimulates the production of type I interferons (IFNs) through a pathway that depends on TRAF3 and the kinase TBK1 (TANK-binding kinase-1). We found that the nonreceptor tyrosine kinase Syk partially mediated the endocytosis of TLR4, but it also played a dual role in TLR4-mediated signaling. LPS-dependent stimulation of TLR4 in Syk-deficient macrophages led to enhanced activation of TAK1 and increased production of proinflammatory cytokines compared to that in wild-type macrophages. In contrast, Syk-deficient macrophages exhibited decreased TLR4-dependent activation of TBK1 signaling and production of type I IFNs. We found that Syk was present in both TRAF6-and TRAF3-containing signaling complexes; however, the LPS-dependent, lysine 63-linked ubiquitination of TRAF6 and TRAF3 was oppositely regulated by Syk. We identified the domains of Syk that interacted with TRAF3, TRAF6, TAK1, and TBK1, factors activated by multiple TLRs, which suggests that Syk may act as a common regulator of various TLR responses. Together, our results demonstrate the opposing regulatory roles of Syk in TLR-mediated TRAF6 and TRAF3 signaling pathways, which suggests that Syk may fine-tune the innate immune response to lessen inflammation. Copyright © 2008 by the American Association for the Advancement of Science.

Li Z.-Y.,University of Virginia | Li Z.-Y.,Academia Sinica, Taiwan | Krasnopolsky R.,Academia Sinica, Taiwan | Shang H.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2013

Stars form in dense cores of molecular clouds that are observed to be significantly magnetized. In the simplest case of a laminar (non-turbulent) core with the magnetic field aligned with the rotation axis, both analytic considerations and numerical simulations have shown that the formation of a large, 102 AU scale, rotationally supported protostellar disk is suppressed by magnetic braking in the ideal MHD limit for a realistic level of core magnetization. This theoretical difficulty in forming protostellar disks is termed the "magnetic braking catastrophe." A possible resolution to this problem, proposed by Hennebelle & Ciardi and Joos et al., is that misalignment between the magnetic field and rotation axis may weaken the magnetic braking enough to enable disk formation. We evaluate this possibility quantitatively through numerical simulations. We confirm the basic result of Joos et al. that the misalignment is indeed conducive to disk formation. In relatively weakly magnetized cores with dimensionless mass-to-flux ratio ≳ 4, it enabled the formation of rotationally supported disks that would otherwise be suppressed if the magnetic field and rotation axis are aligned. For more strongly magnetized cores, disk formation remains suppressed, however, even for the maximum tilt angle of 90°. If dense cores are as strongly magnetized as indicated by OH Zeeman observations (with a mean dimensionless mass-to-flux ratio ∼2), it would be difficult for the misalignment alone to enable disk formation in the majority of them. We conclude that, while beneficial to disk formation, especially for the relatively weak field case, misalignment does not completely solve the problem of catastrophic magnetic braking in general. © 2013. The American Astronomical Society. All rights reserved.

Nakamura F.,Japan National Astronomical Observatory | Takakuwa S.,Academia Sinica, Taiwan | Kawabe R.,Japan National Astronomical Observatory
Astrophysical Journal Letters | Year: 2012

We present combined Submillimeter Array and single-dish images of the (sub)millimeter dust continuum emission toward two prestellar cores, SM1 and B2-N5, in the nearest star-cluster-forming region, ρ Ophiuchus. Our combined images indicate that SM1 and B2-N5 consist of three and four condensations, respectively, with masses of 10-2-10-1 M⊙ and sizes of a few hundred AU. The individual condensations have mean densities of 108-109cm-3 and the masses are comparable to or larger than the critical Bonner-Ebert mass, indicating that self-gravity plays an important role in the dynamical evolution of the condensations. The coalescence timescale of these condensations is estimated to be about 10 4 yr, which is comparable to the local gravitational collapse timescale, suggesting that merging of the condensations, instead of accretion, plays an essential role in the star formation process. These results challenge the standard theory of star formation, where a single, rather featureless, prestellar core collapses to form at most a couple of condensations, each of which potentially evolves into a protostar that is surrounded by a rotating disk where planets are created. © © 2012. The American Astronomical Society. All rights reserved..

Lin S.-C.,National Taiwan University | Yen P.-W.,National Taiwan University | Peng C.-C.,Academia Sinica, Taiwan | Tung Y.-C.,Academia Sinica, Taiwan
Lab on a Chip - Miniaturisation for Chemistry and Biology | Year: 2012

Flow cytometry is a technique capable of optically characterizing biological particles in a high-throughput manner. In flow cytometry, three dimensional (3D) hydrodynamic focusing is critical for accurate and consistent measurements. Due to the advantages of microfluidic techniques, a number of microfluidic flow cytometers with 3D hydrodynamic focusing have been developed in recent decades. However, the existing devices consist of multiple layers of microfluidic channels and tedious fluidic interconnections. As a result, these devices often require complicated fabrication and professional operation. Consequently, the development of a robust and reliable microfluidic flow cytometer for practical biological applications is desired. This paper develops a microfluidic device with a single channel layer and single sheath-flow inlet capable of achieving 3D hydrodynamic focusing for flow cytometry. The sheath-flow stream is introduced perpendicular to the microfluidic channel to encircle the sample flow. In this paper, the flow fields are simulated using a computational fluidic dynamic (CFD) software, and the results show that the 3D hydrodynamic focusing can be successfully formed in the designed microfluidic device under proper flow conditions. The developed device is further characterized experimentally. First, confocal microscopy is exploited to investigate the flow fields. The resultant Z-stack confocal images show the cross-sectional view of 3D hydrodynamic with flow conditions that agree with the simulated ones. Furthermore, the flow cytometric detections of fluorescence beads are performed using the developed device with various flow rate combinations. The measurement results demonstrate that the device can achieve great detection performances, which are comparable to the conventional flow cytometer. In addition, the enumeration of fluorescence-labelled cells is also performed to show its practicality for biological applications. Consequently, the microfluidic flow cytometer developed in this paper provides a practical platform that can be used for routine analysis in biological laboratories. Additionally, the 3D hydrodynamic focusing channel design can also be applied to various applications that can advance the lab on a chip research. © 2012 The Royal Society of Chemistry.

Huang Y.-H.,National Taiwan University | Huang Y.-H.,Academia Sinica, Taiwan | Hirano N.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2013

Two submm/mm sources in the Barnard 1b (B1-b) core, B1-bN and B1-bS, have been observed with the Submillimeter Array (SMA) and the Submillimeter Telescope (SMT). The 1.1 mm continuum map obtained with the SMA reveals that the two sources contain spatially compact components, suggesting that they harbor protostars. The N2D+ and N2H+ J = 3-2 maps were obtained by combining the SMA and SMT data. The N 2D+ map clearly shows two peaks at the continuum positions. The N2H+ map also peaks at the continuum positions, but is more dominated by the spatially extended component. The N 2D+/N2H+ ratio was estimated to be 0.2 at the positions of both B1-bN and B1-bS. The derived N2D +/N2H+ ratio is comparable to those of the prestellar cores in the late evolutionary stage and the class 0 protostars in the early evolutionary stage. Although B1-bN is bright in N2H + and N2D+, this source was barely seen in H13CO+. This implies that the depletion of carbon-bearing molecules is significant in B1-bN. The chemical property suggests that B1-bN is in the earlier evolutionary stage as compared to B1-bS with the H 13CO+ counterpart. The N2H+ and N2D+ lines show that the radial velocities of the two sources are different by 0.9 km s-1. However, the velocity pattern along the line through B1-bN and B1-bS suggests that these two sources were not formed out of a single rotating cloud. It is likely that the B1-b core consists of two velocity components, each of which harbors a very young source. © 2013. The American Astronomical Society. All rights reserved.

Hsieh Y.-Y.,Academia Sinica, Taiwan | Hung P.-H.,Academia Sinica, Taiwan | Hung P.-H.,National Taiwan University | Leu J.-Y.,Academia Sinica, Taiwan | Leu J.-Y.,National Taiwan University
Molecular Cell | Year: 2013

Nongenetic cell-to-cell variability often plays an important role for the survival of a clonal population in the face of fluctuating environments. However, the underlying mechanisms regulating such nongenetic heterogeneity remain elusive in most organisms. We report here that a clonal yeast population exhibits morphological heterogeneity when the level of Hsp90, a molecular chaperone, is reduced. The morphological heterogeneity is driven by the dosage of Cdc28 and Cla4, a key regulator of septin formation. Low Hsp90 levels reduce Cla4 protein stability and cause a subpopulation of cells to switch to a filamentous form that has been previously suggested to be beneficial under certain hostile environments. Moreover, Hsp90-dependent morphological heterogeneity can be induced by environmental stress and is conserved across diverse yeast species. Our results suggest that Hsp90 provides an evolutionarily conserved mechanism that links environmental stress to the induction of morphological diversity. © 2013 Elsevier Inc.

Huang H.-C.,National Taiwan University | Huang H.-C.,Academia Sinica, Taiwan | Chuang Y.-Y.,National Taiwan University | Chen C.-S.,Academia Sinica, Taiwan | Chen C.-S.,National Taiwan University
IEEE Transactions on Fuzzy Systems | Year: 2012

While fuzzy c-means is a popular soft-clustering method, its effectiveness is largely limited to spherical clusters. By applying kernel tricks, the kernel fuzzy c-means algorithm attempts to address this problem by mapping data with nonlinear relationships to appropriate feature spaces. Kernel combination, or selection, is crucial for effective kernel clustering. Unfortunately, for most applications, it is uneasy to find the right combination. We propose a multiple kernel fuzzy c-means (MKFC) algorithm that extends the fuzzy c-means algorithm with a multiple kernel-learning setting. By incorporating multiple kernels and automatically adjusting the kernel weights, MKFC is more immune to ineffective kernels and irrelevant features. This makes the choice of kernels less crucial. In addition, we show multiple kernel k-means to be a special case of MKFC. Experiments on both synthetic and real-world data demonstrate the effectiveness of the proposed MKFC algorithm. © 2012 IEEE.

Krasnopolsky R.,Academia Sinica, Taiwan | Li Z.-Y.,Academia Sinica, Taiwan | Li Z.-Y.,University of Virginia | Shang H.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2010

Disk formation in magnetized cloud cores is hindered by magnetic braking. Previous work has shown that for realistic levels of core magnetization, the magnetic field suppresses the formation of rotationally supported disks during the protostellar mass accretion phase of low-mass star formation both in the ideal MHD limit and in the presence of ambipolar diffusion for typical rates of cosmic-ray ionization. Additional effects, such as ohmic dissipation, the Hall effect, and protostellar outflow, are needed to weaken the magnetic braking and enable the formation of persistent, rotationally supported, protostellar disks. In this paper, we first demonstrate that the classic microscopic resistivity is not large enough to enable disk formation by itself. We then experiment with a set of enhanced values for the resistivity in the range η = 10 17-1022 cm2 s-1. We find that a value of order 1019 cm2 s-1 is needed to enable the formation of a 102 AU scale Keplerian disk; the value depends somewhat on the degree of core magnetization. The required resistivity is a few orders of magnitude larger than the classic microscopic values. Whether it can be achieved naturally during protostellar collapse remains to be determined. © 2010. The American Astronomical Society. All rights reserved.

Liu H.-C.,National Taiwan University | Charng Y.-Y.,Academia Sinica, Taiwan
Plant Signaling and Behavior | Year: 2012

The heat stress (HS) response in eukaryotes is mainly regulated by heat shock factors (HSFs). Genetic disruption of the master HSF gene leads to dramatically reduced HS response and thermo tolerance in several model organisms. However, it is not clear whether organisms devoid of the master regulator can still acclimate to heat. Previously, we showed that Arabidopsis HsfA1a, HsfA1b, and HsfA1d act as master regulators in the HS response. In this study, we examined the heat acclimation capacity of the Arabidopsis quadruple and triple T-DNA knockout mutants of HsfA1a, HsfA1b, HsfA1d, and HsfA1e. Our data showed that in the absence of the master regulators, a minimal but significant level of acquired thermo tolerance could be attained in the Arabidopsis mutants after acclimation. The optimum acclimation temperature for the HsfA1 quadruple mutant was lower than that for the wild type plants, suggesting that plant cells have two HSsensing mechanisms that can be distinguished genetically. The acquired thermo tolerance of the quadruple mutant was likely due to the induction of a small number of HsfA1-independent HS response genes regulated by other transcription factors. Here, we discuss the possible candidates and propose a working model of the transcription network of the HS response by including the HsfA1-dependent and -independent pathways. © 2012 Landes Bioscience.

Shih Y.-L.,Academia Sinica, Taiwan | Shih Y.-L.,National Taiwan University | Zheng M.,Academia Sinica, Taiwan
Environmental Microbiology | Year: 2013

The Min system of Escherichia coli is involved in mediating placement of the cell division site at the midcell; this is accomplished through partitioning of the cell division inhibitor MinC to the cell poles to block aberrant polar division. The partitioning of MinC is achieved through its interaction with MinDE, which alternates its cellular distribution periodically between opposite cell poles throughout the cell cycle. This dynamic oscillation is the result of intricate molecular interactions occurring between the three Min proteins on the membrane in a spatiotemporal manner. In this minireview, we discuss recent developments in understanding the molecular mechanisms of the E. coliMin system from cellular, biochemical and biophysical perspectives. In addition, we propose a model that involves the balancing of different molecular interactions at different stages of the oscillation cycle. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Wang Y.-C.,National Taiwan University | Wang D.-Y.,National Taiwan University | Jiang Y.-T.,National Taiwan Normal University | Chen H.-A.,National Taiwan University | And 5 more authors.
Angewandte Chemie - International Edition | Year: 2013

Calligraphic counter electrodes: An important photovoltaic application using FeS2 nanocrystal (NC) pyrite ink to fabricate a counter electrode as an alternative to Pt in dye-sensitized solar cells is demonstrated. FeS2 NC ink exhibits excellent electrochemical catalytic activity and remarkable electrochemical stability. ITO=indium-doped tin oxide. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chiu H.-Y.,National Taiwan University | Chung S.-L.,National Taiwan University | Zarrinkoub M.H.,Birjand University | Mohammadi S.S.,Birjand University | And 2 more authors.
Lithos | Year: 2013

This study reports zircon LA-ICPMS U-Pb ages of 50 igneous rock samples from the Urumieh-Dokhtar magmatic arc (UDMA) and Sanandaj-Sirjan structural zone (SSZ) in Iran. These results, together with literatures and our unpublished age data, better delineate the magmatic evolution related to the Neotethyan subduction and subsequent Zagros orogeny that resulted from the Arabia-Eurasia collision. Subduction-related magmatism was active during Jurassic time, as evidenced by the presence of widespread I-type granitoids from the Middle to Late Jurassic (176-144. Ma) in the SSZ. After a protracted magmatic quiescence in the Early Cretaceous, igneous activity renewed inland in the UDMA from which we identify Late Cretaceous granitoids (81-72. Ma) in Jiroft and Bazman areas, the southeastern segment of the UDMA. The UDMA volcanism was most active and widespread during the Eocene and Oligocene (55-25. Ma), much longer lasting than previously thought as just an Eocene pulse. Such a prolonged igneous "flare-up" event in the UDMA can be correlated to Armenia where coeval calc-alkaline rocks are common. The UDMA magmatism ceased progressively from northwest to southeast, with magmatic activities ending the Early Miocene (ca. 22. Ma) in Meghri, the Middle Miocene (ca. 16. Ma) in Kashan and the Late Miocene (ca. 10-6. Ma) in Anar, respectively. The southeastward magmatic cessation is consistent with the notion of oblique and diachronous collision between Arabia and Eurasia. Post-collisional volcanism started ca. 11. Ma in Saray, east off the Urumieh Lake, which, along with later eruptions in Sahand (6.5-4.2. Ma) and Sabalan (≤. 0.4. Ma) volcanoes, forms a compositionally unique component of the vast volcanic field covering much of the Lesser Caucasus, NW Iran and eastern Anatolia regions. © 2013 Elsevier B.V.

Usuki T.,Academia Sinica, Taiwan | Lan C.-Y.,Academia Sinica, Taiwan | Wang K.-L.,Academia Sinica, Taiwan | Chiu H.-Y.,National Taiwan University
Tectonophysics | Year: 2013

To constrain the paleoposition of Indochina within Gondwana during the Early Paleozoic, we performed in-situ U-Pb and Hf isotope analyses on detrital zircons from three river sediment samples in the Truong Son Belt of the Indochina block. The age distributions yield dominant Neoarchean (~2.5Ga), Mesoproterozoic (1.7-1.4Ga), Grenvillian (~0.95Ga), and Pan-African (0.65-0.5Ga) age groups and minor Paleo- to Meso-archean zircons. Hf isotope compositions of zircons for each age group exhibit large ranges of εHf(T), suggesting that the zircon host rocks have diverse sources. The oldest Hf model ages for zircons of Neoarchean, Grenvillian, and Pan-African age group yield ~3.7Ga or older, while those of Mesoproterozoic age group show ~3.3Ga. The remarkable similarity of age distribution and Hf isotope compositions among detrital zircons of Indochina and those of Tethyan Himalaya, western Cathaysia, and Qiangtang suggests that Indochina was located outboard of Qiangtang and south of South China in the Indian margin of Gondwana during the Early Paleozoic. Our results are consistent with the paleontological correlations of east Gondwana margin during the Early Paleozoic. © 2012 Elsevier B.V.

Chang Y.J.,National Taiwan University | Watanabe M.,Academia Sinica, Taiwan | Chou P.-T.,National Taiwan University | Chow T.J.,Academia Sinica, Taiwan
Chemical Communications | Year: 2012

Organic dyes consisting of a [2.2]paracyclophane unit along the main chromophore are examined for their application in sensitized solar cells. These materials exhibit considerably high values of open-circuit voltage (V oc) ranging 0.69-0.72 V, and an overall efficiency up to 3.8%. © 2012 The Royal Society of Chemistry.

Lee M.-Y.,National Taiwan University | Hsu H.-H.,Academia Sinica, Taiwan
Journal of Climate | Year: 2013

A multidecadal geopotential height pattern in the upper troposphere of the extratropical Northern Hemisphere (NH) is identified in this study. This pattern is characterized by the nearly zonal symmetry of geopotential height and temperature between 358 and 658N and the equivalent barotropic vertical structure with the largest amplitude in the upper troposphere. This pattern is named the Eurasian-Pacific multidecadal oscillation (EAPMO) to describe its multidecadal time scale and the largest amplitudes over Eurasia and the North Pacific. Although nearly extending over the entire extratropics, theEAPMOexhibits larger amplitudes over western Europe, East Asia, and the North Pacific with a zonal scale equivalent to zonal wavenumbers 4 and 5. The zonally asymmetric perturbation tends to amplify over the major mountain ranges in the region, suggesting a significant topographic influence. The EAPMO has fluctuated concurrently with the Atlantic multidecadal oscillation (AMO) at least since the beginning of the twentieth century. The numerical simulation results suggest that the EAPMO could be induced by the AMO-like sea surface temperature anomaly and strengthened regionally by topography, especially over the Asian highland region, although the amplitude was undersimulated. This study found that the multidecadal variability of the upper-tropospheric geopotential height in the extratropical NH is much more complicated than in the tropics and the Southern Hemisphere (SH). It takes both first (warming trend) and second (multidecadal) EOFs to explain the multidecadal variability in the extratropicalNH, while only the firstEOF, which exhibited a warming trend, is sufficient for the tropics and SH. © 2013 American Meteorological Society.

Okabe N.,University of Tokyo | Okabe N.,Academia Sinica, Taiwan | Futamase T.,Tohoku University | Kajisawa M.,Ehime University | Kuroshima R.,Tohoku University
Astrophysical Journal | Year: 2014

We present a 4 deg2 weak gravitational lensing survey of subhalos in the very nearby Coma cluster using the Subaru/Suprime-Cam. The large apparent size of cluster subhalos allows us to measure the mass of 32 subhalos detected in a model-independent manner, down to the order of 10-3 of the virial mass of the cluster. Weak-lensing mass measurements of these shear-selected subhalos enable us to investigate subhalo properties and the correlation between subhalo masses and galaxy luminosities for the first time. The mean distortion profiles stacked over subhalos show a sharply truncated feature which is well-fitted by a Navarro-Frenk-White (NFW) mass model with the truncation radius, as expected due to tidal destruction by the main cluster. We also found that subhalo masses, truncation radii, and mass-to-light ratios decrease toward the cluster center. The subhalo mass function, dn/dln M sub, in the range of 2 orders of magnitude in mass, is well described by a single power law or a Schechter function. Best-fit power indices of for the former model and for the latter, are in remarkable agreement with slopes of 0.9-1.0 predicted by the cold dark matter paradigm. The tangential distortion signals in the radial range of 0.02-2 h -1 Mpc from the cluster center show a complex structure which is well described by a composition of three mass components of subhalos, the NFW mass distribution as a smooth component of the main cluster, and a lensing model from a large scale structure behind the cluster. Although the lensing signals are 1 order of magnitude lower than those for clusters at z 0.2, the total signal-to-noise ratio, S/N = 13.3, is comparable, or higher, because the enormous number of background source galaxies compensates for the low lensing efficiency of the nearby cluster. © 2014. The American Astronomical Society. All rights reserved.

Cheng A.-C.,Academia Sinica, Taiwan | Tsai I.-H.,Academia Sinica, Taiwan | Tsai I.-H.,National Taiwan University
Biochimica et Biophysica Acta - General Subjects | Year: 2014

Background Snake venoms are rich in Kunitz-type protease inhibitors that may have therapeutic applications. However, apart from trypsin or chymotrypsin inhibition, the functions of most of these inhibitors have not been elucidated. A detailed functional characterization of these inhibitors may lead to valuable drug candidates. Methods A Kunitz-type protease inhibitor, named DrKIn-II, was tested for its ability to inhibit plasmin using various approaches such as far western blotting, kinetic analyses, fibrin plate assay and euglobulin clot lysis assay. In addition, the antifibrinolytic activity of DrKIn-II was demonstrated in vivo. Results DrKIn-II potently decreased the amidolytic activity of plasmin in a dose-dependent manner, with a global inhibition constant of 0.2 nM. Inhibition kinetics demonstrated that the initial binding of DrKIn-II causes the enzyme to isomerize, leading to the formation of a much tighter enzyme-inhibitor complex. DrKIn-II also demonstrated antifibrinolytic activity in fibrin plate assay and significantly prolonged the lysis of the euglobulin clot. Screening of DrKIn-II against a panel of serine proteases indicated that plasmin is the preferential target of DrKIn-II. Furthermore, DrKIn-II treatment prevented the increase of FDP in coagulation-stimulated mice and significantly reduced the bleeding time in a murine tail bleeding model. Conclusion DrKIn-II is a potent, slow and tight-binding plasmin inhibitor that demonstrates antifibrinolytic activity both in vitro and in vivo. General significance This is the first in-depth functional characterization of a plasmin inhibitor from a viperid snake. The potent antifibrinolytic activity of DrKIn-II makes it a potential candidate for the development of novel antifibrinolytic agents. © 2013 Elsevier B.V.

Hirashita H.,Academia Sinica, Taiwan | Li Z.,University of Virginia
Monthly Notices of the Royal Astronomical Society: Letters | Year: 2013

We investigate the condition for the formation of micron-sized grains in dense cores of molecular clouds. This ismotivated by the detection ofmid-infrared emission from deep inside a number of dense cores, the so-called 'coreshine,' which is thought to come from scattering by micron (μm)-sized grains. Based on numerical calculations of coagulation starting from the typical grain-size distribution in the diffuse interstellar medium, we obtain a conservative lower limit to the time t to form μm-sized grains: t/tff 3(5/S)(nH/105 cm-3)-1/4 (where tff is the free-fall time at hydrogen number density nH in the core and S the enhancement factor of the grain-grain collision cross-section to account for non-compact aggregates). At the typical core density nH = 105 cm-3, it takes at least a few free-fall times to form the μm-sized grains responsible for coreshine. The implication is that those dense cores observed in coreshine are relatively long-lived entities in molecular clouds, rather than dynamically transient objects that last for one free-fall time or less. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

Cheng B.H.,Academia Sinica, Taiwan | Lan Y.-C.,National Cheng Kung University | Tsai D.P.,Academia Sinica, Taiwan | Tsai D.P.,National Taiwan University
Optics Express | Year: 2013

We propose and analyze an innovative device called "Hybrid- Super-Hyperlens". This lens is made of two hyperbolic metamaterials with different signs in their dielectric tensor and different isofrequency dispersion curves. The ability of the proposed lens to break the optical diffraction limit is demonstrated using numerical simulations (with the resolution power of about λ/6). Both a pair of nano-slits and a nano-ring can be imaged and resolved by the proposed lens using the radially polarized light source. Such a lens has great potential applications in photolithography and real-time nanoscale imaging. © 2013 Optical Society of America.

Chen Y.,Academia Sinica, Taiwan | Chen Y.,National Tsing Hua University | Chen Y.,National Taiwan University
Biomicrofluidics | Year: 2013

We investigate the fluctuation-relaxation dynamics of entropically restricted DNA molecules in square nanochannels ranging from 0.09 to 19.9 times the persistence length. In nanochannels smaller than the persistence length, the chain relaxation time is found to have cubic dependence on the channel size. It is found that the effective polymer width significantly alter the chain conformation and relaxation time in strong confinement. For thinner chains, looped chain configurations are found in channels with height comparable to the persistence length, with very slow relaxation compared to un-looped chains. Larger effective chain widths inhibit the formation of hairpin loops. © 2013 Author(s).

Shie J.-J.,Academia Sinica, Taiwan | Liu Y.-C.,Academia Sinica, Taiwan | Lee Y.-M.,Academia Sinica, Taiwan | Lim C.,Academia Sinica, Taiwan | And 3 more authors.
Journal of the American Chemical Society | Year: 2014

We have designed a low fluorescent azido-BODIPY-based probe AzBOCEt (Az10) that undergoes copper(I)-catalyzed 1,3-dipolar cycloadditions with alkynes to yield strongly fluorescent triazole derivatives. The fluorescent quantum yield of a triazole product T10 is enhanced by 52-fold as compared to AzBOCEt upon excitation at a wavelength above 500 nm. Quantum mechanical calculations indicate that the increase in fluorescence upon triazole formation is due to the lowering of the HOMO energy level of the aryl moiety to reduce the process of acceptor photoinduced electron transfer. AzBOCEt is shown to label alkyne-functionalized proteins in vitro and glycoproteins in cells with excellent selectivity, and enables cell imaging and visualization of glycoconjugates in alkynyl-saccharide-treated cells at extremely low concentration (0.1 μM). Furthermore, the alkyne-tagged glycoproteins from cell lysates can be directly detected with AzBOCEt in gel electrophoresis. © 2014 American Chemical Society.

Kuo Y.,Academia Sinica, Taiwan | Hsu T.-Y.,National Taiwan University | Wu Y.-C.,Academia Sinica, Taiwan | Wu Y.-C.,National Taiwan University | Chang H.-C.,Academia Sinica, Taiwan
Biomaterials | Year: 2013

This study investigates the intercellular transport of yolk lipoproteins in Caenorhabditis elegans by using fluorescence lifetime imaging microscopy (FLIM) and fluorescent nanodiamonds (FNDs) as photostable labels and tracers. The yolk lipoproteins in the nematode are similar to human serum low-density lipoproteins (LDLs), serving as an intercellular transporter of fat molecules and cholesterol. To study this fundamentally important process, FNDs were first coated with yolk lipoprotein complexes (YLCs) and then microinjected into the intestinal cells of the living organism. Real-time imaging over a time period of more than 50min with FLIM revealed the process of YLC-FND secretion from the intestine to the pseudocoelomic space, followed by transporting into oocytes and subsequent accumulation in the multi-cellular embryos derived from the oocytes. Colocalization studies of the rme-2 adult hermaphrodites expressing green fluorescent protein (GFP)-tagged YLCs confirmed that the injected YLC-FNDs were taken up by oocytes through endocytosis mediated by the LDL receptor, RME-2, functioning as an YLC receptor. Our results demonstrate that FND is useful as a biomolecular nanocarrier without significantly altering the functionality of the cargos for intercellular transport, cell-specific targeting, and long-term imaging applications in vivo. © 2013 Elsevier Ltd.

Yeh J.-W.,National Taiwan University | Yeh J.-W.,Academia Sinica, Taiwan | Taloni A.,Academia Sinica, Taiwan | Taloni A.,CNR Institute for Energetics and Interphases | And 4 more authors.
Nano Letters | Year: 2012

Entropy-driven polymer dynamics at the nanoscale is fundamentally important in biological systems but the dependence of the entropic force on the nanoconfinement remains elusive. Here, we established an entropy-driven single molecule tug-of-war (TOW) at two micro-nanofluidic interfaces bridged by a nanoslit, performed the force analysis from a modified wormlike chain in the TOW scenario and the entropic recoiling process, and determined the associated scalings on the nanoconfinement. Our results provide a direct experimental evidence that the entropic forces in these two regimes, though unequal, are essentially constant at defined slit heights, irrespective of the slit lengths and the DNA segments within. Our findings have the implications to polymer transport at the nanoscale, device design for single molecule analysis, and biotechnological applications. © 2012 American Chemical Society.

Hung H.,National Taiwan University | Wang C.-C.,Academia Sinica, Taiwan
Biostatistics | Year: 2013

Logistic regression has been widely applied in the field of biomedical research for a long time. In some applications, the covariates of interest have a natural structure, such as that of a matrix, at the time of collection. The rows and columns of the covariate matrix then have certain physical meanings, and they must contain useful information regarding the response. If we simply stack the covariate matrix as a vector and fit a conventional logistic regression model, relevant information can be lost, and the problem of inefficiency will arise. Motivated from these reasons, we propose in this paper the matrix variate logistic (MV-logistic) regression model. The advantages of the MV-logistic regression model include the preservation of the inherent matrix structure of covariates and the parsimony of parameters needed. In the EEG Database Data Set, we successfully extract the structural effects of covariate matrix, and a high classification accuracy is achieved. © 2012 The Author.

Wang F.,Academia Sinica, Taiwan | Lin J.-S.,Academia Sinica, Taiwan | Cheng Y.,Academia Sinica, Taiwan | Liu K.,Academia Sinica, Taiwan | And 2 more authors.
Journal of Physical Chemistry Letters | Year: 2013

The vibrational enhancement factor in the Cl + CHD3(v 1 = 1) reaction is revisited over the collisional energy range of 2-5.9 kcal mol-1. Contrary to the previous results obtained by probing the low-|N, K⟩ states of CD3(v = 0) products, CH stretching excitation becomes more efficacious than the same amount of translational energy in promoting the HCl(v) + CD3(v = 0) product pairs when all-|N, K⟩ states are probed. Whereas the new vibrational enhancement factors, which are three to four times larger than the previous report, agree reasonably well with a recent reduced-dimensionality quantum dynamics calculation, a cautious note is made on the different initial |J,K⟩ rotational selections of the CHD3 reactants in the present theory-experiment comparison. © 2013 American Chemical Society.

Zhang X.,Hong Kong Polytechnic University | Chen Y.L.,National Taiwan University | Liu R.-S.,National Taiwan University | Tsai D.P.,National Taiwan University | Tsai D.P.,Academia Sinica, Taiwan
Reports on Progress in Physics | Year: 2013

Plasmonic photocatalysis has recently facilitated the rapid progress in enhancing photocatalytic efficiency under visible light irradiation, increasing the prospect of using sunlight for environmental and energy applications such as wastewater treatment, water splitting and carbon dioxide reduction. Plasmonic photocatalysis makes use of noble metal nanoparticles dispersed into semiconductor photocatalysts and possesses two prominent features - a Schottky junction and localized surface plasmonic resonance (LSPR). The former is of benefit to charge separation and transfer whereas the latter contributes to the strong absorption of visible light and the excitation of active charge carriers. This article aims to provide a systematic study of the fundamental physical mechanisms of plasmonic photocatalysis and to rationalize many experimental observations. In particular, we show that LSPR could boost the generation of electrons and holes in semiconductor photocatalysts through two different effects - the LSPR sensitization effect and the LSPR-powered bandgap breaking effect. By classifying the plasmonic photocatalytic systems in terms of their contact form and irradiation state, we show that the enhancement effects on different properties of photocatalysis can be well-explained and systematized. Moreover, we identify popular material systems of plasmonic photocatalysis that have shown excellent performance and elucidate their key features in the context of our proposed mechanisms and classifications. © 2013 IOP Publishing Ltd.

Hung Y.-H.,Academia Sinica, Taiwan | Hung Y.-H.,National Taiwan University | Chen L.M.-W.,Academia Sinica, Taiwan | Yang J.-Y.,Academia Sinica, Taiwan | And 2 more authors.
Nature Communications | Year: 2013

Lysosomes are the major degradative compartments within cells, harbouring a wide variety of hydrolytic enzymes within their lumen. Release of lysosomal hydrolases from lysosomes into the cell cytoplasm results in cell death. Here we report that damaged lysosomes undergo autophagic turnover. Using a light-induced lysosome impairing scheme that can be controlled spatially and temporally within a cell, we show that damaged lysosomes are selectively ubiquitinated, recruit autophagic proteins and are eventually incorporated into autolysosomes for degradation. We propose that autophagic removal of lysosomes, which we term lysophagy, is a surveillance mechanism that alleviates cells from the adverse effects of lysosomal damage. We envision our method to induce lysosomal damage will enable detailed molecular studies of the lysophagy pathway in the future. © 2013 Macmillan Publishers Limited. All rights reserved.

Li B.-R.,Academia Sinica, Taiwan | Hsieh Y.-J.,National Taiwan University | Chen Y.-X.,National Taiwan University | Chung Y.-T.,National Taiwan University | And 3 more authors.
Journal of the American Chemical Society | Year: 2013

Dopamine (DA) is an important neurotransmitter that is involved in neuronal signal transduction and several critical illnesses. However, the concentration of DA is extremely low in patients and is difficult to detect using existing electrochemical biosensors with detection limits typically around nanomolar levels (∼10-9 M). Here, we developed a nanoelectronic device as a biosensor for ultrasensitive and selective DA detection by modifying DNA-aptamers on a multiple-parallel-connected (MPC) silicon nanowire field-effect transistor (referred to as MPC aptamer/SiNW-FET). Compared with conventional electrochemical methods, the MPC aptamer/SiNW-FET has been demonstrated to improve the limit of DA detection to <10-11 M and to possess a detection specificity that is able to distinguish DA from other chemical analogues, such as ascorbic acid, catechol, phenethylamine, tyrosine, epinephrine, and norepinephrine. This MPC aptamer/SiNW-FET was also applied to monitor DA release under hypoxic stimulation from living PC12 cells. The real-time recording of the exocytotic DA induced by hypoxia reveals that the increase in intracellular Ca2+ that is required to trigger DA secretion is dominated by an extracellular Ca2+ influx, rather than the release of intracellular Ca2+ stores. © 2013 American Chemical Society.

Jego S.,Rice University | Jego S.,Academia Sinica, Taiwan | Jego S.,CNRS Earth Sciences Institute of Orléans | Pichavant M.,CNRS Earth Sciences Institute of Orléans
Geochimica et Cosmochimica Acta | Year: 2012

To investigate the behaviour of gold in sulfur-bearing hydrous intermediate calc-alkaline melts under different redox states typical of subduction-zone settings, we have determined the solubility of Au at 0.4GPa and 1000°C for three dacitic magmas (two adakites and one calc-alkaline composition) from the North-Luzon Arc (Philippines). The experiments were performed over an oxygen fugacity (fO 2) range corresponding to reducing (~NNO-1), moderately oxidizing (~NNO+1.5) and strongly oxidizing (≥NNO+3) conditions as measured by solid Ni-Pd-O sensors. They were carried out in gold containers, serving also as the source of gold, in presence of variable amounts of H 2O and ~1wt.% of elemental sulfur (S). Concentrations of Au in glasses were determined by laser-ablation inductively-coupled plasma mass spectrometry (LA-ICPMS). Gold solubility in S-bearing melts is drastically enhanced compared to S-free melts, by up to two orders of magnitude. In addition, very high gold solubilities are reached under reducing conditions (

Lin Y.-Y.,Academia Sinica, Taiwan | Liu T.-L.,Academia Sinica, Taiwan | Fuh C.-S.,National Taiwan University
IEEE Transactions on Pattern Analysis and Machine Intelligence | Year: 2011

In solving complex visual learning tasks, adopting multiple descriptors to more precisely characterize the data has been a feasible way for improving performance. The resulting data representations are typically high-dimensional and assume diverse forms. Hence, finding a way of transforming them into a unified space of lower dimension generally facilitates the underlying tasks such as object recognition or clustering. To this end, the proposed approach (termed MKL-DR) generalizes the framework of multiple kernel learning for dimensionality reduction, and distinguishes itself with the following three main contributions: First, our method provides the convenience of using diverse image descriptors to describe useful characteristics of various aspects about the underlying data. Second, it extends a broad set of existing dimensionality reduction techniques to consider multiple kernel learning, and consequently improves their effectiveness. Third, by focusing on the techniques pertaining to dimensionality reduction, the formulation introduces a new class of applications with the multiple kernel learning framework to address not only the supervised learning problems but also the unsupervised and semi-supervised ones. © 2006 IEEE.

Chen S.-Y.,Academia Sinica, Taiwan | Ho P.-H.,National Taiwan University | Shiue R.-J.,Academia Sinica, Taiwan | Shiue R.-J.,Columbia University | And 2 more authors.
Nano Letters | Year: 2012

In this article, we present the transport and magnetotransport of high-quality graphene transistors on conventional SiO 2/Si substrates by modification with organic molecule octadecyltrichlorosilane (OTS) self-assembled monolayers (SAMs). Graphene devices on OTS SAM-functionalized substrates with high carrier mobility, low intrinsic doping, suppressed carrier scattering, and reduced thermal activation of resistivity at room temperature were observed. Most interestingly, the remarkable magnetotransport of graphene devices with pronounced quantum Hall effect, strong Shubnikov-de Haas oscillations, a nonzero Berry's phase, and a short carrier scattering time also confirms the high quality of graphene on this ultrasmooth organic SAM-modified platform. The high-performance graphene transistors on the solution-processable OTS SAM-functionalized SiO 2/Si substrates are promising for the future development of large-area and low-cost fabrications of graphene-based nanoelectronics. © 2012 American Chemical Society.

Tu Z.,Academia Sinica, Taiwan | Lin Y.-N.,National Taiwan University | Lin C.-H.,Academia Sinica, Taiwan | Lin C.-H.,National Taiwan University
Chemical Society Reviews | Year: 2013

l-Fucose-containing glycoconjugates are essential for a myriad of physiological and pathological activities, such as inflammation, bacterial and viral infections, tumor metastasis, and genetic disorders. Fucosyltransferases and fucosidases, the main enzymes involved in the incorporation and cleavage of l-fucose residues, respectively, represent captivating targets for therapeutic treatment and diagnosis. We herein review the important breakthroughs in the development of fucosyltransferase and fucosidase inhibitors. To demonstrate how the synthesized small molecules interact with the target enzymes, i.e. delineation of the structure-activity relationship, we cover the reaction mechanisms and resolved X-ray crystal structures, discuss how this information guides the design of enzyme inhibitors, and explain how the molecules were optimized to achieve satisfying potency and selectivity. © 2013 The Royal Society of Chemistry.

Hsieh W.-P.,Academia Sinica, Taiwan | Hsieh W.-P.,National Taiwan University | Hsieh H.-L.,National Taiwan University | Wu S.-H.,Academia Sinica, Taiwan
Plant Cell | Year: 2012

Transcriptomic adjustment plays an important role in Arabidopsis thaliana seed germination and deetiolation in response to environmental light signals. The G-box cis-element is commonly present in promoters of genes that respond positively or negatively to the light signal. In pursuing additional transcriptional regulators that modulate light-mediated transcriptome changes, we identified bZIP16, a basic region/Leu zipper motif transcription factor, by G-box DNA affinity chromatography. We confirmed that bZIP16 has G-box-specific binding activity. Analysis of bzip16 mutants revealed that bZIP16 is a negative regulator in light-mediated inhibition of cell elongation but a positive regulator in light-regulated seed germination. Transcriptome analysis supported that bZIP16 is primarily a transcriptional repressor regulating light-, gibberellic acid (GA)-, and abscisic acid (ABA)-responsive genes. Chromatin immunoprecipitation analysis revealed that bZIP16 could directly target ABA-responsive genes and RGA-LIKE2, a DELLA gene in the GA signaling pathway. bZIP16 could also indirectly repress the expression of PHYTOCHROME INTERACTING FACTOR3-LIKE5, which encodes a basic helix-loop-helix protein coordinating hormone responses during seed germination. By repressing the expression of these genes, bZIP16 functions to promote seed germination and hypocotyl elongation during the early stages of Arabidopsis seedling development. © 2012 American Society of Plant Biologists. All rights reserved.

Hsu C.-H.,National Taiwan University | Wang A.H.-J.,Academia Sinica, Taiwan
Nucleic Acids Research | Year: 2011

Organisms growing at elevated temperatures face the challenge of maintaining the integrity of their genetic materials. Archaea possess unique chromatin proteins for gene organization and information processing. We present the solution structure of Sso7c4 from Sulfolobus solfataricus, which has a homodimeric DNA-binding fold forming a swapped β-loop-β 'Tai-Chi' topology. The fold is reminiscent of the N-terminal DNA-binding domain of AbrB and MazE. In addition, several amide resonances in the heteronuclear single quantum coherence spectra of Sso7c4 are shifted and broadened with the addition of small amounts of duplex DNA oligomers. The locations of the corresponding amides in the Sso7c4 structure define its DNA-interacting surface. NMR spectra of DNA titrated with the protein further indicated that Sso7c4 interacts with DNA in the major groove. Taken together, a plausible model for the Sso7c4-DNA complex is presented, in which the DNA double helix is curved around the protein dimer. © 2011 The Author(s).

Shin L.-J.,A-Life Medical | Shin L.-J.,Academia Sinica, Taiwan | Lo J.-C.,Academia Sinica, Taiwan | Lo J.-C.,National Taiwan University | Yeh K.-C.,Academia Sinica, Taiwan
Plant Physiology | Year: 2012

Copper (Cu) is essential for plant growth but toxic in excess. Specific molecular mechanisms maintain Cu homeostasis to facilitate its use and avoid the toxicity. Cu chaperones, proteins containing a Cu-binding domain(s), are thought to assist Cu intracellular homeostasis by their Cu-chelating ability. In Arabidopsis (Arabidopsis thaliana), two Cu chaperones, Antioxidant Protein1 (ATX1) and ATX1-Like Copper Chaperone (CCH), share high sequence homology. Previously, their Cu-binding capabilities were demonstrated and interacting molecules were identified. To understand the physiological functions of these two chaperones, we characterized the phenotype of atx1 and cch mutants and the cchatx1 double mutant in Arabidopsis. The shoot and root growth of atx1 and cchatx1 but not cch was specifically hypersensitive to excess Cu but not excess iron, zinc, or cadmium. The activities of antioxidant enzymes in atx1 and cchatx1 were markedly regulated in response to excess Cu, which confirms the phenotype of Cu hypersensitivity. Interestingly, atx1 and cchatx1 were sensitive to Cu deficiency. Overexpression of ATX1 not only enhanced Cu tolerance and accumulation in excess Cu conditions but also tolerance to Cu deficiency. In addition, the Cu-binding motif MXCXXC of ATX1 was required for these physiological functions. ATX1 was previously proposed to be involved in Cu homeostasis by its Cu-binding activity and interaction with the Cu transporter Heavy metal-transporting P-type ATPase5. In this study, we demonstrate that ATX1 plays an essential role in Cu homeostasis in conferring tolerance to excess Cu and Cu deficiency. The possible mechanism is discussed. © 2012 American Society of Plant Biologists. All Rights Reserved.

Teng Y.-S.,Academia Sinica, Taiwan | Teng Y.-S.,A-Life Medical | Chan P.-T.,Academia Sinica, Taiwan | Chan P.-T.,National Taiwan University | Li H.-m.,Academia Sinica, Taiwan
PLoS Biology | Year: 2012

Gene-specific, age-dependent regulations are common at the transcriptional and translational levels, while protein transport into organelles is generally thought to be constitutive. Here we report a new level of differential age-dependent regulation and show that chloroplast proteins are divided into three age-selective groups: group I proteins have a higher import efficiency into younger chloroplasts, import of group II proteins is nearly independent of chloroplast age, and group III proteins are preferentially imported into older chloroplasts. The age-selective signal is located within the transit peptide of each protein. A group III protein with its transit peptide replaced by a group I transit peptide failed to complement its own mutation. Two consecutive positive charges define the necessary motif in group III signals for older chloroplast preference. We further show that different members of a gene family often belong to different age-selective groups because of sequence differences in their transit peptides. These results indicate that organelle-targeting signal peptides are part of cells' differential age-dependent regulation networks. The sequence diversity of some organelle-targeting peptides is not a result of the lack of selection pressure but has evolved to mediate regulation. © 2012 Teng et al.

Pu J.,Waseda University | Yomogida Y.,Waseda University | Yomogida Y.,Tohoku University | Liu K.-K.,Academia Sinica, Taiwan | And 4 more authors.
Nano Letters | Year: 2012

Molybdenum disulfide (MoS 2) thin-film transistors were fabricated with ion gel gate dielectrics. These thin-film transistors exhibited excellent band transport with a low threshold voltage (<1 V), high mobility (12.5 cm 2/(V ·s)) and a high on/off current ratio (10 5). Furthermore, the MoS 2 transistors exhibited remarkably high mechanical flexibility, and no degradation in the electrical characteristics was observed when they were significantly bent to a curvature radius of 0.75 mm. The superior electrical performance and excellent pliability of MoS 2 films make them suitable for use in large-area flexible electronics. © 2012 American Chemical Society.

Lee W.-L.,Academia Sinica, Taiwan | Liou K.N.,University of California at Los Angeles | Hall A.,University of California at Los Angeles
Journal of Geophysical Research: Atmospheres | Year: 2011

On the basis of 3-D Monte Carlo photon tracing simulations, we have developed a parameterization of solar fluxes over mountain surfaces by means of the multiple linear regression analysis associated with topographic information, including elevation, solar incident angle, sky view factor, and terrain configuration factor. For clear skies without aerosols and clouds, the regression equation for the direct flux can explain more than 98% of the variation in which the solar incident angle is the dominant factor, except when the Sun is very low or at zenith. About 60% of the variation in the diffuse flux is predicted by the regression equation in which the mean elevation, sky view factor, and solar incident angle are key factors. The terrain-reflected fluxes, proportional to the surface albedo, are well correlated with the terrain configuration factor with more than 80% of the variation that can be explained. The coupled fluxes involve intricate interactions, and the regression analysis is less satisfactory in cases of low albedo values. However, over high-albedo surfaces, the terrain configuration factor becomes most dominant, leading to a significant improvement in regression performance. In these analyses, a surface albedo invariant with wavelength has been used. Using a region over the Sierra Nevada as a testbed, the preceding regression parameterizations have been specifically developed so that the fluxes evaluated from the 3-D Monte Carlo model over intense topography can be used as a perturbation term to correct those computed from the plane-parallel counterpart, commonly used in regional climate models and GCMs. © 2011 by the American Geophysical Union.

Wang C.-I.,National Taiwan University | Wu W.-C.,National Tsing Hua University | Wu W.-C.,Academia Sinica, Taiwan | Periasamy A.P.,National Taiwan University | Chang H.-T.,National Taiwan University
Green Chemistry | Year: 2014

An electrochemical approach has been employed for the preparation of photoluminescent carbon nanodots (C-dots) from glycine under alkaline conditions. The formation of C-dots is through electro-oxidation, electro-polymerization, carbonization, and passivation. The as-prepared C-dots possess excitation-wavelength-dependence and pH sensitive photoluminescence (PL) properties and are stable in solution containing high salt concentration (up to 500 mM NaCl). Detection of hemoglobin using C-dots has been demonstrated through a fluorescence resonance energy transfer (FRET) process. The PL intensity (excitation/emission wavelengths 365/440 nm) of C-dots is inversely proportional to the concentration of hemoglobin over a range of 0.05-250 nM (r = 0.99), with a limit of detection (signal-to-noise ratio 3) of 30 pM. We have validated this assay by determining the concentrations of hemoglobin in five representative diluted blood samples, with results being in good agreement with that obtained by using a commercial hemoglobin meter. The water-dispersible and photostable C-dots have been applied to obtain bloodstained images and fingerprints. © the Partner Organisations 2014.

Liu K.,Academia Sinica, Taiwan | Liu K.,National Taiwan University
Annual Review of Physical Chemistry | Year: 2016

Vibrational motions of a polyatomic molecule are multifold and can be as simple as stretches or bends or as complex as concerted motions of many atoms. Different modes of excitation often possess different capacities in driving a bimolecular chemical reaction, with distinct dynamic outcomes. Reactions with vibrationally excited methane and its isotopologs serve as a benchmark for advancing our fundamental understanding of polyatomic reaction dynamics. Here, some recent progress in this area is briefly reviewed. Particular emphasis is placed on the key concepts developed from those studies. The interconnections among mode and bond selectivity, Polanyi's rules, and newly introduced vibrational-induced steric phenomena are highlighted. Copyright © 2016 by Annual Reviews. All rights reserved.

Maquat L.E.,University of Rochester | Tarn W.-Y.,University of Rochester | Tarn W.-Y.,Academia Sinica, Taiwan | Isken O.,University of Lübeck
Cell | Year: 2010

In mammalian cells, newly synthesized mRNAs undergo a pioneer round of translation that is important for mRNA quality control. Following maturation of messenger ribonucleoprotein particles during and after the pioneer round, steady-state cycles of mRNA translation generate most of the cell's proteins. Translation factors, RNA-binding proteins, and targets of signaling pathways that are particular to newly synthesized mRNAs regulate critical functions of the pioneer round. © 2010 Elsevier Inc.

Mohan N.,National Tsing Hua University | Mohan N.,Academia Sinica, Taiwan | Mohan N.,Institute of Physics | Chen C.-S.,Academia Sinica, Taiwan | And 4 more authors.
Nano Letters | Year: 2010

Nanoscale carbon materials hold great promise for biotechnological and biomedical applications. Fluorescent nanodiamond (FND) is a recent new addition to members of the nanocarbon family. Here, we report long-term in vivo imaging of FNDs in Caenorhabditis elegans (C. elegans) and explore the nano-biointeractions between this novel nanomaterial and the model organism. FNDs are introduced into wild-type C. elegans by either feeding them with colloidal FND solution or microinjecting FND suspension into the gonads of the worms. On feeding, bare FNDs stay in the intestinal lumen, while FNDs conjugated with biomolecules (such as dextran and bovine serum albumin) are absorbed into the intestinal cells. On microinjection, FNDs are dispersed in the gonad and delivered to the embryos and eventually into the hatched larvae in the next generation. The toxicity assessments, performed by employing longevity and reproductive potential as physiological indicators and measuring stress responses with use of reporter genes, show that FNDs are stable and nontoxic and do not cause any detectable stress to the worms. The high brightness, excellent photostability, and nontoxic nature of the nanomaterial have enabled continuous imaging of the whole digestive system and tracking of the cellular and developmental processes of the living organism for several days. © 2010 American Chemical Society.

Chen Y.-C.,Academia Sinica, Taiwan | Hsu C.-Y.,Academia Sinica, Taiwan | Lin R.Y.-Y.,Academia Sinica, Taiwan | Lin R.Y.-Y.,National Taiwan University | And 2 more authors.
ChemSusChem | Year: 2013

Power conversion efficiencies in excess of 7 % have been achieved with bulk heterojunction (BHJ)-type organic solar cells using two components: p- and n-doped materials. The energy level and absorption profile of the active layer can be tuned by introduction of an additional component. Careful design of the additional component is required to achieve optimal panchromatic absorption, suitable energy-level offset, balanced electron and hole mobility, and good light-harvesting efficiency. This article reviews the recent progress on ternary organic photovoltaic systems, including polymer/small molecule/functional fullerene, polymer/polymer/functional fullerene, small molecule/small molecule/functional fullerene, polymer/functional fullerene I/functional fullerene II, and polymer/quantum dot or metal/functional fullerene systems. All good things come in threes: Addition of a third component in bulk heterojunction solar cells (sensitizer or fullerene derivative) may increase the short-circuit current through enhanced light harvesting and/or can increase the open-circuit voltage through enhanced carrier mobility and modification of HOMO/LUMO energy levels. Such ternary organic solar cell systems will be reviewed in this article. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Yu J.-K.S.,Academia Sinica, Taiwan | Yu J.-K.S.,National Taiwan University
Zoology | Year: 2010

The neural crest is an embryonic cell population unique to vertebrates. During vertebrate embryogenesis, neural crest cells are first induced from the neural plate border; subsequently, they delaminate from the dorsal neural tube and migrate to their destination, where they differentiate into a wide variety of derivatives. The emergence of the neural crest is thought to be responsible for the evolution of many complex novel structures of vertebrates that are lacking in invertebrate chordates. Despite its central importance in understanding the origin of vertebrates, the evolutionary origin of the neural crest remains elusive. The basal chordate amphioxus (Branchiostoma floridae) occupies an outgroup position that is useful for investigating this question. In this review, I summarize recent genomic and comparative developmental studies between amphioxus and vertebrates and discuss their implications for the evolutionary origin of neural crest cells. I focus mainly on the origin of the gene regulatory network underlying neural crest development, and suggest several hypotheses regarding how this network could have been assembled during early vertebrate evolution. © 2009 Elsevier GmbH. All rights reserved.

Lin K.-P.,National Taiwan University | Chen M.-S.,National Taiwan University | Chen M.-S.,Academia Sinica, Taiwan
IEEE Transactions on Knowledge and Data Engineering | Year: 2011

The support vector machine (SVM) is a widely used tool in classification problems. The SVM trains a classifier by solving an optimization problem to decide which instances of the training data set are support vectors, which are the necessarily informative instances to form the SVM classifier. Since support vectors are intact tuples taken from the training data set, releasing the SVM classifier for public use or shipping the SVM classifier to clients will disclose the private content of support vectors. This violates the privacy-preserving requirements for some legal or commercial reasons. The problem is that the classifier learned by the SVM inherently violates the privacy. This privacy violation problem will restrict the applicability of the SVM. To the best of our knowledge, there has not been work extending the notion of privacy preservation to tackle this inherent privacy violation problem of the SVM classifier. In this paper, we exploit this privacy violation problem, and propose an approach to postprocess the SVM classifier to transform it to a privacy-preserving classifier which does not disclose the private content of support vectors. The postprocessed SVM classifier without exposing the private content of training data is called Privacy-Preserving SVM Classifier (abbreviated as PPSVC). The PPSVC is designed for the commonly used Gaussian kernel function. It precisely approximates the decision function of the Gaussian kernel SVM classifier without exposing the sensitive attribute values possessed by support vectors. By applying the PPSVC, the SVM classifier is able to be publicly released while preserving privacy. We prove that the PPSVC is robust against adversarial attacks. The experiments on real data sets show that the classification accuracy of the PPSVC is comparable to the original SVM classifier. © 2011 IEEE.

Lee Y.-J.,National Taiwan University of Science and Technology | Yeh Y.-R.,National Taiwan University | Wang Y.-C.F.,Academia Sinica, Taiwan
IEEE Transactions on Knowledge and Data Engineering | Year: 2013

Anomaly detection has been an important research topic in data mining and machine learning. Many real-world applications such as intrusion or credit card fraud detection require an effective and efficient framework to identify deviated data instances. However, most anomaly detection methods are typically implemented in batch mode, and thus cannot be easily extended to large-scale problems without sacrificing computation and memory requirements