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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.


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).


Pu J.,Waseda University | Li L.-J.,Academia Sinica, Taiwan | Takenobu T.,Waseda University
Physical Chemistry Chemical Physics | Year: 2014

The outstanding physical and chemical properties of two-dimensional materials, which include graphene and transition metal dichalcogenides, have allowed significant applications in next generation electronics. In particular, atomically thin molybdenum disulphide (MoS2) is attracting widespread attention because of its large bandgap, effective carrier mobility, and mechanical strength. In addition, recent developments in large-area high-quality sample preparation methods via chemical vapour deposition have enabled the use of MoS2 in novel functional applications, such as flexible and stretchable electronic devices. In this perspective, we focus on the current progress in generating MoS2-based flexible and stretchable thin-film transistors. The reported virtues and novelties of MoS2 provide significant advantages for future flexible and stretchable electronics. This journal is © the Partner Organisations 2014.


Chiang L.-Y.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2014

Tentative evidence for statistical anisotropy in the Wilkinson Microwave Anisotropy Probe data was alleged to be due to "insufficient handling of beam asymmetries." In this paper, we investigate this issue and develop a method to estimate the shape of the inflight effective beam, particularly the asymmetry and azimuthal orientation. We divide the whole map into square patches and exploit the information in the Fourier space. For patches containing bright extragalactic point sources, we can directly estimate their shapes, from which the inflight effective beam can be estimated. For those without, we estimate the pattern from iso-power contours in two-dimensional Fourier space. We show that the inflight effective beam convolving the signal is indeed non-symmetric for most of the sky, and it is not randomly oriented. Around the ecliptic poles, however, the asymmetry is smaller due to the averaging effect from different orientations of the beam from the scan strategy. The orientations of the effective beam with significant asymmetry are parallel to the lines of ecliptic longitude. In the foreground-cleaned Internal Linear Combination map, however, the systematics caused by beam effect is significantly lessened. © 2014. The American Astronomical Society. All rights reserved.


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.


Lin H.-C.,University of California at San Diego | Lin H.-C.,Academia Sinica, Taiwan | Hastings P.A.,University of California at San Diego
BMC Evolutionary Biology | Year: 2013

Background: The Blenniiformes comprises six families, 151 genera and nearly 900 species of small teleost fishes closely associated with coastal benthic habitats. They provide an unparalleled opportunity for studying marine biogeography because they include the globally distributed families Tripterygiidae (triplefin blennies) and Blenniidae (combtooth blennies), the temperate Clinidae (kelp blennies), and three largely Neotropical families (Labrisomidae, Chaenopsidae, and Dactyloscopidae). However, interpretation of these distributional patterns has been hindered by largely unresolved inter-familial relationships and the lack of evidence of monophyly of the Labrisomidae. Results: We explored the phylogenetic relationships of the Blenniiformes based on one mitochondrial (COI) and four nuclear (TMO-4C4, RAG1, Rhodopsin, and Histone H3) loci for 150 blenniiform species, and representative outgroups (Gobiesocidae, Opistognathidae and Grammatidae). According to the consensus of Bayesian Inference, Maximum Likelihood, and Maximum Parsimony analyses, the monophyly of the Blenniiformes and the Tripterygiidae, Blenniidae, Clinidae, and Dactyloscopidae is supported. The Tripterygiidae is the sister group of all other blennies, and the Blenniidae is the sister group of the remaining blennies. The monophyly of the Labrisomidae is supported with the exclusion of the Cryptotremini and inclusion of Stathmonotus, and we elevate two subgenera of Labrisomus to establish a monophyletic classification within the family. The monophyly of the Chaenopsidae is supported with the exclusion of Stathmonotus (placed in the Stathmonotini) and Neoclinus and Mccoskerichthys (placed in the Neoclinini). The origin of the Blenniiformes was estimated in the present-day IndoPacific region, corresponding to the Tethys Sea approximately 60.3 mya. A largely Neotropical lineage including the Labrisomidae, Chaenopsidae and Dactyloscopidae (node IV) evolved around 37.6 mya when the Neotropics were increasingly separated from the IndoPacific, but well before the closure of the Tethys Sea. Conclusions: Relationships recovered in this study are similar to those of earlier analyses within the Clinidae and Chaenopsidae, and partially similar within the Blenniidae, but tripterygiid relationships remain poorly resolved. We present the first comprehensive phylogenetic hypothesis for a monophyletic Labrisomidae with five tribes (Labrisomini, Mnierpini, Paraclinini, Stathmonotini and Starksiini). Global distributions of blenny genera included in our analysis support the evolution of a largely Neotropical clade whose closest relatives (clinids and cryptotremines) are temperate in distribution. © 2013 Lin and Hastings; licensee BioMed Central Ltd.


Wu Y.-C.,Academia Sinica, Taiwan
Culture, Medicine and Psychiatry | Year: 2016

In Japan, the first half of the twentieth century saw a remarkable revival of concern with the cultivation of the belly, with a variety of belly-cultivation techniques, particularly breathing exercise and meditative sitting, widely practiced for improving health and treating diseases. This article carefully examines some practitioners’ experiences of belly-cultivation practice in attempting to understand its healing effects for them within their life histories and contemporary intellectual, social and cultural contexts. It shows that belly-cultivation practice served as a medium for some practitioners to reflect on and retell their life stories, and that the personal charisma of certain masters and the communities developing around them provided practitioners with a valuable sense of belonging in an increasingly industrialized and urbanized society. Moreover, these belly-cultivation techniques provided an embodied way for some to explore and affirm their sense of self and develop individual identity. While they were increasingly promoted as cultural traditions capable of cultivating national character, they also served as healing practices by inspiring practitioners with a sense of collective identity and purpose. With these analyses, this article sheds light on the complicated meanings of belly-cultivation for practitioners, and provides illustrative examples of the multitude of meanings of the body, bodily cultivation and healing. © 2016, Springer Science+Business Media New York.


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.


Lu M.-Y.,National Yang Ming University | Liao F.,National Yang Ming University | Liao F.,Academia Sinica, Taiwan
Cell Death and Differentiation | Year: 2011

Interferons (IFNs) are crucial for host defence against viruses. Many IFN-stimulated genes (ISGs) induced by viral infection exert antiviral effects. Microarray analysis of gene expression induced in liver tissues of mice on dengue virus (DENV) infection has led to identification of the ISG gene ISG12b2. ISG12b2 is also dramatically induced on DENV infection of Hepa 1-6 cells (mouse hepatoma cell line). Here, we performed biochemical and functional analyses of ISG12b2. We demonstrate that ISG12b2 is an inner mitochondrial membrane (IMM) protein containing a cleavable mitochondrial targeting sequence and multiple transmembrane segments. Overexpression of ISG12b2 in Hepa 1-6 induced release of cytochrome c from mitochondria, disruption of the mitochondrial membrane potential, and activation of caspase-9, caspase-3, and caspase-8. Treatment of ISG12b2-overexpressing Hepa 1-6 with inhibitors of pan-caspase, caspase-9, or caspase-3, but not caspase-8, reduced apoptotic cell death, suggesting that ISG12b2 activates the intrinsic apoptotic pathway. Of particular interest, we further demonstrated that ISG12b2 formed oligomers, and that ISG12b2 was able to mediate apoptosis through both Bax/Bak-dependent and Bax/Bak-independent pathways. Our study demonstrates that the ISG12b2 is a novel IMM protein induced by IFNs and regulates mitochondria-mediated apoptosis during viral infection. © 2011 Macmillan Publishers Limited All rights reserved.


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.


Asano R.S.,Nagoya University | Takeuchi T.T.,Nagoya University | Hirashita H.,Academia Sinica, Taiwan | Nozawa T.,University of Tokyo
Monthly Notices of the Royal Astronomical Society | Year: 2014

We investigate the evolution of extinction curves in galaxies based on our evolution model of grain-size distribution. In this model, we considered various processes: dust formation by Type II supernovae and asymptotic giant branch stars, dust destruction by supernova shocks in the interstellar medium, metal accretion onto the surface of grains (referred to as grain growth), shattering and coagulation. We find that the extinction curve is flat in the earliest stage of galaxy evolution. As the galaxy is enriched with dust, shattering becomes effective, producing a large abundance of small grains (a ≤ 0.01 μm). Then, grain growth becomes effective at small grain radii, leading to the formation of a bump at a ̃ 10-3-10-2 μm on the grain-size distribution. Consequently, the extinction curve at ultraviolet (UV) wavelengths becomes steep, and a bump at 1/λ ̃ 4.5 μm-1 (where is the wavelength) on the extinction curve becomes prominent. Once coagulation becomes effective, the extinction curves become flatter, but the UV extinction remains overproduced when compared with the Milky Way extinction curve. This discrepancy can be resolved by introducing a stronger contribution of coagulation. Consequently, the interplay between shattering and coagulation could be important in reproducing the Milky Way extinction curve. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Li P.-L.,Tamkang University | Chiou J.-M.,Academia Sinica, Taiwan
Computational Statistics and Data Analysis | Year: 2011

We propose a new approach, the forward functional testing (FFT) procedure, to cluster number selection for functional data clustering. We present a framework of subspace projected functional data clustering based on the functional multiplicative random-effects model, and propose to perform functional hypothesis tests on equivalence of cluster structures to identify the number of clusters. The aim is to find the maximum number of distinctive clusters while retaining significant differences between cluster structures. The null hypotheses comprise equalities between the cluster mean functions and between the sets of cluster eigenfunctions of the covariance kernels. Bootstrap resampling methods are developed to construct reference distributions of the derived test statistics. We compare several other cluster number selection criteria, extended from methods of multivariate data, with the proposed FFT procedure. The performance of the proposed approaches is examined by simulation studies, with applications to clustering gene expression profiles. © 2011 Elsevier B.V. All rights reserved.


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.


Lee Y.-H.,Beckman Research Institute | Kuo C.-Y.,Beckman Research Institute | Stark J.M.,Beckman Research Institute | Shih H.-M.,Academia Sinica, Taiwan | Ann D.K.,Beckman Research Institute
Nucleic Acids Research | Year: 2013

The DNA damage response (DDR) involves both the control of DNA damage repair and signaling to cell cycle checkpoints. Therefore, unraveling the underlying mechanisms of the DDR is important for understanding tumor suppression and cellular resistance to clastogenic cancer therapeutics. Because the DDR is likely to be influenced by chromatin regulation at the sites of DNA damage, we investigated the role of heterochromatin protein 1 (HP1) during the DDR process. We monitored double-strand breaks (DSBs) using the γH2AX foci marker and found that depleting cells of HP1 caused genotoxic stress, a delay in the repair of DSBs and elevated levels of apoptosis after irradiation. Furthermore, we found that these defects in repair were associated with impaired BRCA1 function. Depleting HP1 reduced recruitment of BRCA1 to DSBs and caused defects in two BRCA1-mediated DDR events: (i) the homologous recombination repair pathway and (ii) the arrest of cell cycle at the G2/M checkpoint. In contrast, depleting HP1 from cells did not affect the non-homologous end-joining (NHEJ) pathway: instead it elevated the recruitment of the 53BP1 NHEJ factor to DSBs. Notably, all three subtypes of HP1 seemed to be almost equally important for these DDR functions. We suggest that the dynamic interaction of HP1 with chromatin and other DDR factors could determine DNA repair choice and cell fate after DNA damage. We also suggest that compromising HP1 expression could promote tumorigenesis by impairing the function of the BRCA1 tumor suppressor. © 2013 The Author(s).


Chen Y.-H.,Academia Sinica, Taiwan
Lifetime Data Analysis | Year: 2012

The "semicompeting risks" include a terminal event and a non-terminal event. The terminal event may censor the non-terminal event but not vice versa. Because times to the two events are usually correlated, the non-terminal event is subject to dependent/informative censoring by the terminal event. We seek to conduct marginal regressions and joint association analyses for the two event times under semicompeting risks. The proposed method is based on the modeling setup where the semiparametric transformation models are assumed for marginal regressions, and a copula model is assumed for the joint distribution. We propose a nonparametric maximum likelihood approach for inferences, which provides a martingale representation for the score function and an analytical expression for the information matrix. Direct theoretical developments and computational implementation are allowed for the proposed approach. Simulations and a real data application demonstrate the utility of the proposed methodology. © 2011 Springer Science+Business Media, LLC.


Jen H.H.,Academia Sinica, Taiwan
Annals of Physics | Year: 2015

We investigate superradiant cascade emissions from an atomic ensemble driven by two-color classical fields. The correlated pair of photons (signal and idler) is generated by adiabatically driving the system with large-detuned light fields via four-wave mixing. The signal photon from the upper transition of the diamond-type atomic levels is followed by the idler one which can be superradiant due to light-induced dipole-dipole interactions. We then calculate the cooperative Lamb shift (CLS) of the idler photon, which is a cumulative effect of interaction energy. We study its dependence on a cylindrical geometry, a conventional setup in cold atom experiments, and estimate the maximum CLS which can be significant and observable. Manipulating the CLS of cascade emissions enables frequency qubits that provide alternative robust elements in quantum network. © 2015 Elsevier Inc..


Krouk G.,New York University | Krouk G.,CNRS Biochemistry and Plant Molecular Physiology Laboratory | Crawford N.M.,University of California at San Diego | Coruzzi G.M.,New York University | Tsay Y.-F.,Academia Sinica, Taiwan
Current Opinion in Plant Biology | Year: 2010

Nitrate (NO 3 -) is a key nutrient as well as a signaling molecule that impacts both metabolism and development of plants. Understanding the complexity of the regulatory networks that control nitrate uptake, metabolism, and associated responses has the potential to provide solutions that address the major issues of nitrate pollution and toxicity that threaten agricultural and ecological sustainability and human health. Recently, major advances have been made in cataloguing the nitrate transcriptome and in identifying key components that mediate nitrate signaling. In this perspective, we describe the genes involved in nitrate regulation and how they influence nitrate transport and assimilation, and we discuss the role of systems biology approaches in elucidating the gene networks involved in NO 3 - signaling adaptation to fluctuating environments. © 2010.


Chen L.-Y.,Ecole Polytechnique Federale de Lausanne | Chen L.-Y.,Academia Sinica, Taiwan | Majerska J.,Ecole Polytechnique Federale de Lausanne | Lingner J.,Ecole Polytechnique Federale de Lausanne
Genes and Development | Year: 2013

Mutations in CTC1 lead to the telomere syndromes Coats Plus and dyskeratosis congenita (DC), but the molecular mechanisms involved remain unknown. CTC1 forms with STN1 and TEN1 a trimeric complex termed CST, which binds ssDNA, promotes telomere DNA synthesis, and inhibits telomerase-mediated telomere elongation. Here we identify CTC1 disease mutations that disrupt CST complex formation, the physical interaction with DNA polymerase a-primase (polα-primase), telomeric ssDNA binding in vitro, accumulation in the nucleus, and/or telomere association in vivo. While having diverse molecular defects, CTC1 mutations commonly lead to the accumulation of internal single-stranded gaps of telomeric DNA, suggesting telomere DNA replication defects as a primary cause of the disease. Strikingly, mutations in CTC1 may also unleash telomerase repression and telomere length control. Hence, the telomere defect initiated by CTC1 mutations is distinct from the telomerase insufficiencies seen in classical forms of telomere syndromes, which cause short telomeres due to reduced maintenance of distal telomeric ends by telomerase. Our analysis provides molecular evidence that CST collaborates with DNA polα-primase to promote faithful telomere DNA replication. © 2013 Chen et al.


Chen Y.-T.,National Penghu University of Science and Technology | Chen M.C.,Academia Sinica, Taiwan
Expert Systems with Applications | Year: 2011

In this paper, we propose using chi-square statistics to measure similarities and chi-square tests to determine the homogeneity of two random samples of term vectors for text categorization. The properties of chi-square tests for text categorization are studied first. One of the advantages of chi-square test is that its significance level is similar to the miss rate that provides a foundation for theoretical performance (i.e. miss rate) guarantee. Generally a classifier using cosine similarities with TF IDF performs reasonably well in text categorization. However, its performance may fluctuate even near the optimal threshold value. To improve the limitation, we propose the combined usage of chi-square statistics and cosine similarities. Extensive experiment results verify properties of chi-square tests and performance of the combined usage. © 2010 Elsevier Ltd. All rights reserved.


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.


Lin Z.,University of Taipei | Li W.-H.,University of Taipei | Li W.-H.,Academia Sinica, Taiwan
Molecular Biology and Evolution | Year: 2012

The sequences of the untranslated regions (UTRs) of mRNAs play important roles in posttranscriptional regulation, but whether a change in UTR length can significantly affect the regulation of gene expression is not clear. In this study, we examined the connection between UTR length and Expression Correlation with cytosolic ribosomal proteins (CRP) genes (ECC), which measures the level of expression similarity of a group of genes with CRP genes under various growth conditions. We used data from the aerobic fermentation yeast Saccharomyces cerevisiae and the aerobic respiration yeast Candida albicans. To reduce statistical fluctuations, we computed the ECC for the genes in a Gene Ontology (GO) functional group. We found that in both species, ECC is strongly correlated with the 5' UTR length but not with the 3' UTR length and that the 5' UTR length is evolutionarily better conserved than the 3' UTR length. Interestingly, we found 11 GO groups that have had a substantial increase in 5' UTR length in the S. cerevisiae lineage and that the length increase was associated with a substantial decrease in ECC. Moreover, 9 of the 11 GO groups of genes are involved in mitochondrial respiration function, whose expression reprogramming has been shown to be a major factor for the evolution of aerobic fermentation. Finally, we found that an increase in 5' UTR length may decrease the +1 nucleosome occupancy. This study provides a new angle to understand the role of 5' UTR in gene expression regulation and evolution. © The Author 2011.


Wang Y.-Y.,National Yang Ming University | Tsaya Y.-F.,Academia Sinica, Taiwan
Plant Cell | Year: 2011

This study of the Arabidopsis thaliana nitrate transporter NRT1.9 reveals an important function for a NRT1 family member in phloem nitrate transport. Functional analysis in Xenopus laevis oocytes showed that NRT1.9 is a low-affinity nitrate transporter. Green fluorescent protein and b-glucuronidase reporter analyses indicated that NRT1.9 is a plasma membrane transporter expressed in the companion cells of root phloem. In nrt1.9 mutants, nitrate content in root phloem exudates was decreased, and downward nitrate transport was reduced, suggesting that NRT1.9 may facilitate loading of nitrate into the root phloem and enhance downward nitrate transport in roots. Under high nitrate conditions, the nrt1.9 mutant showed enhanced root-to-shoot nitrate transport and plant growth. We conclude that phloem nitrate transport is facilitated by expression of NRT1.9 in root companion cells. In addition, enhanced root-to-shoot xylem transport of nitrate in nrt1.9 mutants points to a negative correlation between xylem and phloem nitrate transport. © 2011 American Society of Plant Biologists. All rights reserved.


Yip S.,Academia Sinica, Taiwan
Annual Review of Condensed Matter Physics | Year: 2014

Physics of noncentrosymmetric superconductors is reviewed. We explain the mixing between singlet and triplet superconducting order parameters when parity symmetry is absent. Some exotic properties are summarized, including magnetoelectric effects, the helical phase, topological properties, and unusual surface states. © Copyright 2014 by Annual Reviews. All rights reserved.


Liu H.-L.,Academia Sinica, Taiwan | Cheng S.-C.,A-Life Medical
Molecular and Cellular Biology | Year: 2012

In Saccharomyces cerevisiae, the 3' splice site is not required for the first catalytic reaction of splicing. We have previously reported that at least 24 nucleotides downstream of the branch point is required for the first reaction to take place, but the precatalytic spliceosome forms efficiently on the truncated pre-mRNA with only 5 nucleotides retained downstream of the branch point. The factors that mediate this length-dependent control of the first catalytic step are not known. We show here that Prp2 can be recruited to the spliceosome without interacting with pre-mRNA when the 3' tail is short. Prp2 interacts with the intron when the 3' tail is extended, which results in destabilization of Prp2 and, consequently, progression of the first reaction. An RNA segment at 23 to 33 nucleotides downstream of the branch point is necessary and sufficient for the ATP-dependent action of Prp2. We also show that Prp2 directly interacts with the carboxyl-terminal fragment of Brr2 by pulldown assays. We propose that Prp2 is recruited to the spliceosome via interaction with Brr2 and is spatially positioned to interact with this specific region of the pre-mRNA, which stimulates the ATPase activity of Prp2 to promote the progression of the first catalytic step. © 2012, American Society for Microbiology.


Deloye C.J.,Northwestern University | Deloye C.J.,Mitre Corporation | Taam R.E.,Northwestern University | Taam R.E.,Academia Sinica, Taiwan
Astrophysical Journal Letters | Year: 2010

We have developed a new method for calculating common envelope (CE) events based on explicit consideration of the donor star's structural response to adiabatic mass loss. In contrast to existing CE prescriptions, which specify a priori the donor's remnant mass, we determine this quantity self-consistently and find that it depends on binary and CE parameters. This aspect of our model is particularly important to realistic modeling for upper main-sequence star donors without strongly degenerate cores (and hence without a clear core/envelope boundary). We illustrate the central features of our method by considering CE events involving 10 M⊙ donors on or before their red giant branch. For such donors, the remnant core mass can be as much as 30% larger than the star's He-core mass. Applied across a population of such binaries, our methodology results in a significantly broader remnant mass and final orbital separation distribution and a 20% increase in CE survival rates as compared to previous prescriptions for the CE phase. ©2010. The American Astronomical Society. All rights reserved.


Chou S.-J.,Salk Institute for Biological Studies | Chou S.-J.,Academia Sinica, Taiwan | O'Leary D.D.M.,Salk Institute for Biological Studies
Molecular and Cellular Neuroscience | Year: 2013

The neocortex represents the brain region that has undergone a major increase in its relative size during the course of mammalian evolution. The larger cortex results from a corresponding increase in progenitor cell number. The progenitors giving rise to neocortex are located in the ventricular zone of the dorsal telencephalon and highly express Lhx2, a LIM-homeodomain transcription factor. The neocortex fails to form in the Lhx2 constitutive knockout, indicating a role for Lhx2 in corticogenesis, but mid-embryonic lethality of the Lhx2 knockout requires the use of conditional strategies for further studies. Therefore, to explore Lhx2 function in neocortical progenitors, we generated mice with Lhx2 conditionally deleted from cortical progenitors at the onset of neurogenesis. We find that Lhx2 is critical for maintaining the proliferative state of neocortical progenitors during corticogenesis. In the conditional knockouts, the neocortex is formed but is significantly smaller than wild type. We find that deletion of Lhx2 leads to significantly decreased numbers of cortical progenitors and premature neuronal differentiation. A likely mechanism is indicated by our findings that Lhx2 is required for the expression of Hes1 in cortical progenitors, a key effector in the Notch signaling pathway that maintains the proliferative progenitor state. We conclude that Lhx2 regulates the balance between proliferation and differentiation in cortical progenitors and through this mechanism Lhx2 controls cortical size. © 2013 Elsevier Inc.


Liu S.-H.,Academia Sinica, Taiwan
Medical Anthropology Quarterly | Year: 2011

This article employs the rite of passage concept to analyze why and how heroin use and a subsequent HIV/AIDS epidemic have taken hold among minority Nuosu (Yi) young men in Southwest China. It juxtaposes structural inequalities and sociocultural particularities in social suffering among Nuosu youths as they attempt to create meaningful lives in China's market reform era. Since the 1980s, young Nuosu have ventured out to Han-dominant cities in search of fun and opportunities. This movement has become a new foray into manhood and inadvertently set up their encounter with heroin and the subsequent introduction of HIV into their hometowns. The article is based on my 20-month ethnographic fieldwork in Limu, a mountainous Nuosu community in Liangshan Yi Autonomous Prefecture, Sichuan Province, between 2002 and 2009. © 2011 by the American Anthropological Association.


Lal D.V.,Academia Sinica, Taiwan | Lal D.V.,Harvard - Smithsonian Center for Astrophysics | Ho L.C.,Carnegie Institution for Science
Astronomical Journal | Year: 2010

This paper presents the first high-resolution and high-sensitivity study of the radio properties of optically selected type 2 quasars. We used the Very Large Array at 8.4 GHz to observe 59 sources drawn from the Sloan Digital Sky Survey sample of Zakamska etal.. The detection rate of our survey is 59% (35/59), comparable to the detection rate in FIRST at 1.4GHz. Ongoing star formation, although present, contributes negligible radio emission at the current sensitivity limit. Comparing the radio powers with the [O III] λ5007 luminosities, we find that roughly 15% ± 5% of the sample can be considered radio loud. Intriguingly, the vast majority of the detected sources in our sample fall in a region intermediate between those traditionally occupied by radio loud and radio quiet quasars. Moreover, most of these "radio intermediate" sources tend to have flat or inverted radio spectra, which we speculate may be caused by free-free absorption by ionized gas in the narrow-line region. The incidence of flat-spectrum sources in type 2 quasars appears to be much higher than in type 1 quasars, in apparent violation of the simple orientation-based unified model for active galaxies. © 2010. The American Astronomical Society.


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.


Yang J.Y.,Academia Sinica, Taiwan
Nature communications | Year: 2013

Eukaryotic cells maintain mitochondrial integrity through mitophagy, an autophagic process by which dysfunctional mitochondria are selectively sequestered into double-layered membrane structures, termed phagophores, and delivered to lysosomes for degradation. Here we show that small fragments of parkin-labelled mitochondria at omegasome-marked sites are engulfed by autophagic membranes one at a time. Using a light-activation scheme to impair long mitochondrial tubules, we demonstrate that sites undergoing bit-by-bit mitophagy display preferential ubiquitination, and are situated where parkin-labelled mitochondrial tubules and endoplasmic reticulum intersect. Our observations suggest contact regions between the endoplasmic reticulum and impaired mitochondria are initiation sites for local LC3 recruitment and mitochondrial remodelling that support bit-by-bit, parkin-mediated mitophagy. These results help in understanding how cells manage to fit large and morphologically heterogeneous mitochondria into micron-sized autophagic membranes during mitophagy.


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.


Hsin Y.-C.,Academia Sinica, Taiwan | Qiu B.,University of Hawaii at Manoa | Chiang T.-L.,National Taiwan Normal University | Wu C.-R.,National Taiwan Normal University
Journal of Geophysical Research: Oceans | Year: 2013

Seasonal and interannual changes of surface Kuroshio intensity and central position east of Taiwan during 1993-2012 are investigated by quantitatively analyzing the satellite altimetry product. The Kuroshio moves inshore (offshore) off northeast of Taiwan in winter (summer), whereas it has an offshore (inshore) path off southeast of Taiwan in winter (summer). The seasonal change of heat flux over the East China Sea shelf is found to cause the seasonality of the Kuroshio central position off northeast of Taiwan, whereas the seasonal Kuroshio movement off southeast of Taiwan is found to be induced by the combined effect of the Kuroshio changes through the Luzon Strait and the eastern Luzon Island. In contrast to this y-dependent path changes, the Kuroshio becomes weaker (stronger) as a whole east of Taiwan in winter (summer). On the interannual time scales, the Kuroshio throughout the eastern coast of Taiwan intensifies and has a concurrent offshore path during the periods of 1995-1997 and 2004-2007. The relative intensity of cyclonic eddies to anticyclonic eddies off eastern Taiwan are found to contribute to these interannual Kuroshio changes. © 2013. American Geophysical Union. All Rights Reserved.


Injection of short-lived radionuclides from a nearby core-collapse Type II supernova into the already-formed solar protoplanetary disk was proposed to account for the former presence of 26Al, 41Ca, and 60Fe in the early solar system inferred from isotopic analysis of meteoritic samples. One potential corollary of this "late-injection" scenario is that the disk's initial (pre-injection) oxygen isotopic composition could be significantly altered, as supernova material that carried the short-lived radionuclides would also deliver oxygen components synthesized in that given star. Therefore, the change in the oxygen isotopic composition of the disk caused by injection could in principle be used to constrain the supernova injection models. Previous studies showed that although supernova oxygen could result in a wide range of shifts in 17O/16O and 18O/16O of the disk, a couple of cases existed where the calculated oxygen changes in the disk would be compatible with the meteoritic and solar wind data. Recently, the initial abundances of 41Ca and 60Fe in the solar system were revised to lower values, and the feasibility of supernova injection as a source for the three radionuclides was called into question. In this study, supernova parameters needed for matching 26Al, 41Ca, and 60Fe to their early solar system abundances were reinvestigated and then were used to infer the pre-injection O-isotope composition of the disk. The result suggested that a supernova undergoing mixing fallback might be a viable source for the three radionuclides. © 2014. The American Astronomical Society. All rights reserved.


Rao R.,Institute of Astronomy and Astrophysics | Girart J.M.,Institute Of Ciencies Of Lespai Csic Ieec | Lai S.-P.,National Tsing Hua University | Lai S.-P.,Academia Sinica, Taiwan | Marrone D.P.,University of Arizona
Astrophysical Journal Letters | Year: 2014

We present subarcsecond resolution polarimetric observations of the 878 μm thermal dust continuum emission obtained with the Submillimeter Array toward the IRAS 16293-2422 protostellar binary system. We report the detection of linearly polarized dust emission arising from the circumstellar disk associated with the IRAS 16293-2422 B protostar. The fractional polarization of ≃ 1.4% is only slightly lower than that expected from theoretical calculations in such disks. The magnetic field structure on the plane of the sky derived from the dust polarization suggests a complex magnetic field geometry in the disk, possibly associated with a rotating disk that is wrapping the field lines as expected from the simulations. The polarization around IRAS 16293-2422 A at subarcsecond angular resolution is only marginally detected. © 2014. The American Astronomical Society. All rights reserved..


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.


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.


This study was conducted at a high-latitude location (32°N; Kochi, Japan), where annual seawater temperatures show large fluctuations due to the meandering of the Kuroshio Current, providing a unique opportunity to examine the influence of temperature on coral reproduction. Annual spawning of individual colonies of four reef coral species-two Acropora species (Acropora hyacinthus and A. japonica) and two faviid species (Favites pentagona and Platygyra contorta)-was monitored in situ for 4 years in 2006-2009. The spawning of the four species always occurred around the last quarter moon in the local summer, July or August, irrespective of high annual variations in seawater temperatures (from 23.7 to 29.5 °C) and weather during the spawning period. However, the exact timing of spawning during the spawning period varied among the years and was correlated with the cumulative seawater temperature during the late period of gametogenesis (0-3 months before spawning). When seawater temperatures were higher, spawning occurred in the earlier spawning month (July) and vice versa, except in A. hyacinthus, which always spawned in July. In the case of the two Acropora species, higher (lower) temperatures led to spawning earlier (later) in the lunar cycle. Seawater temperature may have an influence on gametogenesis, causing the shift in spawning timing. © 2012 Marine Biological Laboratory.


Kar S.,Harbin Institute of Technology | Ho Y.K.,Academia Sinica, Taiwan
International Journal of Quantum Chemistry | Year: 2010

We have investigated the effects of screened Coulomb (Yukawa) potentials on the bound 1,3D states and the doubly excited 1,3De resonance states of helium atom using highly correlated exponential basis functions. The Density of resonance states are calculated using stabilization method. Highly correlated exponential basis functions are used to consider the correlation effect between the charged particles. A total of 18 resonances (nine each for 1De and 3De states) below the n = 2 He+ threshold has been calculated. For each spin states, this includes four members in the 2pnp series, three members in the 2snd series, and two members in 2pnf series. The resonance energies and widths for various screening parameters ranging from infinity to a small value for these 1,3De resonance states are reported along with the bound-excited 1s3d 1,3D state energies. Overall behavior of the spectral profile of 1s3d 1D state of helium atom due to electron-electron and electron-nucleus screening are also presented. Accurate resonance energies and widths are also reported for He in vacuum. © 2009 Wiley Periodicals, Inc.


Chen S.-K.,Yuanpei University | Lin S.-J.,Academia Sinica, Taiwan
Journal of Visual Communication and Image Representation | Year: 2012

Based on generalized random grids, this paper proposes two visual cryptography methods denoted as (2, n) GRG and (2, infinity) GRG. The (2, n) GRG is suitable for the pre-decided number of shares, and the (2, infinity) method is suitable for the adjustable number of shares. The proposed (2, n) GRG achieves better contrast on the stacking result, and the proposed (2, infinity) GRG enables extending the number of shares anytime. Based on the definition of contrast in Shyu's work in 2007, we also demonstrate that the stacking result of (2, n) GRG is close to the theoretical bound of the contrast, and the stacking result of (2, infinity) GRG achieves the theoretical bound of the contrast. © 2012 Elsevier Inc. All rights reserved.


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.


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.


He J.H.,CAS Yunnan Astronomical Observatory | Takahashi S.,Academia Sinica, Taiwan | Chen X.,Chinese Academy of Sciences
Astrophysical Journal, Supplement Series | Year: 2012

A northern subsample of 89 Spitzer GLIMPSE extended green objects (EGOs), the candidate massive young stellar objects, are surveyed for molecular lines in two 1GHz ranges: 251.5-252.5 and 260.188-261.188GHz. A comprehensive catalog of observed molecular line data and spectral plots are presented. Eight molecular species are undoubtedly detected: H 13CO +, SiO, SO, CH 3OH, CH 3OCH 3, CH 3CH 2CN, HCOOCH 3, and HN 13C. The H 13CO +3-2 line is detected in 70 EGOs, among which 37 also show the SiO6-5 line, demonstrating their association with dense gas and supporting the outflow interpretation of the extended 4.5 μm excess emission. Our major dense gas and outflow tracers (H 13CO +, SiO, SO, and CH 3OH) are combined with our previous survey of 13CO, 12CO, and C 18O1-0 toward the same sample of EGOs for a multi-line, multi-cloud analysis of linewidth and luminosity correlations. Good log-linear correlations are found among all considered line luminosities, the explanation of which requires a universal similarity of density and thermal structures and probably of shock properties among all EGO clouds. It also requires that the shocks be produced within the natal clouds of the EGOs. Diverse degrees of correlation are found among the linewidths. However, both the linewidth and luminosity correlations tend to progressively worsen across larger cloud subcomponent size scales, depicting the increase of randomness across cloud subcomponent sizes. Moreover, the linewidth correlations among the three isotopic CO1-0 lines show data scatter as linear functions of the linewidth itself, indicating that the velocity randomness also increases with whole cloud sizes in a regular way. © © 2012. The American Astronomical Society. All rights reserved.


Hu C.-K.,Academia Sinica, Taiwan
Journal of Physics: Conference Series | Year: 2015

Many human diseases and the death of most supercentenarians are related to protein aggregation. Neurodegenerative diseases include Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD), frontotemporallobar degeneration, etc. Such diseases are due to progressive loss of structure or function of neurons caused by protein aggregation. For example, AD is considered to be related to aggregation of Aβ40 (peptide with 40 amino acids) and Aβ42 (peptide with 42 amino acids) and HD is considered to be related to aggregation of polyQ (polyglutamine) peptides. In this paper, we briefly review our recent discovery of key factors for protein aggregation. We used a lattice model to study the aggregation rates of proteins and found that the probability for a protein sequence to appear in the conformation of the aggregated state can be used to determine the temperature at which proteins can aggregate most quickly. We used molecular dynamics and simple models of polymer chains to study relaxation and aggregation of proteins under various conditions and found that when the bending-angle dependent and torsion-angle dependent interactions are zero or very small, then protein chains tend to aggregate at lower temperatures. All atom models were used to identify a key peptide chain for the aggregation of insulin chains and to find that two polyQ chains prefer anti-parallel conformation. It is pointed out that in many cases, protein aggregation does not result from protein mis-folding. A potential drug from Chinese medicine was found for Alzheimer's disease. © Published under licence by IOP Publishing Ltd.


Vijayan K.,Academia Sinica, Taiwan
Tree Genetics and Genomes | Year: 2010

Mulberry (Morus L) is one of the economically important trees that have a long history of extensive cultivation in Asia. Mulberry leaf is the sole food for the silkworm Bombyx mori; hence, the sustainability of the sericulture industry is dependent on the continuous supply of nutritious mulberry leaf. Genetic improvement of mulberry for leaf yield, leaf nutritional contents, and adaptability has great socioeconomical importance because the sericulture is the backbone of rutal economy in several Asian countries. Much effort has been made on germplasm collection, characterization, and varietal development through conventional methods. However, the complexity of important agronomic traits, the substantial lag time between germination and sexual maturity, the absence of inbred lines, and the outbreeding nature of mulberry delay the genetic improvement via conventional breeding techniques. In this postgenomic era, having the next generation sequencing facilities in its fold, it is possible to integrate modern genomic tools with conventional breeding techniques to dissect the complex traits into their individual components to gain better control over them. In mulberry, such efforts are lacking. This paper, therefore, summarizes the current position of genetic and genomics research in mulberry and discusses the directions for future research, utilizing the emerging technologies in molecular markers, association genetics, quantitative trait locus mapping, transcriptomics, metabolomics, marker-assisted selection breeding, and transgenesis. © 2010 Springer-Verlag.


Wang C.-W.,Academia Sinica, Taiwan
Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids | Year: 2015

Lipids are essential components for life. Their various structural and physical properties influence diverse cellular processes and, thereby, human health. Lipids are not genetically encoded but are synthesized and modified by complex metabolic pathways, supplying energy, membranes, signaling molecules, and hormones to affect growth, physiology, and response to environmental insults. Lipid homeostasis is crucial, such that excess fatty acids (FAs) can be harmful to cells. To prevent such lipotoxicity, cells convert excess FAs into neutral lipids for storage in organelles called lipid droplets (LDs). These organelles do not simply manage lipid storage and metabolism but also are involved in protein quality management, pathogenesis, immune responses, and, potentially, neurodegeneration. In recent years, a major trend in LD biology has centered around the physiology of lipid mobilization via lipophagy of fat stored within LDs. This review summarizes key findings in LD biology and lipophagy, offering novel insights into this rapidly growing field. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim Levine and Anant K. Menon. © 2015.


Chiang Y.-S.,Chinese University of Hong Kong | Wu C.-I.,Academia Sinica, Taiwan
Evolution and Human Behavior | Year: 2015

Humans tend to treat the ingroup more favorably than the outgroup. The phenomenon of parochial altruism is commonly observed in experimental studies on the division of valuable goods among people from children to adults in modern and indigenous societies. Relatively little known is how parochial altruism evolves in the presence of social influence. We conducted a dictator-game experiment on children and adolescents in different school classes to assess parochial altruism. Subjects divided an endowment of valuable goods with an ingroup and an outgroup person. We then manipulated the social information of how the ingroup and the outgroup person shared their endowments with each other. Our experiment shows that subjects would modify their giving to the two recipients when receiving the information, suggesting that parochial altruism-the difference in how much the ingroup and the ougroup receive-is subject to modification under social influence. Parochialism, in particular, is reduced when social influence is exerted from the ingroup. Our study suggests the research to take into account the social dynamics of interpersonal influence to understand how norms of parochial altruism evolve. © 2015 Elsevier Inc.


Hsieh B.C.,Academia Sinica, Taiwan | Yee H.K.C.,University of Toronto
Astrophysical Journal | Year: 2014

Large direct imaging surveys usually use a template-fitting technique to estimate photometric redshifts for galaxies, which are then applied to derive important galaxy properties such as luminosities and stellar masses. These estimates can be noisy and suffer from systematic biases because of the possible mis-selection of templates and the propagation of the photometric redshift uncertainty. We introduce an algorithm, the Direct Empirical Photometric method (DEmP), that can be used to directly estimate these quantities using training sets, bypassing photometric redshift determination. DEmP also applies two techniques to minimize the effects arising from the non-uniform distribution of training set galaxy redshifts from a flux-limited sample. First, for each input galaxy, fitting is performed using a subset of the training set galaxies with photometry and colors closest to those of the input galaxy. Second, the training set is artificially resampled to produce a flat distribution in redshift or other properties, e.g., luminosity. To test the performance of DEmP, we use a four filter-band mock catalog to examine its ability to recover redshift, luminosity, stellar mass, and luminosity and stellar mass functions. We also compare the results to those from two publicly available template-fitting methods, finding that the DEmP algorithm outperforms both. We find that resampling the training set to have a uniform redshift distribution produces the best results not only in photometric redshift, but also in estimating luminosity and stellar mass. The DEmP method is especially powerful in estimating quantities such as near-IR luminosities and stellar mass using only data from a small number of optical bands. © 2014. The American Astronomical Society. 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..


Tseng M.-C.,Academia Sinica, Taiwan | Yang H.-Y.,National Chung Cheng University | Chu Y.-H.,National Chung Cheng University
Organic and Biomolecular Chemistry | Year: 2010

Using scandium triflate and microwaves, the direct double dehydrocyclization of anthranilate-containing tripeptides was achieved, affording the total syntheses of (i) quinazolino[3,2-a]benzodiazepinediones (1a-f), (ii) diazepino[2,1-b]quinazolinediones (2a-e), and (iii) pyrazino[2,1-b]quinazolinediones (3a-e) with good overall isolated yields (23-43%, 37-47% and 31-56%, respectively). Among the quinazolino[3,2-a] benzodiazepinediones synthesized, 1a (sclerotigenin), 1b (circumdatin F), and 1f (asperlicin C) are natural products. © 2010 The Royal Society of Chemistry.


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.


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.


Yip S.-K.,Academia Sinica, Taiwan
Journal of Low Temperature Physics | Year: 2010

We discuss the topology of the wavefunctions of two-dimensional time-reversal symmetric superconductors. We consider (a) the planar state, (b) a system with broken up-down reflection symmetry, and (c) a system with general spin-orbit interaction. We show explicitly how the relative sign of the order parameter on the two Fermi surfaces determines this topology, and clarify the meaning of the Z 2 classification for these topological states. © 2010 Springer Science+Business Media, LLC.


Hsu Y.-J.,Academia Sinica, Taiwan | Simons M.,California Institute of Technology | Williams C.,Institute of Geological & Nuclear Sciences | Casarotti E.,Italian National Institute of Geophysics and Volcanology
Geochemistry, Geophysics, Geosystems | Year: 2011

Using finite element models (FEMs), we examine the sensitivity of surface displacements to the location of fault slip, topography, and three-dimensional variations in elastic moduli in the context of a 2-D infinite thrust fault. We then evaluate the impact of these factors and fault geometry on surface displacements and estimates of the distribution of coseismic slip associated with the 2005 Mw 8.7 Nias-Simeulue, Sumatra earthquake. Topographic effects can be significant near the trench, where bathymetric gradients are highest and the fault is closest to the free surface. Variations in Young's modulus can significantly alter predicted deformation. Surface displacements are relatively insensitive to perturbations in Poisson's ratio for shear sources, but may play a stronger role when the source has a dilatational component. If we generate synthetic displacements using a heterogeneous elastic model and then use an elastic half-space or layered earth model to estimate the slip distribution and fault geometry, we find systematic residuals of surface displacements and different slip patterns compared to the input fault slip model. The coseismic slip distributions of the 2005 earthquake derived from the same fault geometry and different material models show that the rupture areas are narrower in all tested heterogeneous elastic models compared to that obtained using half-space models. This difference can be understood by the tendency to infer additional sources in elastic half-space models to account for effects that are intrinsically due to the presence of rheological gradients. Although the fit to surface observations in our preferred 3-D FEM model is similar to that from a simple half-space model, the resulting slip distribution may be a more accurate reflection the true fault slip behavior. Copyright 2011 by the American Geophysical Union.


Chen C.-S.,National Center for Theoretical science | Chen C.-S.,Academia Sinica, Taiwan | Lin C.-M.,National Tsing Hua University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2011

In this Letter, we consider a chaotic inflation model where the role of inflaton is played by the Higgs triplet in type II seesaw mechanism for generating the small masses of left-handed neutrinos. Leptogenesis could happen after inflation. This model is constructed without introducing supersymmetry (SUSY). © 2010 Elsevier B.V.


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.


Geng C.Q.,National Tsing Hua University | Geng C.Q.,National Center for Theoretical science | Hsiao Y.K.,Academia Sinica, Taiwan
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2011

We study the four-body exclusive semileptonic baryonic B̄ decays of B-→pp̄ℓ-̄̄ℓ (ℓ=e,μ,τ) in the standard model. We find that their decay branching ratios are about (1.0,1.0,0.5)×10-4, respectively. In particular, the electron mode is close to the corresponding CLEO's upper limit of 5.2×10-3, while all results are about one or two orders of magnitude larger than the previous estimated values for the inclusive modes of B̄→BB̄'ℓ̄̄. Clearly, both B-factories of Belle and BaBar should be able to observe these exclusive four-body modes. © 2011 Elsevier B.V.


Tarn W.,Academia Sinica, Taiwan | Lai M.,National Cheng Kung University
Cell Division | Year: 2011

Regulation of cyclin levels is important for many cell cycle-related processes and can occur at several different steps of gene expression. Translational regulation of cyclins, which occurs by a variety of regulatory mechanisms, permits a prompt response to signal transduction pathways induced by environmental stimuli. This review will summarize translational control of cyclins and its influence on cell cycle progression.© 2011 Tarn and Lai; licensee BioMed Central Ltd.


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.


Wang J.-H.,Academia Sinica, Taiwan
Journal of Geophysical Research: Solid Earth | Year: 2011

On 20 September 1999 the Ms7.6 Chi-Chi earthquake ruptured the Chelungpu fault in central Taiwan. In 2005 the Taiwan Chelungpu Fault Drilling Project was launched to drill two deep holes (holes A and B) cutting across the fault plane. The heat strength (= 7.0°C m), within a heated layer of ∼5 mm, on the fault at hole A due to frictional faulting is evaluated from the values of shear stress and thermal and mechanical parameters measured from the core samples. Based on a 1-D heat conduction equation and 2-D faulting model, with the values of thermal diffusivity evaluated within a representative temperature range, the thermal and pore fluid pressure history at depths 1110.37-1111.34 m in hole A is constructed. Results show that the peak temperature at the center of the heated layer could have been higher than 1100°C during faulting, and temperature rise decreased with increasing distance and time. The possible relationships between the temperatures and chemical reactions of clay minerals are discussed in detail. In the heated layer, pseudotachylites have been formed and quartz plasticity might also have been operative during faulting. Outside this slip zone, the temperature rise was low and thus clay minerals were stable during faulting. The evaluated pore fluid pressure is 22.5 MPa. This suggests the existence of a suprahydrostatic state in the fault zone during the earthquake. Indirect evidence of the existence of fluids in the fault zone during faulting is described. Additionally, rock physics is applied to interpret the observations. Copyright 2011 by the American Geophysical Union.


Fan C.-W.,National Chung Cheng University | Shiue J.,Academia Sinica, Taiwan | Wu C.-Y.,National Chung Cheng University
Organic Geochemistry | Year: 2011

Perylene formation in sediments of water bodies has been a topic of continual discussion and debate. We report the concentration and age (ca. 660. yr) profiles of perylene and other polycyclic aromatic hydrocarbons (PAHs) in a sediment core from Emerald Peak Lake, the largest high mountain lake in Taiwan. Perylene is dominant at all depths of the sediment (ranging from 60% to 98% of total PAHs), a feature not commonly found in other sediments. The concentration profile of perylene with sediment age fits a first order kinetic model, which might be an indication of a steady sedimentary environment. © 2010 Elsevier Ltd.


Lemme M.C.,University of Siegen | Li L.-J.,Academia Sinica, Taiwan | Palacios T.,Massachusetts Institute of Technology | Schwierz F.,TU Hamburg - Harburg
MRS Bulletin | Year: 2014

This article reviews the potential of graphene and related two-dimensional (2D) materials for applications in micro- and nanoelectronics. In addition to graphene, special emphasis is placed on transition metal dichalcogenides (TMDs). First, we discuss potential solutions for application-scale material growth, in particular chemical vapor deposition. We describe challenges for electrical contacts and dielectric interfaces with 2D materials. The device-related sections in this review first weigh the pros and cons of semi-metal graphene as a field-effect transistor (FET) channel material for logic and radio frequency applications. This is followed by an introduction to alternate graphene switch concepts that utilize the particular properties of the material, namely tunnel FETs, vertical devices, and bilayer pseudospin FETs. The final section is dedicated to semiconducting TMDs and their integration in FETs using the examples of n-type molybdenum disulfide (MoS2) and p-type tungsten diselenide (WSe2). © Materials Research Society 2014.


Hirotani K.,Academia Sinica, Taiwan
Astrophysical Journal Letters | Year: 2015

We investigate the particle accelerator that arises in a rotating neutron-star magnetosphere. Simultaneously solving the Poisson equation for the electro-static potential, the Boltzmann equations for relativistic electrons and positrons, and the radiative transfer equation, we demonstrate that the electric field is substantially screened along the magnetic field lines by pairs that are created and separated within the accelerator. As a result, the magnetic-field-aligned electric field is localized in higher altitudes near the light cylinder and efficiently accelerates the positrons created in the lower altitudes outward but does not accelerate the electrons inward. The resulting photon flux becomes predominantly outward, leading to typical double-peak light curves, which are commonly observed from many high-energy pulsars. © 2015. The American Astronomical Society. All rights reserved.


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.


Ozdemir A.,Sakarya University | Chen C.-H.,Academia Sinica, Taiwan
Journal of Mass Spectrometry | Year: 2010

A new ion source has been developed for rapid, noncontact analysis of materials at ambient conditions. The method provides desorption of analytes under ambient conditions directly from different surfaces with little or no sample preparation. The new method, termed electrode-assisted desorption electrospray ionization (EADESI), is on the basis of the ionization of molecules on different surfaces by highly charged droplets produced on a sharp-edged high voltage tip, and ions produced are introduced into themass spectrometer through a capillary. The EADESI technique can be applied to various samples including amino acids, peptides, proteins, drugs and human fluids such as urine and blood. EADESI is promising for routine analyses in different fields such as forensic, environmental andmaterial sciences. EADESI interface can be fit to a conventional ion-trapmass spectrometer. It can be used for various types of samples with a broad mass range. EADESI can also provide real-time analysis which is very valuable for biomedical applications. Copyright © 2010 JohnWiley & Sons, Ltd.


Wang J.-H.,Academia Sinica, Taiwan
Annals of Geophysics | Year: 2016

The scaling of earthquake source displacement spectra is analytically studied based on the continuous form of one-dimensional dynamical spring-slider model in the presence of either linearly slip-weakening friction or linearly velocity-weakening friction. The main parameters of the model are the natural angular frequency, ωo, and the (dimensionless) decreasing rate, Δ, of friction with slip (or the characteristic displacement) for slip-weakening friction as well as the (dimensionless) decreasing rate, υ, of friction with velocity (or the characteristic velocity) for velocity-weakening friction. The analytic solution includes the complementary and particular parts. The former shows the travelling wave and the latter denotes vibrations at a site. The complementary solution exhibits ω-1 scaling in the whole range of ω for both friction laws. For the particular solution, slip-weakening friction results in spectral amplitudes only at three values of ω. For velocity-weakening friction with υ>0.5, the log-log plot of spectral amplitude versus ω exhibits almost ω0 scaling when ω is lower than the corner angular frequency, ωc, which is independent on y and increases with ωo. When ω>ωc, the spectral amplitude monotonically decreases with ω following a line with a slope value of −1, which is the scaling exponent. © 2016 by the Istituto Nazionale di Geofisica e Vulcanologia. All rights reserved.


Chang Y.-C.I.,Academia Sinica, Taiwan
Statistics in Medicine | Year: 2013

Effectively combining many classification instruments or diagnostic measurements together to improve the classification accuracy of individuals is a common idea in disease diagnosis or classification. These ensemble-type diagnostic methods can be constructed with respect to different kinds of performance criterions. Among them, the receiver operating characteristic (ROC) curve is the most popular criterion, which, together with some indexes derived from it, is commonly used to evaluate and summarize the performance of a classification instrument, such as a biomarker or a classifier. However, the usefulness of ROC curve and its related indexes relies on the existence of a binary label for each individual subject. In many disease diagnosis situations, such a binary variable may not exist, but only the continuous measurement of the true disease status is available. This true disease status is often referred to as the 'gold standard'. The modified area under ROC curve (AUC)-type measure defined by Obuchowski is a method proposed to accommodate such a situation. However, there is still no method for finding the optimal combination of diagnostic measurements, with respect to such an index, to have better diagnostic power than that of each individual measurement. In this paper, we propose an algorithm for finding the optimal combination with respect to such an extended AUC-type measure such that the combined measurement can have more diagnostic power. We illustrate the performance of our algorithm by using some synthesized data and a diabetes data set. © 2012 John Wiley & Sons, Ltd.


Chin M.-L.,Mount Sinai School of Medicine | Chin M.-L.,Academia Sinica, Taiwan | Mlodzik M.,Mount Sinai School of Medicine
Developmental Cell | Year: 2013

Establishment of planar cell polarity (PCP) in a tissue requires coordination of directional signals from cell to cell. It is thought that this is mediated by the core PCP factors, which include cell-adhesion molecules. Here, we demonstrate that furrowed, the Drosophila selectin, is required for PCP generation. Disruption of PCP in furrowed-deficient flies results from a primary defect in Fz levels and cell adhesion. Furrowed localizes at or near apical junctions, largely colocalizing with Frizzled and Flamingo (Fmi). It physically interacts with and stabilizes Frizzled, and it mediates intercellular Frizzled-Van Gogh (Vang)/Strabismus interactions, similarly to Fmi. Furrowed does so through a homophilic cell-adhesion role that is distinct from its known carbohydrate-binding function described during vertebrate blood-cell/endothelial cell interactions. Importantly, the carbohydrate function is dispensable for PCP establishment. Invivo studies suggest that Furrowed functions partially redundantly with Fmi, mediating intercellular Frizzled-Vang interactions between neighboring cells. © 2013 Elsevier Inc.


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.


Algaba J.C.,Academia Sinica, Taiwan
Monthly Notices of the Royal Astronomical Society | Year: 2013

We have studied very long baseline array (VLBA) polarimetric observations of eight sources, including quasars and BL Lacertae objects, at 12, 15, 22, 24 and 43 GHz. We present highfrequency rotation-measure maps. We find typical values for the rotation measure in the very long baseline interferometry core of several thousand radm-2. These values are higher than the values given in the literature at lower frequencies. Assuming a dependence of the form RM ∝ νa, where RM is the rotation measure, we obtain an average value of a = 3.6 ± 1.3, which is larger than that expected using theoretical considerations. Rotation measures are detected in the jets of only two sources, and we find that only 0906+430 (and possibly 1633+382) show indications of a robust gradient.We discuss the Faraday-corrected polarization properties of the sources. Our interpretation supports the presence of helical magnetic fields with new, unresolved, components affecting the intrinsic direction of polarization close to the base of the jet of some objects. © 2013 The Author. Published by Oxford University Press on behalf of the Royal Astronomical Society.


Hirashita H.,Academia Sinica, Taiwan | Voshchinnikov N.V.,Saint Petersburg State Polytechnic University
Monthly Notices of the Royal Astronomical Society | Year: 2013

accretion and coagulation. Here we model and test these processes by examining the consistency with the observed variation of the extinction curves in the MilkyWay.We find that, if we simply use the parameters used in previous studies, the model fails to explain the flattening of the far-ultraviolet (far-UV) extinction curve for large RV (flatness of the optical extinction curve) and the existence of a carbon bump even in flat extinction curves. This discrepancy is resolved by adopting a 'tuned' model, in which coagulation of carbonaceous dust is less efficient (by a factor of 2) and that of silicate is more efficient with the coagulation threshold removed. The tuned model is also consistent with the relation between silicon depletion (indicator of accretion) and RV if the duration of accretion and coagulation is >100(nH/103 cm-3)-1 Myr, where nH is the number density of hydrogen nuclei in the cloud.We also examine the relations between each of the extinction curve features (UV slope, far-UV curvature and carbon bump strength) and RV. The correlation between UV slope and RV, which is the strongest among the three correlations, is well reproduced by the tuned model. For the far-UV curvature and carbon bump strength, the observational data are located between the tuned model and the original model without tuning, implying that the large scatters in the observational data can be explained by the sensitive response to the coagulation efficiency. The overall success of the tuned model indicates that accretion and coagulation are promising mechanisms of producing the variation of extinction curves in the Milky Way, although we do not exclude possibilities of other dust-processing mechanisms changing extinction curves. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


Asano R.S.,Nagoya University | Takeuchi T.T.,Nagoya University | Hirashita H.,Academia Sinica, Taiwan | Nozawa T.,University of Tokyo
Monthly Notices of the Royal Astronomical Society | Year: 2013

Dust in galaxies forms and evolves by various processes, and these dust processes change the grain size distribution and amount of dust in the interstellarmedium (ISM). We construct a dust evolutionmodel taking into account the grain size distribution, and investigatewhat kind of dust processes determine the grain size distribution at each stage of galaxy evolution. In addition to the dust production by Type II supernovae (SNe II) and asymptotic giant branch (AGB) stars, we consider three processes in the ISM: (i) dust destruction by SN shocks, (ii) metal accretion on to the surface of pre-existing grains in the cold neutral medium (CNM; called grain growth) and (iii) grain-grain collisions (shattering and coagulation) in the warm neutral medium and CNM. We found that the grain size distribution in galaxies is controlled by stellar sources in the early stage of galaxy evolution, and that afterwards the main processes that govern the size distribution changes to those in the ISM, and this change occurs at earlier stage of galaxy evolution for a shorter star formation time-scale (for star formation time-scales = 0.5, 5 and 50 Gyr, the change occurs about galactic age t~0.6, 2 and 5 Gyr, respectively). If we only take into account the processes which directly affect the total dust mass (dust production by SNe II and AGB stars, dust destruction by SN shocks and grain growth), the grain size distribution is biased to large grains (a≲0.2-0.5 μm, where a is the grain radius). Therefore, shattering is crucial to produce small (a 0.01 μm) grains. Since shattering produces a large abundance of small grains (consequently, the surface-to-volume ratio of grains increases), it enhances the efficiency of grain growth, contributing to the significant increase of the total dust mass. Grain growth creates a large bump in the grain size distribution around a ~ 0.01 μm. Coagulation occurs effectively after the number of small grains is enhanced by shattering, and the grain size distribution is deformed to have a bump at a ~ 0.03-0.05 μm at t ~ 10 Gyr.We conclude that the evolutions of the total dustmass and the grain size distribution in galaxies are closely related to each other, and the grain size distribution changes considerably through the galaxy evolution because the dominant dust processes which regulate the grain size distribution change. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.


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.


Brasser R.,Academia Sinica, Taiwan | Walsh K.J.,Southwest Research Institute | Nesvorny D.,Southwest Research Institute
Monthly Notices of the Royal Astronomical Society | Year: 2013

Evidence in the Solar system suggests that the giant planets underwent an epoch of radial migration that was very rapid, with an e-folding time-scale shorter than 1 Myr. It is probable that the cause of this migration was that the giant planets experienced an orbital instability that caused them to encounter each other, resulting in radial migration. A promising and heavily studied way to accomplish such a fast migration is for Jupiter to have scattered one of the ice giants outwards; this event has been called the 'jumping Jupiter' scenario. Several works suggest that this dynamical instability occurred 'late', long after all the planets had formed and the solar nebula had dissipated. Assuming that the terrestrial planets had already formed, then their orbits would have been affected by the migration of the giant planets as many powerful resonances would sweep through the terrestrial planet region. This raises two questions. First, what is the expected increase in dynamical excitement of the terrestrial planet orbits caused by late and very fast giant planet migration? And secondly, assuming that the migration occurred late, can we use this migration of the giant planets to obtain information on the primordial orbits of the terrestrial planets? In this work, we attempt to answer both of these questions using numerical simulations. We directly model a large number of terrestrial planet systems and their response to the smooth migration of Jupiter and Saturn, and also two jumping Jupiter simulations. We study the total dynamical excitement of the terrestrial planet system with the angular momentum deficit (AMD) value, including the way it is shared among the planets. We conclude that to reproduce the current AMD with a reasonable probability (~20 per cent) after late rapid giant planet migration and a favourable jumping Jupiter evolution, the primordial AMD should have been lower than ~70 per cent of the current value, but higher than 10 per cent. We find that a late giant planet migration scenario that initially had five giant planets rather than four had a higher probability of satisfying the orbital constraints of the terrestrial planets. Assuming late migration, we predict that Mars was initially on an eccentric and inclined orbit while the orbits of Mercury, Venus and Earth were more circular and coplanar. The lower primordial dynamical excitement and the peculiar partitioning between planets impose new constraints for terrestrial planet formation simulations.©2013 The Authors. Published by Oxford University Press on behalf of the Royal Astronomical Society.


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.


Hsu Y.-J.,Academia Sinica, Taiwan | Simons M.,California Institute of Technology | Williams C.,Institute of Geological & Nuclear Sciences | Casarotti E.,Italian National Institute of Geophysics and Volcanology
Geochemistry, Geophysics, Geosystems | Year: 2011

Using finite element models (FEMs), we examine the sensitivity of surface displacements to the location of fault slip, topography, and three-dimensional variations in elastic moduli in the context of a 2-D infinite thrust fault. We then evaluate the impact of these factors and fault geometry on surface displacements and estimates of the distribution of coseismic slip associated with the 2005 Mw 8.7 Nias-Simeulue, Sumatra earthquake. Topographic effects can be significant near the trench, where bathymetric gradients are highest and the fault is closest to the free surface. Variations in Young's modulus can significantly alter predicted deformation. Surface displacements are relatively insensitive to perturbations in Poisson's ratio for shear sources, but may play a stronger role when the source has a dilatational component. If we generate synthetic displacements using a heterogeneous elastic model and then use an elastic half-space or layered earth model to estimate the slip distribution and fault geometry, we find systematic residuals of surface displacements and different slip patterns compared to the input fault slip model. The coseismic slip distributions of the 2005 earthquake derived from the same fault geometry and different material models show that the rupture areas are narrower in all tested heterogeneous elastic models compared to that obtained using half-space models. This difference can be understood by the tendency to infer additional sources in elastic half-space models to account for effects that are intrinsically due to the presence of rheological gradients. Although the fit to surface observations in our preferred 3-D FEM model is similar to that from a simple half-space model, the resulting slip distribution may be a more accurate reflection the true fault slip behavior. Copyright 2011 by the American Geophysical Union.


Kar S.,Harbin Institute of Technology | Ho Y.K.,Academia Sinica, Taiwan
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2012

We have carried out calculations to search Borromean windows for the bound F and G states of the H2+ system, where the nuclei and the electrons interact through a screened Coulomb (Yukawa-type) potential. The bound F and G state energies for different values of the screening parameters are obtained using correlated exponential wave functions in the framework of the Ritz variational principle. The critical values of the screening parameters for the bound F and G states are reported for which the H2+ system is stable, while all the possible fragments are unbound; that is, it shows windows for Borromean binding. © 2012 American Physical Society.


Kar S.,Harbin Institute of Technology | Ho Y.K.,Academia Sinica, Taiwan
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2012

We have searched for S-wave shape resonances in the Ps - system. The calculations are carried out in the framework of the complex-coordinate rotation method using both Hylleraas-type wave functions involving powers of interparticle coordinates, and the exponential correlated wave functions. We have located an S-wave shape resonance lying above the Ps (N = 2) threshold. By changing the mass of the positively charged particle from one unit of the electron mass to infinitely heavy, we have traced this resonance pole from Ps - to H -. Results for the shape resonance in H - are comparable with the available results in the literature. © 2012 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.


The equivalent water thickness (EWT, including mascon) solutions derived from the GRACE time-variable gravity (TVG) data are gaining recognition. We examine the physics of this practice from first principle in light of the non-uniqueness of 3-D gravitational inversion. We raise caveats on the indiscriminate utilization of the EWT solutions, because a surface EWT solution cannot represent an internal process in a physically meaningful way. In practice, EWT is often a good-enough representation of the reality as the predominant TVG signals do originate from surficial processes such as the water cycle, but it should be recognized that all internal geophysical processes leave signatures to different extent in the TVG observations. Treating all TVG as EWT will render physical quantities in general not directly resolvable by gravity to be misinterpreted. As the TVG observations span longer and improve in precision, the gravity itself, rather than EWT, should still be the quantity of choice. This is not just a problem of model uncertainties or numerical errors, but one in the understanding and treatment in the interest of the rigor of physics. © 2016 Springer-Verlag Berlin Heidelberg


The Rothemund reaction and the MacDonald 2+2 condensation are two named reactions widely recognized in porphyrin syntheses. Yet not much has been written about the persons whose work paved the way to various porphyrins and porphyrinoids now realized. Paul Rothemund and S. Ferguson MacDonald both obtained their doctorate under Hans Fischer at Munich. Here I attempt to piece together the life stories of the two chemists, tracing back to the connections with the Fischer School, and giving the historical context to their namesake reactions. The pioneering discoveries of Fischer and his students, with later modifications, have become standard methods in the modern era for the synthesis of sizable quantities of porphyrins and porphyrinoids employed for enzyme models, catalysts, drugs, sensors, and building blocks of materials and biomedical research. This essay highlights the pioneers' achievements, renders history relevant, and recounts the influence they had on my research. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Wang J.-H.,Academia Sinica, Taiwan
Earthquake Science | Year: 2016

During the ruptures of an earthquake, the strain energy, ΔE, will be transferred into, at least, three parts, i.e., the seismic radiation energy (Es), fracture energy (Eg), and frictional energy (Ef), that is, (Formula presented.). Friction, which is represented by a velocity- and state-dependent friction law by some researchers, controls the three parts. One of the main parameters of the law is the characteristic slip displacement, Dc. It is significant and necessary to evaluate the reliable value of Dc from observed and inverted seismic data. Since Dc controls the radiation efficiency, (Formula presented.) , the value of ηR is a good constraint of estimating Dc. Integrating observed data and inverted results of source parameters from recorded seismograms, the values of Es and Eg of an earthquake can be measured, thus leading to the value of ηR. The constraint used to estimate the reliable value of Dc will be described in this work. An example of estimates of Dc based on the observed and inverted values of source parameters of the September 20, 1999 MS 7.6 Chi-Chi (Ji-Ji), Taiwan region, earthquake will be presented. © 2016, The Author(s).


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.


Tseng Y.Y.,University of Chicago | Li W.-H.,University of Chicago | Li W.-H.,Academia Sinica, Taiwan
Nucleic Acids Research | Year: 2012

We recently proposed to classify proteins by their functional surfaces. Using the structural attributes of functional surfaces, we inferred the pairwise relationships of proteins and constructed an expandable database of protein surface classification (PSC). As the functional surface(s) of a protein is the local region where the protein performs its function, our classification may reflect the functional relationships among proteins. Currently, PSC contains a library of 1974 surface types that include 25857 functional surfaces identified from 24170 bound structures. The search tool in PSC empowers users to explore related surfaces that share similar local structures and core functions. Each functional surface is characterized by structural attributes, which are geometric, physicochemical or evolutionary features. The attributes have been normalized as descriptors and integrated to produce a profile for each functional surface in PSC. In addition, binding ligands are recorded for comparisons among homologs. PSC allows users to exploit related binding surfaces to reveal the changes in functionally important residues on homologs that have led to functional divergence during evolution. The substitutions at the key residues of a spatial pattern may determine the functional evolution of a protein. In PSC (http://pocket.uchicago.edu/psc/), a pool of changes in residues on similar functional surfaces is provided. © 2012 The Author(s).


Hsu C.W.,Wesleyan University | Chen Y.-L.,Academia Sinica, Taiwan
Journal of Chemical Physics | Year: 2010

The complexity of the coupling between soft particle deformation and fluid perturbation has limited studies of soft particle hydrodynamics to dilute suspensions. A hybrid Brownian dynamics-lattice Boltzmann method is presented that models nondilute soft spherical deformable particle (DP) suspensions in flow. Dependences on particle size and density are investigated for suspensions with over 100 DP. Multi-DP interactions lead to complex dependence of particle distributions on concentration and flow rate. Flow-induced DP migration toward channel center for DP in narrow channels is found. In wide channels, off-center peaks in the center of mass distribution for DP are found. The migration of DP leads to faster average speed of DP than the flow, which can be exploited for fractionating DPs of different sizes. © 2010 American Institute of Physics.


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).


Wu S.-H.,Academia Sinica, Taiwan
Annual Review of Plant Biology | Year: 2014

Depending on the environment a young seedling encounters, the developmental program following seed germination could be skotomorphogenesis in the dark or photomorphogenesis in the light. Light signals are interpreted by a repertoire of photoreceptors followed by sophisticated gene expression networks, eventually resulting in developmental changes. The expression and functions of photoreceptors and key signaling molecules are highly coordinated and regulated at multiple levels of the central dogma in molecular biology. Light activates gene expression through the actions of positive transcriptional regulators and the relaxation of chromatin by histone acetylation. Small regulatory RNAs help attenuate the expression of light-responsive genes. Alternative splicing, protein phosphorylation/dephosphorylation, the formation of diverse transcriptional complexes, and selective protein degradation all contribute to proteome diversity and change the functions of individual proteins. Copyright © 2014 by Annual Reviews.


Lin K.C.-J.,Academia Sinica, Taiwan | Gollakota S.,Massachusetts Institute of Technology | Katabi D.,Massachusetts Institute of Technology
Proceedings of the ACM SIGCOMM 2011 Conference, SIGCOMM'11 | Year: 2011

This paper presents the design and implementation of 802.11n+, a fully distributed random access protocol for MIMO networks. 802.11n+ allows nodes that differ in the number of antennas to contend not just for time, but also for the degrees of freedom provided by multiple antennas. We show that even when the medium is already occupied by some nodes, nodes with more antennas can transmit concurrently without harming the ongoing transmissions. Furthermore, such nodes can contend for the medium in a fully distributed way. Our testbed evaluation shows that even for a small network with three competing node pairs, the resulting system about doubles the average network throughput. It also maintains the random access nature of today's 802.11n networks. Copyright 2011 ACM.


Wang R.-B.,National Dong Hwa University | Hirotani K.,Academia Sinica, Taiwan | Hirotani K.,National Tsing Hua University
Astrophysical Journal | Year: 2011

We analytically investigate the condition for a particle accelerator to be active in the outer magnetosphere of a rotation-powered pulsar. Within the accelerator (or the gap), the magnetic-field-aligned electric field accelerates electrons and positrons, which emit copious gamma-rays via the curvature process. If one of the gamma-rays emitted by a single pair materializes as a new pair on average, the gap is self-sustained. However, if the neutron-star spin-down rate decreases below a certain limit, the gap becomes no longer self-sustained and the gamma-ray emission ceases. We explicitly compute the multiplicity of cascading pairs and find that the obtained limit corresponds to a modification of the previously derived outer-gap death line. In addition to this traditional death line, we find another death line, which becomes important for millisecond pulsars, by separately considering the threshold of photon-photon pair production. Combining these traditional and new death lines, we give predictions on the detectability of gamma-ray pulsars with Fermi and AGILE. An implication for X-ray observations of heated polar-cap emission is also discussed. © 2011. The American Astronomical Society. All rights reserved.


Cheung K.,National Tsing Hua University | Cheung K.,Konkuk University | Yuan T.-C.,Academia Sinica, Taiwan
Physical Review Letters | Year: 2012

Current Higgs boson searches in various channels at the LHC point to an excess at around 124-126 GeV due to a possibly standard-model-like Higgs boson. If one examines more closely the channels (γγ, WW *, and ZZ *) that have excess, this "Higgs boson" may be the Randall-Sundrum radion ·. Because of the trace anomaly, the radion has stronger couplings to the photon and gluon pairs. Thus, it will enhance the production rates into gg and γγ, while those for WW *, ZZ *, and bb̄ are reduced relative to their standard model values. We show that it can match well with the data from CMS for m ·=124GeV, and the required scale Λ ·∼· is about 0.68 TeV. © 2012 American Physical Society.


Lee C.-F.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2011

The HH 111 protostellar system is a young Class I system with two sources, VLA 1 and VLA 2, at a distance of 400pc. Previously, a flattened envelope has been seen in C18O to be in transition to a rotationally supported disk near the VLA 1 source. The follow-up study here is to confirm the rotationally supported disk at 2-3 times higher angular resolutions, at ∼0".3 (or 120AU) in 1.33mm continuum, and ∼0".6 (or 240AU) in 13CO (J = 2-1) and 12CO (J = 2-1) emission obtained with the Submillimeter Array. The 1.33mm continuum emission shows a resolved dusty disk associated with the VLA 1 source perpendicular to the jet axis, with a Gaussian deconvolved size of ∼240AU. The 13CO and 12CO emissions toward the dusty disk show a Keplerian rotation, indicating that the dusty disk is rotationally supported. The density and temperature distributions in the disk derived from a simple disk model are found to be similar to those found in bright T Tauri disks, suggesting that the disk can evolve into a T Tauri disk in the late stage of star formation. In addition, a hint of a low-velocity molecular outflow is also seen in 13CO and 12CO coming out from the disk. © 2011. The American Astronomical Society. 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.


Shen C.N.,Academia Sinica, Taiwan
Methods in molecular biology (Clifton, N.J.) | Year: 2010

Hepatocytes maintained in culture provide an attractive model system for the study of liver function. Furthermore, hepatocyte transplantation offers an alternative cellular therapy to orthotopic liver transplantation for the treatment of hepatic failure and hereditary liver disease. To overcome the problem of organ shortage, additional source of hepatocytes must be found. Here, we present a strategy and protocol to transdifferentiate (or convert) developmentally related pancreatic cells into hepatocytes based on the addition of the synthetic glucocorticoid dexamethasone.


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

We study theoretically interspecies Cooper pairing in a fermionic system with SU(2) × SU(6) symmetry. We show that, with suitable unitary transformations, the order parameter for the ground state can be reduced to only two nonvanishing complex components. The ground state has a large degeneracy. We find that while some Goldstone modes have linear dispersion, others are quadratic at low frequencies. We compare our results with the case of SU(N). © 2011 American Physical Society.


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

Bose-Einstein condensation in the presence of a synthetic spin-orbit interaction is considered, focusing on the case where a Dirac or Rashba potential is generated via a tripod scheme. We found that the ground states can be either plane-wave states or superpositions of them, each characterized by their unique density distributions. © 2011 American Physical Society.


An orbiting object in a gas-rich environment creates a gravitational density wake containing information about the object and its orbit. Using linear perturbation theory, we analyze the observable properties of the gravitational wake due to the object circularly moving in a static homogeneous gaseous medium, in order to derive the Bondi accretion radius rB , the orbital distance rp , and the Mach number of the object. Supersonic motion, producing a wake of spiral-onion shell structure, exhibits a single-armed Archimedes spiral and two-centered circular arcs with respect to the line of sight. The pitch angle, arm width, and spacing of the spiral pattern are entirely determined by the orbital distance rp and Mach number of the object. The arm-interarm density contrast is proportional to rB , decreasing as a function of distance with a power index of -1. The background density distribution is globally changed from initially uniform to centrally concentrated. The vertical structure of the wake is manifested as circular arcs with the center at the object location. The angular extent of the arcs is determined by the Mach number of the object motion. Diagnostic probes of nonlinear wakes such as a detached bow shock, the absence of the definite inner arm boundary, the presence of turbulent low-density eddies, and elongated shapes of arcs are explained in the extension of the linear analysis. The density enhancement at the center is always rB /rp independent of the nonlinearity, suggesting that massive objects can substantially modify the background distribution. © 2011. The American Astronomical Society. All rights reserved.


Zhao L.,Academia Sinica, Taiwan | Chevrot S.,University Paul Sabatier
Geophysical Journal International | Year: 2011

Seismic tomography has been developed largely on the basis of the Born approximation, in which any waveform-derived seismic observable, such as a perturbation in traveltime, is linearly related to the local perturbation of a model parameter, such as the speed of a seismic wave. This relation defines a Fréchet kernel which can be expressed as the convolution of two strain Green's tensors from the source and receiver to the perturbation location. We develop a new approach for computing the Fréchet kernels using pre-calculated databases of strain Green's tensors. After deriving the general expressions of Fréchet kernels in terms of the strain Green's tensors, we obtain specific expressions for the sensitivities of traveltime and amplitude to both isotropic and anisotropic perturbations of the elastic moduli. We also derive the Fréchet kernels of theSKS-splitting intensity for anisotropic model parameters. Numerical examples of Fréchet kernels are presented for a variety of seismic phases to demonstrate the efficiency and flexibility of this new approach and its potential for both regional and global finite-frequency tomography applications. © 2011 The Authors Geophysical Journal International © 2011 RAS.


Zhao L.,Academia Sinica, Taiwan | Chevrot S.,University Paul Sabatier
Geophysical Journal International | Year: 2011

We propose a new approach to computing the sensitivity kernels used in seismic tomography based on a Green's function database. For any perturbation in the Earth's structural model, the waveform Fréchet derivative can be expressed in terms of strain Green's tensors, which are themselves functions of the reference Earth model only. The Fréchet derivative of any seismic observable can then be obtained from waveform Fréchet derivative. Given a reference model, a strain Green's tensor database can be established, thus eliminating the need for repetitive wavefield evaluations in all subsequent synthetic and kernel calculations, and reducing the CPU time. For a spherically symmetric reference Earth model, the strain Green's tensor database can be constructed on a(r, Δ)grid by normal-mode summation. The stored strain Green's tensors can then be used to quickly evaluate the wavefield between any source and receiver. The generality of the strain Green's tensors makes it possible to compute the Fréchet kernels for any phase on a seismogram (P,S,Pdiff, surface waves, etc.), for any type of data (traveltime, amplitude, splitting intensity, waveform, etc.), and for any parameter (isotropic, anisotropic, attenuation, etc.). The kernel calculation at each point in the medium is reduced to the convolution of two sets of strain Green's tensors extracted from the database, which makes the approach extremely efficient. © 2011 The Authors Geophysical Journal International © 2011 RAS.


Biring S.,Academia Sinica, Taiwan
Physics Letters, Section A: General, Atomic and Solid State Physics | Year: 2011

Using light scattering spectroscopy, I demonstrate an approach to tune particle plasmon resonance in a binary dielectric media where silver nano-rods are embedded partially both in Anodic Aluminum Oxide (AAO) matrix and in air. A systematic experimental study under a controlled variation of the degree of embedding of nano-rods in AAO matrix has been presented. Experimental results have been interpreted based on the Drude model. Finite Difference Time Domain (FDTD) method has been employed to calculate the nature of the silver nano-rod resonance at the experimental conditions. Both the simulation results and theory corroborate the experimental findings. © 2011 Elsevier B.V. All rights reserved.


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.


Liu C.-R.,National Yang Ming University | Chang C.-R.,National Tsing Hua University | Chern Y.,Academia Sinica, Taiwan | Wang T.-H.,National Yang Ming University | And 7 more authors.
Cell | Year: 2012

Lengthy trinucleotide repeats encoding polyglutamine (polyQ) stretches characterize the variant proteins of Huntington's disease and certain other inherited neurological disorders. Using a phenotypic screen to identify events that restore functionality to polyQ proteins in S. cerevisiae, we discovered that transcription elongation factor Spt4 is required to transcribe long trinucleotide repeats located either in ORFs or nonprotein-coding regions of DNA templates. Mutation of SPT4 selectively decreased synthesis of and restored enzymatic activity to expanded polyQ protein without affecting protein lacking long-polyQ stretches. RNA-seq analysis revealed limited effects of Spt4 on overall gene expression. Inhibition of Supt4h, the mammalian ortholog of Spt4, reduced mutant huntingtin protein in neuronal cells and decreased its aggregation and toxicity while not altering overall cellular mRNA synthesis. Our findings identify a cellular mechanism for transcription through repeated trinucleotides and a potential target for countermeasures against neurological disorders attributable to expanded trinucleotide regions. © 2012 Elsevier Inc.


Shih T.-H.,National Taiwan Normal University | Horng J.-L.,Taipei Medical University | Liu S.-T.,National Taiwan Normal University | Hwang P.-P.,Academia Sinica, Taiwan | Lin L.-Y.,National Taiwan Normal University
American Journal of Physiology - Regulatory Integrative and Comparative Physiology | Year: 2012

To investigate whether Na + uptake by zebrafish is dependent on NH 4 + excretion, a scanning ion-selective electrode technique was applied to measure Na + and NH 4 + gradients at the yolk-sac surface of zebrafish larvae. Low-Na + acclimation induced an inward Na + gradient (uptake), and a combination of low Na + and high NH 4 + induced a larger inward Na + gradient. When measuring the ionic gradients, raising the external NH 4 + level (5 mM) blocked NH 4 + excretion and Na + uptake; in contrast, raising the external Na + level (10 mM) simultaneously enhanced Na + uptake and NH 4 + excretion. The addition of MOPS buffer (5 mM), which is known to block NH 4 + excretion, also suppressed Na + uptake. These results showed that Na + uptake and NH 4 + excretion by larval skin are associated when ambient Na + level is low. Knockdown of Rhcg1 translation with morpholino-oligonucleotides decreased both NH 4 + excretion and Na + uptake by the skin and Na + content of whole larvae. Knockdown of nhe3b translation or inhibitor (5-ethylisopropyl amiloride) treatment also decreased both the NH 4 + excretion and Na + uptake. This study provides loss-offunction evidence for the involvement of Rhcg1 and NHE3b in the ammonium-dependent Na + uptake mechanism in zebrafish larvae subjected to low-Na + water. © 2012 the American Physiological 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.


Chang C.-C.,Academia Sinica, Taiwan
Environmental Economics and Policy Studies | Year: 2014

An agricultural sector model based on the principle of economic welfare maximization was modified to derive the supply schedules for carbon sequestered by afforestation in Taiwan. Competition for land between agricultural and forest enterprises provided the basis for simultaneous price determination in both sectors. The land-use shifts that occurred were based on comparisons of endogenously determined returns to cropland for alternative uses. The 1994 baseline results indicated that by reforestation on the idled forest land 5 million to 10 million metric tons of carbon could be sequestered at a annual cost of US$40–$46 per metric ton. Intensified land-use changes were observed in addition to cropland conversion. The cost per metric ton of carbon rose sharply when the sequestration target threshold was more than 15 million metric tons. Our empirical results also indicated that the current afforestation incentive program could achieve, at most, a target of 5 million metric tons. © 1999, Springer Japan.


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.


Machida R.J.,Academia Sinica, Taiwan | Knowlton N.,Smithsonian Institution
PLoS ONE | Year: 2012

Background: Metagenetic analyses, which amplify and sequence target marker DNA regions from environmental samples, are increasingly employed to assess the biodiversity of communities of small organisms. Using this approach, our understanding of microbial diversity has expanded greatly. In contrast, only a few studies using this approach to characterize metazoan diversity have been reported, despite the fact that many metazoan species are small and difficult to identify or are undescribed. One of the reasons for this discrepancy is the availability of universal primers for the target taxa. In microbial studies, analysis of the 16S ribosomal DNA is standard. In contrast, the best gene for metazoan metagenetics is less clear. In the present study, we have designed primers that amplify the nuclear 18S and 28S ribosomal DNA sequences of most metazoan species with the goal of providing effective approaches for metagenetic analyses of metazoan diversity in environmental samples, with a particular emphasis on marine biodiversity. Methodology/Principal Findings: Conserved regions suitable for designing PCR primers were identified using 14,503 and 1,072 metazoan sequences of the nuclear 18S and 28S rDNA regions, respectively. The sequence similarity of both these newly designed and the previously reported primers to the target regions of these primers were compared for each phylum to determine the expected amplification efficacy. The nucleotide diversity of the flanking regions of the primers was also estimated for genera or higher taxonomic groups of 11 phyla to determine the variable regions within the genes. Conclusions/Significance: The identified nuclear ribosomal DNA primers (five primer pairs for 18S and eleven for 28S) and the results of the nucleotide diversity analyses provide options for primer combinations for metazoan metagenetic analyses. Additionally, advantages and disadvantages of not only the 18S and 28S ribosomal DNA, but also other marker regions as targets for metazoan metagenetic analyses, are discussed.


Shade A.,University of Wisconsin - Madison | Chiu C.-Y.,Academia Sinica, Taiwan | McMahon K. D.,University of Wisconsin - Madison
Environmental Microbiology | Year: 2010

Lake mixing disrupts chemical and physical gradients that structure bacterial communities. A transplant experiment was designed to investigate the influence of post-mixing environmental conditions and biotic interactions on bacterial community composition. The experimental design was 3 × 2 factorial, where water was incubated from three different sources (epilimnion, hypolimnion, and mixed epilimnion and hypolimnion) at two different locations in the water column (epilimnion or hypolimnion). Three replicate mesocosms of each treatment were removed every day for 5 days for bacterial community profiling, assessed by automated ribosomal intergenic spacer analysis. There were significant treatment effects observed, and temperature was the strongest measured driver of community change (r = -0.66). Epilimnion-incubated communities changed more than hypolimnion-incubated. Across all treatments, we classified generalist, layer-preferential and layer-specialist populations based on occurrence patterns. Most classified populations were generalists that occurred in both strata, suggesting that communities were robust to mixing. In a network analysis of the mixed-inocula treatments, there was correlative evidence of inter-population biotic interactions, where many of these interactions involved generalists. These results reveal differential responses of bacterial populations to lake mixing and highlight the role of generalist taxa in structuring an emergent community-level response. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.


Saeed I.,University of Melbourne | Tang S.-L.,Academia Sinica, Taiwan | Halgamuge S.K.,University of Melbourne
Nucleic Acids Research | Year: 2012

An approach to infer the unknown microbial population structure within a metagenome is to cluster nucleotide sequences based on common patterns in base composition, otherwise referred to as binning. When functional roles are assigned to the identified populations, a deeper understanding of microbial communities can be attained, more so than gene-centric approaches that explore overall functionality. In this study, we propose an unsupervised, model-based binning method with two clustering tiers, which uses a novel transformation of the oligonucleotide frequency-derived error gradient and GC content to generate coarse groups at the first tier of clustering; and tetranucleotide frequency to refine these groups at the secondary clustering tier. The proposed method has a demonstrated improvement over PhyloPythia, S-GSOM, TACOA and TaxSOM on all three benchmarks that were used for evaluation in this study. The proposed method is then applied to a pyrosequenced metagenomic library of mud volcano sediment sampled in southwestern Taiwan, with the inferred population structure validated against complementary sequencing of 16S ribosomal RNA marker genes. Finally, the proposed method was further validated against four publicly available metagenomes, including a highly complex Antarctic whale-fall bone sample, which was previously assumed to be too complex for binning prior to functional analysis. © 2011 The Author(s).


Kar S.,Harbin Institute of Technology | Ho Y.K.,Academia Sinica, Taiwan
Computer Physics Communications | Year: 2011

We have investigated the Fe1,3 resonance states of positronium negative ion below the N=3, 4 and 5 Ps thresholds using highly correlated exponential wave functions. Resonance parameters (positions and widths) are extracted employing both the stabilization method and the complex-coordinate rotation method. In addition to many Feshbach resonances below the various Ps thresholds, we have identified two Fe1 shape resonances with one each lying above the N=3 and N=5 thresholds, respectively. We have also identified three Fe3 shape resonances with one lying above the N=3 threshold and two lying above N=4 threshold. The Fe1,3 shape resonances associated with N=3 Ps threshold and some other Feshbach resonances are reported for the first time in the literature. © 2010 Elsevier B.V. All rights reserved.


Tsai M.-K.,National Taiwan Normal University | Kuo J.-L.,Academia Sinica, Taiwan | Lu J.-M.,National Center for High Performance Computing | Lu J.-M.,Southern Taiwan University of Science and Technology
Physical Chemistry Chemical Physics | Year: 2012

Water decomposition process was investigated by ab initio molecular dynamic simulations using a model of (H2O)2 + clusters. The proton transfer (PT) process from the cationic H-donor water to the H-acceptor water for the formation of (HO)·H3O+ was predicted as about 90 fs on average calculated at CCSD level of theory. The valence-electron transfer (VET) process through the formation of hemibond interaction between neutral and cationic water, (H2O) 2 +, was also identified in several collected trajectories. Both PT and VET processes were found to propagate along two orthogonal reaction coordinates, the former was through an intermolecular hydrogen bond and the latter required oxygen-oxygen hemibonding. Significant difference of the theoretical electronic transitions along the VET trajectories was also observed in comparison with the non-VET cases, being calculated at SAC-CI level. The strong absorption features of hemibonding (H2O)2 + may introduce an interesting consideration for experimental design to monitor the water decomposition process. © 2012 the Owner Societies.


Noreen R.,French National Center for Scientific Research | Moenner M.,French Institute of Health and Medical Research | Hwu Y.,Academia Sinica, Taiwan | Petibois C.,French National Center for Scientific Research
Biotechnology Advances | Year: 2012

Collagens are a family of at least 30 protein types organized as networks. They constitute the main support material of cells under the form of extracellular matrix as well as for membranes in vessels, organs, and tissue compartments. Collagen network abnormalities are at the origin of many diseases, including myopathies and fibroses. The characterization of collagens remains an analytical challenge due to the insolubility of these molecules and the difficulty encountered in isolating given types without altering their structure or in maintaining network organization, which is critical to diagnosing related pathologies. We have proposed using a vibrational spectroscopy based imaging technique, namely Fourier-transform infrared (FTIR) imaging, for a spatially-resolved analysis of secondary structure of different collagen types in complex samples, and more specifically for characterizing gliomas. With newly developed spectral data treatments and chemometrics using secondary structure parameters of collagen proteins, FTIR imaging is now able to distinguish between several types. On this basis, gliomas have been investigated as specific collagen-rich tissues developing in a non-collagenous environment, providing high specificity to this FTIR imaging utilization. Here, we review the recent advances in this imaging approach for understanding glioma development, with FTIR imaging now being proposed as a molecular histopathology tool for clinicians. © 2012 Elsevier Inc.


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.


Wang C.-W.,Academia Sinica, Taiwan
Cellular and Molecular Life Sciences | Year: 2015

Eukaryotic cells store excess fatty acids as neutral lipids, predominantly triacylglycerols and sterol esters, in organelles termed lipid droplets (LDs) that bulge out from the endoplasmic reticulum. LDs are highly dynamic and contribute to diverse cellular functions. The catabolism of the storage lipids within LDs is channeled to multiple metabolic pathways, providing molecules for energy production, membrane building blocks, and lipid signaling. LDs have been implicated in a number of protein degradation and pathogen infection processes. LDs may be linked to prevalent human metabolic diseases and have marked potential for biofuel production. The knowledge accumulated on LDs in recent years provides a foundation for diverse, and even unexpected, future research. This review focuses on recent advances in LD research, emphasizing the diverse physiological roles of LDs in the model system of budding yeast. © 2015 Springer Basel.


Kar S.,Harbin Institute of Technology | Ho Y.K.,Academia Sinica, Taiwan
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2010

Recently a study on the doubly excited 3Pe states of helium reports some resonance states that are not in conformity with previously published works. Owing to discrepancies between the works, we investigate the resonance parameters (positions and widths) of the doubly excited Feshbach resonances of the 3Pe symmetries associated with N = 3, 4, and 5 He+ thresholds using a different choice of correlated wave functions in the framework of the complex-coordinate rotation method and the stabilization method. Resonance parameters below the N=4 and N=5 He+ thresholds obtained from the present calculations are not consistent with the results and discussions made in the recent work. Here we point out an error in assessment made by Saha and Mukherjee in an earlier work as well as the lack of numerical accuracy of the results for some high-lying doubly excited states reported by Saha and Mukherjee. The bound 2p2-3Pe and 2p3ped from this calculation are consistent with the best reported results but not with the reported values of Saha and Mukherjee. © 2010 The American Physical Society.


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.


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.


Kemper F.,Academia Sinica, Taiwan
Earth, Planets and Space | Year: 2013

The dust reservoir in the interstellar medium of a galaxy is constantly being replenished by dust formed in the stellar winds of evolved stars. Due to their vicinity, nearby irregular dwarf galaxies the Magellanic Clouds provide an opportunity to obtain a global picture of the dust production in galaxies. The Small and Large Magellanic Clouds have been mapped with the Spitzer Space Telescope from 3.6 to 160 μm, and these wavelengths are especially suitable to study thermal dust emission. In addition, a large number of individual evolved stars have been targeted for 5-40 μm spectroscopy, revealing the mineralogy of these sources. Here I present an overview on the work done on determining the total dust production rate in the Large and Small Magellanic Clouds, as well as a first attempt at revealing the global composition of the freshly produced Stardust. © The Society of Geomagnetism and Earth, Planetary and Space Sciences (SGEPSS); The Seismological Society of Japan; The Volcanological Society of Japan; The Geodetic Society of Japan; The Japanese Society for Planetary Sciences; TERRAPUB.


Hirashita H.,Academia Sinica, Taiwan | Nozawa T.,University of Tokyo
Earth, Planets and Space | Year: 2013

We examine a synthetic way of constructing the grain size distribution in the interstellar medium (ISM). First, we formulate a synthetic grain size distribution composed of three grain size distributions processed with the following mechanisms that govern the grain size distribution in the Milky Way: (i) grain growth by accretion and coagulation in dense clouds, (ii) supernova shock destruction by sputtering in diffuse ISM, and (iii) shattering driven by turbulence in diffuse ISM. Then, we examine if the observational grain size distribution in the Milky Way (called MRN) is successfully synthesized or not. We find that the three components actually synthesize the MRN grain size distribution in the sense that the deficiency of small grains by (i) and (ii) is compensated by the production of small grains by (iii). The fraction of each contribution to the total grain processing of (i), (ii), and (iii) (i.e., the relative importance of the three contributions to all grain processing mechanisms) is 30-50%, 20-40%, and 10-40%, respectively. We also show that the Milky Way extinction curve is reproduced with the synthetic grain size distributions. © The Society of Geomagnetism and Earth, Planetary and Space Sciences (SGEPSS); The Seismological Society of Japan; The Volcanological Society of Japan; The Geodetic Society of Japan; The Japanese Society for Planetary Sciences; TERRAPUB.


Asano R.S.,Nagoya University | Takeuchi T.T.,Nagoya University | Hirashita H.,Academia Sinica, Taiwan | Inoue A.K.,Osaka Sangyo University
Earth, Planets and Space | Year: 2013

This paper investigates the main driver of dust mass growth in the interstellar medium (ISM) by using a chemical evolution model of a galaxy with metals (elements heavier than helium) in the dust phase, in addition to the total amount of metals. We consider asymptotic giant branch (AGB) stars, type II supernovae (SNe II), and dust mass growth in the ISM, as the sources of dust, and SN shocks as the destruction mechanism of dust. Furthermore, to describe the dust evolution precisely, our model takes into account the age and metallicity (the ratio of metal mass to ISM mass) dependence of the sources of dust. We have particularly focused on the dust mass growth, and found that in the ISM this is regulated by the metallicity. To quantify this aspect, we introduce a "critical metallicity", which is the metallicity at which the contribution of stars (AGB stars and SNe II) equals that of the dust mass growth in the ISM. If the star-formation timescale is shorter, the value of the critical metallicity is higher, but the galactic age at which the metallicity reaches the critical metallicity is shorter. From observations, it was expected that the dust mass growth was the dominant source of dust in the Milky Way and dusty QSOs at high redshifts. By introducing a critical metallicity, it is clearly shown that the dust mass growth is the main source of dust in such galaxies with various star-formation timescales and ages. The dust mass growth in the ISM is regulated by metallicity, and we emphasize that the critical metallicity serves as an indicator to judge whether the grain growth in the ISM is the dominant source of dust in a galaxy, especially because of the strong, and nonlinear, dependence on the metallicity. © The Society of Geomagnetism and Earth, Planetary and Space Sciences (SGEPSS); The Seismological Society of Japan; The Volcanological Society of Japan; The Geodetic Society of Japan; The Japanese Society for Planetary Sciences; TERRAPUB.


Cortisol is the major endogenous glucocorticoid (GC) both in human and fish, mediated by corticosteroid receptors. Due to the absence of aldosterone production in teleost fish, cortisol is also traditionally accepted to function as mineralocorticoid (MC); but whether it acts through the glucocorticoid receptor (GR) or the mineralocorticoid receptor (MR) remains a subject of debate. Here, we used loss-of-function and rescue assays to determine whether cortisol affects zebrafish epidermal ionocyte development and function via the GR and/or the MR. GR knockdown morphants displayed a significant decrease in the major ionocytes, namely Na(+)-K(+)-ATPase-rich cells (NaRCs) and H(+)-ATPase-rich cells (HRCs), as well as other cells, including epidermal stem cells (ESCs), keratinocytes, and mucus cells; conversely, cell numbers were unaffected in MR knockdown morphants. In agreement, GR morphants, but not MR morphants, exhibited decreased NaRC-mediated Ca(2+) uptake and HRC-mediated H(+) secretion. Rescue via GR capped mRNA injection or exogenous cortisol incubation normalized the number of epidermal ionocytes in GR morphants. We also provide evidence for GR localization in epidermal cells. At the transcript level, GR mRNA is ubiquitously expressed in gill sections and present in both NaRCs and HRCs, supporting the knockdown and functional assay results in embryo. Altogether, we have provided solid molecular evidence that GR is indeed present on ionocytes, where it mediates the effects of cortisol on ionocyte development and function. Hence, cortisol-GR axis performs the roles of both GC and MC in zebrafish skin and gills.


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.


Brasser R.,Academia Sinica, Taiwan | Morbidelli A.,University of Nice Sophia Antipolis
Icarus | Year: 2013

One of the outstanding problems of the dynamical evolution of the outer Solar System concerns the observed population ratio between the Oort cloud (OC) and the Scattered Disc (SD): observations suggest that this ratio lies between 100 and 1000 but simulations that produce these two reservoirs simultaneously consistently yield a value of the order of 10. Here we stress that the populations in the OC and SD are inferred from the observed fluxes of new long period comets (LPCs) and Jupiter-family comets (JFCs), brighter than some reference total magnitude. However, the population ratio estimated in the simulations of formation of the SD and OC refers to objects bigger than a given size. There are multiple indications that LPCs are intrinsically brighter than JFCs, i.e. an LPC is smaller than a JFC with the same total absolute magnitude. When taking this into account we revise the SD/JFC population ratio from our simulations relative to Duncan and Levison (1997), and then deduce from the observations that the size-limited population ratio between the OC and the SD is 44-34+54. This is roughly a factor of four higher than the value 12 ± 1 that we obtain in simulations where the OC and the SD form simultaneously while the planets evolve according to the so-called 'Nice model'. Thus, we still have a discrepancy between model and 'observations', but the agreement cannot be rejected by the null hypothesis. © 2013 Elsevier Inc.


Hwang S.G.,Academia Sinica, Taiwan
Plant physiology and biochemistry : PPB / Société française de physiologie végétale | Year: 2012

ABSCISIC ACID DEFICIENT2 (ABA2) encodes a short-chain dehydrogenase/reductase1 (SDR1) that catalyzes the multi-step conversion of xanthoxin to abscisic aldehyde during abscisic acid (ABA) biosynthesis in Arabidopsis thaliana. In this study, AtSDR2 and AtSDR3, the two closest homologs to AtABA2, were investigated for their potential role in ABA biosynthesis. AtSDR2 showed undetectable transcription in plants grown under normal conditions or under stress. AtSDR3 and AtABA2 have different spatial and temporal expression patterns. Complementation testing demonstrated that the pABA2::SDR3 transgene failed to complement the aba2 mutant phenotype, and that transgenic plants showed the same levels of ABA as the aba2 mutants. These data suggest that AtSDR3 confers no functional redundancy to AtABA2 in ABA biosynthesis. Interestingly, microarray data derived from Genevestigator suggested that AtSDR3 might have a function that is related to plant defense. Pseudomonas syringae pv. tomato (Pst) DC3000 infection and systemic acquired resistance (SAR) activator application further demonstrated that AtSDR3 plays an important role in plant defense responses at least partially through the regulation of AtPR-1 gene expression. Copyright © 2011 Elsevier Masson SAS. All rights reserved.


Wang C.-W.,Academia Sinica, Taiwan
Autophagy | Year: 2014

Delivery of cellular contents to yeast vacuoles/mammalian lysosomes via autophagy ensures long-term cell survival and extends life span. When cultured yeast cells are grown for a prolonged period of time to enter stationary phase, a nondividing state mimicking quiescence, vacuolar membrane proteins partition into either one of the vacuolar microdomains, liquid-ordered (Lo) or liquid-disordered (Ld). We show that during the transition to stationary phase, lipid droplets (LDs), organelles originated from the endoplasmic reticulum (ER), undergo lateral movement to reach the vacuolar surface and are confined within the specific Lo microdomain underlying the network of vacuolar quasi-symmetrical micodomains. Stationary phase lipophagy uses the autophagy machineries to modify the sterolenriched Lo microdomain to engulf LDs and subsequently deposits the LD-containing vesicles inside the vacuole lumen, which is a pathway morphologically resembling microautophagy. Moreover, stationary phase lipophagy supplies quiescent yeast cells with sterols to sustain phase partitioning of lipids for vacuolar microdomain maintenance. A feed forward loop model was proposed to depict that the sterols boosted by LDs via stationary phase lipophagy promote the Lo microdomain maintenance that in turn stimulates lipophagy. © 2014 Taylor & Francis Group, LLC.


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..


Keenan R.C.,Academia Sinica, Taiwan | Barger A.J.,University of Wisconsin - Madison | Barger A.J.,University of Hawaii at Manoa | Cowie L.L.,University of Hawaii at Manoa
Astrophysical Journal | Year: 2013

Galaxy counts and recent measurements of the luminosity density in the near-infrared have indicated the possibility that the local universe may be under-dense on scales of several hundred megaparsecs. The presence of a large-scale under-density in the local universe could introduce significant biases into the interpretation of cosmological observables, and, in particular, into the inferred effects of dark energy on the expansion rate. Here we measure the K-band luminosity density as a function of redshift to test for such a local under-density. For our primary sample in this study, we select galaxies from the UKIDSS Large Area Survey and use spectroscopy from the Sloan Digital Sky Survey (SDSS), the Two-degree Field Galaxy Redshift Survey, the Galaxy And Mass Assembly Survey (GAMA), and other redshift surveys to generate a K-selected catalog of ∼35, 000 galaxies that is ∼95% spectroscopically complete at K AB < 16.3 (K AB < 17 in the GAMA fields). To complement this sample at low redshifts, we also analyze a K-selected sample from the 2M++ catalog, which combines Two Micron All Sky Survey (2MASS) photometry with redshifts from the 2MASS redshift survey, the Six-degree Field Galaxy Redshift Survey, and the SDSS. The combination of these samples allows for a detailed measurement of the K-band luminosity density as a function of distance over the redshift range 0.01 < z < 0.2 (radial distances D ∼ 50-800 Mpc). We find that the overall shape of the z = 0 rest-frame K-band luminosity function (M*-5log (h 70) = -22.15 ± 0.04 and α = -1.02 ± 0.03) appears to be relatively constant as a function of environment and distance from us. We find a local (z < 0.07, D < 300 Mpc) luminosity density that is in good agreement with previous studies. Beyond z ∼ 0.07, we detect a rising luminosity density that reaches a value of roughly ∼1.5 times higher than that measured locally at z > 0.1. This suggests that the stellar mass density as a function of distance follows a similar trend. Assuming that luminous matter traces the underlying dark matter distribution, this implies that the local mass density of the universe may be lower than the global mass density on a scale and amplitude sufficient to introduce significant biases into the determination of basic cosmological observables. An under-density of roughly this scale and amplitude could resolve the apparent tension between direct measurements of the Hubble constant and those inferred by Planck. © 2013. The American Astronomical Society. All rights reserved.


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.


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.


Hasegawa Y.,McMaster University | Hasegawa Y.,Academia Sinica, Taiwan | Pudritz R.E.,McMaster University
Astrophysical Journal | Year: 2013

The rapid growth of observed exoplanets has revealed the existence of several distinct planetary populations in the mass-period diagram. Two of the most surprising are (1) the concentration of gas giants around 1 AU and (2) the accumulation of a large number of low-mass planets with tight orbits, also known as super-Earths and hot Neptunes. We have recently shown that protoplanetary disks have multiple planet traps that are characterized by orbital radii in the disks and halt rapid type I planetary migration. By coupling planet traps with the standard core accretion scenario, we showed that one can account for the positions of planets in the mass-period diagram. In this paper, we demonstrate quantitatively that most gas giants formed at planet traps tend to end up around 1 AU, with most of these being contributed by dead zones and ice lines. We also show that a large fraction of super-Earths and hot Neptunes are formed as "failed" cores of gas giants - this population being constituted by comparable contributions from dead zone and heat transition traps. Our results are based on the evolution of forming planets in an ensemble of disks where we vary only the lifetimes of disks and their mass accretion rates onto the host star. We show that a statistical treatment of the evolution of a large population of planetary cores caught in planet traps accounts for the existence of three distinct exoplanetary populations - the hot Jupiters, the more massive planets around r = 1 AU, and the short-period super-Earths and hot Neptunes. There are very few populations that feed into the large orbital radii characteristic of the imaged Jovian planet, which agrees with recent surveys. Finally, we find that low-mass planets in tight orbits become the dominant planetary population for low-mass stars (M ⊙* ≤ 0.7 M ⊙). © 2013. The American Astronomical Society. All rights reserved.


Hasegawa Y.,Academia Sinica, Taiwan | Ida S.,Tokyo Institute of Technology
Astrophysical Journal | Year: 2013

Planetary migration is one of the most serious problems to systematically understand the observations of exoplanets. We clarify that the theoretically predicted type II, migration (like type I migration) is too fast, by developing detailed analytical arguments in which the timescale of type II migration is compared with the disk lifetime. In the disk-dominated regime, the type II migration timescale is characterized by a local viscous diffusion timescale, while the disk lifetime is characterized by a global diffusion timescale that is much longer than the local one. Even in the planet-dominated regime where the inertia of the planet mass reduces the migration speed, the timescale is still shorter than the disk lifetime except in the final disk evolution stage where the total disk mass decays below the planet mass. This suggests that most giant planets plunge into the central stars within the disk lifetime, and it contradicts the exoplanet observations that gas giants are piled up at r ≳ 1 AU. We examine additional processes that may arise in protoplanetary disks: dead zones, photoevaporation of gas, and gas flow across a gap formed by a type II migrator. Although they make the type II migration timescale closer to the disk lifetime, we show that none of them can act as an effective barrier for rapid type II migration with the current knowledge of these processes. We point out that gas flow across a gap and the fraction of the flow accreted onto the planets are uncertain and they may have the potential to solve the problem. Much more detailed investigation for each process may be needed to explain the observed distribution of gas giants in extrasolar planetary systems. © 2013. The American Astronomical Society. All rights reserved.


Umetsu K.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2013

Lens magnification by galaxy clusters induces characteristic spatial variations in the number counts of background sources, amplifying their observed fluxes and expanding the area of sky, the net effect of which, known as magnification bias, depends on the intrinsic faint-end slope of the source luminosity function. The bias is strongly negative for red galaxies, dominated by the geometric area distortion, whereas it is mildly positive for blue galaxies, enhancing the blue counts toward the cluster center. We generalize the Bayesian approach of Umetsu et al. for reconstructing projected cluster mass profiles, by incorporating multiple populations of background sources for magnification-bias measurements and combining them with complementary lens-distortion measurements, effectively breaking the mass-sheet degeneracy and improving the statistical precision of cluster mass measurements. The approach can be further extended to include strong-lensing projected mass estimates, thus allowing for non-parametric absolute mass determinations in both the weak and strong regimes. We apply this method to our recent CLASH lensing measurements of MACS J1206.2-0847, and demonstrate how combining multi-probe lensing constraints can improve the reconstruction of cluster mass profiles. This method will also be useful for a stacked lensing analysis, combining all lensing-related effects in the cluster regime, for a definitive determination of the averaged mass profile. © 2013. The American Astronomical Society. All rights reserved.


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.


Otsuka M.,Academia Sinica, Taiwan | Tajitsu A.,Subaru Telescope
Astrophysical Journal | Year: 2013

We performed detailed chemical abundance analysis of the extremely metal-poor ([Ar/H] ∼ -2) halo planetary nebula (PN) H4-1 based on the multi-wavelength spectra from Subaru/HDS, GALEX, SDSS, and Spitzer/IRS and determined the abundances of 10 elements. The C and O abundances were derived from collisionally excited lines (CELs) and are almost consistent with abundances from recombination lines (RLs). We demonstrated that the large discrepancy in the C abundance between CEL and RL in H4-1 can be solved using the temperature fluctuation model. We reported the first detection of the [Xe III] λ5846 line in H4-1 and determination of its elemental abundance ([Xe/H] > +0.48). H4-1 is the most Xe-rich PN among the Xe-detected PNe. The observed abundances are close to the theoretical prediction by a 2.0 M single star model with an initially element rich ([r/Fe] = +2.0 dex) rapid neutron-capture process (r-process). The observed Xe abundance would be a product of the r-process in primordial supernovae. The [C/O]-[Ba/(Eu or Xe)] diagram suggests that the progenitor of H4-1 shares the evolution with carbon-enhanced metal-poor (CEMP)-r/s and CEMP-no stars. The progenitor of H4-1 is presumably a binary formed in an r-process-rich environment. © 2013. The American Astronomical Society. All rights reserved..


Chen J.-M.,National Taiwan University | Chen M.-C.,Academia Sinica, Taiwan | Sun Y.S.,National Taiwan University
Computers and Education | Year: 2014

Prior knowledge is an important issue in the study of concept acquisition among students. Traditional studies on prior knowledge generation during reading activities have focused on extracting sentences from reading materials that are manually generated by website administrators and educators. This is time-consuming and strenuous, and hence personalized prior knowledge recommendation is difficult to perform. To cope with this problem, we combine the concept of prior knowledge with social tagging methods to assist the reading comprehension of students studying English. We incorporate tags into a tag based learning approach, which then identifies suitable supplementary materials for quickly constructing a student's prior knowledge reservoir. The experimental results demonstrate that the proposed approach benefits the students by embedding the additional information in social knowledge, and hence significantly improve their on-line reading efficiency. © 2013 Elsevier Ltd. All rights reserved.


Lin H.-W.,Soochow University of Taiwan | Chen Y.-H.,Academia Sinica, Taiwan | Chen Y.-H.,National Yang Ming University
American Journal of Epidemiology | Year: 2014

Bias caused by missing or incomplete information on confounding factors constitutes an important challenge in observational studies. The incorporation of external data on more detailed confounding information into the main study data may help remove confounding bias. This work was motivated by a study of the association between chronic obstructive pulmonary disease and herpes zoster. Analyses were based on administrative databases in which information on important confounders - cigarette smoking and alcohol consumption - was lacking. We consider adjusting for the confounding bias arising from missing confounders by incorporating a validation sample with data on smoking and alcohol consumption obtained from a small-scale National Health Interview Survey study. We propose a 2-stage calibration (TSC) method, which summarizes the confounding information through propensity scores and combines the analysis results from the main and the validation study samples, where the propensity score adjustment from the main sample is crude and that from the validation sample is more precise. Unlike the existing methods, the validity of the TSC approach does not rely on any specific measurement error model. When applying the TSC method to the motivating study above, the odds ratio of herpes zoster associated with chronic obstructive pulmonary disease is 1.91 (95% confidence interval: 1.62, 2.26) after adjustment for cumulative smoking and alcohol consumption. © The Author 2014.


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 H.-Y.,Academia Sinica, Taiwan | Chua C.-K.,Chung Yuan Christian University | Liu K.-F.,University of Kentucky
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

It is commonly believed that the lowest-lying scalar glueball lies somewhere in the isosinglet scalar mesons f0(1370), f0(1500) and f0(1710) denoted generically by f0. In this work we consider lattice calculations and experimental data to infer the glue and qq¯ components of f0. These include the calculations of the scalar glueball masses in quenched and unquenched lattice QCD, measurements of the radiative decays J/ψ→γf0, the ratio of f0 decays to ππ, KK¯ and ηη, the ratio of J/ψ decays to f0(1710)ω and f0(1710)φ, the f0 contributions to Bs→J/ψπ+π-, and the near mass degeneracy of a0(1450) and K0∗(1430). All analyses suggest the prominent glueball nature of f0(1710) and the flavor octet structure of f0(1500). © 2015 American Physical Society.


Cheng H.-Y.,Academia Sinica, Taiwan | Chua C.-K.,Chung Yuan Christian University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

We first give a brief overview of the charmed baryon spectroscopy and discuss their possible structure and spin-parity assignments in the quark model. With the new Belle measurement of the widths of Σc(2455) and Σc(2520) and the recent CDF measurement of the strong decays of Λc(2595) and Λc(2625), we give updated coupling constants in heavy hadron chiral perturbation theory. We find g2=0.565-0.024+0.011 for P-wave transitions between s-wave and s-wave baryons, and h2, one of the couplings responsible for S-wave transitions between s-wave and p-wave baryons, is extracted from Λc(2595)+→Λc+ππ to be 0.63±0.07. It is substantially enhanced compared to the old value of order 0.437. With the help from the quark model, two of the couplings h10 and h11 responsible for D-wave transitions between s-wave and p-wave baryons are determined from Σc(2880) decays. There is a tension for the coupling h2 as its value extracted from Λc(2595)+→Λc+ππ will imply Ξc(2790)0→Ξc′π and Ξc(2815)+→Ξc∗π rates slightly above the current limits. It is conceivable that SU(3) flavor symmetry breaking can help account for the discrepancy. © 2015 American Physical Society.


Hirotani K.,Academia Sinica, Taiwan | Hirotani K.,National Tsing Hua University
Astrophysical Journal | Year: 2013

We investigate the electrodynamic structure of a pulsar outer-magnetospheric particle accelerator and the resulting gamma-ray emission. By considering the condition for the accelerator to be self-sustained, we derive how the trans-magnetic-field thickness of the accelerator evolves with the pulsar age. It is found that the thickness is small but increases steadily if the neutron-star envelope is contaminated by sufficient light elements. For such a light element envelope, the gamma-ray luminosity of the accelerator is kept approximately constant as a function of age in the initial 10,000 yr, forming the lower bound of the observed distribution of the gamma-ray luminosity of rotation-powered pulsars. If the envelope consists of only heavy elements, on the other hand, the thickness is greater, but it increases less rapidly than a light element envelope. For such a heavy element envelope, the gamma-ray luminosity decreases relatively rapidly, forming the upper bound of the observed distribution. The gamma-ray luminosity of a general pulsar resides between these two extreme cases, reflecting the envelope composition and the magnetic inclination angle with respect to the rotation axis. The cutoff energy of the primary curvature emission is regulated below several GeV even for young pulsars because the gap thickness, and hence the acceleration electric field, is suppressed by the polarization of the produced pairs. © 2013. The American Astronomical Society. All rights reserved.


Yu H.-M.,A-Life Medical | Wang T.-C.,Academia Sinica, Taiwan
Food and Chemical Toxicology | Year: 2012

An isogenic pair of cisplatin-susceptible (NTUB1) and -resistant (NTUB1/P) human urothelial carcinoma cell lines was used to elucidate the mechanism of cisplatin resistance. The significantly lower intracellular platinum (IP) concentration, which resulted from the decreased cisplatin uptake, was found in NTUB1/P cells. The enhancement of IP concentration did not increase the susceptibility of NTUB1/P cells to cisplatin treatment. The reduction of IP concentration as well was unable to enhance the cisplatin-resistance in susceptible NTUB1 cells. This indicated that reduction of IP concentration was not the account for the development of cisplatin resistance here. Instead, the over expression of anti-apoptotic Bcl-2, anti-oxidative heme oxygenase-1 (HO-1) and cell cycle regulator p16INK4 seemed to be more important for the gaining of cisplatin in these human urothelial carcinoma cell. © 2012 Elsevier Ltd.


Cheng H.-Y.,Academia Sinica, Taiwan | Chua C.-K.,Chung Yuan Christian University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2015

Based on SU(3) flavor symmetry, we decompose the decay amplitudes of bottom baryon decays to a pseudoscalar meson and an octet (a decuplet) pentaquark in terms of three (two) invariant amplitudes T1 and T2,3 (T∼1 and T∼2) corresponding to external W-emission and internal W-emission diagrams, respectively. For antitriplet bottom baryons Λb0, Ξb0, and Ξb-, their decays to a decuplet pentaquark proceed only through the internal W-emission diagram. Assuming the dominance from the external W-emission amplitudes, we present an estimate of the decay rates relative to Λb0→Pp+K-, where Pp+ is the hidden-charm pentaquark with the same light-quark content as the proton. Hence, our numerical results will provide a very useful guideline to the experimental search for pentaquarks in bottom baryon decays. For example, Ξb0→PΣ+K-, Ξb-→PΣ-K¯0, Ωb-→PΞ-K¯0, and Ωb-→PΞ0K- may have rates comparable to that of Λb0→Pp+K- and these modes should be given the higher priority in the experimental searches for pentaquarks. © 2015 American Physical 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


Nazarov V.U.,Academia Sinica, Taiwan
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

By minimizing the difference between the left- and the right-hand sides of the many-body time-dependent Schrödinger equation with the Slater-determinant wave function, we derive a nonadiabatic and self-interaction-free time-dependent single-particle effective potential, which is the generalization to the time-dependent case of the so-called localized Hartree-Fock potential. The new potential can be efficiently used within the framework of the time-dependent density-functional theory as we demonstrate by the evaluation of the wave vector and frequency-dependent exchange kernel fxh(q,ω) of the homogeneous electron gas. This is found to be nonsingular and causal, and it satisfies the positiveness of the dissipation, in contrast to the earlier known kernel from the first-order perturbation theory, which makes our fxh promising for applications. © 2013 American Physical Society.


Ghoshal A.,University of Burdwan | Ho Y.K.,Academia Sinica, Taiwan
International Journal of Quantum Chemistry | Year: 2011

We have investigated the properties of hydrogen molecular ion (H 2+) interacting with screened Coulomb potentials. Two types of potentials have been considered, namely, static screened Coulomb potential and exponential cosine-screened Coulomb potential. Simulating the localized motion of the nuclei by using high powers of the internuclear coordinate in the generalized Hylleraas-type wave function we have been able to obtain reasonably accurate binding energies for 1 1S(J = 0, ν = 0) and 2 1S(J = 0, ν = 1) states for various values of the screening parameter within the frame work of Ritz variational method. Borromean bindings are found to exist in the ion for a wide range of the screening parameter. Furthermore, expectation values for various operators and cusp condition have been calculated. Results for the unscreened case are in nice agreement with some of the accurate results available in the literature. © 2010 Wiley Periodicals, Inc.


Huang Y.H.,National Taiwan Normal University | Huang W.C.,National Taiwan Normal University | Tzeng W.B.,Academia Sinica, Taiwan
Chemical Physics Letters | Year: 2014

The excitation energy of the S1 ← S0 transition (E1) and the adiabatic ionization energy (IE) of 4-chloro-3- fluoroaniline (4C3FA) are found to be 33 242 and 63 868 cm-1, respectively. Comparing these data with those of 4-chloroaniline, 3-fluoroaniline, and aniline, we find an additivity rule associated with the E1 and IE. This implies that the interaction among the Cl, F, and NH2 substituents is weak. The new vibronic and cation spectra 4C3FA can be used as fingerprints for molecular identification. © 2014 Elsevier B.V. All rights reserved.


Chen K.-Y.,Feng Chia University | Chow T.J.,Academia Sinica, Taiwan
Tetrahedron Letters | Year: 2010

1,7-Dinitroperylene bisimides (1a-1b) and 1-nitroperylene bisimides (2a-2b) were synthesized under mild condition in high yields, and were characterized by FT-IR, 1H NMR, UV-vis, HRMS spectra, cyclic voltammetry, and thermogravimetric analyses. These compounds are stable up to 260 °C according to thermogravimetric analyses. They undergo two quasi-reversible one-electron reductions in THF at modest potentials. The nitro functionalities provide stability of n-type charge carriers by lowering the LUMO to resist ambient oxidation. © 2010 Elsevier Ltd. All rights reserved.


Wen C.-C.,Tamkang University | Chen Y.-H.,Academia Sinica, Taiwan
Statistics in Medicine | Year: 2013

Motivated by an epidemiological survey of fracture in elderly women, we develop a semiparametric regression analysis of current status data with incompletely observed covariate under the proportional odds model. To accommodate both the interval-censored nature of current status failure time data and the incompletely observed covariate data, we propose an analysis based on the validation likelihood (VL), which is derived from likelihood pertaining to the validation sample, namely the subset of the sample where the data are completely observed. The missing data mechanism is assumed to be missing at random and is explicitly modeled and estimated in the VL approach. We propose implementing the VL method by integrating self-consistency and Newton-Raphson algorithms. Asymptotic normality and standard error estimation for the proposed estimator of the regression parameter are guaranteed. Simulation results reveal good performance of the VL estimator. The VL method has some gain in efficiency compared with the naive complete case method. But the VL method leads to unbiased estimators, whereas the complete case method does not when missing covariates are not missing completely at random. Application of the VL approach to the fracture data confirms that osteoporosis (low bone density) is a strong risk factor for the age at onset of fracture in elderly women. © 2012 John Wiley & Sons, Ltd.


Xian L.,Georgia Institute of Technology | Barraza-Lopez S.,Georgia Institute of Technology | Chou M.Y.,Georgia Institute of Technology | Chou M.Y.,Academia Sinica, Taiwan
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

A twisted graphene bilayer consists of two graphene monolayers rotated by an angle θ with respect to each other. Theory predicts that charge-neutral twisted graphene bilayers display a drastic reduction of their Fermi velocity vF for 020 and 4060. In this paper we present evidence for an additional anisotropic reduction of vF in the presence of external electrostatic fields. We also discuss in quantitative detail velocity renormalization for other relevant bands in the vicinity of the K point. Except for a rigid energy shift, electrostatic fields and doping by metal atoms give rise to similar renormalization of the band structure of twisted graphene bilayers. © 2011 American Physical Society.


Jandzik D.,University of Colorado at Boulder | Jandzik D.,Comenius University | Garnett A.T.,University of Colorado at Boulder | Square T.A.,University of Colorado at Boulder | And 3 more authors.
Nature | Year: 2015

A defining feature of vertebrates (craniates) is a pronounced head that is supported and protected by a robust cellular endoskeleton. In the first vertebrates, this skeleton probably consisted of collagenous cellular cartilage, which forms the embryonic skeleton of all vertebrates and the adult skeleton of modern jawless and cartilaginous fish. In the head, most cellular cartilage is derived from a migratory cell population called the neural crest, which arises from the edges of the central nervous system. Because collagenous cellular cartilage and neural crest cells have not been described in invertebrates, the appearance of cellular cartilage derived from neural crest cells is considered a turning point in vertebrate evolution. Here we show that a tissue with many of the defining features of vertebrate cellular cartilage transiently forms in the larvae of the invertebrate chordate Branchiostoma floridae (Florida amphioxus). We also present evidence that during evolution, a key regulator of vertebrate cartilage development, SoxE, gained new cis-regulatory sequences that subsequently directed its novel expression in neural crest cells. Together, these results suggest that the origin of the vertebrate head skeleton did not depend on the evolution of a new skeletal tissue, as is commonly thought, but on the spread of this tissue throughout the head. We further propose that the evolution of cis-regulatory elements near an ancient regulator of cartilage differentiation was a major factor in the evolution of the vertebrate head skeleton. © 2015 Macmillan Publishers Limited. All rights reserved.


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).


Lee C.K.,Academia Sinica, Taiwan | Hua C.C.,National Chung Cheng University | Chen S.A.,National Tsing Hua University
Macromolecules | Year: 2013

Highly efficient and prolonged coarse-grained molecular dynamics simulations revealed a previously unknown pathway of phase transition of (poor-solvent) conjugated polymer solutions, evolving from a rarely explored entangled state into elastic microgels characterized by interconnected fibrous (or arm-like) materials with locally regular segmental packing. These microgels are significant in that their dynamic and structural features are rather universal (i.e., independent of the solvents utilized), in stark contrast with the counterpart dilute/semidilute systems previously shown (and also demonstrated in this work) to be dictated by solvent-sensitive aggregate species. The overall findings shed light on the yet-unresolved gelation phenomena of conjugated polymers, reveal a striking similarity with conventional entangled flexible polymers in light of the effects of solvent and concentration, and prompt a different possibility of maneuvering their thin-film properties in optoelectronics-oriented polymer science and technology. © 2013 American Chemical Society.


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.


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.


Ho I.L.,Academia Sinica, Taiwan
Physica A: Statistical Mechanics and its Applications | Year: 2012

The research herein studies the Langevin dynamics that allows for an exchange of energy between liquid crystals and the thermal environment. This dynamics leads to fluctuation and dissipation behaviors in the motions of liquid crystals, and therefore drives the system toward non-equilibrium evolutional processes. In particular, for the operations of liquid-crystal metastable systems, the fluctuation could allow an excitation (non-equilibrium) transition against energy barriers to the globally-stable state. Implemented with an actual case of liquid crystal π configuration, this work statistically studies the non-equilibrium metastable transitions and shows the dependence of the transition-time on the correlations (of fluctuations). © 2011 Elsevier B.V. All rights reserved.


Hsueh Y.-P.,Academia Sinica, Taiwan
Communicative and Integrative Biology | Year: 2012

Dendritic spines are neuron-specific actin-rich subcellular structures and are the location of excitatory synapses. Neurotransmitters released from presynaptic terminals activate the signals modifying the F-actin dynamics and stability and thus control dendritic spine morphology. Many ubiquitously expressed actin-associated proteins, including cortactin, have been shown to regulate dendritic spine morphology and density. Since dendritic spines are neuron-specific structures, neuron-specific proteins are expected to control F-actin cytoskeletons and dendritic spinogenesis. Recently, we demonstrated that cortactin-binding protein 2 (CTTNBP2), a neuron-specific protein, regulates the mobility and distribution of cortactin and controls the density of dendritic spines. This is the first example of a neuron-specific protein that controls the mobility of an F-actin associated protein and influences the dendritic spines. It provides a platform to explore the specific pathway triggering dendritic spinogenesis. © 2012 Landes Bioscience.


Lee S.-Y.,University of California at Berkeley | Lee S.-Y.,Academia Sinica, Taiwan | Chiang J.C.H.,University of California at Berkeley | Matsumoto K.,University of Minnesota | Tokos K.S.,University of Minnesota
Paleoceanography | Year: 2011

A recent study found enhanced upwelling rates in the Southern Ocean during the last glacial termination that coincided with the deglacial warming in Antarctica and the rise in atmospheric CO2. They hypothesized that the intensification of Southern Hemisphere midlatitude westerlies, the presumed cause of the increased wind-driven upwelling, was triggered by an initial cooling within the glacial North Atlantic whose influence was then communicated to the southern midlatitudes through an atmospheric teleconnection. In this study, we explore the viability of the above hypothesis using a modeling strategy, focusing on the atmospheric teleconnection. In simulations where North Atlantic cooling was applied, the model Intertropical Convergence Zone shifted outhward, and westerlies and wind stress over Southern Ocean increased by as much as 25%. While the perennial westerly anomalies occur over the entire Southern Ocean, they are strongest over the South Pacific during the austral winter. When the wind stress anomalies were applied to an Earth system model incorporating interactive marine biogeochemistry, atmospheric CO2 rises between 20 and 60 ppm, depending on the biological response. We thus confirm the viability of the proposed atmospheric teleconnection hypothesis. The teleconnection appears to involves two distinct steps: first, the North Atlantic cooling shifts the Intertropical Convergence Zone southward, weakening the southern branch of the Hadley circulation, and second, how the altered Hadley circulation in turn modifies the structure of midlatitude westerlies in the South Pacific, via the former's influence on the Southern Hemisphere subtropical jet. This study underscores the control of the Northern Hemisphere has on southern midlatitude westerlies, mediating by tropical circulation, in contrast to past paleoclimate hypotheses that the magnitude and position of the southern midlatitude westerlies was controlled by global mean temperature. Our results do not preclude other potential mechanisms for affecting Southern Ocean ventilation, in particular through oceanic pathways. Copyright © 2011 by the American Geophysical Union.


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.


Yu W.-C.,Academia Sinica, Taiwan
Bulletin of the Seismological Society of America | Year: 2013

This paper examines moderate shallow-focus repeating earthquakes along the Tonga-Kermadec-Vanuatu subduction zones by cross-correlating teleseismically recorded waveforms. A total of 23 clusters and 31 doublets are identified with an average cross-correlation coefficient of >0:8. A master-event algorithm is used to determine the precise relative locations. I then estimate and superpose the source areas among these event pairs. This analysis reveals that most of these correlated pairs are repeating earthquakes, which have similar seismic moments (M0) and completely overlapping source areas. Most of the moderate repeating earthquakes were quasi-periodic with a recurrence interval (Tr) on the order of years, and occurred at the plate interface. The repeating earthquakes are used to study spatial-temporal variations in fault-slip rate (̇d) and interplate coupling. Apart from spatial variations in ̇d, a temporal acceleration in ̇d is observed, associated with large interplate earthquakes in the Vanuatu region. Interplate coupling is weak for most of the study areas, except the northern section 15°-19° S of the Tonga arc. Strong coupling in the northern Tonga interplate region appears to be at odds with the decoupling expected of a region associated with active back-arc extension. Repeating earthquakes are also used to examine the scaling relationship between M0 and Tr derived from the San Andreas fault (SAF). The Tr M0 scaling relationship derived from the SAF can adequately account for the normalized Tr for the Kermadec, Vanuatu, and Tonga interplate regions where it is decoupled, suggesting that the convergence rate is the predominant influence on the recurrence interval in a repeating earthquake sequence.


Knapmeyer-Endrun B.,University of Potsdam | Kruger F.,University of Potsdam | Legendre C.P.,Academia Sinica, Taiwan | Geissler W.H.,Alfred Wegener Institute for Polar and Marine Research
Earth and Planetary Science Letters | Year: 2013

Cratons with their thick lithospheric roots can influence the thermal structure, and thus the convective flow, in the surrounding mantle. As mantle temperatures are hard to measure directly, depth variations in the mantle transition zone (MTZ) discontinuities are often employed as a proxy. Here, we use a large new data set of P-receiver functions to map the 410. km and 660. km discontinuities beneath the western edge of the East European Craton and adjacent Phanerozoic Europe across the most fundamental lithospheric boundary in Europe, the Trans-European Suture Zone (TESZ). We observe significantly shorter travel times for conversions from both MTZ discontinuities within the craton, caused by the high velocities of the cratonic root. By contrast, the differential travel time across the MTZ is normal to only slightly raised. This implies that any insulating effect of the cratonic keel does not reach the MTZ. In contrast to earlier observations in Siberia, we do not find any trace of a discontinuity at 520. km depth, which indicates a rather dry MTZ beneath the western edge of the craton. Within most of covered Phanerozoic Europe, the MTZ differential travel time is remarkably uniform and in agreement with standard Earth models. No widespread thermal effects of the various episodes of Caledonian and Variscan subduction that took place during the amalgamation of the continent remain. Only more recent tectonic events, related to Alpine subduction and Quarternary volcanism in the Eifel area, can be traced. While the East European craton shows no distinct imprint into the MTZ, we discover the signature of the TESZ in the MTZ in the form of a linear region of about 350. km width with a 1.5. s increase in differential travel time, which could either be caused by high water content or decreased temperature. Taking into account results of recent S-wave tomographies, raised water content in the MTZ cannot be the main cause for this observation. Accordingly, we explain the increase, equivalent to a 15. km thicker MTZ, by a temperature decrease of about 80. K. We discuss two alternative models for this temperature reduction, either a remnant of subduction or an indication of downwelling due to small-scale, edge-driven convection caused by the contrast in lithospheric thickness across the TESZ. Any subducted lithosphere found in the MTZ at this location is unlikely to be related to Variscan subduction along the TESZ, though, as Eurasia has moved significantly northward since the Variscan orogeny. © 2013.


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.


Liu B.F.,CAS National Astronomical Observatories | Taam R.E.,Academia Sinica, Taiwan | Taam R.E.,Northwestern University
Astrophysical Journal, Supplement Series | Year: 2013

The magnitude of the viscosity and magnetic field parameters in hot accretion flows is investigated in low luminosity active galactic nuclei (LLAGNs). Theoretical studies show that a geometrically thin, optically thick disk is truncated at mass accretion rates less than a critical value by mass evaporated vertically from the disk to the corona, with the truncated region replaced by an advection dominated accretion flow (ADAF). The critical accretion rate for such a truncation is a function of the viscosity and magnetic field. Observations of X-ray photon indices and spectral fits of a number of LLAGNs published in the literature provide an estimate of the critical rate of mass accretion and the truncation radius, respectively. By comparing the observational results with theoretical predictions, the viscosity and magnetic field parameters in the hot accretion flow region are estimated. Specifically, the mass accretion rates inferred in different sources constrain the viscosity parameter, whereas the truncation radii of the disk, as inferred from spectral fits, further constrain the magnetic field parameter. It is found that the value of the viscosity parameter in the corona/ADAF ranges from 0.17 to 0.5, with values clustered about 0.2-0.3. Magnetic pressure is required by the relatively small truncation radii for some LLAGNs and is found to be as high as its equipartition value with the gas pressure. The inferred values of the viscosity parameter are in agreement with those obtained from the observations of non-stationary accretion in stellar mass black hole X-ray transients. This consistency provides support for the paradigm that a geometrically thin disk is truncated by means of a mass evaporation process from the disk to the corona at low mass accretion rates. © 2013. The American Astronomical Society. All rights reserved.


Wang Z.F.,Georgia Institute of Technology | Wang Z.F.,University of Utah | Liu F.,University of Utah | Chou M.Y.,Georgia Institute of Technology | Chou M.Y.,Academia Sinica, Taiwan
Nano Letters | Year: 2012

The Hofstadter butterfly spectrum for Landau levels in a two-dimensional periodic lattice is a rare example exhibiting fractal properties in a truly quantum system. However, the observation of this physical phenomenon in a conventional material will require a magnetic field strength several orders of magnitude larger than what can be produced in a modern laboratory. It turns out that for a specific range of rotational angles twisted bilayer graphene serves as a special system with a fractal energy spectrum under laboratory accessible magnetic field strengths. This unique feature arises from an intriguing electronic structure induced by the interlayer coupling. Using a recursive tight-binding method, we systematically map out the spectra of these Landau levels as a function of the rotational angle. Our results give a complete description of LLs in twisted bilayer graphene for both commensurate and incommensurate rotational angles and provide quantitative predictions of magnetic field strengths for observing the fractal spectra in these graphene systems. © 2012 American Chemical Society.


Barraza-Lopez S.,Georgia Institute of Technology | Barraza-Lopez S.,University of Arkansas | Kindermann M.,Georgia Institute of Technology | Chou M.Y.,Georgia Institute of Technology | Chou M.Y.,Academia Sinica, Taiwan
Nano Letters | Year: 2012

Graphene is believed to be an excellent candidate material for next-generation electronic devices. However, one needs to take into account the nontrivial effect of metal contacts in order to precisely control the charge injection and extraction processes. We have performed transport calculations for graphene junctions with wetting metal leads (metal leads that bind covalently to graphene) using nonequilibrium Greens functions and density functional theory. Quantitative information is provided on the increased resistance with respect to ideal contacts and on the statistics of current fluctuations. We find that charge transport through the studied two-terminal graphene junction with Ti contacts is pseudo-diffusive up to surprisingly high energies. © 2012 American Chemical Society.


Roberts A.P.,UK National Oceanography Center | Roberts A.P.,Australian National University | Chang L.,UK National Oceanography Center | Rowan C.J.,UK National Oceanography Center | And 3 more authors.
Reviews of Geophysics | Year: 2011

Greigite (Fe3S4) is an authigenic ferrimagnetic mineral that grows as a precursor to pyrite during early diagenetic sedimentary sulfate reduction. It can also grow at any time when dissolved iron and sulfide are available during diagenesis. Greigite is important in paleomagnetic, environmental, biological, biogeochemical, tectonic, and industrial processes. Much recent progress has been made in understanding its magnetic properties. Greigite is an inverse spinel and a collinear ferrimagnet with antiferromagnetic coupling between iron in octahedral and tetrahedral sites. The crystallographic c axis is the easy axis of magnetization, with magnetic properties dominated by magnetocrystalline anisotropy. Robust empirical estimates of the saturation magnetization, anisotropy constant, and exchange constant for greigite have been obtained recently for the first time, and the first robust estimate of the low-field magnetic susceptibility is reported here. The Curie temperature of greigite remains unknown but must exceed 350C. Greigite lacks a low-temperature magnetic transition. On the basis of preliminary micromagnetic modeling, the size range for stable single domain behavior is 17-200 nm for cubic crystals and 17-500 nm for octahedral crystals. Gradual variation in magnetic properties is observed through the pseudo-single-domain size range. We systematically document the known magnetic properties of greigite (at high, ambient, and low temperatures and with alternating and direct fields) and illustrate how grain size variations affect magnetic properties. Recognition of this range of magnetic properties will aid identification and constrain interpretation of magnetic signals carried by greigite, which is increasingly proving to be environmentally important and responsible for complex paleomagnetic records, including widespread remagnetizations. Copyright © 2011 by the American Geophysical Union.


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.


Chen Y.-H.,National Tsing Hua University | Lee M.-J.,National Tsing Hua University | Hung W.,National Tsing Hua University | Chen Y.-C.,National Tsing Hua University | And 3 more authors.
Physical Review Letters | Year: 2012

This study reports the first experimental demonstration that two light pulses were made motionless and interacted with each other through a medium. The scheme with motionless light pulses maximizes the interaction time and can achieve a considerable efficiency even below single-photon level. To demonstrate the enhancement of optical nonlinear efficiency, the experiment in this study used the process of one optical pulse switched by another based on the effect of electromagnetically induced transparency. Moving light pulses activate switching at an energy per area of 2 photons per atomic absorption cross section as discussed in. This study demonstrates that motionless light pulses can activate switching at 0.56 photons per atomic absorption cross section, and that the light level can be further reduced by increasing the optical density of the medium. The result of this work enters a new regime of low-light physics. © 2012 American Physical Society.


Danishefsky S.J.,Sloan Kettering Cancer Center | Shue Y.-K.,OBI Pharma Inc. | Chang M.N.,OBI Pharma Inc. | Wong C.-H.,Academia Sinica, Taiwan | Wong C.-H.,Scripps Research Institute
Accounts of Chemical Research | Year: 2015

The development of anticancer vaccines requires the identification of unique epitope markers, preferably expressed exclusively on the surface of cancer cells. This Account describes the path of development of a carbohydrate-based vaccine for metastatic breast cancer, including the selection and synthesis of Globo-H as the target, the development of the vaccine conjugate and adjuvant design, the study of the immune response and consideration of class switch, and the analysis of Globo-H distribution on the surface of various cancer cells, cancer stem cells, and normal cells.The first synthesis of Globo-H was accomplished through the use of glycal chemistry; this approach delivered sufficient material for evaluation in phase I human trials. The development of a programmable one-pot synthesis method rendered the synthesis more practical and enabled the midstage proof-of-concept phase II trial and late-stage phase III trial. Finally, enzymatic synthesis of Globo-H coupled with cofactor regeneration was used for the late-stage multicenter trials and manufacture of the product. Along this path of development, it was discovered that the vaccine induced antibodies to target not only Globo-H, but also SSEA3 and SSEA4. Moreover, these three glycolipids were found to be uniquely expressed not only on the cell surface of breast cancer but on 15 additional cancer types, suggesting the broad application of this vaccine in cancer treatment and perhaps cancer prevention. In addition, a new glycolipid adjuvant was designed to target the CD1d receptor on dendritic cells and B cells for presentation to and activation of T cells to modulate the immune response and induce a class switch from IgM to IgG, thereby overcoming the common problem of carbohydrate-based vaccines that often induce mainly IgM antibodies.As demonstrated in this vaccine development, the chemical approach to the synthesis and conjugation of carbohydrate-based immunogens provides the flexibility for access to various structures and linkers to identify optimal compositions for development. The enzymatic method was then introduced to enable the practical synthesis of the vaccine candidate for clinical development and commercialization. Overall, this Account illustrates the path of development of a cancer vaccine, from selection of a unique glycan marker on breast cancer cells and the cancer stem cells as target to the use of chemistry in combination with immunology and cancer biology to enable the design and development of the Globo-H vaccine to target three specific glycan markers exclusively expressed on the cell surface of a number of different types of cancer. (Chemical Equation Presented). © 2015 American Chemical Society.


Chan Y.H.,Academia Sinica, Taiwan
Physical Review B - Condensed Matter and Materials Physics | Year: 2015

Based on the density-matrix renormalization group and the infinite time-evolving block decimation methods we study the interacting spin-orbit-coupled 1D Fermi gas in a transverse magnetic field. We find that the system with an attractive interaction can have a polarized insulator phase, a superconducting (SC) phase, a Luther-Emery (LE) phase, and a band insulator phase as we vary the chemical potential and the strength of the magnetic field. Spin-orbit coupling (SOC) enhances the triplet pairing order at zero momentum in both the SC and the LE phase, which leads to an algebraically decaying correlation with the same exponent as that of the singlet pairing one. In contrast to the Fulde-Ferrell-Larkin-Ovchinnikov phase found in the spin imbalanced system without SOC, pairings at finite momentum in these two phases have larger exponents hence do not dictate the long-range behavior. We also test for the presence of Majorana fermions in this system. Unlike results from the mean-field study, we do not find positive evidence of Majorana fermions. © 2015 American Physical Society.


Chang Y.-J.,Harvard University | Chang Y.-J.,Academia Sinica, Taiwan | DeKruyff R.H.,Harvard University | Umetsu D.T.,Harvard University
Journal of Leukocyte Biology | Year: 2013

Asthma is a complex and heterogeneous disease with several phenotypes, including an allergic asthma phe-notype, characterized by Th2 cytokine production and associated with allergen sensitization and adaptive immunity. Asthma also includes nonallergic asthma phenotypes that require innate rather than adaptive immunity. These innate pathways to asthma involve macro-phages, neutrophils, as well as ILCs, newly described cell types that produce a variety of cytokines, including IL-5 and IL-13. We review the recent data regarding ILCs and their role in asthma. © Society for Leukocyte Biology.


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.


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.


Wong H.T.,Academia Sinica, Taiwan
Nuclear Physics A | Year: 2010

The theme of the TEXONO research program is on the studies of low energy neutrino and dark matter physics. The current goals are on the development of germanium detectors with sub-keV sensitivities to realize experiments on neutrino magnetic moments, neutrino-nucleus coherent scattering, as well as WIMP dark matter searches. A threshold of 100-200 eV was achieved with prototype detectors at the Kuo-Sheng Neutrino Laboratory. New limits were placed for low-mass WIMPs. The dark matter program will move to a new underground laboratory currently under construction in Sichuan, China. © 2010 Elsevier B.V.


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.


Sheu S.-Y.,National Yang Ming University | Yang D.-Y.,Academia Sinica, Taiwan
Carbon | Year: 2014

The contact between graphene and metal is crucial in designing high-performance electronic devices. We present a systematic study of the Au-cluster intercalated bilayer graphene (Au-BLG) system. All of the constructed configurations were studied by ab initio density functional theory calculations. The effects of the Au coverage fraction on the gap opening and electron transfer, which are chemically controllable by design, were considered. Based on the analyses of the structure stability, the configurations with Au located at the hollow position are the most stable. Subsequently, a Bader analysis revealed that the Au coverage fraction value of 0.35 is a critical configuration in the direction of electrical charge flow. Our studies indicate that the Au 6s-orbital plays a key role in forming a phase of electronic instability in the Au-BLG system. This demonstration of new Au-BLG structures promises to be of benefit in the development of good potential graphene-based nanodevices in applications. © 2014 Elsevier Ltd. All rights reserved.


Peng C.-Y.,Academia Sinica, Taiwan | Tseng S.-T.,National Tsing Hua University
IEEE Transactions on Reliability | Year: 2010

For highly reliable products with very few test units, a progressive-stress accelerated degradation test (PSADT) has been proposed in the literature to obtain timely information of the product's lifetime distribution. The results, however, are restricted to the case where the product's degradation path follows a Wiener process (Brownian motion) with a linear drift rate. But in practical applications, the product's mean degradation path may be non-linear. Hence, how to address the lifetime distribution in this situation is a worthy topic for reliability analysts. In this paper, a PSADT with a non-linear degradation path is constructed using the cumulative exposure model. Then the product's lifetime distribution can be analytically obtained by the first passage time of its degradation path. Furthermore, we derive an exact relationship between the lifetime distributions of the PSADT, and the conventional constant-stress degradation test (CSDT), which allows us to extrapolate the product's lifetime distribution under typical stress. Finally, the usage of the proposed model, and the efficiency of PSADT to reduce the product's life testing time are demonstrated in the example. © 2010 IEEE.


Yang Y.-H.,Academia Sinica, Taiwan
MM 2012 - Proceedings of the 20th ACM International Conference on Multimedia | Year: 2012

Over recent years there has been a growing interest in finding ways to transform signals/matrices into sparse or low-rank representations, i.e., representations which are sparse in support or of low redundancy. Such decompositions are proving to be particularly powerful for a variety of signal processing and compression problems. In this paper, we investigate the application of this technique to the challenging task of singing voice/accompaniment separation for popular music. The vocal part is modeled as a sparse signal, whereas the instrumental part is considered to be low-rank. In addition, to better account for the particular properties of music, two new algorithms are proposed to improve the decomposition, including the incorporation of harmonicity priors and a back-end drum removal procedure. Evaluations on the MIR-1K benchmark dataset show that the proposed algorithms outperform the state-of-the-art by 0.01-2.41 db. © 2012 ACM.


Ha M.,University of Texas at Austin | Ha M.,University of Chicago | Ng D.W.-K.,University of Texas at Austin | Li W.-H.,University of Chicago | And 2 more authors.
Genome Research | Year: 2011

Histone modifications regulate gene expression in eukaryotes, but their effects on transcriptomes of a multicellular organism and on transcriptomic divergence between species are poorly understood. Here we present the first nucleotideresolution maps of histone acetylation, methylation, and core histone in Arabidopsis thaliana and a comprehensive analysis of these and all other available maps with gene expression data in A. thaliana, Arabidopsis arenosa, and allotetraploids. H3K9 acetylation (H3K9ac) and H3K4 trimethylation (H3K4me3) are correlated, and their distribution patterns are associated with Gene Ontology (GO) functional classifications. Highly dense and narrow distributions of these modifications near transcriptional start sites are associated with constitutive expression of genes involved in translation, whereas broad distributions toward coding regions correlate with expression variation of the genes involved in photosynthesis, carbohydrate metabolism, and defense responses. Compared to animal stem cells, dispersed distributions of H3K27me3 without bivalent H3K4me3 and H3K9ac marks correlate with developmentally repressed genes in Arabidopsis. Finally, genes affected by A. thaliana histone deacetylase 1 mutation tend to show high levels of expression variation within and between species. The data suggest that genome-wide coordinated modifications of histone acetylation and methylation provide a general mechanism for gene expression changes within and between species and in allopolyploids. © 2011 by Cold Spring Harbor Laboratory Press.


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.


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.


Wang W.-H.,Academia Sinica, Taiwan | Barger A.J.,University of Wisconsin - Madison | Barger A.J.,University of Hawaii at Manoa | Cowie L.L.,University of Hawaii at Manoa
Astrophysical Journal | Year: 2012

In order to find the most extreme dust-hidden high-redshift galaxies, we select 196 extremely red objects in the KS and Infrared Array Camera (IRAC) bands (KIEROs, [Ks - 4.5 μm]AB > 1.6) in the 0.06deg2 Great Observatories Origins Deep Surveys-North (GOODS-N) region. This selection avoids the Balmer breaks of galactic spectra at z < 4 and picks up red galaxies with strong dust extinction. The photometric redshifts of KIEROs are between 1.5 and 5, with 70% at z 2-4. KIEROs are very massive, with M 1010-1012 M. They are optically faint and usually cannot be picked out by the Lyman break selection. On the other hand, the KIERO selection includes approximately half of the known millimeter and submillimeter galaxies in the GOODS-N. Stacking analyses in the radio, millimeter, and submillimeter all show that KIEROs are much more luminous than average 4.5 μm-selected galaxies. Interestingly, the stacked fluxes for Advanced Camera for Surveys (ACS)-undetected KIEROs in these wave bands are 2.5-5 times larger than those for ACS-detected KIEROs. With the stacked radio fluxes and the local radio-FIR correlation, we derive mean infrared luminosities of (2-7) × 1012 L and mean star formation rates (SFRs) of 400-1200 Myr -1 for KIEROs with redshifts. We do not find evidence of a significant subpopulation of passive KIEROs. The large stellar masses and SFRs imply that KIEROs are z > 2 massive galaxies in rapid formation. Our results show that a large sample of dusty ultraluminous sources can be selected in this way and that a large fraction of high-redshift star formation is hidden by dust. © 2012 The American Astronomical Society. All rights reserved.


Lee W.-K.,University of California at San Diego | Shu F.H.,University of California at San Diego | Shu F.H.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2012

In this paper, we study the feathering substructures along spiral arms by considering the perturbational gas response to a spiral shock. Feathers are density fluctuations that jut out from the spiral arm to the interarm region at pitch angles given by the quantum numbers of the doubly periodic structure. In a localized asymptotic approximation, related to the shearing sheet except that the inhomogeneities occur in space rather than in time, we derive the linearized perturbation equations for a razor-thin disk with turbulent interstellar gas, frozen-in magnetic field, and gaseous self-gravity. Apart from the modal quantum numbers, the individual normal modes of the system depend on seven dimensionless quantities that characterize the underlying time-independent axisymmetric state plus its steady, nonlinear, two-armed spiral-shock response to a hypothesized background density wave supported by the disk stars of the galaxy. We show that some of these normal modes have positive growth rates. Their overdensity contours in the post-shock region are very reminiscent of observed feathering substructures in full magnetohydrodynamic simulations. The feathering substructures are parasitic instabilities intrinsic to the system; thus, their study not only provides potential diagnostics for important parameters that characterize the interstellar medium of external galaxies, but also yields a deeper understanding of the basic mechanism that drives the formation of the giant molecular clouds and the OB stars that outline observed grand-design spirals. © © 2012. The American Astronomical Society. All rights reserved..


Ricker P.M.,Urbana University | Taam R.E.,Northwestern University | Taam R.E.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2012

The hydrodynamic evolution of the common-envelope (CE) phase of a low-mass binary composed of a 1.05 M red giant and a 0.6 M companion has been followed for five orbits of the system using a high-resolution method in three spatial dimensions. During the rapid inspiral phase, the interaction of the companion with the red giant's extended atmosphere causes about 25% of the CE to be ejected from the system, with mass continuing to be lost at the end of the simulation at a rate 2 M yr-1. In the process the resulting loss of angular momentum and energy reduces the orbital separation by a factor of seven. After this inspiral phase the eccentricity of the orbit rapidly decreases with time. The gravitational drag dominates hydrodynamic drag at all times in the evolution, and the commonly used Bondi-Hoyle-Lyttleton prescription for estimating the accretion rate onto the companion significantly overestimates the true rate. On scales comparable to the orbital separation, the gas flow in the orbital plane in the vicinity of the two cores is subsonic with the gas nearly corotating with the red giant core and circulating about the red giant companion. On larger scales, 90% of the outflow is contained within 30° of the orbital plane, and the spiral shocks in this material leave an imprint on the density and velocity structure. Of the energy released by the inspiral of the cores, only about 25% goes toward ejection of the envelope. © 2012. The American Astronomical Society. All rights reserved.


Takata J.,University of Hong Kong | Cheng K.S.,University of Hong Kong | Taam R.E.,Northwestern University | Taam R.E.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2012

The Fermi Large Area Telescope has revealed that rotation powered millisecond pulsars (MSPs) are a major contributor to the Galactic γ-ray source population. Such pulsars may also be important in modeling the quiescent state of several low-mass X-ray binaries (LMXBs), where optical observations of the companion star suggest the possible existence of rotation powered MSPs. To understand the observational properties of the different evolutionary stages of MSPs, the X-ray and γ-ray emissions associated with the outer gap model are investigated. For rotation powered MSPs, the size of the outer gap and the properties of the high-energy emission are controlled by either the photon-photon pair-creation process or magnetic pair-creation process near the surface. For these pulsars, we find that the outer gap model controlled by the magnetic pair-creation process is preferable in explaining the possible correlations between the γ-ray luminosity or non-thermal X-ray luminosity versus the spin-down power. For the accreting MSPs in quiescent LMXBs, the thermal X-ray emission at the neutron star (NS) surface resulting from deep crustal heating can control the conditions in the outer gap. We argue that the optical modulation observed in the quiescent state of several LMXBs originates from the irradiation of the donor star by γ-rays from the outer gap. In these systems, the irradiation luminosity required for the optical modulation of the source such as SAXJ1808.4-3658 can be achieved for a NS of high mass. Finally, we discuss the high-energy emission associated with an intra-binary shock in black widow systems, e.g., PSRB1957+20. © 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.


Barger V.,University of Wisconsin - Madison | Chiang C.-W.,University of Wisconsin - Madison | Chiang C.-W.,National Central University | Chiang C.-W.,Academia Sinica, Taiwan | And 3 more authors.
Physical Review Letters | Year: 2011

A measurement of the Lamb shift in muonic hydrogen yields a charge radius of the proton that is smaller than the CODATA value by about 5B standard deviations. We explore the possibility that new scalar, pseudoscalar, vector, and tensor flavor-conserving nonuniversal interactions may be responsible for the discrepancy. We consider exotic particles that, among leptons, couple preferentially to muons and mediate an attractive nucleon-muon interaction. We find that the many constraints from low energy data disfavor new spin-0, spin-1, and spin-2 particles as an explanation. © 2011 American Physical Society.


Cheung K.,National Tsing Hua University | Cheung K.,Konkuk University | Lu C.-T.,National Tsing Hua University | Yuan T.-C.,Academia Sinica, Taiwan
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

Motivated by the excess in the diphoton production rate of the Higgs boson at the Large Hadron Collider (LHC), we investigate the possibility that one of the CP-even Higgs bosons of the extra U(1) extended minimal supersymmetric standard model can give a consistent result. We scan the parameter space for a standard-model-like Higgs boson such that the mass is in the range of 124-127 GeV and the production rate σB of the WW*, ZZ* modes is consistent with the standard model (SM) values, while that of γγ is enhanced relative to the SM value. We find that the SM-like Higgs boson is mostly the lightest CP-even Higgs boson and it has a strong mixing with the second lightest one, which is largely singletlike. The implications on Zγ production rate and properties of the other Higgs bosons are also studied. © 2013 American Physical Society.


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.


Chang J.,National Tsing Hua University | Cheung K.,National Tsing Hua University | Cheung K.,Konkuk University | Tseng P.-Y.,National Tsing Hua University | Yuan T.-C.,Academia Sinica, Taiwan
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

The current Large Hadron Collider data indicate that the newly observed resonance has the WW and ZZ modes consistent with the standard model Higgs boson, while the γγ mode is about 1.2-2 times that of the standard model prediction and the tau-pair mode is suppressed. If this pattern persists in the upcoming data, it would be a sign for physics beyond the standard model. In the type II two-Higgs-doublet model, it is the region where sina α≈0 and a moderately large tana β=10-20 that the lighter CP-even Higgs boson can accommodate the current data. We note that in this region the heavier CP-even Higgs boson must have a large decay branching ratio into tau pairs. We find that this heavier Higgs boson can be observable in the associated production with a bb̄ pair and through the decay into a tau pair. © 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.


Cheng H.-Y.,Academia Sinica, Taiwan | Chua C.-K.,Chung Yuan Christian University
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

Charmless three-body decays of B mesons are studied using a simple model based on the framework of the factorization approach. Hadronic three-body decays receive both resonant and nonresonant contributions. Dominant nonresonant contributions to tree-dominated three-body decays arise from the b→u tree transition which can be evaluated using heavy-meson chiral perturbation theory valid in the soft-meson limit. For penguin-dominated decays, nonresonant signals come mainly from the penguin amplitude governed by the matrix elements of scalar densities âŸ̈M1M2|q ̄1q2|0⟩. We use the measurements of B̄0→KSKSKS to constrain the nonresonant component of âŸ̈KK̄|s̄s|0⟠©. The intermediate vector-meson contributions to three-body decays are identified through the vector current, while the scalar-meson resonances are mainly associated with the scalar density. While the calculated direct CP violation in B-→K+K-K- and B-→π+π-π- decays agrees well with experiment in both magnitude and sign, the predicted CP asymmetries in B-→π-K+K- and B-→K-π+π- have incorrect signs when confronted with experiment. It has been conjectured recently that a possible resolution to this CP puzzle may rely on final-state rescattering of π+π- and K+K-. Assuming a large strong phase associated with the matrix element âŸ̈Kπ |s̄q|0⟩ arising from some sort of power corrections, we fit it to the data of K-π+π- and find a correct sign for π-K+K-. We predict some testable CP violation in B̄0→K+K -π0 and K+K-KS. In the low-mass regions of the Dalitz plot, we find that the regional CP violation is indeed largely enhanced with respect to the inclusive one, though it is still significantly below the data. In this work, strong phases arise from effective Wilson coefficients, propagators of resonances, and the matrix element of the scalar density âŸ̈M1M2|q ̄1q2|0⟩. © 2013 American Physical Society.


Nazarov V.U.,Academia Sinica, Taiwan | Vignale G.,University of Missouri
Physical Review Letters | Year: 2011

We calculate the optical spectra of silicon, germanium, and zinc blende semiconductors in the adiabatic time-dependent density-functional formalism, making use of kinetic energy density-dependent [meta-generalized-gradient- approximation (GGA)] exchange-correlation functionals. We find excellent agreement between theory and experiment. The success of the theory on this notoriously difficult problem is traced to the fact that the exchange-correlation kernel of meta-GGA supports a singularity of the form α/q2 (where q is the wave vector and α is a constant), whereas previously employed approximations (e.g., local-density and generalized gradient approximations) do not. Thus, the use of the adiabatic meta-GGA opens a new path for handling the extreme nonlocality of the time-dependent exchange-correlation potential in solid-state systems. © 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..


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.


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..


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.


Chiang L.-Y.,National Taiwan University | Chen F.-F.,Academia Sinica, Taiwan
Astrophysical Journal | Year: 2012

The angular power spectrum of the cosmic microwave background temperature anisotropies is one of the most important characteristics in cosmology that can shed light on the properties of the universe such as its geometry and total density. Using flat sky approximation and Fourier analysis, we estimate the angular power spectrum from an ensemble of the least foreground-contaminated square patches from the Wilkinson Microwave Anisotropy Probe W and V frequency band map. This method circumvents the issue of foreground cleaning and that of breaking orthogonality in spherical harmonic analysis because we are able to mask out the bright Galactic plane region, thereby rendering a direct measurement of the angular power spectrum. We test and confirm the Gaussian statistical characteristic of the selected patches, from which the first and second acoustic peaks of the power spectrum are reproduced, and the third peak is clearly visible, albeit with some noise residual at the tail. © 2012. The American Astronomical Society. All rights reserved.


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.


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.


Feng N.,CAS Wuhan Center for Magnetic Resonance | Wang Q.,CAS Wuhan Center for Magnetic Resonance | Zheng A.,CAS Wuhan Center for Magnetic Resonance | Zhang Z.,CAS Wuhan Center for Magnetic Resonance | And 4 more authors.
Journal of the American Chemical Society | Year: 2013

The origin of the exceptionally high activity of (B, Ag)-codoped TiO 2 catalysts under solar-light irradiation has been investigated by XPS and 11B solid-state NMR spectroscopy in conjunction with density functional theory (DFT) calculations. XPS experimental results demonstrated that a portion of the dopant Ag (Ag3+) ions were implanted into the crystalline lattice of (B, Ag)-codoped TiO2 and were in close proximity to the interstitial B (Bint.) sites, forming [B int.-O-Ag] structural units. In situ XPS experiments were employed to follow the evolution of the chemical states of the B and Ag dopants during UV-vis irradiation. It was found that the [Bint.-O-Ag] units could trap the photoinduced electron to form a unique intermediate structure in the (B, Ag)-codoped TiO2 during the irradiation, which is responsible for the photoinduced shifts of the B 1s and Ag 3d peaks observed in the in situ XPS spectra. Solid-state NMR experiments including 11B triple-quantum and double-quantum magic angle spinning (MAS) NMR revealed that up to six different boron species were present in the catalysts and only the tricoordinated interstitial boron (T) species was in close proximity to the substitutional Ag species, leading to formation of [T-O-Ag] structural units. Furthermore, as demonstrated by DFT calculations, the [T-O-Ag] structural units were responsible for trapping the photoinduced electrons, which prolongs the life of the photoinduced charge carriers and eventually leads to a remarkable enhancement in the photocatalytic activity. All these unprecedented findings are expected to be crucial for understanding the roles of B and Ag dopants and their synergistic effect in numerous titania-mediated photocatalytic reactions. © 2013 American Chemical Society.


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.