Showing papers by "Academia Sinica published in 2004"

Medical genetics: A marker for Stevens-Johnson syndrome

Abstract: Stevens-Johnson syndrome and the related disease toxic epidermal necrolysis are life-threatening reactions of the skin to particular types of medication. Here we show that there is a strong association in Han Chinese between a genetic marker, the human leukocyte antigen HLA-B*1502, and Stevens-Johnson syndrome induced by carbamazepine, a drug commonly prescribed for the treatment of seizures. It should be possible to exploit this association in a highly reliable test to predict severe adverse reaction, as well as for investigation of the pathogenesis of Stevens-Johnson syndrome.

Comparative Analysis of the Receptor-Like Kinase Family in Arabidopsis and Rice

Abstract: Receptor-like kinases (RLKs) belong to the large RLK/Pelle gene family, and it is known that the Arabidopsis thaliana genome contains >600 such members, which play important roles in plant growth, development, and defense responses. Surprisingly, we found that rice (Oryza sativa) has nearly twice as many RLK/Pelle members as Arabidopsis does, and it is not simply a consequence of a larger predicted gene number in rice. From the inferred phylogeny of all Arabidopsis and rice RLK/Pelle members, we estimated that the common ancestor of Arabidopsis and rice had >440 RLK/Pelles and that large-scale expansions of certain RLK/Pelle members and fusions of novel domains have occurred in both the Arabidopsis and rice lineages since their divergence. In addition, the extracellular domains have higher nonsynonymous substitution rates than the intracellular domains, consistent with the role of extracellular domains in sensing diverse signals. The lineage-specific expansions in Arabidopsis can be attributed to both tandem and large-scale duplications, whereas tandem duplication seems to be the major mechanism for recent expansions in rice. Interestingly, although the RLKs that are involved in development seem to have rarely been duplicated after the Arabidopsis–rice split, those that are involved in defense/disease resistance apparently have undergone many duplication events. These findings led us to hypothesize that most of the recent expansions of the RLK/Pelle family have involved defense/resistance-related genes.

Evolution of Red Organic Light-Emitting Diodes: Materials and Devices

Abstract: This short review surveys the development of red fluorescent materials for the application of organic light-emitting diodes (OLEDs) that generate red electroluminescence (EL). The merit and problems of current dopant-based, either fluorescent or phosphorescent, red OLEDs will be addressed first. Materials that offer unique EL characteristics, such as narrow and saturated red EL as well as current density or voltage-independent EL efficiency, are discussed. In addition to dopant-based and assist dopant-based red OLEDs for comparison purposes, the survey emphasizes nondoped red OLEDs that are fabricated with the newly emerging red fluorophores as the host-emitter. The advantage of host-emitting nondoped OLEDs compared with traditional dopant-based red OLEDs is described in view of the chemical and device structures of these materials.

Surface uplift, tectonics, and erosion of eastern Tibet from large-scale drainage patterns

Abstract: [1] A new regional compilation of the drainage history in southeastern Tibet suggests that the modern rivers draining the plateau margin were once tributaries to a single, southward flowing system which drained into the South China Sea. Disruption of the paleo-drainage occurred by river capture and reversal prior to or coeval with the initiation of Miocene (?) uplift in eastern Tibet, including ∼2000 m of surface uplift of the lower plateau margin since reversal of the flow direction of the Yangtze River. Despite lateral changes in course due to capture and reversal, the superposition of eastward and southward draining rivers that cross the southeastern plateau margin suggests that uplift has occurred over long wavelengths (>1000 km), mimicking the present low-gradient topographic slope. Thus reorganization of drainage lines by capture and reversal events explains most of the peculiar patterns of the eastern plateau rivers, without having to appeal to large-magnitude tectonic shear.

Securing web application code by static analysis and runtime protection

Abstract: Security remains a major roadblock to universal acceptance of the Web for many kinds of transactions, especially since the recent sharp increase in remotely exploitable vulnerabilities have been attributed to Web application bugs. Many verification tools are discovering previously unknown vulnerabilities in legacy C programs, raising hopes that the same success can be achieved with Web applications. In this paper, we describe a sound and holistic approach to ensuring Web application security. Viewing Web application vulnerabilities as a secure information flow problem, we created a lattice-based static analysis algorithm derived from type systems and typestate, and addressed its soundness. During the analysis, sections of code considered vulnerable are instrumented with runtime guards, thus securing Web applications in the absence of user intervention. With sufficient annotations, runtime overhead can be reduced to zero. We also created a tool named.WebSSARI (Web application Security by Static Analysis and Runtime Inspection) to test our algorithm, and used it to verify 230 open-source Web application projects on SourceForge.net, which were selected to represent projects of different maturity, popularity, and scale. 69 contained vulnerabilities. After notifying the developers, 38 acknowledged our findings and stated their plans to provide patches. Our statistics also show that static analysis reduced potential runtime overhead by 98.4%.

Identified charged particle spectra and yields in Au + Au collisions at √sNN = 200 GeV

Abstract: The centrality dependence of transverse momentum distributions and yields for ${\ensuremath{\pi}}^{\ifmmode\pm\else\textpm\fi{}},{K}^{\ifmmode\pm\else\textpm\fi{}},p$, and $\overline{p}$ in $\text{Au}+\text{Au}$ collisions at $\sqrt{{s}_{NN}}=200\phantom{\rule{0.3em}{0ex}}\text{GeV}$ at midrapidity are measured by the PHENIX experiment at the Relativistic Heavy Ion Collider. We observe a clear particle mass dependence of the shapes of transverse momentum spectra in central collisions below $\ensuremath{\sim}2\phantom{\rule{0.3em}{0ex}}\text{GeV}∕c$ in ${p}_{T}$. Both mean transverse momenta and particle yields per participant pair increase from peripheral to midcentral and saturate at the most central collisions for all particle species. We also measure particle ratios of ${\ensuremath{\pi}}^{\ensuremath{-}}∕{\ensuremath{\pi}}^{+}$, ${K}^{\ensuremath{-}}∕{K}^{+}$, $\overline{p}∕p$, $K∕\ensuremath{\pi}$, $p∕\ensuremath{\pi}$, and $\overline{p}∕\ensuremath{\pi}$ as a function of ${p}_{T}$ and collision centrality. The ratios of equal mass particle yields are independent of ${p}_{T}$ and centrality within the experimental uncertainties. In central collisions at intermediate transverse momenta $\ensuremath{\sim}1.5--4.5\phantom{\rule{0.3em}{0ex}}\text{GeV}∕c$, proton and antiproton yields constitute a significant fraction of the charged hadron production and show a scaling behavior different from that of pions.

Design, construction and tests of the ICARUS T600 detector

Abstract: We have constructed and operated the ICARUS T600 liquid argon (LAr) time projection chamber (TPC). The ICARUS T600 detector is the largest LAr TPC ever built, with a size of about 500 tons of fully imaging mass. The design and assembly of the detector relied on industrial support and represents the applications of concepts matured in laboratory tests to the kton scale. The ICARUS T600 was commissioned for a technical run that lasted about 3 months. During this period all the detector features were extensively tested with an exposure to cosmic-rays at surface with a resulting data collection of about 30 000 events. The detector was developed as the first element of a modular design. Thanks to the concept of modularity, it will be possible to realize a detector with several ktons active mass, to act as an observatory for astroparticle and neutrino physics at the Gran Sasso Underground Laboratory and a second-generation nucleon decay experiment. In this paper a description of the ICARUS T600 is given, detailing its design specifications, assembly procedures and acceptance tests. Commissioning procedures and results of the technical run are also reported, as well as results from the off-line event reconstruction.

Particle-type dependence of azimuthal anisotropy and nuclear modification of particle production in Au plus Au collisions at root s(NN)=200 GeV

Abstract: We present STAR measurements of the azimuthal anisotropy parameter v{sub 2} and the binary-collision scaled centrality ratio R{sub CP} for kaons and lambdas ({Lambda} + {bar {Lambda}}) at mid-rapidity in Au+Au collisions at {radical}s{sub NN} = 200 GeV. In combination, the v{sub 2} and R{sub CP} particle-type dependencies contradict expectations from partonic energy loss followed by standard fragmentation in vacuum. We establish p{sub T} {approx} 5 GeV/c as the value where the centrality dependent baryon enhancement ends. The K{sub S}{sup 0} and {Lambda} + {bar {Lambda}} v{sub 2} values are consistent with expectations of constituent-quark-number scaling from models of hadron formation by parton coalescence or recombination.

Small molecules targeting severe acute respiratory syndrome human coronavirus

Abstract: Severe acute respiratory syndrome (SARS) is an infectious disease caused by a novel human coronavirus. Currently, no effective antiviral agents exist against this type of virus. A cell-based assay, with SARS virus and Vero E6 cells, was developed to screen existing drugs, natural products, and synthetic compounds to identify effective anti-SARS agents. Of >10,000 agents tested, ≈50 compounds were found active at 10 μM; among these compounds, two are existing drugs (Reserpine 13 and Aescin 5) and several are in clinical development. These 50 active compounds were tested again, and compounds 2–6, 10, and 13 showed active at 3 μM. The 50% inhibitory concentrations for the inhibition of viral replication (EC50) and host growth (CC50) were then measured and the selectivity index (SI = CC50/EC50) was determined. The EC50, based on ELISA, and SI for Reserpine, Aescim, and Valinomycin are 3.4 μM (SI = 7.3), 6.0 μM (SI = 2.5), and 0.85 μM (SI = 80), respectively. Additional studies were carried out to further understand the mode of action of some active compounds, including ELISA, Western blot analysis, immunofluorescence and flow cytometry assays, and inhibition against the 3CL protease and viral entry. Of particular interest are the two anti-HIV agents, one as an entry blocker and the other as a 3CL protease inhibitor (Ki = 0.6 μM).

Quantum confinement and electronic properties of silicon nanowires.

Abstract: We investigate the structural, electronic, and optical properties of hydrogen-passivated silicon nanowires along [110] and [111] directions with diameter d up to 4.2 nm from first principles. The size and orientation dependence of the band gap is investigated and the local-density gap is corrected with the GW approximation. Quantum confinement becomes significant for d<2.2 nm, where the dielectric function exhibits strong anisotropy and new low-energy absorption peaks start to appear in the imaginary part of the dielectric function for polarization along the wire axis.

Observation of the narrow state X(3872) → J/ψπ+π- in p̄p collisions at √s = 1.96 TeV

Abstract: The observation of a state consistent with X(3872) decaying into J/ψπ+π- was reported. The X(3872) mass was measured to be 3871.3±0.7(stat)±0.4(syst)MeV/c2 from a sample of 730±90 candidates. The observed width was consistent with the detector resolution. The results were found to be converging well with the measurements by the Belle Collaboration using b± decays.

A Previously Unknown Maltose Transporter Essential for Starch Degradation in Leaves

Abstract: A previously unknown maltose transporter is essential for the conversion of starch to sucrose in Arabidopsis leaves at night. The transporter was identified by isolating two allelic mutants with high starch levels and very high maltose, an intermediate of starch breakdown. The mutations affect a gene of previously unknown function, MEX1. We show that MEX1is a maltose transporter that is unrelated to other sugar transporters. The severe mex1 phenotype demonstrates that MEX1is the predominant route of carbohydrate export from chloroplasts at night. Homologous genes in plants including rice and potato indicate that maltose export is of widespread significance.

Pre-earthquake ionospheric anomalies registered by continuous GPS TEC measurements

Abstract: . In this paper we examine pre-earthquake ionospheric anomalies by the total electron content (TEC) derived from a ground-based receiver of the Global Positioning System (GPS). A 15-day running median of the TEC and the associated inter-quartile range (IQR) are utilized as a reference for identifying abnormal signals during all of the 20M≥6.0 earthquakes in the Taiwan area from September 1999 to December 2002. Results show that the pre-earthquake ionospheric anomalies appear during 18:00–22:00LT (LT=UT+8h) within 5 days prior to 16 of the 20M≥6.0 earthquakes. This success rate of 80% (=16/20%) suggests that the GPS TEC is useful to register pre-earthquake ionospheric anomalies appearing before large earthquakes. Key words. Ionosphere (ionospheric disturbances; ionosphere-atmosphere interactions)

Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes.

Abstract: We estimated the dates of the monocot–dicot split and the origin of core eudicots using a large chloroplast (cp) genomic dataset. Sixty-one protein-coding genes common to the 12 completely sequenced cp genomes of land plants were concatenated and analyzed. Three reliable split events were used as calibration points and for cross references. Both the method based on the assumption of a constant rate and the Li–Tanimura unequal-rate method were used to estimate divergence times. The phylogenetic analyses indicated that nonsynonymous substitution rates of cp genomes are unequal among tracheophyte lineages. For this reason, the constant-rate method gave overestimates of the monocot–dicot divergence and the age of core eudicots, especially when fast-evolving monocots were included in the analysis. In contrast, the Li–Tanimura method gave estimates consistent with the known evolutionary sequence of seed plant lineages and with known fossil records. Combining estimates calibrated by two known fossil nodes and the Li–Tanimura method, we propose that monocots branched off from dicots 140–150 Myr ago (late Jurassic–early Cretaceous), at least 50 Myr younger than previous estimates based on the molecular clock hypothesis, and that the core eudicots diverged 100–115 Myr ago (Albian–Aptian of the Cretaceous). These estimates indicate that both the monocot–dicot divergence and the core eudicot’s age are older than their respective fossil records.

Mechanisms of Global Warming Impacts on Regional Tropical Precipitation

Abstract: Mechanisms that determine the tropical precipitation anomalies under global warming are examined in an intermediate atmospheric model coupled with a simple land surface and a mixed layer ocean. To compensate for the warm tropospheric temperature, atmospheric boundary layer (ABL) moisture must increase to maintain positive convective available potential energy (CAPE) in convective regions. In nonconvective regions, ABL moisture is controlled by different balances and does not increase as much, creating a spatial gradient of ABL moisture anomalies. Associated with this spatial pattern of the ABL moisture anomalies are two main mechanisms responsible for the anomalous tropical precipitation. In the ‘‘upped-ante mechanism,’’ increases in ABL moisture are opposed by imported dry air wherever inflow from nonconvective regions over margins of convective regions occurs. The ABL moisture is not enough to meet the higher ‘‘convective ante’’ induced by the warmer tropospheric temperature, so precipitation is decreased. In the ‘‘anomalous gross moist stability mechanism,’’ gross moist stability is reduced due to increased ABL moisture. As a result, convection is enhanced and precipitation becomes heavier over convective regions. While the upped-ante mechanism induces negative precipitation anomalies over the margins of convective regions, the anomalous gross moist stability mechanism induces positive precipitation anomalies within convective regions. The importance of variation in gross moist stability, which is likely to differ among climate models, is suggested as a potential factor causing discrepancies in the predicted regional tropical precipitation changes.

Adsorption and Immobilization of Cytochrome c on Nanodiamonds

Abstract: Methods have been developed to immobilize proteins onto the surfaces of nanodiamonds with an average size of 5 ± 1 nm. The immobilization started with carboxylation/oxidization of diamonds with strong acids, followed by coating the surfaces with poly-l-lysine (PL) for covalent attachment of proteins using heterobifunctional cross-linkers. The feasibility of this approach is proven with fluorescent labeling of the PL-coated diamonds by Alexa Fluor 488 and subsequent detection of the emission using a confocal fluorescence microscope. Immobilization of proteins onto the surfaces is also demonstrated with yeast cytochrome c, which possesses a free SH group for linkage and a characteristic Soret absorption band for observation.

Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach.

Abstract: A systematic way of inferring evolutionary relatedness of microbial organisms from the oligopeptide content, i.e., frequency of amino acid K-strings in their complete proteomes, is proposed. The new method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. The only "parameter" in the method is the length K of the oligopeptides, which serves to tune the "resolution power" of the method. The topology of the trees converges with K increasing. Applied to a total of 109 organisms, including 16 Archaea, 87 Bacteria, and 6 Eukarya, it yields an unrooted tree that agrees with the biologists' "tree of life" based on SSU rRNA comparison in a majority of basic branchings, and especially, in all lower taxa.

Molecular events in senescing Arabidopsis leaves.

Abstract: Senescence is the final stage of leaf development. Although it means the loss of vitality of leaf tissue, leaf senescence is tightly controlled by the development to increase the fitness of the whole plant. The molecular mechanisms regulating the induction and progression of leaf senescence are complex. We used a cDNA microarray, containing 11 500 Arabidopsis DNA elements, and the whole-genome Arabidopsis ATH1 Genome Array to examine global gene expression in dark-induced leaf senescence. By monitoring the gene expression patterns at carefully chosen time points, with three biological replicates each time, we identified thousands of up- or down-regulated genes involved in dark-induced senescence. These genes were clustered and categorized according to their expression patterns and responsiveness to dark treatment. Genes with different expression kinetics were classified according to different biological processes. Genes showing significant alteration of expression patterns in all available biochemical pathways were plotted to envision the molecular events occurring in the processes examined. With the expression data, we postulated an innovative biochemical pathway involving pyruvate orthophosphate dikinase in generating asparagine for nitrogen remobilization in dark-treated leaves. We also surveyed the alteration in expression of Arabidopsis transcription factor genes and established an apparent association of GRAS, bZIP, WRKY, NAC, and C2H2 transcription factor families with leaf senescence.

Functional Recovery of Stroke Rats Induced by Granulocyte Colony-Stimulating Factor–Stimulated Stem Cells

Abstract: Background— Stroke is a leading cause of death and disability worldwide; however, no effective treatment currently exists. Methods and Results— Rats receiving subcutaneous granulocyte colony-stimulating factor (G-CSF) showed less cerebral infarction, as evaluated by MRI, and improved motor performance after right middle cerebral artery ligation than vehicle-treated control rats. Subcutaneous administration of G-CSF enhanced the availability of circulating hematopoietic stem cells to the brain and their capacity for neurogenesis and angiogenesis in rats with cerebral ischemia. Conclusions— G-CSF induced increases in bone marrow cell mobilization and targeting to the brain, reducing the volume of cerebral infarction and improving neural plasticity and vascularization.

Color Tuning in Benzo[1,2,5]thiadiazole‐Based Small Molecules by Amino Conjugation/Deconjugation: Bright Red‐Light‐Emitting Diodes

Abstract: Bipolar compounds (referred to in general as btza) containing a benzo[1,2,5]thiadiazole core and peripheral diarylamines and/or 4-tert-butylphenyl moieties have been synthesized via palladium-catalyzed cross-coupling reactions of 4,7-dibromobenzo[1,2,5]thiadiazole with appropriate stannyl compounds. These compounds are fluorescent and the emission color ranges from green to red. The fluorescence of the compounds originates from a charge-transfer process and exhibits solvatochromism. These red-light-emitting materials are amorphous and devices of different configurations were fabricated: I) ITO/btza/TPBI/Mg:Ag; II) ITO/btza/Alq3/Mg:Ag; III) ITO/btza/Mg:Ag (where ITO = indium tin oxide, TPBI = 1,3,5-tris(N-phenylbezimidazol-2-yl)benzene, and Alq3 = tris(8-hydroxyquinoline)aluminum). The performance of some of the red-light-emitting devices appears to be very promising.

Supernova constraints on a holographic dark energy model

Abstract: In this paper, we use the type Ia supernova data to constrain the model of holographic dark energy. For d = 1, the best fit result is Ωm0 = 0.25, the equation of the state of the holographic dark energy wΛ0 = −0.91 and the transition between the decelerating expansion and the accelerating expansion happened when the cosmological red-shift was zT = 0.72. If we set d as a free parameter, the best fit results are d = 0.21, Ωm0 = 0.46, wΛ0 = −2.67, which sounds like a phantom today, and the transition red-shift is zT = 0.28.

A new cluster validity measure and its application to image compression

Abstract: Many validity measures have been proposed for evaluating clustering results. Most of these popular validity measures do not work well for clusters with different densities and/or sizes. They usually have a tendency of ignoring clusters with low densities. In this paper, we propose a new validity measure that can deal with this situation. In addition, we also propose a modified K-means algorithm that can assign more cluster centres to areas with low densities of data than the conventional K-means algorithm does. First, several artificial data sets are used to test the performance of the proposed measure. Then the proposed measure and the modified K-means algorithm are applied to reduce the edge degradation in vector quantisation of image compression.

Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals

Abstract: Only 17% of 111 reef-building coral genera and none of the 18 coral families with reef-builders are considered endemic to the Atlantic, whereas the corresponding percentages for the Indo-west Pacific are 76% and 39%1,2. These figures depend on the assumption that genera and families spanning the two provinces belong to the same lineages (that is, they are monophyletic). Here we show that this assumption is incorrect on the basis of analyses of mitochondrial and nuclear genes. Pervasive morphological convergence at the family level has obscured the evolutionary distinctiveness of Atlantic corals. Some Atlantic genera conventionally assigned to different families are more closely related to each other than they are to their respective Pacific ‘congeners’. Nine of the 27 genera of reef-building Atlantic corals belong to this previously unrecognized lineage, which probably diverged over 34 million years ago. Although Pacific reefs have larger numbers of more narrowly distributed species, and therefore rank higher in biodiversity hotspot analyses3, the deep evolutionary distinctiveness of many Atlantic corals should also be considered when setting conservation priorities.