Showing papers by "University of Tokyo published in 2004"
Macquarie University1, University of Minnesota2, Stanford University3, Simón Bolívar University4, Wageningen University and Research Centre5, Smithsonian Environmental Research Center6, University of Alaska Fairbanks7, VU University Amsterdam8, University of Zurich9, Centre national de la recherche scientifique10, Curtin University11, Tohoku University12, University of Wisconsin–Eau Claire13, Landcare Research14, University of Concepción15, University of Cape Town16, University of Tartu17, Polish Academy of Sciences18, University of Tokyo19, Utrecht University20, University of Western Australia21, Charles Darwin University22, Ural State University23, University of Toronto24, Texas A&M University25, University of Córdoba (Spain)26
TL;DR: Reliable quantification of the leaf economics spectrum and its interaction with climate will prove valuable for modelling nutrient fluxes and vegetation boundaries under changing land-use and climate.
Abstract: Bringing together leaf trait data spanning 2,548 species and 175 sites we describe, for the first time at global scale, a universal spectrum of leaf economics consisting of key chemical, structural and physiological properties. The spectrum runs from quick to slow return on investments of nutrients and dry mass in leaves, and operates largely independently of growth form, plant functional type or biome. Categories along the spectrum would, in general, describe leaf economic variation at the global scale better than plant functional types, because functional types overlap substantially in their leaf traits. Overall, modulation of leaf traits and trait relationships by climate is surprisingly modest, although some striking and significant patterns can be seen. Reliable quantification of the leaf economics spectrum and its interaction with climate will prove valuable for modelling nutrient fluxes and vegetation boundaries under changing land-use and climate.
6,360 citations
TL;DR: A model interface is examined between two insulating perovskite oxides—LaAlO3 and SrTiO3—in which the termination layer at the interface is controlled on an atomic scale, presenting a broad opportunity to tailor low-dimensional charge states by atomically engineered oxide heteroepitaxy.
Abstract: Polarity discontinuities at the interfaces between different crystalline materials (heterointerfaces) can lead to nontrivial local atomic and electronic structure, owing to the presence of dangling bonds and incomplete atomic coordinations. These discontinuities often arise in naturally layered oxide structures, such as the superconducting copper oxides and ferroelectric titanates, as well as in artificial thin film oxide heterostructures such as manganite tunnel junctions. If polarity discontinuities can be atomically controlled, unusual charge states that are inaccessible in bulk materials could be realized. Here we have examined a model interface between two insulating perovskite oxides--LaAlO3 and SrTiO3--in which we control the termination layer at the interface on an atomic scale. In the simple ionic limit, this interface presents an extra half electron or hole per two-dimensional unit cell, depending on the structure of the interface. The hole-doped interface is found to be insulating, whereas the electron-doped interface is conducting, with extremely high carrier mobility exceeding 10,000 cm2 V(-1) s(-1). At low temperature, dramatic magnetoresistance oscillations periodic with the inverse magnetic field are observed, indicating quantum transport. These results present a broad opportunity to tailor low-dimensional charge states by atomically engineered oxide heteroepitaxy.
3,977 citations
University of Pennsylvania1, Massachusetts Institute of Technology2, Princeton University3, New York University4, Los Alamos National Laboratory5, Fermilab6, University of Chicago7, Ohio State University8, University of Arizona9, Drexel University10, Johns Hopkins University11, University of Pittsburgh12, Carnegie Mellon University13, New Mexico State University14, Spanish National Research Council15, University of Sussex16, University of Tokyo17, United States Department of the Navy18, University of Michigan19, Rochester Institute of Technology20, Pennsylvania State University21
TL;DR: In this paper, the authors measured cosmological parameters using the three-dimensional power spectrum P(k) from over 200,000 galaxies in the Sloan Digital Sky Survey (SDSS) in combination with WMAP and other data.
Abstract: We measure cosmological parameters using the three-dimensional power spectrum P(k) from over 200,000 galaxies in the Sloan Digital Sky Survey (SDSS) in combination with WMAP and other data. Our results are consistent with a "vanilla" flat adiabaticCDM model without tilt (ns = 1), running tilt, tensor modes or massive neutrinos. Adding SDSS information more than halves the WMAP-only error bars on some parameters, tightening 1� constraints on the Hubble parameter from h � 0.74 +0.18 −0.07 to h � 0.70 +0.04 −0.03, on the matter density from m � 0.25 ± 0.10 to m � 0.30 ± 0.04 (1�) and on neutrino masses from < 11 eV to < 0.6 eV (95%). SDSS helps even more when dropping prior assumptions about curvature, neutrinos, tensor modes and the equation of state. Our results are in substantial agreement with the joint analysis of WMAP and the 2dF Galaxy Redshift Survey, which is an impressive consistency check with independent redshift survey data and analysis techniques. In this paper, we place particular emphasis on clarifying the physical origin of the constraints, i.e., what we do and do not know when using different data sets and prior assumptions. For instance, dropping the assumption that space is perfectly flat, the WMAP-only constraint on the measured age of the Universe tightens from t0 � 16.3 +2.3
3,938 citations
TL;DR: In this article, the authors identify retinoic acid inducible gene I (RIG-I), which encodes a DExD/H box RNA helicase that contains a caspase recruitment domain, as an essential regulator for dsRNA-induced signaling.
Abstract: Intracellular double-stranded RNA (dsRNA) is a chief sign of replication for many viruses. Host mechanisms detect the dsRNA and initiate antiviral responses. In this report, we identify retinoic acid inducible gene I (RIG-I), which encodes a DExD/H box RNA helicase that contains a caspase recruitment domain, as an essential regulator for dsRNA-induced signaling, as assessed by functional screening and assays. A helicase domain with intact ATPase activity was responsible for the dsRNA-mediated signaling. The caspase recruitment domain transmitted 'downstream' signals, resulting in the activation of transcription factors NF-kappaB and IRF-3. Subsequent gene activation by these factors induced antiviral functions, including type I interferon production. Thus, RIG-I is key in the detection and subsequent eradication of the replicating viral genomes.
3,775 citations
Goddard Space Flight Center1, Brera Astronomical Observatory2, University of Milan3, University College London4, Pennsylvania State University5, University of Leicester6, Sonoma State University7, University of California, Berkeley8, Universities Space Research Association9, National Research Council10, University of Southampton11, Los Alamos National Laboratory12, National Radio Astronomy Observatory13, Space Telescope Science Institute14, Max Planck Society15, California Institute of Technology16, University of Texas at Austin17, French Alternative Energies and Atomic Energy Commission18, University of Toronto19, University of Maryland, College Park20, Princeton University21, Lawrence Livermore National Laboratory22, University of Cambridge23, University of California, Santa Barbara24, Rice University25, University of Tokyo26, Saitama University27, University of Florence28
TL;DR: The Swift mission as discussed by the authors is a multi-wavelength observatory for gamma-ray burst (GRB) astronomy, which is a first-of-its-kind autonomous rapid-slewing satellite for transient astronomy and pioneers the way for future rapid-reaction and multiwavelength missions.
Abstract: The Swift mission, scheduled for launch in 2004, is a multiwavelength observatory for gamma-ray burst (GRB) astronomy. It is a first-of-its-kind autonomous rapid-slewing satellite for transient astronomy and pioneers the way for future rapid-reaction and multiwavelength missions. It will be far more powerful than any previous GRB mission, observing more than 100 bursts yr � 1 and performing detailed X-ray and UV/optical afterglow observations spanning timescales from 1 minute to several days after the burst. The objectives are to (1) determine the origin of GRBs, (2) classify GRBs and search for new types, (3) study the interaction of the ultrarelativistic outflows of GRBs with their surrounding medium, and (4) use GRBs to study the early universe out to z >10. The mission is being developed by a NASA-led international collaboration. It will carry three instruments: a newgeneration wide-field gamma-ray (15‐150 keV) detector that will detect bursts, calculate 1 0 ‐4 0 positions, and trigger autonomous spacecraft slews; a narrow-field X-ray telescope that will give 5 00 positions and perform spectroscopy in the 0.2‐10 keV band; and a narrow-field UV/optical telescope that will operate in the 170‐ 600 nm band and provide 0B3 positions and optical finding charts. Redshift determinations will be made for most bursts. In addition to the primary GRB science, the mission will perform a hard X-ray survey to a sensitivity of � 1m crab (� 2;10 � 11 ergs cm � 2 s � 1 in the 15‐150 keV band), more than an order of magnitude better than HEAO 1 A-4. A flexible data and operations system will allow rapid follow-up observations of all types of
3,753 citations
TL;DR: In this paper, the relation between stellar mass and gas-phase metallicity was studied using the Sloan Digital Sky Survey imaging and spectroscopy of ~53,000 star-forming galaxies at z = 0.1.
Abstract: We utilize Sloan Digital Sky Survey imaging and spectroscopy of ~53,000 star-forming galaxies at z ~ 0.1 to study the relation between stellar mass and gas-phase metallicity. We derive gas-phase oxygen abundances and stellar masses using new techniques that make use of the latest stellar evolutionary synthesis and photoionization models. We find a tight (?0.1 dex) correlation between stellar mass and metallicity spanning over 3 orders of magnitude in stellar mass and a factor of 10 in metallicity. The relation is relatively steep from 108.5 to 1010.5 M? h, in good accord with known trends between luminosity and metallicity, but flattens above 1010.5 M?. We use indirect estimates of the gas mass based on the H? luminosity to compare our data to predictions from simple closed box chemical evolution models. We show that metal loss is strongly anticorrelated with baryonic mass, with low-mass dwarf galaxies being 5 times more metal depleted than L* galaxies at z ~ 0.1. Evidence for metal depletion is not confined to dwarf galaxies but is found in galaxies with masses as high as 1010 M?. We interpret this as strong evidence of both the ubiquity of galactic winds and their effectiveness in removing metals from galaxy potential wells.
3,621 citations
TL;DR: This work has implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs.
Abstract: Summary: We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C.
Availability: The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.
2,815 citations
Goddard Space Flight Center1, National Center for Atmospheric Research2, Meteorological Service of Canada3, Hadley Centre for Climate Prediction and Research4, Geophysical Fluid Dynamics Laboratory5, Commonwealth Scientific and Industrial Research Organisation6, University of Reading7, Science Applications International Corporation8, Princeton University9, Bureau of Meteorology10, University of Tokyo11, Macquarie University12, University of California, Los Angeles13
TL;DR: A multimodel estimation of the regions on Earth where precipitation is affected by soil moisture anomalies during Northern Hemisphere summer indicates potential benefits of this estimation may include improved seasonal rainfall forecasts.
Abstract: Previous estimates of land-atmosphere interaction (the impact of soil moisture on precipitation) have been limited by a lack of observational data and by the model dependence of computational estimates. To counter the second limitation, a dozen climate-modeling groups have recently performed the same highly controlled numerical experiment as part of a coordinated comparison project. This allows a multimodel estimation of the regions on Earth where precipitation is affected by soil moisture anomalies during Northern Hemisphere summer. Potential benefits of this estimation may include improved seasonal rainfall forecasts.
2,522 citations
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TL;DR: In this article, Anderson's idea of the resonating valence bond (RVB) was introduced to describe the spin liquid phase of the undoped Mott insulator, and the slave-boson is introduced to enforce the constraint of no double occupation.
Abstract: This article reviews the effort to understand the physics of high temperature superconductors from the point of view of doping a Mott insulator. The basic electronic structure of the cuprates is reviewed, emphasizing the physics of strong correlation and establishing the model of a doped Mott insulator as a starting point. A variety of experiments are discussed, focusing on the region of the phase diagram close to the Mott insulator (the underdoped region) where the behavior is most anomalous. We introduce Anderson's idea of the resonating valence bond (RVB) and argue that it gives a qualitative account of the data. The importance of phase fluctuation is discussed, leading to a theory of the transition temperature which is driven by phase fluctuation and thermal excitation of quasiparticles. We then describe the numerical method of projected wavefunction which turns out to be a very useful technique to implement the strong correlation constraint, and leads to a number of predictions which are in agreement with experiments. The remainder of the paper deals with an analytic treatment of the t-J model, with the goal of putting the RVB idea on a more formal footing. The slave-boson is introduced to enforce the constraint of no double occupation. The implementation of the local constraint leads naturally to gauge theories. We give a rather thorough discussion of the role of gauge theory in describing the spin liquid phase of the undoped Mott insulator. We next describe the extension of the SU(2) formulation to nonzero doping. We show that inclusion of gauge fluctuation provides a reasonable description of the pseudogap phase.
2,042 citations
TL;DR: Integration of organic transistors and rubber pressure sensors, both of which can be produced by low-cost processing technology such as large-area printing technology, will provide an ideal solution to realize a practical artificial skin.
Abstract: It is now widely accepted that skin sensitivity will be very important for future robots used by humans in daily life for housekeeping and entertainment purposes Despite this fact, relatively little progress has been made in the field of pressure recognition compared to the areas of sight and voice recognition, mainly because good artificial “electronic skin” with a large area and mechanical flexibility is not yet available The fabrication of a sensitive skin consisting of thousands of pressure sensors would require a flexible switching matrix that cannot be realized with present silicon-based electronics Organic field-effect transistors can substitute for such conventional electronics because organic circuits are inherently flexible and potentially ultralow in cost even for a large area Thus, integration of organic transistors and rubber pressure sensors, both of which can be produced by low-cost processing technology such as large-area printing technology, will provide an ideal solution to realize a practical artificial skin, whose feasibility has been demonstrated in this paper Pressure images have been taken by flexible active matrix drivers with organic transistors whose mobility reaches as high as 14 cm2/V·s The device is electrically functional even when it is wrapped around a cylindrical bar with a 2-mm radius
1,804 citations
University of Pennsylvania1, New York University2, Princeton University3, Drexel University4, Ohio State University5, University of Chicago6, Johns Hopkins University7, University of Pittsburgh8, University of Arizona9, Fermilab10, University of Colorado Boulder11, Carnegie Mellon University12, University of Hawaii13, Apache Corporation14, Massachusetts Institute of Technology15, Spanish National Research Council16, University of Sussex17, University of Tokyo18, University of Michigan19, Rochester Institute of Technology20, Pennsylvania State University21
TL;DR: In this paper, the authors employed a matrix-based method using pseudo-Karhunen-Loeve eigenmodes, producing uncorrelated minimum-variance measurements in 22 k-bands of both the clustering power and its anisotropy due to redshift-space distortions.
Abstract: We measure the large-scale real-space power spectrum P(k) by using a sample of 205,443 galaxies from the Sloan Digital Sky Survey, covering 2417 effective square degrees with mean redshift z ≈ 0.1. We employ a matrix-based method using pseudo-Karhunen-Loeve eigenmodes, producing uncorrelated minimum-variance measurements in 22 k-bands of both the clustering power and its anisotropy due to redshift-space distortions, with narrow and well-behaved window functions in the range 0.02 h Mpc-1 < k < 0.3 h Mpc-1. We pay particular attention to modeling, quantifying, and correcting for potential systematic errors, nonlinear redshift distortions, and the artificial red-tilt caused by luminosity-dependent bias. Our results are robust to omitting angular and radial density fluctuations and are consistent between different parts of the sky. Our final result is a measurement of the real-space matter power spectrum P(k) up to an unknown overall multiplicative bias factor. Our calculations suggest that this bias factor is independent of scale to better than a few percent for k < 0.1 h Mpc-1, thereby making our results useful for precision measurements of cosmological parameters in conjunction with data from other experiments such as the Wilkinson Microwave Anisotropy Probe satellite. The power spectrum is not well-characterized by a single power law but unambiguously shows curvature. As a simple characterization of the data, our measurements are well fitted by a flat scale-invariant adiabatic cosmological model with h Ωm = 0.213 ± 0.023 and σ8 = 0.89 ± 0.02 for L* galaxies, when fixing the baryon fraction Ωb/Ωm = 0.17 and the Hubble parameter h = 0.72; cosmological interpretation is given in a companion paper.
TL;DR: It was found that LC-TDDFT clearly reproduces the correct asymptotic behavior of the charge-transfer excitation energy of ethylene-tetrafluoroethylene dimer for the long intramolecular distance, unlike a conventional far-nucleus asymPTotic correction scheme.
Abstract: We apply the long-range correction (LC) scheme for exchange functionals of density functional theory to time-dependent density functional theory (TDDFT) and examine its efficiency in dealing with the serious problems of TDDFT, i.e., the underestimations of Rydberg excitation energies, oscillator strengths, and charge-transfer excitation energies. By calculating vertical excitation energies of typical molecules, it was found that LC-TDDFT gives accurate excitation energies, within an error of 0.5 eV, and reasonable oscillator strengths, while TDDFT employing a pure functional provides 1.5 eV lower excitation energies and two orders of magnitude lower oscillator strengths for the Rydberg excitations. It was also found that LC-TDDFT clearly reproduces the correct asymptotic behavior of the charge-transfer excitation energy of ethylene-tetrafluoroethylene dimer for the long intramolecular distance, unlike a conventional far-nucleus asymptotic correction scheme. It is, therefore, presumed that poor TDDFT results for pure functionals may be due to their lack of a long-range orbital-orbital interaction.
TL;DR: It is concluded that the primary gene mutated in CMT2A is MFN2, and seven large pedigrees affected with Charcot-Marie-Tooth neuropathy type 2A are concluded.
Abstract: We report missense mutations in the mitochondrial fusion protein mitofusin 2 (MFN2) in seven large pedigrees affected with Charcot-Marie-Tooth neuropathy type 2A (CMT2A). Although a mutation in kinesin family member 1B-β (KIF1B) was associated with CMT2A in a single Japanese family, we found no mutations in KIF1B in these seven families. Because these families include all published pedigrees with CMT2A and are ethnically diverse, we conclude that the primary gene mutated in CMT2A is MFN2.
TL;DR: Vitamin A deficiency caused a reduction in alpha4beta7(+) memory/activated T cells in lymphoid organs and a depletion of T cells from the intestinal lamina propria, and revealed a novel role for retinoic acid in the imprinting of gut-homing specificity on T cells.
TL;DR: The complete NAC recognition sequence, containing CATGT and harboring CACG as the core DNA binding site is determined, which indicates that other interacting factors may be necessary for the induction of erd1 in Arabidopsis under stress conditions.
Abstract: The MYC-like sequence CATGTG plays an important role in the dehydration-inducible expression of the Arabidopsis thaliana EARLY RESPONSIVE TO DEHYDRATION STRESS 1 (ERD1) gene, which encodes a ClpA (ATP binding subunit of the caseinolytic ATP-dependent protease) homologous protein. Using the yeast one-hybrid system, we isolated three cDNA clones encoding proteins that bind to the 63-bp promoter region of erd1, which contains the CATGTG motif. These three cDNA clones encode proteins named ANAC019, ANAC055, and ANAC072, which belong to the NAC transcription factor family. The NAC proteins bound specifically to the CATGTG motif both in vitro and in vivo and activated the transcription of a beta-glucuronidase (GUS) reporter gene driven by the 63-bp region containing the CATGTG motif in Arabidopsis T87 protoplasts. The expression of ANAC019, ANAC055, and ANAC072 was induced by drought, high salinity, and abscisic acid. A histochemical assay using P(NAC)-GUS fusion constructs showed that expression of the GUS reporter gene was localized mainly to the leaves of transgenic Arabidopsis plants. Using the yeast one-hybrid system, we determined the complete NAC recognition sequence, containing CATGT and harboring CACG as the core DNA binding site. Microarray analysis of transgenic plants overexpressing either ANAC019, ANAC055, or ANAC072 revealed that several stress-inducible genes were upregulated in the transgenic plants, and the plants showed significantly increased drought tolerance. However, erd1 was not upregulated in the transgenic plants. Other interacting factors may be necessary for the induction of erd1 in Arabidopsis under stress conditions.
TL;DR: In this article, the authors have synthesized chemically modified titanium dioxide photocatalysts in which S (S4+) substitutes for some of the lattice titanium atoms, which showed strong absorption for visible light and high activities for degradation of methylene blue, 2-propanol in aqueous solution and partial oxidation of adamantane under irradiation at wavelengths longer than 440nm.
Abstract: Although titanium dioxide photocatalysts having anatase phase are a promising substrate for photodegradation of pollutants in water and air, their photocatalytic activities show only under ultraviolet (UV) light. For us to utilized a wide range of incident light such as solar light, development of the photocatalysts whose activities show under visible light is one of the most important strategies. We have synthesized chemically modified titanium dioxide photocatalysts in which S (S4+) substitutes for some of the lattice titanium atoms. They show strong absorption for visible light and high activities for degradation of methylene blue, 2-propanol in aqueous solution and partial oxidation of adamantane under irradiation at wavelengths longer than 440 nm. The oxidation state of the S atoms incorporated into the TiO2 particles is determined to be mainly S4+ from X-ray photoelectron spectra (XPS) spectra.
TL;DR: It is shown that although acute injury, acute inflammation, or transient parietal cell loss within the stomach do not lead to BMDC recruitment, chronic infection of C57BL/6 mice with Helicobacter induces repopulation of the stomach with BMDCs, suggesting that epithelial cancers can originate from marrow-derived sources and thus have broad implications for the multistep model of cancer progression.
Abstract: Epithelial cancers are believed to originate from transformation of tissue stem cells. However, bone marrow-derived cells (BMDCs), which are frequently recruited to sites of tissue injury and inflammation, might also represent a potential source of malignancy. We show that although acute injury, acute inflammation, or transient parietal cell loss within the stomach do not lead to BMDC recruitment, chronic infection of C57BL/6 mice with Helicobacter, a known carcinogen, induces repopulation of the stomach with BMDCs. Subsequently, these cells progress through metaplasia and dysplasia to intraepithelial cancer. These findings suggest that epithelial cancers can originate from marrow-derived sources and thus have broad implications for the multistep model of cancer progression.
Kevork N. Abazajian1, Jennifer K. Adelman-McCarthy2, Marcel A. Agüeros3, Sahar S. Allam4 +162 more•Institutions (41)
TL;DR: The second data release of the Sloan Digital Sky Survey (SDSS) as mentioned in this paper is the most recent data set to be publicly available, which consists of 3.5 million unique objects, 367,360 spectra of galaxies, quasars, stars, and calibrating blank sky patches selected over 2627 deg2 of this area.
Abstract: The Sloan Digital Sky Survey (SDSS) has validated and made publicly available its Second Data Release. This data release consists of 3324 deg2 of five-band (ugriz) imaging data with photometry for over 88 million unique objects, 367,360 spectra of galaxies, quasars, stars, and calibrating blank sky patches selected over 2627 deg2 of this area, and tables of measured parameters from these data. The imaging data reach a depth of r ≈ 22.2 (95% completeness limit for point sources) and are photometrically and astrometrically calibrated to 2% rms and 100 mas rms per coordinate, respectively. The imaging data have all been processed through a new version of the SDSS imaging pipeline, in which the most important improvement since the last data release is fixing an error in the model fits to each object. The result is that model magnitudes are now a good proxy for point-spread function magnitudes for point sources, and Petrosian magnitudes for extended sources. The spectroscopy extends from 3800 to 9200 A at a resolution of 2000. The spectroscopic software now repairs a systematic error in the radial velocities of certain types of stars and has substantially improved spectrophotometry. All data included in the SDSS Early Data Release and First Data Release are reprocessed with the improved pipelines and included in the Second Data Release. Further characteristics of the data are described, as are the data products themselves and the tools for accessing them.
TL;DR: This work isolated a large RNase-sensitive granule (size: 1000S approximately) as a binding partner of conventional kinesin (KIF5) and identified a total of 42 proteins with mRNAs for CaMKIIalpha and Arc in the granule.
TL;DR: The results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells.
Abstract: Small, compact genomes of ultrasmall unicellular algae provide information on the basic and essential genes that support the lives of photosynthetic eukaryotes, including higher plants. Here we report the 16,520,305-base-pair sequence of the 20 chromosomes of the unicellular red alga Cyanidioschyzon merolae 10D as the first complete algal genome. We identified 5,331 genes in total, of which at least 86.3% were expressed. Unique characteristics of this genomic structure include: a lack of introns in all but 26 genes; only three copies of ribosomal DNA units that maintain the nucleolus; and two dynamin genes that are involved only in the division of mitochondria and plastids. The conserved mosaic origin of Calvin cycle enzymes in this red alga and in green plants supports the hypothesis of the existence of single primary plastid endosymbiosis. The lack of a myosin gene, in addition to the unexpressed actin gene, suggests a simpler system of cytokinesis. These results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells.
TL;DR: Water retention values of cotton linter can be increased from 60% to about 280% through the introduction of hydrophilic carboxylate groups and morphological changes from fibrous forms to short fragments by the TEMPO-mediated oxidation.
TL;DR: It is shown that TLR-mediated IFN-α induction requires the formation of a complex consisting of MyD88, TRAF6 and IRF7 as well as TRAF 6-dependent ubiquitination.
Abstract: Toll-like receptors (TLRs) are involved in the recognition of microbial pathogens. A subset of TLRs, TLR7, TLR8 and TLR9, induces antiviral responses by producing interferon-alpha (IFN-alpha). Production of IFN-alpha is dependent on the Toll-interleukin-1 receptor domain-containing adaptor MyD88. Here we show that MyD88 formed a complex with the transcription factor IRF7 but not with IRF3. The death domain of MyD88 interacted with an inhibitory domain of IRF7, and this interaction resulted in activation of the IFN-alpha-dependent promoters. Furthermore, the adaptor molecule TRAF6 also bound and activated IRF7. Ubiquitin ligase activity of TRAF6 was required for IRF7 activation. These results indicate that TLR-mediated IFN-alpha induction requires the formation of a complex consisting of MyD88, TRAF6 and IRF7 as well as TRAF6-dependent ubiquitination.
TL;DR: It was demonstrated that Arabidopsis Dicer homologue Dicer-like 1 (DCL1) catalyzes at least the first and second cleavage steps and that double-stranded RNA-binding domains of DCL1 are involved in positioning of the cleavage sites, direct evidence that DCL 1 is involved in processing of pri- and pre-miRNA.
Abstract: Micro-RNAs (miRNAs) are small, noncoding RNAs of 18-25 nt in length that negatively regulate their complementary mRNAs at the posttranscriptional level. Previous work has shown that some RNase III-like enzymes such as Drosha and Dicer are known to be involved in miRNA biogenesis in animals. However, the mechanism of plant miRNA biogenesis still remains poorly understood. In this article, the process of Arabidopsis miR163 biogenesis was examined. The results revealed that two types of miR163 primary transcripts (pri-miR163s) are transcribed from a single gene by RNA polymerase II and that miR163 biogenesis requires at least three cleavage steps by RNase III-like enzymes at 21-nt-long intervals. The first step is from pri-miR163 to long miR163 precursor (premiR163), the second step is from long pre-miR163 to short premiR163, and the last step is from short pre-miR163 to mature miR163 and the remnant. It is interesting that, during the process, four small RNAs including miR163 are released. By using dcl1 mutants, it was demonstrated that Arabidopsis Dicer homologue Dicer-like 1 (DCL1) catalyzes at least the first and second cleavage steps and that double-stranded RNA-binding domains of DCL1 are involved in positioning of the cleavage sites. Our result is direct evidence that DCL1 is involved in processing of pri- and pre-miRNA.
TL;DR: There seems to be a slight bias against GC-rich transcripts in current gene prediction procedures in the “full-length long Japan” collection of sequenced human cDNAs.
Abstract: As a base for human transcriptome and functional genomics, we created the "full-length long Japan" (FLJ) collection of sequenced human cDNAs. We determined the entire sequence of 21,243 selected clones and found that 14,490 cDNAs (10,897 clusters) were unique to the FLJ collection. About half of them (5,416) seemed to be protein-coding. Of those, 1,999 clusters had not been predicted by computational methods. The distribution of GC content of nonpredicted cDNAs had a peak at approximately 58% compared with a peak at approximately 42%for predicted cDNAs. Thus, there seems to be a slight bias against GC-rich transcripts in current gene prediction procedures. The rest of the cDNAs unique to the FLJ collection (5,481) contained no obvious open reading frames (ORFs) and thus are candidate noncoding RNAs. About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at approximately 42%, relatively low compared with that of protein-coding cDNAs.
TL;DR: The rules that may govern siRNA sequence preference are presented and in accordance with which highly effective siRNAs essential for systematic mammalian functional genomics can be readily designed.
Abstract: In the present study, the relationship between short interfering RNA (siRNA) sequence and RNA interference (RNAi) effect was extensively analyzed using 62 targets of four exogenous and two endogenous genes and three mammalian and Drosophila cells. We present the rules that may govern siRNA sequence preference and in accordance with which highly effective siRNAs essential for systematic mammalian functional genomics can be readily designed. These rules indicate that siRNAs which simultaneously satisfy all four of the following sequence conditions are capable of inducing highly effective gene silencing in mammalian cells: (i) A/U at the 5' end of the antisense strand; (ii) G/C at the 5' end of the sense strand; (iii) at least five A/U residues in the 5' terminal one-third of the antisense strand; and (iv) the absence of any GC stretch of more than 9 nt in length. siRNAs opposite in features with respect to the first three conditions give rise to little or no gene silencing in mammalian cells. Essentially the same rules for siRNA sequence preference were found applicable to DNA-based RNAi in mammalian cells and in ovo RNAi using chick embryos. In contrast to mammalian and chick cells, little siRNA sequence preference could be detected in Drosophila in vivo RNAi.
TL;DR: This family of molecularly engineered graphite with a one-dimensional tubular shape and a chemically accessible surface constitutes an important step toward molecular electronics.
Abstract: An amphiphilic hexa-peri-hexabenzocoronene self-assembles to form a π-electronic, discrete nanotubular object. The object is characterized by an aspect ratio greater than 1000 and has a uniform, 14-nanometer-wide, open-ended hollow space, which is an order of magnitude larger than those of carbon nanotubes. The wall is 3 nanometers thick and consists of helical arrays of the π-stacked graphene molecule, whose exterior and interior surfaces are covered by hydrophilic triethylene glycol chains. The graphitic nanotube is redox active, and a single piece of the nanotube across 180-nanometer-gap electrodes shows, upon oxidation, an electrical conductivity of 2.5 megohms at 285 kelvin. This family of molecularly engineered graphite with a one-dimensional tubular shape and a chemically accessible surface constitutes an important step toward molecular electronics.
TL;DR: In this paper, the prevalence of primary open-angle glaucoma (POAG) and its association with intraocular pressure (IOP) in Tajimi City in central Japan was assessed.
TL;DR: This article presented a new keyword extraction algorithm that applies to a single document without using a corpus and showed comparable performance to tfidf without using TFIDF without using any corpus, but the degree of biases of distribution is measured by the χ 2 -measure.
Abstract: We present a new keyword extraction algorithm that applies to a single document without using a corpus. Frequent terms are extracted first, then a set of cooccurrence between each term and the frequent terms, i.e., occurrences in the same sentences, is generated. Co-occurrence distribution shows importance of a term in the documentas follows. If probability distribution of co-occurrence between term a and the frequent terms is biased to a particular subset of frequent terms, then term a is likely to be a keyword. The degree of biases of distribution is measured by the χ 2 -measure. Our algorithm shows comparable performance to tfidf without using a corpus.
TL;DR: The semiclassical equation of motion for the wave packet of light is derived taking into account the Berry curvature in momentum-space, which leads to the shift of wave-packet motion perpendicular to the gradient of the dielectric constant, i.e., the polarization-dependent Hall effect of light.
Abstract: We derive the semiclassical equation of motion for the wave packet of light taking into account the Berry curvature in momentum-space. This equation naturally describes the interplay between orbital and spin angular momenta, i.e., the conservation of the total angular momentum of light. This leads to the shift of wave-packet motion perpendicular to the gradient of the dielectric constant, i.e., the polarization-dependent Hall effect of light. An enhancement of this effect in photonic crystals is also proposed.
TL;DR: The relationships among magnetism, lattice modulation, and dielectric properties have been investigated for RMnO3 and it was found that the IC-C transition is accompanied by a ferroelectric transition, associated with a lattices modulation in the C phase.
Abstract: The relationships among magnetism, lattice modulation, and dielectric properties have been investigated for RMnO3 (R=Eu, Gd, Tb, and Dy). These compounds show a transition to an incommensurate lattice structure below their Neel temperature, and subsequently undergo an incommensurate-commensurate (IC-C) phase transition. For TbMnO3 and DyMnO3 it was found that the IC-C transition is accompanied by a ferroelectric transition, associated with a lattice modulation in the C phase. DyMnO3 shows a gigantic magnetocapacitance with a change of dielectric constant up to Deltaepsilon/epsilon approximately 500%.