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Showing papers by "Tokyo Institute of Technology published in 2014"


Journal ArticleDOI
TL;DR: The Transiting Exoplanet Survey Satellite (TESS) as discussed by the authors will search for planets transiting bright and nearby stars using four wide-field optical charge-coupled device cameras to monitor at least 200,000 main-sequence dwarf stars.
Abstract: The Transiting Exoplanet Survey Satellite (TESS) will search for planets transiting bright and nearby stars. TESS has been selected by NASA for launch in 2017 as an Astrophysics Explorer mission. The spacecraft will be placed into a highly elliptical 13.7-day orbit around the Earth. During its 2-year mission, TESS will employ four wide-field optical charge-coupled device cameras to monitor at least 200,000 main-sequence dwarf stars with I C ≈4−13 for temporary drops in brightness caused by planetary transits. Each star will be observed for an interval ranging from 1 month to 1 year, depending mainly on the star’s ecliptic latitude. The longest observing intervals will be for stars near the ecliptic poles, which are the optimal locations for follow-up observations with the James Webb Space Telescope. Brightness measurements of preselected target stars will be recorded every 2 min, and full frame images will be recorded every 30 min. TESS stars will be 10 to 100 times brighter than those surveyed by the pioneering Kepler mission. This will make TESS planets easier to characterize with follow-up observations. TESS is expected to find more than a thousand planets smaller than Neptune, including dozens that are comparable in size to the Earth. Public data releases will occur every 4 months, inviting immediate community-wide efforts to study the new planets. The TESS legacy will be a catalog of the nearest and brightest stars hosting transiting planets, which will endure as highly favorable targets for detailed investigations.

2,604 citations


Journal ArticleDOI
TL;DR: In this article, a holistic perspective on changing rainfall-driven flood risk is provided for the late 20th and early 21st centuries, which includes an assessment of changes in flood risk in seven of the regions considered in the recent IPCC SREX report.
Abstract: A holistic perspective on changing rainfall-driven flood risk is provided for the late 20th and early 21st centuries. Economic losses from floods have greatly increased, principally driven by the expanding exposure of assets at risk. It has not been possible to attribute rain-generated peak streamflow trends to anthropogenic climate change over the past several decades. Projected increases in the frequency and intensity of heavy rainfall, based on climate models, should contribute to increases in precipitation-generated local flooding (e.g. flash flooding and urban flooding). This article assesses the literature included in the IPCC SREX report and new literature published since, and includes an assessment of changes in flood risk in seven of the regions considered in the recent IPCC SREX report—Africa, Asia, Central and South America, Europe, North America, Oceania and Polar regions. Also considering newer publications, this article is consistent with the recent IPCC SREX assessment finding that ...

957 citations


Journal ArticleDOI
TL;DR: Platanus provides a novel and efficient approach for the assembly of gigabase-sized highly heterozygous genomes and is an attractive alternative to the existing assemblers designed for genomes of lower heterozygosity.
Abstract: Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wild-type samples, in most cases inbred lines or fosmid-based hierarchical sequencing methods are used to overcome such problems. However, these methods are costly and time consuming, forfeiting the advantages of massive parallel sequencing. Here, we describe a novel de novo assembler, Platanus, that can effectively manage high-throughput data from heterozygous samples. Platanus assembles DNA fragments (reads) into contigs by constructing de Bruijn graphs with automatically optimized k-mer sizes followed by the scaffolding of contigs based on paired-end information. The complicated graph structures that result from the heterozygosity are simplified during not only the contig assembly step but also the scaffolding step. We evaluated the assembly results on eukaryotic samples with various levels of heterozygosity. Compared with other assemblers, Platanus yields assembly results that have a larger scaffold NG50 length without any accompanying loss of accuracy in both simulated and real data. In addition, Platanus recorded the largest scaffold NG50 values for two of the three low-heterozygosity species used in the de novo assembly contest, Assemblathon 2. Platanus therefore provides a novel and efficient approach for the assembly of gigabase-sized highly heterozygous genomes and is an attractive alternative to the existing assemblers designed for genomes of lower heterozygosity.

924 citations


Journal ArticleDOI
TL;DR: This work presents a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences.
Abstract: Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.

866 citations


Proceedings ArticleDOI
TL;DR: The Transiting Exoplanet Survey Satellite (TESS) as mentioned in this paper will discover thousands of exoplanets in orbit around the brightest stars in the sky, including Earth-sized to gas giants, around a wide range of stellar types and orbital distances.
Abstract: The Transiting Exoplanet Survey Satellite (TESS) will discover thousands of exoplanets in orbit around the brightest stars in the sky. In a two-year survey, TESS will monitor more than 500,000 stars for temporary drops in brightness caused by planetary transits. This first-ever spaceborne all-sky transit survey will identify planets ranging from Earth-sized to gas giants, around a wide range of stellar types and orbital distances. No ground-based survey can achieve this feat. A large fraction of TESS target stars will be 30-100 times brighter than those observed by Kepler satellite, and therefore TESS . planets will be far easier to characterize with follow-up observations. TESS will make it possible to study the masses, sizes, densities, orbits, and atmospheres of a large cohort of small planets, including a sample of rocky worlds in the habitable zones of their host stars. TESS will provide prime targets for observation with the James Webb Space Telescope (JWST), as well as other large ground-based and space-based telescopes of the future. TESS data will be released with minimal delay (no proprietary period), inviting immediate community-wide efforts to study the new planets. The TESS legacy will be a catalog of the very nearest and brightest main-sequence stars hosting transiting exoplanets, thus providing future observers with the most favorable targets for detailed investigations.

865 citations


Journal ArticleDOI
TL;DR: CRC‐associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor‐related host–microbe interactions.
Abstract: Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here, we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved > 45% relative to the FOBT, while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early- and late-stage cancer and could be validated in independent patient and control populations (N = 335 )f rom different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host–microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients, accompanied by an increase of lipopolysaccharide metabolism.

854 citations


Journal ArticleDOI
David Brawand1, David Brawand2, Catherine E. Wagner3, Catherine E. Wagner4, Yang I. Li2, Milan Malinsky5, Milan Malinsky6, Irene Keller4, Shaohua Fan7, Oleg Simakov7, Alvin Yu Jin Ng8, Zhi Wei Lim8, Etienne Bezault9, Jason Turner-Maier1, Jeremy A. Johnson1, Rosa Alcazar10, Hyun Ji Noh1, Pamela Russell11, Bronwen Aken5, Jessica Alföldi1, Chris T. Amemiya12, Naoual Azzouzi13, Jean-François Baroiller, Frédérique Barloy-Hubler13, Aaron M. Berlin1, Ryan F. Bloomquist14, Karen L. Carleton15, Matthew A. Conte15, Helena D'Cotta, Orly Eshel, Leslie Gaffney1, Francis Galibert13, Hugo F. Gante16, Sante Gnerre1, Lucie Greuter4, Lucie Greuter3, Richard Guyon13, Natalie S. Haddad14, Wilfried Haerty2, Robert M Harris17, Hans A. Hofmann17, Thibaut Hourlier5, Gideon Hulata, David B. Jaffe1, Marcia Lara1, Alison P. Lee8, Iain MacCallum1, Salome Mwaiko3, Masato Nikaido18, Hidenori Nishihara18, Catherine Ozouf-Costaz19, David J. Penman20, Dariusz Przybylski1, Michaelle Rakotomanga13, Suzy C. P. Renn9, Filipe J. Ribeiro1, Micha Ron, Walter Salzburger16, Luis Sanchez-Pulido2, M. Emília Santos16, Steve Searle5, Ted Sharpe1, Ross Swofford1, Frederick J. Tan21, Louise Williams1, Sarah Young1, Shuangye Yin1, Norihiro Okada18, Norihiro Okada22, Thomas D. Kocher15, Eric A. Miska6, Eric S. Lander1, Byrappa Venkatesh8, Russell D. Fernald10, Axel Meyer7, Chris P. Ponting2, J. Todd Streelman14, Kerstin Lindblad-Toh23, Kerstin Lindblad-Toh1, Ole Seehausen3, Ole Seehausen4, Federica Di Palma1, Federica Di Palma24 
18 Sep 2014-Nature
TL;DR: This article found an excess of gene duplications in the East African lineage compared to Nile tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs.
Abstract: Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

832 citations


Journal ArticleDOI
TL;DR: The historical landmarks underpinning the explosion of autophagy research are described with a particular focus on the contribution of yeast as a model organism.
Abstract: The year of 2013 marked the 50th anniversary of C de Duve's coining of the term “autophagy” for the degradation process of cytoplasmic constituents in the lysosome/vacuole. This year we regretfully lost this great scientist, who contributed much during the early years of research to the field of autophagy. Soon after the discovery of lysosomes by de Duve, electron microscopy revealed autophagy as a means of delivering intracellular components to the lysosome. For a long time after the discovery of autophagy, studies failed to yield any significant advances at a molecular level in our understanding of this fundamental pathway of degradation. The first breakthrough was made in the early 1990s, as autophagy was discovered in yeast subjected to starvation by microscopic observation. Next, a genetic effort to address the poorly understood problem of autophagy led to the discovery of many autophagy-defective mutants. Subsequent identification of autophagy-related genes in yeast revealed unique sets of molecules involved in membrane dynamics during autophagy. ATG homologs were subsequently found in various organisms, indicating that the fundamental mechanism of autophagy is well conserved among eukaryotes. These findings brought revolutionary changes to research in this field. For instance, the last 10 years have seen remarkable progress in our understanding of autophagy, not only in terms of the molecular mechanisms of autophagy, but also with regard to its broad physiological roles and relevance to health and disease. Now our knowledge of autophagy is dramatically expanding day by day. Here, the historical landmarks underpinning the explosion of autophagy research are described with a particular focus on the contribution of yeast as a model organism.

769 citations


David Brawand1, David Brawand2, Catherine E. Wagner3, Catherine E. Wagner4, Yang I. Li2, Milan Malinsky5, Milan Malinsky6, Irene Keller4, Shaohua Fan7, Oleg Simakov7, Alvin Yu Jin Ng8, Zhi Wei Lim8, Etienne Bezault9, Jason Turner-Maier1, Jeremy A. Johnson1, Rosa Alcazar10, Hyun Ji Noh1, Pamela Russell11, Bronwen Aken5, Jessica Alföldi1, Chris T. Amemiya12, Naoual Azzouzi13, Jean-François Baroiller, Frédérique Barloy-Hubler13, Aaron M. Berlin1, Ryan F. Bloomquist14, Karen L. Carleton15, Matthew A. Conte15, Helena D'Cotta, Orly Eshel, Leslie Gaffney1, Francis Galibert13, Hugo F. Gante16, Sante Gnerre1, Lucie Greuter3, Lucie Greuter4, Richard Guyon13, Natalie S. Haddad14, Wilfried Haerty2, Robert M Harris17, Hans A. Hofmann17, Thibaut Hourlier5, Gideon Hulata, David B. Jaffe1, Marcia Lara1, Alison P. Lee8, Iain MacCallum1, Salome Mwaiko3, Masato Nikaido18, Hidenori Nishihara18, Catherine Ozouf-Costaz19, David J. Penman20, Dariusz Przybylski1, Michaelle Rakotomanga13, Suzy C. P. Renn9, Filipe J. Ribeiro1, Micha Ron, Walter Salzburger16, Luis Sanchez-Pulido2, M. Emília Santos16, Steve Searle5, Ted Sharpe1, Ross Swofford1, Frederick J. Tan21, Louise Williams1, Sarah Young1, Shuangye Yin1, Norihiro Okada18, Norihiro Okada22, Thomas D. Kocher15, Eric A. Miska6, Eric S. Lander1, Byrappa Venkatesh8, Russell D. Fernald10, Axel Meyer7, Chris P. Ponting2, J. Todd Streelman14, Kerstin Lindblad-Toh23, Kerstin Lindblad-Toh1, Ole Seehausen4, Ole Seehausen3, Federica Di Palma24, Federica Di Palma1 
01 Sep 2014
TL;DR: It is concluded that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
Abstract: Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

666 citations


Journal ArticleDOI
TL;DR: The draft genome sequence of the filamentous terrestrial alga Klebsormidium flaccidum is reported to elucidate the early transition step from aquatic algae to land plants and suggests that, during evolution, this alga acquired the fundamental machinery required for adaptation to terrestrial environments.
Abstract: The colonization of land by plants was a key event in the evolution of life. Here we report the draft genome sequence of the filamentous terrestrial alga Klebsormidium flaccidum (Division Charophyta, Order Klebsormidiales) to elucidate the early transition step from aquatic algae to land plants. Comparison of the genome sequence with that of other algae and land plants demonstrate that K. flaccidum acquired many genes specific to land plants. We demonstrate that K. flaccidum indeed produces several plant hormones and homologues of some of the signalling intermediates required for hormone actions in higher plants. The K. flaccidum genome also encodes a primitive system to protect against the harmful effects of high-intensity light. The presence of these plant-related systems in K. flaccidum suggests that, during evolution, this alga acquired the fundamental machinery required for adaptation to terrestrial environments.

475 citations


Journal ArticleDOI
Adrian John Bevan1, B. Golob2, Th. Mannel3, S. Prell4  +2061 moreInstitutions (171)
TL;DR: The physics of the SLAC and KEK B Factories are described in this paper, with a brief description of the detectors, BaBar and Belle, and data taking related issues.
Abstract: This work is on the Physics of the B Factories. Part A of this book contains a brief description of the SLAC and KEK B Factories as well as their detectors, BaBar and Belle, and data taking related issues. Part B discusses tools and methods used by the experiments in order to obtain results. The results themselves can be found in Part C.

Journal ArticleDOI
TL;DR: The authors investigated abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere.

Journal ArticleDOI
Georges Aad1, Brad Abbott2, Jalal Abdallah3, S. Abdel Khalek4  +2871 moreInstitutions (167)
TL;DR: In this article, the authors presented the electron and photon energy calibration achieved with the ATLAS detector using about 25 fb(-1) of LHC proton-proton collision data taken at center-of-mass energies of root s = 7 and 8 TeV.
Abstract: This paper presents the electron and photon energy calibration achieved with the ATLAS detector using about 25 fb(-1) of LHC proton-proton collision data taken at centre-of-mass energies of root s = 7 and 8 TeV. The reconstruction of electron and photon energies is optimised using multivariate algorithms. The response of the calorimeter layers is equalised in data and simulation, and the longitudinal profile of the electromagnetic showers is exploited to estimate the passive material in front of the calorimeter and reoptimise the detector simulation. After all corrections, the Z resonance is used to set the absolute energy scale. For electrons from Z decays, the achieved calibration is typically accurate to 0.05% in most of the detector acceptance, rising to 0.2% in regions with large amounts of passive material. The remaining inaccuracy is less than 0.2-1% for electrons with a transverse energy of 10 GeV, and is on average 0.3% for photons. The detector resolution is determined with a relative inaccuracy of less than 10% for electrons and photons up to 60 GeV transverse energy, rising to 40% for transverse energies above 500 GeV.

Journal ArticleDOI
TL;DR: In this review, research show that ARLEs achieved a widely variable effect on student performance from a small negative effect to a large effect, with a mean effect size of 0.56 or moderate effect, and a qualitative analysis on the design aspects for ARles: display hardware, software libraries, content authoring solutions, and evaluation techniques.
Abstract: Augmented reality (AR) technology is mature for creating learning experiences for K-12 (pre-school, grade school, and high school) educational settings. We reviewed the applications intended to complement traditional curriculum materials for K-12. We found 87 research articles on augmented reality learning experiences (ARLEs) in the IEEE Xplore Digital Library and other learning technology publications. Forty-three of these articles conducted user studies, and seven allowed the computation of an effect size to the performance of students in a test. In our meta-analysis, research show that ARLEs achieved a widely variable effect on student performance from a small negative effect to a large effect, with a mean effect size of 0.56 or moderate effect. To complement this finding, we performed a qualitative analysis on the design aspects for ARLEs: display hardware, software libraries, content authoring solutions, and evaluation techniques. We explain that AR incur three inherent advantages: real world annotation, contextual visualization, and vision-haptic visualization. We illustrate these advantages through the exemplifying prototypes, and ground these advantages to multimedia learning theory, experiential learning theory, and animate vision theory. Insights from this review are aimed to inform the design of future ARLEs.

Journal ArticleDOI
TL;DR: A comparison of theTaxonomic compositions inferred by the three sequencing experiments indicated that the non-degenerate 342F-806R primer set can characterize the taxonomic composition of the microbial community without substantial bias, and is highly expected to be applicable to the analysis of a wide variety of microbial communities.
Abstract: The deep sequencing of 16S rRNA genes amplified by universal primers has revolutionized our understanding of microbial communities by allowing the characterization of the diversity of the uncultured majority. However, some universal primers also amplify eukaryotic rRNA genes, leading to a decrease in the efficiency of sequencing of prokaryotic 16S rRNA genes with possible mischaracterization of the diversity in the microbial community. In this study, we compared 16S rRNA gene sequences from genome-sequenced strains and identified candidates for non-degenerate universal primers that could be used for the amplification of prokaryotic 16S rRNA genes. The 50 identified candidates were investigated to calculate their coverage for prokaryotic and eukaryotic rRNA genes, including those from uncultured taxa and eukaryotic organelles, and a novel universal primer set, 342F-806R, covering many prokaryotic, but not eukaryotic, rRNA genes was identified. This primer set was validated by the amplification of 16S rRNA genes from a soil metagenomic sample and subsequent pyrosequencing using the Roche 454 platform. The same sample was also used for pyrosequencing of the amplicons by employing a commonly used primer set, 338F-533R, and for shotgun metagenomic sequencing using the Illumina platform. Our comparison of the taxonomic compositions inferred by the three sequencing experiments indicated that the non-degenerate 342F-806R primer set can characterize the taxonomic composition of the microbial community without substantial bias, and is highly expected to be applicable to the analysis of a wide variety of microbial communities.

Journal ArticleDOI
Rasha Abbasi1, M. Abe2, Tareq Abu-Zayyad1, M. Allen1, Robert M. Anderson1, R. Azuma3, Elliott Barcikowski1, John Belz1, Douglas Bergman1, Samuel Blake1, Robert Cady1, M. J. Chae4, Byung Gu Cheon5, Jyunsei Chiba6, Michiyuki Chikawa7, W. R. Cho8, Takahiro Fujii9, Masaki Fukushima9, T. Goto10, William Hanlon1, Y. Hayashi10, Naoaki Hayashida11, K. Hibino11, K. Honda12, Daisuke Ikeda9, N. Inoue2, Takaaki Ishii12, R. Ishimori3, Hidemi Ito, Dmitri Ivanov1, C. C. H. Jui1, Kenichi Kadota13, Fumio Kakimoto3, Oleg Kalashev, K. Kasahara14, H. Kawai15, S. Kawakami10, Shingo Kawana2, Kazumasa Kawata9, Eiji Kido9, Hang Bae Kim5, J. H. Kim1, S. Kitamura3, Yasunori Kitamura3, Vladim Kuzmin, Y. J. Kwon8, J. Lan1, S. I. Lim4, J. P. Lundquist1, Kazuhiro Machida12, K. Martens9, Tomohiro Matsuda, T. Matsuyama10, John N. Matthews1, Mayuko Minamino10, Keijiro Mukai12, Isaac Myers1, K. Nagasawa2, Shigehiro Nagataki, Toru Nakamura16, Toshiyuki Nonaka9, A. Nozato7, Shoichi Ogio10, J. Ogura3, M. Ohnishi9, Hideyuki Ohoka9, K. Oki9, T. Okuda17, Masaomi Ono, Akitoshi Oshima10, S. Ozawa14, Inkyu Park18, Maxim Pshirkov19, D. C. Rodriguez1, Grigory Rubtsov, Dongsu Ryu20, Hiroyuki Sagawa9, Nobuyuki Sakurai10, A. L. Sampson1, L. M. Scott21, Priti Shah1, Fumiya Shibata12, T.-A. Shibata9, Hideaki Shimodaira9, Bokkyun Shin5, J. D. Smith1, Pierre Sokolsky1, R. W. Springer1, B. T. Stokes1, S. R. Stratton21, S. R. Stratton1, Tom Stroman1, T. Suzawa2, Mai Takamura6, M. Takeda9, Ryuji Takeishi9, Akimichi Taketa9, Masato Takita9, Yuichiro Tameda11, Hideki Tanaka10, Kenichi Tanaka22, M. Tanaka, S. B. Thomas1, Gordon Thomson1, Peter Tinyakov19, Igor Tkachev, H. Tokuno3, Takayuki Tomida, Sergey Troitsky, Yoshiki Tsunesada3, K. Tsutsumi3, Y. Uchihori23, S. Udo11, Federico R. Urban19, G. Vasiloff1, Tiffany Wong1, R. Yamane10, Hiroshi Yamaoka, K. Yamazaki10, J. Yang4, Kenta Yashiro6, Y. Yoneda10, S. Yoshida15, H. Yoshii24, R. Zollinger1, Zach Zundel1 
TL;DR: In this paper, the authors search for intermediate-scale anisotropy in the arrival directions of ultra-high-energy cosmic rays with energies above 57 EeV in the northern sky using data collected over a 5-year period by the surface detector of the Telescope Array experiment.
Abstract: We have searched for intermediate-scale anisotropy in the arrival directions of ultrahigh-energy cosmic rays with energies above 57 EeV in the northern sky using data collected over a 5 yr period by the surface detector of the Telescope Array experiment. We report on a cluster of events that we call the hotspot, found by oversampling using 20° radius circles. The hotspot has a Li-Ma statistical significance of 5.1σ, and is centered at R.A. = 146.°7, decl. = 43.°2. The position of the hotspot is about 19° off of the supergalactic plane. The probability of a cluster of events of 5.1σ significance, appearing by chance in an isotropic cosmic-ray sky, is estimated to be 3.7 × 10-4 (3.4σ). © 2014. The American Astronomical Society. All rights reserved.

Journal ArticleDOI
Georges Aad1, Brad Abbott2, Jalal Abdallah3, S. Abdel Khalek4  +2911 moreInstitutions (209)
TL;DR: In this paper, a measurement of the Z/gamma* boson transverse momentum spectrum using ATLAS proton-proton collision data at a centre-of-mass energy of root s = 7TeV at the LHC is described.
Abstract: This paper describes a measurement of the Z/gamma* boson transverse momentum spectrum using ATLAS proton-proton collision data at a centre-of-mass energy of root s = 7TeV at the LHC. The measurement is performed in the Z/gamma* -> e(+)e(-) and Z/gamma* -> mu(+)mu(-) channels, using data corresponding to an integrated luminosity of 4.7 fb(-1). Normalized differential cross sections as a function of the Z/gamma* boson transverse momentum are measured for transverse momenta up to 800 GeV. The measurement is performed inclusively for Z/gamma* rapidities up to 2.4, as well as in three rapidity bins. The channel results are combined, compared to perturbative and resummed QCD calculations and used to constrain the parton shower parameters of Monte Carlo generators.

Journal ArticleDOI
TL;DR: In this article, an effective tar conversion approach during biomass pyrolysis via in-situ dry reforming over rice husk (RH) char and char-supported Ni-Fe catalysts was proposed.
Abstract: This paper aims to propose an effective tar conversion approach during biomass pyrolysis via in-situ dry reforming over rice husk (RH) char and char-supported Ni-Fe catalysts. Utilizing high pyrolysis temperature, tar from biomass pyrolysis could be removed effectively in the gasifier by mixing with the char-supported catalysts, simplifying the follow-up tar removal process. Under the optimized conditions, the conversion efficiencies of condensable tar can reach about 92.3% and 93% using Ni-Fe char (without calcination) and Ni char (with calcination), respectively. It is noteworthy that the condensable tar could be catalytically transformed into the non-condensable tar or small molecule gases resulting in the heating value increase of gaseous products to benefit of the power generation systems. Compared with the other catalysts preparation methods, Ni–Fe char exhibited more advantages of convenient and energy-saving. In the presence of catalysts, the concentration of CO2 (vol.%) was reduced slightly, while the CO concentration (vol.%) increased greatly because of dry reforming. Due to carbon loss, parts of RH char-supported catalysts (C-SiO2 catalysts) could be converted into SiO2-based catalysts because of high-content amorphous nano-sized SiO2 in RH char. In addition, partial metal oxides or ions via carbon (i.e., biochar) and gas (i.e., H2, CO) in-situ reduction were transformed into metallic states contributing to the enhancement of tar conversion. Therefore, RH char plays two significant roles during the process of biomass pyrolysis. On one hand, it works as an intermediate reductant to reduce the metal oxides and CO2; on the other hand, it can be considered as an adsorptive-support to adsorb metal ions and tar. After that, the char-supported catalysts could be used for tar conversion. In particular, since the metal catalysts still remain in the solid residues, the pyrolysis char could be regenerated via thermal regeneration using waste heat or gasified into syngas directly.

Journal ArticleDOI
Georges Aad1, Brad Abbott2, Jalal Abdallah3, S. Abdel Khalek4  +2916 moreInstitutions (211)
TL;DR: In this article, a search for squarks and gluinos in final states containing high-p T jets, missing transverse momentum and no electrons or muons is presented.
Abstract: A search for squarks and gluinos in final states containing high-p T jets, missing transverse momentum and no electrons or muons is presented. The data were recorded in 2012 by the ATLAS experiment in s√=8 TeV proton-proton collisions at the Large Hadron Collider, with a total integrated luminosity of 20.3 fb−1. Results are interpreted in a variety of simplified and specific supersymmetry-breaking models assuming that R-parity is conserved and that the lightest neutralino is the lightest supersymmetric particle. An exclusion limit at the 95% confidence level on the mass of the gluino is set at 1330 GeV for a simplified model incorporating only a gluino and the lightest neutralino. For a simplified model involving the strong production of first- and second-generation squarks, squark masses below 850 GeV (440 GeV) are excluded for a massless lightest neutralino, assuming mass degenerate (single light-flavour) squarks. In mSUGRA/CMSSM models with tan β = 30, A 0 = −2m 0 and μ > 0, squarks and gluinos of equal mass are excluded for masses below 1700 GeV. Additional limits are set for non-universal Higgs mass models with gaugino mediation and for simplified models involving the pair production of gluinos, each decaying to a top squark and a top quark, with the top squark decaying to a charm quark and a neutralino. These limits extend the region of supersymmetric parameter space excluded by previous searches with the ATLAS detector.

Journal ArticleDOI
TL;DR: In this article, a mesoporous nitrogen-doped carbon prepared from (1-methyl-1H-pyrrole-2-yl)methanol in the presence of a meso-SiO2 template (KIT-6) is presented.
Abstract: Electrochemical reduction of oxygen molecules can produce H2O2, which is an important chemical for a green and sustainable society; therefore, the development of catalysts for this reaction is necessary. We propose mesoporous nitrogen-doped carbon prepared from (1-methyl-1H-pyrrole-2-yl)methanol in the presence of a mesoporous SiO2 template (KIT-6). The nitrogen content of the resulting carbon can be controlled in the range of 0–10 at. % and all prepared samples have well-ordered mesopores with diameters of 3.4–4.0 nm. Electrochemical studies indicate the present materials have high catalytic activities with high selectivity toward H2O2 over 90%. Such high selectivity toward H2O2 is probably due to good mass transport in the catalyst layer, which is enhanced by the mesoporous structure.

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TL;DR: The International Axion Observatory (IAXO) as mentioned in this paper is the most powerful axion helioscope, reaching sensitivity to axion-photon couplings down to a few × 10−12 GeV−1 and thus probing a large fraction of the currently unexplored axion and ALP parameter space.
Abstract: The International Axion Observatory (IAXO) will be a forth generation axion helioscope. As its primary physics goal, IAXO will look for axions or axion-like particles (ALPs) originating in the Sun via the Primakoff conversion of the solar plasma photons. In terms of signal-to-noise ratio, IAXO will be about 4–5 orders of magnitude more sensitive than CAST, currently the most powerful axion helioscope, reaching sensitivity to axion-photon couplings down to a few × 10−12 GeV−1 and thus probing a large fraction of the currently unexplored axion and ALP parameter space. IAXO will also be sensitive to solar axions produced by mechanisms mediated by the axion-electron coupling gae with sensitivity — for the first time — to values of gae not previously excluded by astrophysics. With several other possible physics cases, IAXO has the potential to serve as a multi-purpose facility for generic axion and ALP research in the next decade. In this paper we present the conceptual design of IAXO, which follows the layout of an enhanced axion helioscope, based on a purpose-built 20 m-long 8-coils toroidal superconducting magnet. All the eight 60cm-diameter magnet bores are equipped with focusing x-ray optics, able to focus the signal photons into ~ 0.2 cm2 spots that are imaged by ultra-low-background Micromegas x-ray detectors. The magnet is built into a structure with elevation and azimuth drives that will allow for solar tracking for ~ 12 h each day.

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TL;DR: In this article, mild hydrothermal (HT) conversion processes are used to produce clean solid biofuel from high moisture content waste biomass (bio-waste) with high nitrogen (N)/chlorine (Cl) content.

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TL;DR: In this paper, the authors obtained defect energies with errors less than 0.2 eV for 17 defects in 10 compounds; the method is widely applicable to a range of defects and was improved on a previous method for correcting these errors.
Abstract: First-principles defect formation energy calculations can include errors up to several eV. Improving on a previous method for correcting these errors by Freysoldt et al (PRL 102, 016402), the authors obtain defect energies with errors less than 0.2 eV for 17 defects in 10 compounds; the method is widely applicable to a range of defects.

Journal ArticleDOI
TL;DR: It is proposed that mesenchymal remodeling as an overarching role for the matricellular protein periostin, across physiology and disease, is proposed.
Abstract: Periostin, also termed osteoblast-specific factor 2, is a matricellular protein with known functions in osteology, tissue repair, oncology, cardiovascular and respiratory systems, and in various inflammatory settings. However, most of the research to date has been conducted in divergent and circumscribed areas meaning that the overall understanding of this intriguing molecule remains fragmented. Here, we integrate the available evidence on periostin expression, its normal role in development, and whether it plays a similar function during pathologic repair, regeneration, and disease in order to bring together the different research fields in which periostin investigations are ongoing. In spite of the seemingly disparate roles of periostin in health and disease, tissue remodeling as a response to insult/injury is emerging as a common functional denominator of this matricellular molecule. Periostin is transiently upregulated during cell fate changes, either physiologic or pathologic. Combining observations from various conditions, a common pattern of events can be suggested, including periostin localization during development, insult and injury, epithelial–mesenchymal transition, extracellular matrix restructuring, and remodeling. We propose mesenchymal remodeling as an overarching role for the matricellular protein periostin, across physiology and disease. Periostin may be seen as an important structural mediator, balancing appropriate versus inappropriate tissue adaption in response to insult/injury.

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Georges Aad1, Brad Abbott2, Jalal Abdallah3, S. Abdel Khalek4  +2870 moreInstitutions (169)
TL;DR: The performance of the ATLAS muon reconstruction during the LHC run withpp collisions at s=7–8 TeV in 2011–2012 is presented, focusing mainly on data collected in 2012.
Abstract: This paper presents the performance of the ATLAS muon reconstruction during the LHC run with pp collisions at root s = 7-8 TeV in 2011-2012, focusing mainly on data collected in 2012. Measurements ...

Journal ArticleDOI
Georges Aad1, T. Abajyan2, Brad Abbott3, Jalal Abdallah4  +2885 moreInstitutions (169)
TL;DR: In this article, the electron reconstruction and identification efficiencies of the ATLAS detector at the LHC have been evaluated using proton-proton collision data collected in 2011 at TeV and corresponding to an integrated luminosity of 4.7 fb.
Abstract: Many of the interesting physics processes to be measured at the LHC have a signature involving one or more isolated electrons. The electron reconstruction and identification efficiencies of the ATLAS detector at the LHC have been evaluated using proton-proton collision data collected in 2011 at TeV and corresponding to an integrated luminosity of 4.7 fb. Tag-and-probe methods using events with leptonic decays of and bosons and mesons are employed to benchmark these performance parameters. The combination of all measurements results in identification efficiencies determined with an accuracy at the few per mil level for electron transverse energy greater than 30 GeV.

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TL;DR: In this paper, a review of recent developments of radical reactions involving various carbon-centered radicals through photoredox processes mediated by Ru- and Ir-based photocatalysts is presented.
Abstract: Photoredox catalysis by well-known ruthenium(II) polypyridine complexes and the relevant Ir cyclometalated derivatives has become a powerful tool for redox reactions in synthetic organic chemistry, because they can effectively catalyze single-electron-transfer (SET) processes by irradiation with visible light. Remarkably, since 2008, this photocatalytic system has gained importance in radical reactions from the viewpoint of not only a useful and selective protocol but also green chemistry. In this review, we will describe recent developments of radical reactions involving various carbon-centered radicals through photoredox processes mediated by Ru- and Ir-based photocatalysts.

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TL;DR: The Earth, Planets and Space (EPS) as mentioned in this paper is an open access journal for earth and planetary sciences with a focus on geomagnetism, aeronomy, space science, seismology, volcanology, geodesy and planetary science.
Abstract: Editorial This is a new volume of Earth, Planets and Space (EPS) with an open access-style publishing model under SpringerOpen. EPS had a conventional style publication with Terrapub (Tokyo Japan) from 1998 until 2013 as a continuation of the two journals, the Journal of Geomagnetism and Geoelectricity (1949 to 1997) and the Journal of Physics of the Earth (1952 to 1997). We hope that our new open access model as of 2014 will have a greater impact. The scope of EPS is broad, covering earth and planetary sciences, and in particular geomagnetism, aeronomy, space science, seismology, volcanology, geodesy, and planetary science. EPS also covers articles in new and interdisciplinary subjects, including technical topics. We have established four categories for articles: full papers, letters, frontier letters, and technical reports. The full papers are research articles with no page limit. The letters are short papers of eight pages or less in the final PDF version. The frontier letters are letter articles, which are invited by the Editor in Chief, while the technical reports are for the presentations of software tools, experimental or computational methods, or hardware designs.

Journal ArticleDOI
TL;DR: It is shown that by overcoming PCR biases related to amplification and primer mismatch, mi tags may provide more realistic estimates of community richness and evenness than amplicon 454 tags, and is now economically feasible given the dramatic reduction in high-throughput sequencing costs.
Abstract: Summary Sequencing of 16S rDNA polymerase chain reaction (PCR) amplicons is the most common approach for investigating environmental prokaryotic diversity, despite the known biases introduced during PCR. Here we show that 16S rDNA fragments derived from Illumina-sequenced environmental metagenomes (mitags) are a powerful alternative to 16S rDNA amplicons for investigating the taxonomic diversity and structure of prokaryotic communities. As part of the Tara Oceans global expedition, marine plankton was sampled in three locations, resulting in 29 subsamples for which metagenomes were produced by shotgun Illumina sequencing (ca. 700 Gb). For comparative analyses, a subset of samples was also selected for Roche-454 sequencing using both shotgun (m454tags; 13 metagenomes, ca. 2.4 Gb) and 16S rDNA amplicon (454tags; ca. 0.075 Gb) approaches. Our results indicate that by overcoming PCR biases related to amplification and primer mismatch, mitags may provide more realistic estimates of community richness and evenness than amplicon 454tags. In addition, mitags can capture expected beta diversity patterns. Using mitags is now economically feasible given the dramatic reduction in high-throughput sequencing costs, having the advantage of retrieving simultaneously both taxonomic (Bacteria, Archaea and Eukarya) and functional information from the same microbial community.

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TL;DR: This review article focuses on molecular architectures with linear, cyclic, cage, and capsule shapes, each containing three or more anthracene subunits.
Abstract: Anthracene, with its molecular panel-like shape and robust photophysical behaviour, is a versatile building block that is widely used to construct attractive and functional molecules and molecular assemblies through covalent and non-covalent linkages. The intrinsic photophysical, photochemical and chemical properties of the embedded anthracenes often interact to engender desirable chemical behaviours and properties in multi-anthracene assemblies. This review article focuses on molecular architectures with linear, cyclic, cage, and capsule shapes, each containing three or more anthracene subunits.