Showing papers by "University of Tsukuba published in 2014"

Phylogenomics resolves the timing and pattern of insect evolution

Abstract: Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

Abstract: An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

Flood risk and climate change: global and regional perspectives

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 ...

Wearable Photoplethysmographic Sensors—Past and Present

Abstract: Photoplethysmography (PPG) technology has been used to develop small, wearable, pulse rate sensors. These devices, consisting of infrared light-emitting diodes (LEDs) and photodetectors, offer a simple, reliable, low-cost means of monitoring the pulse rate noninvasively. Recent advances in optical technology have facilitated the use of high-intensity green LEDs for PPG, increasing the adoption of this measurement technique. In this review, we briefly present the history of PPG and recent developments in wearable pulse rate sensors with green LEDs. The application of wearable pulse rate monitors is discussed.

Performance of the ALICE experiment at the CERN LHC

Abstract: ALICE is the heavy-ion experiment at the CERN Large Hadron Collider. The experiment continuously took data during the first physics campaign of the machine from fall 2009 until early 2013, using proton and lead-ion beams. In this paper we describe the running environment and the data handling procedures, and discuss the performance of the ALICE detectors and analysis methods for various physics observables.

Reactive cysteine persulfides and S-polythiolation regulate oxidative stress and redox signaling.

Abstract: Using methodology developed herein, it is found that reactive persulfides and polysulfides are formed endogenously from both small molecule species and proteins in high amounts in mammalian cells and tissues. These reactive sulfur species were biosynthesized by two major sulfurtransferases: cystathionine β-synthase and cystathionine γ-lyase. Quantitation of these species indicates that high concentrations of glutathione persulfide (perhydropersulfide >100 μM) and other cysteine persulfide and polysulfide derivatives in peptides/proteins were endogenously produced and maintained in the plasma, cells, and tissues of mammals (rodent and human). It is expected that persulfides are especially nucleophilic and reducing. This view was found to be the case, because they quickly react with H2O2 and a recently described biologically generated electrophile 8-nitroguanosine 3′,5′-cyclic monophosphate. These results indicate that persulfides are potentially important signaling/effector species, and because H2S can be generated from persulfide degradation, much of the reported biological activity associated with H2S may actually be that of persulfides. That is, H2S may act primarily as a marker for the biologically active of persulfide species.

Regulation of water, salinity, and cold stress responses by salicylic acid

Abstract: Salicylic acid (SA) is a naturally occurring phenolic compound. SA plays an important role in the regulation of plant growth, development, ripening, and defense responses. The role of SA in the plant-pathogen relationship has been extensively investigated. In addition to defense responses, SA plays an important role in the response to abiotic stresses, including drought, low temperature, and salinity stresses. It has been suggested that SA has great agronomic potential to improve the stress tolerance of agriculturally important crops. However, the utility of SA is dependent on the concentration of the applied SA, the mode of application, and the state of the plants (e.g., developmental stage and acclimation). Generally, low concentrations of applied SA alleviate the sensitivity to abiotic stresses, and high concentrations of applied induce high levels of oxidative stress, leading to a decreased tolerance to abiotic stresses. In this chapter, the effects of SA on the water stress responses and regulation of stomatal closure are reviewed.

Quantum error correction in a solid-state hybrid spin register

Abstract: Error correction is important in classical and quantum computation Decoherence caused by the inevitable interaction of quantum bits with their environment leads to dephasing or even relaxation Correction of the concomitant errors is therefore a fundamental requirement for scalable quantum computation Although algorithms for error correction have been known for some time, experimental realizations are scarce Here we show quantum error correction in a heterogeneous, solid-state spin system We demonstrate that joint initialization, projective readout and fast local and non-local gate operations can all be achieved in diamond spin systems, even under ambient conditions High-fidelity initialization of a whole spin register (99 per cent) and single-shot readout of multiple individual nuclear spins are achieved by using the ancillary electron spin of a nitrogen-vacancy defect Implementation of a novel non-local gate generic to our electron-nuclear quantum register allows the preparation of entangled states of three nuclear spins, with fidelities exceeding 85 per cent With these techniques, we demonstrate three-qubit phase-flip error correction Using optimal control, all of the above operations achieve fidelities approaching those needed for fault-tolerant quantum operation, thus paving the way to large-scale quantum computation Besides their use with diamond spin systems, our techniques can be used to improve scaling of quantum networks relying on phosphorus in silicon, quantum dots, silicon carbide or rare-earth ions in solids

Somatic RHOA mutation in angioimmunoblastic T cell lymphoma

Abstract: Angioimmunoblastic T cell lymphoma (AITL) is a distinct subtype of peripheral T cell lymphoma characterized by generalized lymphadenopathy and frequent autoimmune-like manifestations. Although frequent mutations in TET2, IDH2 and DNMT3A, which are common to various hematologic malignancies, have been identified in AITL, the molecular pathogenesis specific to this lymphoma subtype is unknown. Here we report somatic RHOA mutations encoding a p.Gly17Val alteration in 68% of AITL samples. Remarkably, all cases with the mutation encoding p.Gly17Val also had TET2 mutations. The RHOA mutation encoding p.Gly17Val was specifically identified in tumor cells, whereas TET2 mutations were found in both tumor cells and non-tumor hematopoietic cells. RHOA encodes a small GTPase that regulates diverse biological processes. We demonstrated that the Gly17Val RHOA mutant did not bind GTP and also inhibited wild-type RHOA function. Our findings suggest that impaired RHOA function in cooperation with preceding loss of TET2 function contributes to AITL-specific pathogenesis.

Mission Design of LiteBIRD

Abstract: LiteBIRD is a next-generation satellite mission to measure the polarization of the cosmic microwave background (CMB) radiation. On large angular scales the B-mode polarization of the CMB carries the imprint of primordial gravitational waves, and its precise measurement would provide a powerful probe of the epoch of inflation. The goal of LiteBIRD is to achieve a measurement of the characterizing tensor to scalar ratio $$r$$ to an uncertainty of $$\delta r=0.001$$ . In order to achieve this goal we will employ a kilo-pixel superconducting detector array on a cryogenically cooled sub-Kelvin focal plane with an optical system at a temperature of 4 K. We are currently considering two detector array options; transition edge sensor (TES) bolometers and microwave kinetic inductance detectors. In this paper we give an overview of LiteBIRD and describe a TES-based polarimeter designed to achieve the target sensitivity of 2 $$\upmu $$ K arcmin over the frequency range 50–320 GHz.

T-bet and Eomes instruct the development of two distinct natural killer cell lineages in the liver and in the bone marrow

Abstract: Trail+DX5−Eomes− natural killer (NK) cells arise in the mouse fetal liver and persist in the adult liver. Their relationships with Trail−DX5+ NK cells remain controversial. We generated a novel Eomes-GFP reporter murine model to address this question. We found that Eomes− NK cells are not precursors of classical Eomes+ NK cells but rather constitute a distinct lineage of innate lymphoid cells. Eomes− NK cells are strictly dependent on both T-bet and IL-15, similarly to NKT cells. We observed that, in the liver, expression of T-bet in progenitors represses Eomes expression and the development of Eomes+ NK cells. Reciprocally, the bone marrow (BM) microenvironment restricts T-bet expression in developing NK cells. Ectopic expression of T-bet forces the development of Eomes− NK cells, demonstrating that repression of T-bet is essential for the development of Eomes+ NK cells. Gene profile analyses show that Eomes− NK cells share part of their transcriptional program with NKT cells, including genes involved in liver homing and NK cell receptors. Moreover, Eomes− NK cells produce a broad range of cytokines, including IL-2 and TNF in vitro and in vivo, during immune responses against vaccinia virus. Thus, mutually exclusive expression of T-bet and Eomes drives the development of different NK cell lineages with complementary functions.

Attosecond band-gap dynamics in silicon

Abstract: Electron transfer from valence to conduction band states in semiconductors is the basis of modern electronics. Here, attosecond extreme ultraviolet (XUV) spectroscopy is used to resolve this process in silicon in real time. Electrons injected into the conduction band by few-cycle laser pulses alter the silicon XUV absorption spectrum in sharp steps synchronized with the laser electric field oscillations. The observed ~450-attosecond step rise time provides an upper limit for the carrier-induced band-gap reduction and the electron-electron scattering time in the conduction band. This electronic response is separated from the subsequent band-gap modifications due to lattice motion, which occurs on a time scale of 60 ± 10 femtoseconds, characteristic of the fastest optical phonon. Quantum dynamical simulations interpret the carrier injection step as light-field–induced electron tunneling.

Global variation in the effects of ambient temperature on mortality: a systematic evaluation.

Abstract: BACKGROUND: Studies have examined the effects of temperature on mortality in a single city, country, or region. However, less evidence is available on the variation in the associations between temperature and mortality in multiple countries, analyzed simultaneously. METHODS: We obtained daily data on temperature and mortality in 306 communities from 12 countries/regions (Australia, Brazil, Thailand, China, Taiwan, Korea, Japan, Italy, Spain, United Kingdom, United States, and Canada). Two-stage analyses were used to assess the nonlinear and delayed relation between temperature and mortality. In the first stage, a Poisson regression allowing overdispersion with distributed lag nonlinear model was used to estimate the community-specific temperature-mortality relation. In the second stage, a multivariate meta-analysis was used to pool the nonlinear and delayed effects of ambient temperature at the national level, in each country. RESULTS: The temperatures associated with the lowest mortality were around the 75th percentile of temperature in all the countries/regions, ranging from 66th (Taiwan) to 80th (UK) percentiles. The estimated effects of cold and hot temperatures on mortality varied by community and country. Meta-analysis results show that both cold and hot temperatures increased the risk of mortality in all the countries/regions. Cold effects were delayed and lasted for many days, whereas heat effects appeared quickly and did not last long. CONCLUSIONS: People have some ability to adapt to their local climate type, but both cold and hot temperatures are still associated with increased risk of mortality. Public health strategies to alleviate the impact of ambient temperatures are important, in particular in the context of climate change.

The Physics of the B Factories

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.

Indistinguishable Photons from Separated Silicon-Vacancy Centers in Diamond

Abstract: We demonstrate that silicon-vacancy (SiV) centers in diamond can be used to efficiently generate coherent optical photons with excellent spectral properties. We show that these features are due to the inversion symmetry associated with SiV centers. The generation of indistinguishable single photons from separated emitters at 5 K is demonstrated in a Hong-Ou-Mandel interference experiment. Prospects for realizing efficient quantum network nodes using SiV centers are discussed. The realization of quantum networks, in which local quantum processing nodes are connected over long distances via optical photons, is an outstanding challenge in quantum information science [1]. Over the past few years, atomlike systems in the solid state have emerged as a promising platform for achieving this goal. Key building blocks have been demonstrated using nitrogen-vacancy (NV) centers in diamond, including long-lived qubit memory [2], spin-photon [3], and spin-spin entanglement [4], as well as teleportation between distant stationary qubits [5]. While NV centers can be used as excellent quantum registers, the current efforts to scale up these proof-of-concept experiments are limited by the small probability of coherent photon emission from NV centers and their spectral stability [6,7]. Here we demonstrate that silicon-vacancy (SiV) centers in diamond can be used to efficiently generate coherent optical photons with excellent spectral stability. We show that these features are due to the inversion symmetry associated with SiV centers and demonstrate generation of indistinguishable single photons

Highly water-soluble, porous, and biocompatible boron nitrides for anticancer drug delivery.

Abstract: Developing materials for "Nano-vehicles" with clinically approved drugs encapsulated is envisaged to enhance drug therapeutic effects and reduce the adverse effects. However, design and preparation of the biomaterials that are porous, nontoxic, soluble, and stable in physiological solutions and could be easily functionalized for effective drug deliveries are still challenging. Here, we report an original and simple thermal substitution method to fabricate perfectly water-soluble and porous boron nitride (BN) materials featuring unprecedentedly high hydroxylation degrees. These hydroxylated BNs are biocompatible and can effectively load anticancer drugs (e.g., doxorubicin, DOX) up to contents three times exceeding their own weight. The same or even fewer drugs that are loaded on such BN carriers exhibit much higher potency for reducing the viability of LNCaP cancer cells than free drugs.

Electron and photon energy calibration with the ATLAS detector using LHC Run 1 data

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.

Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation

Abstract: The brown planthopper, Nilaparvata lugens, the most destructive pest of rice, is a typical monophagous herbivore that feeds exclusively on rice sap, which migrates over long distances. Outbreaks of it have re-occurred approximately every three years in Asia. It has also been used as a model system for ecological studies and for developing effective pest management. To better understand how a monophagous sap-sucking arthropod herbivore has adapted to its exclusive host selection and to provide insights to improve pest control, we analyzed the genomes of the brown planthopper and its two endosymbionts. We describe the 1.14 gigabase planthopper draft genome and the genomes of two microbial endosymbionts that permit the planthopper to forage exclusively on rice fields. Only 40.8% of the 27,571 identified Nilaparvata protein coding genes have detectable shared homology with the proteomes of the other 14 arthropods included in this study, reflecting large-scale gene losses including in evolutionarily conserved gene families and biochemical pathways. These unique genomic features are functionally associated with the animal’s exclusive plant host selection. Genes missing from the insect in conserved biochemical pathways that are essential for its survival on the nutritionally imbalanced sap diet are present in the genomes of its microbial endosymbionts, which have evolved to complement the mutualistic nutritional needs of the host. Our study reveals a series of complex adaptations of the brown planthopper involving a variety of biological processes, that result in its highly destructive impact on the exclusive host rice. All these findings highlight potential directions for effective pest control of the planthopper.

Measurement of the Z/γ* boson transverse momentum distribution in pp collisions at √s = 7 TeV with the ATLAS detector

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.

Search for squarks and gluinos with the ATLAS detector in final states with jets and missing transverse momentum using √s = 8 TeV proton-proton collision data

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.

Measurement of the muon reconstruction performance of the ATLAS detector using 2011 and 2012 LHC proton-proton collision data

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 ...

Electron reconstruction and identification efficiency measurements with the atlas detector using the 2011 lhc proton-proton collision data

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.

Guidelines for obstetrical practice in Japan: Japan Society of Obstetrics and Gynecology (JSOG) and Japan Association of Obstetricians and Gynecologists (JAOG) 2014 edition.

Abstract: The 'Clinical Guidelines for Obstetrical Practice, 2011 edition' were revised and published as a 2014 edition (in Japanese) in April 2014 by the Japan Society of Obstetrics and Gynecology and the Japan Association of Obstetricians and Gynecologists. The aims of this publication include the determination of current standard care practices for pregnant women in Japan, the widespread use of standard care practices, the enhancement of safety in obstetrical practice, the reduction of burdens associated with medico-legal and medico-economical problems, and a better understanding between pregnant women and maternity-service providers. The number of Clinical Questions and Answers items increased from 87 in the 2011 edition to 104 in the 2014 edition. The Japanese 2014 version included a Discussion, a List of References, and some Tables and Figures following the Answers to the 104 Clinical Questions; these additional sections covered common problems and questions encountered in obstetrical practice, helping Japanese readers to achieve a comprehensive understanding. Each answer with a recommendation level of A, B or C was prepared based principally on 'evidence' or a consensus among Japanese obstetricians in situations where 'evidence' was weak or lacking. Answers with a recommendation level of A or B represent current standard care practices in Japan. All 104 Clinical Questions and Answers items, with the omission of the Discussion, List of References, and Tables and Figures, are presented herein to promote a better understanding among English readers of the current standard care practices for pregnant women in Japan.

Multiple intrinsically identical single-photon emitters in the solid state

Abstract: In quantum optical technologies, identical emitters of indistinguishable single photons are difficult to realize due to the inherent dissimilarity of each emitting device Here, Rogers et al demonstrate a solid-state uniform single-photon source, which does not require external tuning of optical properties

The mass spectrum of the first stars

Abstract: We perform cosmological hydrodynamics simulations with non-equilibrium primordial chemistry to obtain 59 minihalos that host first stars. The obtained minihalos are used as initial conditions of local three dimensional radiation hydrodynamics simulations to investigate the formation of the first stars. We find two-thirds of the minihalos host multiple stars, while the rest of them have single stars. The mass of the stars found in our simulations are in the range of 1M⊙ . M . 300M⊙, peaking at several×10M⊙. Most of the very massive stars of & 140M⊙ are born as single stars, although not all of the single stars are very massive. We also find a few stars of . 1M⊙ that are kicked by the gravitational three body interactions to the position distant from the center of mass. The frequency that a star forming minihalo contains a binary system is ∼ 50%. We also investigate the abundance pattern of the stellar remnants by summing up the contributions from the first stars in the simulations. Consequently, the pattern is compatible with that of the low metallicity Damped Lyman−α systems or the Extremely Metal Poor (EMP) stars , if the mass spectrum obtained in our experiment is shifted to the low mass side by 0.2 dex. If we consider the case that an EMP star is born in the remnant of the individual minihalo without mixing with others, the chemical signature of the pair instability supernova is more prominent, because most of them are born as single stars. Subject headings: early Universe—radiative transfer —first stars–metal poor stars

Atomistic Origins of High Rate Capability and Capacity of N-Doped Graphene for Lithium Storage

Abstract: Distinct from pure graphene, N-doped graphene (GN) has been found to possess high rate capability and capacity for lithium storage. However, there has still been a lack of direct experimental evidence and fundamental understanding of the storage mechanisms at the atomic scale, which may shed a new light on the reasons of the ultrafast lithium storage property and high capacity for GN. Here we report on the atomistic insights of the GN energy storage as revealed by in situ transmission electron microscopy (TEM). The lithiation process on edges and basal planes is directly visualized, the pyrrolic N "hole" defect and the perturbed solid-electrolyte-interface configurations are observed, and charge transfer states for three N-existing forms are also investigated. In situ high-resolution TEM experiments together with theoretical calculations provide a solid evidence that enlarged edge {0002} spacings and surface hole defects result in improved surface capacitive effects and thus high rate capability and the high capacity are owing to short-distance orderings at the edges during discharging and numerous surface defects; the phenomena cannot be understood previously by standard electron or X-ray diffraction analyses.