Showing papers by "University of Tsukuba published in 2015"

Combined Measurement of the Higgs Boson Mass in pp Collisions at √s=7 and 8 TeV with the ATLAS and CMS Experiments

Abstract: A measurement of the Higgs boson mass is presented based on the combined data samples of the ATLAS and CMS experiments at the CERN LHC in the H→γγ and H→ZZ→4l decay channels. The results are obtained from a simultaneous fit to the reconstructed invariant mass peaks in the two channels and for the two experiments. The measured masses from the individual channels and the two experiments are found to be consistent among themselves. The combined measured mass of the Higgs boson is mH=125.09±0.21 (stat)±0.11 (syst) GeV.

Comprehensive genomic profiles of small cell lung cancer

Abstract: We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Δex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.

Scheme for Achieving a Topological Photonic Crystal by Using Dielectric Material.

Abstract: We derive in the present work topological photonic states purely based on conventional dielectric material by deforming a honeycomb lattice of cylinders into a triangular lattice of cylinder hexagons. The photonic topology is associated with a pseudo-time-reversal (TR) symmetry constituted by the TR symmetry supported in general by Maxwell equations and the C_{6} crystal symmetry upon design, which renders the Kramers doubling in the present photonic system. It is shown explicitly for the transverse magnetic mode that the role of pseudospin is played by the angular momentum of the wave function of the out-of-plane electric field. We solve Maxwell equations and demonstrate the new photonic topology by revealing pseudospin-resolved Berry curvatures of photonic bands and helical edge states characterized by Poynting vectors.

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

Abstract: Enhancers, critical determinants of cellular identity, are commonly recognized by correlative chromatin marks and gain-of-function potential, although only loss-of-function studies can demonstrate their requirement in the native genomic context. Previously, we identified an erythroid enhancer of human BCL11A, subject to common genetic variation associated with the fetal haemoglobin level, the mouse orthologue of which is necessary for erythroid BCL11A expression. Here we develop pooled clustered regularly interspaced palindromic repeat (CRISPR)-Cas9 guide RNA libraries to perform in situ saturating mutagenesis of the human and mouse enhancers. This approach reveals critical minimal features and discrete vulnerabilities of these enhancers. Despite conserved function of the composite enhancers, their architecture diverges. The crucial human sequences appear to be primate-specific. Through editing of primary human progenitors and mouse transgenesis, we validate the BCL11A erythroid enhancer as a target for fetal haemoglobin reinduction. The detailed enhancer map will inform therapeutic genome editing, and the screening approach described here is generally applicable to functional interrogation of non-coding genomic elements.

Japanese Society for Cancer of the Colon and Rectum (JSCCR) Guidelines 2014 for treatment of colorectal cancer

Abstract: Colorectal cancer is a major cause of death in Japan, where it accounts for the largest number of deaths from malignant neoplasms among women and the third largest number among men. Many new methods of treatment have been developed during recent decades. The Japanese Society for Cancer of the Colon and Rectum Guidelines 2014 for treatment of colorectal cancer (JSCCR Guidelines 2014) have been prepared as standard treatment strategies for colorectal cancer, to eliminate treatment disparities among institutions, to eliminate unnecessary treatment and insufficient treatment, and to deepen mutual understanding among health-care professionals and patients by making these guidelines available to the general public. These guidelines have been prepared as a result of consensuses reached by the JSCCR Guideline Committee on the basis of careful review of evidence retrieved by literature searches and taking into consideration the medical health insurance system and actual clinical practice in Japan. They can, therefore, be used as a guide for treating colorectal cancer in clinical practice. More specifically, they can be used as a guide to obtaining informed consent from patients and choosing the method of treatment for each patient. As a result of the discussions of the Guideline Committee, controversial issues were selected as clinical questions, and recommendations were made. Each recommendation is accompanied by a classification of the evidence and a classification of recommendation categories, on the basis of consensus reached by Guideline Committee members. Here we present the English version of the JSCCR Guidelines 2014.

Four Arabidopsis AREB/ABF transcription factors function predominantly in gene expression downstream of SnRK2 kinases in abscisic acid signalling in response to osmotic stress.

Abstract: Under osmotic stress conditions such as drought and high salinity, the plant hormone abscisic acid (ABA) plays important roles in stress-responsive gene expression mainly through three bZIP transcription factors, AREB1/ABF2, AREB2/ABF4 and ABF3, which are activated by SNF1-related kinase 2s (SnRK2s) such as SRK2D/SnRK2.2, SRK2E/SnRK2.6 and SRK2I/SnRK2.3 (SRK2D/E/I). However, since the three AREB/ABFs are crucial, but not exclusive, for the SnRK2-mediated gene expression, transcriptional pathways governed by SRK2D/E/I are not fully understood. Here, we show that a bZIP transcription factor, ABF1, is a functional homolog of AREB1, AREB2 and ABF3 in ABA-dependent gene expression in Arabidopsis. Despite lower expression levels of ABF1 than those of the three AREB/ABFs, the areb1 areb2 abf3 abf1 mutant plants displayed increased sensitivity to drought and decreased sensitivity to ABA in primary root growth compared with the areb1 areb2 abf3 mutant. Genome-wide transcriptome analyses revealed that expression of downstream genes of SRK2D/E/I, which include many genes functioning in osmotic stress responses and tolerance such as transcription factors and LEA proteins, was mostly impaired in the quadruple mutant. Thus, these results indicate that the four AREB/ABFs are the predominant transcription factors downstream of SRK2D/E/I in ABA signalling in response to osmotic stress during vegetative growth.

Novel scoring system and algorithm for classifying chronic rhinosinusitis: the JESREC Study

Abstract: Background Chronic rhinosinusitis (CRS) can be classified into CRS with nasal polyps (CRSwNP) and CRS without nasal polyps (CRSsNP). CRSwNP displays more intense eosinophilic infiltration and the presence of Th2 cytokines. Mucosal eosinophilia is associated with more severe symptoms and often requires multiple surgeries because of recurrence; however, even in eosinophilic CRS (ECRS), clinical course is variable. In this study, we wanted to set objective clinical criteria for the diagnosis of refractory CRS. Methods This was a retrospective study conducted by 15 institutions participating in the Japanese Epidemiological Survey of Refractory Eosinophilic Chronic Rhinosinusitis (JESREC). We evaluated patients with CRS treated with endoscopic sinus surgery (ESS), and risk of recurrence was estimated using Cox proportional hazard models. Multiple logistic regression models and receiver operating characteristics curves were constructed to create the diagnostic criterion for ECRS. Results We analyzed 1716 patients treated with ESS. To diagnose ECRS, the JESREC scoring system assessed unilateral or bilateral disease, the presence of nasal polyps, blood eosinophilia, and dominant shadow of ethmoid sinuses in computed tomography (CT) scans. The cutoff value of the score was 11 points (sensitivity: 83%, specificity: 66%). Blood eosinophilia (>5%), ethmoid sinus disease detected by CT scan, bronchial asthma, aspirin, and nonsteroidal anti-inflammatory drugs intolerance were associated significantly with recurrence. Conclusion We subdivided CRSwNP in non-ECRS, mild, moderate, and severe ECRS according to our algorithm. This classification was significantly correlated with prognosis. It is notable that this algorithm may give useful information to clinicians in the refractoriness of CRS before ESS or biopsy.

Search for new phenomena in final states with an energetic jet and large missing transverse momentum in pp collisions at √=s=8 TeV with the ATLAS detector

Abstract: Results of a search for new phenomena in final states with an energetic jet and large missing transverse momentum are reported. The search uses 20.3 fb(-1) of root s = 8 TeV data collected in 2012 ...

Subpicotesla Diamond Magnetometry

Abstract: Magnetic fields play roles in a variety of scientific and medical applications. Using solid-state spins in diamond, researchers experimentally demonstrate the measurement of magnetic fields as small as 100 fT in a tiny sensor volume.

MORPHOLOGIES OF ∼190,000 GALAXIES AT z = 0–10 REVEALED WITH HST LEGACY DATA. I. SIZE EVOLUTION

Abstract: We present redshift evolution of galaxy effective radius r_e obtained from the HST samples of ~190,000 galaxies at z=0-10. Our HST samples consist of 176,152 photo-z galaxies at z=0-6 from the 3D-HST+CANDELS catalogue and 10,454 LBGs at z=4-10 identified in CANDELS, HUDF09/12, and HFF parallel fields, providing the largest data set to date for galaxy size evolution studies. We derive r_e with the same technique over the wide-redshift range of z=0-10, evaluating the optical-to-UV morphological K-correction and the selection bias of photo-z galaxies+LBGs as well as the cosmological surface brightness dimming effect. We find that r_e values at a given luminosity significantly decrease towards high-z, regardless of statistics choices. For star-forming galaxies, there is no evolution of the power-law slope of the size-luminosity relation and the median Sersic index (n~1.5). Moreover, the r_e-distribution is well represented by log-normal functions whose standard deviation \sigma_{\ln{r_e}} does not show significant evolution within the range of \sigma_{\ln{r_e}}~0.45-0.75. We calculate the stellar-to-halo size ratio from our r_e measurements and the dark-matter halo masses estimated from the abundance matching study, and obtain a nearly constant value of r_e/r_vir=1.0-3.5% at z=0-8. The combination of the r_e-distribution shape+standard deviation, the constant r_e/r_vir, and n~1.5 suggests a picture that typical high-z star-forming galaxies have disk-like stellar components in a sense of dynamics and morphology over cosmic time of z~0-6. If high-z star-forming galaxies are truly dominated by disks, the r_e/r_vir value and the disk formation model indicate that the specific angular momentum of the disk normalized by the host halo is j_d/m_d=0.5-1. These are statistical results for galaxies' major stellar components, and the detailed study of clumpy sub-components is presented in the paper II.

A Layered P2- and O3-Type Composite as a High-Energy Cathode for Rechargeable Sodium-Ion Batteries

Abstract: A layered composite with P2 and O3 integration is proposed toward a sodium-ion battery with high energy density and long cycle life. The integration of P2 and O3 structures in this layered oxide is clearly characterized by XRD refinement, SAED and HAADF and ABF-STEM at atomic resolution. The biphase synergy in this layered P2+O3 composite is well established during the electrochemical reaction. This layered composite can deliver a high reversible capacity with the largest energy density of 640 mAh g−1, and it also presents good capacity retention over 150 times of sodium extraction and insertion.

Temporal variation in heat-mortality associations: A multicountry study

Abstract: BackgroundRecent investigations have reported a decline in the heat-related mortality risk during the last decades. However, these studies are frequently based on modeling approaches that do not fu...

Jet energy measurement and its systematic uncertainty in proton-proton collisions at s√=7 TeV with the ATLAS detector

Abstract: The jet energy scale (JES) and its systematic uncertainty are determined for jets measured with the ATLAS detector using proton-proton collision data with a centre-of-mass energy of [Formula: see text] TeV corresponding to an integrated luminosity of [Formula: see text][Formula: see text]. Jets are reconstructed from energy deposits forming topological clusters of calorimeter cells using the anti-[Formula: see text] algorithm with distance parameters [Formula: see text] or [Formula: see text], and are calibrated using MC simulations. A residual JES correction is applied to account for differences between data and MC simulations. This correction and its systematic uncertainty are estimated using a combination of in situ techniques exploiting the transverse momentum balance between a jet and a reference object such as a photon or a [Formula: see text] boson, for [Formula: see text] and pseudorapidities [Formula: see text]. The effect of multiple proton-proton interactions is corrected for, and an uncertainty is evaluated using in situ techniques. The smallest JES uncertainty of less than 1 % is found in the central calorimeter region ([Formula: see text]) for jets with [Formula: see text]. For central jets at lower [Formula: see text], the uncertainty is about 3 %. A consistent JES estimate is found using measurements of the calorimeter response of single hadrons in proton-proton collisions and test-beam data, which also provide the estimate for [Formula: see text] TeV. The calibration of forward jets is derived from dijet [Formula: see text] balance measurements. The resulting uncertainty reaches its largest value of 6 % for low-[Formula: see text] jets at [Formula: see text]. Additional JES uncertainties due to specific event topologies, such as close-by jets or selections of event samples with an enhanced content of jets originating from light quarks or gluons, are also discussed. The magnitude of these uncertainties depends on the event sample used in a given physics analysis, but typically amounts to 0.5-3 %.

Recognizing Depression from Twitter Activity

Abstract: In this paper, we extensively evaluate the effectiveness of using a user's social media activities for estimating degree of depression. As ground truth data, we use the results of a web-based questionnaire for measuring degree of depression of Twitter users. We extract several features from the activity histories of Twitter users. By leveraging these features, we construct models for estimating the presence of active depression. Through experiments, we show that (1) features obtained from user activities can be used to predict depression of users with an accuracy of 69%, (2) topics of tweets estimated with a topic model are useful features, (3) approximately two months of observation data are necessary for recognizing depression, and longer observation periods do not contribute to improving the accuracy of estimation for current depression; sometimes, longer periods worsen the accuracy.

ACPN: A Novel Authentication Framework with Conditional Privacy-Preservation and Non-Repudiation for VANETs

Abstract: In Vehicular Ad hoc NETworks (VANETs), authentication is a crucial security service for both inter-vehicle and vehicle-roadside communications. On the other hand, vehicles have to be protected from the misuse of their private data and the attacks on their privacy, as well as to be capable of being investigated for accidents or liabilities from non-repudiation. In this paper, we investigate the authentication issues with privacy preservation and non-repudiation in VANETs. We propose a novel framework with preservation and repudiation (ACPN) for VANETs. In ACPN, we introduce the public-key cryptography (PKC) to the pseudonym generation, which ensures legitimate third parties to achieve the non-repudiation of vehicles by obtaining vehicles’ real IDs. The self-generated PKC-based pseudonyms are also used as identifiers instead of vehicle IDs for the privacy-preserving authentication, while the update of the pseudonyms depends on vehicular demands. The existing ID-based signature (IBS) scheme and the ID-based online/offline signature (IBOOS) scheme are used, for the authentication between the road side units (RSUs) and vehicles, and the authentication among vehicles, respectively. Authentication, privacy preservation, non-repudiation and other objectives of ACPN have been analyzed for VANETs. Typical performance evaluation has been conducted using efficient IBS and IBOOS schemes. We show that the proposed ACPN is feasible and adequate to be used efficiently in the VANET environment.

A mitochondrial superoxide theory for oxidative stress diseases and aging

Abstract: Fridovich identified CuZnSOD in 1969 and manganese superoxide dismutase (MnSOD) in 1973, and proposed ”the Superoxide Theory,” which postulates that superoxide (O2•−) is the origin of most reactive oxygen species (ROS) and that it undergoes a chain reaction in a cell, playing a central role in the ROS producing system. Increased oxidative stress on an organism causes damage to cells, the smallest constituent unit of an organism, which can lead to the onset of a variety of chronic diseases, such as Alzheimer’s, Parkinson’s, amyotrophic lateral sclerosis and other neurological diseases caused by abnormalities in biological defenses or increased intracellular reactive oxygen levels. Oxidative stress also plays a role in aging. Antioxidant systems, including non-enzyme low-molecular-weight antioxidants (such as, vitamins A, C and E, polyphenols, glutathione, and coenzyme Q10) and antioxidant enzymes, fight against oxidants in cells. Superoxide is considered to be a major factor in oxidant toxicity, and mitochondrial MnSOD enzymes constitute an essential defense against superoxide. Mitochondria are the major source of superoxide. The reaction of superoxide generated from mitochondria with nitric oxide is faster than SOD catalyzed reaction, and produces peroxynitrite. Thus, based on research conducted after Fridovich’s seminal studies, we now propose a modified superoxide theory; i.e., superoxide is the origin of reactive oxygen and nitrogen species (RONS) and, as such, causes various redox related diseases and aging.

Application of genomics-assisted breeding for generation of climate resilient crops: Progress and prospects

Abstract: Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.

Search for high-mass diboson resonances with boson-tagged jets in proton-proton collisions at √s=8 TeV with the ATLAS detector

Abstract: A search is performed for narrow resonances decaying into WW, WZ, or ZZ boson pairs using 20.3 fb(-1) of proton-proton collision data at a centre-of-mass energy of root s = TeV recorded with the AT ...

Validation of EULAR primary Sjogren's syndrome disease activity (ESSDAI) and patient indexes (ESSPRI)

Abstract: Objectives To validate the two recently developed disease activity indexes for assessment of primary Sjogren's syndrome (SS): the European League Against Rheumatism (EULAR) SS Patient Reported Index (ESSPRI) and the EULAR SS Disease Activity Index (ESSDAI). Methods A prospective international 6-month duration validation study was conducted in 15 countries. At each visit, physicians completed ESSDAI, SS disease activity index (SSDAI), Sjogren's Systemic Clinical Activity Index (SCAI) and physician global assessment (PhGA); and patients completed ESSPRI, Sicca Symptoms Inventory (SSI), Profile of Fatigue and Discomfort (PROFAD) and patient global assessment (PGA). Psychometric properties (construct validity, responsiveness and reliability) were evaluated and compared between scores. Results Of the 395 patients included, 145 (37%) and 251 (64%) had currently active or current or past systemic manifestations, respectively. EULAR scores had higher correlation with the gold standard than other scores (ESSDAI with PhGA: r= 0.59; ESSRPI with PGA: r= 0.70). Correlations between patient and systemic scores were very low (ranging from 0.07 to 0.29). All systemic scores had similar large responsiveness in improved patients. Responsiveness of patient scores was low but was significantly higher for ESSPRI compared with SSI and PROFAD. Reliability was very good for all scores. Conclusions ESSDAI and ESSPRI had good construct validity. All scores were reliable. Systemic scores had a large sensitivity to change in patients whose disease activity improves. Patient scores had a small sensitivity to change, however, significantly better for ESSPRI. Systemic and patient scores poorly correlated, suggesting that they are 2 complementary components that should be both evaluated, but separately.

Measurements of Higgs boson production and couplings in the four-lepton channel in pp collisions at center-of-mass energies of 7 and 8 TeV with the ATLAS detector

Abstract: The final ATLAS Run 1 measurements of Higgs boson production and couplings in the decay channel H -> ZZ* -> l(+)l(-)l(+)l'(-), where l, l' = e or mu, are presented. These measurements were performed using pp collision data corresponding to integrated luminosities of 4.5 and 20.3 fb(-1) at center-of-mass energies of 7 and 8 TeV, respectively, recorded with the ATLAS detector at the LHC. The H -> ZZ* -> 4l signal is observed with a significance of 8.1 standard deviations, with an expectation of 6.2 standard deviations, at m(H) = 125.36 GeV, the combined ATLAS measurement of the Higgs boson mass from the H -> gamma gamma and H -> ZZ* -> 4l channels. The production rate relative to the Standard Model expectation, the signal strength, is measured in four different production categories in the H -> ZZ* -> 4l channel. The measured signal strength, at this mass, and with all categories combined, is 1.44(-0.33)(+0.40). The signal strength for Higgs boson production in gluon fusion or in association with (tt) over bar or (bb) over bar pairs is found to be 1.7(-0.4)(+0.5), while the signal strength for vector-boson fusion combined with WH/ZH associated production is found to be 0.3(-0.9)(+1.6).

Growth differentiation factor 15 as a useful biomarker for mitochondrial disorders

Abstract: Objective The diagnosis of mitochondrial disorders (MDs) is occasionally difficult because patients often present with solitary, or a combination of, symptoms caused by each organ insufficiency, which may be the result of respiratory chain enzyme deficiency. Growth differentiation factor 15 (GDF-15) has been reported to be elevated in serum of patients with MDs. In this study, we investigated whether GDF-15 is a more useful biomarker for MDs than several conventional biomarkers. Methods We measured the serum levels of GDF-15 and fibroblast growth factor 21 (FGF-21), as well as other biomarkers, in 48 MD patients and in 146 healthy controls in Japan. GDF-15 and FGF-21 concentrations were measured by enzyme-linked immunosorbant assay and compared with lactate, pyruvate, creatine kinase, and the lactate-to-pyruvate ratio. We calculated sensitivity and specificity and also evaluated the correlation based on two rating scales, including the Newcastle Mitochondrial Disease Rating Scale (NMDAS). Results Mean GDF-15 concentration was 6-fold higher in MD patients compared to healthy controls (2,711 ± 2,459 pg/ml vs 462.5 ± 141.0 pg/mL; p < 0.001). Using a receiver operating characteristic curve, the area under the curve was significantly higher for GDF-15 than FGF-21 and other conventional biomarkers. Our date suggest that GDF-15 is the most useful biomarker for MDs of the biomarkers examined, and it is associated with MD severity. Interpretation Our results suggest that measurement of GDF-15 is the most useful first-line test to indicate the patients who have the mitochondrial respiratory chain deficiency. Ann Neurol 2015;78:Ann Neurol 2015;78:679–696

Search for massive, long-lived particles using multitrack displaced vertices or displaced lepton pairs in pp collisions at √s = 8 TeV with the ATLAS detector

Abstract: Many extensions of the Standard Model posit the existence of heavy particles with long lifetimes. This article presents the results of a search for events containing at least one long-lived particle that decays at a significant distance from its production point into two leptons or into five or more charged particles. This analysis uses a data sample of proton-proton collisions at root s = 8 TeV corresponding to an integrated luminosity of 20.3 fb(-1) collected in 2012 by the ATLAS detector operating at the Large Hadron Collider. No events are observed in any of the signal regions, and limits are set on model parameters within supersymmetric scenarios involving R-parity violation, split supersymmetry, and gauge mediation. In some of the search channels, the trigger and search strategy are based only on the decay products of individual long-lived particles, irrespective of the rest of the event. In these cases, the provided limits can easily be reinterpreted in different scenarios.

High-performance symmetric sodium-ion batteries using a new, bipolar O3-type material, Na0.8Ni0.4Ti0.6O2

Abstract: Based on low-cost and rich resources, sodium-ion batteries have been regarded as a promising candidate for next-generation energy storage batteries in the large-scale energy applications of renewable energy and smart grids. However, there are some critical drawbacks limiting its application, such as safety and stability problems. In this work, a stable symmetric sodium-ion battery based on the bipolar, active O3-type material, Na0.8Ni0.4Ti0.6O2, is developed. This bipolar material shows a typical O3-type layered structure, containing two electrochemically active transition metals with redox couples of Ni4+/Ni2+ and Ti4+/Ti3+, respectively. This Na0.8Ni0.4Ti0.6O2-based symmetric cell exhibits a high average voltage of 2.8 V, a reversible discharge capacity of 85 mA h g−1, 75% capacity retention after 150 cycles and good rate capability. This full symmetric cell will greatly contribute to the development of room-temperature sodium-ion batteries with a view towards safety, low cost and long life, and it will stimulate further research on symmetric cells using the same active materials as both cathode and anode.