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- Wang, QBS, et al.
(author)
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The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force
- 2022
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In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 4830-
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Journal article (peer-reviewed)abstract
- Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection.
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- Abe, K., et al.
(author)
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Neutron tagging following atmospheric neutrino events in a water Cherenkov detector
- 2022
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In: Journal of Instrumentation. - : Institute of Physics (IOP). - 1748-0221. ; 17:10
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Journal article (peer-reviewed)abstract
- We present the development of neutron-tagging techniques in Super-Kamiokande IV using a neural network analysis. The detection efficiency of neutron capture on hydrogen is estimated to be 26%, with a mis-tag rate of 0.016 per neutrino event. The uncertainty of the tagging efficiency is estimated to be 9.0%. Measurement of the tagging efficiency with data from an Americium-Beryllium calibration agrees with this value within 10%. The tagging procedure was performed on 3,244.4 days of SK-IV atmospheric neutrino data, identifying 18,091 neutrons in 26,473 neutrino events. The fitted neutron capture lifetime was measured as 218 +/- 9 mu s.
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- Abe, K., et al.
(author)
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J-PARC Neutrino Beamline Upgrade Technical Design Report
- 2019
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Reports (peer-reviewed)abstract
- In this document, technical details of the upgrade plan of the J-PARC neutrino beamline for the extension of the T2K experiment are described. T2K has proposed to accumulate data corresponding to 2×1022 protons-on-target in the next decade, aiming at an initial observation of CP violation with 3σ or higher significance in the case of maximal CP violation. Methods to increase the neutrino beam intensity, which are necessary to achieve the proposed data increase, are described.
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- Bakker, D. C. E., et al.
(author)
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An update to the surface ocean CO2 atlas (SOCAT version 2)
- 2014
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In: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 6:1, s. 69-90
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Journal article (peer-reviewed)abstract
- The Surface Ocean CO2 Atlas (SOCAT), an activity of the international marine carbon research community, provides access to synthesis and gridded fCO2 (fugacity of carbon dioxide) products for the surface oceans. Version 2 of SOCAT is an update of the previous release (version 1) with more data (increased from 6.3 million to 10.1 million surface water fCO 2 values) and extended data coverage (from 1968-2007 to 1968-2011). The quality control criteria, while identical in both versions, have been applied more strictly in version 2 than in version 1. The SOCAT website (http://www.socat.info/) has links to quality control comments, metadata, individual data set files, and synthesis and gridded data products. Interactive online tools allow visitors to explore the richness of the data. Applications of SOCAT include process studies, quantification of the ocean carbon sink and its spatial, seasonal, year-to-year and longerterm variation, as well as initialisation or validation of ocean carbon models and coupled climate-carbon models. © Author(s) 2014. CC Attribution 3.0 License.
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- Addazi, A., et al.
(author)
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New high-sensitivity searches for neutrons converting into antineutrons and/or sterile neutrons at the HIBEAM/NNBAR experiment at the European Spallation Source
- 2021
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In: Journal of Physics G. - : Institute of Physics Publishing (IOPP). - 0954-3899 .- 1361-6471. ; 48:7
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Journal article (peer-reviewed)abstract
- The violation of baryon number, , is an essential ingredient for the preferential creation of matter over antimatter needed to account for the observed baryon asymmetry in the Universe. However, such a process has yet to be experimentally observed. The HIBEAM/NNBAR program is a proposed two-stage experiment at the European Spallation Source to search for baryon number violation. The program will include high-sensitivity searches for processes that violate baryon number by one or two units: free neutron–antineutron oscillation () via mixing, neutron–antineutron oscillation via regeneration from a sterile neutron state (), and neutron disappearance (n → n'); the effective process of neutron regeneration () is also possible. The program can be used to discover and characterize mixing in the neutron, antineutron and sterile neutron sectors. The experiment addresses topical open questions such as the origins of baryogenesis and the nature of dark matter, and is sensitive to scales of new physics substantially in excess of those available at colliders. A goal of the program is to open a discovery window to neutron conversion probabilities (sensitivities) by up to three orders of magnitude compared with previous searches. The opportunity to make such a leap in sensitivity tests should not be squandered. The experiment pulls together a diverse international team of physicists from the particle (collider and low energy) and nuclear physics communities, while also including specialists in neutronics and magnetics.
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- Blondel, A., et al.
(author)
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The SuperFGD Prototype charged particle beam tests
- 2020
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In: Journal of Instrumentation. - : IOP PUBLISHING LTD. - 1748-0221. ; 15:12
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Journal article (peer-reviewed)abstract
- A novel scintillator detector, the SuperFGD, has been selected as the main neutrino target for an upgrade of the T2K experiment ND280 near detector. The detector design will allow nearly 47r coverage for neutrino interactions at the near detector and will provide lower energy thresholds, significantly reducing systematic errors for the experiment. The SuperFGD is made of optically-isolated scintillator cubes of size 10 x 10 x 10 mm(3), providing the required spatial and energy resolution to reduce systematic uncertainties for future T2K runs. The SuperFGD for T2K will have close to two million cubes in a 1920 x 560 x 1840 mm(3) volume. A prototype made of 24 x 8 x 48 cubes was tested at a charged particle beamline at the CERN PS facility. The SuperFGD Prototype was instrumented with readout electronics similar to the future implementation for T2K. Results on electronics and detector response are reported in this paper, along with a discussion of the 3D reconstruction capabilities of this type of detector. Several physics analyses with the prototype data are also discussed, including a study of stopping protons.
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- Morita, Y, et al.
(author)
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ASXL1 mutations with serum EPO levels predict poor response to darbepoetin alfa in lower-risk MDS: W-JHS MDS01 trial
- 2022
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In: International journal of hematology. - : Springer Science and Business Media LLC. - 1865-3774 .- 0925-5710. ; 116:5, s. 659-668
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Journal article (peer-reviewed)abstract
- Darbepoetin alfa (DA) is used to treat anemia in lower-risk (IPSS low or int-1) myelodysplastic syndromes (MDS). However, whether mutations can predict the effectiveness of DA has not been examined. The present study aimed to determine predictive gene mutations. The primary endpoint was a correlation between the presence of highly frequent (≥ 10%) mutations and hematological improvement-erythroid according to IWG criteria 2006 by DA (240 μg/week) until week 16. The study included 79 patients (age 29–90, median 77.0 years; 52 [65.8%] male). Frequently (≥ 10%) mutated genes were SF3B1 (24 cases, 30.4%), TET2 (20, 25.3%), SRSF2 (10, 12.7%), ASXL1 (9, 11.4%), and DNMT3A (8, 10.1%). Overall response rate to DA was 70.9%. Multivariable analysis including baseline erythropoietin levels and red blood cell transfusion volumes as variables revealed that erythropoietin levels and mutations of ASXL1 gene were significantly associated with worse response (odds ratio 0.146, 95% confidence interval 0.042–0.503; p = 0.0023, odds ratio 0.175, 95% confidence interval 0.033–0.928; p = 0.0406, respectively). This study indicated that anemic patients who have higher erythropoietin levels and harbor ASXL1 gene mutations may respond poorly to DA. Alternative strategies are needed for the treatment of anemia in this population. Trial registration number and date of registration: UMIN000022185 and 09/05/2016.
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- Prananingrum, W, et al.
(author)
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Bone ingrowth of various porous titanium scaffolds produced by a moldless and space holder technique : an in vivo study in rabbits
- 2016
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In: Biomedical Materials. - : Institute of Physics Publishing (IOPP). - 1748-6041 .- 1748-605X. ; 11:1
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Journal article (peer-reviewed)abstract
- Porous titanium has long been desired as a bone substitute material because of its ability to reduce the stress shielding in supporting bone. In order to achieve the various pore structures, we have evolved a moldless process combined with a space holder technique to fabricate porous titanium. This study aims to evaluate which pore size is most suitable for bone regeneration using our process. The mixture comprising Ti powder, wax binder and PMMA spacer was prepared manually at 70 °C which depended on the mixing ratio of each group. Group 1 had an average pore size of 60 μm, group 2 had a maximum pore size of 100 μm, group 3 had a maximum pore size of 200 μm and group 4 had a maximum pore size of 600 μm. These specimens were implanted into rabbit calvaria for three and 20 weeks. Thereafter, histomorphometrical evaluation was performed. In the histomorphometrical evaluation after three weeks, the group with a 600 μm pore size showed a tendency to greater bone ingrowth. However, after 20 weeks the group with a pore size of 100 μm showed significantly greater bone ingrowth than the other groups. This study suggested that bone regeneration into porous titanium scaffolds is pore size-dependent, while bone ingrowth was most prominent for the group with 100 μm-sized pores after 20 weeks in vivo.
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- Antonova, M., et al.
(author)
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Synchronization of the distributed readout frontend electronics of the Baby MIND detector
- 2017
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In: 2017 XXVI International Scientific Conference Electronics (ET). - : IEEE. - 9781538617533
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Conference paper (peer-reviewed)abstract
- Baby MIND is a new downstream muon range detector for the WGASCI experiment. This article discusses the distributed readout system and its timing requirements. The paper presents the design of the synchronization subsystem and the results of its test.
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- Fan, G. W., et al.
(author)
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Density distribution of 8Li and 8B$ and capture reaction at low energy
- 2015
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In: Phys. Rev. C. ; 91
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Journal article (peer-reviewed)abstract
- Reaction cross sections of 8Li on stable targets were measured at intermediate energies. With the existing experimental data of interaction cross sections at 790 MeV/nucleon the nucleon density distribution of 8Liwas extracted by the use of the modified Glauber model. Meanwhile, the existing data of 8B have been also reanalyzed. Structures of 8Li and 8B were compared through the density. On the basis of dilute surface densities, the discussion of 7Li(n,γ)8Li and 7Be(p,γ)8B capture reactions was performed within the framework of the direct capture reaction mechanism. The calculations agreed quite well with the experimental data as well as other analyses.
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18. |
- Fan, G. W., et al.
(author)
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Structure of 8Li from a reaction cross-section measurement
- 2014
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In: Phys. Rev. C. - American Physical Society. ; 90, s. 044321-
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Journal article (peer-reviewed)abstract
- We have precisely measured reaction cross sections (σR) for 8Li using 9Be, 12C, 27Al, and proton targets at intermediate energies by the transmission method. From the energy dependence of the σR including the high energy data, the density distribution of 8Li was deduced through a modified Glauber model. It is shown that 8Li has a shorter tail structure in the density as compared with that of 8B and the matter radius of 8Li is similar to those of the other nonhalo Li isotopes. The result is consistent with the previous experiments that there is a tendency for 8Li to be a skin nucleus.
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- Lu, Guo-Wei, 1976, et al.
(author)
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16-QAM transmitter using monolithically integrated quad Mach-Zehnder IQ modulator
- 2010
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In: 36th European Conference and Exhibition on Optical Communication, ECOC 2010; Torino; Italy; 19 September 2010 through 23 September 2010. - 9781424485352 ; 1-2
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Conference paper (peer-reviewed)abstract
- We experimentally demonstrate an optical 16-QAM transmitter using a monolithically integrated quad- Mach-Zehnder in-phase/quadrature (QMZ-IQ) modulator with binary driving electronics.
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- Lu, Guo-Wei, 1976, et al.
(author)
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Monolithically integrated quad mach-zehnder IQ modulator for optical 16-QAM generation
- 2010
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In: Lasers and Electro-Optics/Quantum Electronics and Laser Science Conference: 2010 Laser Science to Photonic Applications, CLEO/QELS 2010; San Jose, CA; United States; 16 May 2010 through 21 May 2010. - 9781557528902 ; , s. Art. no. 5500521-
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Conference paper (peer-reviewed)abstract
- We experimentally demonstrate a 16-QAM transmitter using a monolithicallyintegrated quad Mach-Zehnder in-phase/quadrature (QMZ-IQ) modulator with binary driving electronics.
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- Teke, K., et al.
(author)
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Multi-technique comparison of troposphere zenith delays and gradients during CONT08
- 2011
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In: Journal of Geodesy. - : Springer Science and Business Media LLC. - 0949-7714 .- 1432-1394. ; 85:7, s. 395-413
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Journal article (peer-reviewed)abstract
- CONT08 was a 15 days campaign of continuous Very Long Baseline Interferometry (VLBI) sessions during the second half of August 2008 carried out by the International VLBI Service for Geodesy and Astrometry (IVS). In this study, VLBI estimates of troposphere zenith total delays (ZTD) and gradients during CONT08 were compared with those derived from observations with the Global Positioning System (GPS), Doppler Orbitography and Radiopositioning Integrated by Satellite (DORIS), and water vapor radiometers (WVR) co-located with the VLBI radio telescopes. Similar geophysical models were used for the analysis of the space geodetic data, whereas the parameterization for the least-squares adjustment of the space geodetic techniques was optimized for each technique. In addition to space geodetic techniques and WVR, ZTD and gradients from numerical weather models (NWM) were used from the European Centre for Medium-Range Weather Forecasts (ECMWF) (all sites), the Japan Meteorological Agency (JMA) and Cloud Resolving Storm Simulator (CReSS) (Tsukuba), and the High Resolution Limited Area Model (HIRLAM) (European sites). Biases, standard deviations, and correlation coefficients were computed between the troposphere estimates of the various techniques for all eleven CONT08 co-located sites. ZTD from space geodetic techniques generally agree at the sub-centimetre level during CONT08, and-as expected-the best agreement is found for intra-technique comparisons: between the Vienna VLBI Software and the combined IVS solutions as well as between the Center for Orbit Determination (CODE) solution and an IGS PPP time series; both intra-technique comparisons are with standard deviations of about 3-6 mm. The best inter space geodetic technique agreement of ZTD during CONT08 is found between the combined IVS and the IGS solutions with a mean standard deviation of about 6 mm over all sites, whereas the agreement with numerical weather models is between 6 and 20 mm. The standard deviations are generally larger at low latitude sites because of higher humidity, and the latter is also the reason why the standard deviations are larger at northern hemisphere stations during CONT08 in comparison to CONT02 which was observed in October 2002. The assessment of the troposphere gradients from the different techniques is not as clear because of different time intervals, different estimation properties, or different observables. However, the best inter-technique agreement is found between the IVS combined gradients and the GPS solutions with standard deviations between 0.2 and 0.7 mm.
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