| 1. |
- Namkoong, H, et al.
(author)
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DOCK2 is involved in the host genetics and biology of severe COVID-19
- 2022
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 609:7928, s. 754-
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Journal article (peer-reviewed)abstract
- Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge1–5. Here we conducted a genome-wide association study (GWAS) involving 2,393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3,289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target.
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| 2. |
- 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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| 3. |
- 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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| 4. |
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| 5. |
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| 6. |
- Kato, Norihiro, et al.
(author)
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Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation
- 2015
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In: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 47:11, s. 1282-1293
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Journal article (peer-reviewed)abstract
- We carried out a trans-ancestry genome-wide association and replication study of blood pressure phenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 new loci to be associated with blood pressure (P = 3.9 × 10−11 to 5.0 × 10−21). The sentinel blood pressure SNPs are enriched for association with DNA methylation at multiple nearby CpG sites, suggesting that, at some of the loci identified, DNA methylation may lie on the regulatory pathway linking sequence variation to blood pressure. The sentinel SNPs at the 12 new loci point to genes involved in vascular smooth muscle (IGFBP3, KCNK3, PDE3A and PRDM6) and renal (ARHGAP24, OSR1, SLC22A7 and TBX2) function. The new and known genetic variants predict increased left ventricular mass, circulating levels of NT-proBNP, and cardiovascular and all-cause mortality (P = 0.04 to 8.6 × 10−6). Our results provide new evidence for the role of DNA methylation in blood pressure regulation.
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| 7. |
- Molina, F., et al.
(author)
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Tz=-1 → 0 β-Decays of 54Ni, 50Fe, 46Cr, and 42Ti and Comparison With Mirror (3He,t) Measurements
- 2015
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In: Physical Review C (Nuclear Physics). - 0556-2813. ; 91:1
-
Journal article (peer-reviewed)abstract
- We have studied the β decay of the Tz=−1, f7/2 shell nuclei Ni54, Fe50, Cr46, and Ti42 produced in fragmentation reactions. The proton separation energies in the daughter Tz=0 nuclei are relatively large (≈4–5 MeV) so studies of the γ rays are essential. The experiments were performed at GSI as part of the Stopped-beam campaign with the RISING setup consisting of 15 Euroball Cluster Ge detectors. From the newly obtained high precision β-decay half-lives, excitation energies, and β branching ratios, we were able to extract Fermi and Gamow-Teller transition strengths in these β decays. With these improved results it was possible to compare in detail the Gamow-Teller (GT) transition strengths observed in beta decay including a sensitivity limit with the strengths of the Tz=+1 to Tz=0 transitions derived from high resolution (3He,t) reactions on the mirror target nuclei at RCNP, Osaka. The accumulated B(GT) strength obtained from both experiments looks very similar although the charge exchange reaction provides information on a broader energy range. Using the “merged analysis” one can obtain a full picture of the B(GT) over the full Qβ range. Looking at the individual transitions some differences are observed, especially for the weak transitions. Their possible origins are discussed.
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| 8. |
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| 9. |
- Ryu, Y. -H., et al.
(author)
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OGLE-2016-BLG-1190Lb : The First Spitzer Bulge Planet Lies Near the Planet/Brown-dwarf Boundary
- 2018
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In: Astronomical Journal. - : American Astronomical Society. - 0004-6256 .- 1538-3881. ; 155:1
-
Journal article (peer-reviewed)abstract
- We report the discovery of OGLE-2016-BLG-1190Lb, which is likely to be the first Spitzer microlensing planet in the Galactic bulge/ bar, an assignation that can be confirmed by two epochs of high-resolution imaging of the combined source-lens baseline object. The planet's mass, M-p = 13.4 +/- 0.9 M-J, places it right at the deuteriumburning limit, i. e., the conventional boundary between planets and brown dwarfs. Its existence raises the question of whether such objects are really planets (formed within the disks of their hosts) or failed stars (lowmass objects formed by gas fragmentation). This question may ultimately be addressed by comparing disk and bulge/bar planets, which is a goal of the Spitzer microlens program. The host is a G dwarf, M-host = 0.89. +/- 0.07 M-circle dot, and the planet has a semimajor axis a similar to 2.0 au. We use Kepler K2 Campaign 9 microlensing data to break the lens-mass degeneracy that generically impacts parallax solutions from Earth-Spitzer observations alone, which is the first successful application of this approach. The microlensing data, derived primarily from near-continuous, ultradense survey observations from OGLE, MOA, and three KMTNet telescopes, contain more orbital information than for any previous microlensing planet, but not quite enough to accurately specify the full orbit. However, these data do permit the first rigorous test of microlensing orbital-motion measurements, which are typically derived from data taken over < 1% of an orbital period.
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| 10. |
- Fransson, Jens H.M., et al.
(author)
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Transition induced by free-stream turbulence
- 2005
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In: Journal of Fluid Mechanics. - 0022-1120 .- 1469-7645. ; 527, s. 1-25
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Journal article (peer-reviewed)abstract
- Free-stream turbulence (FST) is perhaps the most important source inducing by-pass transition in boundary layer flows. The present study describes the initial energy growth of streamwise-oriented disturbances in the boundary layer originating from the presence of FST with intensities between 1.4% and 6.7%, but the study is mainly focused on the modelling of the transition zone. For this study three passive and one active turbulence-gene rating grids were used. The active grid was used in order to vary the turbulence intensity (Tu(2)) without changing the setup in the test section. It is shown that the initial disturbance energy in the boundary layer is proportional to Tu(2). The experiments also show that the energy grows in linear proportion to the Reynolds number based on the downstream distance. Furthermore the transitional Reynolds number is shown to be inversely proportional to Tu(2) for the whole range of Tu studied. The intermittency in the transitional zone was determined and it was shown that the intermittency function has a universal shape if the downstream distance is scaled with the length of the transition zone. The Reynolds number based on this transition zone length was found to increase linearly with the transition Reynolds number; however it was also noted that this non-dimensional length has a minimum value. With these results we were able to formulate an expression for the spot production rate which has a better physical base than previous models.
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| 11. |
- Gould, A., et al.
(author)
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MOA-2010-BLG-523:" Failed Planet"= RS CVn Star
- 2013
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In: Astrophysical Journal. - 0004-637X. ; 763:2
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Journal article (peer-reviewed)abstract
- The Galactic bulge source MOA-2010-BLG-523S exhibited short-term deviations from a standard microlensing light curve near the peak of an A(max) similar to 265 high-magnification microlensing event. The deviations originally seemed consistent with expectations for a planetary companion to the principal lens. We combine long-term photometric monitoring with a previously published high-resolution spectrum taken near peak to demonstrate that this is an RS CVn variable, so that planetary microlensing is not required to explain the light-curve deviations. This is the first spectroscopically confirmed RS CVn star discovered in the Galactic bulge.
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| 12. |
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| 13. |
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| 14. |
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| 15. |
- Sumi, T., et al.
(author)
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The first Neptune analog or super-earth with a Neptune-like orbit : MOA-2013-BLG-605LB
- 2016
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In: Astrophysical Journal. - 0004-637X. ; 825:2
-
Journal article (peer-reviewed)abstract
- We present the discovery of the first Neptune analog exoplanet or super-Earth with a Neptune-like orbit, MOA-2013-BLG-605Lb. This planet has a mass similar to that of Neptune or a super-Earth and it orbits at 9 ∼ 14 times the expected position of the snow line, a snow, which is similar to Neptune's separation of 11 a snow from the Sun. The planet/host-star mass ratio is q = (3.6 ± 0.7) × 10-4 and the projected separation normalized by the Einstein radius is s = 2.39 ± 0.05. There are three degenerate physical solutions and two of these are due to a new type of degeneracy in the microlensing parallax parameters, which we designate "the wide degeneracy." The three models have (i) a Neptune-mass planet with a mass of Mp = 21-7 +6M⊕ orbiting a low-mass M-dwarf with a mass of Mh = 0.19-0.06 +0.05M⊙, (ii) a mini-Neptune with Mp = 7.9-1.2 +1.8M⊕ orbiting a brown dwarf host with Mh = 0.068-0.011 +0.019M⊙, and (iii) a super-Earth with Mp = 3.2-0.3 +0.5MM⊕ orbiting a low-mass brown dwarf host with Mh = 0.025-0.0004 +0.005M⊙, which is slightly favored. The 3D planet-host separations are 4.6-1.2 +4.7au, 2.1-0.2 +1.0au, and 0.94-0.02 +0.67au, which are 8.9-1.4 +10.5, 12-1 +7, or 14-1 +11 times larger than a snow for these models, respectively. Keck adaptive optics observations confirm that the lens is faint. This discovery suggests that low-mass planets with Neptune-like orbits are common. Therefore processes similar to the one that formed Neptune in our own solar system or cold super-Earths may be common in other solar systems.
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| 16. |
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| 17. |
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| 18. |
- Matsubara, N., et al.
(author)
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Neutron powder diffraction study of NaMn2O4 and Li0.92Mn2O4: Insights on spin-charge-orbital ordering
- 2020
-
In: Physical Review Research. - 2643-1564. ; 2:4
-
Journal article (peer-reviewed)abstract
- High-pressure synthesized quasi-one-dimensional NaMn2O4 and Li0.92Mn2O4 are both antiferromagnetic insulators. Here their atomic and magnetic structures are investigated using neutron powder diffraction. The present crystal structural analyses of NaMn2O4 reveal that a Mn3+/Mn4+ charge-ordering state exists even at low temperature (down to 1.5 K). It is evident that one of the Mn sites shows a strongly distorted Mn3+ octahedron due to the Jahn-Teller effect. Above T-N = 35 K, a two-dimensional short-range correlation is observed, as indicated by asymmetric diffuse scattering. Below T-N, two antiferromagnetic transitions are observed: (i) a commensurate long-range Mn3+ spin ordering below T-N1 = 35 K and (ii) an incommensurate Mn4+ spin ordering below T-N2 = 11 K. Surprisingly, the two antiferromagnetic orders are found to be independent of each other. The commensurate magnetic structure (k(C) = 0.5, 0.5, 0.5) follows the magnetic anisotropy of the local easy axes of Mn3+, while the incommensurate Mn4+ one shows a spin-density-wave or a cycloidal order with k(IC) = (0, 0, 0.216). For Li0.92Mn2O4, on the other hand, the absence of a long-range spin-ordered state is confirmed down to 1.5 K.
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| 19. |
- Matsubara, Nami, et al.
(author)
-
Neutron powder diffraction study of NaMn2O4 and Li0.92Mn2O4 : Insights on spin-charge-orbital ordering
- 2020
-
In: Physical Review Research. - : American Physical Society (APS). - 2643-1564. ; 2:4
-
Journal article (peer-reviewed)abstract
- High-pressure synthesized quasi-one-dimensional NaMn2O4 and Li0.92Mn2O4 are both antiferromagnetic insulators. Here their atomic and magnetic structures are investigated using neutron powder diffraction. The present crystal structural analyses of NaMn2O4 reveal that a Mn3+/Mn4+ charge-ordering state exists even at low temperature (down to 1.5 K). It is evident that one of the Mn sites shows a strongly distorted Mn3+ octahedron due to the Jahn-Teller effect. Above TN=35 K, a two-dimensional short-range correlation is observed, as indicated by asymmetric diffuse scattering. Below TN, two antiferromagnetic transitions are observed: (i) a commensurate long-range Mn3+ spin ordering below TN1=35 K and (ii) an incommensurate Mn4+ spin ordering below TN2=11 K. Surprisingly, the two antiferromagnetic orders are found to be independent of each other. The commensurate magnetic structure (kC=0.5,0.5,0.5) follows the magnetic anisotropy of the local easy axes of Mn3+, while the incommensurate Mn4+ one shows a spin-density-wave or a cycloidal order with kIC=(0,0,0.216). For Li0.92Mn2O4, on the other hand, the absence of a long-range spin-ordered state is confirmed down to 1.5 K.
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| 20. |
- Nocerino, Elisabetta, et al.
(author)
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Competition between magnetic interactions and structural instabilities leading to itinerant frustration in the triangular lattice antiferromagnet LiCrSe2
- 2023
-
In: Communications Materials. - : Springer Nature. - 2662-4443. ; 4:1
-
Journal article (peer-reviewed)abstract
- LiCrSe2 constitutes a recent valuable addition to the ensemble of two-dimensional triangular lattice antiferromagnets. In this work, we present a comprehensive study of the low temperature nuclear and magnetic structure established in this material. Being subject to a strong magnetoelastic coupling, LiCrSe2 was found to undergo a first order structural transition from a trigonal crystal system (P3 ¯ m1) to a monoclinic one (C2/m) at T s = 30 K. Such restructuring of the lattice is accompanied by a magnetic transition at T N = 30 K. Refinement of the magnetic structure with neutron diffraction data and complementary muon spin rotation analysis reveal the presence of a complex incommensurate magnetic structure with a up-up-down-down arrangement of the chromium moments with ferromagnetic double chains coupled antiferromagnetically. The spin axial vector is also modulated both in direction and modulus, resulting in a spin density wave-like order with periodic suppression of the chromium moment along the chains. This behavior is believed to appear as a result of strong competition between direct exchange antiferromagnetic and superexchange ferromagnetic couplings established between both nearest neighbor and next nearest neighbor Cr3+ ions. We finally conjecture that the resulting magnetic order is stabilized via subtle vacancy/charge order within the lithium layers, potentially causing a mix of two co-existing magnetic phases within the sample.
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| 21. |
- Ohishi, Kazuki, et al.
(author)
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The internal magnetic field in a ferromagnetic compound Y 2 Co 12 P 7
- 2023
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In: Journal of Physics: Conference Series. - : IOP Publishing. - 1742-6588 .- 1742-6596. ; 2462:1
-
Conference paper (peer-reviewed)abstract
- The internal magnetic field in a ferromagnetic compound, Y2Co12P7 with T C = 150 K, was studied with μ +SR using a powder sample down to 2 K. The wTF-μ +SR measurements revealed the presence of a sharp magnetic transition at T C = 151 K, and the ZF-μ +SR measurements clarified the formation of static magnetic order below T C. The presence of two muon spin precession signals in the ZF-μ +SR spectrum below T C indicates the existence of the two different muon sites in the lattice. By considering the muon sites and local spin densities at the muon sites predicted with DFT calculations, the ordered magnetic moments of Co were successfully determined.
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| 22. |
- Ohishi, Kazuki, et al.
(author)
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The internal magnetic field in a ferromagnetic compound Y2Co12P7
- 2023
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In: Proceedings 15th International Conference on Muon Spin Rotation, Relaxation and Resonance (SR). - : IOP Publishing. ; 2462
-
Conference paper (peer-reviewed)abstract
- The internal magnetic field in a ferromagnetic compound, Y2Co12P7 with T-C = 150 K, was studied with mu(+) SR using a powder sample down to 2 K. The wTF-mu(+) SR measurements revealed the presence of a sharp magnetic transition at T-C = 151 K, and the ZF-mu(+) SR measurements clarified the formation of static magnetic order below T-C. The presence of two muon spin precession signals in the ZF-mu(+) SR spectrum below TC indicates the existence of the two different muon sites in the lattice. By considering the muon sites and local spin densities at the muon sites predicted with DFT calculations, the ordered magnetic moments of Co were successfully determined.
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| 23. |
- Patrinos, George P., et al.
(author)
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Human variome project country nodes: Documenting genetic information within a country
- 2012
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In: Human Mutation. - : Hindawi Limited. - 1059-7794. ; 33:11, s. 1513-1519
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Journal article (peer-reviewed)abstract
- The Human Variome Project (http://www.humanvariomeproject.org) is an international effort aiming to systematically collect and share information on all human genetic variation. The two main pillars of this effort are gene/disease-specific databases and a network of Human Variome Project Country Nodes. The latter are nationwide efforts to document the genomic variation reported within a specific population. The development and successful operation of the Human Variome Project Country Nodes are of utmost importance to the success of Human Variome Project's aims and goals because they not only allow the genetic burden of disease to be quantified in different countries, but also provide diagnosticians and researchers access to an up-to-date resource that will assist them in their daily clinical practice and biomedical research, respectively. Here, we report the discussions and recommendations that resulted from the inaugural meeting of the International Confederation of Countries Advisory Council, held on 12th December 2011, during the 2011 Human Variome Project Beijing Meeting. We discuss the steps necessary to maximize the impact of the Country Node effort for developing regional and country-specific clinical genetics resources and summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects. Hum Mutat 33:15131519, 2012. (c) 2012 Wiley Periodicals, Inc.
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| 24. |
- Schmitt, T, et al.
(author)
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Resonant soft X-ray emission spectroscopy of doped and undoped vanadium oxides
- 2004
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In: Journal of Alloys and Compounds. - 0925-8388 .- 1873-4669. ; 362:1-2, s. 143-150
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Journal article (peer-reviewed)abstract
- Resonant soft X-ray emission (RSXE) spectra of NaV2O5, MoxV1-xO2 and V2O3 have been recorded for a series of excitation energies at resonances of the V L- and O K-absorption band. Resonant excitation allows us, firstly, to separate V 3d and O 2p projected density-of-states of the valence band and, secondly, to study charge-neutral low-energy excitations due to resonant inelastic X-ray scattering (RIXS). We found that both the V L- and the O K-emission spectra clearly show components originating from O 2p- and V 3d-states, reflecting the high degree of hybridization of the valence band in all compounds. At threshold excitation we observed that NaV2O5 spectra are dominated by RIXS whereas MoxV1-xO2 and V2O3 spectra show bandlike features, which may be due to differences in the correlation effects of the compounds. We compared the RSXE spectra with cluster model calculations, which gives a good account for NaV2O5 whereas the RSXE spectra of the other compounds show RIXS only at certain energies well above the threshold. In fact, we interpret the trend in the RSXE spectra of the MoxV1-xO2 compound system as a successive filling of the (rigid) V 3d band with increasing Mo content. (C) 2003 Elsevier B.V. All rights reserved.
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| 25. |
- Sugiyama, Jun, et al.
(author)
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Lithium diffusion in LiMnPO4 detected with mu +/- SR
- 2020
-
In: Physical Review Research. - : American Physical Society (APS). - 2643-1564. ; 2:3
-
Journal article (peer-reviewed)abstract
- Positive- and negative-muon spin rotation and relaxation (mu(+/-) SR) was first used to investigate fluctuations of nuclear magnetic fields in an olivine-type battery material, LiMnPO4, in order to clarify the diffusive species, namely, to distinguish between a mu(+) hopping among interstitial sites and Li+ ions diffusing in the LiMnPO4 lattice. Muon diffusion can only occur in mu+SR, because the implanted mu(-) forms a stable muonic atom at the lattice site, and therefore any change in linewidth measured with mu-SR must be due to Li+ diffusion. Since the two measurements exhibit a similar increase in the field fluctuation rate with temperature above 100 K, it is confirmed that Li+ ions are in fact diffusing. The diffusion coefficient of Li+ at 300 K and its activation energy were estimated to be 1.4(3) x 10(-10) cm(2)/s and 0.19(3) eV, respectively. Such combined mu(SR)-S-+/- measurements are thus shown to be a suitable tool for detecting ion diffusion in solid-state energy materials.
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| 26. |
- Takahashi, Harumi, et al.
(author)
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Correlations between the enantio- and regio-selective metabolisms of warfarin
- 2017
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In: Pharmacogenomics (London). - : Future Medicine Ltd. - 1462-2416 .- 1744-8042. ; 18:2, s. 133-142
-
Journal article (peer-reviewed)abstract
- Aim: To clarify whether the activities of multiple CYPs associated with warfarin metabolism would be correlated with each other. Methods: Oral clearances (CLpo) of warfarin enantiomers were estimated in 378 Chinese, Caucasians and African-Americans. The partial metabolic clearances (CLm) for 7-hydroxywarfarin enantiomers were also measured. In addition, CLpo and CLm were determined in a patient on warfarin and rifampicin. Results: Correlations between CLpo for warfarin enantiomers existed across the three populations. In addition, there was a significant correlation between the CLm for 7-hydroxylation of warfarin enantiomers. Under induced conditions by rifampicin, there were significant correlations between the enantio-and regio-selective metabolisms of warfarin. Conclusion: Metabolic activities of CYP2C9, CYP1A2 and CYP3A4 may be regulated by common transcriptional mechanism(s).
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| 27. |
- Tiemeyer, Michael, et al.
(author)
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GlyTouCan: an accessible glycan structure repository.
- 2017
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In: Glycobiology. - : Oxford University Press (OUP). - 1460-2423 .- 0959-6658. ; 27:10, s. 915-919
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Journal article (peer-reviewed)abstract
- Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data. In order to facilitate continued growth and expanded accessibility of glycomic data, the authors strongly encourage the glycomics community to coordinate the submission of their glycan structures to the GlyTouCan Repository and to make use of GlyTouCan identifiers in their communications and publications. The authors also deeply encourage journals to recommend a submission workflow in which submitted publications utilize GlyTouCan identifiers as a standard reference for explicitly describing glycan structures cited in manuscripts.
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| 28. |
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