Quantitative evaluation of temporal partial coherence using 3D Fourier transforms of through-focus TEM images

AbstractWe evaluate the temporal partial coherence of transmission electron microscopy (TEM) using the three-dimensional (3D) Fourier transform (FT) of through-focus images. Young's fringe method often indicates the unexpected high-frequency information due to non-linear imaging terms. We have already used the 3D FT of axial (non-tilted) through-focus images to reduce the effect of non-linear terms on the linear imaging term, and demonstrated the improvement of monochromated lower-voltage TEM performance [Kimoto et al., Ultramicroscopy 121 (2012) 31–39]. Here we apply the 3D FT method with intentionally tilted incidence to normalize various factors associated with a TEM specimen and an imaging device. The temporal partial coherence of two microscopes operated at 30, 60 and 80kV is evaluated. Our method is applicable to such cases where the non-linear terms become more significant in lower acceleration voltage or aberration-corrected high spatial resolution TEM

High-pressure synthesis, crystal structure determination, and a Ca substitution study of the metallic rhodium oxide NaRh2O4

The sodium rhodate NaRh2O4 was synthesized for the first time and characterized by neutron and X-ray diffraction studies and measurements of magnetic susceptibility, specific heat, electrical resistivity, and the Seebeck coefficient. NaRh2O4 crystallizes in the CaFe2O4-type structure, which is comprised of a characteristic RhO6 octahedral network. The compound is metallic in nature, probably reflecting the 1:1 mixed valence character of Rh(III) and Rh(IV) in the network. For further studies of the compound, the Rh valence was varied significantly by means of an aliovalent substitution: the full-range solid solution between NaRh2O4 and CaRh2O 4 was achieved and characterized as well. The metallic state was dramatically altered, and a peculiar magnetism developed in the low Na concentration range

A Rhombic Dodecahedral Honeycomb Structure with Cation Vacancy Ordering in a γ-Ga2O3 Crystal

The crystal structure of a γ-Ga2O3 layer grown epitaxially on an MgO substrate by a vapor phase transport method was investigated by transmission electron microscopy, electron diffraction, and scanning transmission electron microscopy with aberration correctors. Some forbidden reflections were excited in electron diffraction patterns by double reflection from the vicinity of the substrate interface. Phase boundaries are observed in atomic column images using high-angle annular dark field images. A structure model is proposed to explain the experimental results. Cation vacancy ordering is introduced in the structure model to distort the γ-Ga2O3 crystal lattice along one axis and reduce the lattice mismatch with the substrate. Some grains are formed and alter the directions to reduce the distortion for the other axis. The grains are stacked with {110} phase boundaries and form a rhombic dodecahedral honeycomb. The rhombic dodecahedral honeycomb structure model with cation vacancy ordering is stabilized by the lattice mismatch between the γ-Ga2O3 crystal and the MgO substrate, and it disappears at a depth of 170 nm from the interface

Experimental inspection of a computationally-designed NiCrMnSi Heusler alloy with high Curie temperature

Nowadays advanced magnetic tunnel junction applications demand very high tunnel magnetoresistance at room temperature, thus it is quite important to explore high Curie temperature Tc half-metallic Heusler alloys. In this article rst-principles calculation unveiled that NiCrMnSi has Tc of 1200 K comparable to that of the traditional Co2MnSi Heusler alloys, even though it does not contain Co element. In addition, we examined whether NiCrMnSi Heulser phase lms can be obtained by a magnetron sputtering on MgO substrates. The results of the structural analysis and rst-principles calculations indicated that NiCrMnSi Heusler phase is metastable. A possible route to obtain metastable NiCrMnSi Heusler alloy is to utilize appropriate templates

Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. 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

Mechanical design of the optical modules intended for IceCube-Gen2

IceCube-Gen2 is an expansion of the IceCube neutrino observatory at the South Pole that aims to increase the sensitivity to high-energy neutrinos by an order of magnitude. To this end, about 10,000 new optical modules will be installed, instrumenting a fiducial volume of about 8 km3. Two newly developed optical module types increase IceCube’s current sensitivity per module by a factor of three by integrating 16 and 18 newly developed four-inch PMTs in specially designed 12.5-inch diameter pressure vessels. Both designs use conical silicone gel pads to optically couple the PMTs to the pressure vessel to increase photon collection efficiency. The outside portion of gel pads are pre-cast onto each PMT prior to integration, while the interiors are filled and cast after the PMT assemblies are installed in the pressure vessel via a pushing mechanism. This paper presents both the mechanical design, as well as the performance of prototype modules at high pressure (70 MPa) and low temperature (−40∘C), characteristic of the environment inside the South Pole ice

The next generation neutrino telescope: IceCube-Gen2

The IceCube Neutrino Observatory, a cubic-kilometer-scale neutrino detector at the geographic South Pole, has reached a number of milestones in the field of neutrino astrophysics: the discovery of a high-energy astrophysical neutrino flux, the temporal and directional correlation of neutrinos with a flaring blazar, and a steady emission of neutrinos from the direction of an active galaxy of a Seyfert II type and the Milky Way. The next generation neutrino telescope, IceCube-Gen2, currently under development, will consist of three essential components: an array of about 10,000 optical sensors, embedded within approximately 8 cubic kilometers of ice, for detecting neutrinos with energies of TeV and above, with a sensitivity five times greater than that of IceCube; a surface array with scintillation panels and radio antennas targeting air showers; and buried radio antennas distributed over an area of more than 400 square kilometers to significantly enhance the sensitivity of detecting neutrino sources beyond EeV. This contribution describes the design and status of IceCube-Gen2 and discusses the expected sensitivity from the simulations of the optical, surface, and radio components