Direct Integration of the Collisionless Boltzmann Equation in Six-dimensional Phase Space: Self-gravitating Systems

We present a scheme for numerical simulations of collisionless self-gravitating systems which directly integrates the Vlasov--Poisson equations in six-dimensional phase space. By the results from a suite of large-scale numerical simulations, we demonstrate that the present scheme can simulate collisionless self-gravitating systems properly. The integration scheme is based on the positive flux conservation method recently developed in plasma physics. We test the accuracy of our code by performing several test calculations including the stability of King spheres, the gravitational instability and the Landau damping. We show that the mass and the energy are accurately conserved for all the test cases we study. The results are in good agreement with linear theory predictions and/or analytic solutions. The distribution function keeps the property of positivity and remains non-oscillatory. The largest simulations are run on 64^6 grids. The computation speed scales well with the number of processors, and thus our code performs efficiently on massively parallel supercomputers.Comment: 35 pages, 19 figures. Submitted to the Astrophysical Journa

RNAウイルスに対する迅速な全ゲノム決定法の構築

RNA viruses are the etiological agents of many infectious diseases. Since RNA viruses are error-prone during genome replication, rapid, accurate and economical whole RNA viral genome sequence determination is highly demanded. Next generation sequencing (NGS) techniques perform whole viral genome sequencing due to their high-throughput sequencing capacity. However, the NGS techniques involve a significant burden for sample preparation. Since to generate complete viral genome coverage, genomic nucleic acid enrichment is required by reverse transcription PCR using virus-specific primers or by viral particle concentration. Furthermore, conventional NGS techniques cannot determine the 5′ and 3′ terminal sequences of the RNA viral genome. Therefore, the terminal sequences are determined one by one using rapid amplification of cDNA ends (RACE). However, since some RNA viruses have segmented genomes, the burden of the determination using RACE is proportional to the number of segments. To date, there is only one study attempting whole genome sequencing of multiple RNA viruses without using above mentioned methods, but the generated sequences’ accuracy compared to the reference sequences was up to 97% and did not reach 100% due to the low read depth. Hence, we established novel methods, named PCR-NGS and RCA-NGS, that were optimized for an NGS machine, MinION. These methods do not require nucleic acid amplification with virus-specific PCR primers, physical viral particle enrichment, and RACE. These methods enable whole RNA viral genome sequencing by combining the following techniques: (1) removal of unwanted DNA and RNA other than the RNA viral genome by nuclease treatment; (2) the terminal of viral genome sequence determination by barcoded linkers ligation; (3) amplification of the viral genomic cDNA using ligated linker sequences-specific PCR or an isothermal DNA amplification technique, such as rolling circle amplification (RCA). The established method was evaluated using isolated RNA viruses with single-stranded, double-stranded, positive-stranded, negative-stranded, non-segmented or multi-segmented genomes. As a result, all the viral genome sequences could be determined with 100% accuracy, and these mean read depths were greater than 2,500×, at least using either of the methods. This method should allow for easy and economical determination of accurate RNA viral genomes.権利情報：© 2023 Misu, Yoshikawa, Sugimoto, Takamatsu, Kurosu, Ouji, Yoshikawa, Shimojima, Ebihara and Saijo. This is an open-access article distributed under　the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is　permitted which does not comply with these terms

Single cell analysis of neutrophils NETs by Microscopic LSPR imaging system

A simple microengraving cell monitoring method for neutrophil extracellular traps (NETs) released from single neutrophils has been realized using a polydimethylsiloxane (PDMS) microwell array (MWA) sheet on a plasmon chip platform. An imbalance between NETs formation and the succeeding degradation (NETosis) are considered associated with autoimmune disease and its pathogenesis. Thus, an alternative platform that can conduct monitoring of this activity on single cell level at minimum cost but with great sensitivity is greatly desired. The developed MWA plasmon chips allow single cell isolation of neutrophils from 150 μL suspension (6.0 × 105 cells/mL) with an efficiency of 36.3%; 105 microwells with single cell condition. To demonstrate the utility of the chip, trapped cells were incubated between 2 to 4 h after introducing with 100 nM phorbol 12- myristate 13-acetate (PMA) before measurement. Under observation using a hyperspectral imaging system that allows high-throughput screening, the neutrophils stimulated by PMA solution show a significant release of fibrils and NETs after 4 h, with observed maximum areas between 314–758 μm2. An average absorption peak wavelength shows a redshift of Δλ = 1.5 nm as neutrophils release NETs

Coreference based event-argument relation extraction on biomedical text

This paper presents a new approach to exploit coreference information for extracting event-argument (E-A) relations from biomedical documents. This approach has two advantages: (1) it can extract a large number of valuable E-A relations based on the concept of salience in discourse; (2) it enables us to identify E-A relations over sentence boundaries (cross-links) using transitivity of coreference relations. We propose two coreference-based models: a pipeline based on Support Vector Machine (SVM) classifiers, and a joint Markov Logic Network (MLN). We show the effectiveness of these models on a biomedical event corpus. Both models outperform the systems that do not use coreference information. When the two proposed models are compared to each other, joint MLN outperforms pipeline SVM with gold coreference information

[3H]9-Methyl-7-bromoeudistomin D, a caffeine-like powerful Ca2+ releaser, binds to caffeine-binding sites distinct from the ryanodine receptors in brain microsomes

Abstract[3H]9-Methyl-7-bromoeudistomin D ([3H]MBED), the most powerful Ca2+ releaser from sarcoplasmic reticulum, specifically bound to the brain microsomes. Caffeine competitively inhibited [3H]MBED binding. [3H]MBED binding was markedly blocked by procaine, whereas that was enhanced by adenosine-5′-(β,γ-methylene)triphosphate. The Bmax value was 170 times more than that of [3H]ryanodine binding. The profile of sucrose-density gradient centrifugation of solubilized microsomes indicated that [3H]MBED binding protein was different from [3H]ryanodine binding protein. These results suggest that there are MBED/caffeine-binding sites in brain that are distinct from the ryanodine receptor and that MBED becomes an essential molecular probe for characterizing caffeine-binding protein in the central nervous system

大強度相対論的電子ビーム・プラズマ相互作用による強いラングミュア乱流電場の分光測定及び高出力広帯域マイクロ波放射との相関に関する研究

取得学位：博士(理学)，学位授与番号：博甲第122号，学位授与年月日：平成6年9月30日,学位授与年：199

ミエン語（勉語）藍山匯源方言調査報告

調査報

MOIRCS Deep Survey. X. Evolution of Quiescent Galaxies as a Function of Stellar Mass at 0.5<z<2.5

We study the evolution of quiescent galaxies at 0.5<z<2.5 as a function of stellar mass, using very deep NIR imaging data taken with the Multi-Object Infrared Camera and Spectrograph on the Subaru Telescope in the GOODS-North region. The deep NIR data allow us to construct a stellar mass-limited sample of quiescent galaxies down to ~10^{10} Msun even at z~2 for the first time. We selected quiescent galaxies with age/tau>6 by performing SED fitting of the multi broad-band photometry from the U to Spitzer 5.8um bands with the population synthesis model of Bruzual & Charlot (2003) where exponentially decaying star formation histories are assumed. The number density of quiescent galaxies increases by a factor of ~3 from 1.0<z<1.5 to 0.5<z<1.0, and by a factor of ~10 from 1.5<z<2.5 to 0.5<z<1.0, while that of star-forming galaxies with age/tau<4 increases only by factors of ~2 and ~3 in the same redshift ranges. At 0.5<z<2.5, the low-mass slope of the stellar mass function of quiescent galaxies is alpha ~ 0 -- 0.6, which is significantly flatter than those of star-forming galaxies (alpha ~ -1.3 -- -1.5). As a result, the fraction of quiescent galaxies in the overall galaxy population increases with stellar mass in the redshift range. The fraction of quiescent galaxies at 10^{11}-10^{11.5} Msun increases from ~20-30% at z~2 to ~40-60% at z~0.75, while that at 10^{10}-10^{10.5} Msun increases from <~ 5% to ~15% in the same redshift range. These results could suggest that the quenching of star formation had been more effective in more massive galaxies at 1<~z<~2. Such a mass-dependent quenching could explain the rapid increase of the number density of ~M* galaxies relative to lower-mass galaxies at z >~ 1-1.5.Comment: 12 pages, 7 figures, accepted for publication in PASJ (Subaru special issue). Updated to accepted versio

ARGOT: Accelerated radiative transfer on grids using oct-tree

We present two types of numerical prescriptions that accelerate the radiative transfer calculation around point sources within a three-dimensional Cartesian grid by using the oct-tree structure for the distribution of radiation sources. In one prescription, distant radiation sources are grouped as a bright extended source when the group's angular size, $\theta_{\rm s}$, is smaller than a critical value, $\theta_{\rm crit}$, and radiative transfer is solved on supermeshes whose angular sizes are similar to that of the group of sources. The supermesh structure is constructed by coarse-graining the mesh structure. With this method, the computational time scales with $N_{\rm m} \log(N_{\rm m}) \log(N_{\rm s})$ where $N_{\rm m}$ and $N_{\rm s}$ are the number of meshes and that of radiation sources, respectively. While this method is very efficient, it inevitably overestimates the optical depth when a group of sources acts as an extended powerful radiation source and affects distant meshes. In the other prescription, a distant group of sources is treated as a bright point source ignoring the spatial extent of the group and the radiative transfer is solved on the meshes rather than the supermeshes. This prescription is simply a grid-based version of {\scriptsize START} by Hasegawa & Umemura and yields better results in general with slightly more computational cost ($\propto N_{\rm m}^{4/3} \log(N_{\rm s})$) than the supermesh prescription. Our methods can easily be implemented to any grid-based hydrodynamic codes and are well-suited to the adaptive mesh refinement methods.Comment: 13 pages, 12 figures, submitted to MNRAS. Revised according to referee's comment