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- Wang, QBS, et al.
(författare)
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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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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1, s. 4830-
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Tidskriftsartikel (refereegranskat)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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- Yabuta, Hikaru, et al.
(författare)
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Macromolecular organic matter in samples of the asteroid (162173) Ryugu
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 379:6634
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Tidskriftsartikel (refereegranskat)abstract
- Samples of the carbonaceous asteroid (162173) Ryugu were collected and brought to Earth by the Hayabusa2 spacecraft. We investigated the macromolecular organic matter in Ryugu samples and found that it contains aromatic and aliphatic carbon, ketone, and carboxyl functional groups. The spectroscopic features of the organic matter are consistent with those in chemically primitive carbonaceous chondrite meteorites that experienced parent-body aqueous alteration (reactions with liquid water). The morphology of the organic carbon includes nanoglobules and diffuse carbon associated with phyllosilicate and carbonate minerals. Deuterium and/or nitrogen-15 enrichments indicate that the organic matter formed in a cold molecular cloud or the presolar nebula. The diversity of the organic matter indicates variable levels of aqueous alteration on Ryugus parent body.
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- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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- Annese, Emilia, et al.
(författare)
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Nonvortical Rashba Spin Structure on a Surface with C1h Symmetry
- 2016
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Ingår i: Physical Review Letters. - 0031-9007. ; 117:1
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Tidskriftsartikel (refereegranskat)abstract
- A totally anisotropic peculiar Rashba-Bychkov (RB) splitting of electronic bands was found on the Tl/Si(110)-(1×1) surface with C1h symmetry by angle- and spin-resolved photoelectron spectroscopy and first-principles theoretical calculation. The constant energy contour of the upper branch of the RB split band has a warped elliptical shape centered at a k point located between Γ and the edge of the surface Brillouin zone, i.e., at a point without time-reversal symmetry. The spin-polarization vector of this state is in-plane and points almost the same direction along the whole elliptic contour. This novel nonvortical RB spin structure is confirmed as a general phenomenon originating from the C1h symmetry of the surface.
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- Kimura, K., et al.
(författare)
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End-to-end throughput aware adaptive channel and route selection for enhancing system throughput in multi-hop radio networks
- 2008
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Konferensbidrag (refereegranskat)abstract
- A distributed power, channel, and route selection scheme for multi-hop radio networks is proposed by extending Multichannel Asynchronous Distributed Pricing (MADP) algorithm, which is a power and channel selection scheme for single-hop radio networks. MADP algorithm achieves suboptimal system throughput in single-hop radio networks, however, since MADP algorithm allocates more resources to links with good quality, there may be a large difference in throughput among communication links. Particularly in multi-hop radio networks, MADP algorithm might not necessarily achieve high system throughput because the link with the lowest throughput limits the end-to-end throughput of a given multi-hop route. In order to achieve high system throughput in multi-hop radio networks, a modification of MADP algorithm named End-to-end Throughput Aware MADP (ETA-MADP) algorithm is proposed. It is proved that all links in a given multi-hop route have the same throughput through the use of ETA-MADP algorithm. Simulation results reveal that the introduction of the proposed algorithm achieves high spectral efficiency in multi-hop radio networks even with lower transmit power compared to that in single-hop radio networks.
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- Otsubo, Toshimichi, et al.
(författare)
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Effective expansion of satellite laser ranging network to improve global geodetic parameters
- 2016
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Ingår i: Earth, Planets and Space. - : Springer Science and Business Media LLC. - 1880-5981 .- 1343-8832. ; 68:1
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study is to find an effective way to expand the ground tracking network of satellite laser ranging on the assumption that a new station is added to the existing network. Realistic numbers of observations for a new station are numerically simulated, based on the actual data acquisition statistics of the existing stations. The estimated errors are compared between the cases with and without a new station after the covariance matrices are created from a simulation run that contains six-satellite-combined orbit determination. While a station placed in the southern hemisphere is found to be useful in general, it is revealed that the most effective place differs according to the geodetic parameter. The X and Y components of the geocenter and the sectoral terms of the Earth’s gravity field are largely improved by a station in the polar regions. A middle latitude station best contributes to the tesseral gravity terms, and, to a lesser extent, a low latitude station best performs for the Z component of the geocenter and the zonal gravity terms.
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- Sakamoto, Kazuyuki, et al.
(författare)
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Valley spin polarization by using the extraordinary Rashba effect on silicon
- 2013
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Ingår i: Nature Communications. - : Nature Publishing Group: Nature Communications. - 2041-1723. ; 4:2073
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Tidskriftsartikel (refereegranskat)abstract
- The addition of the valley degree of freedom to a two-dimensional spin-polarized electronic system provides the opportunity to multiply the functionality of next-generation devices. So far, however, such devices have not been realized due to the difficulty to polarize the valleys, which is an indispensable step to activate this degree of freedom. Here we show the formation of 100% spin-polarized valleys by a simple and easy way using the Rashba effect on a system with C-3 symmetry. This polarization, which is much higher than those in ordinary Rashba systems, results in the valleys acting as filters that can suppress the backscattering of spin-charge. The present system is formed on a silicon substrate, and therefore opens a new avenue towards the realization of silicon spintronic devices with high efficiency.
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- Shibata, Naotaka, et al.
(författare)
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Channel-Gain-Based Transmission Scheduling for Cooperative Relaying
- 2010
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Ingår i: IEICE transactions on communications. - 0916-8516 .- 1745-1345. ; E93B:3, s. 776-779
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Tidskriftsartikel (refereegranskat)abstract
- A cooperative relaying. system with transmission scheduling is investigated Cooperative relaying, is composed of multiple links because the source;ends the data to more than one receiver, and the destination receive; multiple data transmitted by more than one transmitter Therefore. tithe source can transmit the data when the channel gains of the links are high, it is not clear which channel gains should he high in order to achieve high spectral efficiency In the present letter. the spectral efficiency of a cooperative relay me system is theoretically derived under the assumption that the source transmits the data only when the channel gains of links are above certain threshold values Numerical results reveal that a high spectral efficiency can be achieved by assuring a high channel gain for the link with the highest average received power among links to the destination.
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