| 1. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 2. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 3. |
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| 4. |
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| 5. |
- Namkoong, H, et al.
(författare)
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DOCK2 is involved in the host genetics and biology of severe COVID-19
- 2022
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 609:7928, s. 754-
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Tidskriftsartikel (refereegranskat)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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| 6. |
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| 7. |
- 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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| 8. |
- Carninci, P, et al.
(författare)
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The transcriptional landscape of the mammalian genome
- 2005
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 309:5740, s. 1559-1563
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Tidskriftsartikel (refereegranskat)abstract
- This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5′ and 3′ boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
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| 9. |
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| 10. |
- Forrest, ARR, et al.
(författare)
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A promoter-level mammalian expression atlas
- 2014
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 507:7493, s. 462-
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Tidskriftsartikel (refereegranskat)
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| 11. |
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| 12. |
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| 13. |
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| 14. |
- Noguchi, S, et al.
(författare)
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FANTOM5 CAGE profiles of human and mouse samples
- 2017
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
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Tidskriftsartikel (refereegranskat)abstract
- In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.
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| 15. |
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| 16. |
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| 17. |
- Miyoshi, Y., et al.
(författare)
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The energization and radiation in geospace (ERG) project
- 2012
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Ingår i: Dynamics of The Earth's Radiation Belts and Inner Magnetosphere. - : American Geophysical Union (AGU). - 9780875904894 ; , s. 103-116
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Konferensbidrag (refereegranskat)abstract
- The Energization and Radiation in Geospace (ERG) project for solar cycle 24 will explore how relativistic electrons in the radiation belts are generated during space storms. This geospace exploration project consists of three research teams: the ERG satellite observation team, the ground-based network observation team, and the integrated data analysis/simulation team. Satellite observation will provide in situ measurements of features such as the plasma distribution function, electric and magnetic fields, and plasma waves, whereas remote sensing by ground-based observations using, for example, HF radars, magnetometers, optical instruments, and radio wave receivers will provide the global state of the geospace. Various kinds of data will be integrated and compared with numerical simulations for quantitative understanding. Such a synergetic approach is essential for comprehensive understanding of relativistic electron generation/loss processes through crossenergy and cross-regional coupling in which different plasma populations and regions are dynamically coupled with each other. In addition, the ERG satellite will utilize a new and innovative measurement technique for wave-particle interactions that can directly measure the energy exchange process between particles and plasma waves. In this paper, we briefly review some of the profound problems regarding relativistic electron accelerations and losses that will be solved by the ERG project, and we provide an overview of the project.
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| 18. |
- Müller, T D, et al.
(författare)
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Ghrelin.
- 2015
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Ingår i: Molecular metabolism. - : Elsevier BV. - 2212-8778. ; 4:6, s. 437-60
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Tidskriftsartikel (refereegranskat)abstract
- The gastrointestinal peptide hormone ghrelin was discovered in 1999 as the endogenous ligand of the growth hormone secretagogue receptor. Increasing evidence supports more complicated and nuanced roles for the hormone, which go beyond the regulation of systemic energy metabolism.
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| 19. |
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| 20. |
- Fustin, JM, et al.
(författare)
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Methylation deficiency disrupts biological rhythms from bacteria to humans
- 2020
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Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1, s. 211-
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Tidskriftsartikel (refereegranskat)abstract
- The methyl cycle is a universal metabolic pathway providing methyl groups for the methylation of nuclei acids and proteins, regulating all aspects of cellular physiology. We have previously shown that methyl cycle inhibition in mammals strongly affects circadian rhythms. Since the methyl cycle and circadian clocks have evolved early during evolution and operate in organisms across the tree of life, we sought to determine whether the link between the two is also conserved. Here, we show that methyl cycle inhibition affects biological rhythms in species ranging from unicellular algae to humans, separated by more than 1 billion years of evolution. In contrast, the cyanobacterial clock is resistant to methyl cycle inhibition, although we demonstrate that methylations themselves regulate circadian rhythms in this organism. Mammalian cells with a rewired bacteria-like methyl cycle are protected, like cyanobacteria, from methyl cycle inhibition, providing interesting new possibilities for the treatment of methylation deficiencies.
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| 21. |
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| 22. |
- Milillo, A., et al.
(författare)
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Investigating Mercury's Environment with the Two-Spacecraft BepiColombo Mission
- 2020
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Ingår i: Space Science Reviews. - : Springer Science and Business Media LLC. - 0038-6308 .- 1572-9672. ; 216:5
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Forskningsöversikt (refereegranskat)abstract
- The ESA-JAXA BepiColombo mission will provide simultaneous measurements from two spacecraft, offering an unprecedented opportunity to investigate magnetospheric and exospheric dynamics at Mercury as well as their interactions with the solar wind, radiation, and interplanetary dust. Many scientific instruments onboard the two spacecraft will be completely, or partially devoted to study the near-space environment of Mercury as well as the complex processes that govern it. Many issues remain unsolved even after the MESSENGER mission that ended in 2015. The specific orbits of the two spacecraft, MPO and Mio, and the comprehensive scientific payload allow a wider range of scientific questions to be addressed than those that could be achieved by the individual instruments acting alone, or by previous missions. These joint observations are of key importance because many phenomena in Mercury's environment are highly temporally and spatially variable. Examples of possible coordinated observations are described in this article, analysing the required geometrical conditions, pointing, resolutions and operation timing of different BepiColombo instruments sensors.
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| 23. |
- Ramilowski, JA, et al.
(författare)
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Functional annotation of human long noncoding RNAs via molecular phenotyping
- 2020
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Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 30:7, s. 1060-1072
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Tidskriftsartikel (refereegranskat)abstract
- Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
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| 24. |
- Blomberg, Lars G., et al.
(författare)
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MEFISTO - An electric field instrument for BepiColombo/MMO
- 2006
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Ingår i: Advances in Space Research. - : Elsevier BV. - 0273-1177 .- 1879-1948. ; 38:4, s. 672-679
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Tidskriftsartikel (refereegranskat)abstract
- MEFISTO, together with the companion instrument WPT, are planning the first-ever in situ measurements of the electric field in the magnetosphere of planet Mercury. The instruments have been selected by JAXA for inclusion in the BepiColombo/MMO payload, as part of the Plasma Wave Investigation coordinated by Kyoto University. The magnetosphere of Mercury was discovered by Mariner 10 in 1974 and will be studied further by Messenger starting in 2011. However, neither spacecraft did or will measure the electric field. Electric fields are crucial in the dynamics of a magnetosphere and for the energy and plasma transport between different regions within the magnetosphere as well as between the magnetosphere and the surrounding regions. The MEFISTO instrument will be capable of measuring electric fields from DC to 3 MHz, and will thus also allow diagnostics of waves at all frequencies of relevance to the Hermean magnetosphere. MEFISTO is a double-probe electric field instrument. The double-probe technique has strong heritage and is well proven on missions such as Viking, Polar, and Cluster. For BepiColombo, a newly developed deployment mechanism is planned which reduces the mass by a factor of about 5 compared to conventional mechanisms for 15 in long booms. We describe the basic characteristics of the instrument and briefly discuss the new developments made to tailor the instrument to flight in Mercury orbit.
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| 25. |
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| 26. |
- Green, Richard E., et al.
(författare)
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Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1335-
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Tidskriftsartikel (refereegranskat)abstract
- To provide context for the diversification of archosaurs-the group that includes crocodilians, dinosaurs, and birds-we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
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| 27. |
- Hattori, T, et al.
(författare)
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Administration of umbilical cord blood cells transiently decreased hypoxic-ischemic brain injury in neonatal rats
- 2015
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Ingår i: Developmental neuroscience. - : S. Karger AG. - 1421-9859 .- 0378-5866. ; 37:2, s. 95-104
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Tidskriftsartikel (refereegranskat)abstract
- This study aimed to investigate whether the administration of mononuclear cells derived from human umbilical cord blood cells (UCBCs) could ameliorate hypoxic-ischemic brain injury in a neonatal rat model. The left carotid arteries of 7-day-old rats were ligated, and the rats were then exposed to 8% oxygen for 60 min. Mononuclear cells derived from UCBCs using the Ficoll-Hypaque technique were injected intraperitoneally 6 h after the insult (1.0 × 10<sup>7</sup> cells). Twenty-four hours after the insult, the number of cells positive for the oxidative stress markers 4-hydroxy-2-nonenal and nitrotyrosine, in the dentate gyrus of the hippocampus in the UCBC-treated group, decreased by 36 and 42%, respectively, compared with those in the control group. In addition, the number of cells positive for the apoptosis markers active caspase-3 and apoptosis-inducing factor decreased by 53 and 58%, respectively. The number of activated microglia (ED1-positive cells) was 51% lower in the UCBC group compared with the control group. In a gait analysis performed 2 weeks after the insult, there were no significant differences among the sham-operated, control and UCBC groups. An active avoidance test using a shuttle box the following week also revealed no significant differences among the groups. Neither the volumes of the hippocampi, corpus callosum and cortices nor the numbers of neurons in the hippocampus were different between the UCBC and control groups. In summary, a single intraperitoneal injection of UCBC-derived mononuclear cells 6 h after an ischemic insult was associated with a transient reduction in numbers of apoptosis and oxidative stress marker-positive cells, but it did not induce long-term morphological or functional protection. Repeated administration or a combination treatment may be required to achieve sustained protection.
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| 28. |
- Karlsson, Tomas, 1964-, et al.
(författare)
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The MEFISTO and WPT Electric Field Sensors of the Plasma Wave Investigation on the BepiColombo Mio Spacecraft Measurements of Low and High Frequency Electric Fields at Mercury
- 2020
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Ingår i: Space Science Reviews. - : Springer Nature. - 0038-6308 .- 1572-9672. ; 216:8
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Forskningsöversikt (refereegranskat)abstract
- This paper describes the design of MEFISTO (Mercury Electric Field In-Situ Tool) and WPT (Wire Probe Antenna) electric field sensors for Plasma Wave Investigation (PWI) on the BepiColombo Mio spacecraft (Mercury Magnetospheric Orbiter, MMO). The two sensors will enable the first observations of electric fields, plasma waves and radio waves in and around the Hermean magnetosphere and exosphere. MEFISTO and WPT are dipole antennas with 31.6 m tip-to-tip length. Each antenna element has a spherical probe at each end of the wire (15 m length). They are extended orthogonally in the spin plane of the spacecraft and enable measurements of the electric field in the frequency range of DC to 10 MHz by the connection to two sets of receivers, EWO for a lower frequency range and SORBET for higher frequencies. In the initial operations after the launch (20 Oct. 2018), we succeeded to confirm the health of both antennas and to release the launch lock of the WPT. After Mercury orbit insertion planned at the end of 2025, both sensors will be fully deployed and activate full operations of the PWI electric field measurements.
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| 29. |
- Kojima, K., et al.
(författare)
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Nonlinearity-Tolerant Four-Dimensional 2A8PSK Family for 5-7 Bits/Symbol Spectral Efficiency
- 2017
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Ingår i: Journal of Lightwave Technology. - : Institute of Electrical and Electronics Engineers (IEEE). - 0733-8724 .- 1558-2213. ; 35:8, s. 1383-1391
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Tidskriftsartikel (refereegranskat)abstract
- We describe in detail the recently proposed four-dimensional modulation format family based on 2-ary amplitude 8-ary phase-shift keying (2A8PSK), supporting spectral efficiencies of 5, 6, and 7 bits/symbol. These formats nicely fill the spectral efficiency gap between the dual-polarization (DP) quadrature PSK (QPSK) and DP 16-ary quadrature-amplitude modulation (16QAM), with excellent linear and nonlinear performance. Since these modulation formats just use different parity bit expressions in the same constellation, similar digital signal processing can be seamlessly used for different spectral efficiency. A series of nonlinear transmission simulation results shows that this modulation format family outperforms the conventional modulation formats at the corresponding spectral efficiency. We also investigate the adaptive equalizer for these modulation formats.
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| 30. |
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| 31. |
- Belitsky, Victor, 1955, et al.
(författare)
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ALMA Band 2 Cold Cartridge Assembly Design
- 2022
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Ingår i: 32nd International Symposium of Space Terahertz Technology, ISSTT 2022.
-
Konferensbidrag (refereegranskat)abstract
- As part of the ALMA development, we present the design of the ALMA Band 2 Cold Cartridge Assembly (CCA). The Band 2 is the last band that completes the suit of the 10 receiver channels of ALMA. The originally planned ALMA Band 2 receiver cartridge should cover the RF band of 67 - -90 GHz. The recent progress in technology, optics, OMT design and mm-wave amplifiers, however allowed to implement receiver that has an extended RF band up to 116 GHz. Furthermore, the Band 2 receiver pursues 2SB layout and provides 4-18 GHz IF band for two sidebands in a dual-polarization configuration. Here, we describe the design of the Band 2 CCA that includes optics, amplifier assembly, internal RF transport, mechanics and cryogenics. The downconverter part and performances are described elsewhere.
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| 32. |
- Fujimoto, Seiji, et al.
(författare)
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JWST and ALMA Multiple-line Study in and around a Galaxy at z =8.496: Optical to Far-Infrared Line Ratios and the Onset of an Outflow Promoting Ionizing Photon Escape
- 2024
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Ingår i: Astrophysical Journal. - 1538-4357 .- 0004-637X. ; 964:2
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Tidskriftsartikel (refereegranskat)abstract
- We present Atacama Large Millimeter/submillimeter Array (ALMA) deep spectroscopy for a lensed galaxy at z(spec) = 8.496 with log(M-star/M-circle dot) similar to 7.8 whose optical nebular lines and stellar continuum are detected by JWST/NIRSpec and NIRCam Early Release Observations in the field of SMACS J0723.3-7327. Our ALMA spectrum shows [O III] 88 mu m and [C II] 158 mu m line detections at 4.0 sigma and 4.5 sigma, respectively. The redshift and position of the [O III] line coincide with those of the JWST source, while the [C II] line is blueshifted by 90 km s(-1) with a spatial offset of 0.'' 5 (approximate to 0.5 kpc in the source plane) from the centroid of the JWST source. The NIRCam F444W image, including [O III] lambda 5007 and H beta line emission, spatially extends beyond the stellar components by a factor of >8. This indicates that the z = 8.5 galaxy has already experienced strong outflows as traced by extended [O III] lambda 5007 and offset [C II] emission, which would promote ionizing photon escape and facilitate reionization. With careful slit-loss corrections and the removal of emission spatially outside the galaxy, we evaluate the [O III] 88 mu m/lambda 5007 line ratio, and derive the electron density n (e) by photoionization modeling to be 220(-130)(+230) cm(-3), which is comparable with those of z similar to 2-3 galaxies. We estimate an [O III] 88 mu m/[C II] 158 mu m line ratio in the galaxy of >4, as high as those of known z similar to 6-9 galaxies. This high [O III] 88 mu m/[C II] 158 mu m line ratio is generally explained by the high n(e) as well as the low metallicity (Z(gas)/Z(circle dot)=0.04(-0.02)(+0.02)), high ionization parameter (log U > -2.27), and low carbon-to-oxygen abundance ratio (log(C/O) = [-0.52: -0.24]) obtained from the JWST/NIRSpec data; further [C II] follow-up observations will constrain the covering fraction of photodissociation regions.
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| 33. |
- Golob-Schwarzi, Nicole, et al.
(författare)
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High Keratin 8/18 Ratio Predicts Aggressive Hepatocellular Cancer Phenotype
- 2019
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Ingår i: Translational Oncology. - : ELSEVIER SCIENCE INC. - 1944-7124 .- 1936-5233. ; 12:2, s. 256-268
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND amp; AIMS: Steatohepatitis (SH) and SH-associated hepatocellular carcinoma (HCC) are of considerable clinical significance. SH is morphologically characterized by steatosis, liver cell ballooning, cytoplasmic aggregates termedMallory-Denk bodies (MDBs), inflammation, and fibrosis at late stage. Disturbance of the keratin cytoskeleton and aggregation of keratins (KRTs) are essential for MDB formation. METHODS: Weanalyzed livers of aged Krt18(-/-) mice that spontaneously developed in the majority of cases SH-associated HCC independent of sex. Interestingly, the hepatic lipid profile in Krt18(-/-) mice, which accumulate KRT8, closely resembles human SH lipid profiles and shows that the excess of KRT8 over KRT18 determines the likelihood to develop SH-associated HCC linked with enhanced lipogenesis. RESULTS: Our analysis of the genetic profile of Krt18(-/-) mice with 26 human hepatoma cell lines and with data sets of amp;gt;300 patients with HCC, where Krt18(-/-) gene signatures matched human HCC. Interestingly, a high KRT8/18 ratio is associated with an aggressive HCC phenotype. CONCLUSIONS: We can prove that intermediate filaments and their binding partners are tightly linked to hepatic lipid metabolism and to hepatocarcinogenesis. We suggest KRT8/18 ratio as a novel HCC biomarker for HCC.
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| 34. |
- Hashimoto, K, et al.
(författare)
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CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors
- 2015
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Ingår i: Genome research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 25:12, s. 1812-1824
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Tidskriftsartikel (refereegranskat)abstract
- An increasing number of noncoding RNAs (ncRNAs) have been implicated in various human diseases including cancer; however, the ncRNA transcriptome of hepatocellular carcinoma (HCC) is largely unexplored. We used CAGE to map transcription start sites across various types of human and mouse HCCs with emphasis on ncRNAs distant from protein-coding genes. Here, we report that retroviral LTR promoters, expressed in healthy tissues such as testis and placenta but not liver, are widely activated in liver tumors. Despite HCC heterogeneity, a subset of LTR-derived ncRNAs were more than 10-fold up-regulated in the vast majority of samples. HCCs with a high LTR activity mostly had a viral etiology, were less differentiated, and showed higher risk of recurrence. ChIP-seq data show that MYC and MAX are associated with ncRNA deregulation. Globally, CAGE enabled us to build a mammalian promoter map for HCC, which uncovers a new layer of complexity in HCC genomics.
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| 35. |
- Kasaba, Y., et al.
(författare)
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The Plasma Wave Investigation (PWI) onboard the BepiColombo/MMO : First measurement of electric fields, electromagnetic waves, and radio waves around Mercury
- 2010
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Ingår i: Planetary and Space Science. - : Elsevier BV. - 0032-0633 .- 1873-5088. ; 58:1-2, s. 238-278
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Tidskriftsartikel (refereegranskat)abstract
- The BepiColombo Mercury Magnetospheric Orbiter (MMO) spacecraft includes the plasma and radio wave observation system called Plasma Wave Investigation (PWI). Since the receivers for electric field, plasma waves, and radio waves are not installed in any of the preceding spacecraft to Mercury, the PWI will provide the first opportunity for conducting in-situ and remote-sensing observations of electric fields, plasma waves, and radio waves in the Hermean magnetosphere and exosphere. These observations are valuable in studying structure, dynamics, and energy exchange processes in the unique magnetosphere of Mercury. They are characterized by the key words of the non-MHD environment and the peculiar interaction between the relatively large planet without ionosphere and the solar wind with high dynamic pressure. The PWI consists of three sets of receivers (EWO, SORBET, and AM(2)P), connected to two sets of electric field sensors (MEFISTO and WPT) and two kinds of magnetic field sensors (LF-SC and DB-SC). The PWI will observe both waveforms and frequency spectra in the frequency range from DC to 10 MHz for the electric field and from 0.3 Hz to 640kHz for the magnetic field. From 2008, we will start the development of the engineering model, which is conceptually consistent with the flight model design. The present paper discusses the significance and objectives of plasma/radio wave observations in the Hermean magnetosphere, and describes the PWI sensors, receivers and their performance as well as the onboard data processing.
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| 36. |
- Kojima, T, et al.
(författare)
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The Effects of High Molecular Weight Hyaluronic Acid Eye Drop Application in Environmental Dry Eye Stress Model Mice
- 2020
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Ingår i: International journal of molecular sciences. - : MDPI AG. - 1422-0067. ; 21:10
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Tidskriftsartikel (refereegranskat)abstract
- Hyaluronic acid (HA) ophthalmic solution is widely used in dry eye treatment worldwide. However, there are no reports comparing the dry eye treatment effects of high molecular weight HA with low molecular weight HA. Sixty eight-week-old C57BL/6 mice were assigned to the following 6 groups and exposed to environmental dry eye stress (EDES) that mimics office work environment: (1) 0.1% low molecular weight HA (LMWHA) eye drops, (2) 0.3% LMWHA eye drops, (3) 3% diquafosol sodium (DQ) eye drops, (4) 0.15% high molecular weight HA (HMWHA) eye drops, (5) no treatment with exposure to EDES (EDES+/Treatment−), and (6) no treatment without exposure to EDES (EDES−/Treatment−). After EDES, the HMWHA group had significantly longer break-up time (BUT) than the 0.1%, 0.3% LMWHA groups and the DQ group. After EDES, the HMWHA group had significantly lower lissamine green staining scores than the LMWHA and DQ groups. Subepithelial presumed dendritic cell density in the HMWHA group was significantly lower than the EDES+/Treatment− group. After EDES exposure, Conjunctival Muc5AC mRNA expression in the HMWHA group was significantly higher than the 0.1 and 0.3% LMWHA groups. Ophthalmic HMWHA solution may have a better dry eye treatment effect than LMWHA or DQ solution, owing to its anti-inflammatory effect.
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| 37. |
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| 38. |
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| 39. |
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| 40. |
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| 41. |
- Martin, Maria A., et al.
(författare)
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Ten new insights in climate science 2021 : a horizon scan
- 2021
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Ingår i: Global Sustainability. - : Cambridge University Press (CUP). - 2059-4798. ; 4, s. 1-20
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Forskningsöversikt (refereegranskat)abstract
- Non-technical summary: We summarize some of the past year's most important findings within climate change-related research. New research has improved our understanding about the remaining options to achieve the Paris Agreement goals, through overcoming political barriers to carbon pricing, taking into account non-CO2 factors, a well-designed implementation of demand-side and nature-based solutions, resilience building of ecosystems and the recognition that climate change mitigation costs can be justified by benefits to the health of humans and nature alone. We consider new insights about what to expect if we fail to include a new dimension of fire extremes and the prospect of cascading climate tipping elements.Technical summary: A synthesis is made of 10 topics within climate research, where there have been significant advances since January 2020. The insights are based on input from an international open call with broad disciplinary scope. Findings include: (1) the options to still keep global warming below 1.5 °C; (2) the impact of non-CO2 factors in global warming; (3) a new dimension of fire extremes forced by climate change; (4) the increasing pressure on interconnected climate tipping elements; (5) the dimensions of climate justice; (6) political challenges impeding the effectiveness of carbon pricing; (7) demand-side solutions as vehicles of climate mitigation; (8) the potentials and caveats of nature-based solutions; (9) how building resilience of marine ecosystems is possible; and (10) that the costs of climate change mitigation policies can be more than justified by the benefits to the health of humans and nature.Social media summary: How do we limit global warming to 1.5 °C and why is it crucial? See highlights of latest climate science.
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| 42. |
- Moncuquet, M., et al.
(författare)
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The radio waves and thermal electrostatic noise spectroscopy (SORBET) experiment on BEPICOLOMBO/MMO/PWI : Scientific objectives and performance
- 2006
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Ingår i: Advances in Space Research. - : Elsevier. - 0273-1177 .- 1879-1948. ; 38:4, s. 680-685
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Tidskriftsartikel (refereegranskat)abstract
- SORBET (Spectroscopie des Ondes Radio and du Bruit Electrostatique Thermique) is a radio HF spectrometer designed for the radio and Plasma Waves Instrument onboard BepiColombo/Mercury Magnetospheric Orbiter (MMO), which performs remote and in situ measurements of waves (electromagnetic and electrostatic). Technically, SORBET includes a plasma wave spectrometer, with two E-field inputs from the two perpendicular electric antennas and one B-field input from a search coil, in the range 2.5-640 kHz. This frequency band includes the local gyrofrequency and plasma frequency expected on most part of the MMO orbits. SORBET also includes a higher frequency radio receiver for remote sensing in the range 500 kHz-10.2 MHz. Owing to its capabilities, SORBET will be able to address the following scientific objectives: High resolution mapping(similar to 30 km) of electron density and temperature in the solar wind and in the Hermean magnetosphere and exo-ionosphere, via the technique of Quasi-Thermal Noise (QTN) spectroscopy. These QTN measurements will be determinant for the dynamic modeling of the magnetosphere and will provide a fundamental input for the chemistry of cold ionized species (Na, K, O, . . .) in Mercury's environment. Detection and study of Hermean radio emissions, including possible cyclotron emissions (up to similar to 10-20 kHz) from mildly energetic electrons in most highly magnetized (polar?) regions, and possible synchrotron radiation (up to a few MHz?) from more energetic electrons. Monitoring of solar radio emissions up to similar to 10 MHz in order to create a solar activity index from the view point of Mercury, allowing to correlate it with the Hermean magnetospheric response. We especially discuss the capabilities of SORBET for performing the QTN spectroscopy in Mercury's magnetosphere, using the two electric dipole antennas equipping MMO, called MEFISTO and WPT.
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| 43. |
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| 44. |
- Nanda, V, et al.
(författare)
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Membership spotlight
- 2015
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Ingår i: Vascular medicine (London, England). - 1477-0377. ; 20:3, s. 274-274
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 45. |
- Nguyen, Thao K. N., et al.
(författare)
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Dimerized Glycosaminoglycan Chains Increase FGF Signaling during Zebrafish Development
- 2013
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Ingår i: ACS Chemical Biology. - : American Chemical Society (ACS). - 1554-8929 .- 1554-8937. ; 8:5, s. 939-948
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Tidskriftsartikel (refereegranskat)abstract
- Proteoglycans (PGs) modulate numerous signaling pathways during development through binding of their glycosaminoglycan (GAG) side chains to various signaling molecules, including fibroblast growth factors (FGFs). A majority of PGs possess two or more GAG side chains, suggesting that GAG multivalency is imperative for biological functions in vivo. However, only a few studies have examined the biological significance of GAG multivalency. In this report, we utilized a library of bis- and tris-xylosides that produce two and three GAG chains on the same scaffold, respectively, thus mimicking PGs, to examine the importance of GAG valency and chain type in regulating FGF/FGFR interactions in vivo in zebrafish. A number of bis- and tris-xylosides, but not mono-xylosides, caused an elongation phenotype upon their injection into embryos. In situ hybridization showed that elongated embryos have elevated expression of the FGF target gene mkp3 but unchanged expression of reporters for other pathways, indicating that FGF/FGFR signaling was specifically hyperactivated. In support of this observation, elongation can be reversed by the tyrosine kinase inhibitor SU5402, mRNA for the FGFR antagonist sprouty4, or FGF8 morpholino. Endogenous GAGs seem to be unaffected after xyloside treatment, suggesting that this is a gain-of-function phenotype. Furthermore, expression of a multivalent but not a monovalent GAG containing syndecan-1 proteoglycan recapitulates the elongation phenotype observed with the bivalent xylosides. On the basis of these in vivo findings, we propose a new model for GAG/FGF/FGFR interactions in which dimerized GAG chains can activate FGF-mediated signal transduction pathways.
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| 46. |
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| 47. |
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| 48. |
- Smith, Stuart W., et al.
(författare)
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Tree species that 'live slow, die older' enhance tropical peat swamp restoration : Evidence from a systematic review
- 2022
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Ingår i: Journal of Applied Ecology. - : Wiley. - 0021-8901 .- 1365-2664. ; 59:8, s. 1950-1966
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Forskningsöversikt (refereegranskat)abstract
- 1. Degraded tropical peatlands lack tree cover and are often subject to seasonal flooding and repeated burning. These harsh environments for tree seedlings to survive and grow are therefore challenging to revegetate. Knowledge on species performance from previous plantings represents an important evidence base to help guide future tropical peat swamp forest (TPSF) restoration efforts.2. We conducted a systematic review of the survival and growth of tree species planted in degraded peatlands across Southeast Asia to examine (1) species differences, (2) the impact of seedling and site treatments on survival and growth and (3) the potential use of plant functional traits to predict seedling survival and growth rates.3. Planted seedling monitoring data were compiled through a systematic review of journal articles, conference proceedings, reports, theses and unpublished datasets. In total, 94 study-sites were included, spanning three decades from 1988 to 2019, and including 141 indigenous peatland tree and palm species. Accounting for variable planting numbers and monitoring durations, we analysed three measures of survival and growth: (1) final survival weighted by the number of seedlings planted, (2) half-life, that is, duration until 50% mortality and (3) relative growth rates (RGR) corrected for initial planting height of seedlings.4. Average final survival was 62% and half-life was 33 months across all species, sites and treatments. Species differed significantly in survival and half-life. Seedling and site treatments had small effects with the strongest being higher survival of mycorrhizal fungi inoculated seedlings; lower survival, half-life and RGR when shading seedlings; and lower RGR and higher survival when fertilising seedlings. Leaf nutrient and wood density traits predicted TPSF species survival, but not half-life and RGR. RGR and half-life were negatively correlated, meaning that slower growing species survived for longer.5. Synthesis and applications. To advance tropical peat swamp reforestation requires expanding the number and replication of species planted and testing treatments by adopting control vs. treatment experimental designs. Species selection should involve slower growing species (e.g. Lophopetalum rigidum, Alstonia spatulata, Madhuca motleyana) that survive for longer and explore screening species based on functional traits associated with nutrient acquisition, flooding tolerance and recovery from fire.
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| 49. |
- Suh, Alexander, et al.
(författare)
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Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes
- 2015
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Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 7:1, s. 205-217
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Tidskriftsartikel (refereegranskat)abstract
- Chicken repeat 1 (CR1) retroposons are long interspersed elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of 12 crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggests the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians.
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| 50. |
- Trotignon, J. G., et al.
(författare)
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Active measurement of the thermal electron density and temperature on the Mercury Magnetospheric Orbiter of the BepiColombo mission
- 2006
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Ingår i: Advances in Space Research. - : Elsevier BV. - 0273-1177 .- 1879-1948. ; 38:4, s. 686-692
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Tidskriftsartikel (refereegranskat)abstract
- The thermal component of Mercury's electron population has never been measured. One scientific objective of the Plasma Wave Investigation consortium, PWI, is to determine the influence of the thermal plasma upon the formation and dynamics of the planetary magnetosphere, as a function of solar activity. The Active Measurement of Mercury's Plasma experiment, AM(2)p, has been proposed as part of PWI, to monitor the density and temperature of the thermal electron population, during the whole mission of the Mercury Magnetospheric Orbiter of BepiColombo. These two physical parameters will be deduced from the measurements of the self- and mutual-impedances of the MEFISTO (Mercury Electric Field In Situ Tool) double-sphere antenna, in a frequency range comprising the expected plasma frequency. The in situ measurement of the antenna impedance is also essential for calibrating the electric antenna which measures the natural waves; it will allow, in particular, the effective length of the antenna to be calculated as a function of frequency and plasma conditions. The purpose of this paper is to define the scientific objectives of AM(2)p, to explain the principle of the measurement, to describe the electronic device, and to show the ability of AM 2p to make reliable and accurate measurements of the thermal plasma density and temperature in the Hermean magnetosphere, as well as in the solar wind at heliocentric distances of 0.31-0.47 AU. The potential performance of this instrument has been evaluated using both an analytical approach and numerical simulations.
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