| 1. |
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| 2. |
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| 3. |
- Ramdas, S., et al.
(author)
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A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids
- 2022
-
In: American Journal of Human Genetics. - : Elsevier BV. - 0002-9297 .- 1537-6605. ; 109:8, s. 1366-1387
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Journal article (peer-reviewed)abstract
- A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.
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| 4. |
- Bouyoucef, S E, et al.
(author)
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Poster Session 2 : Monday 4 May 2015, 08
- 2015
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In: European Heart Journal Cardiovascular Imaging. - : Oxford University Press (OUP). - 2047-2404 .- 2047-2412. ; 16 Suppl 1
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Journal article (peer-reviewed)
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| 5. |
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| 6. |
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| 7. |
- Adcox, K, et al.
(author)
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PHENIX detector overview
- 2003
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In: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - 0167-5087. ; 499:2-3, s. 469-479
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Journal article (peer-reviewed)abstract
- The PHENIX detector is designed to perform a broad study of A-A, p-A, and p-p collisions to investigate nuclear matter under extreme conditions. A wide variety of probes, sensitive to all timescales, are used to study systematic variations with species and energy as well as to measure the spin structure of the nucleon. Designing for the needs of the heavy-ion and polarized-proton programs has produced a detector with unparalleled capabilities. PHENIX measures electron and muon pairs, photons, and hadrons with excellent energy and momentum resolution. The detector consists of a large number of subsystems that are discussed in other papers in this volume. The overall design parameters of the detector are presented. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 8. |
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| 9. |
- Kanoni, Stavroula, et al.
(author)
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Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
-
In: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
-
Journal article (peer-reviewed)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 10. |
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| 11. |
- Sampson, Joshua N., et al.
(author)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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In: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
-
Journal article (peer-reviewed)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 12. |
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| 13. |
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| 14. |
- Sugita, S., et al.
(author)
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The geomorphology, color, and thermal properties of Ryugu: Implications for parent-body processes
- 2019
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In: Science. - : AAAS. - 0036-8075 .- 1095-9203. ; 364:6437
-
Journal article (peer-reviewed)abstract
- Asteroids fall to Earth in the form of meteorites, but these provide little information about their origins. The Japanese mission Hayabusa2 is designed to collect samples directly from the surface of an asteroid and return them to Earth for laboratory analysis. Three papers in this issue describe the Hayabusa2 team's study of the near-Earth carbonaceous asteroid 162173 Ryugu, at which the spacecraft arrived in June 2018 (see the Perspective by Wurm). Watanabeet al.measured the asteroid's mass, shape, and density, showing that it is a “rubble pile” of loose rocks, formed into a spinning-top shape during a prior period of rapid spin. They also identified suitable landing sites for sample collection. Kitazatoet al.used near-infrared spectroscopy to find ubiquitous hydrated minerals on the surface and compared Ryugu with known types of carbonaceous meteorite. Sugitaet al.describe Ryugu's geological features and surface colors and combined results from all three papers to constrain the asteroid's formation process. Ryugu probably formed by reaccumulation of rubble ejected by impact from a larger asteroid. These results provide necessary context to understand the samples collected by Hayabusa2, which are expected to arrive on Earth in December 2020.Science, this issue p.268, p.272, p.eaaw0422; see also p.230
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| 15. |
- Mahajan, Anubha, et al.
(author)
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Multi-ancestry genetic study of type 2 diabetes highlights the power of diverse populations for discovery and translation
- 2022
-
In: Nature Genetics. - : Springer Nature. - 1061-4036 .- 1546-1718. ; 54:5, s. 560-572
-
Journal article (peer-reviewed)abstract
- We assembled an ancestrally diverse collection of genome-wide association studies (GWAS) of type 2 diabetes (T2D) in 180,834 affected individuals and 1,159,055 controls (48.9% non-European descent) through the Diabetes Meta-Analysis of Trans-Ethnic association studies (DIAMANTE) Consortium. Multi-ancestry GWAS meta-analysis identified 237 loci attaining stringent genome-wide significance (P < 5 x 10(-9)), which were delineated to 338 distinct association signals. Fine-mapping of these signals was enhanced by the increased sample size and expanded population diversity of the multi-ancestry meta-analysis, which localized 54.4% of T2D associations to a single variant with >50% posterior probability. This improved fine-mapping enabled systematic assessment of candidate causal genes and molecular mechanisms through which T2D associations are mediated, laying the foundations for functional investigations. Multi-ancestry genetic risk scores enhanced transferability of T2D prediction across diverse populations. Our study provides a step toward more effective clinical translation of T2D GWAS to improve global health for all, irrespective of genetic background. Genome-wide association and fine-mapping analyses in ancestrally diverse populations implicate candidate causal genes and mechanisms underlying type 2 diabetes. Trans-ancestry genetic risk scores enhance transferability across populations.
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| 16. |
- Sakatani, N., et al.
(author)
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Anomalously porous boulders on (162173) Ryugu as primordial materials from its parent body
- 2021
-
In: Nature Astronomy. - : Springer Nature. - 2397-3366. ; 5:8, s. 766-774
-
Journal article (peer-reviewed)abstract
- Planetesimals—the initial stage of the planetary formation process—are considered to be initially very porous aggregates of dusts1,2, and subsequent thermal and compaction processes reduce their porosity3. The Hayabusa2 spacecraft found that boulders on the surface of asteroid (162173) Ryugu have an average porosity of 30–50% (refs. 4,5,6), higher than meteorites but lower than cometary nuclei7, which are considered to be remnants of the original planetesimals8. Here, using high-resolution thermal and optical imaging of Ryugu’s surface, we discovered, on the floor of fresh small craters (<20 m in diameter), boulders with reflectance (~0.015) lower than the Ryugu average6 and porosity >70%, which is as high as in cometary bodies. The artificial crater formed by Hayabusa2’s impact experiment9 is similar to these craters in size but does not have such high-porosity boulders. Thus, we argue that the observed high porosity is intrinsic and not created by subsequent impact comminution and/or cracking. We propose that these boulders are the least processed material on Ryugu and represent remnants of porous planetesimals that did not undergo a high degree of heating and compaction3. Our multi-instrumental analysis suggests that fragments of the highly porous boulders are mixed within the surface regolith globally, implying that they might be captured within collected samples by touch-down operations10,11.
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| 17. |
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| 18. |
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| 19. |
- 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
-
In: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 47:11, s. 1282-1293
-
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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| 20. |
- Kitamura, N., et al.
(author)
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Energy Transfer Between Hot Protons and Electromagnetic Ion Cyclotron Waves in Compressional Pc5 Ultra-low Frequency Waves
- 2021
-
In: Journal of Geophysical Research - Space Physics. - : AMER GEOPHYSICAL UNION. - 2169-9380 .- 2169-9402. ; 126:5
-
Journal article (peer-reviewed)abstract
- The Magnetospheric Multiscale (MMS) spacecraft observed many enhancements of electromagnetic ion cyclotron (EMIC) waves in an event in the late afternoon outer magnetosphere. These enhancements occurred mainly in the troughs of magnetic field intensity associated with a compressional ultralow frequency (ULF) wave. The ULF wave had a period of similar to 2-5 min (Pc5 frequency range) and was almost static in the plasma rest frame. The magnetic and ion pressures were in antiphase. They are consistent with mirror-mode type structures. We apply the Wave-Particle Interaction Analyzer method, which can quantitatively investigate the energy transfer between hot anisotropic protons and EMIC waves, to burst-mode data obtained by the four MMS spacecraft. The energy transfer near the cyclotron resonance velocity was identified in the vicinity of the center of troughs of magnetic field intensity, which corresponds to the maxima of ion pressure in the compressional ULF wave. This result is consistent with the idea that the EMIC wave generation is modulated by ULF waves, and preferential locations for the cyclotron resonant energy transfer are the troughs of magnetic field intensity. In these troughs, relatively low resonance velocity due to the lower magnetic field intensity and the enhanced hot proton flux likely contribute to the enhanced energy transfer from hot protons to the EMIC waves by cyclotron resonance. Due to the compressional ULF wave, regions of the cyclotron resonant energy transfer can be narrow (only a few times of the gyroradii of hot resonant protons) in magnetic local time.
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| 21. |
- Oimatsu, S., et al.
(author)
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Drift-Bounce Resonance Between Pc5 Pulsations and Ions at Multiple Energies in the Nightside Magnetosphere : Arase and MMS Observations
- 2018
-
In: Geophysical Research Letters. - : American Geophysical Union (AGU). - 0094-8276 .- 1944-8007. ; 45:15, s. 7277-7286
-
Journal article (peer-reviewed)abstract
- A Pc5 wave is observed by the Exploration of energization and Radiation in Geospace Arase satellite in the inner magnetosphere (L similar to 5.4-6.1) near postmidnight (L-magnetic local time similar to 1.8-2.5 hr) during the storm recovery phase on 27 March 2017. Its azimuthal wave number (m-number) is estimated using two independent methods with satellites and ground observations to be -8 to -15. The direct measurement of the m-number enables us to calculate the resonance energy. The flux oscillations of H+ and O+ ions at >= 56.3 keV are caused by drift resonance and those of O+ ions at <= 18.6 keV by bounce resonance. Resonances of O+ ions at multiple energies are simultaneously observed for the first time. The enhancement of the O+/H+ flux ratio at <= 18.6 keV indicates selective acceleration of O+ ions through bounce resonance. Plain Language Summary Geomagnetic pulsations are magnetic fluctuations excited by solar wind or plasma instabilities in the magnetosphere. Pc5 waves are continuous geomagnetic pulsations with a period of 150-600 s. A Pc5 wave was observed in the inner magnetosphere during a magnetic storm on 27 March 2017. It propagated westward with a wave number of 8 to 15 and resonated with charged particles, resulting in oscillations of the H+ and O+ ion fluxes at >= 56.3 keV and the O+ ion fluxes at <= 18.6 keV. Resonances of O+ ions at multiple energies are simultaneously observed for the first time. At the same time, the O+/H+ flux ratio at <= 18.6 keV enhanced corresponding to the O+ ion flux oscillations, which indicates selective acceleration of O+ ions through resonances.
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| 22. |
- Farrell, William M., et al.
(author)
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The dust, atmosphere, and plasma at the moon
- 2024
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In: Reviews in Mineralogy and Geochemistry, Mineralogical Society of America. - : Walter de Gruyter. - 1529-6466 .- 1943-2666. ; 89, s. 563-609
-
Journal article (peer-reviewed)
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| 23. |
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| 24. |
- Hrycik, Allison R., et al.
(author)
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Earlier winter/spring runoff and snowmelt during warmer winters lead to lower summer chlorophyll-a in north temperate lakes
- 2021
-
In: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 27:19, s. 4615-4629
-
Journal article (peer-reviewed)abstract
- Winter conditions, such as ice cover and snow accumulation, are changing rapidly at northern latitudes and can have important implications for lake processes. For example, snowmelt in the watershed—a defining feature of lake hydrology because it delivers a large portion of annual nutrient inputs—is becoming earlier. Consequently, earlier and a shorter duration of snowmelt are expected to affect annual phytoplankton biomass. To test this hypothesis, we developed an index of runoff timing based on the date when 50% of cumulative runoff between January 1 and May 31 had occurred. The runoff index was computed using stream discharge for inflows, outflows, or for flows from nearby streams for 41 lakes in Europe and North America. The runoff index was then compared with summer chlorophyll-a (Chl-a) concentration (a proxy for phytoplankton biomass) across 5–53 years for each lake. Earlier runoff generally corresponded to lower summer Chl-a. Furthermore, years with earlier runoff also had lower winter/spring runoff magnitude, more protracted runoff, and earlier ice-out. We examined several lake characteristics that may regulate the strength of the relationship between runoff timing and summer Chl-a concentrations; however, our tested covariates had little effect on the relationship. Date of ice-out was not clearly related to summer Chl-a concentrations. Our results indicate that ongoing changes in winter conditions may have important consequences for summer phytoplankton biomass and production.
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| 25. |
- Jane, Stephen F., et al.
(author)
-
Widespread deoxygenation of temperate lakes
- 2021
-
In: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 594:7861, s. 66-70
-
Journal article (peer-reviewed)abstract
- The concentration of dissolved oxygen in aquatic systems helps to regulate biodiversity(1,2), nutrient biogeochemistry(3), greenhouse gas emissions(4), and the quality of drinking water(5). The long-term declines in dissolved oxygen concentrations in coastal and ocean waters have been linked to climate warming and human activity(6,7), but little is known about the changes in dissolved oxygen concentrations in lakes. Although the solubility of dissolved oxygen decreases with increasing water temperatures, long-term lake trajectories are difficult to predict. Oxygen losses in warming lakes may be amplified by enhanced decomposition and stronger thermal stratification(8,9) or oxygen may increase as a result of enhanced primary production(10). Here we analyse a combined total of 45,148 dissolved oxygen and temperature profiles and calculate trends for 393 temperate lakes that span 1941 to 2017. We find that a decline in dissolved oxygen is widespread in surface and deep-water habitats. The decline in surface waters is primarily associated with reduced solubility under warmer water temperatures, although dissolved oxygen in surface waters increased in a subset of highly productive warming lakes, probably owing to increasing production of phytoplankton. By contrast, the decline in deep waters is associated with stronger thermal stratification and loss of water clarity, but not with changes in gas solubility. Our results suggest that climate change and declining water clarity have altered the physical and chemical environment of lakes. Declines in dissolved oxygen in freshwater are 2.75 to 9.3 times greater than observed in the world's oceans(6,7) and could threaten essential lake ecosystem services(2,3,5,11).
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| 26. |
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| 27. |
- Rojo, M., et al.
(author)
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Electron moments derived from the Mercury Electron Analyzer during the cruise phase of BepiColombo
- 2024
-
In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 683
-
Journal article (peer-reviewed)abstract
- Aims. We derive electron density and temperature from observations obtained by the Mercury Electron Analyzer on board Mio during the cruise phase of BepiColombo while the spacecraft is in a stacked configuration. Methods. In order to remove the secondary electron emission contribution, we first fit the core electron population of the solar wind with a Maxwellian distribution. We then subtract the resulting distribution from the complete electron spectrum, and suppress the residual count rates observed at low energies. Hence, our corrected count rates consist of the sum of the fitted Maxwellian core electron population with a contribution at higher energies. We finally estimate the electron density and temperature from the corrected count rates using a classical integration method. We illustrate the results of our derivation for two case studies, including the second Venus flyby of BepiColombo when the Solar Orbiter spacecraft was located nearby, and for a statistical study using observations obtained to date for distances to the Sun ranging from 0.3 to 0.9 AU. Results. When compared either to measurements of Solar Orbiter or to measurements obtained by HELIOS and Parker Solar Probe, our method leads to a good estimation of the electron density and temperature. Hence, despite the strong limitations arising from the stacked configuration of BepiColombo during its cruise phase, we illustrate how we can retrieve reasonable estimates for the electron density and temperature for timescales from days down to several seconds.
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| 28. |
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| 29. |
- Amano, T., et al.
(author)
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Observational Evidence for Stochastic Shock Drift Acceleration of Electrons at the Earth's Bow Shock
- 2020
-
In: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 124:6
-
Journal article (peer-reviewed)abstract
- The first-order Fermi acceleration of electrons requires an injection of electrons into a mildly relativistic energy range. However, the mechanism of injection has remained a puzzle both in theory and observation. We present direct evidence for a novel stochastic shock drift acceleration theory for the injection obtained with Magnetospheric Multiscale observations at the Earth's bow shock. The theoretical model can explain electron acceleration to mildly relativistic energies at high-speed astrophysical shocks, which may provide a solution to the long-standing issue of electron injection.
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| 30. |
- Ejiri, M.K., et al.
(author)
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Validation of the Improved Limb Atmospheric Spectrometer-II (ILAS-II) Version 1.4 nitrous oxide and methane profiles
- 2006
-
In: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 111:D22
-
Journal article (peer-reviewed)abstract
- This study assesses polar stratospheric nitrous oxide (N(2)O) and methane (CH(4)) data from the Improved Limb Atmospheric Spectrometer-II (ILAS-II) on board the Advanced Earth Observing Satellite-II (ADEOS-II) retrieved by the Version 1.4 retrieval algorithm. The data were measured between January and October 2003. Vertical profiles of ILAS-II volume mixing ratio (VMR) data are compared with data from two balloon-borne instruments, the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS-B) and the MkIV instrument, as well as with two satellite sensors, the Odin Sub-Millimetre Radiometer (SMR) for N(2)O and the Halogen Occultation Experiment (HALOE) for CH(4). Relative percentage differences between the ILAS-II and balloon/satellite data and their median values are calculated in 10-ppbv-wide bins for N(2)O (from 0 to 400 ppbv) and in 0.05-ppmv-wide bins for CH(4) (from 0 to 2 ppmv) in order to assess systematic differences between the ILAS-II and balloon/satellite data. According to this study, the characteristics of the ILAS-II Version 1.4 N(2)O and CH(4) data differ between hemispheres. For ILAS-II N(2)O VMR larger than 250 ppbv, the ILAS-II N(2)O agrees with the balloon/SMR N(2)O within +/- 20% in both hemispheres. The ILAS-II N(2)O in the VMR range from 30-50 to 250 ppbv (corresponding to altitudes of similar to 17-30 km in the Northern Hemisphere (NH, mainly outside the polar vortex) and similar to 13-21 km in the Southern Hemisphere (SH, mainly inside the polar vortex) is smaller by similar to 10-30% than the balloon/SMR N(2)O. For ILAS-II N(2)O VMR smaller than 30 ppbv (>similar to 21 km) in the SH, the differences between the ILAS-II and SMR N(2)O are within +/- 10 ppbv. For ILAS-II CH(4) VMR larger than 1 ppmv (similar to 30 km) and the ILAS-II CH(4) for its VMR smaller than 1 ppmv (>similar to 25 km) only in the NH, are abnormally small compared to the balloon/satellite data.
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| 31. |
- Floriddia, Elisa M., et al.
(author)
-
Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury
- 2020
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
-
Journal article (peer-reviewed)abstract
- Mature oligodendrocytes (MOLs) show transcriptional heterogeneity, the functional consequences of which are unclear. MOL heterogeneity might correlate with the local environment or their interactions with different neuron types. Here, we show that distinct MOL populations have spatial preference in the mammalian central nervous system (CNS). We found that MOL type 2 (MOL2) is enriched in the spinal cord when compared to the brain, while MOL types 5 and 6 (MOL5/6) increase their contribution to the OL lineage with age in all analyzed regions. MOL2 and MOL5/6 also have distinct spatial preference in the spinal cord regions where motor and sensory tracts run. OL progenitor cells (OPCs) are not specified into distinct MOL populations during development, excluding a major contribution of OPC intrinsic mechanisms determining MOL heterogeneity. In disease, MOL2 and MOL5/6 present different susceptibility during the chronic phase following traumatic spinal cord injury. Our results demonstrate that the distinct MOL populations have different spatial preference and different responses to disease.
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| 32. |
- George, Julie, et al.
(author)
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Comprehensive genomic profiles of small cell lung cancer
- 2015
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 524:7563, s. 47-U73
-
Journal article (peer-reviewed)abstract
- We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Dex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
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| 33. |
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| 34. |
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| 35. |
- Jensen, Lasse, et al.
(author)
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Disruption of the Extracellular Matrix Progressively Impairs Central Nervous System Vascular Maturation Downstream of beta-Catenin Signaling
- 2019
-
In: Arteriosclerosis, Thrombosis and Vascular Biology. - : LIPPINCOTT WILLIAMS & WILKINS. - 1079-5642 .- 1524-4636. ; 39:7, s. 1432-1447
-
Journal article (peer-reviewed)abstract
- Objective- The Wnt/beta-catenin pathway orchestrates development of the blood-brain barrier, but the downstream mechanisms involved at different developmental windows and in different central nervous system (CNS) tissues have remained elusive. Approach and Results- Here, we create a new mouse model allowing spatiotemporal investigations of Wnt/beta-catenin signaling by induced overexpression of Axin1, an inhibitor of beta-catenin signaling, specifically in endothelial cells (Axin1(iEC)-(OE)). AOE (Axin1 overexpression) in Axin1(iEC)-(OE) mice at stages following the initial vascular invasion of the CNS did not impair angiogenesis but led to premature vascular regression followed by progressive dilation and inhibition of vascular maturation resulting in forebrain-specific hemorrhage 4 days post-AOE. Analysis of the temporal Wnt/beta-catenin driven CNS vascular development in zebrafish also suggested that Axin1(iEC)-(OE) led to CNS vascular regression and impaired maturation but not inhibition of ongoing angiogenesis within the CNS. Transcriptomic profiling of isolated, beta-catenin signaling-deficient endothelial cells during early blood-brain barrier-development (E11.5) revealed ECM (extracellular matrix) proteins as one of the most severely deregulated clusters. Among the 20 genes constituting the forebrain endothelial cell-specific response signature, 8 (Adamtsl2, Apod, Ctsw, Htra3, Pglyrp1, Spock2, Ttyh2, and Wfdc1) encoded bona fide ECM proteins. This specific beta-catenin-responsive ECM signature was also repressed in Axin1(iEC)-(OE) and endothelial cell-specific beta-catenin-knockout mice (Ctnnb1-KOiEC) during initial blood-brain barrier maturation (E14.5), consistent with an important role of Wnt/beta-catenin signaling in orchestrating the development of the forebrain vascular ECM. Conclusions- These results suggest a novel mechanism of establishing a CNS endothelium-specific ECM signature downstream of Wnt-beta-catenin that impact spatiotemporally on blood-brain barrier differentiation during forebrain vessel development.
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| 36. |
- Kitamura, N., et al.
(author)
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Direct observations of energy transfer from resonant electrons to whistler-mode waves in magnetosheath of Earth
- 2022
-
In: Nature Communications. - : Springer Nature. - 2041-1723. ; 13:1
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Journal article (peer-reviewed)abstract
- Excitation of whistler-mode waves by cyclotron instability is considered as the likely generation process of the waves. Here, the authors show direct observational evidence for locally ongoing secular energy transfer from the resonant electrons to the whistler-mode waves in Earth's magnetosheath. Electromagnetic whistler-mode waves in space plasmas play critical roles in collisionless energy transfer between the electrons and the electromagnetic field. Although resonant interactions have been considered as the likely generation process of the waves, observational identification has been extremely difficult due to the short time scale of resonant electron dynamics. Here we show strong nongyrotropy, which rotate with the wave, of cyclotron resonant electrons as direct evidence for the locally ongoing secular energy transfer from the resonant electrons to the whistler-mode waves using ultra-high temporal resolution data obtained by NASA's Magnetospheric Multiscale (MMS) mission in the magnetosheath. The nongyrotropic electrons carry a resonant current, which is the energy source of the wave as predicted by the nonlinear wave growth theory. This result proves the nonlinear wave growth theory, and furthermore demonstrates that the degree of nongyrotropy, which cannot be predicted even by that nonlinear theory, can be studied by observations.
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| 37. |
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| 38. |
- Kukanja, Petra, et al.
(author)
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Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology
- 2024
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In: Cell. - : Cell Press. - 0092-8674 .- 1097-4172. ; 187:8, s. 1990-2009
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Journal article (peer-reviewed)abstract
- Multiple sclerosis (MS) is a neurological disease characterized by multifocal lesions and smoldering pathology. Although single -cell analyses provided insights into cytopathology, evolving cellular processes underlying MS remain poorly understood. We investigated the cellular dynamics of MS by modeling temporal and regional rates of disease progression in mouse experimental autoimmune encephalomyelitis (EAE). By performing single -cell spatial expression profiling using in situ sequencing (ISS), we annotated disease neighborhoods and found centrifugal evolution of active lesions. We demonstrated that disease -associated (DA)-glia arise independently of lesions and are dynamically induced and resolved over the disease course. Single -cell spatial mapping of human archival MS spinal cords confirmed the differential distribution of homeostatic and DA-glia, enabled deconvolution of active and inactive lesions into sub -compartments, and identified new lesion areas. By establishing a spatial resource of mouse and human MS neuropathology at a single -cell resolution, our study unveils the intricate cellular dynamics underlying MS.
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| 39. |
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| 40. |
- Lavraud, B., et al.
(author)
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Currents and associated electron scattering and bouncing near the diffusion region at Earth's magnetopause
- 2016
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In: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 43:7, s. 3042-3050
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Journal article (peer-reviewed)abstract
- Based on high-resolution measurements from NASA's Magnetospheric Multiscale mission, we present the dynamics of electrons associated with current systems observed near the diffusion region of magnetic reconnection at Earth's magnetopause. Using pitch angle distributions (PAD) and magnetic curvature analysis, we demonstrate the occurrence of electron scattering in the curved magnetic field of the diffusion region down to energies of 20 eV. We show that scattering occurs closer to the current sheet as the electron energy decreases. The scattering of inflowing electrons, associated with field-aligned electrostatic potentials and Hall currents, produces a new population of scattered electrons with broader PAD which bounce back and forth in the exhaust. Except at the center of the diffusion region the two populations are collocated and appear to behave adiabatically: the inflowing electron PAD focuses inward (toward lower magnetic field), while the bouncing population PAD gradually peaks at 90 degrees away from the center (where it mirrors owing to higher magnetic field and probable field-aligned potentials).
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| 41. |
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| 42. |
- Milz, Mathias, et al.
(author)
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Validation of water vapour profiles (version 13) retrieved by the IMK/IAA scientific retrieval processor based on full resolution spectra measured by MIPAS on board Envisat
- 2009
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In: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 2:2, s. 379-399
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Journal article (peer-reviewed)abstract
- Vertical profiles of stratospheric water vapour measured by the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) with the full resolution mode between September 2002 and March 2004 and retrieved with the IMK/IAA scientific retrieval processor were compared to a number of independent measurements in order to estimate the bias and to validate the existing precision estimates of the MIPAS data. The estimated precision for MIPAS is 5 to 10% in the stratosphere, depending on altitude, latitude, and season. The independent instruments were: the Halogen Occultation Experiment (HALOE), the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS), the Improved Limb Atmospheric Spectrometer-II (ILAS-II), the Polar Ozone and Aerosol Measurement (POAM III) instrument, the Middle Atmospheric Water Vapour Radiometer (MIAWARA), the Michelson Interferometer for Passive Atmospheric Sounding, balloon-borne version (MIPAS-B), the Airborne Microwave Stratospheric Observing System(AMSOS), the Fluorescent Stratospheric Hygrometer for Balloon (FLASH-B), the NOAA frostpoint hygrometer, and the Fast In Situ Hygrometer (FISH). For the in-situ measurements and the ground based, air- and balloon borne remote sensing instruments, the measurements are restricted to central and northern Europe. The comparisons to satellite-borne instruments are predominantly at mid- to high latitudes on both hemispheres. In the stratosphere there is no clear indicationof a bias in MIPAS data, because the independent measurements in some cases are drier and in some cases are moister than the MIPAS measurements. Compared to the infrared measurements of MIPAS, measurements in the ultraviolet and visible have a tendency to be high, whereas microwave measurements have a tendency to be low. Theresults of chi2-based precision validation are somewhat controversial among the comparison estimates. However, for comparison instruments whose error budget also includes errors due to uncertainties in spectrally interfering species and where good coincidences were found, the chi2 values found are in the expected range or even below. This suggests that there is no evidence of systematically underestimated MIPAS random errors.
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| 43. |
- Reinl, Kaitlin L., et al.
(author)
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Blooms also like it cold
- 2023
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In: Limnology and Oceanography Letters. - : John Wiley & Sons. - 2378-2242. ; 8:4, s. 546-564
-
Research review (peer-reviewed)abstract
- Cyanobacterial blooms have substantial direct and indirect negative impacts on freshwater ecosystems including releasing toxins, blocking light needed by other organisms, and depleting oxygen. There is growing concern over the potential for climate change to promote cyanobacterial blooms, as the positive effects of increasing lake surface temperature on cyanobacterial growth are well documented in the literature; however, there is increasing evidence that cyanobacterial blooms are also being initiated and persisting in relatively cold-water temperatures (< 15 °C), including ice-covered conditions. In this work, we provide evidence of freshwater cold-water cyanobacterial blooms, review abiotic drivers and physiological adaptations leading to these blooms, offer a typology of these lesser-studied cold-water cyanobacterial blooms, and discuss their occurrence under changing climate conditions.
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| 44. |
- Takahashi, H., et al.
(author)
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A thermal-neutron detector with a phoswich system of LiCaAlF6 and BGO crystal scintillators onboard PoGOLite
- 2010
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In: 2010 IEEE Nuclear Science Symposium, Medical Imaging Conference, NSS/MIC 2010 and 17th International Workshop on Room-Temperature Semiconductor X-ray and Gamma-ray Detectors, RTSD 2010. ; , s. 32-37
-
Conference paper (peer-reviewed)abstract
- To measure the flux of atmospheric neutrons and study the neutron contribution to the background of the main detector of the PoGOLite (Polarized Gamma-ray Observer) balloon-borne experiment, a thermal-neutron detector with a phoswich system of LiCaAlF6 (Eu) and BGO crystal scintillators is developed. The performance to separate thermal-neutron events from those of gamma-rays and charged particles is validated with 252Cf on ground. The detector is attached to the PoGOLite instrument and is launched in 2011 from the Esrange facility in the North of Sweden. Although the emission wavelength of the LiCaAlF6 (Ce) is 300 nm and overlaps with the absorption wavelength of the BGO, the phoswich capability of the LiCaAlF6 (Ce) with the BGO is also confirmed with installing a waveform shifter.
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| 45. |
- Dinoto, Achmad, et al.
(author)
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Population dynamics of Bifidobacterium species in human feces during raffinose administration monitored by fluorescence in situ hybridization-flow cytometry
- 2006
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In: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 72:12, s. 7739-47
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Journal article (peer-reviewed)abstract
- The population dynamics of bifidobacteria in human feces during raffinose administration were investigated at the species level by using fluorescence in situ hybridization (FISH) coupled with flow cytometry (FCM) analysis. Although double-staining FISH-FCM using both fluorescein isothiocyanate (FITC) and indodicarbocyanine (Cy5) as labeling dyes for fecal samples has been reported, the analysis was interfered with by strong autofluorescence at the FITC fluorescence region because of the presence of autofluorescence particles/debris in the fecal samples. We circumvented this problem by using only Cy5 fluorescent dye in the FISH-FCM analysis. Thirteen subjects received 2 g of raffinose twice a day for 4 weeks. Fecal samples were collected, and the bifidobacterial populations were monitored using the established FISH-FCM method. The results showed an increase in bifidobacteria from about 12.5% of total bacteria in the prefeeding period to about 28.7 and 37.2% after the 2-week and 4-week feeding periods, respectively. Bifidobacterium adolescentis, the Bifidobacterium catenulatum group, and Bifidobacterium longum were the major species, in that order, at the prefeeding period, and these bacteria were found to increase nearly in parallel during the raffinose administration. During the feeding periods, indigenous bifidobacterial populations became more diverse, such that minor species in human adults, such as Bifidobacterium breve, Bifidobacterium bifidum, Bifidobacterium dentium, and Bifidobacterium angulatum, proliferated. Four weeks after raffinose administration was stopped, the proportion of each major bifidobacterial species, as well as that of total bifidobacteria, returned to approximately the original values for the prefeeding period, whereas that of each minor species appeared to differ considerably from its original value. To the best of our knowledge, these results provide the first clear demonstration of the population dynamics of indigenous bifidobacteria at the species level in response to raffinose administration.
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| 46. |
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| 47. |
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| 48. |
- Fadanelli, S., et al.
(author)
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Four-Spacecraft Measurements of the Shape and Dimensionality of Magnetic Structures in the Near-Earth Plasma Environment
- 2019
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In: Journal of Geophysical Research - Space Physics. - 2169-9380 .- 2169-9402. ; 124:8, s. 6850-6868
-
Journal article (peer-reviewed)abstract
- We present a new method for determining the main relevant features of the local magnetic field configuration, based entirely on the knowledge of the magnetic field gradient four‐spacecraft measurements. The method, named “magnetic configuration analysis” (MCA), estimates the spatial scales on which the magnetic field varies locally. While it directly derives from the well‐known magnetic directional derivative and magnetic rotational analysis procedures (Shi et al., 2005, htpps://doi.org/10.1029/2005GL022454; Shen et al., 2007, https://doi.org/10.1029/2005JA011584), MCA was specifically designed to address the actual magnetic field geometry. By applying MCA to multispacecraft data from the Magnetospheric Multiscale (MMS) satellites, we perform both case and statistical analyses of local magnetic field shape and dimensionality at very high cadence and small scales. We apply this technique to different near‐Earth environments and define a classification scheme for the type of configuration observed. While our case studies allow us to benchmark the method with those used in past works, our statistical analysis unveils the typical shape of magnetic configurations and their statistical distributions. We show that small‐scale magnetic configurations are generally elongated, displaying forms of cigar and blade shapes, but occasionally being planar in shape like thin pancakes (mostly inside current sheets). Magnetic configurations, however, rarely show isotropy in their magnetic variance. The planar nature of magnetic configurations and, most importantly, their scale lengths strongly depend on the plasma β parameter. Finally, the most invariant direction is statistically aligned with the electric current, reminiscent of the importance of electromagnetic forces in shaping the local magnetic configuration.
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| 49. |
- Hilscher, Markus M., et al.
(author)
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Spatial and temporal heterogeneity in the lineage progression of fine oligodendrocyte subtypes
- 2022
-
In: BMC Biology. - : Springer Science and Business Media LLC. - 1741-7007. ; 20:1
-
Journal article (peer-reviewed)abstract
- Background: Oligodendrocytes are glial cells that support and insulate axons in the central nervous system through the production of myelin. Oligodendrocytes arise throughout embryonic and early postnatal development from oligodendrocyte precursor cells (OPCs), and recent work demonstrated that they are a transcriptional heterogeneous cell population, but the regional and functional implications of this heterogeneity are less clear. Here, we apply in situ sequencing (ISS) to simultaneously probe the expression of 124 marker genes of distinct oligodendrocyte populations, providing comprehensive maps of the corpus callosum, cingulate, motor, and somatosensory cortex in the brain, as well as gray matter (GM) and white matter (WM) regions in the spinal cord, at postnatal (P10), juvenile (P20), and young adult (P60) stages. We systematically compare the abundances of these populations and investigate the neighboring preference of distinct oligodendrocyte populations.Results: We observed that oligodendrocyte lineage progression is more advanced in the juvenile spinal cord compared to the brain, corroborating with previous studies. We found myelination still ongoing in the adult corpus callosum while it was more advanced in the cortex. Interestingly, we also observed a lateral-to-medial gradient of oligodendrocyte lineage progression in the juvenile cortex, which could be linked to arealization, as well as a deep-to-superficial gradient with mature oligodendrocytes preferentially accumulating in the deeper layers of the cortex. The ISS experiments also exposed differences in abundances and population dynamics over time between GM and WM regions in the brain and spinal cord, indicating regional differences within GM and WM, and we found that neighboring preferences of some oligodendroglia populations are altered from the juvenile to the adult CNS.Conclusions: Overall, our ISS experiments reveal spatial heterogeneity of oligodendrocyte lineage progression in the brain and spinal cord and uncover differences in the timing of oligodendrocyte differentiation and myelination, which could be relevant to further investigate functional heterogeneity of oligodendroglia, especially in the context of injury or disease.
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| 50. |
- Inagaki, Shunsuke, et al.
(author)
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Effects of adsorbed molecular ordering to the superconductivity of a two-dimensional atomic layer crystal
- 2023
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In: Physical Review Materials. - : American Physical Society. - 2475-9953. ; 7:2
-
Journal article (peer-reviewed)abstract
- The effect of 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) adsorption on the physical properties of the two-dimensional (2D) atomic layer superconductor (ALSC) In/Si(111)-(7×3) has been studied by angle-resolved photoelectron spectroscopy, transport measurements, and scanning tunneling microscopy. Hole doping from the adsorbed molecules has been reported to increase the superconducting transition temperature Tc of this ALSC, and the molecular spin tends to decrease it. Owing to its large electron affinity and its nonexistent spin state, the adsorption of PTCDA was expected to increase Tc. However, the PTCDA adsorption dopes only a small number of holes in the In layers and causes a suppression of Tc with a sharp increase in the normal-state sheet resistance followed by an insulating transition. Taking the disordering of the arrangement of PTCDA into account, we conclude that the increase in resistance is due to the localization effect originating from the random potential that is induced by the disordered PTCDA molecules. The present result also indicates the importance of the crystallinity of a 2D molecular film adsorbed on ALSCs.
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