| 11. |
- Noguchi, S, et al.
(author)
-
FANTOM5 CAGE profiles of human and mouse samples
- 2017
-
In: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4, s. 170112-
-
Journal article (peer-reviewed)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.
|
|
| 12. |
- Bonnefoy, M., et al.
(author)
-
The GJ 504 system revisited Combining interferometric, radial velocity, and high contrast imaging data
- 2018
-
In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 618
-
Journal article (peer-reviewed)abstract
- Context. The G-type star GJ504A is known to host a 3-35 M-Jup companion whose temperature, mass, and projected separation all contribute to making it a test case for planet formation theories and atmospheric models of giant planets and light brown dwarfs. Aims. We aim at revisiting the system age, architecture, and companion physical and chemical properties using new complementary interferometric, radial-velocity, and high-contrast imaging data. Methods. We used the CHARA interferometer to measure GJ504A's angular diameter and obtained an estimation of its radius in combination with the HIPPARCOS parallax. The radius was compared to evolutionary tracks to infer a new independent age range for the system. We collected dual imaging data with IRDIS on VLT/SPHERE to sample the near-infrared (1.02-2.25 mu m) spectral energy distribution (SED) of the companion. The SED was compared to five independent grids of atmospheric models (petitCODE, Exo-REM, BT-SETTL, Morley et al., and ATMO) to infer the atmospheric parameters of GJ 504b and evaluate model-to-model systematic errors. In addition, we used a specific model grid exploring the effect of different C/O ratios. Contrast limits from 2011 to 2017 were combined with radial velocity data of the host star through the MESS2 tool to define upper limits on the mass of additional companions in the system from 0.01 to 100 au. We used an MCMC fitting tool to constrain the companion's orbital parameters based on the measured astrometry, and dedicated formation models to investigate its origin. Results. We report a radius of 1.35 +/- 0.04 R-circle dot for GJ504A. The radius yields isochronal ages of 21 +/- 2 Myr or 4.0 +/- 1.8 Gyr for the system and line-of-sight stellar rotation axis inclination of 162.4(-4.3)(+3.8) degrees or 18.6(-3.8)(+4.3) degrees. We re-detect the companion in the Y2, Y3, J3, H2, and K1 dual-band images. The complete 1-4 mu m SED shape of GJ504b is best reproduced by T8-T9.5 objects with intermediate ages (<= 1.5Gyr), and/or unusual dusty atmospheres and/or super-solar metallicities. All atmospheric models yield T-eff = 550 +/- 50 K for GJ504b and point toward a low surface gravity (3.5-4.0 dex). The accuracy on the metallicity value is limited by model-to-model systematics; it is not degenerate with the C/O ratio. We derive log L/L-circle dot = 6.15 +/- 0.15 dex for the companion from the empirical analysis and spectral synthesis. The luminosity and T-eff yield masses of M = 1.3(-0.3)(+0.6) M-Jup and M = 23(-9)(+10) M-Jup for the young and old age ranges, respectively. The semi-major axis (sma) is above 27.8 au and the eccentricity is lower than 0.55. The posterior on GJ 504b's orbital inclination suggests a misalignment with the rotation axis of GJ 504A. We exclude additional objects (90% prob.) more massive than 2.5 and 30 M-Jup with semi-major axes in the range 0.01-80 au for the young and old isochronal ages, respectively. Conclusions. The mass and semi-major axis of GJ 504b are marginally compatible with a formation by disk-instability if the system is 4 Gyr old. The companion is in the envelope of the population of planets synthesized with our core-accretion model. Additional deep imaging and spectroscopic data with SPHERE and JWST should help to confirm the possible spin-orbit misalignment and refine the estimates on the companion temperature, luminosity, and atmospheric composition.
|
|
| 13. |
|
|
| 14. |
- Naruse, M., et al.
(author)
-
Percolation of optical excitation mediated by near-field interactions
- 2017
-
In: Physica A: Statistical Mechanics and its Applications. - : Elsevier. - 0378-4371. ; 471, s. 162-168
-
Journal article (peer-reviewed)abstract
- Optical excitation transfer in nanostructured matter has been intensively studied in various material systems for versatile applications. Herein, we theoretically and numerically discuss the percolation of optical excitations in randomly organized nanostructures caused by optical near-field interactions governed by Yukawa potential in a two-dimensional stochastic model. The model results demonstrate the appearance of two phases of percolation of optical excitation as a function of the localization degree of near-field interaction. Moreover, it indicates sublinear scaling with percolation distances when the light localization is strong. Furthermore, such a character is maximized at a particular size of environments. The results provide fundamental insights into optical excitation transfer and will facilitate the design and analysis of nanoscale signal-transfer characteristics.
|
|
| 15. |
- Duffy, J. E., et al.
(author)
-
Biodiversity mediates top-down control in eelgrass ecosystems: a global comparative-experimental approach
- 2015
-
In: Ecology Letters. - : Wiley. - 1461-023X .- 1461-0248. ; 18:7, s. 696-705
-
Journal article (peer-reviewed)abstract
- Nutrient pollution and reduced grazing each can stimulate algal blooms as shown by numerous experiments. But because experiments rarely incorporate natural variation in environmental factors and biodiversity, conditions determining the relative strength of bottom-up and top-down forcing remain unresolved. We factorially added nutrients and reduced grazing at 15 sites across the range of the marine foundation species eelgrass (Zostera marina) to quantify how top-down and bottom-up control interact with natural gradients in biodiversity and environmental forcing. Experiments confirmed modest top-down control of algae, whereas fertilisation had no general effect. Unexpectedly, grazer and algal biomass were better predicted by cross-site variation in grazer and eelgrass diversity than by global environmental gradients. Moreover, these large-scale patterns corresponded strikingly with prior small-scale experiments. Our results link global and local evidence that biodiversity and top-down control strongly influence functioning of threatened seagrass ecosystems, and suggest that biodiversity is comparably important to global change stressors.
|
|
| 16. |
|
|
| 17. |
|
|
| 18. |
- Ruesink, JL., et al.
(author)
-
Form–function relationships in a marine foundation species depend on scale: a shoot to global perspective from a distributed ecological experiment
- 2018
-
In: Oikos. - : Wiley. - 0030-1299 .- 1600-0706. ; 127:3, s. 364-374
-
Journal article (peer-reviewed)abstract
- Form–function relationships in plants underlie their ecosystem roles in supporting higher trophic levels through primary production, detrital pathways, and habitat provision. For widespread, phenotypically-variable plants, productivity may differ not only across abiotic conditions, but also from distinct morphological or demographic traits. A single foundation species, eelgrass Zostera marina, typically dominates north temperate seagrass meadows, which we studied across 14 sites spanning 32–61°N latitude and two ocean basins. Body size varied by nearly two orders of magnitude through this range, and was largest at mid-latitudes and in the Pacific Ocean. At the global scale, neither latitude, site-level environmental conditions, nor body size helped predict productivity (relative growth rate 1–2% day-1 at most sites), suggesting a remarkable capacity of Z. marina to achieve similar productivity in summer. Furthermore, among a suite of stressors applied within sites, only ambient leaf damage reduced productivity; grazer reduction and nutrient addition had no effect on eelgrass size or growth. Scale-dependence was evident in different allometric relationships within and across sites for productivity and for modules (leaf count) relative to size. Zostera marina provides a range of ecosystem functions related to both body size (habitat provision, water flow) and growth rates (food, carbon dynamics). Our observed decoupling of body size and maximum production suggests that geographic variation in these ecosystem functions may be independent, with a future need to resolve how local adaptation or plasticity of body size might actually enable more consistent peak productivity across disparate environmental conditions.
|
|
| 19. |
|
|
| 20. |
|
|
