| 1. |
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| 2. |
- Kanai, M, et al.
(författare)
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- 2023
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swepub:Mat__t
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| 3. |
- Glasbey, JC, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 4. |
- Tabiri, S, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 5. |
- Bravo, L, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 6. |
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| 7. |
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| 8. |
- Bradnam, K. R., et al.
(författare)
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Assemblathon 2 : Evaluating de novo methods of genome assembly in three vertebrate species
- 2013
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Ingår i: GigaScience. - : BioMed Central (BMC). - 2047-217X. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
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| 9. |
- Hoyer, S., et al.
(författare)
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TOI-220b: a warm sub-Neptune discovered by TESS
- 2021
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Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 505:3, s. 3361-3379
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we report the discovery of TOI-220b, a new sub-Neptune detected by the Transiting Exoplanet Survey Satellite (TESS) and confirmed by radial velocity follow-up observations with the HARPS spectrograph. Based on the combined analysis of TESS transit photometry and high precision radial velocity measurements, we estimate a planetary mass of 13.8 +/- 1.0M(circle plus) and radius of 3.03 +/- 0.15R(circle plus), implying a bulk density of 2.73 +/- 0.47. TOI-220b orbits a relative bright (V=10.4) and old (10.1 +/- 1.4Gyr) K dwarf star with a period of similar to 10.69d. Thus, TOI-220b is a new warm sub-Neptune with very precise mass and radius determinations. A Bayesian analysis of the TOI-220b internal structure indicates that due to the strong irradiation it receives, the low density of this planet could be explained with a steam atmosphere in radiative-convective equilibrium and a supercritical water layer on top of a differentiated interior made of a silicate mantle and a small iron core.
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| 10. |
- Jorda, L., et al.
(författare)
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The global shape, density and rotation of Comet 67P/Churyumov-Gerasimenko from preperihelion Rosetta/OSIRIS observations
- 2016
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Ingår i: Icarus. - : Elsevier BV. - 0019-1035 .- 1090-2643. ; 277, s. 257-278
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Tidskriftsartikel (refereegranskat)abstract
- The Rosetta spacecraft reached Comet 67P/Churyumov-Gerasimenko (hereafter 67P/C-G) in August 2014 at an heliocentric distance of 3.6 a.u. and was then put in orbit around its nucleus to perform detailed observations. Among the collected data are the images acquired by the OSIRIS instrument up to the perihelion passage of the comet in August 2015, which allowed us to map the entire nucleus surface at high-resolution in the visible. Stereophotoclinometry methods have been used to reconstruct a global high-resolution shape model and to monitor its rotational parameters using data collected up to perihelion. The nucleus has a conspicuous bilobate shape with overall dimensions along its principal axes of (4.34 +/- 0.02) x (2.60 +/- 0.02) x (2.12 +/- 0.06) km. The best-fit ellipsoid dimensions of the individual lobes along their principal axes of inertia are found to be 4.10 x 3.52 x 1.63 km and 2.50 x 2.14 x 1.641cm. Their volume amounts to 66% and 27% of the total volume of the nucleus. The two lobes are connected by a "neck" whose volume has been estimated to represent similar to 7% of the total volume of the comet. Combining the derived volume of 18.8 +/- 0.3 km(3) with the mass of 9.982 +/- 0.003 x 10(12) kg determined by the Rosetta/RSI experiment, we obtained a bulk density of the nucleus of 532 +/- 7 kg m(-3). Together with the companion value of 535 35 kg m-3 deduced from the stereophotogrammetry shape model of the nucleus (Preusker et al. [2015] Astron. Astrophys. 583, A33), these constitute the first reliable and most accurate determination of the density of a cometary nucleus to date. The calculated porosity is quite large, ranging approximately from 70% to 75% depending upon the assumed density of the dust grains and the dust-to-ice mass ratio. The nature of the porosity, either micro or macro or both, remains unconstrained. The coordinates of the center of gravity are not compatible with a uniform nucleus density. The direction of the offset between the center of gravity and the center of figure suggests that the big lobe has a slightly higher bulk density compared to the small one. the center of mass position cannot be explained by different, but homogenous densities in the two lobes. The initial rotational period of 12.4041 +/- 0.0001 h of the nucleus persisted until October 2014. It then slightly increased to a maximum of 12.4304h reached on 19 May 2015 and finally dropped to 12.305 h just before perihelion on August 10, 2015. A periodogram analysis of the (RA, Dec) direction of the Z-axis of the comet obtained in parallel with the shape reconstruction exhibits a highly significant minima at 11.5 +/- 0.5 day clearly indicating an excited rotational state with an amplitude of 0.15 +/- 0.03 degrees.
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| 11. |
- Huybrighs, H. L. F., et al.
(författare)
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Energetic Proton Losses Reveal Io's Extended and Longitudinally Asymmetrical Atmosphere
- 2024
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Ingår i: Journal of Geophysical Research - Space Physics. - : American Geophysical Union (AGU). - 2169-9380 .- 2169-9402. ; 129:7
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Tidskriftsartikel (refereegranskat)abstract
- Along the I24, I27, and I31 flybys of Io (1999-2001), the Energetic Particle Detector (EPD) onboard the Galileo spacecraft observed localized regions of energetic protons losses (155-1,250 keV). Using back-tracking particle simulations combined with a prescribed atmospheric distribution and a magnetohydrodynamics (MHD) model of the plasma/atmosphere interaction, we investigate the possible causes of these depletions. We focus on a limited region within two Io radii, which is dominated by Io's SO2 atmosphere. Our results show that charge exchange of protons with the SO2 atmosphere, absorption by the surface and the configuration of the electromagnetic field contribute to the observed proton depletion along the Galileo flybys. In the 155-240 keV energy range, charge exchange is either a major or the dominant loss process, depending on the flyby altitude. In the 540-1,250 keV range, as the charge exchange cross sections are small, the observed decrease of the proton flux is attributed to absorption by the surface and the perturbed electromagnetic fields, which divert the protons away from the detector. From a comparison between the modeled losses and the data we find indications of an extended atmosphere on the day/downstream side of Io, a lack of atmospheric collapse on the night/upstream side as well as a more global extended atmospheric component (>1 Io radius). Our results demonstrate that observations and modeling of proton depletion around the moon constitute an important tool to constrain the electromagnetic field configuration around Io and the radial and longitudinal atmospheric distribution, which is still poorly understood.
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| 12. |
- Blanc, M., et al.
(författare)
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Saturn Plasma Sources and Associated Transport Processes
- 2015
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Ingår i: Space Science Reviews. - : Springer Science and Business Media LLC. - 0038-6308 .- 1572-9672. ; 192:1-4, s. 237-283
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Forskningsöversikt (refereegranskat)abstract
- This article reviews the different sources of plasma for Saturn's magnetosphere, as they are known essentially from the scientific results of the Cassini-Huygens mission to Saturn and Titan. At low and medium energies, the main plasma source is the cloud produced by the "geyser" activity of the small satellite Enceladus. Impact ionization of this cloud occurs to produce on the order of 100 kg/s of fresh plasma, a source which dominates all the other ones: Titan (which produces much less plasma than anticipated before the Cassini mission), the rings, the solar wind (a poorly known source due to the lack of quantitative knowledge of the degree of coupling between the solar wind and Saturn's magnetosphere), and the ionosphere. At higher energies, energetic particles are produced by energy diffusion and acceleration of lower energy plasma produced by the interchange instabilities induced by the rapid rotation of Saturn, and possibly, for the highest energy range, by contributions from the CRAND process acting inside Saturn's magnetosphere. Discussion of the transport and acceleration processes acting on these plasma sources shows the importance of rotation-induced radial transport and energization of the plasma, and also shows how much the unexpected planetary modulation of essentially all plasma parameters of Saturn's magnetosphere remains an unexplained mystery.
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| 13. |
- Edberg, Niklas J. T., et al.
(författare)
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Effects of Saturn's magnetospheric dynamics on Titan's ionosphere
- 2015
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Ingår i: Journal of Geophysical Research - Space Physics. - 2169-9380 .- 2169-9402. ; 120:10, s. 8884-8898
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Tidskriftsartikel (refereegranskat)abstract
- We use the Cassini Radio and Plasma Wave Science/Langmuir probe measurements of the electron density from the first 110 flybys of Titan to study how Saturn's magnetosphere influences Titan's ionosphere. The data is first corrected for biased sampling due to varying solar zenith angle and solar energy flux (solar cycle effects). We then present results showing that the electron density in Titan's ionosphere, in the altitude range 1600-2400km, is increased by about a factor of 2.5 when Titan is located on the nightside of Saturn (Saturn local time (SLT) 21-03h) compared to when on the dayside (SLT 09-15 h). For lower altitudes (1100-1600km) the main dividing factor for the ionospheric density is the ambient magnetospheric conditions. When Titan is located in the magnetospheric current sheet, the electron density in Titan's ionosphere is about a factor of 1.4 higher compared to when Titan is located in the magnetospheric lobes. The factor of 1.4 increase in between sheet and lobe flybys is interpreted as an effect of increased particle impact ionization from approximate to 200eV sheet electrons. The factor of 2.5 increase in electron density between flybys on Saturn's nightside and dayside is suggested to be an effect of the pressure balance between thermal plus magnetic pressure in Titan's ionosphere against the dynamic pressure and energetic particle pressure in Saturn's magnetosphere.
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| 14. |
- Singer, Andrew C, et al.
(författare)
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Meeting Report : Risk Assessment of Tamiflu Use Under Pandemic Conditions
- 2008
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Ingår i: Environmental Health Perspectives. ; 116:11, s. 1563-7
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Tidskriftsartikel (refereegranskat)abstract
- On 3 October 2007, 40 participants with diverse expertise attended the workshop Tamiflu and the Environment: Implications of Use under Pandemic Conditions to assess the potential human health impact and environmental hazards associated with use of Tamiflu during an influenza pandemic. Based on the identification and risk-ranking of knowledge gaps, the consensus was that oseltamivir ethylester-phosphate (OE-P) and oseltamivir carboxylate (OC) were unlikely to pose an ecotoxicologic hazard to freshwater organisms. OC in river water might hasten the generation of OC-resistance in wildfowl, but this possibility seems less likely than the potential disruption that could be posed by OC and other pharmaceuticals to the operation of sewage treatment plants. The workgroup members agreed on the following research priorities: a) available data on the ecotoxicology of OE-P and OC should be published ; b) risk should be assessed for OC-contaminated river water generating OC-resistant viruses in wildfowl ; c) sewage treatment plant functioning due to microbial inhibition by neuraminidase inhibitors and other antimicrobials used during a pandemic should be investigated ; and d) realistic worst-case exposure scenarios should be developed. Additional modeling would be useful to identify localized areas within river catchments that might be prone to high pharmaceutical concentrations in sewage treatment plant effluent. Ongoing seasonal use of Tamiflu in Japan offers opportunities for researchers to assess how much OC enters and persists in the aquatic environment.
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| 15. |
- Connolly, L. J., et al.
(författare)
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Effects of small-volume soccer and vibration training on body composition, aerobic fitness, and muscular PCr kinetics for inactive women aged 20-45
- 2014
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Ingår i: Journal of Sport and Health Science. - : Elsevier BV. - 2095-2546. ; 3:4, s. 284-292
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: The present study investigated the effects of 16 weeks of small-volume, small-sided soccer training soccer group (SG, n = 13) and oscillating whole-body vibration training vibration group (VG, n = 17) on body composition, aerobic fitness, and muscle PCr kinetics in healthy inactive premenopausal women in comparison with an inactive control group (CO, n = 14). Methods: Training for SG and VG consisted of twice-weekly 15-min sessions with average heart rates (HRs) of similar to 155 and 90 bpm respectively. Pre- and post-measurements of body composition (DXA), phosphocreatine (PCr) on-and off-kinetics, and HR measurements during standardised submaximal exercise were performed. Results: After 16 weeks of training in SG, fat percentage was lowered (p = 0.03) by 1.7% +/- 2.4% from 37.5% +/- 6.9% to 35.8% +/- 6.2% and the PCr decrease in the quadriceps during knee-extension ramp exercise was attenuated (4% +/- 8%, p = 0.04), with no changes in VG or CO (time-group effect: p = 0.03 and p = 0.03). Submaximal exercise HR was also reduced in SG after 16 weeks of training (6% +/- 5% of HRmax, p = 0.01). Conclusion: Short duration soccer training for 16 weeks appears to be sufficient to induce favourable changes in body composition and indicators of aerobic fitness and muscle oxidative capacity in untrained premenopausal women. Copyright (C) 2014, Shanghai University of Sport. Production and hosting by Elsevier B.V. All rights reserved.
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| 16. |
- Krustrup, P., et al.
(författare)
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The Yo-Yo IE2 Test: Physiological Response for Untrained Men versus Trained Soccer Players
- 2015
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Ingår i: Medicine and Science in Sports and Exercise. - : Ovid Technologies (Wolters Kluwer Health). - 0195-9131. ; 47:1, s. 100-108
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Tidskriftsartikel (refereegranskat)abstract
- Purpose This study aimed to examine the physical capacity and physiological response to the Yo-Yo Intermittent Endurance level 2 test (IE2) for untrained individuals (UTR) and trained male soccer players (TR) and to investigate the determinants of intense intermittent exercise performance. Methods Thirty-four healthy UTR males and 15 age-matched TR performed a maximal incremental treadmill test and a Yo-Yo IE2 test. Muscle biopsies and blood samples were obtained, and heart rate (HR) was measured before, during, and after tests. Results UTR had a 67% lower (P < 0.01) Yo-Yo IE2 performance (665 271 vs 2027 +/- 298 m; effect size (ES), 4.8), 34% lower VO2max (P < 0.01), and 19% lower resting muscle glycogen (P < 0.05) than those of TR. Blood lactate concentration and HR during the first 560 m of the Yo-Yo IE2 test were higher (P < 0.01) in UTR than those in TR (560 m, 7.4 +/- 2.8 vs 2.4 +/- 0.8 mM; ES, 1.7-2.8; 188 +/- 11 vs 173 +/- 8 bpm; ES, 0.9-1.5), with no differences at exhaustion. Time >95% HRmax was lower (P < 0.01) in UTR than that in TR (1.0 +/- 1.1 vs 6.3 +/- 2.9 min; ES, 3.1). Mean rates of muscle creatine phosphate utilization (16.5 +/- 9.5 vs 4.3 +/- 2.7 mmolkg(-1) d.wmin(-1)), muscle lactate accumulation (16.8 +/- 9.1 vs 4.2 +/- 2.9 mmolkg(-1) d.w.min(-1)), and glycogen breakdown (29.6 +/- 14.2 vs 7.7 +/- 5.4 mmolkg(-1) d.w.min(-1)) were fourfold higher (P < 0.01; ES, 1.4-1.7) in UTR than those in TR. For UTR, correlations (P < 0.01) were observed between Yo-Yo IE2 performance and VO2max (r = 0.77), incremental treadmill test performance (r = 0.79), and muscle citrate synthase activity (r = 0.57) but not for TR (r = -0.12 to 0.50; P > 0.05). Conclusions The Yo-Yo IE2 test was shown to possess high construct validity by showing large differences in performance, HR, and anaerobic metabolism between UTR and TR. In addition, VO2max seemed to be important for intermittent exercise performance in UTR but not for TR.
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| 17. |
- Mazzola, F., et al.
(författare)
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Simultaneous Conduction and Valence Band Quantization in Ultrashallow High-Density Doping Profiles in Semiconductors
- 2018
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Ingår i: Physical Review Letters. - 0031-9007. ; 120:4
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate simultaneous quantization of conduction band (CB) and valence band (VB) states in silicon using ultrashallow, high-density, phosphorus doping profiles (so-called Si:P δ layers). We show that, in addition to the well-known quantization of CB states within the dopant plane, the confinement of VB-derived states between the subsurface P dopant layer and the Si surface gives rise to a simultaneous quantization of VB states in this narrow region. We also show that the VB quantization can be explained using a simple particle-in-a-box model, and that the number and energy separation of the quantized VB states depend on the depth of the P dopant layer beneath the Si surface. Since the quantized CB states do not show a strong dependence on the dopant depth (but rather on the dopant density), it is straightforward to exhibit control over the properties of the quantized CB and VB states independently of each other by choosing the dopant density and depth accordingly, thus offering new possibilities for engineering quantum matter.
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