| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Appeltans, W., et al.
(författare)
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The Magnitude of Global Marine Species Diversity
- 2012
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Ingår i: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 22:23, s. 2189-2202
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Tidskriftsartikel (refereegranskat)abstract
- Background: The question of how many marine species exist is important because it provides a metric for how much we do and do not know about life in the oceans. We have compiled the first register of the marine species of the world and used this baseline to estimate how many more species, partitioned among all major eukaryotic groups, may be discovered. Results: There are similar to 226,000 eukaryotic marine species described. More species were described in the past decade (similar to 20,000) than in any previous one. The number of authors describing new species has been increasing at a faster rate than the number of new species described in the past six decades. We report that there are similar to 170,000 synonyms, that 58,000-72,000 species are collected but not yet described, and that 482,000-741,000 more species have yet to be sampled. Molecular methods may add tens of thousands of cryptic species. Thus, there may be 0.7-1.0 million marine species. Past rates of description of new species indicate there may be 0.5 +/- 0.2 million marine species. On average 37% (median 31%) of species in over 100 recent field studies around the world might be new to science. Conclusions: Currently, between one-third and two-thirds of marine species may be undescribed, and previous estimates of there being well over one million marine species appear highly unlikely. More species than ever before are being described annually by an increasing number of authors. If the current trend continues, most species will be discovered this century.
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| 3. |
- van Dishoeck, E. F., et al.
(författare)
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Water in star-forming regions: Physics and chemistry from clouds to disks as probed by Herschel spectroscopy
- 2021
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 648
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Tidskriftsartikel (refereegranskat)abstract
- Context. Water is a key molecule in the physics and chemistry of star and planet formation, but it is difficult to observe from Earth. The Herschel Space Observatory provided unprecedented sensitivity as well as spatial and spectral resolution to study water. The Water In Star-forming regions with Herschel (WISH) key program was designed to observe water in a wide range of environments and provide a legacy data set to address its physics and chemistry. Aims. The aim of WISH is to determine which physical components are traced by the gas-phase water lines observed with Herschel and to quantify the excitation conditions and water abundances in each of these components. This then provides insight into how and where the bulk of the water is formed in space and how it is transported from clouds to disks, and ultimately comets and planets. Methods. Data and results from WISH are summarized together with those from related open time programs. WISH targeted ∼80 sources along the two axes of luminosity and evolutionary stage: from low- to high-mass protostars (luminosities from <1 to > 10Lpdbl) and from pre-stellar cores to protoplanetary disks. Lines of H2O and its isotopologs, HDO, OH, CO, and [O I], were observed with the HIFI and PACS instruments, complemented by other chemically-related molecules that are probes of ultraviolet, X-ray, or grain chemistry. The analysis consists of coupling the physical structure of the sources with simple chemical networks and using non-LTE radiative transfer calculations to directly compare models and observations. Results. Most of the far-infrared water emission observed with Herschel in star-forming regions originates from warm outflowing and shocked gas at a high density and temperature (> 10cm-3, 300-1000 K, v ∼ 25 km s-1), heated by kinetic energy dissipation. This gas is not probed by single-dish low-J CO lines, but only by CO lines with Jup > 14. The emission is compact, with at least two different types of velocity components seen. Water is a significant, but not dominant, coolant of warm gas in the earliest protostellar stages. The warm gas water abundance is universally low: orders of magnitude below the H2O/H2 abundance of 4 × 10-4 expected if all volatile oxygen is locked in water. In cold pre-stellar cores and outer protostellar envelopes, the water abundance structure is uniquely probed on scales much smaller than the beam through velocity-resolved line profiles. The inferred gaseous water abundance decreases with depth into the cloud with an enhanced layer at the edge due to photodesorption of water ice. All of these conclusions hold irrespective of protostellar luminosity. For low-mass protostars, a constant gaseous HDO/H2O ratio of ∼0.025 with position into the cold envelope is found. This value is representative of the outermost photodesorbed ice layers and cold gas-phase chemistry, and much higher than that of bulk ice. In contrast, the gas-phase NH3 abundance stays constant as a function of position in low-mass pre- and protostellar cores. Water abundances in the inner hot cores are high, but with variations from 5 × 10-6 to a few × 10-4 for low- and high-mass sources. Water vapor emission from both young and mature disks is weak. Conclusions. The main chemical pathways of water at each of the star-formation stages have been identified and quantified. Low warm water abundances can be explained with shock models that include UV radiation to dissociate water and modify the shock structure. UV fields up to 102-10times the general interstellar radiation field are inferred in the outflow cavity walls on scales of the Herschel beam from various hydrides. Both high temperature chemistry and ice sputtering contribute to the gaseous water abundance at low velocities, with only gas-phase (re-)formation producing water at high velocities. Combined analyses of water gas and ice show that up to 50% of the oxygen budget may be missing. In cold clouds, an elegant solution is that this apparently missing oxygen is locked up in larger μm-sized grains that do not contribute to infrared ice absorption. The fact that even warm outflows and hot cores do not show H2O at full oxygen abundance points to an unidentified refractory component, which is also found in diffuse clouds. The weak water vapor emission from disks indicates that water ice is locked up in larger pebbles early on in the embedded Class I stage and that these pebbles have settled and drifted inward by the Class II stage. Water is transported from clouds to disks mostly as ice, with no evidence for strong accretion shocks. Even at abundances that are somewhat lower than expected, many oceans of water are likely present in planet-forming regions. Based on the lessons for galactic protostars, the low-J H2O line emission (Eup < 300 K) observed in extragalactic sources is inferred to be predominantly collisionally excited and to originate mostly from compact regions of current star formation activity. Recommendations for future mid- to far-infrared missions are made.
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| 4. |
- Aidas, Kestutis, et al.
(författare)
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The Dalton quantum chemistry program system
- 2014
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Ingår i: WIREs Computational Molecular Science. - : Wiley. - 1759-0876 .- 1759-0884. ; 4:3, s. 269-284
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Tidskriftsartikel (refereegranskat)abstract
- Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.
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| 5. |
- Fedorov, R V, et al.
(författare)
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Structure of ribosomal protein TL5 complexed with RNA provides new insights into the CTC family of stress proteins
- 2001
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Ingår i: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; D57:7, s. 968-976
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Tidskriftsartikel (refereegranskat)abstract
- The crystal structure of Thermus thermophilus ribosomal protein TL5 in complex with a fragment of Escherichia coli 5S rRNA has been determined at 2.3 Å resolution. The protein consists of two domains. The structure of the N-terminal domain is close to the structure of E. coli ribosomal protein L25, but the C-terminal domain represents a new fold composed of seven -strands connected by long loops. TL5 binds to the RNA through its N-terminal domain, whereas the C-terminal domain is not included in this interaction. Cd2+ ions, the presence of which improved the crystal quality significantly, bind only to the protein component of the complex and stabilize the protein molecule itself and the interactions between the two molecules in the asymmetric unit of the crystal. The TL5 sequence reveals homology to the so-called general stress protein CTC. The hydrophobic cores which stabilize both TL5 domains are highly conserved in CTC proteins. Thus, all CTC proteins may fold with a topology close to that of TL5.
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| 6. |
- Saevarsdottir, S., et al.
(författare)
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Multiomics analysis of rheumatoid arthritis yields sequence variants that have large effects on risk of the seropositive subset
- 2022
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Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 0003-4967 .- 1468-2060. ; 81:8
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Tidskriftsartikel (refereegranskat)abstract
- Objectives To find causal genes for rheumatoid arthritis (RA) and its seropositive (RF and/or ACPA positive) and seronegative subsets. Methods We performed a genome-wide association study (GWAS) of 31 313 RA cases (68% seropositive) and similar to 1 million controls from Northwestern Europe. We searched for causal genes outside the HLA-locus through effect on coding, mRNA expression in several tissues and/or levels of plasma proteins (SomaScan) and did network analysis (Qiagen). Results We found 25 sequence variants for RA overall, 33 for seropositive and 2 for seronegative RA, altogether 37 sequence variants at 34 non-HLA loci, of which 15 are novel. Genomic, transcriptomic and proteomic analysis of these yielded 25 causal genes in seropositive RA and additional two overall. Most encode proteins in the network of interferon-alpha/beta and IL-12/23 that signal through the JAK/STAT-pathway. Highlighting those with largest effect on seropositive RA, a rare missense variant in STAT4 (rs140675301-A) that is independent of reported non-coding STAT4-variants, increases the risk of seropositive RA 2.27-fold (p=2.1x10(-9)), more than the rs2476601-A missense variant in PTPN22 (OR=1.59, p=1.3x10(-160)). STAT4 rs140675301-A replaces hydrophilic glutamic acid with hydrophobic valine (Glu128Val) in a conserved, surface-exposed loop. A stop-mutation (rs76428106-C) in FLT3 increases seropositive RA risk (OR=1.35, p=6.6x10(-11)). Independent missense variants in TYK2 (rs34536443-C, rs12720356-C, rs35018800-A, latter two novel) associate with decreased risk of seropositive RA (ORs=0.63-0.87, p=10(-9)-10(-27)) and decreased plasma levels of interferon-alpha/beta receptor 1 that signals through TYK2/JAK1/STAT4. Conclusion Sequence variants pointing to causal genes in the JAK/STAT pathway have largest effect on seropositive RA, while associations with seronegative RA remain scarce.
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| 7. |
- Calcutt, H., et al.
(författare)
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The ALMA-PILS survey: complex nitriles towards IRAS 16293-2422
- 2018
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 616
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Tidskriftsartikel (refereegranskat)abstract
- Context. Complex organic molecules are readily detected in the inner regions of the gaseous envelopes of forming protostars. Their detection is crucial to understanding the chemical evolution of the Universe and exploring the link between the early stages of star formation and the formation of solar system bodies, where complex organic molecules have been found in abundance. In particular, molecules that contain nitrogen are interesting due to the role nitrogen plays in the development of life and the compact scales such molecules have been found to trace around forming protostars. Aims. The goal of this work is to determine the inventory of one family of nitrogen-bearing organic molecules, complex nitriles (molecules with a -C N functional group) towards two hot corino sources in the low-mass protostellar binary IRAS 16293-2422. This work explores the abundance differences between the two sources, the isotopic ratios, and the spatial extent derived from molecules containing the nitrile functional group. Methods. Using data from the Protostellar Interferometric Line Survey (PILS) obtained with ALMA, we determine abundances and excitation temperatures for the detected nitriles. We also present a new method for determining the spatial structure of sources with high line density and large velocity gradients-Velocity-corrected INtegrated emission (VINE) maps. Results. We detect methyl cyanide (CH3CN) as well as five of its isotopologues, including CHD2CN, which is the first detection in the interstellar medium (ISM). We also detect ethyl cyanide (C2H5CN), vinyl cyanide (C2H3CN), and cyanoacetylene (HC3N). We find that abundances are similar between IRAS 16293A and IRAS 16293B on small scales except for vinyl cyanide which is only detected towards the latter source. This suggests an important difference between the sources either in their evolutionary stage or warm-up timescales. We also detect a spatially double-peaked emission for the first time in molecular emission in the A source, suggesting that this source is showing structure related to a rotating toroid of material. Conclusions. With high-resolution observations, we have been able to show for the first time a number of important similarities and differences in the nitrile chemistry in these objects. These illustrate the utility of nitriles as potential tracers of the physical conditions in star-forming regions.
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| 8. |
- Dionatos, Odysseas, et al.
(författare)
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Feedback of molecular outflows from protostars in NGC 1333 revealed by Herschel and Spitzer spectro-imaging observations
- 2020
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 641
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Tidskriftsartikel (refereegranskat)abstract
- Context. Far infrared cooling of excited gas around protostars has been predominantly studied in the context of pointed observations. Large-scale spectral maps of star forming regions enable the simultaneous, comparative study of the gas excitation around an ensemble of sources at a common frame of reference, therefore, providing direct insights in the multitude of physical processes involved.Aims. We employ extended spectral-line maps to decipher the excitation, the kinematical, and dynamical processes in NGC 1333 as revealed by a number of different molecular and atomic lines, aiming to set a reference for the applicability and limitations of different tracers in constraining particular physical processes.Methods. We reconstructed line maps for H-2, CO, H2O, and [CI] using data obtained with the Spitzer infrared spectrograph and the Herschel HIFI and SPIRE instruments. We compared the morphological features revealed in the maps and derive the gas excitation conditions for regions of interest employing local thermodynamic equilibrium (LTE) and non-LTE methods. We also calculated the kinematical and dynamical properties for each outflow tracer in a consistent manner for all observed outflows driven by protostars in NGC 1333. We finally measured the water abundance in outflows with respect to carbon monoxide and molecular hydrogen.Results. CO and H-2 are highly excited around B-stars and, at lower, levels trace protostellar outflows. H2O emission is dominated by a moderately fast component associated with outflows. H2O also displays a weak, narrow-line component in the vicinity of B-stars associated to their ultraviolet (UV) field. This narrow component is also present in a few of outflows, indicating UV radiation generated in shocks. Intermediate J CO lines appear brightest at the locations traced by the narrow H2O component, indicating that beyond the dominating collisional processes, a secondary, radiative excitation component can also be active. The morphology, kinematics, excitation, and abundance variations of water are consistent with its excitation and partial dissociation in shocks. Water abundance ranges between 5 x 10(-7) and similar to 10(-5), with the lower values being more representative. Water is brightest and most abundant around IRAS 4A, which is consistent with the latter hosting a hot corino source. [CI] traces dense and warm gas in the envelopes surrounding protostars. Outflow mass flux is highest for CO and decreases by one and two orders of magnitude for H-2 and H2O, respectively.Conclusions. Large-scale spectral line maps can provide unique insights into the excitation of gas in star-forming regions. A comparative analysis of line excitation and morphologies at different locations allows us to decipher the dominant excitation conditions in each region in addition to isolating exceptional cases.
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| 9. |
- Harsono, D., et al.
(författare)
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Missing water in Class i protostellar disks
- 2020
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 636
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Tidskriftsartikel (refereegranskat)abstract
- Context. Water is a key volatile that provides insight into the initial stages of planet formation. The low water abundances inferred from water observations toward low-mass protostellar objects may point to a rapid locking of water as ice by large dust grains during star and planet formation. However, little is known about the water vapor abundance in newly formed planet-forming disks. Aims. We aim to determine the water abundance in embedded Keplerian disks through spatially-resolved observations of H218O lines to understand the evolution of water during star and planet formation. Methods. We present H218O line observations with ALMA and NOEMA millimeter interferometers toward five young stellar objects. NOEMA observed the 31,3-22,0 line (Eup? kB = 203.7 K) while ALMA targeted the 41,4-32,1 line (Eup? kB = 322.0 K). Water column densities were derived considering optically thin and thermalized emission. Our observations were sensitive to the emission from the known Keplerian disks around three out of the five Class I objects in the sample. Results. No H218O emission is detected toward any of our five Class I disks. We report upper limits to the integrated line intensities. The inferred water column densities in Class I disks are NH218O < 1015 cm-2 on 100 au scales, which include both the disk and envelope. The upper limits imply a disk-averaged water abundance of ? 10-6 with respect to H2 for Class I objects. After taking the physical structure of the disk into account, the upper limit to the water abundance averaged over the inner warm disk with T > 100 K is between ~10-7 and 10-5. Conclusions. Water vapor is not abundant in warm protostellar envelopes around Class I protostars. Upper limits to the water vapor column densities in Class I disks are at least two orders of magnitude lower than values found in Class 0 disk-like structures.
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| 10. |
- Jensen, S. S., et al.
(författare)
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ALMA observations of doubly deuterated water: Inheritance of water from the prestellar environment
- 2021
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 650
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Tidskriftsartikel (refereegranskat)abstract
- Context. Establishing the origin of the water D/H ratio in the Solar System is central to our understanding of the chemical trail of water during the star and planet formation process. Recent modeling suggests that comparisons of the D2O/HDO and HDO/H2O ratios are a powerful way to trace the chemical evolution of water and, in particular, determine whether the D/H ratio is inherited from the molecular cloud or established locally. Aims. We seek to determine the D2O column density and derive the D2O/HDO ratios in the warm region toward the low-mass Class 0 sources B335 and L483. The results are compared with astrochemical models and previous observations to determine their implications for the chemical evolution of water. Methods. We present ALMA observations of the D2O 11,0-10,1 transition at 316.8 GHz toward B335 and L483 at 0.′′5 ( 100 au) resolution, probing the inner warm envelope gas. The column densities of D2O, HDO, and H218O are determined by synthetic spectrum modeling and direct Gaussian fitting, under the assumption of a single excitation temperature and similar spatial extent for the three water isotopologs. Results. D2O is detected toward both sources in the inner warm envelope. The derived D2O/HDO ratio is (1.0 ± 0.2) × 10-2 for L483 and (1.4 ± 0.1) × 10-2 for B335. These values indicate that the D2O/HDO ratio is higher than the HDO/H2O ratios by a factor of 2 toward both sources. Conclusions. The high D2O/HDO ratios are a strong indication of chemical inheritance of water from the prestellar phase down to the inner warm envelope. This implies that the local cloud conditions in the prestellar phase, such as temperatures and timescales, determine the water chemistry at later stages and could provide a source of chemical differentiation in young systems. In addition, the observed D2O/H2O ratios support an observed dichotomy in the deuterium fractionation of water toward isolated and clustered protostars, namely, a higher D/H ratio toward isolated sources.
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