| 1. |
- Imanishi, T., et al.
(author)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
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In: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
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Journal article (peer-reviewed)abstract
- The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
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| 2. |
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| 3. |
- Spinoglio, L., et al.
(author)
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- 2017
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In: Publications Astronomical Society of Australia. - : Cambridge University Press (CUP). - 1323-3580 .- 1448-6083. ; 34
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Journal article (peer-reviewed)abstract
- IR spectroscopy in the range 12-230 mu m with the SPace IR telescope for Cosmology and Astrophysics (SPICA) will reveal the physical processes governing the formation and evolution of galaxies and black holes through cosmic time, bridging the gap between the James Webb Space Telescope and the upcoming Extremely Large Telescopes at shorter wavelengths and the Atacama Large Millimeter Array at longer wavelengths. The SPICA, with its 2.5-m telescope actively cooled to below 8 K, will obtain the first spectroscopic determination, in the mid-IR rest-frame, of both the star-formation rate and black hole accretion rate histories of galaxies, reaching lookback times of 12 Gyr, for large statistically significant samples. Densities, temperatures, radiation fields, and gas-phase metallicities will be measured in dust-obscured galaxies and active galactic nuclei, sampling a large range in mass and luminosity, from faint local dwarf galaxies to luminous quasars in the distant Universe. Active galactic nuclei and starburst feedback and feeding mechanisms in distant galaxies will be uncovered through detailed measurements of molecular and atomic line profiles. The SPICA's large-area deep spectrophotometric surveys will provide mid-IR spectra and continuum fluxes for unbiased samples of tens of thousands of galaxies, out to redshifts of z similar to 6.
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| 4. |
- Fernandez-Ontiveros, J. A., et al.
(author)
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A CO molecular gas wind 340 pc away from the Seyfert 2 nucleus in ESO420-G13 probes an elusive radio jet*
- 2020
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 633
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Journal article (peer-reviewed)abstract
- A prominent jet-driven outflow of CO(2-1) molecular gas is found along the kinematic minor axis of the Seyfert 2 galaxy ESO 420-G13, at a distance of 340-600 pc from the nucleus. The wind morphology resembles the characteristic funnel shape, formed by a highly collimated filamentary emission at the base, and likely traces the jet propagation through a tenuous medium, until a bifurcation point at 440 pc. Here the jet hits a dense molecular core and shatters, dispersing the molecular gas into several clumps and filaments within the expansion cone. We also trace the jet in ionised gas within the inner less than or similar to 340 pc using the [NeII](12.8 mu m) line emission, where the molecular gas follows a circular rotation pattern. The wind outflow carries a mass of similar to 8 x 10(6) M-circle dot at an average wind projected speed of similar to 160 km s(-1), which implies a mass outflow rate of similar to 14 M-circle dot yr(-1). Based on the structure of the outflow and the budget of energy and momentum, we discard radiation pressure from the active nucleus, star formation, and supernovae as possible launching mechanisms. ESO 420-G13 is the second case after NGC 1377 where a previously unknown jet is revealed through its interaction with the interstellar medium, suggesting that unknown jets in feeble radio nuclei might be more common than expected. Two possible jet-cloud configurations are discussed to explain an outflow at this distance from the AGN. The outflowing gas will likely not escape, thus a delay in the star formation rather than quenching is expected from this interaction, while the feedback effect would be confined within the central few hundred parsecs of the galaxy.
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| 5. |
- Izumi, T., et al.
(author)
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ALMA OBSERVATIONS OF THE SUBMILLIMETER DENSE MOLECULAR GAS TRACERS IN THE LUMINOUS TYPE-1 ACTIVE NUCLEUS OF NGC 7469
- 2015
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In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 811:1, s. Article Number: 39-
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Journal article (peer-reviewed)abstract
- We present Atacama Large Millimeter/submillimeter Array (ALMA) Cycle 1 observations of the central kiloparsec region of the luminous type. 1 Seyfert galaxy NGC 7469 with unprecedented high resolution (0.'' 5x0.'' 4 = 165 x 132 pc) at submillimeter wavelengths. Utilizing the wide. bandwidth of ALMA, we simultaneously obtained HCN(4-3), HCO+(4-3), CS(7-6), and partially CO(3-2) line maps, as well as the 860 mu m continuum. The region consists of the central similar to 1 '' component and the surrounding starburst ring with a radius of similar to 1.'' 5-2.'' 5. Several structures connect these components. Except for CO(3-2), these dense gas tracers are significantly concentrated toward the central similar to 1 '', suggesting their suitability to probe the nuclear regions of galaxies. Their spatial distribution resembles well those of centimeter and mid-infrared continuum emissions, but it is anticorrelated with the optical one, indicating the existence of dust-obscured star formation. The integrated intensity ratios of HCN(4-3)/HCO+(4-3) and HCN(4-3)/CS(7-6) are higher at the active galactic nucleus (AGN) position than at the starburst ring, which is consistent with our previous findings (submillimeter-HCN enhancement). However, the HCN(4-3)/HCO+(4-3) ratio at the AGN position of NGC 7469 (1.11 +/- 0.06) is almost half of the corresponding value of the low-luminosity type. 1 Seyfert galaxy NGC 1097 (2.0 +/- 0.2), despite the more than two orders of magnitude higher X-ray luminosity of NGC 7469. But the ratio is comparable to that of the close vicinity of the AGN of NGC 1068 (similar to 1.5). Based on these results, we speculate that some heating mechanisms other than X-ray (e.g., mechanical heating due to an AGN jet) can contribute significantly for shaping the chemical composition in NGC 1097.
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| 6. |
- Belete, A. Bewketu, et al.
(author)
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Molecular gas kinematics in the nuclear region of nearby Seyfert galaxies with ALMA
- 2021
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 654
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Journal article (peer-reviewed)abstract
- Context. The study of the distribution, morphology, and kinematics of cold molecular gas in the nuclear and circumnuclear regions of active galactic nuclei (AGNs) helps to characterise and hence to quantify the impact of the AGNs on the host galaxy over its lifetime. Aims. We present the analysis of the molecular gas in the nuclear regions of three Seyfert galaxies, NGC 4968, NGC 4845, and MCG-06-30-15, using Atacama Large sub-Millimetre Array (ALMA) observations of the CO(2-1) emission line. The aim is to determine the kinematics of the gas in the central (∼1 kpc) region and thereby to probe nuclear fueling and feedback of AGNs. Methods. We used two different softwares, namely the 3D-Based Analysis of Rotating Object via Line Observations and DiskFit, to model the kinematics of the gas in the molecular disc, and thereby to determine the gas rotation and any kinematical perturbations. Results. Circular motions dominate the kinematics of the molecular gas in the central discs, mainly in NGC 4845 and MCG-06-30-15; however there is clear evidence of non-circular motions in the central (∼1 kpc) region of NGC 4845 and NGC 4968. The strongest non-circular motion is detected in the inner disc of NGC 4968, mainly along the minor kinematic axis, with a velocity ∼115 km s-1. Of all DiskFit models, the bisymmetric model is found to give the best fit for NGC 4968 and NGC 4845, indicating that the observed non-circular motions in the inner disc of these galaxies could result from the nuclear barred structure, where the gas streams in elliptical orbits aligned along the bar. If the dynamics of NGC 4968 is modelled as a corotation pattern just outside of the bar, the bar pattern speed becomes ωb = 52 km s-1 kpc-1; the corotation is set at 3.5 kpc; and the inner Lindblad resonance (ILR) ring is R = 300 pc, corresponding to the CO emission ring. In the NGC 4968 galaxy, the torques exerted on the gas by the bar are positive in the centre, within the gas nuclear ring, and negative outside. This shows that the gas is transiently trapped in the ILR. The comparison of the CO intensity maps with the map of the cold dust emission shows an absence of CO in the centre of NGC 4968; also the dust distribution and CO emission in and around the centre of NGC 4845 have similar extensions. The 1.2 mm ALMA continuum is peaked and compact in NGC 4968 and MCG-06-30-15, but their CO(2-1) emissions have extended distributions. Allowing the CO-to-H2 conversion factor αCO between 0.8 and 3.2, which is typical of nearby galaxies of the same type, the molecular mass M(H2) is estimated to be ∼3 - 12 × 107 M⊙ (NGC 4968), ∼9 - 36 × 107 M⊙ (NGC 4845), and ∼1 - 4 × 107 M⊙ (MCG-06-30-15). Conclusions. We conclude that the observed non-circular motions in the molecular disc of NGC 4968 and likely those seen in NGC 4845 are due to the presence of the bar in the nuclear region. We discuss the possibility that the observed pattern in the kinematics might be a consequence of the presence of AGNs, and this might be the case for NGC 4845. At the current spectral and spatial resolution and sensitivity, we cannot claim any strong evidence in these sources of the long sought feedback or feeding effect resulting from the presence of AGNs.
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| 7. |
- Izumi, T., et al.
(author)
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SUBMILLIMETER-HCN DIAGRAM FOR ENERGY DIAGNOSTICS IN THE CENTERS OF GALAXIES
- 2016
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In: Astrophysical Journal. - : American Astronomical Society. - 1538-4357 .- 0004-637X. ; 818:1
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Journal article (peer-reviewed)abstract
- Compiling data from literature and the Atacama Large Millimeter/submillimeter Array archive, we show enhanced HCN(4-3)/HCO+(4-3) and/or HCN(4-3)/CS(7-6) integrated intensity ratios in circumnuclear molecular gas around active galactic nuclei (AGNs) compared to those in starburst (SB) galaxies (submillimeter HCN. enhancement). The number of sample galaxies is significantly increased from our previous work. We expect that this feature could potentially be an extinction-free energy diagnostic tool of nuclear regions of galaxies. Non-LTE radiative transfer modelings of the above molecular emission lines involving both collisional and radiative excitation, as well as a photon trapping effect, were conducted to investigate the cause of the high line ratios in AGNs. As a result, we found that enhanced abundance ratios of HCN to HCO+ and HCN to CS in AGNs as compared to SB galaxies by a factor of a few to even greater than or similar to 10 are a plausible explanation for the submillimeter HCN. enhancement. However, a counterargument of a systematically higher gas density in AGNs than in SB galaxies can also be a plausible scenario. Although we cannot fully distinguish. these two scenarios at this moment owing to an insufficient amount of multi-transition, multi-species data, the former scenario is indicative of abnormal chemical composition in AGNs. Regarding the actual mechanism to realize the composition, we suggest that it is difficult with conventional gas-phase X-ray-dominated region ionization models to reproduce the observed high line ratios. We might have to take into account other mechanisms such as neutral-neutral reactions that are efficiently activated in high-temperature environments and/or mechanically heated regions to further understand the high line ratios in AGNs.
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| 8. |
- Martin, S., et al.
(author)
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Multimolecule ALMA observations toward the Seyfert 1 galaxy NGC 1097
- 2015
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 573
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Journal article (peer-reviewed)abstract
- Context. The nearby Sy 1 galaxy NGC 1097 represents an ideal laboratory for exploring the molecular chemistry in the surroundings of an active galactic nucleus (AGN). Aims. Exploring the distribution of different molecular species allows us to understand the physical processes affecting the interstellar medium both in the AGN vicinity and in the outer star forming molecular ring. Methods. We carried out 3 mm ALMA observations that include seven different molecular species, namely HCN, HCO+, CCH, CS, HNCO, SiO, HC3N, and SO, as well as the C-13 isotopologues of the first two. Spectra were extracted from selected positions and all species were imaged over the central 2 kpc (similar to 30 '') of the galaxy at a resolution of similar to 2.2 '' x 1.5 '' (150 pc x 100 pc). Results. HCO+ and CS appear to be slightly enhanced in the star forming ring. CCH shows the largest variations across NGC 1097 and is suggested to be a good tracer of both obscured and early stage star formation. HNCO, SiO, and HC3N are significantly enhanced in the inner circumnuclear disk surrounding the AGN. Conclusions. Differences in the molecular abundances are observed between the star forming ring and the inner circumnuclear disk. We conclude that the HCN/HCO+ and HCN/CS differences observed between AGN-dominated and starburst (SB) galaxies are not due to a HCN enhancement due to X-rays, but rather this enhancement is produced by shocked material at distances of 200 pc from the AGN. Additionally, we claim that lower HCN/CS is a combination of a small underabundance of CS in AGNs, together with excitation effects, where a high density gas component (similar to 10(6) cm(-3)) may be more prominent in SB galaxies. However, the most promising are the differences found among the dense gas tracers that, at our modest spatial resolution, seem to outline the physical structure of the molecular disk around the AGN. In this picture, HNCO probes the well-shielded gas in the disk, surrounding the dense material moderately exposed to the X-ray radiation traced by HC3N. Finally SiO might be the innermost molecule in the disk structure.
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| 9. |
- Falstad, Niklas, 1987, et al.
(author)
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CON-quest: Searching for the most obscured galaxy nuclei
- 2021
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 649
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Journal article (peer-reviewed)abstract
- Context. Some luminous and ultraluminous infrared galaxies (LIRGs and ULIRGs) host extremely compact (r < 100 pc) and dusty nuclei. The high extinction associated with large column densities of gas and dust toward these objects render them hard to detect at many wavelengths. The intense infrared radiation arising from warm dust in these sources can provide a significant fraction of the bolometric luminosity of the galaxy and is prone to excite vibrational levels of molecules such as HCN. This results in emission from the rotational transitions of vibrationally excited HCN (HCN-vib); the brightest emission is found in compact obscured nuclei (CONs; ςHCN-vib > 1 L⊙ pc-2 in the J = 3-2 transition). However, there have been no systematic searches for CONs, and it is unknown how common they are. Aims. We aim to establish how common CONs are in the local Universe (z < 0.08), and whether their prevalence depends on the luminosity or other properties of the host galaxy. Methods. We conducted an Atacama Large Millimeter/submillimeter Array survey of the rotational J = 3-2 transition of HCN-vib in a volume-limited sample of 46 far-infrared luminous galaxies. Results. Compact obscured nuclei are identified in 38-13+18% of the ULIRGs, 21-6+12% of the LIRGs, and 0-0+9% of the lower luminosity galaxies. We find no dependence on the inclination of the host galaxy, but strong evidence of lower IRAS 25 μm to 60 μm flux density ratios (f25/f60) in CONs (with the exception of one galaxy, NGC 4418) compared to the rest of the sample. Furthermore, we find that CONs have stronger silicate features (s9.7 μm), but similar polycyclic aromatic hydrocarbon equivalent widths (EQW6.2 μm) compared to other galaxies. Along with signatures of molecular inflows seen in the far-infrared in most CONs, submillimeter observations also reveal compact, often collimated, outflows. Conclusions. In the local Universe, CONs are primarily found in (U)LIRGs, in which they are remarkably common. As such systems are often highly disturbed, inclinations are difficult to estimate, and high-resolution continuum observations of the individual nuclei are required to determine if the CON phenomenon is related to the inclinations of the nuclear disks. Further studies of the in- A nd outflow properties of CONs should also be conducted to investigate how these are connected to each other and to the CON phenomenon. The lower f25/f60 ratios in CONs as well as the results for the mid-infrared diagnostics investigated (EQW6.2 μm and s9.7 μm) are consistent with the notion that large dust columns gradually shift the radiation from the hot nucleus to longer wavelengths, making the mid- A nd far-infrared "photospheres"significantly cooler than the interior regions. Finally, to assess the importance of CONs in the context of galaxy evolution, it is necessary to extend this study to higher redshifts where (U)LIRGs are more common.
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| 10. |
- Falstad, Niklas, 1987, et al.
(author)
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Hidden or missing outflows in highly obscured galaxy nuclei?
- 2019
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 623
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Journal article (peer-reviewed)abstract
- Understanding the nuclear growth and feedback processes in galaxies requires investigating their often obscured central regions. One way to do this is to use (sub)millimeter line emission from vibrationally excited HCN (HCN-vib), which is thought to trace warm and highly enshrouded galaxy nuclei. It has been suggested that the most intense HCN-vib emission from a galaxy is connected to a phase of nuclear growth that occurs before the nuclear feedback processes have been fully developed. Aims. We aim to investigate if there is a connection between the presence of strong HCN-vib emission and the development of feedback in (ultra)luminous infrared galaxies ((U)LIRGs). Methods. We collected literature and archival data to compare the luminosities of rotational lines of HCN-vib, normalized to the total infrared luminosity, to the median velocities of 119 μm OH absorption lines, potentially indicating outflows, in a total of 17 (U)LIRGs. Results. The most HCN-vib luminous systems all lack signatures of significant molecular outflows in the far-infrared OH absorption lines. However, at least some of the systems with bright HCN-vib emission have fast and collimated outflows that can be seen in spectral lines at longer wavelengths, including in millimeter emission lines of CO and HCN (in its vibrational ground state) and in radio absorption lines of OH. Conclusions. We conclude that the galaxy nuclei with the highest L HCN-vib /L IR do not drive wide-angle outflows that are detectable using the median velocities of far-infrared OH absorption lines. This is possibly because of an orientation effect in which sources oriented in such a way that their outflows are not along our line of sight also radiate a smaller proportion of their infrared luminosity in our direction. It could also be that massive wide-angle outflows destroy the deeply embedded regions responsible for bright HCN-vib emission, so that the two phenomena cannot coexist. This would strengthen the idea that vibrationally excited HCN traces a heavily obscured stage of evolution before nuclear feedback mechanisms are fully developed.
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