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  • 1.
    Adolfsson, Emma
    et al.
    Örebro University, School of Medical Sciences. Department of Laboratory Medicine.
    Jonasson, Jon
    Department of Laboratory Medicine, Örebro University Hospital, Örebro, Sweden.
    Kashyap, Aniruddh
    Department of Laboratory Medicine, Örebro University Hospital, Örebro, Sweden.
    Nordensköld, Anna
    Department of Cardiology, Faculty of Medicine and Health, Örebro University Hospital, Örebro, Sweden.
    Green, Anna
    Örebro University, School of Medical Sciences. Örebro University Hospital. Department of Laboratory Medicine.
    CNV-Z; a new tool for detecting copy number variation in next generation sequencing data2023In: SoftwareX, E-ISSN 2352-7110, Vol. 24, article id 101530Article in journal (Refereed)
    Abstract [en]

    We developed an efficient approach to diagnostic copy number analysis of targeted gene panel or whole exome sequence (WES) data. Here we present CNV-Z as a new tool for detection of copy number variants (CNVs). Deletions and duplications of chromosomal regions are widely implicated in both genomic evolution and genetic disorders. However, calling CNVs from targeted or exome sequence data is challenging. In most cases, the copy number of a chromosomal region is estimated as the depth of reads mapping to a certain bin or sliding window divided by the expected number of reads derived from a set of reference samples. This approach will inevitably miss smaller CNVs on an irregular basis, and quite frequently results in a disturbing number of false positive CNVs. We developed an alternative approach to detect CNVs based on deviation from expected read depth per position, instead of region. Cautiously used, the cohort of samples in the same run will do as a reference. With appropriate filtering, given high quality DNA and a set of suitable reference samples, CNV-Z detects CNVs ranging in length from one nucleotide to an entire chromosome, with few false positives. Performance is proved by benchmarking using both in-house targeted gene panel NGS data and a publicly available NGS dataset, both sets with multiplex ligation-dependent amplification probe (MLPA) validated CNVs. The outcome shows that CNV-Z detects single- and multi-exonic CNVs with high specificity and sensitivity using different kind of NGS data. On gene level, CNV-Z shows both excellent sensitivity and specificity. Compared to competing CNV callers, CNV-Z shows higher specificity and positive predictive value for detecting exonic CNVs.

  • 2.
    Adolfsson, Emma
    et al.
    Örebro University, School of Medical Sciences. Department of Laboratory Medicine, Örebro University Hospital, Sweden.
    Qvick, Alvida
    Örebro University, School of Medical Sciences. Department of Laboratory Medicine, Örebro University Hospital, Sweden.
    Gréen, Henrik
    Division of Drug Research, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.
    Kling, Daniel
    Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.
    Gunnarsson, Cecilia
    Department of Clinical Genetics and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Centre for Rare Diseases in South East Region of Sweden, Linköping University, Linköping, Sweden.
    Jonasson, Jon
    Department of Laboratory Medicine, Örebro University Hospital, Sweden; Department of Clinical Genetics and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
    Green, Anna
    Örebro University, School of Medical Sciences. Örebro University Hospital. Department of Laboratory Medicine, Örebro University Hospital, Sweden.
    Technical in-depth comparison of two massive parallel DNA-sequencing methods for formalin-fixed paraffin-embedded tissue from victims of sudden cardiac death2021In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 53, article id 102522Article in journal (Refereed)
    Abstract [en]

    Sudden cardiac death (SCD) is a tragic and traumatic event. SCD is often associated with hereditary genetic disease and in such cases, sequencing of stored formalin fixed paraffin embedded (FFPE) tissue is often crucial in trying to find a causal genetic variant. This study was designed to compare two massive parallel sequencing assays for differences in sensitivity and precision regarding variants related to SCD in FFPE material. From eight cases of SCD where DNA from blood had been sequenced using HaloPlex, corresponding FFPE samples were collected six years later. DNA from FFPE samples were amplified using HaloPlex HS, sequenced on MiSeq, representing the first method, as well as amplified using modified Twist and sequenced on NextSeq, representing the second method. Molecular barcodes were included to distinguish artefacts from true variants. In both approaches, read coverage, uniformity and variant detection were compared using genomic DNA isolated from blood and corresponding FFPE tissue, respectively. In terms of coverage uniformity, Twist performed better than HaloPlex HS for FFPE samples. Despite higher overall coverage, amplicon-based HaloPlex technologies, both for blood and FFPE tissue, suffered from design and/or performance issues resulting in genes lacking complete coverage. Although Twist had considerably lower overall mean coverage, high uniformity resulted in equal or higher fraction of genes covered at ≥ 20X. By comparing variants found in the matched samples in a pre-defined cardiodiagnostic gene panel, HaloPlex HS for FFPE material resulted in high sensitivity, 98.0% (range 96.6-100%), and high precision, 99.9% (range 99.5-100%) for moderately fragmented samples, but suffered from reduced sensitivity (range 74.2-91.1%) in more severely fragmented samples due to lack of coverage. Twist had high sensitivity, 97.8% (range 96.8-98.7%) and high precision, 99.9% (range 99.3-100%) in all analyzed samples, including the severely fragmented samples.

  • 3. Benmahi, B.
    et al.
    Cavali, T.
    Dobrijevic, M.
    Biver, N.
    Bermudez-Diaz, K.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Lellouch, E.
    Moreno, R.
    Fouchet, T.
    Hue, V
    Hartogh, P.
    Billebaud, F.
    Lecacheux, A.
    Hjalmarson, Å.
    Frisk, U.
    Olberg, M.
    Monitoring of the evolution of H2O vapor in the stratosphere of Jupiter over an 18-yr period with the Odin space telescope2020In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 641, article id A140Article in journal (Refereed)
    Abstract [en]

    Context. The comet Shoemaker-Levy 9 impacted Jupiter in July 1994, leaving its stratosphere with several new species, with water vapor (H2O) among them.

    Aims. With the aid of a photochemical model, H2O can be used as a dynamical tracer in the Jovian stratosphere. In this paper, we aim to constrain the vertical eddy diffusion (Kzz) at levels where H2O is present.

    Methods. We monitored the H2O disk-averaged emission at 556.936 GHz with the space telescope between 2002 and 2019, covering nearly two decades. We analyzed the data with a combination of 1D photochemical and radiative transfer models to constrain the vertical eddy diffusion in the stratosphere of Jupiter. Results. Odin observations show us that the emission of H2O has an almost linear decrease of about 40% between 2002 and 2019. We can only reproduce our time series if we increase the magnitude of Kzz in the pressure range where H2O diffuses downward from 2002 to 2019, that is, from ~0.2 mbar to ~5 mbar. However, this modified Kzz is incompatible with hydrocarbon observations. We find that even if an allowance is made for the initially large abundances of H2O and CO at the impact latitudes, the photochemical conversion of H2O to CO2 is not sufficient to explain the progressive decline of the H2O line emission, which is suggestive of additional loss mechanisms.

    Conclusions. The Kzz we derived from the Odin observations of H2O can only be viewed as an upper limit in the ~0.2 mbar to ~5 mbar pressure range. The incompatibility between the interpretations made from H2O and hydrocarbon observations probably results from 1D modeling limitations. Meridional variability of H2O, most probably at auroral latitudes, would need to be assessed and compared with that of hydrocarbons to quantify the role of auroral chemistry in the temporal evolution of the H2O abundance since the SL9 impacts. Modeling the temporal evolution of SL9 species with a 2D model would naturally be the next step in this area of study.

  • 4. Biver, N. ...
    et al.
    Floren, H.G. ...
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sandqvist, Aa. et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Odin observations of water emission variation in comet 103P/Hartley 22010In: Central Bureau Electronic Telegrams (CBET), Vol. CBET, no 2524Article in journal (Other academic)
  • 5. Biver, N.
    et al.
    Lellouch, E.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Florén, H.G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Observation of Saturn and the Enceladus water torus at 557 GHz with Odin2011In: EPSC Abstracts, 2011, p. 912-1-2Conference paper (Refereed)
  • 6. Biver, N.
    et al.
    Moreno, R.
    Bockelée-Morvan, D.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Colom, P.
    Crovisier, J.
    Lis, D. C.
    Boissier, J.
    Debout, V.
    Paubert, G.
    Milam, S.
    Hjalmarson, A.
    Lundin, S.
    Karlsson, T.
    Battelino, M.
    Frisk, U.
    Murtagh, D.
    Isotopic ratios of H, C, N, O, and S in comets C/2012 F6 (Lemmon) and C/2014 Q2 (Lovejoy)2016In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 589, article id A78Article in journal (Refereed)
    Abstract [en]

    The apparition of bright comets C/2012 F6 (Lemmon) and C/2014 Q2 (Lovejoy) in March-April 2013 and January 2015, combined with the improved observational capabilities of submillimeter facilities, offered an opportunity to carry out sensitive compositional and isotopic studies of the volatiles in their coma. We observed comet Lovejoy with the IRAM 30 m telescope between 13 and 26 January 2015, and with the Odin submillimeter space observatory on 29 January-3 February 2015. We detected 22 molecules and several isotopologues. The (H2O)-O-16 and (H2O)-O-18 production rates measured with Odin follow a periodic pattern with a period of 0.94 days and an amplitude of similar to 25%. The inferred isotope ratios in comet Lovejoy are O-16/O-18 = 499 +/- 24 and D/H = 1.4 +/- 0.4 x 10(-4) in water, S-32/S-34 = 24.7 +/- 3.5 in CS, all compatible with terrestrial values. The ratio C-12/C-13 = 109 +/- 14 in HCN is marginally higher than terrestrial and N-14/N-15 = 145 +/- 12 in HCN is half the Earth ratio. Several upper limits for D/H or C-12/C-13 in other molecules are reported. From our observation of HDO in comet C/2014 Q2 (Lovejoy), we report the first D/H ratio in an Oort Cloud comet that is not larger than the terrestrial value. On the other hand, the observation of the same HDO line in the other Oort-cloud comet, C/2012 F6 (Lemmon), suggests a D/H value four times higher. Given the previous measurements of D/H in cometary water, this illustrates that a diversity in the D/H ratio and in the chemical composition, is present even within the same dynamical group of comets, suggesting that current dynamical groups contain comets formed at very different places or times in the early solar system.

  • 7. Biver, N.,....
    et al.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Floren, H.-G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Molecular composition and outgassing variability of 103P/Hartley 2 from mm and submm observations2011In: EPSC Abstracts, EPSC , 2011, p. 938-1-2Conference paper (Refereed)
  • 8. Biver, Nicolas
    et al.
    Bockelée-Morvan, Dominique
    Moreno, Raphaël
    Crovisier, Jacques
    Colom, Pierre
    Lis, Dariusz C.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Boissier, Jérémie
    Despois, Didier
    Milam, Stefanie N.
    Ethyl alcohol and sugar in comet C/2014 Q2 (Lovejoy)2015In: Science Advances, E-ISSN 2375-2548, Vol. 1, no 9, article id e1500863Article in journal (Refereed)
    Abstract [en]

    The presence of numerous complex organic molecules (COMs; defined as those containing six or more atoms) around protostars shows that star formation is accompanied by an increase of molecular complexity. These COMs may be part of the material from which planetesimals and, ultimately, planets formed. Comets represent some of the oldest and most primitive material in the solar system, including ices, and are thus our best window into the volatile composition of the solar protoplanetary disk. Molecules identified to be present in cometary ices include water, simple hydrocarbons, oxygen, sulfur, and nitrogen-bearing species, as well as a few COMs, such as ethylene glycol and glycine. We report the detection of 21 molecules in comet C/2014 Q2 (Lovejoy), including the first identification of ethyl alcohol (ethanol, C2H5OH) and the simplest monosaccharide sugar glycolaldehyde (CH2OHCHO) in a comet. The abundances of ethanol and glycolaldehyde, respectively 5 and 0.8% relative to methanol (0.12 and 0.02% relative to water), are somewhat higher than the values measured in solar-type protostars. Overall, the high abundance of COMs in cometary ices supports the formation through grain-surface reactions in the solar system protoplanetary disk.

  • 9. Biver, Nicolas
    et al.
    Florén, Hans-Gustav
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Radio observations of Comet 9P/Tempel 1 before and after Deep Impact2007In: Icarus (Supplement), Vol. 191, no 2, p. 494-512Article in journal (Refereed)
  • 10. Biver, Nicolas
    et al.
    Florén, Hans-Gustav
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Radio observations of Comet 9P/Tempel 1 before and after Deep Impact2007In: Icarus, Vol. 187, no 1, p. 253-271Article in journal (Refereed)
  • 11. Biver, Nicolas
    et al.
    Florén, Hans-Gustav
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Submillimetre observations of comets with Odin: 2001 20052007In: Planetary and Space Science, Vol. 55, no 9, p. 1058-1068Article in journal (Refereed)
    Abstract [en]

    The Odin satellite, launched in February 2001, is equipped with a 1.1-m submillimetre telescope. Odin was used to observe the 557 GHz line of water with high spectral resolution in 12 comets between 2001 and 2005. Line shapes and spatial mapping provide information on the anisotropy of the outgassing and constraints on water excitation, enabling accurate measurements of the water production rate. Five comets were regularly observed over periods of more than one month to monitor the variation of their water outgassing rate with heliocentric distance. Observing campaigns have been generally coordinated with ground-based observations of molecular lines at Nançay, CSO or IRAM 30-m telescopes to obtain molecular abundances relative to water. Thanks to Odin's frequency coverage, it was also possible to detect the H218O 548 GHz line, first in comet 153P/Ikeya Zhang in April 2002 [Lecacheux, A., Biver, N., Crovisier, J. et al., 2003, Observations of water in comets with Odin. Astron. Astrophys. 402, L55 L58.] and then in comets C/2002 T7 (LINEAR), C/2001 Q4 (NEAT) and C/2004 Q2 (Machholz). The 16O/18O isotopic ratio (≈450) is consistent with the terrestrial value. Ammonia has been searched for in three comets through its J=1 0 line at 572 GHz and was tentatively detected in C/2001 Q4 and C/2002 T7. The derived abundances of NH3 relative to water are 0.5% and 0.3%, respectively, similar to values obtained in other comets with different techniques.

  • 12. Cavalie, T.
    et al.
    Biver, N.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Odin space telescope monitoring of water vapor in the stratosphere of Jupiter2012In: Planetary and Space Science, ISSN 0032-0633, E-ISSN 1873-5088, Vol. 61, no 1, p. 3-14Article in journal (Refereed)
    Abstract [en]

    The Odin space telescope has monitored the H2O (110–101) line in Jupiter's stratosphere over the 2003–2009 period. When comparing these data with previous spectra obtained with SWAS and Odin over the 1999–2002 period, we see no significant variations in the line-to-continuum ratio of the H2O line over the whole period. We have however tentatively identified a decrease by ∼15% of the line-to-continuum ratio between 2002 and 2007–2009, indicating that there was less H2O in the stratosphere of Jupiter in 2007–2009 than anticipated. We have tested the IDP (interplanetary dust particles) and SL9 (Shoemaker-Levy 9) 1D time-dependent models presented in Cavalié et al. [2008, Observation of water vapor in the stratosphere 613 of Jupiter with the Odin space telescope. Planetary and Space Science 56, 1573–1584]. We present a series of scenarios that lead to satisfactory fits of the whole data set (1999–2002 and 2003–2009 periods) based on IDP and SL9 models. The evolution of Jupiter's stratospheric H2O that we have tentatively observed has however to be confirmed by Herschel/HIFI observations. If the decrease of the line-to-continuum ratio is confirmed by future observations, it would be a direct evidence that Jupiter's H2O comes from SL9. In addition, this study shows that new constraints on Jupiter's eddy diffusion coefficient profile could be obtained (in the pressure ranges that are probed) from the monitoring of SL9 species in its stratosphere.

  • 13. Cavalie, T.
    et al.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Contribution of the Odin Space Telescope to the Understanding of the Origin of Water Vapor in the Atmosphere of Jupiter2007In: Societe Francaise d'Astronomie et d'Astrophysique, Vol. SF2A, p. 1-5Article, review/survey (Other (popular science, discussion, etc.))
  • 14.
    Engström, Karolina
    et al.
    Department of Clinical Genetics and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
    Vánky, Farkas
    Department of Cardiothoracic and Vascular Surgery and Department of Medical and Health Sciences, Linköping University, Linköping, Sweden.
    Rehnberg, Malin
    Department of Clinical Genetics and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
    Trinks, Cecilia
    Department of Clinical Genetics and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
    Jonasson, Jon
    Department of Clinical Genetics and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
    Green, Anna
    Örebro University, School of Medical Sciences. Örebro University Hospital. Department of Laboratory Medicine.
    Gunnarsson, Cecilia
    Department of Clinical Genetics and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
    Novel SMAD3 p.Arg386Thr genetic variant co-segregating with thoracic aortic aneurysm and dissection2020In: Molecular Genetics & Genomic Medicine, ISSN 2324-9269, Vol. 8, no 4, article id e1089Article in journal (Refereed)
    Abstract [en]

    Background: Pathogenic variants in the SMAD3 gene affecting the TGF-beta/SMAD3 signaling pathway with aortic vessel involvement cause Loeys-Dietz syndrome 3, also known as aneurysms-osteoarthritis syndrome.

    Methods: Description of clinical history of a family in Sweden using clinical data, DNA sequencing, bioinformatics, and pedigree analysis.

    Results: We report a novel SMAD3 variant, initially classified as a genetic variant of uncertain clinical significance (VUS), and later found to be co-segregating with aortic dissection in the family. The index patient presented with a dissecting aneurysm of the aorta including the ascending, descending, and abdominal parts. Genotype analysis revealed a heterozygous missense SMAD3 variant: NM_005902.3(SMAD3): c.11576G > C (p.Arg386Thr). The same variant was also identified in a 30 years old formalin-fixed paraffin-embedded block of tissue from a second cousin, who died at 26 years of age from a dissecting aneurysm of the aorta.

    Conclusion: A "variant of uncertain significance" according to the ACMG guidelines has always a scope for reappraisal. Genetic counselling to relatives, and the offering of surveillance service is important to families with aortic aneurysm disease. The report also highlight the potential use of FFPE analysis from deceased relatives to help in the interpretation of variants.

  • 15. Goldsmith, Paul F.
    et al.
    Liseau, Rene
    Larsson, Bengt
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    HERSCHEL Measurements of Molecular Oxygen in Orion2011In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 737, no 2, p. 96-Article in journal (Refereed)
    Abstract [en]

    We report observations of three rotational transitions of molecular oxygen (O2) in emission from the H2 Peak 1 position of vibrationally excited molecular hydrogen in Orion. We observed the 487 GHz, 774 GHz, and 1121 GHz lines using the Heterodyne Instrument for the Far Infrared on the Herschel Space Observatory, having velocities of 11 km s–1 to 12 km s–1 and widths of 3 km s–1. The beam-averaged column density is N(O2) = 6.5 × 1016 cm–2, and assuming that the source has an equal beam-filling factor for all transitions (beam widths 44, 28, and 19''), the relative line intensities imply a kinetic temperature between 65 K and 120 K. The fractional abundance of O2 relative to H2 is (0.3-7.3) × 10–6. The unusual velocity suggests an association with a ~5'' diameter source, denoted Peak A, the Western Clump, or MF4. The mass of this source is ~10 M and the dust temperature is ≥150 K. Our preferred explanation of the enhanced O2 abundance is that dust grains in this region are sufficiently warm (T ≥ 100 K) to desorb water ice and thus keep a significant fraction of elemental oxygen in the gas phase, with a significant fraction as O2. For this small source, the line ratios require a temperature ≥180 K. The inferred O2 column density 5 × 1018 cm–2 can be produced in Peak A, having N(H2) 4 × 1024 cm–2. An alternative mechanism is a low-velocity (10-15 km s–1) C-shock, which can produce N(O2) up to 1017 cm–2.

  • 16.
    Green, Anna
    et al.
    Örebro University, School of Medical Sciences. Örebro University Hospital. Department of Laboratory Medicine.
    Alonso, Consuelo
    Bionano Genomics, Evry Cedex, France.
    Jonasson, Jon
    Örebro University, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro, Sweden.
    Kashyap, Aniruddh
    Örebro University, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro, Sweden.
    Adolfsson, Emma
    Örebro University, School of Medical Sciences. Department of Laboratory Medicine.
    Nordenskjöld, Anna M.
    Örebro University, School of Medical Sciences. Örebro University Hospital. Department of Cardiology.
    Copy number variants in familial hypercholesterolemia genes using targeted NGS, validated through optical genome mapping2024In: European Journal of Human Genetics, ISSN 1018-4813, E-ISSN 1476-5438, Vol. 32, no Suppl. 1, p. 159-159, article id EP06.039Article in journal (Other academic)
    Abstract [en]

    Background/Objectives: Familial hypercholesterolemia (FH) is a common genetic disorder which is primarily caused by pathogenic variants in the LDLR, APOB, and PCSK9 genes. Approximately 10% of pathogenic variants in LDLR may be CNVs. Here, we combine NGS, MLPA, and Optical Genome Mapping (OGM) to investigate CNVs in LDLR.

    Methods: A NGS panel was designed for whole gene sequencing (8 genes) of 100 FH patients using Twist technology and Illumina platform. CNVs were detected using CNVexpo, and an in-house pipeline for base-resolved normalized coverage. Identified CNVs were validated using MLPA and OGM. Bionano Services Lab performed the OGM procedure. Purified gDNA was labeled using Direct Label and Stain DNA Labeling Kit. Saphyr chip was run aiming for 100X coverage. De novo assembly and Variant Annotation pipelines were executed on Bionano Solve v3.7. Bionano Access v1.7 was used for CNV reporting and visualization.

    Results: In five out of 100 samples NGS and MLPA data showed heterozygous deletions in LDLR. Three deletions, affecting different exons, was analyzed and confirmed using OGM. In two samples, OGM better defined the breakpoints as well as the size of the event, which expanded far beyond the gene of interest. In one sample, an additional CNV of SLCO1B1, a pharmaco-gene, important for transport of statins used for FH treatment was identified.

    Conclusion: CNVs in FH genes in FH patients could be detected using targeted NGS, which was further confirmed by MLPA and characterized using OGM.

  • 17. Hjalmarson, Å.
    et al.
    Frisk, U.
    Olberg, M.
    Bergman, P.
    Bernath, P.
    Biver, N.
    Black, J. H.
    Booth, R. S.
    Buat, V.
    Crovisier, J.
    Curry, C. L.
    Dahlgren, M.
    Encrenaz, P. J.
    Falgarone, E.
    Feldman, P. A.
    Fich, M.
    Florén, H. G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Fredrixon, M.
    Gerin, M.
    Gregersen, E. M.
    Hagström, M.
    Harju, J.
    Hasegawa, T.
    Horellou, C.
    Johansson, L. E. B.
    Kyrölä, E.
    Kwok, S.
    Larsson, B.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Lecacheux, A.
    Liljeström, T.
    Lindqvist, M.
    Liseau, R.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Llewellyn, E. J.
    Mattila, K.
    Mégie, G.
    Mitchell, G. F.
    Murtagh, D.
    Nyman, L.-Å.
    Nordh, H. L.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Olofsson, A. O. H.
    Olofsson, G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Olofsson, H.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Pagani, L.
    Persson, G.
    Plume, R.
    Rickman, H.
    Ristorcelli, I.
    Rydbeck, G.
    Sandqvist, Aa.
    Stockholm University, Faculty of Science, Department of Astronomy.
    von Schéele, F.
    Serra, G.
    Torchinsky, S.
    Tothill, N. F.
    Volk, K.
    Wiklind, T.
    Wilson, C. D.
    Winnberg, A.
    Witt, G.
    Highlights from the first year of Odin observations2003In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 402, p. L39-L46Article in journal (Refereed)
    Abstract [en]

    Key Odin operational and instrumental features and highlights from our sub-millimetre and millimetre wave observations of H2O, H218O, NH3, 15NH3 and O2 are presented, with some insights into accompanying Odin Letters in this A&A issue. We focus on new results where Odin's high angular resolution, high frequency resolution, large spectrometer bandwidths, high sensitivity or/and frequency tuning capability are crucial: H2O mapping of the Orion KL, W3, DR21, S140 regions, and four comets; H2O observations of Galactic Centre sources, of shock enhanced H2O towards the SNR IC443, and of the candidate infall source IRAS 16293-2422; H218O detections in Orion KL and in comet Ikeya-Zhang; sub-mm detections of NH3 in Orion KL (outflow, ambient cloud and bar) and ρ Oph, and very recently, of 15NH3 in~Orion KL. Simultaneous sensitive searches for the 119 GHz line of O2 have resulted in very low abundance limits, which are difficult to accomodate in chemical models. We also demonstrate, by means of a quantitative comparison of Orion KL H2O results, that the Odin and SWAS observational data sets are very consistently calibrated. Odin is a Swedish-led satellite project funded jointly by the Swedish National Space Board (SNSB), the Canadian Space Agency (CSA), the National Technology Agency of Finland (Tekes), and the Centre National d'études Spatiales (CNES, France). The Swedish Space Corporation (SSC) has been the prime industrial contractor, and is also responsible for the satellite operation from its Odin Mission Control Centre at SSC in Solna and its Odin Control Centre at ESRANGE near Kiruna in northern Sweden. See also the SNSB Odin web page: http://www.snsb.se/eng_odin_intro.shtml

  • 18. Hjalmarson, Åke
    et al.
    Bergman, Per
    Biver, Nicolas
    Florén, H.-G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Frisk, Urban
    Hasegawa, Tatsuhiko
    Justtanont, Kay
    Stockholm University, Faculty of Science, Department of Astronomy.
    Larsson, Bengt
    Stockholm University, Faculty of Science, Department of Astronomy.
    Lundin, Stefan
    Olberg, Michael
    Olofsson, Henrik
    Persson, Glenn
    Rydbeck, Gustaf
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    The Odin Team,
    Recent astronomy highlights from the Odin satellite2005In: Advances in Space Research, ISSN 0273-1177, E-ISSN 1879-1948, Vol. 36, p. 1031-1047Article in journal (Refereed)
    Abstract [en]

    Astronomy highlights, mainly from the third year of Odin observations time shared 50/50% with aeronomy are presented: the very low O2 abundance limits achieved, the highly pressure broadened absorption lines of H2O, H218O, and CO (5 → 4) in the atmosphere of Mars, the high precision H2O and H218O observations of comets, the detections of NH3 and H2O around the C-rich star IRC+10216 (CW Leo) and of H2O around the O-rich star W Hya, NH3 and H2O observations of infall/outflow interactions, observations of H2O, H218O, H217O as well as NH3 and 15NH3 in multiple absorptions towards Sgr B2, and in emission towards Orion KL, the H2O detection of several new outflows in the DR21 W75S region. We also discuss the results of deconvolution of high S/N H2O, CO and 13CO (5 → 4) maps of the Orion KL region to 40″ resolution (the beam size of the Herschel telescope) and the first results from our ongoing “spectral scan” of Orion KL in bands around 555 and 570 GHz. Finally, a search for primordial molecules is presented.

  • 19. Hjalmarson, Åke
    et al.
    Florén, Hans-Gustav
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    On the progress in Odin’s hunt for molecules2007In: Advances in Space Research, Vol. 40, no 5, p. 630-638Article in journal (Refereed)
  • 20.
    Justtanont, K.
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Bergman, P.
    Onsala Space Observatory.
    Larsson, B.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Olofsson, H.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Schöier, F. L.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Frisk, U.
    Hasegawa, T.
    Hjalmarson, Å.
    Kwok, S.
    Olberg, M.
    Sandqvist, Aa.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Volk, K.
    Elitzur, M.
    W Hya through the eye of Odin. Satellite observations of circumstellar submillimetre H2O line emission2005In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 439, p. 627-633Article in journal (Refereed)
    Abstract [en]

    We present Odin observations of the AGB star W Hya in the ground-state transition of ortho-H{2}O, 1{10}-101, at 557 GHz. The line is clearly of circumstellar origin. Radiative transfer modelling of the water lines observed by Odin and ISO results in a mass-loss rate of (2.5±0.5)×10-7 Mȯ yr-1, and a circumstellar H{2}O abundance of (2.0±1.0)×10-3. The inferred mass-loss rate is consistent with that obtained from modelling the circumstellar CO radio line emission, and also with that obtained from the dust emission modelling combined with a dynamical model for the outflow. The very high water abundance, higher than the cosmic oxygen abundance, can be explained by invoking an injection of excess water from evaporating icy bodies in the system. The required extra mass of water is quite small, on the order of 0.1 Moplus.

  • 21.
    Karlsson, Roland
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Fathi, Kambiz
    Stockholm University, Faculty of Science, Department of Astronomy. Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC).
    Martin, Sergio
    The OH-streamer in Sagittarius A revisited: Analysis of hydroxyl absorption within 10 pc from the Galactic centre2015In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 582, article id A118Article in journal (Refereed)
    Abstract [en]

    Aims. We study the structure and kinematics of the OH-streamer and the +80 km s(-1) cloud and their interactions with the circumnu-clear disk (CND) and with other molecular clouds in the vicinity of the Galactic centre (GC), and we map OH absorption at about 6 '' resolution at R <= 10 pc from the GC, with about 9 km s(-1) of velocity resolution. Methods. The VLA was used to map OH line absorption at the 1665 and 1667 MHz lambda doublet main lines of the (2)Pi(3/2) state towards the Sagittarius A complex. Results. Strong OH absorption was found in the OH-streamer, the southern streamer (SS), the +20, +50, and +80 km s(-1) molecular clouds, the molecular belt, the CND, the expanding molecular ring (EMR), and the high negative velocity gas (HNVG). The OH-streamer was found to comprise three parts, head, mid, and tail, and to interact with the SS/+20, +80 km s(-1) clouds and the CND. Optical depths and column densities divided by excitation temperatures have been calculated for the OH-streamer and the +80 km s(-1) cloud. Conclusions. The OH-streamer, the SS, the +20 and +80 km s(-1) clouds, and the CND are intimately related in position and velocity space. The OH-streamer was found to be a clumpy object stretching in projection from the inner radius of the CND at about 1.8 pc from Sgr A*towards and partly engulfing Sgr A*. As a side result of our data, a possible link between the near side of the EMR and the CND's southwest lobe was found. Additionally, we found OH absorption against all four of the previously known compact H II regions A-D, located east of Sgr A East, indicating their close association with the +50 km s(-1) cloud.

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  • 22.
    Karlsson, Roland
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Fathi, Kambiz
    Stockholm University, Faculty of Science, Department of Astronomy.
    Martin, Sergio
    VizieR Online Data Catalog: OH-streamer in SgrA at 1665 and 1667MHz (Karlsson+, 2015)2015Other (Other academic)
    Abstract [en]

    The VLA was used to map OH line absorption at the 1665 and 1667MHz lambda doublet main lines of the 2{Pi}3/2 state towards the Sagittarius A complex. Strong OH absorption was found in the OH-streamer, the southern streamer (SS), the +20, +50, and +80km/s molecular clouds, the molecular belt, the CND, the expanding molecular ring (EMR), and the high negative velocity gas (HNVG).

    Data cubes of VLA observations of the Sgr A complex at 1667- and 1665MHz OH-absorption at 7"x5" angular and 8.8km/s velocity resolution in 63 spectral channels centered at -38km/s (LSR). OH-absorption is defined as "continuum flux minus line flux". The continuum is taken as the average of 1665 and 1667 MHz maps of line free channels. Observations with the VLA in BnA and DnC arrays have been concatenated with AIPS, and data were calibrated and CLEANed with NRAO AIPS standard procedures.

    (2 data files).

  • 23.
    Karlsson, Roland
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Hjalmarson, A.
    Winnberg, A.
    Fathi, Kambiz
    Stockholm University, Faculty of Science, Department of Astronomy.
    Frisk, U.
    Olberg, M.
    Hydroxyl, water, ammonia, carbon monoxide, and neutral carbon towards the Sagittarius A complex VLA, Odin, and SEST observations2013In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 554, article id A141Article in journal (Refereed)
    Abstract [en]

    Aims. The Sagittarius A complex in the Galactic centre comprises an ensemble of molecular clouds of different species with a variety of geometrical and kinematic properties. This work aims to study molecular abundances, morphology, and kinematics by comparing hydroxyl, water, carbon monoxide, ammonia, and atomic carbon and some of their isotopologues, in the +50 km s(-1) cloud, the circumnuclear disk (CND), the +20 km s(-1) cloud, the expanding molecular ring and the line-of-sight spiral arm features, including the Local/Sgr arm, the -30 km s(-1) arm, and the 3-kpc arm. Methods. We observed the +50 km s(-1) cloud, the CND and the +20 km s(-1) cloud, and other selected positions at the Galactic centre with the VLA, and the Odin satellite. The VLA was used to map the 1665 and 1667 MHz OH lambda doublet main lines of the (H-2(3/2)) state, and the Odin satellite was used to map the 557 GHz H2O (1(10)-1(01)) line as well as to observe the 548 GHz (H2O)-O-18 (1(10)-1(01)) line, the 572 GHz NH3 (1(0)-0(0)) line, the 576 GHz CO J = 5-4 line and the 492 GHz C-I (P-3(1)-P-3(0)) line. Furthermore, the SEST was used to map a 4'.5 x 6' region of the SgrAcomplex in the 220 GHz (CO)-O-18 J = 2-1 line. Results. Strong OH absorption, H2O emission and absorption lines were seen at all observed positions, and the (H2O)-O-18 line was detected in absorption towards the +50 km s(-1) cloud, the CND, the +20 km s(-1)cloud, the expanding molecular ring, and the 3-kpc arm. Strong CO J = 5-4, (CO)-O-18 J = 2-1, and neutral carbon C-I emissions were seen towards the +50 and +20 km s(-1) clouds. NH3 was only detected in weak absorption originating in the line-of-sight spiral arm features. The abundances of OH and H2O in the +50 and +20 km s(-1) clouds reflect the different physical environments in the clouds, where shocks and star formation prevail in the +50 km s(-1) cloud and giving rise to a higher rate of H2O production there than in the +20 km s(-1) cloud. In the CND, cloud collisions and shocks are frequent, and the CND is also subject to intense UV-radiation emanating from the supermassive black hole and the central star cluster. The CND is rich in (HO)-O-2 and OH, and these abundances are considerably higher than in the +50 and +20 km s(-1) clouds. We compare our estimated abundances of OH, H2O, and NH3 with similar and differing results for some other sources available in the literature. As compared to the quiescent cloud values of a few x 10(-9), or lower, the H2O abundance is markedly enhanced in the front sides of the Sgr A molecular cloud cores, (2-7) x 10(-8), as observed in absorption, and highest in the CND. A similar abundance enhancement is seen in OH. The likely explanation is PDR chemistry including grain surface reactions, and perhaps also the influence of shocks. In the redward high-velocity line wings of the +50 and +20 km s(-1) clouds and the CND, the H2O abundances are estimated to be (1-6) x 10(-6) or higher, i.e., similar to the water abundances in outflows of the Orion KL and DR21 molecular clouds, which are said to be caused by the combined action of shock desorption from icy grain mantles and high-temperature, gas-phase shock chemistry.

  • 24.
    Karlsson, Roland
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Hjalmarson, Åke
    Winnberg, Anders
    Fathi, Kambiz
    Stockholm University, Faculty of Science, Department of Astronomy.
    Frisk, Urban
    Olberg, Mikael
    Hydroxyl, water, ammonia, carbon monoxide and neutral carbon towards the Sgr A complex2014In: Proceedings of the International Astronomical Union, ISSN 1743-9213, E-ISSN 1743-9221, Vol. 9, no 303, p. 97-99Article in journal (Refereed)
    Abstract [en]

    We observed Hydroxyl, water, ammonia, carbon monoxide and neutral carbon towards the +50 km s−1 cloud (M−0.02−0.07), the circumnuclear disk (CND) and the +20 km s−1 (M−0.13−0.08) cloud in the Sgr A complex with the VLA, Odin and SEST. Strong OH absorption, H2O emission and absorption lines were seen at all three positions. Strong C18O emissions were seen towards the +50 and +20 km s−1 clouds. The CND is rich in H2O and OH, and these abundances are considerably higher than in the surrounding clouds, indicating that shocks, star formation and clump collisions prevail in those objects. A comparison with the literature reveals that it is likely that PDR chemistry including grain surface reactions, and perhaps also the influences of shocks has led to the observed abundances of the observed molecular species studied here. In the redward high-velocity line wings of both the +50 and +20 km s−1 clouds and the CND, the very high H2O abundances are suggested to be caused by the combined action of shock desorption from icy grain mantles and high-temperature, gas-phase shock chemistry. Only three of the molecules are briefly discussed here. For OH and H2O three of the nine observed positions are shown, while a map of the C18O emission is provided. An extensive paper was recently published with Open Access (Karlsson et al. 2013, A&A 554, A141).

  • 25.
    Karlsson, Roland
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sjouwerman, Lorant O.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Whiteoak, John B.
    18-cm VLA observations of OH towards the Galactic Centre: Absorption and emission in the four ground-state OH lines2003In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 403, p. 1011-1021Article in journal (Refereed)
    Abstract [en]

    The OH distribution in the Sgr A Complex has been observed in the 1612-, 1665-, 1667- and 1720-MHz OH transitions with the Very Large Array (VLA) in BnA configuration. Maps are presented with a channel velocity resolution of about 9 km s -1 and with angular resolutions of  . Some clear results are highlighted here, such as absorption from the Circumnuclear Disk (CND) and the OH-Streamer inside the CND near Sgr , strong absorption towards most of the eastern and western parts of the Sgr A East shell, lack of absorption towards both Sgr A West and the compact H II-regions to the east of Sgr A East, and double-lobed structure of the High Negative Velocity Gas (HNVG) oriented northeast and southwest of Sgr , and finally compact, point-like maser emission in all four transitions, in particular a 1720-MHz maser at -132 km s -1 in the CND as counterpart to a 1720-MHz maser at +132 km s -1 in the CND.

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  • 26.
    Koskela, Anita
    et al.
    University Hospital Örebro, Örebro, Sweden.
    Qvick, Alvida
    University Hospital Örebro, Örebro, Sweden.
    Jakobsen, Ingrid
    University Hospital Örebro, Örebro, Sweden.
    Lindqvist, Carl Mårten
    University Hospital Örebro, Örebro, Sweden.
    Farkas, Sanja A.
    Örebro University Hospital.
    Green, Anna
    Örebro University Hospital.
    Isaksson, Helena S.
    Örebro University Hospital.
    Holmgren, Benjamin
    Halland Hospital, Halmstad, Sweden.
    Levéen, Per
    Region Skåne and Lund University, Lund, Sweden.
    Thankaswamy, Subazini
    University Hospital Örebro, Örebro, Sweden.
    Fredriksson, Johan
    Örebro University, Örebro Sweden.
    Andersson, Lina
    University Hospital Örebro, Örebro, Sweden.
    Helenius, Gisela
    Örebro University, School of Medical Sciences.
    Evaluation of Microsatellite instability score from GMS560 DNA panel2022Conference paper (Other academic)
    Abstract [en]

    Microsatellite instability is characterised by gains or losses of nucleotides in short tandem repeat sequences, microsatellites, dispersed throughout the human genome. Microsatellite instability status is a molecular fingerprint for DNA mismatch repair deficiency. Clinical detection of microsatellite instability status is important for identifying inherited disease in patients with colorectal and endometrial cancer but has also a prognostic value for survival and prediction of treatment response. Lately, microsatellite instability has been used as a tumor agnostic biomarker that predicts response to immune checkpoint inhibitors. To identify microsatellite instability status clinically, PCR and immunohistochemistry have been the gold standard. On the contrary, next generation sequencing provide simultaneous accession of large number of microsatellite loci and can be combined with detection of several other biomarkers. 

    The national collaboration Genome Medicine Sweden have developed a solid tumour gene panel composed of 560 cancer associated genes with integrated microsatellite instability score. Our aim was to validate the microsatellite instability status based on microsatellite instability score from GMS560 DNA panel against the clinically used methods. Extracted DNA (100 ng) from formalin fixed paraffin embedded tissue sections with various tumour cell content >10% were analysed. During target enrichment sequencing analysis, allelic distribution from 5000 microsatellite markers were calculated by MSIsensor Pro to generate an instability score. 

    The cohort consisted of microsatellite instable verified colorectal cancer samples (n=20), microsatellite stable solid tumour material (n=60). Preliminary results generated a microsatellite instability score for the colorectal cancer samples with a mean of 26.5 % (CI: 23.4-29.6, range: 16.9-32.3). Microsatellite stable tumour samples had a mean microsatellite instability score of 1.5 % (CI: 0.93-2.07, range: 1-4.45). 

    In conclusion, we found the microsatellite instability score from GMS560 DNA panel to be both diagnostically sensitive and specific for determining MSI status due to obvious separation in instability. 

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    Poster
  • 27.
    Larsson, B.
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Liseau, R.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Bergman, P.
    Bernath, P.
    Black, J. H.
    Booth, R. S.
    Buat, V.
    Curry, C. L.
    Encrenaz, P.
    Falgarone, E.
    Feldman, P.
    Fich, M.
    Florén, H. G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Frisk, U.
    Gerin, M.
    Gregersen, E. M.
    Harju, J.
    Hasegawa, T.
    Johansson, L. E. B.
    Kwok, S.
    Lecacheux, A.
    Liljeström, T.
    Mattila, K.
    Mitchell, G. F.
    Nordh, L. H.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Olberg, M.
    Olofsson, G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Pagani, L.
    Plume, R.
    Ristorcelli, I.
    Sandqvist, Aa.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Schéele, F. v.
    Tothill, N. F. H.
    Volk, K.
    Wilson, C. D.
    Hjalmarson, Å.
    First NH3 detection of the Orion Bar2003In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 402, p. L69-L72Article in journal (Refereed)
    Abstract [en]

    Odin has successfully observed three regions in the Orion A cloud, i.e. Ori KL, Ori S and the Orion Bar, in the 572.5 GHz rotational ground state line of ammonia, ortho-NH3 (J,K) = (1,0) -> (0,0), and the result for the Orion Bar represents the first detection in an ammonia line. Several velocity components are present in the data. Specifically, the observed line profile from the Orion Bar can be decomposed into two components, which are in agreement with observations in high-J CO lines by Wilson et al. (\cite{wilson01}). Using the source model for the Orion Bar by these authors, our Odin observation implies a total ammonia abundance of NH3/H2 = 5x 10-9. Based on observations with Odin, a Swedish-led satellite project funded jointly by the Swedish National Space Board (SNSB), the Canadian Space Agency (CSA), the National Technology Agency of Finland (Tekes) and Centre National d'Études Spatiales (CNES). The Swedish Space Corporation has been the industrial prime contractor.

  • 28.
    Larsson, Bengt
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Liseau, Rene
    Stockholm University, Faculty of Science, Department of Astronomy.
    Pagani, Laurent
    Bergman, Per
    Bernath, Peter
    Biver, Nicolas
    Black, John
    Booth, Roy
    Buat, Veronique
    Crovisier, Jacques
    Curry, Charles
    Dahlgren, Magnus
    Encrenaz, Pierre
    Falgarone, Edith
    Feldman, Paul
    Fish, Michel
    Florén, Hans-Gustav
    Stockholm University, Faculty of Science, Department of Astronomy.
    Fredrixon,
    Frisk, Urban
    Gahm, Gösta
    Stockholm University, Faculty of Science, Department of Astronomy.
    Gerin, Maryvonne
    Hagström, Magne
    Harju, Jorma
    Hasegawa, Tatsuhiko
    Hjalmarsson, Åke
    Johansson, Lars
    Justtanout, Kay
    Stockholm University, Faculty of Science, Department of Astronomy.
    Klotz, Alain
    Kytölä, Erikii
    Kwok, Sun
    Lecacheux, Alain
    Liljeström, Tarja
    Llewellyn, Edward
    Lundin, Stefan
    Mégie, Gérard
    Mitchell, Gary
    Murtagh, Donal
    Nordh, Lennart
    Nyman, Lars-Åke
    Olberg, Michael
    Olofsson, Henrik
    Olofsson, Göran
    Stockholm University, Faculty of Science, Department of Astronomy.
    Olofsson, Hans
    Stockholm University, Faculty of Science, Department of Astronomy.
    Persson, Glen
    Plume, Rene
    Rickman, Hans
    Ristorcelli, Isabelle
    Rydbeck, Gustaf
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    von Scheele, Fredrik
    Serra, Guy
    Torchinsky, Steve
    Tothill, Nick
    Volk, Kevin
    Wiklind, Tommy
    Wilson, Christine
    Winnberg, Anders
    Witt, George
    Department of Meteorology.
    Molecular oxygen in the rho Ophiuchi cloud2007In: Astronomy & Astrophysics, ISSN 0004-6361, Vol. 466, no 3, p. 5-Article in journal (Refereed)
    Abstract [en]

    Context: Molecular oxygen, O2, has been expected historically to be an abundant component of the chemical species in molecular clouds and, as such, an important coolant of the dense interstellar medium. However, a number of attempts from both ground and from space have failed to detect O2 emission.

    Aims: The work described here uses heterodyne spectroscopy from space to search for molecular oxygen in the interstellar medium. Methods: The Odin satellite carries a 1.1 m sub-millimeter dish and a dedicated 119 GHz receiver for the ground state line of O2. Starting in 2002, the star forming molecular cloud core ρ Oph A was observed with Odin for 34 days during several observing runs.

    Results: We detect a spectral line at v_LSR =+3.5 km s-1 with Δ v_FWHM=1.5 km s-1, parameters which are also common to other species associated with ρ Oph A. This feature is identified as the O2 (NJ = 11 - 1_0) transition at 118 750.343 MHz.

    Conclusions: The abundance of molecular oxygen, relative to H{2} , is 5 × 10-8 averaged over the Odin beam. This abundance is consistently lower than previously reported upper limits.

    Based on observations with Odin, a Swedish-led satellite project funded jointly by the Swedish National Space Board (SNSB), the Canadian Space Agency (CSA), the National Technology Agency of Finland (Tekes) and Centre National d'Étude Spatiale (CNES). The Swedish Space Corporation has been the industrial prime contractor and also is operating the satellite. Appendix A is only available in electronic form at http://www.aanda.org

  • 29. Liseau, R.
    et al.
    Goldsmith, P. F.
    Larsson, Bengt
    Stockholm University, Faculty of Science, Department of Astronomy.
    Pagani, L.
    Bergman, P.
    Le Bourlot, J.
    Bell, T. A.
    Benz, A. O.
    Bergin, E. A.
    Bjerkeli, P.
    Black, J. H.
    Bruderer, S.
    Caselli, P.
    Caux, E.
    Chen, J. -H
    de Luca, M.
    Encrenaz, P.
    Falgarone, E.
    Gerin, M.
    Goicoechea, J. R.
    Hjalmarson, A.
    Hollenbach, D. J.
    Justtanont, K.
    Kaufman, M. J.
    Le Petit, F.
    Li, D.
    Lis, D. C.
    Melnick, G. J.
    Nagy, Z.
    Olofsson, A. O. H.
    Olofsson, Göran
    Stockholm University, Faculty of Science, Department of Astronomy.
    Roueff, E.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Snell, R. L.
    van der Tak, F. F. S.
    van Dishoeck, E. F.
    Vastel, C.
    Viti, S.
    Yildiz, U. A.
    Multi-line detection of O-2 toward rho Ophiuchi A2012In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 541, p. A73-Article in journal (Refereed)
    Abstract [en]

    Context. Models of pure gas-phase chemistry in well-shielded regions of molecular clouds predict relatively high levels of molecular oxygen, O-2, and water, H2O. These high abundances imply high cooling rates, leading to relatively short timescales for the evolution of gravitationally unstable dense cores, forming stars and planets. Contrary to expectations, the dedicated space missions SWAS and Odin typically found only very small amounts of water vapour and essentially no O-2 in the dense star-forming interstellar medium. Aims. Only toward rho OphA did Odin detect a very weak line of O-2 at 119 GHz in a beam of size 10 arcmin. The line emission of related molecules changes on angular scales of the order of some tens of arcseconds, requiring a larger telescope aperture such as that of the Herschel Space Observatory to resolve the O-2 emission and pinpoint its origin. Methods. We use the Heterodyne Instrument for the Far Infrared (HIFI) aboard Herschel to obtain high resolution O-2 spectra toward selected positions in the rho Oph A core. These data are analysed using standard techniques for O2 excitation and compared to recent PDR-like chemical cloud models. Results. The N-J = 3(3)-1(2) line at 487.2 GHz is clearly detected toward all three observed positions in the rho Oph A core. In addition, an oversampled map of the 5(4)-3(4) transition at 773.8 GHz reveals the detection of the line in only half of the observed area. On the basis of their ratios, the temperature of the O-2 emitting gas appears to vary quite substantially, with warm gas (greater than or similar to 50 K) being adjacent to a much colder region, of temperatures lower than 30 K. Conclusions. The exploited models predict that the O-2 column densities are sensitive to the prevailing dust temperatures, but rather insensitive to the temperatures of the gas. In agreement with these models, the observationally determined O-2 column densities do not seem to depend strongly on the derived gas temperatures, but fall into the range N(O-2) = 3 to greater than or similar to 6 x 10(15) cm(-2). Beam-averaged O-2 abundances are about 5 x 10(-8) relative to H-2. Combining the HIFI data with earlier Odin observations yields a source size at 119 GHz in the range of 4 to 5 arcmin, encompassing the entire rho Oph A core. We speculate that one of the reasons for the generally very low detection rate of O-2 is the short period of time during which O-2 molecules are reasonably abundant in molecular clouds.

  • 30.
    Liseau, R.
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Larsson, B.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Brandeker, A.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Bergman, P.
    Bernath, P.
    Black, J. H.
    Booth, R.
    Buat, V.
    Curry, C.
    Encrenaz, P.
    Falgarone, E.
    Feldman, P.
    Fich, M.
    Florén, H.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Frisk, U.
    Gerin, M.
    Gregersen, E.
    Harju, J.
    Hasegawa, T.
    Hjalmarson, Å.
    Johansson, L.
    Kwok, S.
    Lecacheux, A.
    Liljeström, T.
    Mattila, K.
    Mitchell, G.
    Nordh, L.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Olberg, M.
    Olofsson, G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Pagani, L.
    Plume, R.
    Ristorcelli, I.
    Sandqvist, Aa.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Schéele, F. v.
    Serra, G.
    Tothill, N.
    Volk, K.
    Wilson, C.
    First detection of NH3 (10 -> 00) from a low mass cloud core. On the low ammonia abundance of the rho Oph A core2003In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 402, p. L73-L76Article in journal (Refereed)
    Abstract [en]

    Odin has successfully observed the molecular core rho Oph A in the 572.5 GHz rotational ground state line of ammonia, NH3 (JK = 10 -> 00). The interpretation of this result makes use of complementary molecular line data obtained from the ground (C17O and CH3OH) as part of the Odin preparatory work. Comparison of these observations with theoretical model calculations of line excitation and transfer yields a quite ordinary abundance of methanol, X(CH3OH)= 3 x 10-9. Unless NH3 is not entirely segregated from C17O and CH3OH, ammonia is found to be significantly underabundant with respect to typical dense core values, viz. X(NH3) = 8 x 10-10. Based on observations with Odin, a Swedish-led satellite project funded jointly by the Swedish National Space Board (SNSB), the Canadian Space Agency (CSA), the National Technology Agency of Finland (Tekes) and Centre National d'Études Spatiales (CNES). The Swedish Space Corporation has been the industrial prime contractor. and based on observations collected with the Swedish ESO Submillimeter Telescope, SEST, in La Silla, Chile.

  • 31.
    Maercker, Matthias
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Schöier, F.L.
    Olofsson, Hans
    Stockholm University, Faculty of Science, Department of Astronomy. Onsala Space Observatory, Sweden.
    Bergman, P.
    Frisk, U.
    Hjalmarson, Å.
    Justannont, K.
    Kwok, S.
    Larsson, Bengt
    Stockholm University, Faculty of Science, Department of Astronomy.
    Olberg, M.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Circumstellar water vapour in M-type AGB stars: constraints from H2O(1,10-1,01) lines obtained with odin2009In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 494, p. 243-252Article in journal (Refereed)
    Abstract [en]

    Context. A detailed radiative transfer code has been previously used to model circumstellar ortho-H2O line emission towards six M-type asymptotic giant branch stars using Infrared Space Observatory Long Wavelength Spectrometer data. Collisional and radiative excitation, including the v(2) = 1 state, was considered. Aims. Spectrally resolved circumstellar H2O(1(10)-1(01)) lines have been obtained towards three M-type AGB stars using the Odin satellite. This provides additional strong constraints on the properties of circumstellar H2O, in particular on the chemistry in the stellar atmosphere, and the photodissociation in the outer envelope. Methods. Infrared Space Observatory and Odin satellite H2O line data are used as constraints for radiative transfer models. Special consideration is taken to the spectrally resolved Odin line profiles, and the effect of excitation to the first excited vibrational states of the stretching modes (v(1) = 1 and v(3) = 1) on the derived abundances is estimated. A non-local, radiative transfer code based on the accelerated lambda iteration formalism is used. A statistical analysis is performed to determine the best-fit models. Results. The H2O abundance estimates are in agreement with previous estimates. The inclusion of the Odin data sets stronger constraints on the size of the H2O envelope. The H2O(1(10)-1(01)) line profiles require a significant reduction in expansion velocity compared to the terminal gas expansion velocity determined in models of CO radio line emission, indicating that the H2O emission lines probe a region where the wind is still being accelerated. Including the v(3) = 1 state significantly lowers the estimated abundances for the low-mass-loss-rate objects. This shows the importance of detailed modelling, in particular the details of the infrared spectrum in the range 3 to 6 mu m, to estimate accurate circumstellar H2O abundances. Conclusions. Spectrally resolved circumstellar H2O emission lines are important probes of the physics and chemistry in the inner regions of circumstellar envelopes around asymptotic giant branch stars. Predictions for H2O emission lines in the spectral range of the upcoming Herschel/HIFI mission indicate that these observations will be very important in this context.

  • 32. Meech, K.J.
    et al.
    Florén, Hans-Gustav
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    EPOXI: Comet 103P/Hartley 2 Observations from a Worldwide Campaign2011In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 734, no L1, p. 1-9Article in journal (Refereed)
    Abstract [en]

    Earth- and space-based observations provide synergistic information for space mission encounters by providing data over longer timescales, at different wavelengths and using techniques that are impossible with an in situ flyby. We report here such observations in support of the EPOXI spacecraft flyby of comet 103P/Hartley 2. The nucleus is small and dark, and exhibited a very rapidly changing rotation period. Prior to the onset of activity, the period was ~16.4 hr. Starting in 2010 August the period changed from 16.6 hr to near 19 hr in December. With respect to dust composition, most volatiles and carbon and nitrogen isotope ratios, the comet is similar to other Jupiter-family comets. What is unusual is the dominance of CO2-driven activity near perihelion, which likely persists out to aphelion. Near perihelion the comet nucleus was surrounded by a large halo of water-ice grains that contributed significantly to the total water production.

  • 33. Neufeld, David A.
    et al.
    Roueff, Evelyne
    Snell, Ronald L.
    Lis, Dariusz
    Benz, Arnold O.
    Bruderer, Simon
    Black, John H.
    De Luca, Massimo
    Gerin, Maryvonne
    Goldsmith, Paul F.
    Gupta, Harshal
    Indriolo, Nick
    Le Bourlot, Jacques
    Le Petit, Franck
    Larsson, Bengt
    Melnick, Gary J.
    Menten, Karl M.
    Monje, Raquel
    Nagy, Zsofia
    Phillips, Thomas G.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Sonnentrucker, Paule
    van der Tak, Floris
    Wolfire, Mark G.
    HERSCHEL OBSERVATIONS OF INTERSTELLAR CHLORONIUM2012In: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 748, no 1, p. 37-Article in journal (Refereed)
    Abstract [en]

    Using the Herschel Space Observatory's Heterodyne Instrument for the Far-Infrared, we have observed parachloronium (H2Cl+) toward six sources in the Galaxy. We detected interstellar chloronium absorption in foreground molecular clouds along the sight lines to the bright submillimeter continuum sources Sgr A (+50 km s(-1) cloud) and W31C. Both the para-(H2Cl+)-Cl-35 and para-(H2Cl+)-Cl-37 isotopologues were detected, through observations of their 1(11)-0(00) transitions at rest frequencies of 485.42 and 484.23 GHz, respectively. For an assumed ortho-to-para ratio (OPR) of 3, the observed optical depths imply that chloronium accounts for similar to 4%-12% of chlorine nuclei in the gas phase. We detected interstellar chloronium emission from two sources in the Orion Molecular Cloud 1: the Orion Bar photodissociation region and the Orion South condensation. For an assumed OPR of 3 for chloronium, the observed emission line fluxes imply total beam-averaged column densities of similar to 2 x 10(13) cm(-2) and similar to 1.2 x 10(13) cm(-2), respectively, for chloronium in these two sources. We obtained upper limits on the para-(H2Cl+)-Cl-35 line strengths toward H-2 Peak 1 in the Orion Molecular cloud and toward the massive young star AFGL 2591. The chloronium abundances inferred in this study are typically at least a factor similar to 10 larger than the predictions of steady-state theoretical models for the chemistry of interstellar molecules containing chlorine. Several explanations for this discrepancy were investigated, but none has proven satisfactory, and thus the large observed abundances of chloronium remain puzzling.

  • 34. Olberg, M.
    et al.
    Frisk, U.
    Lecacheux, A.
    Olofsson, A. O. H.
    Baron, P.
    Bergman, P.
    Florin, G.
    Hjalmarson, Å..
    Larsson, B.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Murtagh, D.
    Olofsson, G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Pagani, L.
    Sandqvist, Aa.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Teyssier, D.
    Torchinsky, S. A.
    Volk, K.
    The Odin satellite. II. Radiometer data processing and calibration2003In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 402, p. L35-L38Article in journal (Refereed)
    Abstract [en]

    The radiometer on-board the Odin satellite comprises four different sub-mm receivers covering the 486-581 GHz frequency range and one fixed frequency 119 GHz receiver. Two auto-correlators and one acousto-optical spectrometer serve as backends. This article gives an overview over the processing of the data delivered by these instruments and discusses calibration issues. Odin is a Swedish-led satellite project funded jointly by the Swedish National Space Board (SNSB), the Canadian Space Agency (CSA), the National Technology Agency of Finland (Tekes) and the Centre National d'Études Spatiales (CNES, France). Odin is operated by the Swedish Space Corporation (SSC), the project's prime industrial contractor.

  • 35. Olofsson, A. O. H.
    et al.
    Olofsson, G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Hjalmarson, Å.
    Bergman, P.
    Black, J. H.
    Booth, R. S.
    Buat, V.
    Curry, C. L.
    Encrenaz, P. J.
    Falgarone, E.
    Feldman, P.
    Fich, M.
    Florén, H. G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Frisk, U.
    Gerin, M.
    Gregersen, E. M.
    Harju, J.
    Hasegawa, T.
    Johansson, L. E. B.
    Kwok, S.
    Larsson, B.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Lecacheux, A.
    Liljeström, T.
    Liseau, R.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Mattila, K.
    Mitchell, G. F.
    Nordh, H. L.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Olberg, M.
    Olofsson, H.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Pagani, L.
    Plume, R.
    Ristorcelli, I.
    Rydbeck, G.
    Sandqvist, Aa.
    Stockholm University, Faculty of Science, Department of Astronomy.
    von Schéele, F.
    Serra, G.
    Tothill, N. F.
    Volk, K.
    Wilson, C. D.
    Odin water mapping in the Orion KL region2003In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 402, p. L47-L54Article in journal (Refereed)
    Abstract [en]

    New results from water mapping observations of the Orion KL region using the submm/mm wave satellite Odin (2.1\arcmin beam size at 557 GHz), are presented. The ortho-H2O \jkktrans{1}{1}{0}{1}{0}{1} ground state transition was observed in a 7arcminx 7arcmin rectangular grid with a spacing of 1\arcmin, while the same line of H218O was measured in two positions, Orion KL itself and 2\arcmin south of Orion KL. In the main water species, the KL molecular outflow is largely resolved from the ambient cloud and it is found to have an extension of 60\arcsec-110\arcsec. The H2O outflow profile exhibits a rather striking absorption-like asymmetry at the line centre. Self-absorption in the near (or ``blue'') part of the outflow (and possibly in foreground quiescent halo gas) is tentatively suggested to play a role here. We argue that the dominant part of the KL H218O outflow emission emanates from the compact (size ~ 15\arcsec) low-velocity flow and here estimate an H2O abundance of circa 10-5 compared to all H2 in the flow - an order of magnitude below earlier estimates of the H2O abundance in the shocked gas of the high-velocity flow. The narrow ambient cloud lines show weak velocity trends, both in the N-S and E-W directions. H218O is detected for the first time in the southern position at a level of ~ 0.15 K and we here estimate an H2O abundance of (1-8) x 10-8. Odin is a Swedish-led satellite project funded jointly by the Swedish National Space Board (SNSB), the Canadian Space Agency (CSA), the National Technology Agency of Finland (Tekes), and the Centre National d'Études Spatiales (CNES, France). The Swedish Space Corporation (SSC) was the industrial prime contractor and is also responsible for the satellite operation.

  • 36.
    Olofsson, Emma
    et al.
    Örebro University, School of Medical Sciences. Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
    Kling, Daniel
    Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.
    Gunnarsson, Cecilia
    Department of Clinical Genetics and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden; Centre for Rare Diseases in South East Region of Sweden, Linköping University, Linköping, Sweden.
    Jonasson, Jon
    Department of Clinical Genetics and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
    Gréen, Henrik
    Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.
    Green, Anna
    Örebro University, School of Medical Sciences. Örebro University Hospital. Department of Laboratory Medicine.
    Whole exome sequencing of FFPE samples-expanding the horizon of forensic molecular autopsies2023In: International journal of legal medicine, ISSN 0937-9827, E-ISSN 1437-1596, Vol. 137, no 4, p. 1215-1234Article in journal (Refereed)
    Abstract [en]

    Forensic molecular autopsies have emerged as a tool for medical examiners to establish the cause of death. It is particularly useful in sudden unexplained deaths where the cause of death cannot be determined with a regular medical autopsy. We provide the first study of exome data from formalin-fixed paraffin-embedded samples (FFPE) paired with data from high-quality blood samples in forensic applications. The approach allows exploration of the potential to use FFPE samples for molecular autopsies and identify variants in extensive exome data. We leverage the high uniformity of the hybridization capture approach provided by Twist Bioscience to target the complete exome and sequence the libraries on a NextSeq 550. Our findings suggest that exome sequencing is feasible for 24 out of a total of 35 included FFPE samples. When successful, the coverage across the exome is comparatively high (> 90% covered to 20X) and uniform (fold80 below 1.5). Detailed variant comparisons for matched FFPE and blood samples show high concordance with few false variants (positive predictive value of 0.98 and a sensitivity of 0.97) with no distinct FFPE artefacts. Ultimately, we apply carefully constructed forensic gene panels in a stepwise manner to find genetic variants associated with the clinical phenotype and with relevance to the sudden unexplained death.

  • 37. Olofsson, henrik
    et al.
    Persson, Carina
    Koning, N
    Bergman, Per
    Bernath, Peter
    black, John
    Frisk, Urban
    Geppert, Wolf
    Stockholm University, Faculty of Science, Department of Physics.
    Hasegawa, T
    Hjalmarsson, Åke
    Kwok, Sun
    Larsson, Bengt
    Department of Astronomy.
    Nummelin, albert
    Olberg, Mikael
    Sandqvist, Aage
    Department of Astronomy.
    Wirsröm, Eva
    A spectral line survey of Orion KL in the bands 486-492 and 541-577 GHz with the Odin satellite.: I. The observational data2007In: Astronomy and Astrophysics, Vol. 476, no 2Article in journal (Refereed)
  • 38. Pagani, L.
    et al.
    Olofsson, A. O. H.
    Bergman, P.
    Bernath, P.
    Black, J. H.
    Booth, R. S.
    Buat, V.
    Crovisier, J.
    Curry, C. L.
    Encrenaz, P. J.
    Falgarone, E.
    Feldman, P. A.
    Fich, M.
    Floren, H. G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Frisk, U.
    Gerin, M.
    Gregersen, E. M.
    Harju, J.
    Hasegawa, T.
    Hjalmarson, Å.
    Johansson, L. E. B.
    Kwok, S.
    Larsson, B.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Lecacheux, A.
    Liljeström, T.
    Lindqvist, M.
    Liseau, R.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Mattila, K.
    Mitchell, G. F.
    Nordh, L. H.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Olberg, M.
    Olofsson, G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Ristorcelli, I.
    Sandqvist, Aa.
    Stockholm University, Faculty of Science, Department of Astronomy.
    von Scheele, F.
    Serra, G.
    Tothill, N. F.
    Volk, K.
    Wiklind, T.
    Wilson, C. D.
    Low upper limits on the O2 abundance from the Odin satellite2003In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 402, p. L77-L81Article in journal (Refereed)
    Abstract [en]

    For the first time, a search has been conducted in our Galaxy for the 119 GHz transition connecting to the ground state of O2, using the Odin satellite. Equipped with a sensitive 3 mm receiver (Tsys(SSB) = 600 K), Odin has reached unprecedented upper limits on the abundance of O2, especially in cold dark clouds where the excited state levels involved in the 487 GHz transition are not expected to be significantly populated. Here we report upper limits for a dozen sources. In cold dark clouds we improve upon the published SWAS upper limits by more than an order of magnitude, reaching N(O2)/N(H2) <= 10-7 in half of the sources. While standard chemical models are definitively ruled out by these new limits, our results are compatible with several recent studies that derive lower O2 abundances. Goldsmith et al. (\cite{SWAS2002}) recently reported a SWAS tentative detection of the 487 GHz transition of O2 in an outflow wing towards rho Oph A in a combination of 7 beams covering approximately 10arcmin x 14arcmin . In a brief (1.3 hour integration time) and partial covering of the SWAS region (~65% if we exclude their central position), we did not detect the corresponding 119 GHz line. Our 3 sigma upper limit on the O2 column density is 7.3x 1015 cm-2. We presently cannot exclude the possibility that the SWAS signal lies mostly outside of the 9\arcmin Odin beam and has escaped our sensitive detector. Based on observations with Odin, a Swedish-led satellite project funded jointly by the Swedish National Space Board (SNSB), the Canadian Space Agency (CSA), the National Technology Agency of Finland (Tekes) and Centre National d'Études Spatiales (CNES). The Swedish Space Corporation was the industrial prime contractor and is operating Odin.

  • 39.
    Persson, C. M. ...
    et al.
    Onsala Space Observatory.
    Sandqvist, Aa.; et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    The first spectral line surveys searching for signals from the dark ages2010In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 515, p. A72 1-18Article in journal (Refereed)
    Abstract [en]

    Aims. Our aim is to observationally investigate the cosmic Dark Ages in order to constrain star and structure formation models, as well as the chemical evolution in the early Universe.

    Methods. Spectral lines from atoms and molecules in primordial perturbations at high redshifts can give information about the conditions in the early universe before and during the formation of the first stars in addition to the epoch of reionisation. The lines may arise from moving primordial perturbations before the formation of the first stars (resonant scattering lines), or could be thermal absorption or emission lines at lower redshifts. The difficulties in these searches are that the source redshift and evolutionary state, as well as molecular species and transition are unknown, which implies that an observed line can fall within a wide range of frequencies. The lines are also expected to be very weak. Observations from space have the advantages of stability and the lack of atmospheric features which is important in such observations. We have therefore, as a first step in our searches, used the Odin (Odin is a Swedish-led satellite project funded jointly by the Swedish National Space Board (SNSB), the Canadian Space Agency (CSA), the National Technology Agency of Finland (Tekes) and Centre National d'Etudes Spatiales (CNES). The Swedish Space Corporation was the prime contractor and also is responsible for the satellite operation.) satellite to perform two sets of spectral line surveys towards several positions. The first survey covered the band 547–578 GHz towards two positions, and the second one covered the bands 542.0–547.5 GHz and 486.5–492.0 GHz towards six positions selected to test different sizes of the primordial clouds. Two deep searches centred at 543.250 and 543.100 GHz with 1 GHz bandwidth were also performed towards one position. The two lowest rotational transitions of H2 will be redshifted to these frequencies from z ~ 20–30, which is the predicted epoch of the first star formation.

    Results. No lines are detected at an rms level of 14–90 and 5–35 mK for the two surveys, respectively, and 2–7 mK in the deep searches with a channel spacing of 1–16 MHz. The broad bandwidth covered allows a wide range of redshifts to be explored for a number of atomic and molecular species and transitions. From the theoretical side, our sensitivity analysis show that the largest possible amplitudes of the resonant lines are about 1 mK at frequencies 200 GHz, and a few μK around 500–600 GHz, assuming optically thick lines and no beam-dilution. However, if existing, thermal absorption lines have the potential to be orders of magnitude stronger than the resonant lines. We make a simple estimation of the sizes and masses of the primordial perturbations at their turn-around epochs, which previously has been identified as the most favourable epoch for a detection. This work may be considered as an important pilot study for our forthcoming observations with the Herschel Space Observatory

  • 40. Persson, Carina
    et al.
    Olofsson, Henrik
    Koning, N
    Bergman, Per
    Bernath, Peter
    black, John
    Frisk, Urban
    Geppert, Wolf
    Stockholm University, Faculty of Science, Department of Physics.
    Hasegawa, T
    Hjalmarsson, Åke
    Kwok, Sam
    Larsson, Bengt
    Department of Astronomy.
    Lecacheux, A
    Olberg, Mikael
    Sandqvist, Aage
    Department of Astronomy.
    Wirsröm, Eva
    A spectral line survey of Orion KL in the bands 486-492 and 541-577 GHz with the Odin satellite.: II. Data analysis2007In: Astronomy and Astrophysics, Vol. 476, no 2Article in journal (Refereed)
  • 41.
    Sandqvist, Aa
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Bergman, P.
    Bernath, P.
    Frisk, U.
    Hjalmarson, Å.
    Larsson, B.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Lindqvist, M.
    Olberg, M.
    Olofsson, A. O. H.
    Pagani, L.
    Odin spectral line observations of Sgr A and Sgr B2 at submm wavelengths and in the 118-GHz band2006In: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 54, p. 72-76Article in journal (Refereed)
    Abstract [en]

    Since its launch in 2001, the Odin satellite has been observing the Galactic Centre Sgr A Complex (CND, +20 and +50 km s-1 Clouds) as well as the nearby star formation region, Sgr B2, a number of times. Observations have been made in the 118-119 GHz and 486-581 GHz bands. A limited mapping of the Sgr A Complex in the H162O line has been performed and new observations of the H182O line took place in 2006. In the 118-119 GHz band, a strong line of HC3N (J = 13 - 12) has been detected at a number of positions - sensitive upper limits have been obtained for the O2 (11 - 10) and the SiC (3Π2, J = 3 - 2) lines. Towards Sgr B2, submm observations have yielded absorption profles of H162O, H182O, H172O, NH3, and 15NH3.

  • 42.
    Sandqvist, Aa.
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Bergman, P.
    Black, J. H.
    Booth, R.
    Buat, V.
    Curry, C. L.
    Encrenaz, P.
    Falgarone, E.
    Feldman, P.
    Fich, M.
    Floren, H. G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Frisk, U.
    Gerin, M.
    Gregersen, E. M.
    Harju, J.
    Hasegawa, T.
    Hjalmarson, Å.
    Johansson, L. E. B.
    Kwok, S.
    Larsson, B.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Lecacheux, A.
    Liljeström, T.
    Lindqvist, M.
    Liseau, R.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Mattila, K.
    Mitchell, G. F.
    Nordh, L.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Olberg, M.
    Olofsson, A. O. H.
    Olofsson, G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Pagani, L.
    Plume, R.
    Ristorcelli, I.
    Schéele, F. v.
    Serra, G.
    Tothill, N. F. H.
    Volk, K.
    Wilson, C. D.
    Winnberg, A.
    Odin observations of H2O in the Galactic Centre2003In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 402, p. L63-L67Article in journal (Refereed)
    Abstract [en]

    The Odin satellite has been used to detect emission and absorption in the 557-GHz H216O line in the Galactic Centre towards the Sgr Astar Circumnuclear Disk (CND), and the Sgr A +20 km s-1 and +50 km s-1 molecular clouds. Strong broad H2O emission lines have been detected in all three objects. Narrow H2O absorption lines are present at all three positions and originate along the lines of sight in the 3-kpc Spiral Arm, the -30 km s-1 Spiral Arm and the Local Sgr Spiral Arm. Broad H2O absorption lines near -130 km s-1 are also observed, originating in the Expanding Molecular Ring. A new molecular feature (the ``High Positive Velocity Gas'' - HPVG) has been identified in the positive velocity range of ~+120 to +220 km s-1, seen definitely in absorption against the stronger dust continuum emission from the +20 km s-1 and +50 km s-1 clouds and possibly in emission towards the position of Sgr Astar CND. The 548-GHz H218O isotope line towards the CND is not detected at the 0.02 K (rms) level. Based on observations with Odin, a Swedish-led satellite project funded jointly by the Swedish National Space Board (SNSB), the Canadian Space Agency (CSA), the National Technology Agency of Finland (Tekes) and Centre National d'Études Spatiales (CNES). The Swedish Space Corporation was the industrial prime contractor and is also responsible for the satellite operation.

  • 43.
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    COSMONOVA och Odin, en personlig återblick2007In: Den Svenska Almanackan 2008, 2007Chapter in book (Other (popular science, discussion, etc.))
  • 44.
    Sandqvist, Aage
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Hjalmarson, A.
    Frisk, U.
    Lundin, S.
    Nordh, L.
    Stockholm Univ, AlbaNova Univ Ctr, Stockholm Observ, S-10691 Stockholm, Sweden.
    Olberg, M.
    Olofsson, Göran
    Stockholm University, Faculty of Science, Department of Astronomy.
    Odin observations of ammonia in the SgrA+50 km s(-1) cloud and circumnuclear disk2017In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 599, article id A135Article in journal (Refereed)
    Abstract [en]

    Context. The Odin satellite is now into its sixteenth year of operation, much surpassing its design life of two years. One of the sources which Odin has observed in great detail is the Sgr A complex in the centre of the Milky Way.

    Aims. To study the presence of NH3 in the Galactic centre and spiral arms.

    Methods. Recently, Odin has made complementary observations of the 572 GHz NH3 line towards the SgrA + 50 km s(-1) cloud and circumnuclear disk (CND).

    Results. Significant NH3 emission has been observed in both the + 50 km s(-1) cloud and the CND. Clear NH3 absorption has also been detected in many of the spiral arm features along the line of sight from the Sun to the core of our Galaxy.

    Conclusions. The very large velocity width (80 km s 1) of the NH3 emission associated with the shock region in the southwestern part of the CND may suggest a formation / desorption scenario similar to that of gas-phase H2O in shocks / outflows.

  • 45.
    Sandqvist, Aage
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Hjalmarson, Å.
    Larsson, Bengt
    Stockholm University, Faculty of Science, Department of Astronomy.
    Frisk, U.
    Lundin, S.
    Rydbeck, G.
    Herschel and Odin observations of H2O, CO, CH, CH+, and [NII] in the barred spiral galaxy NGC 1365 Bar-induced activity in the outer and inner circumnuclear tori2021In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 647, article id A86Article in journal (Refereed)
    Abstract [en]

    Context. The Odin satellite is now into its twentieth year of operation, much surpassing its design life of two years. One of its major astronomical pursuits was the search for and study of water vapor in diverse regions of the Solar System and the Milky Way galaxy. The Herschel space observatory was needed to detect water vapor in external galaxies.

    Aims. Our goal is to study the distribution and excitation of water vapor and other molecules in the barred spiral galaxy NGC 1365.

    Methods. Herschel has observed the central region of NGC 1365 in two positions, and both its SPIRE and PACS observations are available in the Herschel Science Archive. Herschel PACS images have been produced of the 70 and 160 mu m infrared emission from the whole galaxy, and also of the cold dust distribution as obtained from the ratio of the 160 to 70 mu m images. The Herschel SPIRE observations have been used to produce simultaneously observed maps of the 557 GHz o-H2O, 752 GHz p-H2O, 691 GHz CO(6-5), 1037 GHz CO(9-8), 537 GHz CH, 835 GHz CH', and the 1461 GHz [N IT] lines (efficiently probing the warm ionized medium) in the inner bar and circumnuclear torus region; - however, these observations have no effective velocity resolution. For this reason Odin has recently observed the 557 GHz ortho-H2O ground state line in the central region with high (5 km s(-1)) spectral resolution.

    Results. The emission and absorption of H2O at 557 GHz, with a velocity resolution of 5 km s(-1), has been marginally detected in NGC 1365 with Odin. The water vapor is predominantly located in a shocked 15 '' (1.3 kpc) region near some central compact radio sources and hot-spot HIT regions, close to the northeast component of the molecular torus surrounding the nucleus. An analysis of the H2O line intensities and velocities indicates that a shock-region is located here. This is corroborated by a statistical image deconvolution of our SEST CO(3-2) observations, yielding 5 '' resolution, and a study of our Very Large Array HI absorption observations, as well as comparisons with published interferometric CO observations. Additionally, an enticing 20 '' HI ridge is found to extend south-southeast from the nucleus, coinciding in position with the southern edge of an O III outflow cone, emanating from the nucleus. The molecular chemistry of the shocked central region of NGC 1365 is analyzed with special emphasis on the CO, H2O and CH, CH+ results.

    Conclusions. The dominating activity near the northeast (NE) torus component may have been triggered by the rapid bar-driven inflow into the circumnuclear torus causing cloud-cloud collisions and shocks, leading to the formation of stellar superclusters and, hence, also to more efficient PDR chemistry, which, here, may also benefit from cosmic ray focusing caused by the observed aligned magnetic field. The very high activity near the NE torus component may reflect the fact that the eastern bar-driven gas inflow into the NE region is much more massive than the corresponding western gas inflow into the southwest region. The H2O and CH+ emissions peak in the NE torus region, but the CO and CH emissions are more evenly distributed across the whole circumnuclear torus. The higher energy CO spectral line energy distribution (SLED) is nicely modeled by a low velocity (10 km s(-1)) shock, which may as well explain the required CH excitation and its high abundance in denser gas. The higher velocity (40 km s(-1)) shock required to model the H2O SLED in the NE torus region, paired with the intense UV radiation from the observed massive young stellar superclusters, may also explain the high abundance of CH+ in this region. The nuclear H I ridge may have been created by the action of outflow-driving X-ray photons colliding with ice-covered dust grains. A precessing nuclear engine, as is suggested by the tilted massive inner gas torus, may be necessary to explain the various nuclear outflows encountered.

  • 46.
    Sandqvist, Aage
    et al.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Larsson, Bengt
    Stockholm University, Faculty of Science, Department of Astronomy.
    Hjalmarson, Å.
    Encrenaz, P.
    Gerin, M.
    Goldsmith, P. F.
    Lis, D. C.
    Liseau, R.
    Pagani, L.
    Roueff, E.
    Viti, S.
    Herschel HIFI observations of the Sgr A+50 km s(-1) Cloud Deep searches for O-2 in emission and foreground absorption2015In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 584, article id A118Article in journal (Refereed)
    Abstract [en]

    Context: The Herschel Oxygen Project (HOP) is an open time key program, awarded 140 h of observing time to search for molecular oxygen (O-2) in a number of interstellar sources. To date O-2 has definitely been detected in only two sources, namely rho Oph A and Orion, reflecting the extremely low abundance of O-2 in the interstellar medium.

    Aims: One of the sources in the HOP program is the + 50 km s(-1) Cloud in the Sgr A Complex in the centre of the Milky Way. Its environment is unique in the Galaxy and this property is investigated to see if it is conducive to the presence of O-2. Methods. The Herschel Heterodyne Instrument for the Far Infrared (HIFI) is used to search for the 487 and 774 GHz emission lines of O-2.

    Results: No O-2 emission is detected towards the Sgr A + 50 km s(-1) Cloud, but a number of strong emission lines of methanol (CH3OH) and absorption lines of chloronium (H2Cl+) are observed.

    Conclusions: A 3 sigma upper limit for the fractional abundance ratio of [O-2]/[H-2] in the Sgr A + 50 km s(-1) Cloud is found to be X(O-2) <= 5x 10(-8). However, since we can find no other realistic molecular candidate than O-2 itself, we very tentatively suggest that two weak absorption lines at 487.261 and 487.302 GHz may be caused by the 487 GHz line of O-2 in two foreground spiral arm clouds. By considering that the absorption may only be apparent, the estimated upper limit to the O-2 abundance of <=(10-20) x 10(-6) in these foreground clouds is very high, as opposed to the upper limit in the Sgr A + 50 km s(-1) Cloud itself, but similar to what has been reached in recent chemical shock models for Orion. This abundance limit was determined also using Odin non-detection limits, and assumes that O-2 fills the beam. If the absorption is due to a differential Herschel OFF-ON emission, the O-2 fractional abundance may be of the order of approximate to(5-10) x 10 (6). With the assumption of pure absorption by foreground clouds, the unreasonably high abundance of (1.4-2.8) x 10(-4) was obtained. The rotation temperatures for CH3OH-A and CH3OH-E lines in the + 50 km s(-1) Cloud are found to be approximate to 64 and 79 K, respectively, and the fractional abundance of CH3OH is approximately 5 x 10(-7).

  • 47. Wilson, C. D.
    et al.
    Mason, A.
    Gregersen, E.
    Olofsson, A. O. H.
    Bergman, P.
    Booth, R.
    Boudet, N.
    Buat, V.
    Curry, C. L.
    Encrenaz, P.
    Falgarone, E.
    Feldman, P.
    Fich, M.
    Floren, H. G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Frisk, U.
    Gerin, M.
    Harju, J.
    Hasegawa, T.
    Hjalmarson, Å.
    Juvela, M.
    Kwok, S.
    Larsson, B.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Lecacheux, A.
    Liljestrom, T.
    Liseau, R.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Mattila, K.
    Mitchell, G.
    Nordh, L.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Olberg, M.
    Olofsson, G.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Pagani, L.
    Plume, R.
    Ristorcelli, I.
    Sandqvist, Aa.
    Stockholm University, Faculty of Science, Department of Astronomy.
    Serra, G.
    Tothill, N.
    Volk, K.
    von Scheele, F.
    Submillimeter emission from water in the W3 region2003In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 402, p. L59-L62Article in journal (Refereed)
    Abstract [en]

    Using the Odin satellite, we have mapped the submillimeter emission from the 110-101 transition of ortho-water in the W3 star-forming region. A 5arcminx 5arcmin map of the W3 IRS4 and W3 IRS5 region reveals strong water lines at half the positions in the map. The relative strength of the Odin lines compared to previous observations by SWAS suggests that we are seeing water emission from an extended region. Across much of the map the lines are double-peaked, with an absorption feature at -39 km s-1; however, some positions in the map show a single strong line at -43 km s-1. We interpret the double-peaked lines as arising from optically thick, self-absorbed water emission near the W3 IRS5, while the narrower blue-shifted lines originate in emission near W3 IRS4. In this model, the unusual appearance of the spectral lines across the map results from a coincidental agreement in velocity between the emission near W3 IRS4 and the blue peak of the more complex lines near W3 IRS5. The strength of the water lines near W3 IRS4 suggests we may be seeing water emission enhanced in a photon-dominated region. Based on observations with Odin, a Swedish-led satellite project funded jointly by the Swedish National Space Board (SNSB), the Canadian Space Agency (CSA), the National Technology Agency of Finland (Tekes), and Centre National d'Études Spatiales (CNES). The Swedish Space Corporation was the industrial prime contractor and is also responsible for the satellite operation.

  • 48. Wilson, Christine
    et al.
    Booth, Roy
    Olofsson, A
    Olberg, Michael
    Persson, C
    Sandqvist, Aage
    Stockholm University, Faculty of Science, Department of Astronomy.
    Upper limits to the water abundance in starburst galaxies2007In: Astronomy & Astrophysics, ISSN 0004-6361, Vol. 469, p. 121-124Article in journal (Refereed)
    Abstract [en]

    Aims.We have searched for emission from the 557 GHz ortho-water line in the interstellar medium of six nearby starburst galaxies. Methods: We used the Odin satellite to observe the 110{-}101 transition of o-H2O in the galaxies NGC 253, IC 342, M 82, NGC 4258, CenA, and M 51. None of the galaxies in our sample was detected. Results: We derive three sigma upper limits to the H2O abundance relative to H2 ranging from 2×10-9 to 1×10-8. The best of these upper limits are comparable to the measured abundance of H2O in the Galactic star forming region W3. However, if only 10% of the molecular gas is in very dense cores, then the water abundance limits in the cores themselves would be larger by a factor of 10 i.e. 2×10-8 to 1×10-7. Conclusions: These observations suggest that detections of H2O emission in galaxies with the upcoming Herschel Space Observatory are likely to require on-source integration times of an hour or more except in the very brightest extragalactic targets such as M 82 and NGC 253.

1 - 48 of 48
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