| 1. |
- Griffin, M. J., et al.
(författare)
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The Herschel-SPIRE instrument and its in-flight performance
- 2010
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 518, s. L3-
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Tidskriftsartikel (refereegranskat)abstract
- The Spectral and Photometric Imaging REceiver (SPIRE), is the Herschel Space Observatory`s submillimetre camera and spectrometer. It contains a three-band imaging photometer operating at 250, 350 and 500 mu m, and an imaging Fourier-transform spectrometer (FTS) which covers simultaneously its whole operating range of 194-671 mu m (447-1550 GHz). The SPIRE detectors are arrays of feedhorn-coupled bolometers cooled to 0.3 K. The photometer has a field of view of 4' x 8', observed simultaneously in the three spectral bands. Its main operating mode is scan-mapping, whereby the field of view is scanned across the sky to achieve full spatial sampling and to cover large areas if desired. The spectrometer has an approximately circular field of view with a diameter of 2.6'. The spectral resolution can be adjusted between 1.2 and 25 GHz by changing the stroke length of the FTS scan mirror. Its main operating mode involves a fixed telescope pointing with multiple scans of the FTS mirror to acquire spectral data. For extended source measurements, multiple position offsets are implemented by means of an internal beam steering mirror to achieve the desired spatial sampling and by rastering of the telescope pointing to map areas larger than the field of view. The SPIRE instrument consists of a cold focal plane unit located inside the Herschel cryostat and warm electronics units, located on the spacecraft Service Module, for instrument control and data handling. Science data are transmitted to Earth with no on-board data compression, and processed by automatic pipelines to produce calibrated science products. The in-flight performance of the instrument matches or exceeds predictions based on pre-launch testing and modelling: the photometer sensitivity is comparable to or slightly better than estimated pre-launch, and the spectrometer sensitivity is also better by a factor of 1.5-2.
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| 2. |
- Gomez-Cabrero, D, et al.
(författare)
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STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse
- 2019
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Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 6:1, s. 256-
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Tidskriftsartikel (refereegranskat)abstract
- Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive systems models of cellular physiology and regulation. However, most multi-omics projects still include a limited number of molecular assays and there have been very few multi-omic studies that evaluate dynamic processes such as cellular growth, development and adaptation. Hence, we lack formal analysis methods and comprehensive multi-omics datasets that can be leveraged to develop true multi-layered models for dynamic cellular systems. Here we present the STATegra multi-omics dataset that combines measurements from up to 10 different omics technologies applied to the same biological system, namely the well-studied mouse pre-B-cell differentiation. STATegra includes high-throughput measurements of chromatin structure, gene expression, proteomics and metabolomics, and it is complemented with single-cell data. To our knowledge, the STATegra collection is the most diverse multi-omics dataset describing a dynamic biological system.
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| 3. |
- Bernhardt, A. M., et al.
(författare)
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A unified classification approach rating clinical utility of protein biomarkers across neurologic diseases
- 2023
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Ingår i: Ebiomedicine. - : Elsevier BV. - 2352-3964. ; 89
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Tidskriftsartikel (refereegranskat)abstract
- A major evolution from purely clinical diagnoses to biomarker supported clinical diagnosing has been occurring over the past years in neurology. High-throughput methods, such as next-generation sequencing and mass spectrometry-based proteomics along with improved neuroimaging methods, are accelerating this development. This calls for a consensus framework that is broadly applicable and provides a spot-on overview of the clinical validity of novel biomarkers. We propose a harmonized terminology and a uniform concept that stratifies biomarkers according to clinical context of use and evidence levels, adapted from existing frameworks in oncology with a strong focus on (epi) genetic markers and treatment context. We demonstrate that this framework allows for a consistent assessment of clinical validity across disease entities and that sufficient evidence for many clinical applications of protein biomarkers is lacking. Our framework may help to identify promising biomarker candidates and classify their applications by clinical context, aiming for routine clinical use of (protein) biomarkers in neurology. Copyright (c) 2023 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
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| 4. |
- Decin, L., et al.
(författare)
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Silicon in the dust formation zone of IRC+10216
- 2010
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 518, s. L143-
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Tidskriftsartikel (refereegranskat)abstract
- The interstellar medium is enriched primarily by matter ejected from evolved low and intermediate mass stars. The outflows from these stars create a circumstellar envelope in which a rich gas-phase and dust-nucleation chemistry takes place. We observed the nearest carbon-rich evolved star, IRC + 10216, using the PACS (55-210 mu m) and SPIRE (194-672 mu m) spectrometers on board Herschel. We find several tens of lines from SiS and SiO, including lines from the v = 1 vibrational level. For SiS these transitions range up to J = 124-123, corresponding to energies around 6700 K, while the highest detectable transition is J = 90-89 for SiO, which corresponds to an energy around 8400 K. Both species trace the dust formation zone of IRC + 10216, and the broad energy ranges involved in their detected transitions permit us to derive the physical properties of the gas and the particular zone in which each species has been formed. This allows us to check the accuracy of chemical thermodynamical equilibrium models and the suggested depletion of SiS and SiO due to accretion onto dust grains.
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| 5. |
- Decin, L., et al.
(författare)
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Warm water vapour in the sooty outflow from a luminous carbon star
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 467:7311, s. 64-67
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Tidskriftsartikel (refereegranskat)abstract
- The detection(1) of circumstellar water vapour around the ageing carbon star IRC + 10216 challenged the current understanding of chemistry in old stars, because water was predicted(2) to be almost absent in carbon-rich stars. Several explanations for the water were postulated, including the vaporization of icy bodies (comets or dwarf planets) in orbit around the star(1), grain surface reactions(3), and photochemistry in the outer circumstellar envelope(4). With a single water line detected so far from this one carbon-rich evolved star, it is difficult to discriminate between the different mechanisms proposed. Here we report the detection of dozens of water vapour lines in the far-infrared and sub-millimetre spectrum of IRC + 10216 using the Herschel satellite(5). This includes some high-excitation lines with energies corresponding to similar to 1,000 K, which can be explained only if water is present in the warm inner sooty region of the envelope. A plausible explanation for the warm water appears to be the penetration of ultraviolet photons deep into a clumpy circumstellar envelope. This mechanism also triggers the formation of other molecules, such as ammonia, whose observed abundances(6) are much higher than hitherto predicted(7).
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| 6. |
- Royer, P., et al.
(författare)
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PACS and SPIRE spectroscopy of the red supergiant VY CMa
- 2010
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 518, s. L145-
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Tidskriftsartikel (refereegranskat)abstract
- With a luminosity > 10(5) L-circle dot and a mass-loss rate of similar to 2 x 10(-4) M-circle dot yr(-1), the red supergiant VY CMa truly is a spectacular object. Because of its extreme evolutionary state, it could explode as supernova any time. Studying its circumstellar material, into which the supernova blast will run, provides interesting constraints on supernova explosions and on the rich chemistry taking place in such complex circumstellar envelopes. We have obtained spectroscopy of VY CMa over the full wavelength range offered by the PACS and SPIRE instruments of Herschel, i.e. 55-672 micron. The observations show the spectral fingerprints of more than 900 spectral lines, of which more than half belong to water. In total, we have identified 13 different molecules and some of their isotopologues. A first analysis shows that water is abundantly present, with an ortho-to-para ratio as low as similar to 1.3:1, and that chemical non-equilibrium processes determine the abundance fractions in the inner envelope.
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| 7. |
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| 8. |
- Tarazona, S, et al.
(författare)
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Harmonization of quality metrics and power calculation in multi-omic studies
- 2020
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1, s. 3092-
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Tidskriftsartikel (refereegranskat)abstract
- Multi-omic studies combine measurements at different molecular levels to build comprehensive models of cellular systems. The success of a multi-omic data analysis strategy depends largely on the adoption of adequate experimental designs, and on the quality of the measurements provided by the different omic platforms. However, the field lacks a comparative description of performance parameters across omic technologies and a formulation for experimental design in multi-omic data scenarios. Here, we propose a set of harmonized Figures of Merit (FoM) as quality descriptors applicable to different omic data types. Employing this information, we formulate the MultiPower method to estimate and assess the optimal sample size in a multi-omics experiment. MultiPower supports different experimental settings, data types and sample sizes, and includes graphical for experimental design decision-making. MultiPower is complemented with MultiML, an algorithm to estimate sample size for machine learning classification problems based on multi-omic data.
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| 9. |
- Cernicharo, J., et al.
(författare)
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Detection of anhydrous hydrochloric acid, HCl, in IRC+10216 with the Herschel SPIRE and PACS spectrometers Detection of HCI in IRC+10216
- 2010
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 518, s. L136-
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Tidskriftsartikel (refereegranskat)abstract
- We report on the detection of anhydrous hydrochloric acid (hydrogen chlorine, HCl) in the carbon-rich star IRC+10216 using the spectroscopic facilities onboard the Herschel satellite. Lines from J = 1-0 up to J = 7-6 have been detected. From the observed intensities, we conclude that HCl is produced in the innermost layers of the circumstellar envelope with an abundance relative to H-2 of 5 x 10(-8) and extends until the molecules reach its photodissociation zone. Upper limits to the column densities of AlH, MgH, CaH, CuH, KH, NaH, FeH, and other diatomic hydrides have also been obtained.
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| 10. |
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