| 1. |
- Roueff, Antoine, et al.
(författare)
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Bias versus variance when fitting multi-species molecular lines with a non-LTE radiative transfer model: Application to the estimation of the gas temperature and volume density
- 2024
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 686
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Tidskriftsartikel (refereegranskat)abstract
- Context. Robust radiative transfer techniques are requisite for efficiently extracting the physical and chemical information from molecular rotational lines. Aims. We study several hypotheses that enable robust estimations of the column densities and physical conditions when fitting one or two transitions per molecular species. We study the extent to which simplifying assumptions aimed at reducing the complexity of the problem introduce estimation biases and how to detect them. Methods. We focus on the CO and HCO+ isotopologues and analyze maps of a 50 square arcminutes field. We used the RADEX escape probability model to solve the statistical equilibrium equations and compute the emerging line profiles, assuming that all species coexist. Depending on the considered set of species, we also fixed the abundance ratio between some species and explored different values. We proposed a maximum likelihood estimator to infer the physical conditions and considered the effect of both the thermal noise and calibration uncertainty. We analyzed any potential biases induced by model misspecifications by comparing the results on the actual data for several sets of species and confirmed with Monte Carlo simulations. The variance of the estimations and the efficiency of the estimator were studied based on the Cramér-Rao lower bound. Results. Column densities can be estimated with 30% accuracy, while the best estimations of the volume density are found to be within a factor of two. Under the chosen model framework, the peak 12CO (1 -0) is useful for constraining the kinetic temperature. The thermal pressure is better and more robustly estimated than the volume density and kinetic temperature separately. Analyzing CO and HCO+ isotopologues and fitting the full line profile are recommended practices with respect to detecting possible biases. Conclusions. Combining a non-local thermodynamic equilibrium model with a rigorous analysis of the accuracy allows us to obtain an efficient estimator and identify where the model is misspecified. We note that other combinations of molecular lines could be studied in the future.
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| 2. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Einig, Lucas, et al.
(författare)
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Deep learning denoising by dimension reduction: Application to the ORION-B line cubes
- 2023
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 677
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Tidskriftsartikel (refereegranskat)abstract
- Context. The availability of large bandwidth receivers for millimeter radio telescopes allows for the acquisition of position-position-frequency data cubes over a wide field of view and a broad frequency coverage. These cubes contain a lot of information on the physical, chemical, and kinematical properties of the emitting gas. However, their large size coupled with an inhomogenous signal-to-noise ratio (S/N) are major challenges for consistent analysis and interpretation. Aims. We searched for a denoising method of the low S/N regions of the studied data cubes that would allow the low S/N emission to be recovered without distorting the signals with a high S/N. Methods. We performed an in-depth data analysis of the 13CO and C17O (1-0) data cubes obtained as part of the ORION-B large program performed at the IRAM 30 m telescope. We analyzed the statistical properties of the noise and the evolution of the correlation of the signal in a given frequency channel with that of the adjacent channels. This has allowed us to propose significant improvements of typical autoassociative neural networks, often used to denoise hyperspectral Earth remote sensing data. Applying this method to the 13CO (1-0) cube, we were able to compare the denoised data with those derived with the multiple Gaussian fitting algorithm ROHSA, considered as the state-of-the-art procedure for data line cubes. Results. The nature of astronomical spectral data cubes is distinct from that of the hyperspectral data usually studied in the Earth remote sensing literature because the observed intensities become statistically independent beyond a short channel separation. This lack of redundancy in data has led us to adapt the method, notably by taking into account the sparsity of the signal along the spectral axis. The application of the proposed algorithm leads to an increase in the S/N in voxels with a weak signal, while preserving the spectral shape of the data in high S/N voxels. Conclusions. The proposed algorithm that combines a detailed analysis of the noise statistics with an innovative autoencoder architecture is a promising path to denoise radio-astronomy line data cubes. In the future, exploring whether a better use of the spatial correlations of the noise may further improve the denoising performances seems to be a promising avenue. In addition, dealing with the multiplicative noise associated with the calibration uncertainty at high S/N would also be beneficial for such large data cubes.
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| 4. |
- Rodriguez, Sébastien, et al.
(författare)
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Science goals and new mission concepts for future exploration of Titan's atmosphere, geology and habitability : titan POlar scout/orbitEr and in situ lake lander and DrONe explorer (POSEIDON)
- 2022
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Ingår i: Experimental astronomy. - : Springer Science and Business Media LLC. - 0922-6435 .- 1572-9508. ; 54:2-3, s. 911-973
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Tidskriftsartikel (refereegranskat)abstract
- In response to ESA’s “Voyage 2050” announcement of opportunity, we propose an ambitious L-class mission to explore one of the most exciting bodies in the Solar System, Saturn’s largest moon Titan. Titan, a “world with two oceans”, is an organic-rich body with interior-surface-atmosphere interactions that are comparable in complexity to the Earth. Titan is also one of the few places in the Solar System with habitability potential. Titan’s remarkable nature was only partly revealed by the Cassini-Huygens mission and still holds mysteries requiring a complete exploration using a variety of vehicles and instruments. The proposed mission concept POSEIDON (Titan POlar Scout/orbitEr and In situ lake lander DrONe explorer) would perform joint orbital and in situ investigations of Titan. It is designed to build on and exceed the scope and scientific/technological accomplishments of Cassini-Huygens, exploring Titan in ways that were not previously possible, in particular through full close-up and in situ coverage over long periods of time. In the proposed mission architecture, POSEIDON consists of two major elements: a spacecraft with a large set of instruments that would orbit Titan, preferably in a low-eccentricity polar orbit, and a suite of in situ investigation components, i.e. a lake lander, a “heavy” drone (possibly amphibious) and/or a fleet of mini-drones, dedicated to the exploration of the polar regions. The ideal arrival time at Titan would be slightly before the next northern Spring equinox (2039), as equinoxes are the most active periods to monitor still largely unknown atmospheric and surface seasonal changes. The exploration of Titan’s northern latitudes with an orbiter and in situ element(s) would be highly complementary in terms of timing (with possible mission timing overlap), locations, and science goals with the upcoming NASA New Frontiers Dragonfly mission that will provide in situ exploration of Titan’s equatorial regions, in the mid-2030s.
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| 5. |
- Santa-Maria, Miriam G., et al.
(författare)
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HCN emission from translucent gas and UV-illuminated cloud edges revealed by wide-field IRAM 30 m maps of the Orion B GMC: Revisiting its role as a tracer of the dense gas reservoir for star formation
- 2023
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 679
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Tidskriftsartikel (refereegranskat)abstract
- Context. Massive stars form within dense clumps inside giant molecular clouds (GMCs). Finding appropriate chemical tracers of the dense gas (n(H2) > several 104 cm-3 or AV > 8 mag) and linking their line luminosity with the star formation rate is of critical importance. Aims. Our aim is to determine the origin and physical conditions of the HCN-emitting gas and study their relation to those of other molecules. Methods. In the context of the IRAM 30m ORION-B large program, we present 5 deg2 (~250 pc2) HCN, HNC, HCO+, and CO J =1-0 maps of the Orion B GMC, complemented with existing wide-field [CI] 492 GHz maps, as well as new pointed observations of rotationally excited HCN, HNC, H13CN, and HN13C lines. We compare the observed HCN line intensities with radiative transfer models including line overlap effects and electron excitation. Furthermore, we study the HCN/HNC isomeric abundance ratio with updated photochemical models. Results. We spectroscopically resolve the HCN J = 1-0 hyperfine structure (HFS) components (and partially resolved J = 2-1 and 3-2 components). We detect anomalous HFS line intensity (and line width) ratios almost everywhere in the cloud. About 70% of the total HCN J = 1-0 luminosity, L′(HCN J = 1-0) = 110 K km s-1 pc-2, arises from AV < 8 mag. The HCN/CO J = 1-0 line intensity ratio, widely used as a tracer of the dense gas fraction, shows a bimodal behavior with an inflection point at AV < 3 mag typical of translucent gas and illuminated cloud edges. We find that most of the HCN J = 1-0 emission arises from extended gas with n(H2) < 104 cm-3, and even lower density gas if the ionization fraction is χe ≥10-5 and electron excitation dominates. This result contrasts with the prevailing view of HCN J = 1-0 emission as a tracer of dense gas and explains the low-AV branch of the HCN/CO J = 1-0 intensity ratio distribution. Indeed, the highest HCN/CO ratios (~ 0.1) at AV < 3 mag correspond to regions of high [CI] 492 GHz/CO J = 1-0 intensity ratios (>1) characteristic of low-density photodissociation regions. The low surface brightness (≲ 1 K km s-1) and extended HCN and HCO+ J = 1-0 emission scale with IFIR -a proxy of the stellar far-ultraviolet (FUV) radiation field -in a similar way. Together with CO J = 1-0, these lines respond to increasing IFIR up to G0 ≅ 20. On the other hand, the bright HCN J = 1-0 emission (> 6 K km s-1) from dense gas in star-forming clumps weakly responds to IFIR once the FUV field becomes too intense (G0 > 1500). In contrast, HNC J = 1-0 and [CI] 492 GHz lines weakly respond to IFIR for all G0. The different power law scalings (produced by different chemistries, densities, and line excitation regimes) in a single but spatially resolved GMC resemble the variety of Kennicutt-Schmidt law indexes found in galaxy averages. Conclusions. Given the widespread and extended nature of the [CI] 492 GHz emission, as well as its spatial correlation with that of HCO+, HCN, and 13CO J = 1-0 lines (in this order), we argue that the edges of GMCs are porous to FUV radiation from nearby massive stars. Enhanced FUV radiation favors the formation and excitation of HCN on large scales, not only in dense star-forming clumps, and it leads to a relatively low value of the dense gas mass to total luminosity ratio, α (HCN) = 29 M⊙ /(K km s-1pc2) in Orion B. As a corollary for extragalactic studies, we conclude that high HCN/CO J = 1-0 line intensity ratios do not always imply the presence of dense gas, which may be better traced by HNC than by HCN.
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| 6. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 7. |
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| 8. |
- Elyn, Antoine, et al.
(författare)
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End of life care practice and symptom management outcomes of nursing home residents with dementia : secondary analyses of IQUARE trial
- 2019
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Ingår i: European Geriatric Medicine. - : Springer Science and Business Media LLC. - 1878-7649 .- 1878-7657. ; 10:6, s. 947-955
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Tidskriftsartikel (refereegranskat)abstract
- Purpose End-of-life care is a central issue in nursing homes. Poor care outcomes have been reported, especially among residents with dementia. Our aim was two-fold: to assess whether the diagnosis of dementia was associated with specific patterns of care and symptom management for residents with dementia during the last 6 months of life, and to compare these patterns of care between residents with dementia who died within 6 months and those who survived longer. Methods Secondary prospective analyses of the IQUARE trial (trial registration number NCT01703689). 175 nursing homes in South West France. Residents with and without dementia at baseline (May-June 2011), stratified according to their vital status at 6-month follow-up. Results Of 6275 residents enrolled in IQUARE study (including 2688 with dementia), 494 (7.9%) died within 6 months. Compared to residents without dementia (n = 254), those with dementia (n = 240) were less likely to be self-sufficient (OR = 0.08, 95% CI 0.01-0.64). They were more likely to have physical restraints (OR = 1.65, 95% CI 1.08-2.51) and less likely to be prescribed benzodiazepines (OR = 0.58, 95% CI 0.38-0.88). Among residents with dementia, those who died during the first 6 months of follow-up were more likely to be identified with a formal end-of-life status (OR = 5.71, 95% CI 3.48-9.37) although such identification remains low with only 15% of them. They were more likely to experience pain (OR = 1.43, 95% CI 1.04-1.97) and to be physically restrained (OR = 1.46, 95% CI 1.08-1.98). However, pain relief and psychological distress management were not improved. Conclusions Poor quality indicators such as physical restraints are associated with end-of-life care for residents with dementia. Among symptom management outcomes, pain medication remains low even if pain complaint increased at life end.
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| 9. |
- Gaballa, Ahmed, et al.
(författare)
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Evaluating Thymic Function After Human Hematopoietic Stem Cell Transplantation in the Personalized Medicine Era
- 2020
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Ingår i: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 11
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Forskningsöversikt (refereegranskat)abstract
- Hematopoietic stem cell transplantation (HSCT) is an effective treatment option for several malignant and non-malignant hematological diseases. The clinical outcome of this procedure relies to a large extent on optimal recovery of adaptive immunity. In this regard, the thymus plays a central role as the primary site forde novogeneration of functional, diverse, and immunocompetent T-lymphocytes. The thymus is exquisitely sensitive to several insults during HSCT, including conditioning drugs, corticosteroids, infections, and graft-vs.-host disease. Impaired thymic recovery has been clearly associated with increased risk of opportunistic infections and poor clinical outcomes in HSCT recipients. Therefore, better understanding of thymic function can provide valuable information for improving HSCT outcomes. Recent data have shown that, besides gender and age, a specific single-nucleotide polymorphism affects thymopoiesis and may also influence thymic output post-HSCT, suggesting that the time of precision medicine of thymic function has arrived. Here, we review the current knowledge about thymic role in HSCT and the recent work of genetic control of human thymopoiesis. We also discuss different transplant-related factors that have been associated with impaired thymic recovery and the use of T-cell receptor excision circles (TREC) to assess thymic output, including its clinical significance. Finally, we present therapeutic strategies that could boost thymic recovery post-HSCT.
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| 10. |
- Patty, C. H.Lucas, et al.
(författare)
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Biosignatures of the Earth : I. Airborne spectropolarimetric detection of photosynthetic life
- 2021
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 651
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Tidskriftsartikel (refereegranskat)abstract
- Context. Homochirality is a generic and unique property of life on Earth and is considered a universal and agnostic biosignature. Homochirality induces fractional circular polarization in the incident light that it reflects. Because this circularly polarized light can be sensed remotely, it can be one of the most compelling candidate biosignatures in life detection missions. While there are also other sources of circular polarization, these result in spectrally flat signals with lower magnitude. Additionally, circular polarization can be a valuable tool in Earth remote sensing because the circular polarization signal directly relates to vegetation physiology. Aims. While high-quality circular polarization measurements can be obtained in the laboratory and under semi-static conditions in the field, there has been a significant gap to more realistic remote sensing conditions. Methods. In this study, we present sensitive circular spectropolarimetric measurements of various landscape elements taken from a fast-moving helicopter. Results. We demonstrate that during flight, within mere seconds of measurements, we can differentiate (S∕ N > 5) between grass fields, forests, and abiotic urban areas. Importantly, we show that with only nonzero circular polarization as a discriminant, photosynthetic organisms can even be measured in lakes. Conclusions. Circular spectropolarimetry can be a powerful technique to detect life beyond Earth, and we emphasize the potential of utilizing circular spectropolarimetry as a remote sensing tool to characterize and monitor in detail the vegetation physiology and terrain features of Earth itself.
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