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| 2. |
- Borrero, J. M., et al.
(författare)
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Combining magneto-hydrostatic constraints with Stokes profiles inversions. II. Application to Hinode/SP observations
- 2021
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 647
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Tidskriftsartikel (refereegranskat)abstract
- Context. Inversion techniques applied to the radiative transfer equation for polarized light are capable of inferring the physical parameters in the solar atmosphere (temperature T, magnetic field B, and line-of-sight velocity v(los)) from observations of the Stokes vector (i.e., spectropolarimetric observations) in spectral lines. Inferences are usually performed in the (x, y, tau (c)) domain, where tau (c) refers to the optical-depth scale. Generally, their determination in the (x, y, z) volume is not possible due to the lack of a reliable estimation of the gas pressure, particularly in regions of the solar surface harboring strong magnetic fields.Aims. We aim to develop a new inversion code capable of reliably inferring the physical parameters in the (x, y, z) domain.Methods. We combine, in a self-consistent way, an inverse solver for the radiative transfer equation (Firtez-DZ) with a solver for the magneto-hydrostatic equilibrium, which derives realistic values of the gas pressure by taking the magnetic pressure and tension into account.Results. We test the correct behavior of the newly developed code with spectropolarimetric observations of two sunspots recorded with the spectropolarimeter (SP) instrument on board the Hinode spacecraft, and we show how the physical parameters are inferred in the (x, y, z) domain, with the Wilson depression of the sunspots arising as a natural consequence of the force balance. In particular, our approach significantly improves upon previous determinations that were based on semiempirical models.Conclusions. Our results open the door for the possibility of calculating reliable electric currents in three dimensions, j(x, y, z), in the solar photosphere. Further consistency checks would include a comparison with other methods that have recently been proposed and which achieve similar goals.
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| 4. |
- Noda, C. Quintero, et al.
(författare)
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Chromospheric polarimetry through multiline observations of the 850-nm spectral region - II. A magnetic flux tube scenario
- 2017
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 472:1, s. 727-737
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Tidskriftsartikel (refereegranskat)abstract
- In this publication, we continue the work started in Quintero Noda et al., examining this time a numerical simulation of a magnetic flux tube concentration. Our goal is to study if the physical phenomena that take place in it, in particular, the magnetic pumping, leaves a specific imprint on the examined spectral lines. We find that the profiles from the interior of the flux tube are periodically doppler shifted following an oscillation pattern that is also reflected in the amplitude of the circular polarization signals. In addition, we analyse the properties of the Stokes profiles at the edges of the flux tube discovering the presence of linear polarization signals for the Ca II lines, although they are weak with an amplitude around 0.5 per cent of the continuum intensity. Finally, we compute the response functions to perturbations in the longitudinal field, and we estimate the field strength using the weak-field approximation. Our results indicate that the height of formation of the spectral lines changes during the magnetic pumping process, which makes the interpretation of the inferred magnetic field strength and its evolution more difficult. These results complement those from previous works, demonstrating the capabilities and limitations of the 850-nm spectrum for chromospheric Zeeman polarimetry in a very dynamic and complex atmosphere.
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| 5. |
- Noda, C. Quintero, et al.
(författare)
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Diagnostic capabilities of spectropolarimetric observations for understanding solar phenomena : I. Zeeman-sensitive photospheric lines
- 2021
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 652
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Tidskriftsartikel (refereegranskat)abstract
- Future ground-based telescopes will expand our capabilities for simultaneous multi-line polarimetric observations in a wide range of wavelengths, from the near-ultraviolet to the near-infrared. This creates a strong demand to compare candidate spectral lines to establish a guideline of the lines that are most appropriate for each observation target. We focused in this first work on Zeeman-sensitive photospheric lines in the visible and infrared. We first examined their polarisation signals and response functions using a 1D semi-empirical atmosphere. Then we studied the spatial distribution of the line core intensity and linear and circular polarisation signals using a realistic 3D numerical simulation. We ran inversions of synthetic profiles, and we compared the heights at which we obtain a high correlation between the input and the inferred atmosphere. We also used this opportunity to revisit the atomic information we have on these lines and computed the broadening cross-sections due to collisions with neutral hydrogen atoms for all the studied spectral lines. The results reveal that four spectral lines stand out from the rest for quiet-Sun and network conditions: Fe I 5250.2, 6302, 8468, and 15 648 angstrom. The first three form higher in the atmosphere, and the last line is mainly sensitive to the atmospheric parameters at the bottom of the photosphere. However, as they reach different heights, we strongly recommend using at least one of the first three candidates together with the Fe I 15 648 angstrom line to optimise our capabilities for inferring the thermal and magnetic properties of the lower atmosphere.
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| 6. |
- Oliver, J, et al.
(författare)
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Association of Circular RNA and Long Non-Coding RNA Dysregulation with the Clinical Response to Immune Checkpoint Blockade in Cutaneous Metastatic Melanoma
- 2022
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Ingår i: Biomedicines. - : MDPI AG. - 2227-9059. ; 10:10
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Tidskriftsartikel (refereegranskat)abstract
- Cutaneous melanoma (CM) is the most lethal form of skin cancer if it becomes metastatic, where treatment options and survival chances decrease dramatically. Immunotherapy treatments based on the immunologic checkpoint inhibitors programmed death cell protein 1 (PD-1) and cytotoxic T-lymphocyte antigen 4 (CTLA-4) constituted a main breakthrough in the treatment of metastatic CM, particularly for the achievement of long-term benefits. Even though it is a very promising therapy, resistance to primary immune checkpoint blockade (ICB) arises in about 70% of CM patients treated with a CTLA-4 inhibitor, and 40–65% of CM patients administered with a PD-1-targeting treatment. Some long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) are implicated in triggering pro- and anti-tumorigenic responses to various cancer treatments. The relationship between lncRNAs, circRNAs and ICB immunotherapy has not been explored in cutaneous metastatic melanoma (CMM). The aim of this pilot study is to evaluate the potential role of circRNA and lncRNA expression variability as pre-treatment predictor of the clinical response to immunotherapy in CMM patients. RNA-seq from 12 formalin-fixed paraffin-embedded (FFPE) samples from the metastatic biopsies of CMM patients treated with nivolumab was used to identify response-associated transcripts. Our findings indicate that specific lncRNAs and circRNAs, probably acting as competitive endogenous RNAs (ceRNAs), are involved in the regulatory networks of the immune response against metastatic melanoma that these patients have under treatment with nivolumab. Moreover, we established a risk score that yields predictions of the overall survival (OS) and progression-free survival (PFS) of CMM patients with high accuracy. This proof-of-principle work provides a possible insight into the function of ceRNAs, contributing to efforts to decipher the complex molecular mechanisms of ICB cancer treatment response.
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| 8. |
- Onieva, JL, et al.
(författare)
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High IGKC-Expressing Intratumoral Plasma Cells Predict Response to Immune Checkpoint Blockade
- 2022
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Ingår i: International journal of molecular sciences. - : MDPI AG. - 1422-0067. ; 23:16
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Tidskriftsartikel (refereegranskat)abstract
- Resistance to Immune Checkpoint Blockade (ICB) constitutes the current limiting factor for the optimal implementation of this novel therapy, which otherwise demonstrates durable responses with acceptable toxicity scores. This limitation is exacerbated by a lack of robust biomarkers. In this study, we have dissected the basal TME composition at the gene expression and cellular levels that predict response to Nivolumab and prognosis. BCR, TCR and HLA profiling were employed for further characterization of the molecular variables associated with response. The findings were validated using a single-cell RNA-seq data of metastatic melanoma patients treated with ICB, and by multispectral immunofluorescence. Finally, machine learning was employed to construct a prediction algorithm that was validated across eight metastatic melanoma cohorts treated with ICB. Using this strategy, we have unmasked a major role played by basal intratumoral Plasma cells expressing high levels of IGKC in efficacy. IGKC, differentially expressed in good responders, was also identified within the Top response-related BCR clonotypes, together with IGK variants. These results were validated at gene, cellular and protein levels; CD138+ Plasma-like and Plasma cells were more abundant in good responders and correlated with the same RNA-seq-defined fraction. Finally, we generated a 15-gene prediction model that outperformed the current reference score in eight ICB-treated metastatic melanoma cohorts. The evidenced major contribution of basal intratumoral IGKC and Plasma cells in good response and outcome in ICB in metastatic melanoma is a groundbreaking finding in the field beyond the role of T lymphocytes.
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| 9. |
- Pastor Yabar, Adur, et al.
(författare)
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Inference of electric currents in the solar photosphere
- 2021
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 656
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Tidskriftsartikel (refereegranskat)abstract
- Context. Despite their importance, routine and direct measurements of electric currents, j, in the solar atmosphere have generally not been possible.Aims. We aim at demonstrating the capabilities of a newly developed method for determining electric currents in the solar photosphere.Methods. We employ three-dimensional radiative magneto-hydrodynamic (MHD) simulations to produce synthetic Stokes profiles in several spectral lines with a spatial resolution similar to what the newly operational 4-meter Daniel K. Inouye Solar Telescope solar telescope should achieve. We apply a newly developed inversion method of the polarized radiative transfer equation with magneto-hydrostatic (MHS) constraints to infer the magnetic field vector in the three-dimensional Cartesian domain, B(x,y,z), from the synthetic Stokes profiles. We then apply Ampere's law to determine the electric currents, j, from the inferred magnetic field, B(x,z), and compare the results with the electric currents present in the original MHD simulation.Results. We show that the method employed here is able to attain reasonable reliability (close to 50% of the cases are within a factor of two, and this increases to 60%-70% for pixels with B300 G) in the inference of electric currents for low atmospheric heights (optical depths at 500 nm tau(5)is an element of[1, 0.1]) regardless of whether a small or large number of spectral lines are inverted. Above these photospheric layers, the method's accuracy strongly deteriorates as magnetic fields become weaker and as the MHS approximation becomes less accurate. We also find that the inferred electric currents have a floor value that is related to low-magnetized plasma, where the uncertainty in the magnetic field inference prevents a sufficiently accurate determination of the spatial derivatives.Conclusions. We present a method that allows the inference of the three components of the electric current vector at deep atmospheric layers (photospheric layers) from spectropolarimetric observations.
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| 10. |
- Quintero Noda, C., et al.
(författare)
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A study of the capabilities for inferring atmospheric information from high-spatial-resolution simulations
- 2023
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Ingår i: Astronomy and Astrophysics. - 0004-6361 .- 1432-0746. ; 675
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Tidskriftsartikel (refereegranskat)abstract
- In this work, we study the accuracy that can be achieved when inferring the atmospheric information from realistic numerical magnetohydrodynamic simulations that reproduce the spatial resolution we will obtain with future observations made by the 4 m class telescopes DKIST and EST. We first study multiple inversion configurations using the SIR code and the Fe i transitions at 630 nm until we obtain minor differences between the input and the inferred atmosphere in a wide range of heights. Also, we examine how the inversion accuracy depends on the noise level of the Stokes profiles. The results indicate that when the majority of the inverted pixels come from strongly magnetised areas, there are almost no restrictions in terms of the noise, obtaining good results for noise amplitudes up to 1 x 10(-3) of I-c. At the same time, the situation is different for observations where the dominant magnetic structures are weak, and noise restraints are more demanding. Moreover, we find that the accuracy of the fits is almost the same as that obtained without noise when the noise levels are on the order of 1 x 10(-4) of I-c. We, therefore, advise aiming for noise values on the order of or lower than 5 x 10(-4) of I-c if observers seek reliable interpretations of the results for the magnetic field vector reliably. We expect those noise levels to be achievable by next-generation 4m class telescopes thanks to an optimised polarisation calibration and the large collecting area of the primary mirror.
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