Spectropolarimetric NLTE inversion code SNAPI

Inversion codes are computer programs that fit a model atmosphere to the observed Stokes spectra, thus retrieving the relevant atmospheric parameters. The rising interest in the solar chromosphere, where spectral lines are formed by scattering, requires developing, testing, and comparing new non-local thermal equilibrium (NLTE) inversion codes. We present a new NLTE inversion code that is based on the analytical computation of the response functions. We named the code SNAPI, which is short for spectropolarimetic NLTE analytically powered inversion. SNAPI inverts full Stokes spectrum in order to obtain a depth-dependent stratification of the temperature, velocity, and the magnetic field vector. It is based on the so-called node approach, where atmospheric parameters are free to vary in several fixed points in the atmosphere, and are assumed to behave as splines in between. We describe the inversion approach in general and the specific choices we have made in the implementation. We test the performance on one academic problem and on two interesting NLTE examples, the Ca\,II\,8542 and Na\,I\,D spectral lines. The code is found to have excellent convergence properties and outperforms a finite-difference based code in this specific implementation by at least a factor of three. We invert synthetic observations of Na lines from a small part of a simulated solar atmosphere and conclude that the Na lines reliably retrieve the magnetic field and velocity in the range $-3<\log \tau < -0.5$.Comment: To appear in A&

Peripheral downflows in sunspot penumbrae

Sunspot penumbrae show high-velocity patches along the periphery. The high-velocity downflow patches are believed to be the return channels of the Evershed flow. We aim to investigate their structure in detail using Hinode SOT/SP observations. We employ Fourier interpolation in combination with spatially coupled height dependent LTE inversions of Stokes profiles to produce high-resolution, height-dependent maps of atmospheric parameters of these downflows and investigate their properties. High-speed downflows are observed over a wide range of viewing angles. They have supersonic line-of-sight velocities, some in excess of 20km/s, and very high magnetic field strengths, reaching values of over 7 kG. A relation between the downflow velocities and the magnetic field strength is found, in good agreement with MHD simulations. The coupled inversion at high resolution allows for the accurate determination of small-scale structures. The recovered atmospheric structure indicates that regions with very high downflow velocities contain some of the strongest magnetic fields that have ever been measured on the Sun.Comment: A&A, in press, 14 pages, 15 figure

Vigorous convection in a sunspot granular light bridge

Light bridges are the most prominent manifestation of convection in sunspots. The brightest representatives are granular light bridges composed of features that appear to be similar to granules. An in-depth study of the convective motions, temperature stratification, and magnetic field vector in and around light bridge granules is presented with the aim of identifying similarities and differences to typical quiet-Sun granules. Spectropolarimetric data from the Hinode Solar Optical Telescope were analyzed using a spatially coupled inversion technique to retrieve the stratified atmospheric parameters of light bridge and quiet-Sun granules. Central hot upflows surrounded by cooler fast downflows reaching 10 km/s clearly establish the convective nature of the light bridge granules. The inner part of these granules in the near surface layers is field free and is covered by a cusp-like magnetic field configuration. We observe hints of field reversals at the location of the fast downflows. The quiet-Sun granules in the vicinity of the sunspot are covered by a low-lying canopy field extending radially outward from the spot. The similarities between quiet-Sun and light bridge granules point to the deep anchoring of granular light bridges in the underlying convection zone. The fast, supersonic downflows are most likely a result of a combination of invigorated convection in the light bridge granule due to radiative cooling into the neighboring umbra and the fact that we sample deeper layers, since the downflows are immediately adjacent to the slanted walls of the Wilson depression.Comment: 10 pages, 11 figure

Recent advancements in the EST project

The European Solar Telescope (EST) is a project of a new-generation solar telescope. It has a large aperture of 4~m, which is necessary for achieving high spatial and temporal resolution. The high polarimetric sensitivity of the EST will allow to measure the magnetic field in the solar atmosphere with unprecedented precision. Here, we summarise the recent advancements in the realisation of the EST project regarding the hardware development and the refinement of the science requirements.Comment: accepted to Advances in Space Researc

Structure of sunspot penumbral filaments: a remarkable uniformity of properties

The sunspot penumbra comprises numerous thin, radially elongated filaments that are central for heat transport within the penumbra, but whose structure is still not clear. To investigate the fine-scale structure of these filaments, we perform a depth-dependent inversion of spectropolarimetric data of a sunspot very close to solar disk center obtained by Hinode (SOT/SP). We have used a recently developed spatially coupled 2D inversion scheme which allows us to analyze the fine structure of individual penumbral filaments up to the diffraction limit of the telescope. Filaments of different sizes in all parts of penumbra display very similar magnetic field strengths, inclinations and velocity patterns. The similarities allowed us to average all these filaments and to extract the physical properties common to all of them. This average filament shows upflows associated with an upward pointing field at its inner, umbral end and along its axis, downflows along the lateral edge and strong downflows in the outer end associated with a nearly vertical, strong and downward pointing field. The upflowing plasma is significantly hotter than the downflowing plasma. The hot, tear-shaped head of the averaged filament can be associated with a penumbral grain. The central part of the filament shows nearly horizontal fields with strengths of ~1kG. The field above the filament converges, whereas a diverging trend is seen in the deepest layers near the head of the filament. We put forward a unified observational picture of a sunspot penumbral filament. It is consistent with such a filament being a magneto-convective cell, in line with recent MHD simulations. The uniformity of its properties over the penumbra sets constraints on penumbral models and simulations. The complex and inhomogeneous structure of the filament provides a natural explanation for a number of long-running controversies in the literature.Comment: 19 pages; 12 figures; accepted for publication in A&

Adaptation to high ethanol reveals complex evolutionary pathways

Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts

Neoadjuvant immunotherapy with nivolumab and ipilimumab induces major pathological responses in patients with head and neck squamous cell carcinoma

Surgery for locoregionally advanced head and neck squamous cell carcinoma (HNSCC) results in 30‒50% five-year overall survival. In IMCISION (NCT03003637), a non-randomized phase Ib/IIa trial, 32 HNSCC patients are treated with 2 doses (in weeks 1 and 3) of immune checkpoint blockade (ICB) using nivolumab (NIVO MONO, n = 6, phase Ib arm A) or nivolumab plus a single dose of ipilimumab (COMBO, n = 26, 6 in phase Ib arm B, and 20 in phase IIa) prior to surgery. Primary endpoints are feasibility to resect no later than week 6 (phase Ib) and primary tumor pathological response (phase IIa). Surgery is not delayed or suspended for any patient in phase Ib, meeting the primary endpoint. Grade 3‒4 immune-related adverse events are seen in 2 of 6 (33%) NIVO MONO and 10 of 26 (38%) total COMBO patients. Pathological response, defined as the %-change in primary tumor viable tumor cell percentage from baseline biopsy to on-treatment resection, is evaluable in 17/20 phase IIa patients and 29/32 total trial patients (6/6 NIVO MONO, 23/26 COMBO). We observe a major pathological response (MPR, 90‒100% response) in 35% of patients after COMBO ICB, both in phase IIa (6/17) and in the whole trial (8/23), meeting the phase IIa primary endpoint threshold of 10%. NIVO MONO’s MPR rate is 17% (1/6). None of the MPR patients develop recurrent HSNCC during 24.0 months median postsurgical follow-up. FDG-PET-based total lesion glycolysis identifies MPR patients prior to surgery. A baseline AID/APOBEC-associated mutational profile and an on-treatment decrease in hypoxia RNA signature are observed in MPR patients. Our data indicate that neoadjuvant COMBO ICB is feasible and encouragingly efficacious in HNSCC

Multidimensional Radiative Transfer

A multidimensional radiative transfer code is presented, using the short characteristics scheme and the ALI method. The code uses the 2-level atom formulation, appropriate for strong resonance lines, and can operate with Cartesian, cylindrical and spherical coordinate systems, the last two assuming rotational symmetry about the z-axis. The emphasis of the code is on accurately treating large, three-dimensional velocity fields on a large number of spatial points and with high angular resolution, in order to deal with complete objects. To keep the code fast and reduce memory requirements, the code was parallelized for use on a cluster of networked PCs by using a spatial parallelization method, where the computational domain is divided spatially in independent subdomains. It is shown that such a method is both efficient and reliable. The accuracy of the code was tested at length and was found to be ~ 5% in most cases of interest. A spectrum synthesis code is then presented, using the long characteristics method and an Adaptive Mesh Refinement technique. The code can accurately calculate the emergent line profile for a specified inclination angle on a two-dimensional structure with a specified source function assuming rotational symmetry, in cylindrical and spherical coordinate systems. The accuracy of the code was determined to be of the order of 1%, given the structure and line source function. Both codes were then applied to the problem of rotation in expanding stellar winds. The spectroscopic effects of rotation were found to be significant for large inclination angles only, with the largest differences with respect to non-rotating of ~ 20%. The direction of the radiation volume force was found to change at most by a similar amount. Finally, the codes were applied to calculate line profiles for the disks in cataclysmic variables. The differences due to rotation were found to be significant, with the cores of strong resonance lines brightened by about 50% for small inclination angles. The radiation force was not found to be strongly affected