PyMieDAP: a Python--Fortran tool to compute fluxes and polarization signals of (exo)planets

PyMieDAP (the Python Mie Doubling-Adding Programme) is a Python--based tool for computing the total, linearly, and circularly polarized fluxes of incident unpolarized sun- or starlight that is reflected by, respectively, Solar System planets or moons, or exoplanets at a range of wavelengths. The radiative transfer computations are based on an adding--doubling Fortran algorithm and fully include polarization for all orders of scattering. The model (exo)planets are described by a model atmosphere composed of a stack of homogeneous layers containing gas and/or aerosol and/or cloud particles bounded below by an isotropically, depolarizing surface (that is optionally black). The reflected light can be computed spatially--resolved and/or disk--integrated. Spatially--resolved signals are mostly representative for observations of Solar System planets (or moons), while disk--integrated signals are mostly representative for exoplanet observations. PyMieDAP is modular and flexible, and allows users to adapt and optimize the code according to their needs. PyMieDAP keeps options open for connections with external programs and for future additions and extensions. In this paper, we describe the radiative transfer algorithm that PyMieDAP is based on and the code's principal functionalities. And we provide benchmark results of PyMieDAP that can be used for testing its installation and for comparison with other codes. PyMieDAP is available online under the GNU GPL license at http://gitlab.com/loic.cg.rossi/pymiedapComment: 15 pages, 7 figures, 4 tables. Accepted for publication in Astronomy and Astrophysic

Traces of exomoons in computed flux and polarization phase curves of starlight reflected by exoplanets

Context: Detecting moons around exoplanets is a major goal of current and future observatories. Moons are suspected to influence rocky exoplanet habitability, and gaseous exoplanets in stellar habitable zones could harbour abundant and diverse moons to target in the search for extraterrestrial habitats. Exomoons will contribute to exoplanetary signals but are virtually undetectable with current methods. Aims: We identify and analyse traces of exomoons in the temporal variation of total and polarised fluxes of starlight reflected by an Earth-like exoplanet and its spatially unresolved moon across all phase angles, with both orbits viewed in an edge-on geometry. Methods: We compute the total and linearly polarised fluxes, and the degree of linear polarization P of starlight that is reflected by the exoplanet with its moon along their orbits, accounting for the temporal variation of the visibility of the planetary and lunar disks, and including effects of mutual transits and mutual eclipses. Our computations pertain to a wavelength of 450 nm. Results: Total flux F shows regular dips due to planetary and lunar transits and eclipses. Polarization P shows regular peaks due to planetary transits and lunar eclipses, and P can increase and/or slightly decrease during lunar transits and planetary eclipses. Changes in F and P will depend on the radii of the planet and moon, on their reflective properties, and their orbits, and are about one magnitude smaller than the smooth background signals. The typical duration of a transit or an eclipse is a few hours. Conclusions: Traces of an exomoon due to planetary and lunar transits and eclipses show up in F and P of sunlight reflected by planet-moon systems and could be searched for in exoplanet flux and/or polarisation phase functions.Comment: Accepted for publication in Astronomy & Astrophysic

Deletion patterns, genetic variability and protein structure of pfhrp2 and pfhrp3: implications for malaria rapid diagnostic test in Amhara region, Ethiopia

Background: Although rapid diagnostic tests (RDTs) play a key role in malaria-control strategies, their efficacy has been threatened by deletion and genetic variability of the genes pfhrp2/3. This study aims to characterize the deletion, genetic patterns and diversity of these genes and their implication for malaria RDT effectiveness, as well as their genetic evolution in the Amhara region of Ethiopia. Methods: The study included 354 isolates from symptomatic patients from the Amhara region of Ethiopia who tested positive by microscopy. Exon 1-2 and exon 2 of genes pfhrp2 and -3 were amplified, and exon 2 was sequenced to analyse the genetic diversity, phylogenetic relationship and epitope availability. Results: The deletion frequency in exon 1-2 and exon 2 was 22 and 4.6% for pfhrp2, and 68 and 18% for pfhrp3, respectively. Double deletion frequency for pfhrp2 and pfhrp3 was 1.4%. High genetic diversity, lack of clustering by phylogenetic analysis and evidence of positive selection suggested a diversifying selection for both genes. The amino-acid sequences, classified into different haplotypes, varied widely in terms of frequency of repeats, with novel amino-acid changes. Aminoacidic repetition type 2 and type 7 were the most frequent in all the sequences. The most frequent epitopes among protein sequences were those recognized by MAbs 3A4 and C1-13. Conclusion: Deletions and high amino acidic variation in pfhrp2 and pfhrp3 suggest their possible impact on RDT use in the Amhara region, and the high genetic diversity of these genes could be associated with a diversifying selection in Ethiopia. Surveillance of these genes is, therefore, essential to ensure the effectiveness of public health interventions in this region.This work was supported by the project TRPY 111/18 funded by the Institute of Health Carlos III; and IMF received a research fellowship from the University of Alcalá that enables her to develop this study.S

Deletion patterns, genetic variability and protein structure of pfhrp2 and pfhrp3: implications for malaria rapid diagnostic test in Amhara region, Ethiopia

Background: Although rapid diagnostic tests (RDTs) play a key role in malaria-control strategies, their efficacy has been threatened by deletion and genetic variability of the genes pfhrp2/3. This study aims to characterize the deletion, genetic patterns and diversity of these genes and their implication for malaria RDT effectiveness, as well as their genetic evolution in the Amhara region of Ethiopia. Methods: The study included 354 isolates from symptomatic patients from the Amhara region of Ethiopia who tested positive by microscopy. Exon 1?2 and exon 2 of genes pfhrp2 and -3 were amplified, and exon 2 was sequenced to analyse the genetic diversity, phylogenetic relationship and epitope availability. Results: The deletion frequency in exon 1?2 and exon 2 was 22 and 4.6% for pfhrp2, and 68 and 18% for pfhrp3, respectively. Double deletion frequency for pfhrp2 and pfhrp3 was 1.4%. High genetic diversity, lack of clustering by phylogenetic analysis and evidence of positive selection suggested a diversifying selection for both genes. The amino-acid sequences, classified into different haplotypes, varied widely in terms of frequency of repeats, with novel amino-acid changes. Aminoacidic repetition type 2 and type 7 were the most frequent in all the sequences. The most frequent epitopes among protein sequences were those recognized by MAbs 3A4 and C1-13. Conclusion: Deletions and high amino acidic variation in pfhrp2 and pfhrp3 suggest their possible impact on RDT use in the Amhara region, and the high genetic diversity of these genes could be associated with a diversifying selection in Ethiopia. Surveillance of these genes is, therefore, essential to ensure the effectiveness of public health interventions in this region.Instituto de Salud Carlos II

Traces of exomoons in flux and polarization signals of starlight reflected by exoplanets

The detection of moons around extrasolar planets is one of the main focuses of current and future observatories. These silent companions contribute to the planets' observed signals but are barely detectable with current methods. Numerous gaseous exoplanets are known to orbit in the habitable zones of stars, and the expected abundance of natural satellites and their diversity in composition make them ideal targets when looking for habitable celestial bodies. And moons are suspected to play key roles in stabilizing a planet's rotational axis and hence its climate. We show that an exomoon orbiting an Earth-like exoplanet could be identified by measuring the flux and polarization of starlight reflected by the planet-moon system, allowing the characterization of their orbital motions and physical properties.Astrodynamics & Space Mission

Additional file 6 of Deletion patterns, genetic variability and protein structure of pfhrp2 and pfhrp3: implications for malaria rapid diagnostic test in Amhara region, Ethiopia

Additional file 6: Figure S2. Structural organisation of pfhrp2 amino acid repeats types. Type 1, when is present, appeared always at the beginning of the sequence with 1 to 5 consecutives repeats following by various consecutive type 2 repeats. In the middle of the sequences, there were different numbers of consecutive type 2 repeats usually mixed with type 4, type 5, type 6, type 7 and type 8, but there was not any clear pattern. At the end of the sequence, usually appeared a unique type 12 repeat, preceded by type 10 repeat

Additional file 3 of Deletion patterns, genetic variability and protein structure of pfhrp2 and pfhrp3: implications for malaria rapid diagnostic test in Amhara region, Ethiopia

Additional file 3: Table S2. Frequencies of deletion patterns of exon 2 of pfhrp2 and pfhrp3 genes by location

Additional file 5 of Deletion patterns, genetic variability and protein structure of pfhrp2 and pfhrp3: implications for malaria rapid diagnostic test in Amhara region, Ethiopia

Additional file 5: Table S4. Occurrence and number of variations of Baker’s amino acid repeats types in pfhrp2 and pfhrp3 sequences. *Amino acid repeats types described by Nderu et al. [61]. ^New amino acid repeats type

Additional file 4 of Deletion patterns, genetic variability and protein structure of pfhrp2 and pfhrp3: implications for malaria rapid diagnostic test in Amhara region, Ethiopia

Additional file 4: Table S3. Haplotypes frequency of not—unique samples in pfhrp2 and pfhrp3 by sampling located in Ahmara region. Figure S1. Haplotype networks of pfhpr2 (a) and pfhrp3 (b). Colour represents different sample The size of the circles are proportional to the number of sequences include in each haplotype

Additional file 8 of Deletion patterns, genetic variability and protein structure of pfhrp2 and pfhrp3: implications for malaria rapid diagnostic test in Amhara region, Ethiopia

Additional file 8: Figure S4. Tertiary protein structure models according to template-based prediction