Comparison of the solophenyl-red polarization method and the immunohistochemical analysis for collagen type III

In the present study, we have compared the staining pattern of the Solophenyl-Red 3 BL-method for the visualization of collagen type III with the immunohistochemical staining in serial sections from 7 skin wounds (wound age 3 days up to 4 weeks) to elucidate the specifity of the histochemical staining method. Large amounts of collagen type III were clearly detectable in the investigated wounds using the immunohistochemical technique. In the sections stained with Solophenyl-Red, however, only 3 out of 7 skin lesions showed a significant positive red staining at the wound margin or in the granulation tissue, while the adjacent normal connective tissue revealed a typical intensive staining. Using polarization microscopy no characteristic bright green fibrils, as reported for collagen type 111, could be seen in the wound areas without positive Solophenyl-Red staining. Since the localization of collagen type III detected by immunohistochemistry and the presumed distribution of this collagen type by the Solophenyl-Red method was not identical, the histochemical polarization method has to be regarded as non-specific for visualization of this collagen type

An L Band Spectrum of the Coldest Brown Dwarf

The coldest brown dwarf, WISE 0855, is the closest known planetary-mass, free-floating object and has a temperature nearly as cold as the solar system gas giants. Like Jupiter, it is predicted to have an atmosphere rich in methane, water, and ammonia, with clouds of volatile ices. WISE 0855 is faint at near-infrared wavelengths and emits almost all its energy in the mid-infrared. Skemer et al. 2016 presented a spectrum of WISE 0855 from 4.5-5.1 micron (M band), revealing water vapor features. Here, we present a spectrum of WISE 0855 in L band, from 3.4-4.14 micron. We present a set of atmosphere models that include a range of compositions (metallicities and C/O ratios) and water ice clouds. Methane absorption is clearly present in the spectrum. The mid-infrared color can be better matched with a methane abundance that is depleted relative to solar abundance. We find that there is evidence for water ice clouds in the M band spectrum, and we find a lack of phosphine spectral features in both the L and M band spectra. We suggest that a deep continuum opacity source may be obscuring the near-infrared flux, possibly a deep phosphorous-bearing cloud, ammonium dihyrogen phosphate. Observations of WISE 0855 provide critical constraints for cold planetary atmospheres, bridging the temperature range between the long-studied solar system planets and accessible exoplanets. JWST will soon revolutionize our understanding of cold brown dwarfs with high-precision spectroscopy across the infrared, allowing us to study their compositions and cloud properties, and to infer their atmospheric dynamics and formation processes.Comment: 19 pages, 21 figures. Accepted for publication in Ap

Reptile enamel matrix proteins: Selection, divergence, and functional constraint

The three major enamel matrix proteins (EMPs): amelogenin (AMEL), ameloblastin (AMBN), and enamelin (ENAM), are intrinsically linked to tooth development in tetrapods. However, reptiles and mammals exhibit significant differences in dental patterning and development, potentially affecting how EMPs evolve in each group. In most reptiles, teeth are replaced continuously throughout life, while mammals have reduced replacement to only one or two generations. Reptiles also form structurally simple, aprismatic enamel while mammalian enamel is composed of highly organized hydroxyapatite prisms. These differences, combined with reported low sequence homology in reptiles, led us to predict that reptiles may experience lower selection pressure on their EMPs as compared with mammals. However, we found that like mammals, reptile EMPs are under moderate purifying selection, with some differences evident between AMEL, AMBN, and ENAM. We also demonstrate that sequence homology in reptile EMPs is closely associated with divergence times, with more recently diverged lineages exhibiting high homology, along with strong phylogenetic signal. Lastly, despite sequence divergence, none of the reptile species in our study exhibited mutations consistent with diseases that cause degeneration of enamel (e.g. amelogenesis imperfecta). Despite short tooth retention time and simplicity in enamel structure, reptile EMPs still exhibit purifying selection required to form durable enamel.We calculated the percent identity between amino acid sequences of ameloblastin from various reptile groups. Crocodilians exhibit the highest sequence identity, while identity across squamates was substantially lower. Upon closer examination of the individual squamate clades, however, we found that identity values are actually much higher in snakes, with much of the variation existing between the various lizard infraorders.HIGHLIGHTSReptile enamel matrix proteins are under moderate purifying selection despite polyphyodonty and simple enamel structure.Sequence identity in reptile enamel matrix proteins exhibit correlation with divergence times in spite of differences in substitution rates.Reptile amelogenin operates under a distinct selection regime compared with ameloblastin and enamelin.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/150577/1/jezb22857.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150577/2/jezb22857-sup-0001-Supplementary_file.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150577/3/jezb22857-sup-0007-Supplementary_file_S8-DAMBE-Saturation.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150577/4/jezb22857-sup-0002-Supplementary_file_S1-SpeciesTable.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150577/5/jezb22857-sup-0003-Supplementary_file_S2_Alignments.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150577/6/jezb22857-sup-0008-Supplementary_File_S9.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150577/7/jezb22857-sup-0005-Supplementary_file_S6.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150577/8/jezb22857_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150577/9/jezb22857-sup-0009-Supplementary_file_Reptiles.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150577/10/jezb22857-sup-0006-Supplementary_file_S7-DIVERGE.pd

Uniform Atmospheric Retrieval Analysis of Ultracool Dwarfs I : Characterizing Benchmarks, Gl570D and HD3651B

Michael Line, et al, 'UNIFORM ATMOSPHERIC RETRIEVAL ANALYSIS OF ULTRACOOL DWARFS. I. CHARACTERIZING BENCHMARKS, Gl 570D AND HD 3651B', The Astrophysical Journal, Vol. 802 (2), July 2015, doi: https://doi.org/10.1088/0004-637X/807/2/183, published by IOP.Interpreting the spectra of brown dwarfs is key to determining the fundamental physical and chemical processes occurring in their atmospheres. Powerful Bayesian atmospheric retrieval tools have recently been applied to both exoplanet and brown dwarf spectra to tease out the thermal structures and molecular abundances to understand those processes. In this manuscript we develop a significantly upgraded retrieval method and apply it to the SpeX spectral library data of two benchmark late T-dwarfs, Gl570D and HD3651B, to establish the validity of our upgraded forward model parameterization and Bayesian estimator. Our retrieved metallicities, gravities, and effective temperature are consistent with the metallicity and presumed ages of the systems. We add the carbon-to-oxygen ratio as a new dimension to benchmark systems and find good agreement between carbon-to-oxygens ratio derived in the brown dwarfs and the host stars. Furthermore, we have for the first time unambiguously determined the presence of ammonia in the low-resolution spectra of these two late T-dwarfs. We also show that the retrieved results are not significantly impacted by the possible presence of clouds, though some quantities are significantly impacted by uncertainties in photometry. This investigation represents a watershed study in establishing the utility of atmospheric retrieval approaches on brown dwarf spectra.Peer reviewedFinal Published versio

On the asymptotics of higher-dimensional partitions

We conjecture that the asymptotic behavior of the numbers of solid (three-dimensional) partitions is identical to the asymptotics of the three-dimensional MacMahon numbers. Evidence is provided by an exact enumeration of solid partitions of all integers <=68 whose numbers are reproduced with surprising accuracy using the asymptotic formula (with one free parameter) and better accuracy on increasing the number of free parameters. We also conjecture that similar behavior holds for higher-dimensional partitions and provide some preliminary evidence for four and five-dimensional partitions.Comment: 30 pages, 8 tables, 4 figures (v2) New data (63-68) for solid partitions added; (v3) published version, new subsection providing an unbiased estimate of the leading for the leading coefficient added, some tables delete

Neutral Iron Emission Lines From The Day-side Of KELT-9b -- The GAPS Programme With HARPS-N At TNG XX

We present the first detection of atomic emission lines from the atmosphere of an exoplanet. We detect neutral iron lines from the day-side of KELT-9b (Teq $\sim$ 4, 000 K). We combined thousands of spectrally resolved lines observed during one night with the HARPS-N spectrograph (R $\sim$ 115, 000), mounted at the Telescopio Nazionale Galileo. We introduce a novel statistical approach to extract the planetary parameters from the binary mask cross-correlation analysis. We also adapt the concept of contribution function to the context of high spectral resolution observations, to identify the location in the planetary atmosphere where the detected emission originates. The average planetary line profile intersected by a stellar G2 binary mask was found in emission with a contrast of 84 $\pm$ 14 ppm relative to the planetary plus stellar continuum (40 $\pm$ 5$\%$ relative to the planetary continuum only). This result unambiguously indicates the presence of an atmospheric thermal inversion. Finally, assuming a modelled temperature profile previously published (Lothringer et al. 2018), we show that an iron abundance consistent with a few times the stellar value explains the data well. In this scenario, the iron emission originates at the $10^{-3}$-$10^{-5}$ bar level.Comment: Accepted for publication on ApJL; 19 pages, 4 figures, 3 table

Gridded and direct Epoch of Reionisation bispectrum estimates using the Murchison Widefield Array

We apply two methods to estimate the 21~cm bispectrum from data taken within the Epoch of Reionisation (EoR) project of the Murchison Widefield Array (MWA). Using data acquired with the Phase II compact array allows a direct bispectrum estimate to be undertaken on the multiple redundantly-spaced triangles of antenna tiles, as well as an estimate based on data gridded to the $uv$-plane. The direct and gridded bispectrum estimators are applied to 21 hours of high-band (167--197~MHz; $z$=6.2--7.5) data from the 2016 and 2017 observing seasons. Analytic predictions for the bispectrum bias and variance for point source foregrounds are derived. We compare the output of these approaches, the foreground contribution to the signal, and future prospects for measuring the bispectra with redundant and non-redundant arrays. We find that some triangle configurations yield bispectrum estimates that are consistent with the expected noise level after 10 hours, while equilateral configurations are strongly foreground-dominated. Careful choice of triangle configurations may be made to reduce foreground bias that hinders power spectrum estimators, and the 21~cm bispectrum may be accessible in less time than the 21~cm power spectrum for some wave modes, with detections in hundreds of hours.Comment: 19 pages, 10 figures, accepted for publication in PAS

Uniform Atmospheric Retrieval Analysis of Ultracool Dwarfs II : Properties of 11 T-dwarfs

Accepted ApJ. Supplemental material including full posteriors will be included through the link in the published ApJ article © 2017 The American Astronomical Society. All rights reserved.Brown dwarf spectra are rich in information revealing of the chemical and physical processes operating in their atmospheres. We apply a recently developed atmospheric retrieval tool to an ensemble of late T-dwarf (600-800K) near infrared spectra. With these spectra we are able to place direct constraints the molecular abundances of H$_2$O, CH$_4$, CO, CO$_2$, NH$_3$, H$_2$S, and Na+K, gravity, thermal structure (and effective temperature), photometric radius, and cloud optical depths. We find that ammonia, water, methane, and the alkali metals are present and well constrained in all 11 objects. From the abundance constraints we find no significant trend in the water, methane, or ammonia abundances with temperature, but find a very strong ($>$25$\sigma$) increasing trend in the alkali metal abundances with effective temperature, indicative of alkali rainout. We also find little evidence for optically thick clouds. With the methane and water abundances, we derive the intrinsic atmospheric metallicity and carbon-to-oxygen ratios. We find in our sample, that metallicities are typically sub solar and carbon-to-oxygen ratios are somewhat super solar, different than expectations from the local stellar population. We also find that the retrieved vertical thermal profiles are consistent with radiative equilibrium over the photospheric regions. Finally, we find that our retrieved effective temperatures are lower than previous inferences for some objects and that our radii are larger than expectations from evolutionary models, possibly indicative of un-resolved binaries. This investigation and methodology represents a paradigm in linking spectra to the determination of the fundamental chemical and physical processes governing cool brown dwarf atmospheres.Peer reviewe

Evidence for disequilibrium chemistry from vertical mixing in hot Jupiter atmospheres. A comprehensive survey of transiting close-in gas giant exoplanets with warm-Spitzer/IRAC

[Abridged] Aims. We present a large atmospheric study of 49 gas giant exoplanets using infrared transmission photometry with Spitzer/IRAC at 3.6 and 4.5um. Methods. We uniformly analyze 70 photometric light curves of 33 transiting planets using our custom pipeline, which implements pixel level decorrelation. We use this survey to understand how infrared photometry traces changes in atmospheric chemical properties as a function of planetary temperature. We compare our measurements to a grid of 1D radiative-convective equilibrium forward atmospheric models which include disequilibrium chemistry. We explore various strengths of vertical mixing (Kzz = 0 - 10^12 cm2/s) as well as two chemical compositions (1x and 30x solar). Results. We find that, on average, Spitzer probes a difference of 0.5 atmospheric scale heights between 3.6 and 4.5um, which is measured at 7.5sigma level of significance. We find that the coolest planets show a lack of methane compared to expectations, which has also been reported by previous studies of individual objects. We show that the sample of coolest planets rule out 1x solar composition with >3sigma confidence while supporting low vertical mixing (Kzz = 10^8 cm2/s). On the other hand, we find that the hot planets are best explained by models with 1x solar metallicity and high vertical mixing (Kzz = 10^12 cm2/s). We interpret this as the lofting of CH4 to the upper atmospheric layers. Changing the interior temperature changes the expectation for equilibrium chemistry in deep layers, hence the expectation of disequilibrium chemistry higher up. We also find a significant scatter in the transmission signatures of the mid-temperate and ultra-hot planets, likely due to increased atmospheric diversity, without the need to invoke higher metallicities. Additionally, we compare Spitzer transmission with emission for the same planets and find no evidence for correlation.Comment: 43 pages, 17 Figures. Accepted on 9 Feb 2021 in Astronomy & Astrophysic