Journal articles on the topic 'Opacity phase variation'

ABSTRACTAcinetobacter baumanniistrain AB5075 produces colonies with two opacity phenotypes, designated opaque and translucent. These phenotypes were unstable and opaque and translucent colony variants were observed to interconvert at high frequency, suggesting that a phase-variable mechanism was responsible. The frequency of phase variation both within colonies and in broth cultures increased in a cell density-dependent manner and was mediated by the accumulation of an extracellular factor. This factor was distinct from the knownA. baumanniisignaling molecule 3-OH C12-homoserine lactone. Opaque and translucent colony variants exhibited a number of phenotypic differences, including cell morphology, surface motility, biofilm formation, antibiotic resistance, and virulence in aGalleria mellonellamodel. Additional clinical isolates exhibited a similar phase-variable control of colony opacity, suggesting that this may be a common feature ofA. baumannii.IMPORTANCEA novel phase-variable mechanism has been identified inAcinetobacter baumanniithat results in an interconversion between opaque and translucent colony phenotypes. This phase variation also coordinately regulates motility, cell shape, biofilm formation, antibiotic resistance, and virulence. The frequency of phase variation is increased at high cell density via a diffusible extracellular signal. To our knowledge, this report presents the first example of phase variation inA. baumanniiand also the first example of quorum sensing-mediated control of phase variation in a bacterium. The findings are important, as this phase-variable mechanism can be identified only via changes in colony opacity using oblique light; therefore, many researchers studyingA. baumanniimay unknowingly be working with different colony variants.

Simulation studies have proposed a significant thermal effect of water ice clouds on the Martian atmosphere and climate. However, previous studies focused more on seasonal variations but less on short-term changes. In this work, we used the MCS multi-local time data to investigate the water ice diurnal variations on Mars. We quantified its diurnal variations with amplitude and phase by applying the tidal fitting method to the water ice abundance. In addition, we found a close correlation (antiphase relation) between the thermal tide and water ice diurnal variations during the aphelion seasons that was not sensitive to both the background water ice and dust opacity but increased with the tidal amplitude. In the perihelion seasons, the antiphase relation was sensitive to the water ice and dust opacity, both affected by the dust storm activity. Finally, the statistic results suggested an unexpected low threshold of diurnal tide amplitude (2 to 3 K) for generating a relevant water ice diurnal variation, accounting for the ubiquitous water ice diurnal variations in the Martian atmosphere. These new observational results can help further understand the phase transition process between ice and vapor in the Martian atmosphere and better constrain the Martian global climate model in the future.

ABSTRACT The neisserial opacity (Opa) proteins are a family of antigenically distinct outer membrane proteins that undergo phase-variable expression. Opa+ variants of Neisseria gonorrhoeae strain FA1090 are selected in a cyclical pattern from the lower genital tract of estradiol-treated mice. Here we show that cyclical recovery of Opa+ gonococci does not occur in ovariectomized mice; therefore, the reproductive cycle plays a role in the selection kinetics in vivo. As predicted by the selection pattern shown by wild-type gonococci, we demonstrated that a constitutive Opa-expressing strain was more fit than an Opa-deficient mutant in the early and late phases of infection. We found no evidence that Opa-mediated colonization selects for Opa+ variants during murine infection based on adherence assays with cultured murine epithelial cells. We also tested the hypothesis that complement selects for Opa protein expression during infection. Although some Opa+ variants of a serum-sensitive derivative of strain FA1090 were more resistant to the bactericidal activity of normal human serum, selection for Opa expression was not abrogated in C3-depleted mice. Finally, as previously reported, Opa+ gonococci were more sensitive to serine proteases. Thus, proteases or protease inhibitors may contribute to the observed in vivo selection pattern. We concluded that Opa proteins promote persistence of N. gonorrhoeae in the female genital tract and that opa gene phase variation allows gonococci to evade or capitalize upon unidentified host factors of the mammalian reproductive cycle. This work revealed an intimate interaction between pathogen and host and provides evidence that hormonally related factors shape bacterial adaptation.

ABSTRACT Phase variation in the colonial opacity of Streptococcus pneumoniae has been implicated as a factor in bacterial adherence, colonization, and invasion in the pathogenesis of pneumococcal disease. Additionally, the synergistic effects of influenza A virus and S. pneumoniae in the development of otitis media (OM) have been reported. This study examined the ability of opaque or transparent S. pneumoniae from the same strain in combination with an antecedent influenza A virus infection to colonize the nasopharynx and invade the middle ear in the chinchilla model. Our data indicated that there was no significant difference in the level of nasopharyngeal colonization and induction of OM between the opaque and transparent variants unless there was a prior challenge with influenza A virus. Subsequent to influenza A virus infection, there was a significant difference between the variants in the ability to colonize and persist in the nasopharynx and middle ear. The concentrations of the opaque variant in nasopharyngeal-lavage samples and middle-ear fluid remained consistently higher than those of the transparent variant for 10 days postinoculation. Data from this study indicate that the effects of influenza A virus on the pathogenesis of experimental S. pneumoniae-induced OM differ depending on the opacity phenotype involved.

Streptococcus pneumoniae (pneumococcus) is a respiratory commensal pathogen that causes a range of infections, particularly in young children and the elderly. Pneumococci undergo spontaneous phase variation in colony opacity phenotype, in which DNA rearrangements within the Type I restriction-modification (R-M) system specificity gene hsdS can potentially generate up to six different hsdS alleles with differential DNA methylation activity, resulting in changes in gene expression. To gain a broader perspective of this system, we performed bioinformatic analyses of Type I R-M loci from 18 published pneumococcal genomes, and one R-M locus sequenced for this study, to compare genetic content, organization, and homology. All 19 loci encoded the genes hsdR, hsdM, hsdS, and at least one hsdS pseudogene, but differed in gene order, gene orientation, and hsdS target recognition domain (TRD) content. We determined the coding sequences of 87 hsdS TRDs and excluded seven from further analysis due to the presence of premature stop codons. Comparative analyses revealed that the TRD 1.1, 1.2, and 2.1 protein sequences had single amino acid substitutions, and TRD 2.2 and 2.3 each had seven differences. The results of this study indicate that variability exists among the gene content and arrangements within Type I R-M loci may provide an additional level of divergence between pneumococcal strains, such that phase variation-mediated control of virulence factors may vary significantly between individual strains. These findings are consistent with presently available transcript profile data.

The opacity (Opa) proteins of Neisseria gonorrhoeae are a family of outer membrane proteins demonstrating phase and antigenic variation. N. gonorrhoeae strain FA0190 has 11 opa loci that encode at least 8 antigenically distinct Opa proteins. To determine if expression of one Opa protein or a subset of them is favored during gonococcal infection, we inoculated Opa-negative variants of strain FA1090 intraurethrally into male volunteers. The Opa phenotype of gonococci isolated from urine and urethral swab cultures from nine infected subjects was determined. Opa proteins were expressed in a large proportion of the reisolates from the infected subjects. Gonococci cultured from urine or urethral swab samples from six of the subjects were uniformly Opa positive, with the predominant Opa variants differing among subjects. Three different Opa proteins were represented as the predominant type in at least one subject each. In three subjects, there was more heterogeneity in Opa phenotype of the reisolates, including the presence of Opa-negative variants. An increase in the proportion of isolates expressing multiple Opa proteins occurred over time in most subjects. Passage of the inoculum in vitro did not result in similar changes in Opa expression. There was no detectable difference in infectivity of an Opa-negative variant and one expressing an Opa protein (OpaF) that was highly represented in reisolates from the original nine subjects. Reisolates from three infected volunteers inoculated with the OpaF variant showed continued expression of OpaF alone or in conjunction with other Opa proteins. These results demonstrate that there is strong selection for expression of one or more Opa proteins by strain FA1090 in vivo, but that no single protein is preferentially expressed during early infection in the male urethra.

ABSTRACT Phase variation in the colonial opacity phenotype of Streptococcus pneumoniae has been implicated as a factor in bacterial adherence, colonization, and invasion in the pathogenesis of pneumococcal otitis media (OM). The purpose of this study was to determine whether S. pneumoniae opacity variants influence the induction of gene expression for proinflammatory mediators in vivo using the rat model of OM. Both the opaque and transparent phenotype variants induced a significant up-regulation in gene expression for interleukin-1α (IL-1α), IL-1β, IL-6, IL-10, tumor necrosis factor alpha, and inducible nitric oxide synthase (iNOS) compared to saline sham-inoculated controls at both 4 and 24 h postinoculation (P < 0.05 in all cases). Furthermore, whereas a significant difference in gene expression was evident for only IL-6 (greater following challenge with the opaque variant) and IL-1β (greater following challenge with the transparent variant) at 4 h, by 24 h the opaque variant cohort demonstrated a significant increase in gene expression for IL-1α, IL-1β, IL-6, IL-10, and iNOS relative to animals inoculated with the transparent phenotype variant (P < 0.05 in all cases). Enzyme-linked immunosorbent assay results confirmed the gene expression data as determined by real-time PCR. Moreover, the concentrations of the opaque variant in the middle ear lavage fluid were a full log higher than those of the transparent variant. The aforementioned results indicate that the opaque phenotype variant is more efficient at survival and multiplication within the middle ear space, resulting in the accumulation of more inflammatory cells and the enhanced expression and production of inflammatory mediators. However, when the data were normalized to account for differences in middle ear bacterial titers, it became apparent that the transparent variant of S. pneumoniae is a more potent inducer of inflammation, triggering the accumulation of more inflammatory cells and substantially greater fold increases in the expression and production of inflammatory mediators. Data from this study indicate that S. pneumoniae opacity variants influence the temporal mRNA expression of inflammatory mediators within the middle ear.

During natural infection, gonococcal opacity proteins (Opa) undergo rapid phase variation, but how this phenomenon contributes to the virulence of the bacteria is not well understood. In the present immunomorphological study we examined the actual Opa status of individual gonococci during various stages of gonococcal infection of Chang epithelial cells, by probing ultrathin sections of infected specimens with Opa-specific monoclonal antibodies. Our results demonstrate a heterogeneous Opa expression during the initial interaction of the bacteria, but an almost 100% expression of one of the probed Opas during their secondary attachment and entry into the host cells, suggesting a role for distinct Opas in cellular penetration. The association between Opa expression, tight attachment, and bacterial invasion into the host cells could be confirmed with isogenic variants that expressed different Opa proteins. Once inside the epithelial cells, both morphologically intact, Opa positive and morphologically disintegrated, Opa negative bacteria were observed. The loss of Opa immunoreactivity in intracellular gonococci could not be related to the presence of a particular Opa protein, but could be mimicked by incubating the organisms with extracts of sonicated uninfected epithelial cells, suggesting that it was caused by host cell proteolytic activity. Taken together, our data suggest that Opa phase transitions confer a functional adaptation of the bacteria enabling host cell penetration.

ABSTRACT Phase variation in the colonial opacity of Streptococcus pneumoniae has been implicated as a factor in the pathogenesis of pneumococcal disease. This study examined the relationship between membrane characteristics and colony morphology in a few selected opaque-transparent couples of S. pneumoniae strains carrying different capsular types. Membrane fluidity was determined on the basis of intermolecular excimerization of pyrene and fluorescence polarization of 1,6-diphenyl 1,3,5-hexatriene (DPH). A significant decrease, 16 to 26% (P ≤ 0.05), in the excimerization rate constant of the opaque variants compared with that of the transparent variants was observed, indicating higher microviscosity of the membrane of bacterial cells in the opaque variants. Liposomes prepared from phospholipids of the opaque phenotype showed an even greater decrease, 27 to 38% (P ≤ 0.05), in the pyrene excimerization rate constant compared with that of liposomes prepared from phospholipids of bacteria with the transparent phenotype. These findings agree with the results obtained with DPH fluorescence anisotropy, which showed a 9 to 21% increase (P ≤ 0.001) in the opaque variants compared with the transparent variants. Membrane fatty acid composition, determined by gas chromatography, revealed that the two variants carry the same types of fatty acids but in different proportions. The trend of modification points to the presence of a lower degree of unsaturated fatty acids in the opaque variants compared with their transparent counterparts. The data presented here show a distinct correlation between phase variation and membrane fluidity in S. pneumoniae. The changes in membrane fluidity most probably stem from the observed differences in fatty acid composition.

ABSTRACT Vibrio parahaemolyticus, a biofouling marine bacterium and human pathogen, undergoes phase variation displaying translucent (TR) and opaque (OP) colony morphologies. Prior studies demonstrated that OP colonies produce more capsular polysaccharide (CPS) than TR colonies and that opacity is controlled by the Vibrio harveyi LuxR-type transcriptional activator OpaR. CPS has also been shown to be regulated by the scrABC signaling pathway, which involves a GGDEF-EAL motif-containing sensory protein. The present study identifies cps genes and examines their regulation. Transposon insertions in the cps locus, which contains 11 genes, abolished opacity. Such mutants failed to produce CPS and were defective in pellicle formation in microtiter wells and in a biofilm attachment assay. Reporter fusions to cpsA, the first gene in the locus, showed ∼10-fold-enhanced transcription in the OP (opaR +) strain compared to a TR (ΔopaR) strain. Two additional transcriptional regulators were discovered. One potential activator, CpsR, participates in the scrABC GGDEF-EAL-signaling pathway; CpsR was required for the increased cps expression observed in scrA ΔopaR strains. CpsR, which contains a conserved module found in members of the AAA+ superfamily of ATP-interacting proteins, is homologous to Vibrio cholerae VpsR; however, unlike VpsR, CpsR was not essential for cps expression. CpsS, the second newly identified regulator, contains a CsgD-type DNA-binding domain and appears to act as a repressor. Mutants with cpsS defects have greatly elevated cps transcription; their high level of cpsA expression was CpsR dependent in ΤR strains and primarily OpaR dependent in OP strains. Thus, a network of positive and negative regulators modulates CPS production in V. parahaemolyticus.

Marbling refers to the appearance of white flecks of fatty tissue between muscle fibre bundles. The whiteness and opacity of the fat is important for visual assessment of marbling and depends on the crystallisation of the triacylglycerols within the fat cells. In the living animal, fat is in a liquid state. With chilling, the triacylglycerols undergo phase changes (solidify) and become opaque. The temperature at which this occurs is largely dependent upon the melting points of the individual fatty acids. Marbling fat can comprise a diverse range of fatty acids and each has an individual melting point (e.g. palmitoleic melts at 0°C; stearic melts at 70°C). The visual appearance of marbling will thus depend on the melting points of the constituent fatty acids at chiller temperature. The high melting point stearic acid can vary significantly in content across groups of cattle and has a major influence on the physical properties and visual appearance of marbling fat. The effects of nutrition, seasonal and climatic variation are reviewed and linked to marbling appearance and fat hardness.

During the past 30 years, seismic attributes have evolved beyond simple measures of amplitude, frequency, and phase to include measures of waveform similarity, amplitude variation with offset (AVO), spectral content, and structural deformation. Although neural networks and geostatistics are effective ways of combining the information content of these many attributes, such analyses cannot replicate the pattern-recognition capabilities of an experienced interpreter. For this reason, careful visualization and display of multiple attributes remains one of the most powerful interpretation tools at our disposal. The two most important color display models are based on red, green, and blue (RGB) or hue, lightness, and saturation (HLS). Each of these color models in turn can be modulated by transparency. We recommend using the RGB color model to map attributes of similar type, such as-volumes of near-, mid-, and far-angle amplitude or low-, moder-ate-, and high-frequency spectral components. The HLS model is preferred when one attribute modulates another, such as dip magnitude modulating dip azimuth or amplitude of the peak spectral frequency modulating the phase measured at the peak frequency. Transparency/opacity provides a fourth color dimension and additional attribute modulation capabilities. This tutorial demonstrates those attributes best displayed in each of the two basic color models with examples from the Gulf of Mexico and Fort Worth Basin, Texas, U.S.A. Sometimes these combinations can be achieved using commercial voxel-based interpretation software. By careful use of color and transparency applied to modern volumetric attributes, one can display the strike of faults and flexures in three dimensions, isolate collapse features, and qualitatively display the geomorphology and thickness of channels.

ABSTRACT Streptococcus pneumoniae undergoes spontaneous phase variation resulting in opaque and transparent colony forms. Differences in colony opacity correlate with differences in virulence: the transparent variants are more capable of colonizing the nasopharynx, whereas the opaque variants show increased virulence during systemic infections. To gain insight into the pathogenesis of pneumococcal disease at the molecular level, protein expression patterns of the phenotypic variants of two pneumococcal strains were compared by high-resolution two-dimensional protein electrophoresis. In comparison with transparent variants, the opaque variants reduced the expression of two proteins and overexpressed one protein. The proteins were identified by mass spectrometric analysis. The protein overexpressed in the opaque phenotype revealed significant homology to elongation factor Ts of Helicobacter pylori. One of the two proteins that were underexpressed in the opaque variants revealed significant homology to the proteinase maturation protein PrtM ofLactocobacillus paracasei, a member of the family of peptidyl-prolyl cis/trans isomerases. A consensus lipoprotein signal sequence suggests that the putative proteinase maturation protein A, designated PpmA, is located at the surface of the pneumococcus and may play a role in the maturation of surface or secreted proteins. The second underexpressed protein was identified as pyruvate oxidase, SpxB. The lower SpxB expression in opaque variants most probably explains the reduced production of hydrogen peroxide, a reaction product of SpxB, in this variant. Since aspxB-defective pneumococcal mutant has decreased ability to colonize the nasopharynx (B. Spellerberg, D. R. Cundell, J. Sandros, B. J. Pearce, I. Idanpaan-Heikkila, C. Rosenow, and H. R. Masure, 1996. Mol. Microbiol. 19:803–813, 1996), our data suggest that SpxB plays an important role in enhancing the ability of transparent variants to efficiently colonize the nasopharynx.

Abstract Thanks to ground-based infrared and submillimeter observations the study of the dusty torus of nearby active galactic nuclei has greatly advanced in the last years. With the aim of further investigating the nuclear mid-infrared emission of the archetypal Seyfert 2 galaxy NGC 1068, here we present a fitting to the N- and Q-band Michelle/Gemini spectra. We initially test several available spectral energy distribution (SED) libraries, including smooth, clumpy and two-phase torus models, and a clumpy disk+wind model. We find that the spectra of NGC 1068 cannot be reproduced with any of these models. Although, the smooth torus models describe the spectra of NGC 1068 if we allow variation of some model parameters among the two spectral bands. Motivated by this result, we produced new SEDs using the radiative transfer code SKIRT. We use two concentric tori that allow us to test a more complex geometry. We test different values for the inner and outer radii, half-opening angle, radial, and polar exponent of the power-law density profile, opacity, and viewing angle. Furthermore, we also test the dust grains’ size and different optical and calorimetric properties of silicate grains. The best-fitting model consists of two concentric components with outer radii of 1.8 and 28 pc, respectively. We find that the size and the optical and calorimetric properties of graphite and silicate grains in the dust structure are key to reproducing the spectra of NGC 1068. A maximum grain size of 1 μm leads to a significant improvement in the fit. We conclude that the dust in NGC 1068 reaches different scales, where the highest contribution to the mid-infrared is given by a central and compact component. A less dense and extended component is present, which can be either part of the same torus (conforming a flared disk) or can represent the emission of a polar dust component, as already suggested from interferometric observations.

AbstractThe long-term visible spectrophotometric variations depicted by the following parameters: V the apparent visual magnitude; Φrb the gradient of the observed Paschen energy distribution and D the total Balmer discontinuity (BD) of 49 Be stars in different spectrophotometric phases (SPh-E: spectrophotometric phase where the second component of the BD is in emission; SPh-A: spectrophotometric phase where the second component of the BD is in absorption) were translated into CE physical parameters. These parameters are: R/R* the mean extent of the CE zone that produces the visible energy distribution; Tenv its mean temperature; τ the continuum opacity at λ0.56μm. The results obtained show that the triplet of parameters (V, Φrb, D) do not depend on the (R/R*, Tenv, τ) set of parameters in the same way if Be stars are in a SPh-E or in a SPh-A phase. Independently of the spectrophotometric phase, Tenv always decreases as a linear function of (R/R*)−1. In SPh-E it is (R/R*,)−1 ≤ 0.7, and in SPh-A it is (R/R*)−1 ≥ 0.7. All SPh behaviours can be summarized by the relation ∂Tenv/∂(R*/R) = ∂Tenv/∂τ × ∂τ/∂(R*/R) ≥ 0, which describes different spectrophotometric behaviours in both SPh-E and SPh-A phases.

Aims. We have explored the capabilities of dust extinction and γ rays to probe the properties of the interstellar medium in the nearby anti-centre region. In particular, we aim at quantifying the variations of the dust properties per gas nucleon across the different gas phases and different clouds. The comparison of dust extinction and emission properties with other physical quantities of large grains (emission spectral index β, dust colour temperature Tdust, total-to-selective extinction factor RV) helps the theoretical modelling of grains as they evolve from diffuse to dense cloud environments. Methods. We have jointly modelled the γ-ray intensity, recorded between 0.4 and 100 GeV with the Fermi Large Area Telescope (LAT), and the stellar reddening, E(B − V), inferred from Pan-STARRS and 2MASS photometry, as a combination of HI-bright, CO-bright, and ionised gas components. The complementary information from dust reddening and γ rays is used to reveal the gas not seen, or poorly traced, by HI, free-free, and 12CO emissions, namely (i) the opaque HI and diffuse H2 present in the dark neutral medium (DNM) at the atomic-molecular transition, and (ii) the dense H2 to be added where 12CO lines saturate (COsat). We compare the total gas column densities, NH, derived from the γ rays and stellar reddening with those inferred from a similar, previously published analysis of γ rays and of the optical depth of the thermal dust emission, τ353, at 353 GHz. We can therefore compare environmental variations in specific dust reddening, E(B − V)∕NH, and in dust emission opacity (dust optical depth per gas nucleon), τ353∕NH. Results. The gas column densities obtained when combining γ rays with either dust reddening or dust emission compare reasonably well in the atomic and DNM gas phases and over most of the CO-bright phase, but we find localised differences in the dense media (COsat component) due to differences in the two dust tracers. Over the whole anti-centre region, we find an average E(B − V)∕NH ratio of (2.02 ± 0.48) ×10−22 mag cm2, with maximum local variations of about ± 30% at variance with the two to six fold coincident increase seen in emission opacity as the gas column density increases. We show how the specific reddening and opacity vary with the colour temperature and spectral index of the thermal emission of the large grains. Additionally, we find a better agreement between the XCO = N(H2)/WCO conversion factors derived with dust reddening or with γ rays than with those inferred from dust emission, especially towards clouds with large τ353 optical depths. The comparison confirms that the high XCO values found with dust emission are biased by the significant rise in emission opacity inside molecular clouds. Conclusions. In the diffuse medium, we find only small variations in specific reddening, E(B − V)∕NH, compatible with the dispersion in the RV factor reported by other studies. This implies a relatively uniform dust-to-gas mass ratio in the diffuse parts of the anti-centre clouds. The small amplitude of the E(B − V)∕NH variations with increasing NH column density confirms that the large opacity τ353∕NH rise seen towards dense CO clouds is primarily due to changes in dust emissivity. The environmental changes are qualitatively compatible with model predictions based on mantle accretion on the grains and the formation of grain aggregates.

AbstractWe have undertaken an extensive program to investigate atmospheric shock dynamics in Mira variables through monitoring the MgII emission strengths versus phase. Theoretical calculations of Bowen (1987), which represent the structural variations in the extended atmosphere of a pulsating Mira, are presented in addition to the MgII observations. The model calculations generate density, temperature and velocity structures as determined by stellar parameters and by interactions of the driving amplitude, dust opacity and thermal relaxation processes. The main diagnostic provided by the models is the total emitted shock luminosity versus phase, which can be compared to the observed MgII emission. Models and observations are presented for three Miras: S Car, R Car and T Cep.

Context. Umbral flashes (UF) and running penumbral waves (RPWs) in sunspot chromospheres leave a dramatic imprint in the intensity profile of the Ca II 8542 Å line. Recent studies have focussed on also explaining the observed polarization profiles, which show even more dramatic variations during the passage of these shock fronts. While most of these variations can be explained with an almost constant magnetic field as a function of time, several studies have reported changes in the inferred magnetic field strength during UF phases. These changes could be explained by opacity effects or by intrinsic changes in the magnetic field strength. Aims. In this study we investigate the origin of these periodic variations of the magnetic field strength by analyzing a time-series of high-temporal-cadence observations acquired in the Ca II 8542 Å line with the CRISP instrument at the Swedish 1-m Solar Telescope. In particular, we analyze how the inferred geometrical height scale changes between quiescent and UF phases, and whether those changes are enough to explain the observed changes in the magnetic field, B. Methods. We have performed non local thermodynamical equilibrium (non-LTE) data inversions with the NICOLE code of a time-series of very high spatio-temporal-resolution observations in the Ca II 8542 Å, Fe I 6301.5, and Fe I 6302.5 Å lines. We analyze in detail the variations of the different physical parameters of the model as a function of time. Results. Our results indicate that the Ca II 8542 Å line in sunspots is greatly sensitive to magnetic fields at log τ500 = −5 (hereafter log τ = −5) during UFs and quiescence. However this optical depth value does not correspond to the same geometrical height during the two phases. Our results indicate that during UFs and RPWs the log τ = −5 is located at a higher geometrical height than during quiescence. Additionally, the inferred magnetic field values are higher in UFs (up to ∼270 G) and in RPWs (∼100 G). Conclusions. Our results suggest that opacity changes caused by UFs and RPWs cannot explain the observed temporal variations in the magnetic field, as the line seems to form at higher geometrical heights where the field is expected to be lower.

Abstract Twenty-four spectra of 52 Her (A1p SiSrCr) obtained through the large apertures of the SWP and LWP cameras on board International Ultraviolet Explorer are compared to look for variations of the absolute flux over the spectral range 1200–3000 Å. Large variations of the spectral energy distribution occur in the far-ultraviolet shortwards of 2000 Å. In contrast, the flux at wavelengths larger than 2000 Å does not vary but several lines are variable between phases of FUV maximum and FUV minimum. The large FUV variability is probably caused by changes in the continuous and line opacity driven by modest horizontal gradients of the abundances of chemical elements over the surface of 52 Her. The TESS lightcurve of 52 Her is slightly asymetric and has a period close to 3.83 days.

ABSTRACT The crucial initial step in planet formation is the agglomeration of micron-sized dust into macroscopic aggregates. This phase is likely to happen very early during the protostellar disc formation, which is characterized by active gas dynamics. We present numerical simulations of protostellar/protoplanetary disc long-term evolution, which includes gas dynamics with self-gravity in the thin-disc limit, and bidisperse dust grain evolution due to coagulation, fragmentation, and drift through the gas. We show that the decrease of the grain size to the disc periphery leads to sharp outer edges in dust millimetre emission, which are explained by a drop in dust opacity coefficient rather than by dust surface density variations. These visible outer edges are at the location where average grain size ≈λ/2$\pi$, where λ is the observational wavelength, so discs typically look more compact at longer wavelengths if dust size decreases outwards. This allows a simple recipe for reconstructing grain sizes in disc outer regions. Discs may look larger at longer wavelengths if grain size does not reach λ/2$\pi$ for some wavelength. Disc visible sizes evolve non-monotonically over the first million years and differ from dust and gas physical sizes by factor of a few. We compare our model with recent observation data on gas and dust disc sizes, far-infrared fluxes, and spectral indices of protoplanetary discs in Lupus. We also show that non-monotonic variations of the grain size in radial direction can cause wavelength-dependent opacity gaps, which are not associated with any physical gaps in the dust density distribution.

Results of the recent stability surveys (Dziembowski and Pamyatnykh 1993; Gautschy and Saio 1993) leave no doubts that the opacity mechanism is responsible for oscillations observed in β Cephei stars. The linear nonadiabatic analysis used to determine the instability domains in the HR diagram, yields also quantities that may be compared with observations. These nonadiabatic observables are evaluated from the complex eigenfunctions y(r) and f(r) describing variations of the radial displacement and the bolometric flux, respectively. Both y and f are very nearly constant within the stellar atmosphere. The eigenfunctions describing the horizontal displacement and variations of thermodynamical quantities may be expressed in terms of y and f. Since the linear eigenfunctions may be arbitrarily normalized, there are only two real independent observables. We may choose them to be and ψ = arg(f/y). Using static atmosphere models, with the inertial term included in the effective gravity, we may evaluate amplitude ratios and phase differences for integrated changes in directly measured parameters (Dziembowski 1977, Stamford and Watson 1981, Watson 1988).

Abstract Forty-one spectra of 78 Vir (A2p ScrCrEu) obtained through the large apertures of the SWP and LWP/LWR cameras on board International Ultraviolet Explorer (IUE) are compared to look for variations of the absolute flux of 78 Vir over the spectral range 1200–3000 Å. Large variations of the spectral energy distribution occur in the far ultraviolet shortwards of 2000 Å. In contrast, the flux at wavelengths larger than 2000 Å does not vary but several lines are variable between phases of far-UV (FUV) maximum and FUV minimum. The large FUV variability is probably caused by changes in the continuous and line opacity driven by modest horizontal gradients of the abundances of chemical elements over the surface of 78 Vir as the star is probably seen at a low inclination angle. The FUV flux at 1500 Å varies in anticorrelation with the FES counts (optical brightness) recorded before each exposure by the Fine Error Sensor on board IUE.

Context. Dust grains are determinant for setting the chemical, physical, dynamical, and radiative properties of all the media in which they are present. Their influence depends on the grain composition, size, and geometrical structure which vary throughout the life cycle of dust. In particular, grain growth arises in dense molecular clouds and protoplanetary disks as traced by an enhancement of the dust far-IR emissivity and by the effects of cloudshine and coreshine. Aims. Our aim is to investigate the imprint of the grain characteristics on the dust unpolarised optical properties from the visible to the far-IR wavelengths for isolated grains as well as for aggregates. Methods. Using optical constants for both carbonaceous and silicate materials, we have derived the absorption and scattering efficiencies, the asymmetry factor of the phase function, the single scattering albedo, and the mass opacity for isolated grains and aggregates, using either the Mie theory or the discrete dipole approximation (DDA). We investigated the effects of the size, porosity, and shape of the grains, and of the monomers constituting the aggregates, on the optical properties. Besides this, for aggregates we studied the influence of the number of monomers and of mixing monomer sizes. Results. Grain structure changes result in optical property variations at all wavelengths. Porosity, grain elongation, as well as aggregation all produce an increase in the far-IR opacity. The spectral dependence of this increase depends on the nature of the material composing the grain: it is independent of the wavelength for insulators but not for conductors. In the case of aggregates, the far-IR increase does not depend on the monomer size and saturates for aggregates containing six or more monomers. In the visible and near-IR, the aggregate behaviour is reminiscent of a compact sphere of the same mass whereas at longer wavelengths, it is closer to the effect of porosity. Finally, for silicates, the mid-IR spectral feature at 18 μm is more sensitive to the details of the grain structure than the 10 μm feature. Conclusions. Dust optical properties, from the visible to the far-IR, are highly dependent upon the grain composition, size, and structure. This study provides a basis for understanding the range of variations achievable as a result of varying the grain characteristics. It emphasises the importance of considering the detailed grain structure in determining the dust optical properties and of using exact methods because approximate methods cannot reproduce the entire range of the observed variations at all wavelengths.

Aims. The rotational spectral modulation (spectro-photometric variability) of brown dwarfs is usually interpreted as a sign indicating the presence of inhomogeneous cloud covers in the atmosphere. This paper is aimed at exploring the role of temperature fluctuations in these spectral modulations. These fluctuations could naturally arise in a convective atmosphere impacted by such diabatic processes as complex chemistry, namely, a mechanism recently proposed to explain the L/T transition: CO/CH4 radiative convection. Methods. After exploring the observed spectral-flux ratios between different objects along the cooling sequence, we used the 1D radiative-convective code ATMO, with ad hoc modifications of the temperature gradient, to model the rotational spectral modulation of 2MASS 1821, 2MASS 0136, and PSO 318.5-22. We also explored the impact of CH4 abundance fluctuations on the spectral modulation of 2MASS 0136. Results. The spectral-flux ratio of different objects along the cooling sequence and the rotational spectral modulation within individual objects at the L/T transition have similar characteristics. This strongly suggests that the main parameter varying along the cooling sequence, namely, temperature, might play a key role in the rotational spectral modulations at the L/T transition. Modeling the spectral bright-to-faint ratio of the modulation of 2MASS 1821, 2MASS 0136, and PSO 318.5-22 shows that most spectral characteristics can be reproduced by temperature variations alone. Furthermore, the approximately anti-correlated variability between different wavelengths can be easily interpreted as a change in the temperature gradient in the atmosphere, which is a consequence we expect from CO/CH4 radiative convection as an explanation of the L/T transition. The deviation from an exact anti-correlation could then be interpreted as a phase shift similar to the hot-spot shift at different bandpasses in the atmospheres of hot Jupiters. Conclusions. Our results suggest that the rotational spectral modulation from cloud opacity and temperature variations are degenerate. If the nearly anti-correlated signal between different wavelengths is, indeed, a strong sign of a change in the temperature gradient, the detection of direct cloud spectral signatures, for instance, the silicate absorption feature at 10 μm, would help to confirm the presence of clouds and their contribution to spectral modulations (which does not exclude temperature variations or other mechanisms that may also be at play). Future studies considering the differences in the spectral modulation of objects with and without the silicate absorption feature may give us some insight into how to distinguish cloud-opacity fluctuations from temperature fluctuations.

Context. Despite being the best studied red supergiant star in our Galaxy, the physics behind the photometric variability and mass loss of Betelgeuse is poorly understood. Moreover, recently the star has experienced an unusual fading with its visual magnitude reaching a historical minimum. The nature of this event was investigated by several studies where mechanisms, such as episodic mass loss and the presence of dark spots in the photosphere, were invoked. Aims. We aim to relate the atmospheric dynamics of Betelgeuse to its photometric variability, with the main focus on the dimming event. Methods. We used the tomographic method which allowed us to probe different depths in the stellar atmosphere and to recover the corresponding disk-averaged velocity field. The method was applied to a series of high-resolution HERMES observations of Betelgeuse. Variations in the velocity field were then compared with photometric and spectroscopic variations. Results. The tomographic method reveals that the succession of two shocks along our line-of-sight (in February 2018 and January 2019), the second one amplifying the effect of the first one, combined with underlying convection and/or outward motion present at this phase of the 400 d pulsation cycle, produced a rapid expansion of a portion of the atmosphere of Betelgeuse and an outflow between October 2019 and February 2020. This resulted in a sudden increase in molecular opacity in the cooler upper atmosphere of Betelgeuse and, thus, in the observed unusual decrease of the star’s brightness.

A scattering process can be a natural process or a process carried out in a laboratory. The scattering of particles from targets has resulted in important discoveries in physics. We discuss various scattering theories of electrons and positrons and their applications to elastic scattering, resonances, photoabsorption, excitation, and solar and stellar atmospheres. Among the most commonly employed approaches are the Kohn variational principle, close-coupling approximation, method of polarized orbitals, R-matrix formulation, and hybrid theory. In every formulation, an attempt is made to include exchange, long-range and short-range correlations, and to make the approach variationally correct. The present formulation, namely, hybrid theory, which is discussed in greater detail compared to other approximations, includes exchange, long-range correlations, and short-range correlations at the same time, and is variationally correct. It was applied to calculate the phase shifts for elastic scattering, the resonance parameters of two-electron systems, photoabsorption in two-electron systems, excitation of atomic hydrogen by an electron and positron impact, and to study the opacity of the Sun’s atmosphere. Calculations of polarizabilities, Rydberg states, and bound states of atoms are also discussed.

Abstract. Sulfur-rich degassing, which is mostly composed of sulfur dioxide (SO2), plays a major role in the overall impact of volcanism on the atmosphere and climate. The accurate assessment of this impact is currently hampered by the poor knowledge of volcanic SO2 emissions. Here, using an inversion procedure, we show how assimilating snapshots of the volcanic SO2 load derived from the Infrared Atmospheric Sounding Interferometer (IASI) allows for reconstructing both the flux and altitude of the SO2 emissions with an hourly resolution. For this purpose, the regional chemistry-transport model CHIMERE is used to describe the dispersion of SO2 when released in the atmosphere. As proof of concept, we study the 10 April 2011 eruption of the Etna volcano (Italy), which represents one of the few volcanoes instrumented on the ground for the continuous monitoring of SO2 degassing. We find that the SO2 flux time-series retrieved from satellite imagery using the inverse scheme is in agreement with ground observations during ash-poor phases of the eruption. However, large discrepancies are observed during the ash-rich paroxysmal phase as a result of enhanced plume opacity affecting ground-based ultraviolet (UV) spectroscopic retrievals. As a consequence, the SO2 emission rate derived from the ground is underestimated by almost one order of magnitude. Altitudes of the SO2 emissions predicted by the inverse scheme are validated against a RGB MODIS image capturing the near-source atmospheric pathways followed by Etna plumes, in combination with forward trajectories from the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model. At large distance from the source, modeled SO2 altitudes are confronted with independent information on the volcanic cloud height. We find that the altitude predicted by the inverse scheme is in agreement with snapshots of the SO2 height retrieved from recent algorithms exploiting the high spectral resolution of IASI. The validity of the modeled SO2 altitude is further confirmed by the detection of a layer of particles at the same altitude by the spaceborne CALIOP LiDAR. Analysis of CALIOP color and depolarization ratios suggests that these particles consist of sulfate aerosols formed from precursory volcanic SO2. The reconstruction of emission altitude, through inversion procedures which assimilate volcanic SO2 column amounts, requires specific meteorological conditions, especially sufficient wind shear so that gas parcels emitted at different altitudes follow distinct trajectories. We consequently explore the possibility and limits of assimilating in inverse schemes infrared (IR) imagery of the volcanic SO2 cloud altitude which will render the inversion procedure independent of the wind shear prerequisite.

Abstract. Sulfur-rich degassing, which is mostly composed of sulfur dioxide (SO2), plays a major role in the overall impact of volcanism on the atmosphere and climate. The accurate assessment of this impact is currently hampered by the poor knowledge of volcanic SO2 emissions. Here, using an inversion procedure, we show how assimilating snapshots of the volcanic SO2 load derived from the Infrared Atmospheric Sounding Interferometer (IASI) allows for reconstructing both the flux and altitude of the SO2 emissions with an hourly resolution. For this purpose, the regional chemistry-transport model CHIMERE is used to describe the dispersion of SO2 when released in the atmosphere. As proof of concept, we study the 10 April 2011 eruption of the Etna volcano (Italy), which represents one of the few volcanoes instrumented on the ground for the continuous monitoring of SO2 degassing. We find that the SO2 flux time-series retrieved from satellite imagery using the inverse scheme is in agreement with ground observations during ash-poor phases of the eruption. However, large discrepancies are observed during the ash-rich paroxysmal phase as a result of enhanced plume opacity affecting ground-based ultraviolet (UV) spectroscopic retrievals. As a consequence, the SO2 emission rate derived from the ground is underestimated by almost one order of magnitude. Altitudes of the SO2 emissions predicted by the inverse scheme are validated against an RGB image of the Moderate Resolution Imaging Spectroradiometer (MODIS) capturing the near-source atmospheric pathways followed by Etna plumes, in combination with forward trajectories from the Hybrid Single Particle Lagrangian Integrated Trajectory (HYSPLIT) model. At a large distance from the source, modelled SO2 altitudes are compared with independent information on the volcanic cloud height. We find that the altitude predicted by the inverse scheme is in agreement with snapshots of the SO2 height retrieved from recent algorithms exploiting the high spectral resolution of IASI. The validity of the modelled SO2 altitude is further confirmed by the detection of a layer of particles at the same altitude by the spaceborne Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP). Analysis of CALIOP colour and depolarization ratios suggests that these particles consist of sulfate aerosols formed from precursory volcanic SO2. The reconstruction of emission altitude, through inversion procedures which assimilate volcanic SO2 column amounts, requires specific meteorological conditions, especially sufficient wind shear so that gas parcels emitted at different altitudes follow distinct trajectories. We consequently explore the possibility and limits of assimilating in inverse schemes infrared (IR) imagery of the volcanic SO2 cloud altitude which will render the inversion procedure independent of the wind shear prerequisite.

High-resolution optical spectra were taken of the carbon star V Hydrae at 10 different epochs spanning two stellar periods using the Hamilton Echelle Spectrograph at Lick Observatory. Velocities were determined at each epoch by performing a cross-correlation analysis against the spectra of standard stars with previously-determined velocities. The velocities of individual atomic absorption and emission lines, and their variations with phase, were also determined. The rising and falling of the photosphere is clearly in evidence, with an amplitude about the mean of ± 5 km s−1 and a phase consistent with the expectation that maximum light occurs at minimum radius. In addition, the spectra were subjected to a rotational broadening analysis, in which we determined V sin(i), where V is the presumed equatorial rotation velocity, by minimizing the differences between the spectra of V Hya and a number of artificially broadened comparison stars showing no evidence for broadening. Mechanisms other than stellar rotation, including both turbulence and opacity, were found to be unlikely contributors to the broadening. The very unusual rotation velocity (for a red giant) was found to vary between about 10 and 18 km s−1, with an average of ≈ 14 km s−1. The relative phase of the rotation velocity curve is consistent with the hypothesis that the pulsation leads to a periodically varying moment of inertia. The assumption of angular momentum conservation, coupled with the radial velocity and V sin(i) curves, permits a deduction of the equilibrium stellar radius: The similar magnitudes of the rotation and pulsation velocities imply that they are dynamically coupled, leading to a latitude–dependent circulation which probably affects the mass loss. This interaction should also have a strong effect on the convective structure of the envelope. The angular momentum implied for the V Hya atmosphere leads us to the conclusion that it is a common-envelope binary, and that it is a precursor of a binary nucleus in a bipolar planetary nebula.

Context. The initial conditions for mass loss during the asymptotic giant branch (AGB) phase are set in their extended atmospheres, where, among others, convection and pulsation driven shocks determine the physical conditions. Aims. High resolution observations of AGB stars at (sub)millimetre wavelengths can now directly determine the morphology, activity, density, and temperature close to the stellar photosphere. Methods. We used Atacama Large Millimeter/submillimeter Array (ALMA) high angular resolution observations to resolve the extended atmospheres of four of the nearest AGB stars: W Hya, Mira A, R Dor, and R Leo. We interpreted the observations using a parameterised atmosphere model. Results. We resolve all four AGB stars and determine the brightness temperature structure between 1 and 2 stellar radii. For W Hya and R Dor we confirm the existence of hotspots with brightness temperatures > 3000 to 10 000 K. All four stars show deviations from spherical symmetry. We find variations on a timescale of days to weeks, and for R Leo we directly measure an outward motion of the millimetre wavelength surface with a velocity of at least 10.6 ± 1.4 km s−1. For all objects but W Hya we find that the temperature-radius and size-frequency relations require the existence of a (likely inhomogeneous) layer of enhanced opacity. Conclusions. The ALMA observations provide a unique probe of the structure of the extended AGB atmosphere. We find highly variable structures of hotspots and likely convective cells. In the future, these observations can be directly compared to multi-dimensional chromosphere and atmosphere models that determine the temperature, density, velocity, and ionisation structure between the stellar photosphere and the dust formation region. However, our results show that for the best interpretation, both very accurate flux calibration and near-simultaneous observations are essential.

Abstract The dense network of the Surface Heat Budget of the Arctic (SHEBA) observations is used to assess relationships between winter surface and atmospheric variables as the SHEBA site came under the influence of cyclonic and anticyclonic atmospheric circulation systems. Two distinct and preferred states of subsurface, surface, atmosphere, and clouds occur during the SHEBA winter, extending from the oceanic mixed layer through the troposphere and preceded by same-sign variations in the stratosphere. These states are apparent in distributions of surface temperature, sensible heat and longwave radiation fluxes, ocean heat conduction, cloud-base height and temperature, and in the atmospheric humidity and temperature structure. Surface and atmosphere are in radiative–turbulent–conductive near-equilibrium during a warm opaquely cloudy-sky state, which persists up to 10 days and usually occurs during the low surface pressure phase of a baroclinic wave, although occasionally occurs during the high surface pressure phase because of low, scattered clouds. Clouds occurring in this state have near-unity emissivity and the lowest bases in the vicinity of, or below, the temperature inversion peak. A cold radiatively clear-sky state persists up to two weeks, and occurs only in the high surface pressure phase of a baroclinic wave. The radiatively clear state has clouds that are too tenuous when surface based or, irrespective of opacity, located too far aloft to contribute significantly to the surface energy budget. There is a 13-K surface temperature difference between the two states, and atmospheric inversion peak temperatures are linearly related to the surface temperature in both states. The snow–sea ice interface temperature oscillates over the course of the winter season, as it cools during the radiatively clear state and is warmed from atmospheric emission above and ocean heat conduction from below during the opaquely cloudy state. Analysis of satellite data over the Arctic from 70°–90°N indicates that the radiatively clear and opaquely cloudy states observed at SHEBA may be representative of the entire Arctic basin. The results suggest that model formulation inadequacies should be easier to diagnose if modeled energy transfers are compared with observations using process-based metrics that acknowledge the bimodal nature of the Arctic ocean–ice–snow–atmosphere column, rather than monthly and regionally averaged quantities. Climate change projections of thinner Arctic sea ice and larger advective water vapor influxes into the Arctic could yield different frequencies of occupation of the radiatively clear and opaquely cloudy states and higher wintertime temperatures of SHEBA ocean, ice, snow, atmosphere, and clouds—in particular, a wintertime warming of the snow–sea ice interface temperature.

<span lang="EN-US"><span>The present study aimed to investigate the metacognitive ability of students using e-portfolio assessment in project-based learning classes. The projects were a set out a critical analysis based on the selected references (project 1) and set out of field activities based on the selected theme content (project 2). Student metacognitive ability consists of three phases, planning, implementation, and evaluation abilities that were assessed through e-portfolio assignments. There were 87 participants who divided into groups consisted of four to five students, conducted the projects, and submitted the progress of their projects in every decided step into online report assignments. The rubric of metacognition was used to acquire the quantitative score of skill that was separated into six levels category: not yet, at risk, not-really, developing, OK, and super. The result revealed that 44.83% of the students belong to the last three of those levels and the rest are otherwise. The lowest and highest metacognitive ability of the student is “not really” and “developing” respectively. Student metacognitive ability through conducting the project 2 activities is higher than project 1. The findings showed that project-based learning (PBL) enables to foster the student metacognitive ability that developed through e-portfolio-based documents that student conducted during fulfilling all projects assignments.</span>The aim of present study was to investigate the metacognitive ability of student using e-portfolio assessment in the project-based learning classes. The projects were the set out a critical analysis based on the selected references (project 1) and the set out of field activities based on the selected theme content (project 2). Student metacognitive ability consists of three phases, planning, implementation and evaluation abilities that were assessed through e-portfolio assignments. Eighty-seven participants divided into groups consisted of four to five students, conducted the projects, and submitted the progress of their projects in every decided step into online report assignments. The rubric of metacognition was used to acquire the quantitative score of skill that was separated into six levels category; not yet, at risk, not really, developing, OK, and super. The result revealed that 44.83% of the students belong to the last three of those levels and the rest are otherwise. The lowest and highest metacognitive ability of student is "not really" and "developing” respectively. Student metacognitive ability through conducting the project 2 activities is higher than the project 1. The findings showed that PjBl enable to foster the student metacognitive ability that developed through e-portfolio-based documents that student conducted during fulfilling all projects assignments.</span><div class="ms-editor-squiggler" style="color: initial; font: initial; font-feature-settings: initial; font-kerning: initial; font-optical-sizing: initial; font-variation-settings: initial; forced-color-adjust: initial; text-orientation: initial; text-rendering: initial; -webkit-font-smoothing: initial; -webkit-locale: initial; -webkit-text-orientation: initial; -webkit-writing-mode: initial; writing-mode: initial; zoom: initial; place-content: initial; place-items: initial; place-self: initial; alignment-baseline: initial; animation: initial; appearance: initial; aspect-ratio: initial; backdrop-filter: initial; backface-visibility: initial; background: initial; background-blend-mode: initial; baseline-shift: initial; block-size: initial; border-block: initial; border: initial; border-radius: initial; 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Aims. Hydrogen Lyman continuum emission is greatly enhanced in the impulsive kernels of solar flares, with observations of Lyman lines showing impulsive brightening and both red and blue wing asymmetries, based on the images with low spatial resolution. A spate of proposed instruments will study Lyman emission in more detail from bright, impulsive flare kernels. In support of new instrumentation we aim to apply an improved interpretation of Lyman emission with the hydrodynamic radiative code, HYDRO2GEN, which has already successfully explained Hα emission with large redshifts and sources of white light emission in solar flares. The simulations can interpret the existing observations and propose observations in the forthcoming missions. Methods. A flaring atmosphere is considered to be produced by a 1D hydrodynamic response to injection of an electron beam, defining depth variations of electron and ion kinetic temperatures, densities, and macro-velocities. Radiative responses in this flaring atmosphere affected by the beams with different parameters are simulated using a fully non-local thermodynamic equilibrium (NLTE) approach for a five-level plus continuum model hydrogen atom with excitation and ionisation by spontaneous, external, and internal diffusive radiation, and by inelastic collisions with thermal and beam electrons. Integral radiative transfer equations for all optically thick transitions are solved using the L2 approximation simultaneously with steady state equations. Results. During a beam injection in the impulsive phase there is a large increase of collisional ionisation and excitation by non-thermal electrons that strongly (by orders of magnitude) increases excitation and the ionisation degree of hydrogen atoms from all atomic levels. These non-thermal collisions combined with plasma heating caused by beam electrons lead to an increase in Lyman line and continuum radiation, which is highly optically thick. During a beam injection phase the Lyman continuum emission is greatly enhanced in a large range of wavelengths resulting in a flattened distribution of Lyman continuum over wavelengths. After the beam is switched off, Lyman continuum emission, because of its large opacity, sustains, for a very long time, the high ionisation degree of the flaring plasma gained during the beam injection. This leads to a long enhancement of hydrogen ionisation, occurrence of white light flares, and an increase of Lyman line emission in cores and wings, whose shapes are moved closer to those from complete redistribution (CRD) in frequencies, and away from the partial ones (PRD) derived in the non-flaring atmospheres. In addition, Lyman line profiles can reflect macro-motions of a flaring atmosphere caused by downward hydrodynamic shocks produced in response to the beam injection reflected in the enhancements of Ly-line red wing emission. These redshifted Ly-line profiles are often followed by the enhancement of Ly-line blue wing emission caused by the chromospheric evaporation. The ratio of the integrated intensities in the Lyα and Lyβ lines is lower for more powerful flares and agrees with reported values from observations, except in the impulsive phase in flaring kernels which were not resolved in previous observations, in which the ratio is even lower. These results can help observers to design the future observations in Lyman lines and continuum emission in flaring atmospheres.

Context.The Andromeda (M 31) galaxy subtends nearly 100 square degrees on the sky. Any study of its halo must therefore account for the severe contamination from the Milky Way halo stars whose surface density displays a steep gradient across the entire M 31 field of view.Aims.Our goal is to identify a population of stars firmly associated with the M 31 galaxy. Planetary nebulae (PNe) are one such population that are excellent tracers of light, chemistry, and motion in galaxies. We present a 16 square degree survey of the disc and inner halo of M 31 with the MegaCam wide-field imager at the CFHT to identify PNe, and characterise the luminosity-specific PN number and PN luminosity function (PNLF) in M 31.Methods.PNe were identified via automated detection techniques based on their bright [O III] 5007 Å emission and absence of a continuum. Subsamples of the faint PNe were independently confirmed by matching with resolvedHubbleSpace Telescope sources from the PanchromaticHubbleAndromeda Treasury and spectroscopic follow-up observations with HectoSpec at the MMT.Results.The current survey reaches two magnitudes fainter than the previous most sensitive survey. We thus identify 4289 PNe, of which only 1099 were previously known. By comparing the PN number density with the surface brightness profile of M 31 out to ∼30 kpc along the minor axis, we find that the stellar population in the inner halo has a luminosity-specific PN number value that is seven times higher than that of the disc. We measure the luminosity function of the PN population and find a bright cut-off and a slope consistent with previous determinations. Interestingly, it shows a significant rise at the faint end, present in all radial bins covered by the survey. This rise in the M 31 PNLF is much steeper than that observed for the Magellanic clouds and Milky Way bulge.Conclusions.The significant radial variation of the PN specific frequency value indicates that the stellar population at deprojected minor-axis radii larger than ∼10 kpc is different from that in the disc of M 31. The rise at the faint end of the PNLF is a property of the late phases of the stellar population. M 31 shows two major episodes of star formation and the rise at the faint end of the PNLF is possibly associated with the older stellar population. It may also be a result of varying opacity of the PNe.

ABSTRACT A growing number of bacterial species undergo epigenetic phase variation due to variable expression or specificity of DNA-modifying enzymes. For pneumococci, this phase variation has long been appreciated as being revealed by changes in colony opacity, which are reflected in changes in expression or accessibility of factors on the bacterial surface. Recent work showed that recombination-generated variation in alleles of the HsdS DNA methylase specificity subunit mediated pneumococcal phase variation. We generated phase-locked populations of S. pneumoniae TIGR4 expressing a single nonvariant hsdS allele and observed significant differences in gene expression and virulence. These results highlight the importance of focused pathogenesis studies within specific phase types. Moreover, the generation of single-allele hsdS constructs will greatly facilitate such studies. Streptococcus pneumoniae (pneumococcus) is a leading human pathogen that can cause serious localized and invasive diseases. Pneumococci can undergo a spontaneous and reversible phase variation that is reflected in colony opacity and which allows the population to adapt to different host environments. Generally, transparent variants are adapted for nasopharyngeal colonization, whereas opaque variants are associated with invasive disease. In recent work, colony phase variation was shown to occur by means of recombination events to generate multiple alleles of the hsdS targeting domain of a DNA methylase complex, which mediates epigenetic changes in gene expression. A panel of isogenic strains were created in the well-studied S. pneumoniae TIGR4 background that are “locked” in the transparent (n = 4) or opaque (n = 2) colony phenotype. The strains had significant differences in colony size which were stable over multiple passages in vitro and in vivo. While there were no significant differences in adherence for the phase-locked mutant strains to immortalized epithelial cells, biofilm formation and viability were reduced for the opaque variants in static assays. Nasopharyngeal colonization was stable for all strains, but the mortality rates differed between them. Transcript profiling by transcriptome sequencing (RNA-seq) analyses revealed that the expression levels of certain virulence factors were increased in a phase-specific manner. As epigenetic regulation of phase variation (often referred to as "phasevarion") is emerging as a common theme for mucosal pathogens, these results serve as a model for future studies of host-pathogen interactions. IMPORTANCE A growing number of bacterial species undergo epigenetic phase variation due to variable expression or specificity of DNA-modifying enzymes. For pneumococci, this phase variation has long been appreciated as being revealed by changes in colony opacity, which are reflected in changes in expression or accessibility of factors on the bacterial surface. Recent work showed that recombination-generated variation in alleles of the HsdS DNA methylase specificity subunit mediated pneumococcal phase variation. We generated phase-locked populations of S. pneumoniae TIGR4 expressing a single nonvariant hsdS allele and observed significant differences in gene expression and virulence. These results highlight the importance of focused pathogenesis studies within specific phase types. Moreover, the generation of single-allele hsdS constructs will greatly facilitate such studies.

AbstractNon-stoichiometric perovskites with the general formula SrFeO2.5+x have potential in oxygen sensing applications. Thin films of these compositions have been grown onto various substrates by pulsed laser deposition techniques. At elevated temperatures, (T > 550K), the films react rapidly and reversibly with oxygen and the bulk oxygen content, x, of the films changes. Accompanying the change in oxygen stoichiometry are significant changes in the optical transmittance and reflectance of the films. Transmission spectrophotometry in the uv-vis region has been used to determine the relationship of transmittance with oxygen composition in the gas phase. Spectrophotometric data have been obtained by a batch method and also in-situ in a flow cell at T = 690K. The data show a large variation in transmittance, exceeding 103 for the batch measurements, with SrFeO3 showing the highest opacity. The design of the flow cell is also described.

ABSTRACT Recently, a novel phase-variable colony opacity phenotype was discovered in Acinetobacter baumannii strain AB5075, where colonies interconvert between opaque and translucent variants. Opaque colonies become mottled or sectored after 24 h of growth due to translucent variants arising within the colony. This easily distinguishable opaque-colony phenotype was used to screen for random transposon insertions that increased the frequency of sectoring at a time point when wild-type colonies were uniformly opaque. A colony was identified that contained multiple papillae of translucent variants, and the insertion in this mutant mapped to an ortholog of the two-component system response regulator ompR. Subsequent investigation of in-frame deletions of ompR and the sensor kinase envZ (located adjacent to ompR) showed that the switching frequency from opaque to translucent was increased 401- and 281-fold, respectively. The ompR mutant also exhibited sensitivity to sodium chloride in growth medium, whereas the envZ mutation did not elicit sensitivity to sodium chloride. Mutation of either gene reduced motility in A. baumannii strain AB5075, but a mutation in both ompR and envZ produced a more profound effect. The ompR and envZ genes were cotranscribed but were not subject to autoregulation by OmpR. Both ompR and envZ mutant opaque variants were attenuated in virulence in the Galleria mellonella infection model, whereas mutation of ompR had no effect on the virulence of the translucent variant. IMPORTANCE Acinetobacter baumannii is a well-known antibiotic-resistant pathogen; many clinical isolates can only be treated by a very small number of antibiotics (including colistin), while some exhibit panresistance. The current antimicrobial arsenal is nearing futility in the treatment of Acinetobacter infections, and new avenues of treatment are profoundly needed. Since phase variation controls the transition between opaque (virulent) and translucent (avirulent) states in A. baumannii, this may represent an “Achilles' heel” that can be targeted via the development of small molecules that lock cells in the translucent state and allow the host immune system to clear the infection. A better understanding of how phase variation is regulated may allow for the development of methods to target this process. The ompR-envZ two-component system ortholog negatively regulates phase variation in A. baumannii, and perturbation of this system leads to the attenuation of virulence in an invertebrate infection model.

Abstract In this paper, we investigate the photometric variability of magnetic O-type stars. Such stars possess oblique, predominantly dipolar magnetic fields that confine their winds roughly axisymmetrically about the magnetic equator, thus forming a magnetosphere. We interpret their photometric variability as phase-dependent magnetospheric occultations. For massive star winds dominated by electron scattering opacity in the optical and NIR, we can compute synthetic light curves from simply knowing the magnetosphere’s mass density distribution. We exploit the newly-developed Analytical Dynamical Magnetosphere model (ADM) in order to obtain the predicted circumstellar density structures of magnetic O-type stars. The simplicity in our light curve synthesis model allows us to readily conduct a parameter space study. For validation purposes, we first apply our algorithm to HD 191612, the prototypical Of?p star. Next, we attempt to model the photometric variability of the Of?p-type stars identified in the Magellanic Clouds using OGLE photometry. We evaluate the compatibility of the ADM predictions with the observed photometric variations, and discuss the magnetic field properties that are implied by our modelling.

Abstract Satellite imager estimates of cloud-top pressure (CTP) have many applications in both operations and in studying long-term variations in cloud properties. Recently, machine learning (ML) approaches have shown improvement upon physically-based algorithms. However, ML approaches, and especially neural networks, can suffer from a lack of interpretability making it difficult to understand what information is most useful for accurate predictions of cloud properties. We trained several neural networks to estimate CTP from the infrared channels of the Visible Infrared Imaging Radiometer Suite (VIIRS) and the Advanced Baseline Imager (ABI). The main focus of this work is assessing the relative importance of each instrument’s infrared channels in neural networks trained to estimate CTP. We use several ML explainability methods to offer different perspectives on feature importance. These methods show many differences in the relative feature importance depending on the exact method used, but most agree on a few points. Overall, the 8.4- and 8.6-μm channels appear to be the most useful for CTP estimation on ABI and VIIRS, respectively, with other native infrared window channels and the 13.3-μm channel playing a moderate role. Furthermore, we find that the neural networks learn relationships that may account for properties of clouds such as opacity and cloud-top phase that otherwise complicate the estimation of CTP.