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Geminiviruses are major plant pathogens that threaten food security globally. They have a unique architecture built from two incomplete icosahedral particles, fused to form a geminate capsid. However, despite their importance to agricultural economies and fundamental biological interest, the details of how this is realized in 3D remain unknown. Here we report the structure of A geratum yellow vein virus at 3.3 Å resolution, using single-particle cryo-electron microscopy, together with an atomic model that shows that the N-terminus of the single capsid protein (CP) adopts three different conformations essential for building the interface between geminate halves. Our map also contains density for ~7 bases of single-stranded DNA bound to each CP, and we show that the interactions between the genome and CPs are different at the interface than in the rest of the capsid. With additional mutagenesis data, this suggests a central role for DNA binding-induced conformational change in directing the assembly of geminate capsids. Geminiviruses are an important plant pathogen that causes large food crop losses globally. Here the authors describe a high resolution cryo-EM structure of the Ageratum yellow vein virus and reveal the molecular details of how a single capsid protein sequence can adopt the different conformations needed to build that geminate capsid.

Infectious meningoencephalitides represent an important differential diagnosis for meningoencephalitis of unknown origin (MUO) in dogs. Treatment of the latter requires immunosuppression, but laboratory test results for infectious agents may take several days to return. This study investigated whether the presence of masticatory muscle changes on magnetic resonance imaging (MRI) of the head can be used to distinguish dogs with neosporosis from those with MUO at the time of diagnosis. Cases diagnosed with neosporosis or MUO at two referral centers in the United Kingdom (UK) were retrospectively collected. Clinical data were reviewed, and each MRI study was blindly assessed by a radiologist, a neurologist, and a neurology resident for the presence of masticatory muscle changes by consensus opinion. Statistical analysis was performed on obtained data. Twenty-two neosporosis cases and 23 MUO cases were enrolled. In the neosporosis group, six dogs (27%) had masticatory muscle changes, compared to one dog (4%) in the MUO group ( p  = 0.047). All six neosporosis cases had bilateral, multifocal, T2W and FLAIR hyperintense, contrast enhancing muscular changes, with three having concurrent masticatory muscle atrophy. The only MUO case with muscle changes had a mild, focal, unilateral temporal muscle lesion which was only visible in the T1W post-contrast images. Within the neosporosis group, dogs with masticatory muscle lesions had significantly higher cerebrospinal fluid WBC counts ( p  = 0.017) and protein concentrations ( p  = 0.025) compared to those without muscle changes. In conclusion, characteristic bilateral, multifocal masticatory muscle changes should raise the index of suspicion for neosporosis in dogs with an imaging diagnosis of meningoencephalitis and starting early antimicrobial treatment is recommended. However, the absence of masticatory muscle abnormalities does not exclude active Neospora caninum infection. In these cases, whether immunosuppressive or antimicrobial treatments are started prior to receiving further test results should still be based on the clinical status of the animal and index of suspicion using a combination of all available clinical information at that time.

ABSTRACT A primary objective of exoplanet atmosphere characterization is to learn about planet formation and evolution, however, this is challenged by degeneracies. To determine whether differences in atmospheric composition can be reliably traced to differences in evolution, we are undertaking a transmission spectroscopy survey with JWST to compare the compositions of a sample of hot Jupiters that have different orbital alignments around F stars above the Kraft break. Under the assumption that aligned planets migrate through the inner disc, while misaligned planets migrate after disc dispersal, the act of migrating through the inner disc should cause a measurable difference in the C/O between aligned and misaligned planets. We expect the amplitude and sign of this difference to depend on the amount of planetesimal accretion and whether silicates accreted from the inner disc release their oxygen. Here, we identify all known exoplanets that are suitable for testing this hypothesis, describe our JWST survey, and use noise simulations and atmospheric retrievals to estimate our survey’s sensitivity. With the selected sample of four aligned and four misaligned hot Jupiters, we will be sensitive to the predicted differences in C/O between aligned and misaligned hot Jupiters for a wide range of model scenarios.

The use of machine learning is becoming ubiquitous in astronomy 1 – 3 , but remains rare in the study of the atmospheres of exoplanets. Given the spectrum of an exoplanetary atmosphere, a multi-parameter space is swept through in real time to find the best-fit model 4 – 6 . Known as atmospheric retrieval, this technique originates in the Earth and planetary sciences 7 . Such methods are very time-consuming, and by necessity there is a compromise between physical and chemical realism and computational feasibility. Machine learning has previously been used to determine which molecules to include in the model, but the retrieval itself was still performed using standard methods 8 . Here, we report an adaptation of the ‘random forest’ method of supervised machine learning 9 , 10 , trained on a precomputed grid of atmospheric models, which retrieves full posterior distributions of the abundances of molecules and the cloud opacity. The use of a precomputed grid allows a large part of the computational burden to be shifted offline. We demonstrate our technique on a transmission spectrum of the hot gas-giant exoplanet WASP-12b using a five-parameter model (temperature, a constant cloud opacity and the volume mixing ratios or relative abundances of molecules of water, ammonia and hydrogen cyanide) 11 . We obtain results consistent with the standard nested-sampling retrieval method. We also estimate the sensitivity of the measured spectrum to the model parameters, and we are able to quantify the information content of the spectrum. Our method can be straightforwardly applied using more sophisticated atmospheric models to interpret an ensemble of spectra without having to retrain the random forest. A method of atmospheric retrieval for exoplanets that uses supervised ‘random forest’ machine learning, less time-consuming than standard techniques, is presented. Tests on Hubble spectra of WASP-12b give results consistent with standard atmospheric retrievals.

Study Analysis Group 21 (SAG21) of NASA’s Exoplanet Exploration Program Analysis Group was organized to study the effect of stellar contamination on space-based transmission spectroscopy, a method for studying exoplanetary atmospheres by measuring the wavelength-dependent radius of a planet as it transits its star. Transmission spectroscopy relies on a precise understanding of the spectrum of the star being occulted. However, stars are not homogeneous, constant light sources but have temporally evolving photospheres and chromospheres with inhomogeneities like spots, faculae, plages, granules, and flares. This SAG brought together an interdisciplinary team of more than 100 scientists, with observers and theorists from the heliophysics, stellar astrophysics, planetary science, and exoplanetary atmosphere research communities, to study the current research needs that can be addressed in this context to make the most of transit studies from current NASA facilities like Hubble Space Telescope and JWST. The analysis produced 14 findings, which fall into three science themes encompassing (i) how the Sun is used as our best laboratory to calibrate our understanding of stellar heterogeneities (‘The Sun as the Stellar Benchmark’), (ii) how stars other than the Sun extend our knowledge of heterogeneities (‘Surface Heterogeneities of Other Stars’), and (iii) how to incorporate information gathered for the Sun and other stars into transit studies (‘Mapping Stellar Knowledge to Transit Studies’). In this invited review, we largely reproduce the final report of SAG21 as a contribution to the peer-reviewed literature.

This hermeneutic phenomenological study aims to understand how mental health practitioners experience and respond to climate-related concerns when working with clients. Equally important to this study is the absence of climate-related issues in therapy sessions. Five participants, all working as clinicians in private practices, served as the sample for this research. Data were collected through semi-structured interviews and interpreted through a hermeneutic phenomenological lens. The data analysis revealed four themes: 1) Prioritization of Immediate Issues; 2) Not Wanting to Attend to Impending Catastrophe; 3) Misnaming or Mispunctuating; 4) Therapist’s Approach. Participants in this study indicated they felt unprepared to handle climate-related issues during client sessions and reported insufficient training in graduate school. This study highlights the need for a transformative approach to psychotherapy that makes environmental concerns central. It will be important to view the therapeutic process through an environmental lens where therapists engage with sociopolitical issues instead of remaining neutral. As climate change continues to escalate, integrating environmental awareness into therapy will be essential, becoming a standard part of the therapeutic process.

The temperature of an atmosphere decreases with increasing altitude, unless a shortwave absorber that causes a temperature inversion exists 1 . Ozone plays this role in the Earth’s atmosphere. In the atmospheres of highly irradiated exoplanets, the shortwave absorbers are predicted to be titanium oxide (TiO) and vanadium oxide (VO) 2 . Detections of TiO and VO have been claimed using both low- 3 – 6 and high- 7 spectral-resolution observations, but subsequent observations have failed to confirm these claims 8 – 10 or overturned them 11 – 13 . Here we report the unambiguous detection of TiO in the ultra-hot Jupiter WASP-189 b 14 using high-resolution transmission spectroscopy. This detection is based on applying the cross-correlation technique 15 to many spectral lines of TiO from 460 to 690 nm. Moreover, we report detections of metals, including neutral and singly ionized iron and titanium, as well as chromium, magnesium, vanadium and manganese (Fe, Fe + , Ti, Ti + , Cr, Mg, V, Mn). The line positions of the detected species differ, which we interpret as a consequence of spatial gradients in their chemical abundances, such that they exist in different regions or dynamical regimes. This is direct observational evidence for the three-dimensional thermochemical stratification of an exoplanet atmosphere derived from high-resolution ground-based spectroscopy. The rich transmission spectrum of exoplanet WASP-189 b reveals its dynamical atmosphere with a three-dimensional thermochemical stratification, requiring the unification of dynamical, thermal and chemical models for its study.

The initial motivations of this thesis were to dope paraelectric SrTiO3 with niobium alongside an A-site vacancy compensation scheme so as to study the resulting chemical defects and potentially manipulate them in order to create a macroscopic dipole to induce a piezoelectric effect. However, it is made clear that this thesis is not an attempt at creating a new, nor modifying an existing, ferroelectric system. This thesis will cover an introduction to piezoelectric and ferroelectric materials, due to the author's inclusion within a piezoelectric research group, from which stemmed the idea for this research. A literature review into the defect chemistry of SrTiO3 was carried out, including the effects of non-stoichiometric SrTiO3, acceptor and donor doping, followed by a review of existing defect dipole research. Samples of Sr1-x/2Ti1-xNbxO3, Sr0.9Ti1-xNbxO3, SrTi1-xNbxO3, SrTi1-xMnxO3 and SrTi1-xCoxO3 were produced via the mixed oxide solid state reaction technique. Samples were characterised using X-ray diffraction and scanning electron microscopy. Following this electrical characterisation was carried out and impedance, electric modulus and permittivity data were examined in order to better understand the defect mechanisms taking place. Complex impedance analysis was used as an initial comparison of conductivity before deeper analysis of the frequency dependence of impedance and modulus data was conducted. Detailed analysis of the impedance and modulus data showed that electronic conduction dominated the electrical behaviour of all Nb-doped SrTiO3 samples. The conductivity was much more electron-dominated in the B-site Nb-doped samples compared to the A-site vacancy samples. This resulted in a blue colouration of sample pellets, indicating the reduction of Ti4+ to Ti3+ and higher conductivities. The influence of Sr vacancies is also apparent from the lack of increase in conductivity in the Sr1-x/2 samples despite ten times the increase in Nb content. It was shown that the addition of large concentrations of A-site vacancies to the perovskite system enabled it structurally to accommodate large amounts of Nb, but it also significantly reduced the increase in conductivity seen by Nb doping. Equally, the large amount of Nb doping enabled the SrTiO3 system to accept large amounts of Sr deficiencies (up to 15%) by charge compensation. The vacancy/donor compensation scheme is shown to be key to maintaining the SrTiO3 perovskite structure by charge compensation, proven by the Sr0.9 sample set which began to eject TiO2 as a secondary phase as Nb dopant decreased.

The construction and implementation of atmospheric model grids is a popular tool in exoplanet characterisation. These typically vary a number of parameters linearly, containing one model for every combination of parameter values. Here we investigate alternative methods of sampling parameters, including random sampling and Latin hypercube (LH) sampling, and how these compare to linearly sampled grids. We use a random forest to analyse the performance of these grids for two different models, as well as investigate the information content of the particular model grid from Goyal et al. 2019. We also use nested-sampling to implement mock atmospheric retrievals on simulated JWST transmission spectra by interpolating on linearly sampled model grids. Our results show that random or LH sampling out-performs linear sampling in parameter predictability for our higher dimensional models, requiring fewer models in the grid, and thus allowing for more computationally intensive forward models to be used. We also find that using a traditional retrieval with interpolation on a linear grid can produce biased posterior distributions, especially for parameters with non-linear effects on the spectrum. In particular, we advise caution when performing linear interpolation on the C/O ratio, cloud properties, and metallicity. Finally, we find that the information content analysis of the grid from Goyal et al. 2019 is able to highlight key areas of the spectra where the presence or absence of certain molecules can be detected, providing good indicators for parameters such as temperature and C/O ratio.