A Supplementary Description of Cypridina mariae and Rediagnosis of the Genus Cylindroleberis (Ostracoda: Myodocopa: Cylindroleberididae)

The ostracod family Cylindroleberididae is based on the genus Cylindroleberis Brady, 1868, and has a complicated nomenclatural history. The type species of Cylindroleberis is Cypridina mariae Baird, 1850. Baird described only the carapace, which had been considered lost. Thus, there was no reference point for the concept C. mariae or the genus Cylindroleberis. Baird's material has now been found in the Natural History Museum, London, U.K., and is illustrated here. To clarify the taxonomic status of C. mariae and Cylindroleberis, specimens were obtained from near the type locality, and a supplementary description is presented. This includes description of appendages, particularly the first antenna and mandible, which contain important diagnostic characters. This supplementary description provides important information about C. mariae, allowing a revision of the genus Cylindroleberis, and establishing a framework for future biological research on this ostracod group

Computational Molecular Spectroscopy Towards New Physics

Several theories of modern physics go beyond the standard model of particle physics to describe as of yet unexplained phenomena of the universe. A common method of testing new theories of physics is using spectroscopy to compare transition positions at different times. Non-trivial calculations are required to determine the sensitivity coefficients of transitions to a variation of fundamental constants. These calculations can be done using nuclear motion programs with adequate spectroscopic models. In this work, 27 small molecules with spectroscopic models are evaluated as molecular probes to constrain the variation of the proton-to-electron mass ratio. The diatomic radical CN is used as a case study to develop and explain the construction of spectroscopic models. Over 40,000 experimental transitions from 22 unique sources were validated to generate a network of 8083 interconnected spin-rovibronic energy levels. These empirical energy levels, along with ab initio dipole moment curves have been used to construct and fit a spectroscopic model for the three lowest coupled electronic states of CN in the nuclear motion program Duo. The resultant line list is further refined in a novel hybrid style with the replacement of energy levels from empirical and perturbative sources to produce over 2.2 million transitions up to 60,000 cm-1. A comprehensive high-throughput methodology is developed to calculate the sensitivity coefficients for transitions in CN, 21 other diatomic and 5 small polyatomic molecules of astrophysical relevance. In diatomics, near degenerate vibronic levels and parity transitions within non-singlet-sigma ground states can cause enhanced transition sensitivity. Unfortunately, many of the enhanced transitions, especially those showing anomalously large sensitivities, have extremely low intensities at 100 K. Expanding to polyatomic molecules, tunnelling transitions (a natural progression from parity transitions) show enhanced sensitivity, especially combination rotation-tunnelling transitions. Enhanced transitions are compared against previous calculations, and some previously identified enhanced transitions are excluded from astrophysical consideration based on their very low intensity at 100 K. Selection criteria that consider factors both sensitivity and observability of transitions to be used as molecular probes for a variation in the proton-to-electron mass ratio are considered for both diatomic and polyatomic molecules

Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach

<p>Abstract</p> <p>Background</p> <p>Duplication and divergence of genes and genetic networks is hypothesized to be a major driver of the evolution of complexity and novel features. Here, we examine the history of genes and genetic networks in the context of eye evolution by using new approaches to understand patterns of gene duplication during the evolution of metazoan genomes. We hypothesize that 1) genes involved in eye development and phototransduction have duplicated and are retained at higher rates in animal clades that possess more distinct types of optical design; and 2) genes with functional relationships were duplicated and lost together, thereby preserving genetic networks. To test these hypotheses, we examine the rates and patterns of gene duplication and loss evident in 19 metazoan genomes, including that of <it>Daphnia pulex </it>- the first completely sequenced crustacean genome. This is of particular interest because the pancrustaceans (hexapods+crustaceans) have more optical designs than any other major clade of animals, allowing us to test specifically whether the high amount of disparity in pancrustacean eyes is correlated with a higher rate of duplication and retention of vision genes.</p> <p>Results</p> <p>Using protein predictions from 19 metazoan whole-genome projects, we found all members of 23 gene families known to be involved in eye development or phototransduction and deduced their phylogenetic relationships. This allowed us to estimate the number and timing of gene duplication and loss events in these gene families during animal evolution. When comparing duplication/retention rates of these genes, we found that the rate was significantly higher in pancrustaceans than in either vertebrates or non-pancrustacean protostomes. Comparing patterns of co-duplication across Metazoa showed that while these eye-genes co-duplicate at a significantly higher rate than those within a randomly shuffled matrix, many genes with known functional relationships in model organisms did not co-duplicate more often than expected by chance.</p> <p>Conclusions</p> <p>Overall, and when accounting for factors such as differential rates of whole-genome duplication in different groups, our results are broadly consistent with the hypothesis that genes involved in eye development and phototransduction duplicate at a higher rate in Pancrustacea, the group with the greatest variety of optical designs. The result that these genes have a significantly high number of co-duplications and co-losses could be influenced by shared functions or other unstudied factors such as synteny. Since we did not observe co-duplication/co-loss of genes for all known functional modules (e.g. specific regulatory networks), the interactions among suites of known co-functioning genes (modules) may be plastic at the temporal scale of analysis performed here. Other factors in addition to gene duplication - such as cis-regulation, heterotopy, and co-option - are also likely to be strong factors in the diversification of eye types.</p

Computational Infrared Spectroscopy of 958 Phosphorus-Bearing Molecules

Phosphine is now well-established as a biosignature, which has risen to prominence with its recent tentative detection on Venus. To follow up this discovery and related future exoplanet biosignature detections, it is important to spectroscopically detect the presence of phosphorus-bearing atmospheric molecules that could be involved in the chemical networks producing, destroying or reacting with phosphine. We start by enumerating phosphorus-bearing molecules (P-molecules) that could potentially be detected spectroscopically in planetary atmospheres and collecting all available spectral data. Gaseous P-molecules are rare, with speciation information scarce. Very few molecules have high accuracy spectral data from experiment or theory; instead, the best current spectral data was obtained using a high-throughput computational algorithm, RASCALL, relying on functional group theory to efficiently produce approximate spectral data for arbitrary molecules based on their component functional groups. Here, we present a high-throughput approach utilizing established computational quantum chemistry methods (CQC) to produce a database of approximate infrared spectra for 958 P-molecules. These data are of interest for astronomy and astrochemistry (importantly identifying potential ambiguities in molecular assignments), improving RASCALL's underlying data, big data spectral analysis and future machine learning applications. However, this data will probably not be sufficiently accurate for secure experimental detections of specific molecules within complex gaseous mixtures in laboratory or astronomy settings. We chose the strongly performing harmonic ωB97X-D/def2-SVPD model chemistry for all molecules and test the more sophisticated and time-consuming GVPT2 anharmonic model chemistry for 250 smaller molecules. Limitations to our automated approach, particularly for the less robust GVPT2 method, are considered along with pathways to future improvements. Our CQC calculations significantly improve on existing RASCALL data by providing quantitative intensities, new data in the fingerprint region (crucial for molecular identification) and higher frequency regions (overtones, combination bands), and improved data for fundamental transitions based on the specific chemical environment. As the spectroscopy of most P-molecules have never been studied outside RASCALL and this approach, the new data in this paper is the most accurate spectral data available for most P-molecules and represent a significant advance in the understanding of the spectroscopic behavior of these molecules.</jats:p

Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke

Genetic factors have been implicated in stroke risk but few replicated associations have been reported. We conducted a genome-wide association study (GWAS) in ischemic stroke and its subtypes in 3,548 cases and 5,972 controls, all of European ancestry. Replication of potential signals was performed in 5,859 cases and 6,281 controls. We replicated reported associations between variants close to PITX2 and ZFHX3 with cardioembolic stroke, and a 9p21 locus with large vessel stroke. We identified a novel association for a SNP within the histone deacetylase 9(HDAC9) gene on chromosome 7p21.1 which was associated with large vessel stroke including additional replication in a further 735 cases and 28583 controls (rs11984041, combined P = 1.87×10−11, OR=1.42 (95% CI) 1.28-1.57). All four loci exhibit evidence for heterogeneity of effect across the stroke subtypes, with some, and possibly all, affecting risk for only one subtype. This suggests differing genetic architectures for different stroke subtypes

LEARN: A multi-centre, cross-sectional evaluation of Urology teaching in UK medical schools

OBJECTIVE: To evaluate the status of UK undergraduate urology teaching against the British Association of Urological Surgeons (BAUS) Undergraduate Syllabus for Urology. Secondary objectives included evaluating the type and quantity of teaching provided, the reported performance rate of General Medical Council (GMC)-mandated urological procedures, and the proportion of undergraduates considering urology as a career. MATERIALS AND METHODS: LEARN was a national multicentre cross-sectional study. Year 2 to Year 5 medical students and FY1 doctors were invited to complete a survey between 3rd October and 20th December 2020, retrospectively assessing the urology teaching received to date. Results are reported according to the Checklist for Reporting Results of Internet E-Surveys (CHERRIES). RESULTS: 7,063/8,346 (84.6%) responses from all 39 UK medical schools were included; 1,127/7,063 (16.0%) were from Foundation Year (FY) 1 doctors, who reported that the most frequently taught topics in undergraduate training were on urinary tract infection (96.5%), acute kidney injury (95.9%) and haematuria (94.4%). The most infrequently taught topics were male urinary incontinence (59.4%), male infertility (52.4%) and erectile dysfunction (43.8%). Male and female catheterisation on patients as undergraduates was performed by 92.1% and 73.0% of FY1 doctors respectively, and 16.9% had considered a career in urology. Theory based teaching was mainly prevalent in the early years of medical school, with clinical skills teaching, and clinical placements in the later years of medical school. 20.1% of FY1 doctors reported no undergraduate clinical attachment in urology. CONCLUSION: LEARN is the largest ever evaluation of undergraduate urology teaching. In the UK, teaching seemed satisfactory as evaluated by the BAUS undergraduate syllabus. However, many students report having no clinical attachments in Urology and some newly qualified doctors report never having inserted a catheter, which is a GMC mandated requirement. We recommend a greater emphasis on undergraduate clinical exposure to urology and stricter adherence to GMC mandated procedures