Mass-radius relationships for exoplanets

For planets other than Earth, interpretation of the composition and structure depends largely on comparing the mass and radius with the composition expected given their distance from the parent star. The composition implies a mass-radius relation which relies heavily on equations of state calculated from electronic structure theory and measured experimentally on Earth. We lay out a method for deriving and testing equations of state, and deduce mass-radius and mass-pressure relations for key materials whose equation of state is reasonably well established, and for differentiated Fe/rock. We find that variations in the equation of state, such as may arise when extrapolating from low pressure data, can have significant effects on predicted mass- radius relations, and on planetary pressure profiles. The relations are compared with the observed masses and radii of planets and exoplanets. Kepler-10b is apparently 'Earth- like,' likely with a proportionately larger core than Earth's, nominally 2/3 of the mass of the planet. CoRoT-7b is consistent with a rocky mantle over an Fe-based core which is likely to be proportionately smaller than Earth's. GJ 1214b lies between the mass-radius curves for H2O and CH4, suggesting an 'icy' composition with a relatively large core or a relatively large proportion of H2O. CoRoT-2b is less dense than the hydrogen relation, which could be explained by an anomalously high degree of heating or by higher than assumed atmospheric opacity. HAT-P-2b is slightly denser than the mass-radius relation for hydrogen, suggesting the presence of a significant amount of matter of higher atomic number. CoRoT-3b lies close to the hydrogen relation. The pressure at the center of Kepler-10b is 1.5+1.2-1.0 TPa. The central pressure in CoRoT-7b is probably close to 0.8TPa, though may be up to 2TPa.Comment: Added more recent exoplanets. Tidied text and references. Added extra "rock" compositions. Responded to referee comment

High Protein Binding and Cidal Activity against Penicillin-Resistant S. pneumoniae: A Cefditoren In Vitro Pharmacodynamic Simulation

BACKGROUND: Although protein binding is a reversible phenomenon, it is assumed that antibacterial activity is exclusively exerted by the free (unbound) fraction of antibiotics. METHODOLOGY/PRINCIPAL FINDINGS: Activity of cefditoren, a highly protein bound 3(rd) generation cephalosporin, over 24h after an oral 400 mg cefditoren-pivoxil bid regimen was studied against six S. pneumoniae strains (penicillin/cefditoren MICs; microg/ml): S1 (0.12/0.25), S2 (0.25/0.25), S3 and S4 (0.5/0.5), S5 (1/0.5) and S6 (4/0.5). A computerized pharmacodynamic simulation with media consisting in 75% human serum and 25% broth (mean albumin concentrations = 4.85+/-0.12 g/dL) was performed. Protein binding was measured. The cumulative percentage of a 24h-period that drug concentrations exceeded the MIC for total (T > MIC) and unbound concentrations (fT > MIC), expressed as percentage of the dosing interval, were determined. Protein binding was 87.1%. Bactericidal activity (> or = 99.9% initial inocula reduction) was obtained against strains S1 and S2 at 24h (T > MIC = 77.6%, fT > MIC = 23.7%). With T > MIC of 61.6% (fT > MIC = 1.7%), reductions against S3 and S4 ranged from 90% to 97% at 12h and 24h; against S5, reduction was 45.1% at 12h and up to 85.0% at 24h; and against S6, reduction was 91.8% at 12h, but due to regrowth of 52.9% at 24h. Cefditoren physiological concentrations exerted antibacterial activity against strains exhibiting MICs of 0.25 and 0.5 microg/ml under protein binding conditions similar to those in humans. CONCLUSIONS/SIGNIFICANCE: The results of this study suggest that, from the pharmacodynamic perspective, the presence of physiological albumin concentrations may not preclude antipneumococcal activity of highly bound cephalosporins as cefditoren

Protein prediction for trait mapping in diverse populations

Genetically regulated gene expression has helped elucidate the biological mechanisms underlying complex traits. Improved high-throughput technology allows similar interrogation of the genetically regulated proteome for understanding complex trait mechanisms. Here, we used the Trans-omics for Precision Medicine (TOPMed) Multi-omics pilot study, which comprises data from Multi-Ethnic Study of Atherosclerosis (MESA), to optimize genetic predictors of the plasma proteome for genetically regulated proteome-wide association studies (PWAS) in diverse populations. We built predictive models for protein abundances using data collected in TOPMed MESA, for which we have measured 1,305 proteins by a SOMAscan assay. We compared predictive models built via elastic net regression to models integrating posterior inclusion probabilities estimated by fine-mapping SNPs prior to elastic net. In order to investigate the transferability of predictive models across ancestries, we built protein prediction models in all four of the TOPMed MESA populations, African American (n = 183), Chinese (n = 71), European (n = 416), and Hispanic/Latino (n = 301), as well as in all populations combined. As expected, fine-mapping produced more significant protein prediction models, especially in African ancestries populations, potentially increasing opportunity for discovery. When we tested our TOPMed MESA models in the independent European INTERVAL study, fine-mapping improved cross-ancestries prediction for some proteins. Using GWAS summary statistics from the Population Architecture using Genomics and Epidemiology (PAGE) study, which comprises ∼50,000 Hispanic/Latinos, African Americans, Asians, Native Hawaiians, and Native Americans, we applied S-PrediXcan to perform PWAS for 28 complex traits. The most protein-trait associations were discovered, colocalized, and replicated in large independent GWAS using proteome prediction model training populations with similar ancestries to PAGE. At current training population sample sizes, performance between baseline and fine-mapped protein prediction models in PWAS was similar, highlighting the utility of elastic net. Our predictive models in diverse populations are publicly available for use in proteome mapping methods at https://doi.org/10.5281/zenodo.4837327

A Model for Using a Concept Inventory as a Tool for Students' Assessment and Faculty Professional Development

This essay describes how the use of a concept inventory has enhanced professional development and curriculum reform efforts of a faculty teaching community. The Host Pathogen Interactions (HPI) teaching team is composed of research and teaching faculty with expertise in HPI who share the goal of improving the learning experience of students in nine linked undergraduate microbiology courses. To support evidence-based curriculum reform, we administered our HPI Concept Inventory as a pre- and postsurvey to approximately 400 students each year since 2006. The resulting data include student scores as well as their open-ended explanations for distractor choices. The data have enabled us to address curriculum reform goals of 1) reconciling student learning with our expectations, 2) correlating student learning with background variables, 3) understanding student learning across institutions, 4) measuring the effect of teaching techniques on student learning, and 5) demonstrating how our courses collectively form a learning progression. The analysis of the concept inventory data has anchored and deepened the team's discussions of student learning. Reading and discussing students' responses revealed the gap between our understanding and the students' understanding. We provide evidence to support the concept inventory as a tool for assessing student understanding of HPI concepts and faculty development

Monte-Carlo dosimetry on a realistic cell monolayer geometry exposed to alpha particles

The energy and specific energy absorbed in the main cell compartments (nucleus and cytoplasm) in typical radiobiology experiments are usually estimated by calculations as they are not accessible for a direct measurement. In most of the work, the cell geometry is modelled using the combination of simple mathematical volumes. We propose a method based on high resolution confocal imaging and ion beam analysis (IBA) in order to import realistic cell nuclei geometries in Monte-Carlo simulations and thus take into account the variety of different geometries encountered in a typical cell population. Seventy-six cell nuclei have been imaged using confocal microscopy and their chemical composition has been measured using IBA. A cellular phantom was created from these data using the ImageJ image analysis software and imported in the Geant4 Monte-Carlo simulation toolkit. Total energy and specific energy distributions in the 76 cell nuclei have been calculated for two types of irradiation protocols: a 3 MeV alpha particle microbeam used for targeted irradiation and a 239Pu alpha source used for large angle random irradiation. Qualitative images of the energy deposited along the particle tracks have been produced and show good agreement with images of DNA double strand break signalling proteins obtained experimentally. The methodology presented in this paper provides microdosimetric quantities calculated from realistic cellular volumes. It is based on open-source oriented software that is publicly available

Cottrell Scholars Collaborative New Faculty Workshop: Professional Development for New Chemistry Faculty and Initial Assessment of Its Efficacy

The Cottrell Scholars Collaborative New Faculty Workshop (CSC NFW) is a professional development program that was initiated in 2012 to address absences in the preparation of chemistry faculty at research universities as funded researchers and educators (i.e., teacher–scholars). The primary focus of the workshop is an introduction to evidence-based teaching methods; other topics including mentoring, work–life balance, time management, and grant writing are also addressed. A longer-term aim of the workshop is to develop lifelong teacher–scholars by encouraging workshop participants to engage with teaching-focused faculty learning communities through the CSC NFW and at their institutions. The workshop also provides a platform to investigate the adoption of student-centered pedagogies among new faculty, and a study of that process was initiated concurrently. Thus, the aim of the workshop program is to address professional development needs as well as understand the efficacy of that effort