Planktic foraminiferal diversity: logistic growth overprinted by a varying environment

This study statistically assesses the relationship between the planktic foraminiferal long-term diversity pattern (~170 Ma to Recent) and four major paleobiological diversification models: (i) the ‘Red Queen’ (Van Valen, 1973; Raup et al., 1973), (ii) the turnover-pulse (Vrba, 1985; Brett and Baird, 1995), (iii) the diversity-equilibrium (Sepkoski, 1978; Rosenzweig, 1995), and (iv) the ‘complicated logistic growth’ (Alroy, 2010a). Our results suggest that the long-term standing diversity pattern and the interplay between origination and extinction rates displayed by this group do not correspond to the first three models, but can be more readily explained by the fourth scenario. Consequently, these patterns are likely controlled by a combination of planktic foraminiferal interspecific competition as well as various environmental changes such as marine global temperatures that could impacted the niches within the upper mixed layer within the oceans. Moreover, as other global long-term patterns have been interpreted as reflecting ‘complicated logistic growth’, this study further suggests that the interplay between abiotic and biotic factors are fundamental elements influencing the evolutionary processes over the extensive history of the biota.Este estudio evalúa estadísticamente la relación entre el patrón de diversidad global de los foraminíferos planctónicos en el largo plazo (~170 Ma al Reciente) y los cuatro modelos de diversificación propuestos desde la rama de la paleobiología: (i) “Reina Roja” (Van Valen, 1973; Raup et al., 1973), (ii) remplazo pausado (Vrba, 1985; Brett y Baird, 1995), (iii) diversidad en equilibrio (Sepkoski, 1978; Rosenzweig, 1995), y (iv) el “crecimiento logístico complicado” (Alroy, 2010a). Nuestros resultados sugieren que la forma de este patrón global de diversidad y la inter-relación entre las tasas de extinción y originación de este grupo no corresponden con los primeros tres modelos anteriormente citados. Sin embargo, estos pueden ser explicados bajo el cuarto escenario. Consecuentemente, las dinámicas de diversidad (i.e. patrón de diversidad y tasas de extinción y originación) de este grupo posiblemente son controladas por la combinación de la competencia interespecífica de los foraminíferos planctónicos y varios cambios ambientales tales como temperaturas globales marinas que pudieron impactar el número de nichos dentro de la capa superior de los océanos.  Además, otros patrones globales de diversidad en el largo plazo han sido interpretados como el reflejo del modelo de crecimiento logístico complicado, lo que sugiere que la relación entre factores abióticos y bióticos tiene un carácter fundamental en los procesos evolutivos que han sucedido a lo largo de la historia de la vida

Confronting Standard Models of Proto--Planetary Disks With New Mid--Infrared Sizes from the Keck Interferometer

We present near and mid-infrared interferometric observations made with the Keck Interferometer Nuller and near-contemporaneous spectro-photometry from the IRTF of 11 well known young stellar objects, several observed for the first time in these spectral and spatial resolution regimes. With AU-level spatial resolution, we first establish characteristic sizes of the infrared emission using a simple geometrical model consisting of a hot inner rim and mid-infrared disk emission. We find a high degree of correlation between the stellar luminosity and the mid-infrared disk sizes after using near-infrared data to remove the contribution from the inner rim. We then use a semi-analytical physical model to also find that the very widely used "star + inner dust rim + flared disk" class of models strongly fails to reproduce the SED and spatially-resolved mid-infrared data simultaneously; specifically a more compact source of mid-infrared emission is required than results from the standard flared disk model. We explore the viability of a modification to the model whereby a second dust rim containing smaller dust grains is added, and find that the two-rim model leads to significantly improved fits in most cases. This complexity is largely missed when carrying out SED modelling alone, although detailed silicate feature fitting by McClure et al. 2013 recently came to a similar conclusion. As has been suggested recently by Menu et al. 2015, the difficulty in predicting mid-infrared sizes from the SED alone might hint at "transition disk"-like gaps in the inner AU; however, the relatively high correlation found in our mid-infrared disk size vs. stellar luminosity relation favors layered disk morphologies and points to missing disk model ingredients instead

Predicting the long-term impact of antiretroviral therapy scale-up on population incidence of tuberculosis.

OBJECTIVE: To investigate the impact of antiretroviral therapy (ART) on long-term population-level tuberculosis disease (TB) incidence in sub-Saharan Africa. METHODS: We used a mathematical model to consider the effect of different assumptions about life expectancy and TB risk during long-term ART under alternative scenarios for trends in population HIV incidence and ART coverage. RESULTS: All the scenarios we explored predicted that the widespread introduction of ART would initially reduce population-level TB incidence. However, many modelled scenarios projected a rebound in population-level TB incidence after around 20 years. This rebound was predicted to exceed the TB incidence present before ART scale-up if decreases in HIV incidence during the same period were not sufficiently rapid or if the protective effect of ART on TB was not sustained. Nevertheless, most scenarios predicted a reduction in the cumulative TB incidence when accompanied by a relative decline in HIV incidence of more than 10% each year. CONCLUSIONS: Despite short-term benefits of ART scale-up on population TB incidence in sub-Saharan Africa, longer-term projections raise the possibility of a rebound in TB incidence. This highlights the importance of sustaining good adherence and immunologic response to ART and, crucially, the need for effective HIV preventive interventions, including early widespread implementation of ART

The paracladistic approach to phylogenetic taxonomy

The inclusion of some paraphyletic groups in a temporally and taxonomically comprehensive phylogenetic classification is inevitable because cladistic methodology is incapable of excluding the possibility that a structurally (i.e., based on the branching pattern of a given cladogram) monophyletic group contains the ancestor of another group, i.e., that it is historically paraphyletic. Paracladistics is proposed as a pragmatic synthesis of phylogenetic and evolutionary taxonomy in which true monophyly is distinguished from structural monophyly with historical paraphyly, some structurally paraphyletic groups are retained in the interest of nomenclatorial continuity and stability, and both unranked and suprageneric ranked taxon names are defined phylogenetically. Ancestral groups are structurally paraphyletic or structurally monophyletic but historically paraphyletic sets of species that are believed to contain the ancestor for the most recent common ancestor of a descendent group. Historical paraphyly is determined by considering evidence of nesting in cladistic analyses, timing of first appearances in the fossil record, polarity in character evolution, and taxa that are morphologically intermediate between groups of species. The decision to name an ancestral group is based on the same criteria as the decision to name a clade. Ancestral groups are defined in the same manner as clades, except that their descendent group(s) are designated as external specifiers. Recognizing that two supposedly monophyletic, cladistically defined sister taxa can represent ancestral and descendent groups has implications for inferring their times of origination. To illustrate the advantages of the paracladistic approach to phylogenetic taxonomy, alternative paracladistic and phylogenetic classifications of the crown group families of Nuculanoidea (Mollusca, Bivalvia) are presented

Community-based pre-pregnancy care programme improves pregnancy preparation in women with pregestational diabetes.

AIMS/HYPOTHESIS: Women with diabetes remain at increased risk of adverse pregnancy outcomes associated with poor pregnancy preparation. However, women with type 2 diabetes are less aware of and less likely to access pre-pregnancy care (PPC) compared with women with type 1 diabetes. We developed and evaluated a community-based PPC programme with the aim of improving pregnancy preparation in all women with pregestational diabetes. METHODS: This was a prospective cohort study comparing pregnancy preparation measures before and during/after the PPC intervention in women with pre-existing diabetes from 1 June 2013 to 28 February 2017. The setting was 422 primary care practices and ten National Health Service specialist antenatal diabetes clinics. A multifaceted approach was taken to engage women with diabetes and community healthcare teams. This included identifying and sending PPC information leaflets to all eligible women, electronic preconception care templates, online education modules and resources, and regional meetings and educational events. Key outcomes were preconception folic acid supplementation, maternal HbA1c level, use of potentially harmful medications at conception and gestational age at first presentation, before and during/after the PPC programme. RESULTS: A total of 306 (73%) primary care practices actively participated in the PPC programme. Primary care databases were used to identify 5075 women with diabetes aged 18-45 years. PPC leaflets were provided to 4558 (89.8%) eligible women. There were 842 consecutive pregnancies in women with diabetes: 502 before and 340 during/after the PPC intervention. During/after the PPC intervention, pregnant women with type 2 diabetes were more likely to achieve target HbA1c levels ≤48 mmol/mol (6.5%) (44.4% of women before vs 58.5% of women during/after PPC intervention; p = 0.016) and to take 5 mg folic acid daily (23.5% and 41.8%; p = 0.001). There was an almost threefold improvement in 'optimal' pregnancy preparation in women with type 2 diabetes (5.8% and 15.1%; p = 0.021). Women with type 1 diabetes presented for earlier antenatal care during/after PPC (54.0% vs 67.3% before 8 weeks' gestation; p = 0.003) with no other changes. CONCLUSIONS/INTERPRETATION: A pragmatic community-based PPC programme was associated with clinically relevant improvements in pregnancy preparation in women with type 2 diabetes. To our knowledge, this is the first community-based PPC intervention to improve pregnancy preparation for women with type 2 diabetes. DATA AVAILABILITY: Further details of the data collection methodology, individual clinic data and the full audit reports for healthcare professionals and service users are available from https://digital.nhs.uk/data-and-information/clinical-audits-and-registries/our-clinical-audits-and-registries/national-pregnancy-in-diabetes-audit

Confronting standard models of proto-planetary disks with new mid-infrared sizes from the Keck Interferometer

This is the author accepted manuscript. The final version is available from American Astronomical Society/IOP Publishing via the DOI in this record.The published version is in ORE at http://hdl.handle.net/10871/30943We present near and mid–infrared interferometric observations made with the Keck Interferometer Nuller and near–contemporaneous spectro–photometry from the IRTF of 11 well known young stellar objects, several observed for the first time in these spectral and spatial resolution regimes. With AU–level spatial resolution, we first establish characteristic sizes of the infrared emission using a simple geometrical model consisting of a hot inner rim and mid–infrared disk emission. We find a high degree of correlation between the stellar luminosity and the mid–infrared disk sizes after using near–infrared data to remove the contribution from the inner rim. We then use a semi–analytical physical model to also find that the very widely used “star + inner dust rim+ flared disk” class of models strongly fails to reproduce the SED and spatially–resolved mid–infrared data simultaneously; specifically a more compact source of mid–infrared emission is required than results from the standard flared disk model. We explore the viability of a modification to the model whereby a second dust rim containing smaller dust grains is added, and find that the two–rim model leads to significantly improved fits in most cases. This complexity is largely missed when carrying out SED modelling alone, although detailed silicate feature fitting by McClure et al. (2013) recently came to a similar conclusion. As has been suggested recently by Menu et al. (2015), the difficulty in predicting mid–infrared sizes from the SED alone might hint at “transition disk”–like gaps in the inner AU; however, the relatively high correlation found in our mid–infrared disk size vs. stellar luminosity relation favors layered disk morphologies and points to missing disk model ingredients instead.The authors wish to acknowledge fruitful discussions with Nuria Calvet and Melissa McClure. Part of this work was performed while X. C. was a Visiting Graduate Student Research Fellow at the Infrared Processing and Analysis Center (IPAC), California Institute of Technology. The Keck Interferometer was funded by the National Aeronautics and Space Administration as part of its Exoplanet Exploration Program. Data presented herein were obtained at the W.M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W.M. Keck Foundation. The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Mauna Kea has always had within the indigenous Hawaiian community. We are most fortunate to have the opportunity to conduct observations from this mountain. Data presented in this paper were obtained at the Infrared Telescope Facility, which is operated by the University of Hawaii under contract NNH14CK55B with the National Aeronautics and Space Administration. We gratefully acknowledge support and participation in the IRTF/BASS observing runs by Daryl Kim, The Aerospace Corporation. This work has made use of services produced by the NASA Exoplanet Science Institute at the California Institute of Technology. M. S. was supported by NASA ADAP grant NNX09AC73G. R. W. R. was supported by the IR&D program of The Aerospace Corporatio

Genetic Incorporation of Unnatural Amino Acids into Proteins in Mycobacterium tuberculosis

New tools are needed to study the intracellular pathogen Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), to facilitate new drug discovery and vaccine development. We have developed methodology to genetically incorporate unnatural amino acids into proteins in Mycobacterium smegmatis, BCG and Mtb, grown both extracellularly in culture and inside host cells. Orthogonal mutant tRNATyr/tyrosyl-tRNA synthetase pairs derived from Methanococcus jannaschii and evolved in Escherichia coli incorporate a variety of unnatural amino acids (including photocrosslinking, chemically reactive, heavy atom containing, and immunogenic amino acids) into proteins in response to the amber nonsense codon. By taking advantage of the fidelity and suppression efficiency of the MjtRNA/pIpaRS pair in mycobacteria, we are also able to use p-iodophenylalanine to induce the expression of proteins in mycobacteria both extracellularly in culture and inside of mammalian host cells. This provides a new approach to regulate the expression of reporter genes or mycobacteria endogenous genes of interest. The establishment of the unnatural amino acid expression system in Mtb, an intracellular pathogen, should facilitate studies of TB biology and vaccine development

Spectropolarimetry of the Type Ib Supernova iPTF 13bvn: revealing the complex explosion geometry of a stripped-envelope core-collapse supernova

We present six epochs of spectropolarimetric observations and one epoch of spectroscopy of the Type Ib SN iPTF 13bvn. The epochs of these observations correspond to −10 to +61 d with respect to the r-band light-curve maximum. The continuum is intrinsically polarized to the 0.2–0.4 per cent level throughout the observations, implying asphericities of ∼10 per cent in the shape of the photosphere. We observe significant line polarization associated with the spectral features of Ca II IR3, He I/Na I D, He I λλ6678, 7065, Fe II λ4924 and O I λ7774. We propose that an absorption feature at ∼6200 Å, usually identified as Si II λ6355, is most likely to be high-velocity H α at −16 400 km s−1. Two distinctly polarized components, separated in velocity, are detected for both He I/Na I D and Ca II IR3 , indicating the presence of two discrete line-forming regions in the ejecta in both radial velocity space and in the plane of the sky. We use the polarization of He I λ5876 as a tracer of sources of non-thermal excitation in the ejecta; finding that the bulk of the radioactive nickel was constrained to lie interior to ∼50–65 per cent of the ejecta radius. The observed polarization is also discussed in the context of the possible progenitor system of iPTF 13bvn, with our observations favouring the explosion of a star with an extended, distorted envelope rather than a compact Wolf–Rayet star