Developing and applying heterogeneous phylogenetic models with XRate

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog

Quasielastic 12C(e,e'p) Reaction at High Momentum Transfer

We measured the 12C(e,e'p) cross section as a function of missing energy in parallel kinematics for (q,w) = (970 MeV/c, 330 MeV) and (990 MeV/c, 475 MeV). At w=475 MeV, at the maximum of the quasielastic peak, there is a large continuum (E_m > 50 MeV) cross section extending out to the deepest missing energy measured, amounting to almost 50% of the measured cross section. The ratio of data to DWIA calculation is 0.4 for both the p- and s-shells. At w=330 MeV, well below the maximum of the quasielastic peak, the continuum cross section is much smaller and the ratio of data to DWIA calculation is 0.85 for the p-shell and 1.0 for the s-shell. We infer that one or more mechanisms that increase with $\omega$ transform some of the single-nucleon-knockout into multinucleon knockout, decreasing the valence knockout cross section and increasing the continuum cross section.Comment: 14 pages, 7 figures, Revtex (multicol, prc and aps styles), to appear in Phys Rev

The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata)

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ The file attached is the published version of the article

Integrated Methane Inversion (IMI 1.0): a user-friendly, cloud-based facility for inferring high-resolution methane emissions from TROPOMI satellite observations

We present a user-friendly, cloud-based facility for quantifying methane emissions with 0.25∘ × 0.3125∘ (≈ 25 km × 25 km) resolution by inverse analysis of satellite observations from the TROPOspheric Monitoring Instrument (TROPOMI). The facility is built on an Integrated Methane Inversion optimal estimation workflow (IMI 1.0) and supported for use on the Amazon Web Services (AWS) cloud. It exploits the GEOS-Chem chemical transport model and TROPOMI data already resident on AWS, thus avoiding cumbersome big-data download. Users select a region and period of interest, and the IMI returns an analytical solution for the Bayesian optimal estimate of period-average emissions on the 0.25∘ × 0.3125∘ grid including error statistics, information content, and visualization code for inspection of results. The inversion uses an advanced research-grade algorithm fully documented in the literature. An out-of-the-box inversion with rectilinear grid and default prior emission estimates can be conducted with no significant learning curve. Users can also configure their inversions to infer emissions for irregular regions of interest, swap in their own prior emission inventories, and modify inversion parameters. Inversion ensembles can be generated at minimal additional cost once the Jacobian matrix for the analytical inversion has been constructed. A preview feature allows users to determine the TROPOMI information content for their region and time period of interest before actually performing the inversion. The IMI is heavily documented and is intended to be accessible by researchers and stakeholders with no expertise in inverse modelling or high-performance computing. We demonstrate the IMI's capabilities by applying it to estimate methane emissions from the US oil-producing Permian Basin in May 2018.</p

Evidence for Centromere Drive in the Holocentric Chromosomes of Caenorhabditis

In monocentric organisms with asymmetric meiosis, the kinetochore proteins, such as CENH3 and CENP-C, evolve adaptively to counterbalance the deleterious effects of centromere drive, which is caused by the expansion of centromeric satellite repeats. The selection regimes that act on CENH3 and CENP-C genes have not been analyzed in organisms with holocentric chromosomes, although holocentrism is speculated to have evolved to suppress centromere drive. We tested both CENH3 and CENP-C for positive selection in several species of the holocentric genus Caenorhabditis using the maximum likelihood approach and sliding-window analysis. Although CENP-C did not show any signs of positive selection, positive selection has been detected in the case of CENH3. These results support the hypothesis that centromere drive occurs in Nematoda, at least in the telokinetic meiosis of Caenorhabditis

Optical properties of MgH2 measured in situ in a novel gas cell for ellipsometry/spectrophotometry

The dielectric properties of alpha-MgH2 are investigated in the photon energy range between 1 and 6.5 eV. For this purpose, a novel sample configuration and experimental setup are developed that allow both optical transmission and ellipsometric measurements of a transparent thin film in equilibrium with hydrogen. We show that alpha-MgH2 is a transparent, colour neutral insulator with a band gap of 5.6 +/- 0.1 eV. It has an intrinsic transparency of about 80% over the whole visible spectrum. The dielectric function found in this work confirms very recent band structure calculations using the GW approximation by Alford and Chou [J.A. Alford and M.Y. Chou (unpublished)]. As Pd is used as a cap layer we report also the optical properties of PdHx thin films.Comment: REVTeX4, 15 pages, 12 figures, 5 table

Gene expression microarray analysis of early oxygen-induced retinopathy in the rat

Different inbred strains of rat differ in their susceptibility to oxygen-induced retinopathy (OIR), an animal model of human retinopathy of prematurity. We examined gene expression in Sprague–Dawley (susceptible) and Fischer 344 (resistant) neonatal rats after 3 days exposure to cyclic hyperoxia or room air, using Affymetrix rat Genearrays. False discovery rate analysis was used to identify differentially regulated genes. Such genes were then ranked by fold change and submitted to the online database, DAVID. The Sprague–Dawley list returned the term “response to hypoxia,” absent from the Fischer 344 output. Manual analysis indicated that many genes known to be upregulated by hypoxia-inducible factor-1α were downregulated by cyclic hyperoxia. Quantitative real-time RT-PCR analysis of Egln3, Bnip3, Slc16a3, and Hk2 confirmed the microarray results. We conclude that combined methodologies are required for adequate dissection of the pathophysiology of strain susceptibility to OIR in the rat