A new chelonioid turtle from the Paleocene of Cabinda, Angola

Sem PDF.We report a new chelonioid turtle on the basis of a nearly complete skull collected in lower Paleocene, shallow marine deposits, equivalent to the offshore Landana Formation, near the town of Landana in Cabinda Province, Angola. Chelonioid material previously reported from this locality is likely referable to this new taxon. The well-preserved skull is missing the left quadrate, squamosal, and prootic, both opisthotics, and the mandible. The skull possesses a rod-like basisphenoid rostrum, which is a synapomorphy of Chelonioidea, but it differs from other chelonioid skulls in that the contact between the parietal and squamosal is absent, and the posterior palatine foramen is present. Phylogenetic analysis recovers the new taxon as a basal chelonioid. The Paleocenetextendash Eocene strata near Landana have produced a wealth of turtle fossils, including the holotype of the pleurodire Taphrosphys congolensis. A turtle humerus collected from the Landana locality differs morphologically from the humeri of chelonioids and Taphrosphys, indicating the presence of a third taxon. Chelonioid fossil material in the Landana assemblage is rare compared to the abundant fragmentary remains of Taphrosphys that are found throughout the stratigraphic section. This disparity in abundance suggests the new chelonioid taxon preferred open marine habitats, whereas Taphrosphys frequented nearshore environments.publishe

Calculating Ensemble Averaged Descriptions of Protein Rigidity without Sampling

Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently calculated using the integer body-bar Pebble Game (PG) algorithm. However, thermodynamic properties require averaging over many samples from the ensemble of accessible conformations to accurately account for fluctuations in network topology. We have developed a mean field Virtual Pebble Game (VPG) that represents the ensemble of networks by a single effective network. That is, all possible number of distance constraints (or bars) that can form between a pair of rigid bodies is replaced by the average number. The resulting effective network is viewed as having weighted edges, where the weight of an edge quantifies its capacity to absorb degrees of freedom. The VPG is interpreted as a flow problem on this effective network, which eliminates the need to sample. Across a nonredundant dataset of 272 protein structures, we apply the VPG to proteins for the first time. Our results show numerically and visually that the rigidity characterizations of the VPG accurately reflect the ensemble averaged properties. This result positions the VPG as an efficient alternative to understand the mechanical role that chemical interactions play in maintaining protein stability

Learning automata with side-effects

Automata learning has been successfully applied in the verification of hardware and software. The size of the automaton model learned is a bottleneck for scalability, and hence optimizations that enable learning of compact representations are important. This paper exploits monads, both as a mathematical structure and a programming construct, to design and prove correct a wide class of such optimizations. Monads enable the development of a new learning algorithm and correctness proofs, building upon a general framework for automata learning based on category theory. The new algorithm is parametric on a monad, which provides a rich algebraic structure to capture non-determinism and other side-effects. We show that this allows us to uniformly capture existing algorithms, develop new ones, and add optimizations

Cosmology of a Scalar Field Coupled to Matter and an Isotropy-Violating Maxwell Field

Motivated by the couplings of the dilaton in four-dimensional effective actions, we investigate the cosmological consequences of a scalar field coupled both to matter and a Maxwell-type vector field. The vector field has a background isotropy-violating component. New anisotropic scaling solutions which can be responsible for the matter and dark energy dominated epochs are identified and explored. For a large parameter region the universe expands almost isotropically. Using that the CMB quadrupole is extremely sensitive to shear, we constrain the ratio of the matter coupling to the vector coupling to be less than 10^(-5). Moreover, we identify a large parameter region, corresponding to a strong vector coupling regime, yielding exciting and viable cosmologies close to the LCDM limit.Comment: Refs. added, some clarifications. Published in JHEP10(2012)06

Distinct Visual Working Memory Systems for View-Dependent and View-Invariant Representation

Background: How do people sustain a visual representation of the environment? Currently, many researchers argue that a single visual working memory system sustains non-spatial object information such as colors and shapes. However, previous studies tested visual working memory for two-dimensional objects only. In consequence, the nature of visual working memory for three-dimensional (3D) object representation remains unknown. Methodology/Principal Findings: Here, I show that when sustaining information about 3D objects, visual working memory clearly divides into two separate, specialized memory systems, rather than one system, as was previously thought. One memory system gradually accumulates sensory information, forming an increasingly precise view-dependent representation of the scene over the course of several seconds. A second memory system sustains view-invariant representations of 3D objects. The view-dependent memory system has a storage capacity of 3–4 representations and the view-invariant memory system has a storage capacity of 1–2 representations. These systems can operate independently from one another and do not compete for working memory storage resources. Conclusions/Significance: These results provide evidence that visual working memory sustains object information in two separate, specialized memory systems. One memory system sustains view-dependent representations of the scene, akin to the view-specific representations that guide place recognition during navigation in humans, rodents and insects. Th

Enriching Peptide Libraries for Binding Affinity and Specificity Through Computationally Directed Library Design

Peptide reagents with high affinity or specificity for their target protein interaction partner are of utility for many important applications. Optimization of peptide binding by screening large libraries is a proven and powerful approach. Libraries designed to be enriched in peptide sequences that are predicted to have desired affinity or specificity characteristics are more likely to yield success than random mutagenesis. We present a library optimization method in which the choice of amino acids to encode at each peptide position can be guided by available experimental data or structure-based predictions. We discuss how to use analysis of predicted library performance to inform rounds of library design. Finally, we include protocols for more complex library design procedures that consider the chemical diversity of the amino acids at each peptide position and optimize a library score based on a user-specified input model.National Institute of General Medical Sciences (U.S.) (Award R01 GM110048

Low Serum Glutathione Peroxidase Activity Is Associated with Increased Cardiovascular Mortality in Individuals with Low HDLc’s

Background Since oxidized LDL is thought to initiate atherosclerosis and the serum glutathione peroxidase (GPx3) reduces oxidized lipids, we investigated whether high GPx3 activity reduces cardiovascular disease (CVD) mortality. Methods We determined GPx3 in stored samples from the Minnesota Heart Survey of 130 participants who after 5 to 12 years of follow-up had died of CVD and 240 controls. Participants were 26 to 85 years old and predominantly white. In a nested case-control, study we performed logistic regressions to calculate odds ratios (OR) adjusted for age, sex, baseline year, body mass index, smoking, alcohol intake, physical activity, total and HDL cholesterols, systolic blood pressure, serum glucose and gamma glutamyltransferase (GTT) activity. The referent was the quartile with the highest GPx3 activity (quartile 4). Results OR’s for CVD mortality for increasing quartiles of GPx3 were 2.37, 2.14, 1.83 and 1.00 (P for trend 0.02). This inverse correlation was confined to those with HDLc’s below the median (P for interaction, 0.006). The OR’s for increasing quartiles of GPx3 in this group were 6.08, 5.00, 3.64 and 1.00 (P for trend, 0.002). Conclusions Individuals with both low HDLc and GPx3 activity are at markedly increased risk for death from CVD

Traffic Air Pollution and Oxidized LDL

BACKGROUND: Epidemiologic studies indirectly suggest that air pollution accelerates atherosclerosis. We hypothesized that individual exposure to particulate matter (PM) derived from fossil fuel would correlate with plasma concentrations of oxidized low-density lipoprotein (LDL), taken as a marker of atherosclerosis. We tested this hypothesis in patients with diabetes, who are at high risk for atherosclerosis. METHODOLOGY/PRINCIPAL FINDINGS: In a cross-sectional study of non-smoking adult outpatients with diabetes we assessed individual chronic exposure to PM by measuring the area occupied by carbon in airway macrophages, collected by sputum induction and by determining the distance from the patient's residence to a major road, through geocoding. These exposure indices were regressed against plasma concentrations of oxidized LDL, von Willebrand factor and plasminogen activator inhibitor 1 (PAI-1). We could assess the carbon load of airway macrophages in 79 subjects (58 percent). Each doubling in the distance of residence from major roads was associated with a 0.027 µm(2) decrease (95% confidence interval (CI): -0.048 to -0.0051) in the carbon load of airway macrophages. Independently from other covariates, we found that each increase of 0.25 µm(2) [interquartile range (IQR)] in carbon load was associated with an increase of 7.3 U/L (95% CI: 1.3 to 13.3) in plasma oxidized LDL. Each doubling in distance of residence from major roads was associated with a decrease of -2.9 U/L (95% CI: -5.2 to -0.72) in oxidized LDL. Neither the carbon load of macrophages nor the distance from residence to major roads, were associated with plasma von Willebrand factor or PAI-1. CONCLUSIONS: The observed positive association, in a susceptible group of the general population, between plasma oxidized LDL levels and either the carbon load of airway macrophages or the proximity of the subject's residence to busy roads suggests a proatherogenic effect of traffic air pollution