A Bayesian framework to estimate diversification rates and their variation through time and space

Background: Patterns of species diversity are the result of speciation and extinction processes, and molecular phylogenetic data can provide valuable information to derive their variability through time and across clades. Bayesian Markov chain Monte Carlo methods offer a promising framework to incorporate phylogenetic uncertainty when estimating rates of diversification. Results: We introduce a new approach to estimate diversification rates in a Bayesian framework over a distribution of trees under various constant and variable rate birth-death and pure-birth models, and test it on simulated phylogenies. Furthermore, speciation and extinction rates and their posterior credibility intervals can be estimated while accounting for non-random taxon sampling. The framework is particularly suitable for hypothesis testing using Bayes factors, as we demonstrate analyzing dated phylogenies of Chondrostoma (Cyprinids) and Lupinus (Fabaceae). In addition, we develop a model that extends the rate estimation to a meta-analysis framework in which different data sets are combined in a single analysis to detect general temporal and spatial trends in diversification. Conclusions: Our approach provides a flexible framework for the estimation of diversification parameters and hypothesis testing while simultaneously accounting for uncertainties in the divergence times and incomplete taxon sampling

CATRA: Interactive Measuring and Modeling of Cataracts

We introduce an interactive method to assess cataracts in the human eye by crafting an optical solution that measures the perceptual impact of forward scattering on the foveal region. Current solutions rely on highly-trained clinicians to check the back scattering in the crystallin lens and test their predictions on visual acuity tests. Close-range parallax barriers create collimated beams of light to scan through sub-apertures, scattering light as it strikes a cataract. User feedback generates maps for opacity, attenuation, contrast and sub-aperture point-spread functions. The goal is to allow a general audience to operate a portable high-contrast light-field display to gain a meaningful understanding of their own visual conditions. User evaluations and validation with modified camera optics are performed. Compiled data is used to reconstruct the individual's cataract-affected view, offering a novel approach for capturing information for screening, diagnostic, and clinical analysis.Alfred P. Sloan Foundation (Research Fellowship)United States. Defense Advanced Research Projects Agency (Young Faculty Award

Madagascar’s extraordinary biodiversity: Threats and opportunities

Madagascar's unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar's terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as themost prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar

Madagascar’s extraordinary biodiversity: Evolution, distribution, and use

Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique living laboratory for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth's biodiversity

Doppler ultrasonography in evaluation of hemodynamic parameters of transjugular intrahepatic portosystemic shunt (TIPS)

OBJECTIVE. The purpose of the study was to evaluate the long-term clinical efficacy of Doppler sonography in revealing failure of transjugular intrahepatic portosystemic shunt (TIPS). SUBJECTS AND METHODS. Over a five-year period, 1192 Doppler examinations were performed in 21 patients with TIPS. No regular follow-up shunt venograms were performed. Doppler examinations were retrospectively compared to the results of shunt revisions. Negative sonograms were compared to the patients' clinical status so that the number of false negative sonographic findings leading to an episode of shunt failure (recurrence of gastrointestinal bleeding or ascites) could be ascertained. Sonographic parameters assessed included diameter, velocity, flow volume, and congestion index of the portal vein together with shunt velocities. RESULTS. Doppler sonography revealed shunt occlusion in 25 of 26 angiographically proven cases (sensitivity 96%). The combination of velocity criteria (peak intrashunt velocity greater than or equal to 250 cm/sec and/or maximum velocity measured in the portal third of the shunt less than or equal to 50 cm/sec and/or maximum portal vein velocity less than or equal to 2/3 of the baseline value) revealed shunt stenosis in 103 of 110 cases (sensitivity 94%). Within the course of the study, Doppler sonography missed a significant shunt stenosis leading to an episode of gastrointestinal bleeding or ascites recurrence only in seven cases. Congestion index of the portal vein showed significant differences between the groups of patent and malfunctioning shunts (p<0,001). To the best of our knowledge, this is the first study describing the evolution of congestion index before and after TIPS creation and during the long-term follow-up of patients with TIPSAvailable from STL Prague, CZ / NTK - National Technical LibrarySIGLECZCzech Republi

Advances in Computer Science, Engineering & Applications : Proceedings of the Second International Conference on Computer Science, Engineering & Applications

The International conference series on Computer Science, Engineering & Applications (ICCSEA) aims to bring together researchers and practitioners from academia and industry to focus on understanding computer science, engineering and applications and to establish new collaborations in these areas. The Second International Conference on Computer Science, Engineering & Applications (ICCSEA-2012), held in Delhi, India, during May 25-27, 2012 attracted many local and international delegates, presenting a balanced mixture of  intellect and research both from the East and from the West. Upon a strenuous peer-review process the best submissions were selected leading to an exciting, rich and a high quality technical conference program, which featured high-impact presentations in the latest developments of various areas of computer science, engineering and applications research