955 research outputs found

    A Mutagenetic Tree Hidden Markov Model for Longitudinal Clonal HIV Sequence Data

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    RNA viruses provide prominent examples of measurably evolving populations. In HIV infection, the development of drug resistance is of particular interest, because precise predictions of the outcome of this evolutionary process are a prerequisite for the rational design of antiretroviral treatment protocols. We present a mutagenetic tree hidden Markov model for the analysis of longitudinal clonal sequence data. Using HIV mutation data from clinical trials, we estimate the order and rate of occurrence of seven amino acid changes that are associated with resistance to the reverse transcriptase inhibitor efavirenz.Comment: 20 pages, 6 figure

    Allocating Public Spending Efficiently: Is There a Need for a Better Mechanism to Inform Decisions in the UK and Elsewhere?

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    In the UK few if any regular processes explicitly address comparisons of value for money between spending in different government departments, despite the existence of mechanisms that could in principle achieve that. This leaves a very important gap in evidence and means that decisions about public spending allocations are likely to miss opportunities to improve social welfare from existing budgets. Greater attention to the development of methods and evidence to better inform the allocation of public sector spending between departments is therefore urgently needed. We identify a number of possible approaches to this—some of which are being used in different countries—and highlight their strengths and weaknesses. We propose a new, pragmatic approach that incorporates a generic descriptive system to measure the disparate outcomes produced by public sector activities in a commensurate manner. Discrete-choice experiments could be used to generate evidence of the relative importance placed on different aspects of public sector outcomes by members of the general public. The proposed approach would produce evidence on value for money across departments, and the generation of evidence on public preferences to support that

    Multiple-relaxation-time lattice Boltzmann simulation of natural convection flow in a partitioned cavity using GPU computing

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    © 2019 Author(s). In this paper, we demonstrated the implementation of General Purpose Graphics Processing Unit (GPGPU) programming in Compute Unified Device Architecture (CUDA) C for the simulation of natural convection flow in a side-heated three-dimensional (3D) rectangular cavity with a partition. In the present lattice Boltzmann method (LBM) D3Q19 multiple-relaxation-time (MRT) and D3Q6 single relaxation-time (SRT) model are implemented for the simulation of fluid flow and temperature phenomena, respectively. The parallel code is validated with the benchmark problem of a side heated cubic cavity. The results are presented by the temperature distribution in terms of isotherms, local and average Nusselt number and 3D view of iso-surface for the different Rayleigh number (Ra) and the Prandtl number fixed at Pr = 0.71. It is also observed that the present parallel implementation of the MRT-lattice Boltzmann simulation in GPU has a substantial computational effciency rather than the sequential programming in central processing units (CPU)

    Sea Level Muon Spectrum Below I Tev Range Derived from the Latest Primary Spectrum

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    Governing change: a dynamical systems approach to understanding the stability of environmental governance

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    The ability to adapt to social and environmental change is an increasingly critical feature of environmental governance. However, an understanding of how specific features of governance systems influence how they respond to change is still limited. Here we focus on how system features like diversity, heterogeneity, and connectedness impact stability, which indicates a system's capacity to recover from perturbations. Through a framework that combines agent-based modeling with “generalized” dynamical systems modeling, we model the stability of thousands of governance structures consisting of groups of resource users and non-government organizations interacting strategically with the decision centers that mediate their access to a shared resource. Stabilizing factors include greater effort dedicated to venue shopping and a greater fraction of non-government organizations in the system. Destabilizing factors include greater heterogeneity among actors, a greater diversity of decision centers, and greater interdependence between actors. The results suggest that while complexity tends to be destabilizing, there are mitigating factors that may help balance adaptivity and stability in complex governance. This study demonstrates the potential in applying the insights of complex systems theory to managing complex and highly uncertain human–natural systems in the face of rapid social and environmental change.</p

    Differences in carbon and nitrogen abundances between field and cluster early-type galaxies

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    Central line-strength indices were measured in the blue spectral region for a sample of 98 early-type galaxies in different environments. For most indices (Mgb and in particular) ellipticals in rich clusters and in low-density regions follow the same index-sigma relations. However, striking spectral differences between field ellipticals and their counterparts in the central region of the Coma cluster are found for the first time, with galaxies in the denser environment showing significantly lower C4668 and CN2 absorption strengths. The most convincing interpretation of these results is a difference in abundance ratios, arising from a distinct star formation and chemical enrichment histories of galaxies in different environments. An scenario in which elliptical galaxies in clusters are fully assembled at earlier stages than their low-density counterparts is discussed.Comment: 12 pages, including 3 figures, accepted for publication in ApJ

    Evaluation and Quantification of Angiogenesis Activity of Terminalia Bellirica Roxb, by Mice Sponge Implantation Method

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    Angiogenesis represents an excellent therapeutic target for the treatment of cardiovascular diseases. It is a potent physiological process that underlies the natural manner in which our bodies respond to a diminution of blood supply to vital organs, namely the production of new collateral vessels to overcome the ischemic state. This present study is aimed to evaluate and quantify the Angiogenic potential of Terminalia bellirica Roxb, by in vivo mice sponge implantation assay. Here, gelatin sponge with or without Ethanolic extract of Terminalia bellirica leaf (EETB - 0.3 mg and 0.5 mg, respectively) were subcutaneously injected into Swiss albino mice, and 14 days later, the implanted sponges was excised and histologically examined. The stained section showed that sponge containing EETB had produced more vessels in gels than sponges alone. The new vessels were abundantly filled with intact Red blood corpuscles (RBCs), which indicate the formation of a functional vasculature inside the sponges and blood circulation in newly formed vessels by angiogenesis which is induced by EETB. It also measured that the hemoglobin content inside the sponges: Whereas, hemoglobin in control was nearly 0.3 μg, EETB cases the hemoglobin quantity was markedly enhanced to about 17 μg. Taken together, it demonstrated that Ethanolic extract of Terminalia bellirica leaf exhibited a profound angiogenic activity in vivo. The phytochemical screening and qualitative instrumental analysis of EETB reveals the presence of proteins and Phytosterols. The promising angiogenic potential may be due to the presence of the above chemical constituents. Further study is required to define more precisely the molecular mechanisms by which Ethanolic extract of Terminalia bellirica leaf modulates endothelial cell function and gene expression, as well as the pathological relevance of these findings
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