Effects of passage history and sampling bias on phylogenetic reconstruction of human influenza A evolution

In this paper we determine the extent to which host-mediated mutations and a known sampling bias affect evolutionary studies of human influenza A. Previous phylogenetic reconstruction of influenza A (H3N2) evolution using the hemagglutinin gene revealed an excess of nonsilent substitutions assigned to the terminal branches of the tree. We investigate two hypotheses to explain this observation. The first hypothesis is that the excess reflects mutations that were either not present or were at low frequency in the viral sample isolated from its human host, and that these mutations increased in frequency during passage of the virus in embryonated eggs. A set of 22 codons known to undergo such “host-mediated” mutations showed a significant excess of mutations assigned to branches attaching sequences from egg-cultured (as opposed to cell-cultured) isolates to the tree. Our second hypothesis is that the remaining excess results from sampling bias. Influenza surveillance is purposefully biased toward sequencing antigenically dissimilar strains in an effort to identify new variants that may signal the need to update the vaccine. This bias produces an excess of mutations assigned to terminal branches simply because an isolate with no close relatives is by definition attached to the tree by a relatively long branch. Simulations show that the magnitude of excess mutations we observed in the hemagglutinin tree is consistent with expectations based on our sampling protocol. Sampling bias does not affect inferences about evolution drawn from phylogenetic analyses. However, if possible, the excess caused by host-mediated mutations should be removed from studies of the evolution of influenza viruses as they replicate in their human hosts.

Accurate reconstruction of a known HIV-1 transmission history by phylogenetic tree analysis.

Phylogenetic analyses are increasingly used in attempts to clarify transmission patterns of human immunodeficiency virus type 1 (HIV-1), but there is a continuing discussion about their validity because convergent evolution and transmission of minor HIV variants may obscure epidemiological patterns. Here we have studied a unique HIV-1 transmission cluster consisting of nine infected individuals, for whom the time and direction of each virus transmission was exactly known. Most of the transmissions occurred between 1981 and 1983, and a total of 13 blood samples were obtained approximately 2-12 years later. The p17 gag and env V3 regions of the HIV-1 genome were directly sequenced from uncultured lymphocytes. A true phylogenetic tree was constructed based on the knowledge about when the transmissions had occurred and when the samples were obtained. This complex, known HIV-1 transmission history was compared with reconstructed molecular trees, which were calculated from the DNA sequences by several commonly used phylogenetic inference methods [Fitch-Margoliash, neighbor-joining, minimum-evolution, maximum-likelihood, maximum-parsimony, unweighted pair group method using arithmetic averages (UPGMA), and a Fitch-Margoliash method assuming a molecular clock (KITSCH)]. A majority of the reconstructed trees were good estimates of the true phylogeny; 12 of 13 taxa were correctly positioned in the most accurate trees. The choice of gene fragment was found to be more important than the choice of phylogenetic method and substitution model. However, methods that are sensitive to unequal rates of change performed more poorly (such as UPGMA and KITSCH, which assume a constant molecular clock). The rapidly evolving V3 fragment gave better reconstructions than p17, but a combined data set of both p17 and V3 performed best. The accuracy of the phylogenetic methods justifies their use in HIV-1 research and argues against convergent evolution and selective transmission of certain virus variants.

The best thermoelectric.

What electronic structure provides the largest figure of merit for thermoelectric materials? To answer that question, we write the electrical conductivity, thermopower, and thermal conductivity as integrals of a single function, the transport distribution. Then we derive the mathematical function for the transport distribution, which gives the largest figure of merit. A delta-shaped transport distribution is found to maximize the thermoelectric properties. This result indicates that a narrow distribution of the energy of the electrons participating in the transport process is needed for maximum thermoelectric efficiency. Some possible realizations of this idea are discussed.

In vivo estimates of division and death rates of human T lymphocytes.

We present data on the decay, after radiotherapy, of naive and memory human T lymphocytes with stable chromosome damage. These data are analyzed in conjunction with existing data on the decay of naive and memory T lymphocytes with unstable chromosome damage and older data on unsorted lymphocytes. The analyses yield in vivo estimates for some life-history parameters of human T lymphocytes. Best estimates of proliferation rates have naive lymphocytes dividing once every 3.5 years and memory lymphocytes dividing once every 22 weeks. It appears that memory lymphocytes can revert to the naive phenotype, but only, on average, after 3.5 years in the memory class. The lymphocytes with stable chromosome damage decay very slowly, yielding surprisingly low estimates of their death rate. The estimated parameters are used in a simple mathematical model of the population dynamics of undamaged naive and memory lymphocytes. We use this model to illustrate that it is possible for the unprimed subset of a constantly stimulated clone to stay small, even when there is a large population of specific primed cells reverting to the unprimed state.

Perspectivas em exercício: Uma investigação sobre a lógica administrativa e o engajamento subjetivo no trabalho

Esta pesquisa tem como tema os discursos que circulam e estruturam o ambiente de trabalho nas empresas. De forma geral, busca-se compreender a lógica administrativa que, no limite, exerce uma condução da subjetividade dos trabalhadores. Temos por objetivos: 1) identificar como nas escolas do pensamento administrativo do século XX o engajamento do trabalho é requerido dos trabalhadores; 2) pretendemos discutir uma possível caracterização do discurso e dos usos da administração, como campo de conhecimento sobre o trabalho, dentro das organizações. Para tanto, estabelecemos como panorama teórico-metodológico nas ideias centrais de Michel Foucault em suas análises sobre a funcionalidade do poder e seus dispositivos. Propusemos uma perspectiva arqueogenealógica para a estudar o tema trabalho por meio da lógica da administração e do engajamento. Para estruturar esta análise, selecionamos disciplinas oferecidas e examinamos ementas e referências de leituras nos cursos de graduação da Escola de Administração de Empresas de São Paulo da Fundação Getúlio Vargas (EAESP-FGV) e do curso de Administração da Faculdade de Economia, Administração e Contabilidade da Universidade de São Paulo (FEA-USP). Diante do contato com a discursividade administrativa pudemos formular algumas reflexões. A Administração de Empresas é a ciência da demonstração, pautada na dominação da realidade por uma dita eficiência. É o que se faz produtivo da realidade ou o que se produz nela que se torna científico. Não há discussão, nos registros aqui investigados, de um questionamento sobre o discurso de eficiência, de melhores práticas e da localização das organizações como construções historicamente produzidas, apenas como produtoras de determinações. Não parece haver a possibilidade de desnaturalizar a empresa. A administração parece estar pautada em uma duplicação da dominação como a profissão que é moldada ao moldar o trabalho. Partimos também da análise do que se nomeia engajamento para compreender o que é requerido do trabalhador para além do contrato de trabalho e de sua produtividade material. Neste sentido, o trabalho torna-se uma experiência de educação em contínua e ininterrupta vigilância pedagógica. O efeito moral das técnicas e das provas nas correntes de pensamento da administração permite uma condução técnica e do modo de viver dos trabalhadores. Nesse sentido, a administração, propõe o aperfeiçoamento do cuidado de si no trabalho e para o trabalho. As disciplinas então se duplicam: pelo exterior, por meio da regra pautada na estrutura formal da autoridade da fábrica/empresa com o governo dos corpos; e pelo interior por meio de uma sujeição por identidade, pela estilização da vida

An Analysis of U.S. Air Force Policy and Installation CO2 Emissions to Determine Best Practices for the Implementation of Executive Order 13514

United States Air Force (USAF) energy policy is a measured but aggressive response to federal energy policy guidance. Previous USAF efforts, like those of the federal government, focused primarily on energy intensity reduction, cost, and BTU savings, and in certain cases have resulted in facility greenhouse gas (GHG) emission reductions. The USAF now faces the challenge of integrating GHG reduction goals and inventory requirements set forth in Executive Order 13514. Using USAF reported energy consumption data, facility GHG emission estimates have been synthesized to identify trends and elucidate existing energy best practices to be applied as part of overarching USAF GHG mitigation efforts and to highlight areas of possible concern for the integration of EO 13514 into operational USAF policy.

Russia's best ally: The situation of the Russian oil sector and forecast for its future. OSW Study 39/2012

Oil is a strategic raw material for Russia and one of fundamental significance for the functioning of the state and its future. Taxes on oil production and exports are the most important source of state budget revenues which guarantee Russia maintains its political and economic stability. Russia is building its international position on the basis of its vast raw material and energy potential. While a great number of various publications have been devoted to Russian gas and Gazprom, surprisingly little research has been done into the present condition and possible future developments of the Russian oil sector, despite the fact that oil has and will have a much greater impact than gas on the functioning and the future of Russia. The main objective of this text is to describe the present situation of the Russian oil sector, its problems and the challenges it is posing, as well as the government’s policy towards this key branch of the Russian economy. This will be an introduction to an attempt to answer to the questions about the possible future production and the export levels of Russian oil, also broken down into the European and Asian directions.

Is Independence Possible in an Interdependent World? Scotland vs. the UK's Participation in the European Economy. Bruges European Economic Policy (BEEP) Briefing 30/2013

Many commentators have criticised the strategy used to finance regional governments such as the Scottish Parliament – both the block grant system and the limited amount of fiscal autonomy devised in the Scotland Act of 2012. This lecture sets out to identify what level of autonomy or independence would best suit a regional economy in a currency union, and also the institutional changes needed to sustain those arrangements. Our argument is developed along three lines. First, we set out the advantages of a fiscal federalism framework and the institutions needed to support it, but which the Euro-zone currently lacks. The second is to elaborate a model of fiscal federalism where comprehensive powers of taxation and spending are devolved (an independent Scotland and the UK remain constituent members of the EU and European economy). Third, we evaluate the main arguments for the breakup of nations or economic unions with Scotland and the UK as leading examples. We note that greater autonomy may not result in increases in long run economic growth rate, but it does imply that enhancing the fiscal competence and responsibility of regional governments would result in productivity gains and hence higher levels of GDP per head. That means the population is permanently richer than before, even if ultimately their incomes continue to grow at the same rate. It turns out that these improvements can be achieved through devolved tax powers, but not through devolved spending powers or shared taxes.

The History and Challenges of Cohesion Policies. Jean Monnet/Robert Schuman Paper Series Vol. 14 No. 2, February 2014

From Introduction. Regional economic disequilibria was viewed as both an obstacle to and result of integration (European Commission 1965; European Commission 1962; European Commission 1969). Even within the Treaty of Rome, the Community tried to establish mechanisms to alleviate regional inequality. However, it was not until 1975 that the main mechanism of regional policy was established as a result of British and Irish enlargement: the European Regional Development Fund (ERDF). Since then, cohesion policy has become a significant EU expenditure accounting for €347bn, or 35.7% of the total EU budget for 2007-13(European Commission Regional Policy-Info Regio 2012). It has also become a key policy linked to enlargement. The underlying principle of cohesion policy assumes that the market alone cannot solve development problems and therefore government intervention is needed. This notion is in direct contrast to the underlying principle of EU competition policy, which asserts that the free market can solve economic development problems (Meadows, interview by author, 2003). The logic underlying cohesion policy is not only counter to EU competition policy, but also regulatory policies. Unlike other EU policies, cohesion policy is not a sectoral policy, but rather territorial in nature (Leonardi, 2006). Thus at times EU regulatory policy has also unintentionally worked counter to the goals of regional policy, sometimes disadvantaging poorer regions (Dudek, 2005). As the Community has sought to ameliorate regional disparities, it meant that all levels of government: local, regional, national and supranational would need to be involved, however, member states have different territorial governance and European regional development programs have to varying degrees impacted the relationship and policy responsibility of different levels of government (Leonardi, 2006; Bachtler and Michie 1993; Marks, 1993). The very nature of regional development policy has provoked a re-examination of subsidiarity, or which level of government is the lowest and most appropriate level. The discussion of policy formulation and implementation at the lowest level possible also addresses the issue of the democratic deficit. Some argue that the closer government is to the people the more responsive and representative it is. Democracy, however, also implies that public funds are used in a transparent way and for public rather than private good. Yet, as we examine the history and current situation of EU regional funds we find that corruption and misuse still abound. Thus, to understand the history of regional policy it is imperative to look at the major transformations of the policy, how regional policy has impacted subsidiarity and the quality of democracy, become an important instrument of enlargement and contradicted or conflicted with other EU policies.

Possible Approaches to Commercializing Applied University Research: a Russian Case Study

This paper discusses the environment around universities in Russia and possible approaches to analyzing and choosing the method for applied research results commercialization as well as selecting promising applied research areas in that environment. Conceptual foundations for decision making during the commercialization and roadmap/action plan creation processes are outlined. These can be useful to both universities for planning their activities aswell as for organizations that plan to cooperate with universities or that are interested in university generated research. This being said, obtained models and used evaluation parameters may be unique and may depend upon the particular project, university, region, and personal preferences of decision makers. Thus, consideration of these parameters and characteristics only has merit when making decisions in the dynamics of change of these parameters. For this purpose statistical information is needed that characterizes the competencies of the research organization (university) inquestion, needs of partner organizations, governmental and societal requirements, and science and technology prospects. After determining the promising research areas it’s time to look at particular projects, which in turn are also characterized by various parameters dependent upon their objectives. Considering the values of these parameters in their dynamics allows control of project parameters in the course of its execution. This in turn allows prediction of negative situations and alleviation of such by setting the target values of parameters and using best practices and standardization of management processes to achieve those values.

A bibliography of philosophy : being the sections relating to that subject in the Best books and the Reader's guide /

Mode of access: Internet.

History of Fulton County, Illinois : together with sketches of its cities, villages and townships, educational, civil, military, and political history ...

The reproduction ... made possible through the sponsorship of the Fulton County Historical and Genealogical Society, Canton, Illinois.

Why is history rewritten?

"The publication of this book was made possible by the Lucy Maynard Salmon Fund for Research."--p. [v]

The Literature of all nations and all ages : history, character, and incident /

"One hundred demi-teinte plates from paintings by the world's best artists."