Enclosing the Maximum Likelihood of the Simplest DNA Model Evolving on Fixed Topologies: Towards a Rigorous Framework for Phylogenetic Inference

This issue was undated. The date given is an estimate.14 pages, 1 article*Enclosing the Maximum Likelihood of the Simplest DNA Model Evolving on Fixed Topologies: Towards a Rigorous Framework for Phylogenetic Inference* (Sainudiin, Raazesh) 14 page

Maximum likelihood estimation of Gene family specific duplication and deletion rates

Genes can be divided into gene families, which are defined by homology, and let presume that the genes evolved from a common ancestral gene. In this content the size of a gene family is subject to evolutionary change. We model gene duplications and deletions using a birth-and-death process. Based on the number of gene copies in a set of extant species, we apply a maximum likelihood approach to infer the birth-rate and the death-rate due to duplications and deletions respectively. Furthermore we determine the number of gene copies of the most recent common ancestor. To validate this strategy, we performed simulation studies. Assuming a fixed number of gene copies for the ancestor and specific rates for duplication and deletion of genes, we simulated the evolution of the number of gene copies along a phylogenetic tree. Using our maximum likelihood framework, we subsequently estimated the rates and the ancestral number used for the simulation. A collection of different simulation studies showed that the maximum likelihood approach infers the given parameter quite good. We further applied our method to biological gene family data from vertebrates of the Inparanoid and the Ensembl databases. Compared to previous reported rates our estimates are about one magnitude lower. The data was also considered with regards to model violations, since it is assumed that e.g. large-scale duplication, like whole genome duplications, have occurred during evolution. Hence, extensions of our method and future work are discussed.Genes can be divided into gene families, which are defined by homology, and let presume that the genes evolved from a common ancestral gene. In this content the size of a gene family is subject to evolutionary change. We model gene duplications and deletions using a birth-and-death process. Based on the number of gene copies in a set of extant species, we apply a maximum likelihood approach to infer the birth-rate and the death-rate due to duplications and deletions respectively. Furthermore we determine the number of gene copies of the most recent common ancestor. To validate this strategy, we performed simulation studies. Assuming a fixed number of gene copies for the ancestor and specific rates for duplication and deletion of genes, we simulated the evolution of the number of gene copies along a phylogenetic tree. Using our maximum likelihood framework, we subsequently estimated the rates and the ancestral number used for the simulation. A collection of different simulation studies showed that the maximum likelihood approach infers the given parameter quite good. We further applied our method to biological gene family data from vertebrates of the Inparanoid and the Ensembl databases. Compared to previous reported rates our estimates are about one magnitude lower. The data was also considered with regards to model violations, since it is assumed that e.g. large-scale duplication, like whole genome duplications, have occurred during evolution. Hence, extensions of our method and future work are discussed

Machineries of Oil

Machineries of Oil is an investigation into oil infrastructure in modern society, examining local power struggles over the construction of the global oil industry in a non-western context. This history is crucial for understanding the twentieth-century politics of the Middle East and the peculiar ways in which countries of the Global South have served as irreplaceable laboratories for producing knowledge and know-how on nature and society. This book will come at a time when tensions between the US and Iran, and tensions surrounding the politics of the oil industry in the Middle East in particular, have become unfortunately heightened in the wake of the change in US administration. We feel this book is particularly suited to the Knowledge Unlatched program because our reach to Middle East studies audiences is somewhat limited, and we’d like this book to be available to as many readers as possible, despite limited marketing resources to go beyond our usual channels

Motions 1988 volume 1 number 5

https://digital.sandiego.edu/motions/1004/thumbnail.jp

RISK VS. RISK TRADE-OFFS: PRESIDENTIAL DECISION-MAKING AND THE EMERGENCE OF FOREIGN POLICY CRISES

With the radicalisation of the ‘War on Terror’ and the chaos following the 2003 Iraq War, the concept of ‘risk’ emerged as central to a wide-ranging set of claims about the extent and significance of the changed post-Cold War strategic environment and its impact on policy-making. International Relations (IR) scholars argued that ‘risk’ and ‘risk management’ defined foreign policy-making, with the US as the principal exemplar of such a change. The thesis explores the two, sociologically rooted, accounts of risk that underpin this literature – indebted to Ulrich Beck and Michel Foucault respectively – to identify the deeply contrasting and contradictory conceptualisations of risk they produce. Returning to some classic, and badly neglected, writing on risk and highlighting an alternative account originally developed by John Graham and Jonathan Wiener, the thesis establishes Presidential decision-making in foreign policy as a series of ‘risk versus risk trade-offs.’ This framework focuses on the ways in which risk operates simultaneously in different environments via concepts of ‘political risks’ focusing on the domestic environment and ‘strategic risks’ focusing on the international dimension. The concept of trade-off elucidates the ways in which actions aimed at countering a ‘target risk’ frequently produce ‘countervailing risks’ of their own. Using this approach, the thesis assesses the build-up to three crises in US foreign policy; two from the Cold War (the Cuban Missile Crisis, and the Iran hostage crisis) and one from the post-Cold War period (the road to Srebrenica). The case studies, based on archival research and interviews, effectively challenge the claim that the end of the Cold War represented the onset of an era of foreign policy-making as risk management, by showing how the Kennedy and Carter administrations engaged in policy-making practices and processes that are not markedly dissimilar from Clinton’s. In addition, the case studies enrich the ‘risk literature’ and demonstrate how the analysis of crises can be advanced by understanding the moment of crisis as the culmination of a series of neglected ‘countervailing risks.’ More generally, the thesis points to the initial validity of an approach that can be applied to diverse issues in foreign policy-making

America's Perceptions of Political Islam: Roots of Geopolitical Image and Implications for U.S. Middle East Policy

This thesis examins America's perceptions of Islamism with a view both to identify the geopolitical dynamics that shape the U.S. Middle East prefernces and predict the trajectories of the U.S.-Islamist relations. the importance of this topic lies in the fact that the mainstream Islamism has increasingly established itself as an unrivaled force, emerging as a leading catalyst for change, and hence posing a threat to the U.S.-backed authoritarian power structures. focusing on the presidencies of Bill Clinton (1993-2001), George W. Bush (2001-2009), and Barck Obama (2009-2016), this research seeks to develop an empirical-based argument, offering a compelling interpretation of the post-Cold War's U.S. approaches towards Islamism in power. The outbreak of the Arab Spring at the outset of 2011 further reinforced the centrality of this theme, where moderate Islamists dominated the political scene in Egypt, Tunisa, Libya, and Yemen. The West in general, and the United States in particular, appeared to have depicted Islamism in power as a security threat rather than political challenge. Howvere, This study concludes that the U.S. conceptualizations of the contemporary Politica Islam are primarily rooted in a maltitude of historical, political, and ideological factors

Investing in Development: A Practical Plan to Achieve the Millennium Development Goals

The UN Millennium Project has been a unique undertaking. Its 10 task forces, Secretariat, and broad array of participants from academia, government, UN agencies, international financial institutions, nongovernmental organizations, donor agencies, and the private sector created a worldwide network of development practitioners and experts across an enormous range of countries, disciplines, and organizations. The Project was made possible by the unique commitment, skills, and convictions of the task force coordinators, who led their groups to take on some of the most challenging development questions of our generation, and by the task force members, who gave remarkably of their time. This has been a global effort, in the service of a great global cause—the Millennium Development Goals (MDGs). Our Project has been a microcosm of a larger truth: achieving the Millennium Development Goals will require a global partnership suitable for an interconnected world. The world truly shares a common fate. This has been a labor of love for the many participants in the task forces and Secretariat. Individuals have volunteered vast amounts of effort and expertise to the Project. Their contributions, far beyond any reasonable expectation, have immeasurably sharpened and strengthened the messages contained in the Project’s many outputs, including this report, the task force final reports, the newly developed tools for needs assessment, and the advisory support for MDG-based planning in several countries.https://www.scams.info/unmillenniumproject-org

Network analysis of the cellular circuits of memory

Intuitively, memory is conceived as a collection of static images that we accumulate as we experience the world. But actually, memories are constantly changing through our life, shaped by our ongoing experiences. Assimilating new knowledge without corrupting pre-existing memories is then a critical brain function. However, learning and memory interact: prior knowledge can proactively influence learning, and new information can retroactively modify memories of past events. The hippocampus is a brain region essential for learning and memory, but the network-level operations that underlie the continuous integration of new experiences into memory, segregating them as discrete traces while enabling their interaction, are unknown. Here I show a network mechanism by which two distinct memories interact. Hippocampal CA1 neuron ensembles were monitored in mice as they explored a familiar environment before and after forming a new place-reward memory in a different environment. By employing a network science representation of the co-firing relationships among principal cells, I first found that new associative learning modifies the topology of the cells’ co-firing patterns representing the unrelated familiar environment. I fur- ther observed that these neuronal co-firing graphs evolved along three functional axes: the first segregated novelty; the second distinguished individual novel be- havioural experiences; while the third revealed cross-memory interaction. Finally, I found that during this process, high activity principal cells rapidly formed the core representation of each memory; whereas low activity principal cells gradually joined co-activation motifs throughout individual experiences, enabling cross-memory in- teractions. These findings reveal an organizational principle of brain networks where high and low activity cells are differentially recruited into coactivity motifs as build- ing blocks for the flexible integration and interaction of memories. Finally, I employ a set of manifold learning and related approaches to explore and characterise the complex neural population dynamics within CA1 that underlie sim- ple exploration.Open Acces