Re-imagining the Borders of US Security after 9/11: Securitisation, Risk, and the Creation of the Department of Homeland Security

The articulation of international and transnational terrorism as a key issue in US security policy, as a result of the 9/11 attacks, has not only led to a policy rethink, it has also included a bureaucratic shift within the US, showing a re-thinking of the role of borders within US security policy. Drawing substantively on the 'securitisation' approach to security studies, the article analyses the discourse of US security in order to examine the founding of the Department of Homeland Security, noting that its mission provides a new way of conceptualising 'borders' for US national security. The securitisation of terrorism is, therefore, not only represented by marking terrorism as a security issue, it is also solidified in the organisation of security policy-making within the US state. As such, the impact of a 'war on terror' provides an important moment for analysing the re-articulation of what security is in the US, and, in theoretical terms, for reaffirming the importance of a relationship between the production of threat and the institutionalisation of threat response. © 2007 Taylor & Francis

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton: Fish phenotypes

The rich phenotypic diversity that characterizes the vertebrate skeleton results from evolutionary changes in regulation of genes that drive development. Although relatively little is known about the genes that underlie the skeletal variation among fish species, significant knowledge of genetics and development is available for zebrafish. Because developmental processes are highly conserved, this knowledge can be leveraged for understanding the evolution of skeletal diversity. We developed the Phenoscape Knowledgebase (KB; http://kb.phenoscape.org) to yield testable hypotheses of candidate genes involved in skeletal evolution. We developed a community anatomy ontology for fishes and ontology-based methods to represent complex free-text character descriptions of species in a computable format. With these tools, we populated the KB with comparative morphological data from the literature on over 2500 teleost fishes (mainly Ostariophysi) resulting in over 500,000 taxon phenotype annotations. The KB integrates these data with similarly structured phenotype data from zebrafish genes (http://zfin.org). Using ontology-based reasoning, candidate genes can be inferred for the phenotypes that vary across taxa, thereby uniting genetic and phenotypic data to formulate evo-devo hypotheses. The morphological data in the KB can be browsed, sorted, and aggregated in ways that provide unprecedented possibilities for data mining and discovery

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex

BackgroundPhenex (http://phenex.phenoscape.org/) is a desktop application for semantically annotating the phenotypic character matrix datasets common in evolutionary biology. Since its initial publication, we have added new features that address several major bottlenecks in the efficiency of the phenotype curation process: allowing curators during the data curation phase to provisionally request terms that are not yet available from a relevant ontology; supporting quality control against annotation guidelines to reduce later manual review and revision; and enabling the sharing of files for collaboration among curators.ResultsWe decoupled data annotation from ontology development by creating an Ontology Request Broker (ORB) within Phenex. Curators can use the ORB to request a provisional term for use in data annotation; the provisional term can be automatically replaced with a permanent identifier once the term is added to an ontology. We added a set of annotation consistency checks to prevent common curation errors, reducing the need for later correction. We facilitated collaborative editing by improving the reliability of Phenex when used with online folder sharing services, via file change monitoring and continual autosave.ConclusionsWith the addition of these new features, and in particular the Ontology Request Broker, Phenex users have been able to focus more effectively on data annotation. Phenoscape curators using Phenex have reported a smoother annotation workflow, with much reduced interruptions from ontology maintenance and file management issues

Open Science principles for accelerating trait-based science across the Tree of Life.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges

Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation

A novel method for quantifying the similarity between phenotypes by the use of ontologies can be used to search for candidate genes, pathway members, and human disease models on the basis of phenotypes alone

Conceptualising and historicising the US foreign policy establishment in a racialised class structure

In recent years critical scholars of U.S. foreign policy have challenged the mainstream paradigm that fails to account for the racial dimensions of international relations. This article introduces a conceptual and historical analysis of the US foreign policy establishment that posits race and racism at its centre. While alluding to conventional theories of American power such as pluralism and statism, the article also highlights classical Marxism’s failure to acknowledge that US exceptionalism and racism conjoined in a manner that conferred a racial dimension to class politics. The article argues that the U.S. foreign policy establishment has been presided over by an elite or ruling elite; and irrespective of challenges from below, increasing diversity, or the insistence that America is a meritocratic classless society, the U.S establishment is at heart, elitist, racialised and generally Anglo-centric. The article identifies links between the racial dimensions of U.S. foreign policy and the identity profile of the power elite. The paper extends and critiques C. Wright Mills’ definition of the power elite by mapping its racial dimension. Finally the article argues that although the election of Obama represented a more inclusive and cosmopolitan version of the establishment, Obama’s presence has helped to consolidate the status quo as the structural constraints on the executive branch and symbolism associated with the election of the first African-American president has generally silenced the Left and quietly fostered the suggestion that an unconventional identity profile will not necessarily result in the change we can believe in

Cathepsin L Inhibition Prevents Murine Autoimmune Diabetes via Suppression of CD8+ T Cell Activity

Background: Type 1 diabetes (T1D) is an autoimmune disease resulting from defects in central and peripheral tolerance and characterized by T cell-mediated destruction of islet b cells. To determine whether specific lysosomal proteases might influence the outcome of a T cell–mediated autoimmune response, we examined the functional significance of cathepsin inhibition on autoimmune T1D-prone non-obese diabetic (NOD) mice. Methods and Findings: Here it was found that specific inhibition of cathepsin L affords strong protection from cyclophosphamide (CY)-induced insulitis and diabetes of NOD mice at the advanced stage of CD8 + T cell infiltration via inhibiting granzyme activity. It was discovered that cathepsin L inhibition prevents cytotoxic activity of CD8 + T cells in the pancreatic islets through controlling dipeptidyl peptidase I activity. Moreover, the gene targeting for cathepsin L with application of in vivo siRNA administration successfully prevented CY-induced diabetes of NOD mice. Finally, cathepsin L mRNA expression of peripheral CD8 + T cells from NOD mice developing spontaneous T1D was significantly increased compared with that from control mice. Conclusions: Our results identified a novel function of cathepsin L as an enzyme whose activity is essential for the progression of CD8 + T cell-mediated autoimmune diabetes, and inhibition of cathepsin L as a powerful therapeutic strateg

A critical appraisal of appendage disparity and homology in fishes

Fishes are both extremely diverse and morphologically disparate. Part of this disparity can be observed in the numerous possible fin configurations that may differ in terms of the number of fins as well as fin shapes, sizes and relative positions on the body. Here, we thoroughly review the major patterns of disparity in fin configurations for each major group of fishes and discuss how median and paired fin homologies have been interpreted over time. When taking into account the entire span of fish diversity, including both extant and fossil taxa, the disparity in fin morphologies greatly complicates inferring homologies for individual fins. Given the phylogenetic scope of this review, structural and topological criteria appear to be the most useful indicators of fin identity. We further suggest that it may be advantageous to consider some of these fin homologies as nested within the larger framework of homologous fin‐forming morphogenetic fields. We also discuss scenarios of appendage evolution and suggest that modularity may have played a key role in appendage disparification. Fin modules re‐expressed within the boundaries of fin‐forming fields could explain how some fins may have evolved numerous times independently in separate lineages (e.g., adipose fin), or how new fins may have evolved over time (e.g., anterior and posterior dorsal fins, pectoral and pelvic fins). We favour an evolutionary scenario whereby median appendages appeared from a unique field of competence first positioned throughout the dorsal and ventral midlines, which was then redeployed laterally leading to paired appendages.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151971/1/faf12402_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151971/2/faf12402.pd

Finding Our Way through Phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility