Identification of candidate small-molecule therapeutics to cancer by gene-signature perturbation in connectivity mapping.

Connectivity mapping is a recently developed technique for discovering the underlying connections between different biological states based on gene-expression similarities. The sscMap method has been shown to provide enhanced sensitivity in mapping meaningful connections leading to testable biological hypotheses and in identifying drug candidates with particular pharmacological and/or toxicological properties. Challenges remain, however, as to how to prioritise the large number of discovered connections in an unbiased manner such that the success rate of any following-up investigation can be maximised. We introduce a new concept, gene-signature perturbation, which aims to test whether an identified connection is stable enough against systematic minor changes (perturbation) to the gene-signature. We applied the perturbation method to three independent datasets obtained from the GEO database: acute myeloid leukemia (AML), cervical cancer, and breast cancer treated with letrozole. We demonstrate that the perturbation approach helps to identify meaningful biological connections which suggest the most relevant candidate drugs. In the case of AML, we found that the prevalent compounds were retinoic acids and PPAR activators. For cervical cancer, our results suggested that potential drugs are likely to involve the EGFR pathway; and with the breast cancer dataset, we identified candidates that are involved in prostaglandin inhibition. Thus the gene-signature perturbation approach added real values to the whole connectivity mapping process, allowing for increased specificity in the identification of possible therapeutic candidates.

Disowning our shadow: a psychoanalytic approach to understanding punitive public attitudes

Punitive public attitudes cannot be easily explained by pointing to instrumental concerns (e.g., fear of crime, personal victimization, or rea or perceived levels of crime). Instead, numerous observers have suggested that public punitiveness is more a symptom of free-floating anxieties and insecurities resulting from social change than a rational response to crime problems. We argue that these public concerns might be better understood by drawing on the insights of psychoanalytic theory, and we review relevant theoretical work to that effect.

Novel breast cancer biomarkers identified by integrative proteomic and gene expression mapping

Proteomic and transcriptomic platforms both play important roles in cancer research, with differing strengths and limitations. Here, we describe a proteo-transcriptomic integrative strategy for discovering novel cancer biomarkers, combining the direct visualization of differentially expressed proteins with the high-throughput scale of gene expression profiling. Using breast cancer as a case example, we generated comprehensive two-dimensional electrophoresis (2DE)/mass spectrometry (MS) proteomic maps of cancer (MCF-7 and HCC-38) and control (CCD-1059Sk) cell lines, identifying 1724 expressed protein spots representing 484 different protein species. The differentially expressed cell-line proteins were then mapped to mRNA transcript databases of cancer cell lines and primary breast tumors to identify candidate biomarkers that were concordantly expressed at the gene expression level. Of the top nine selected biomarker candidates, we reidentified ANX1, a protein previously reported to be differentially expressed in breast cancers and normal tissues, and validated three other novel candidates, CRAB, 6PGL, and CAZ2, as differentially expressed proteins by immunohistochemistry on breast tissue microarrays. In total, close to half (4/9) of our protein biomarker candidates were successfully validated. Our study thus illustrates how the systematic integration of proteomic and transcriptomic data from both cell line and primary tissue samples can prove advantageous for accelerating cancer biomarker discovery.

Controlling the Shadow Trade

From tackling illicit flows of small arms to combating nuclear smuggling, the shadow trade has become a central target of attempts to control the means of violence. This article argues that much of this practice and literature is framed in unhelpful terms that posit two distinct worlds, an upperworld and underworld, that separates illicit flow networks from the familiar world of state security policy. This implies that the possibilities for controlling the shadow trade are limited or require expansive and expensive controls. The article then examines the formation of illicit flow networks, drawing on examples including narcotics, small arms, nuclear materials, nuclear technology, major conventional arms, dual use technologies, and chemical weapons precursors; and finds that state and hybrid actors rather than extensive private networks are constitutive of illicit networks in many ways. It concludes by reclaiming hope for controlling the means of violence in this hybridity.

Business representation and the UK regions: mapping institutional change

Political devolution in Scotland, Wales and Northern Ireland and the developing regional agenda in England are prompting changes in the organization of business interest representation within the devolved and decentralized territories. In this paper we seek to describe the realignment of business interest representation at the 'regional' scale, first through a detailed review of changes underway across specific business associations and representative fora, and secondly through an initial attempt to compare and 'map' the patterns of institutional change recorded in the various territories. In broad terms the overall scale, operation and degree of formalization of the new political arrangements for business representation tend broadly to reflect the established institutional and political contexts of the respective nations and regions and the level of devolution ceded to the territories. However, there are important variations in a complex process of uneven development. In the concluding section we present some initial thoughts on the nature of the changes observed in the institutional framework for business representation. A key argument is that to date such changes suggest a reconfiguration of business political activity rather than a step-change in the institutional foundation for sub-national business interest representation in the UK. (C) 2003 Elsevier Ltd. All rights reserved.

Mapping biological to clinical phenotypes during the development (21 days) and resolution (21 days) of experimental gingivitis

Aim: To characterize and map temporal changes in the biological and clinical phenotype during a 21-day experimental gingivitis study. Materials and Methods: Experimental gingivitis was induced over 21 days in healthy human volunteers (n = 56), after which normal brushing was resumed (resolution phase). Gingival and plaque indices were assessed. Gingival crevicular fluid was collected from four paired test and contra-lateral control sites in each volunteer during induction (Days 0, 7, 14 and 21) and resolution (Days 28 and 42) of experimental gingivitis. Fluid volumes were measured and a single analyte was quantified from each site-specific, 30s sample. Data were evaluated by analysis of repeated measurements and paired sample tests. Results: Clinical indices and gingival crevicular fluid volumes at test sites increased from Day 0, peaking at Day 21 (test/control differences all p

Mapping a Colonial Borderland: Objectifying the Geo-Body of India's Northeast

India’s Northeast frontier is at the margins of three study areas: South Asia, Southeast Asia, and East Asia. This paper attempts a history of “mapping” in its broader sense as a cultural universal over a relatively long period. It is not a history of cartography, but focuses on the interface between cartography and cosmography, which were, in turn, shaped by imperial power and geographical knowledge. This approach offers a high-altitude view of this Asian borderland as the imperial frontier of both the Mughals and the British, and the national fringe of Republican India. The authors argue that imperial geographical discourses invested the colonial Northeast (British Assam) with a new kind of territorial identity. Surveyors and mapmakers objectified the “geo-body” of this borderland in a spatial fix and visualized it as a Northeast-on-the-map. Cartographic territoriality naturalized traditional frontiers into colonial borderlands, which, in turn, forged national boundaries.