338 research outputs found

    The Marker State Space (MSS) Method for Classifying Clinical Samples

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    The development of accurate clinical biomarkers has been challenging in part due to the diversity between patients and diseases. One approach to account for the diversity is to use multiple markers to classify patients, based on the concept that each individual marker contributes information from its respective subclass of patients. Here we present a new strategy for developing biomarker panels that accounts for completely distinct patient subclasses. Marker State Space (MSS) defines "marker states" based on all possible patterns of high and low values among a panel of markers. Each marker state is defined as either a case state or a control state, and a sample is classified as case or control based on the state it occupies. MSS was used to define multi-marker panels that were robust in cross validation and training-set/test-set analyses and that yielded similar classification accuracy to several other classification algorithms. A three-marker panel for discriminating pancreatic cancer patients from control subjects revealed subclasses of patients based on distinct marker states. MSS provides a straightforward approach for modeling highly divergent subclasses of patients, which may be adaptable for diverse applications. Β© 2013 Fallon et al

    Differential Requirements for Clathrin-dependent Endocytosis at Sites of Cell–Substrate Adhesion

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    Little is known about the influences of cell–substrate attachment in clathrin-mediated endocytosis. We find that cell–substrate adhesion reduces the rate of endocytosis. In addition, we demonstrate that actin assembly is differentially required for efficient endocytosis, with a stronger requirement for actin dynamics at sites of adhesion

    Stress Generation and Filament Turnover during Actin Ring Constriction

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    We present a physical analysis of the dynamics and mechanics of contractile actin rings. In particular, we analyze the dynamics of ring contraction during cytokinesis in the Caenorhabditis elegans embryo. We present a general analysis of force balances and material exchange and estimate the relevant parameter values. We show that on a microscopic level contractile stresses can result from both the action of motor proteins, which cross-link filaments, and from the polymerization and depolymerization of filaments in the presence of end-tracking cross-linkers

    Vesicular Stomatitis Virus Enters Cells through Vesicles Incompletely Coated with Clathrin That Depend upon Actin for Internalization

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    Many viruses that enter cells by clathrin-dependent endocytosis are significantly larger than the dimensions of a typical clathrin-coated vesicle. The mechanisms by which viruses co-opt the clathrin machinery for efficient internalization remain uncertain. Here we examined how clathrin-coated vesicles accommodate vesicular stomatitis virus (VSV) during its entry into cells. Using high-resolution imaging of the internalization of single viral particles into cells expressing fluorescent clathrin and adaptor molecules, we show that VSV enters cells through partially clathrin-coated vesicles. We found that on average, virus-containing vesicles contain more clathrin and clathrin adaptor molecules than conventional vesicles, but this increase is insufficient to permit full coating of the vesicle. We further show that virus-containing vesicles depend upon the actin machinery for their internalization. Specifically, we found that components of the actin machinery are recruited to virus-containing vesicles, and chemical inhibition of actin polymerization trapped viral particles in vesicles at the plasma membrane. By analysis of multiple independent virus internalization events, we show that VSV induces the nucleation of clathrin for its uptake, rather than depending upon random capture by formation of a clathrin-coated pit. This work provides new mechanistic insights into the process of virus internalization as well as uptake of unconventional cargo by the clathrin-dependent endocytic machinery

    Challenging Masculinity in CSR Disclosures: Silencing of Women’s Voices in Tanzania’s Mining Industry

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    This paper presents a feminist analysis of corporate social responsibility (CSR) in a male-dominated industry within a developing country context. It seeks to raise awareness of the silencing of women’s voices in CSR reports produced by mining companies in Tanzania. Tanzania is one of the poorest countries in Africa, and women are often marginalised in employment and social policy considerations. Drawing on work by HΓ©lΓ¨ne Cixous, a post-structuralist/radical feminist scholar, the paper challenges the masculinity of CSR discourses that have repeatedly masked the voices and concerns of β€˜other’ marginalised social groups, notably women. Using interpretative ethnographic case studies, the paper provides much-needed empirical evidence to show how gender imbalances remain prevalent in the Tanzanian mining sector. This evidence draws attention to the dynamics faced by many women working in or living around mining areas in Tanzania. The paper argues that CSR, a discourse enmeshed with the patriarchal logic of the contemporary capitalist system, is entangled with tensions, class conflicts and struggles which need to be unpacked and acknowledged. The paper considers the possibility of policy reforms in order to promote gender balance in the Tanzanian mining sector and create a platform for women’s concerns to be voiced
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