Measuring overlap in logistic regression

In this paper we show that the recent notion of regression depth can be used as a data-analytic tool to measure the amount of separation between successes and failures in the binary response framework. Extending this algorithm allows us to compute the overlap in data sets which are commonly fitted by logistic regression models. The overlap is the number of observations that would need to be removed to obtain complete or quasicomplete separation, i.e. the situation where the logistic regression parameters are no longer identifiable and the maximum likelihood estimate does not exist. It turns out that the overlap is often quite small

The role of microRNA-155/liver X receptor pathway in experimental and idiopathic pulmonary fibrosis

Background: Idiopathic Pulmonary Fibrosis (IPF) is progressive and rapidly fatal. Improved understanding of pathogenesis is required to prosper novel therapeutics. Epigenetic changes contribute to IPF therefore microRNAs may reveal novel pathogenic pathways. Objectives: To determine the regulatory role of microRNA(miR)-155 in the pro-fibrotic function of murine lung macrophages and fibroblasts, IPF lung fibroblasts and its contribution to experimental pulmonary fibrosis. Methods: Bleomycin-induced lung fibrosis in wild-type and miR-155-/- mice was analyzed by histology, collagen and pro-fibrotic gene expression. Mechanisms were identified by in silico and molecular approaches; validated in mouse lung fibroblasts and macrophages, and in IPF lung fibroblasts, using loss-and-gain of function assays, and in vivo using specific inhibitors. Results: miR-155-/- mice developed exacerbated lung fibrosis, increased collagen deposition, collagen 1 and 3 mRNA expression, TGFβ production, and activation of alternatively-activated macrophages, contributed by deregulation of the microRNA-155 target gene the liver X receptor (LXR)α in lung fibroblasts and macrophages. Inhibition of LXRα in experimental lung fibrosis and in IPF lung fibroblasts reduced the exacerbated fibrotic response. Similarly, enforced expression of miR-155 reduced the pro-fibrotic phenotype of IPF and miR-155-/- fibroblasts. Conclusion: We describe herein a molecular pathway comprising miR-155 and its epigenetic LXRα target that when deregulated enables pathogenic pulmonary fibrosis. Manipulation of the miR-155/LXR pathway may have therapeutic potential for IPF

Progress towards a public chemogenomic set for protein kinases and a call for contributions

Protein kinases are highly tractable targets for drug discovery. However, the biological function and therapeutic potential of the majority of the 500+ human protein kinases remains unknown. We have developed physical and virtual collections of small molecule inhibitors, which we call chemogenomic sets, that are designed to inhibit the catalytic function of almost half the human protein kinases. In this manuscript we share our progress towards generation of a comprehensive kinase chemogenomic set (KCGS), release kinome profiling data of a large inhibitor set (Published Kinase Inhibitor Set 2 (PKIS2)), and outline a process through which the community can openly collaborate to create a KCGS that probes the full complement of human protein kinases

Coupled counterrotating polariton condensates in optically defined annular potentials.

Polariton condensates are macroscopic quantum states formed by half-matter half-light quasiparticles, thus connecting the phenomena of atomic Bose-Einstein condensation, superfluidity, and photon lasing. Here we report the spontaneous formation of such condensates in programmable potential landscapes generated by two concentric circles of light. The imposed geometry supports the emergence of annular states that extend up to 100 μm, yet are fully coherent and exhibit a spatial structure that remains stable for minutes at a time. These states exhibit a petal-like intensity distribution arising due to the interaction of two superfluids counterpropagating in the circular waveguide defined by the optical potential. In stark contrast to annular modes in conventional lasing systems, the resulting standing wave patterns exhibit only minimal overlap with the pump laser itself. We theoretically describe the system using a complex Ginzburg-Landau equation, which indicates why the condensate wants to rotate. Experimentally, we demonstrate the ability to precisely control the structure of the petal condensates both by carefully modifying the excitation geometry as well as perturbing the system on ultrafast timescales to reveal unexpected superfluid dynamics.We acknowledge grants EPSRC EP/G060649/1, EU INDEX 289968, Spanish MEC (MAT2008-01555), Greek GSRT ARISTEIA programs Irakleitos II and Apollo and the Skolkovo Foundation.This version is the author accepted manuscript. The final published version can be found on the PNAS website here: http://www.pnas.org/content/early/2014/05/30/1401988111.abstrac

Human seroreactivity to gut microbiota antigens

Background: Although immune responses directed against antigens from the intestinal microbiota are observed in certain diseases, the normal human adaptive immune response to intestinal microbiota is poorly defined. Objective: Our goal was to assess the adaptive immune response to the intestinal microbiota present in 143 healthy adults and compare this response with the response observed in 52 children and their mothers at risk of having allergic disease. Methods: Human serum was collected from adults and children followed from birth to 7 years of age, and the serum IgG response to a panel of intestinal microbiota antigens was assessed by using a novel protein microarray. Results: Nearly every subject tested, regardless of health status, had serum IgG that recognized a common set of antigens. Seroreactivity to the panel of antigens was significantly lower in atopic adults. Healthy infants expressed the highest level of IgG seroreactivity to intestinal microbiota antigens. This adaptive response developed between 6 and 12 months of age and peaked around 2 years of age. Low IgG responses to certain clusters of microbiota antigens during infancy were associated with allergy development during childhood. Conclusions: There is an observed perturbation of the adaptive response to antigens from the microbiota in allergic subjects. These perturbations are observable even in childhood, suggesting that optimal stimulation of the adaptive immune system by the microbiota might be needed to prevent certain immune-mediated diseases.Funding Agencies|National Institutes of Health [DK071176]; Swedish Research Council [K2011-56X-21854-01-06]; Swedish Heart-Lung Foundation [20050514]; Ekhaga Foundation [210-53]; Research Council for the South-East Sweden; Olle Engqvist Foundation; Swedish Asthma and Allergy Association; Vardal Foundation for Health Care Science and Allergy Research, Sweden [B2007 042]; University Hospital of Linkoping, Sweden</p