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      Generation of a microglial developmental index in mice and in humans reveals a sex difference in maturation and immune reactivity : HANAMSAGAR et al.

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          Abstract

          <p class="first" id="P1">Evidence suggests many neurological disorders emerge when normal neurodevelopmental trajectories are disrupted, i.e. when circuits or cells do not reach their fully mature state. Microglia play a critical role in normal neurodevelopment and are hypothesized to contribute to brain disease. We used whole transcriptome profiling with Next Generation sequencing of purified developing microglia to identify a microglial developmental gene expression program involving thousands of genes whose expression levels change monotonically (up or down) across development. Importantly, the gene expression program was delayed in males relative to females and exposure of adult male mice to LPS, a potent immune activator, accelerated microglial development in males. Next, a microglial developmental index (MDI) generated from gene expression patterns obtained from purified mouse microglia, was applied to human brain transcriptome datasets to test the hypothesis that variability in microglial development is associated with human diseases such as Alzheimer’s and autism where microglia have been suggested to play a role. MDI was significantly increased in both Alzheimer’s Disease and in autism, suggesting that accelerated microglial development may contribute to neuropathology. In conclusion, we identified a microglia-specific gene expression program in mice that was used to create a microglia developmental index, which was applied to human datasets containing heterogeneous cell types to reveal differences between healthy and diseased brain samples, and between males and females. This powerful tool has wide ranging applicability to examine microglial development within the context of disease and in response to other variables such as stress and pharmacological treatments. </p><p id="P2"> <div class="figure-container so-text-align-c"> <img alt="" class="figure" src="/document_file/c20d873c-82b1-496b-afef-3a0c5149099e/PubMedCentral/image/nihms877395u1.jpg"/> </div> </p>

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          Most cited references25

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          The operated Markov´s chains in economy (discrete chains of Markov with the income)

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            Cortical inhibitory neurons and schizophrenia.

            Impairments in certain cognitive functions, such as working memory, are core features of schizophrenia. Convergent findings indicate that a deficiency in signalling through the TrkB neurotrophin receptor leads to reduced GABA (gamma-aminobutyric acid) synthesis in the parvalbumin-containing subpopulation of inhibitory GABA neurons in the dorsolateral prefrontal cortex of individuals with schizophrenia. Despite both pre- and postsynaptic compensatory responses, the resulting alteration in perisomatic inhibition of pyramidal neurons contributes to a diminished capacity for the gamma-frequency synchronized neuronal activity that is required for working memory function. These findings reveal specific targets for therapeutic interventions to improve cognitive function in individuals with schizophrenia.
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              Fast R Functions for Robust Correlations and Hierarchical Clustering.

              Many high-throughput biological data analyses require the calculation of large correlation matrices and/or clustering of a large number of objects. The standard R function for calculating Pearson correlation can handle calculations without missing values efficiently, but is inefficient when applied to data sets with a relatively small number of missing data. We present an implementation of Pearson correlation calculation that can lead to substantial speedup on data with relatively small number of missing entries. Further, we parallelize all calculations and thus achieve further speedup on systems where parallel processing is available. A robust correlation measure, the biweight midcorrelation, is implemented in a similar manner and provides comparable speed. The functions cor and bicor for fast Pearson and biweight midcorrelation, respectively, are part of the updated, freely available R package WGCNA.The hierarchical clustering algorithm implemented in R function hclust is an order n(3) (n is the number of clustered objects) version of a publicly available clustering algorithm (Murtagh 2012). We present the package flashClust that implements the original algorithm which in practice achieves order approximately n(2), leading to substantial time savings when clustering large data sets.
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                Author and article information

                Journal
                Glia
                Glia
                Wiley
                08941491
                September 2017
                September 2017
                June 15 2017
                : 65
                : 9
                : 1504-1520
                Affiliations
                [1 ]Department of Pediatrics; Lurie Center for Autism, Massachusetts General Hospital for Children, Harvard Medical School; Boston Massachusetts 02129
                [2 ]Department of Psychiatry; University of Pennsylvania; Philadelphia Pennsylvania 19104
                [3 ]Department of Psychology and Neuroscience; Duke University; Durham North Carolina 27708
                Article
                10.1002/glia.23176
                5540146
                28618077
                f3a086d7-17a1-41d3-863b-5de068c97172
                © 2017

                http://doi.wiley.com/10.1002/tdm_license_1.1

                http://onlinelibrary.wiley.com/termsAndConditions

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