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  • 1
    Publication Date: 2012-03-15
    Description: The aim of this work is to explore the effectiveness of theoretical information approaches for the reduction of data complexity in multimodel ensemble systems. We first exploit a weak form of independence, i.e. uncorrelation, as a mechanism for detecting linear relationships. Then, stronger and more general forms of independence measure, such as mutual information, are used to investigate dependence structures for model selection. A distance matrix, measuring the interdependence between data, is derived for the investigated measures, with the scope of clustering correlated/dependent models together. Redundant information is discarded by selecting a few representative models from each cluster. We apply the clustering analysis in the context of atmospheric dispersion modeling, by using the ETEX-1 data set. We show how the selection of a small subset of models, according to uncorrelation or mutual information distance criteria, usually suffices to achieve a statistical performance comparable to, or even better than, that achieved from the whole ensemble data set, thus providing a simpler description of ensemble results without sacrificing accuracy.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
    Publication Date: 2013-02-20
    Description: Paternal duplications of chromosome 6q24, a region that contains the imprinted PLAGL1 and HYMAI transcripts, are associated with transient neonatal diabetes mellitus. A common feature of imprinted genes is that they tend to cluster together, presumably as a result of sharing common cis -acting regulatory elements. To determine the extent of this imprinted cluster in human and mouse, we have undertaken a systematic analysis of allelic expression and DNA methylation of the genes mapping within an ~1.4-Mb region flanking PLAGL1/Plagl1 . We confirm that all nine neighbouring genes are biallelically expressed in both species. In human we identify two novel paternally expressed PLAGL1 coding transcripts that originate from unique promoter regions. Chromatin immunoprecipitation for CTCF and the cohesin subunits RAD21 and SMC3 reveals evolutionarily conserved binding sites within unmethylated regions ~5 kb downstream of the PLAGL1 differentially methylated region and within the PLAGL1 3' untranslated region (UTR). Higher-order chromatin looping occurs between these regions in both expressing and non-expressing tissues, forming a non-allelic chromatin loop around the PLAGL1/Plagl1 gene. In placenta and brain tissues, we identify an additional interaction between the PLAGL1 P3/P4 promoters and the unmethylated element downstream of the PLAGL1 differentially methylated region that we propose facilitates imprinted expression of these alternative isoforms.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2011-12-28
    Description: Analytical Chemistry DOI: 10.1021/ac2031805
    Print ISSN: 0003-2700
    Electronic ISSN: 1520-6882
    Topics: Chemistry and Pharmacology
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  • 4
    Publication Date: 2014-07-04
    Description: CXCR4 and CXCR7 transduce through mTOR in human renal cancer cells Cell Death and Disease 5, e1310 (July 2014). doi:10.1038/cddis.2014.269 Authors: C Ieranò, S Santagata, M Napolitano, F Guardia, A Grimaldi, E Antignani, G Botti, C Consales, A Riccio, M Nanayakkara, M V Barone, M Caraglia & S Scala
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 5
    Publication Date: 1999-12-22
    Description: Nerve growth factor (NGF) and other neurotrophins support survival of neurons through processes that are incompletely understood. The transcription factor CREB is a critical mediator of NGF-dependent gene expression, but whether CREB family transcription factors regulate expression of genes that contribute to NGF-dependent survival of sympathetic neurons is unknown. CREB-mediated gene expression was both necessary for NGF-dependent survival and sufficient on its own to promote survival of sympathetic neurons. Moreover, expression of Bcl-2 was activated by NGF and other neurotrophins by a CREB-dependent transcriptional mechanism. Overexpression of Bcl-2 reduced the death-promoting effects of CREB inhibition. Together, these data support a model in which neurotrophins promote survival of neurons, in part through a mechanism involving CREB family transcription factor-dependent expression of genes encoding prosurvival factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Riccio, A -- Ahn, S -- Davenport, C M -- Blendy, J A -- Ginty, D D -- NS34814-04/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 1999 Dec 17;286(5448):2358-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10600750" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis ; Axons/drug effects/metabolism ; Brain-Derived Neurotrophic Factor/pharmacology ; Cell Nucleus/metabolism ; Cell Survival ; Cells, Cultured ; Cyclic AMP Response Element-Binding Protein/antagonists & inhibitors/*metabolism ; *Gene Expression Regulation ; Genes, bcl-2 ; Genetic Vectors ; Nerve Growth Factor/*pharmacology ; Neurons/*cytology/drug effects/metabolism ; PC12 Cells ; Promoter Regions, Genetic ; Proto-Oncogene Proteins c-bcl-2/genetics/metabolism ; Rats ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Sympathetic Nervous System/*cytology/drug effects/metabolism ; Transfection
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 1997-08-22
    Description: Nerve growth factor (NGF) is a neurotrophic factor secreted by cells that are the targets of innervation of sympathetic and some sensory neurons. However, the mechanism by which the NGF signal is propagated from the axon terminal to the cell body, which can be more than 1 meter away, to influence biochemical events critical for growth and survival of neurons has remained unclear. An NGF-mediated signal transmitted from the terminals and distal axons of cultured rat sympathetic neurons to their nuclei regulated phosphorylation of the transcription factor CREB (cyclic adenosine monophosphate response element-binding protein). Internalization of NGF and its receptor tyrosine kinase TrkA, and their transport to the cell body, were required for transmission of this signal. The tyrosine kinase activity of TrkA was required to maintain it in an autophosphorylated state upon its arrival in the cell body and for propagation of the signal to CREB within neuronal nuclei. Thus, an NGF-TrkA complex is a messenger that delivers the NGF signal from axon terminals to cell bodies of sympathetic neurons.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Riccio, A -- Pierchala, B A -- Ciarallo, C L -- Ginty, D D -- New York, N.Y. -- Science. 1997 Aug 22;277(5329):1097-100.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neuroscience, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9262478" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Newborn ; *Axonal Transport ; Axons/*metabolism ; Carbazoles/pharmacology ; Cell Membrane/metabolism ; Cells, Cultured ; Cyclic AMP Response Element-Binding Protein/*metabolism ; Indole Alkaloids ; Microspheres ; Nerve Growth Factors/*metabolism/pharmacology ; Neurons/*metabolism ; Phosphorylation ; Proto-Oncogene Proteins/antagonists & inhibitors/*metabolism ; Rats ; Receptor Protein-Tyrosine Kinases/antagonists & inhibitors/*metabolism ; Receptor, trkA ; Receptors, Nerve Growth Factor/antagonists & inhibitors/*metabolism ; Signal Transduction ; Superior Cervical Ganglion/cytology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2011-11-05
    Description: Non-mammalian vertebrates have an intrinsically photosensitive iris and thus a local pupillary light reflex (PLR). In contrast, it is thought that the PLR in mammals generally requires neuronal circuitry connecting the eye and the brain. Here we report that an intrinsic component of the PLR is in fact widespread in nocturnal and crepuscular mammals. In mouse, this intrinsic PLR requires the visual pigment melanopsin; it also requires PLCbeta4, a vertebrate homologue of the Drosophila NorpA phospholipase C which mediates rhabdomeric phototransduction. The Plcb4(-/-) genotype, in addition to removing the intrinsic PLR, also essentially eliminates the intrinsic light response of the M1 subtype of melanopsin-expressing, intrinsically photosensitive retinal ganglion cells (M1-ipRGCs), which are by far the most photosensitive ipRGC subtype and also have the largest response to light. Ablating in mouse the expression of both TRPC6 and TRPC7, members of the TRP channel superfamily, also essentially eliminated the M1-ipRGC light response but the intrinsic PLR was not affected. Thus, melanopsin signalling exists in both iris and retina, involving a PLCbeta4-mediated pathway that nonetheless diverges in the two locations.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3270891/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3270891/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xue, T -- Do, M T H -- Riccio, A -- Jiang, Z -- Hsieh, J -- Wang, H C -- Merbs, S L -- Welsbie, D S -- Yoshioka, T -- Weissgerber, P -- Stolz, S -- Flockerzi, V -- Freichel, M -- Simon, M I -- Clapham, D E -- Yau, K-W -- EY14596/EY/NEI NIH HHS/ -- R01 DC006904/DC/NIDCD NIH HHS/ -- R01 DC006904-07/DC/NIDCD NIH HHS/ -- R01 DC006904-08/DC/NIDCD NIH HHS/ -- R01 DC006904-09/DC/NIDCD NIH HHS/ -- R01 EY006837/EY/NEI NIH HHS/ -- R01 EY006837-22/EY/NEI NIH HHS/ -- R01 EY006837-23/EY/NEI NIH HHS/ -- R01 EY006837-24/EY/NEI NIH HHS/ -- R37 EY006837/EY/NEI NIH HHS/ -- R37 EY006837-13/EY/NEI NIH HHS/ -- R37 EY006837-14/EY/NEI NIH HHS/ -- R37 EY006837-15/EY/NEI NIH HHS/ -- R37 EY006837-15S1/EY/NEI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Nov 2;479(7371):67-73. doi: 10.1038/nature10567.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA. txue77@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22051675" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Iris/anatomy & histology/cytology/*metabolism/*radiation effects ; Light Signal Transduction/physiology/*radiation effects ; Mammals/*physiology ; Mice ; Phospholipase C beta/metabolism ; Photic Stimulation ; Primates/physiology ; Reflex, Pupillary/physiology/radiation effects ; Retina/cytology/*metabolism/*radiation effects ; Retinal Ganglion Cells/metabolism/radiation effects ; Rod Opsins/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Computing and visualization in science 2 (1999), S. 1-13 
    ISSN: 1433-0369
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract. In this paper we analyze the efficiency of some stiff ode solvers, applied to the coupled solution of vertical turbulent diffusion and chemical kinetics in Air Quality Models. We consider four general-purpose solvers, based on bdf or Rosenbrock methods, and two special-purpose solvers, developed for odes from atmospheric chemistry, and compare their performance on three test problems using different chemical models. The general-purpose solvers have been modified to take advantage of the sparsity of the Jacobian matrices arising in the application of implicit methods. The obtained results show that general-purpose solvers, provided with suitable sparse matrix techniques, perform generally better than special-purpose ones. Our analysis extends to the diffusion-reaction equations the recent work of other research groups, comparing ode solvers on atmospheric chemical kinetics equations.
    Type of Medium: Electronic Resource
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  • 9
  • 10
    Publication Date: 2013-11-04
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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