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  • 1
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    Global Ionosphere Estimation Based on Data Fusion From Multisource: Multi‐GNSS, IRI Model, and Satellite Altimetry (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract Traditionally, the ionosphere determination just uses American Global Positioning System and Russian GLObal NAvigation Satellite System dual‐frequency data and has a low precision particularly on oceans. With the rapid development of Chinese BeiDou and European Galileo systems, they are playing an increasingly important role for modeling global ionosphere. Meanwhile, satellite altimetry provides valuable and precise ionosphere delay over the oceans. Through introducing priori ionosphere values from an advanced empirical ionosphere model, combining the advantages of Global Navigation Satellite System (GNSS) and satellite altimetry technologies, the precision of global ionosphere estimation can be further improved. To assess the improvement, we collect satellite altimetry data from Jason‐2/3 and more than 300 global GNSS stations, the data are processed in 2014 and 2018 when the Sun is in a high and a low activity conditions. The results suggest that the ionosphere determination based on multitechnique fusion in a solar‐geomagnetic reference frame is well suitable to represent the ionosphere and its structure. The determined ionosphere achieves a better global consistency, and its formal accuracy is significantly reduced. By comparing with the International GNSS Service products, evaluating by satellite altimetry measurements, and independently validating with ionosonde techniques, it is proved that the ionosphere results are further improved through employing additional available data, especially for the ionosphere over the oceans.
    Print ISSN: 2169-9380
    Electronic ISSN: 2169-9402
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
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    Paracrine Wingless signalling controls self-renewal of Drosophila intestinal stem cells (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-09-23
    Description: In the Drosophila midgut, multipotent intestinal stem cells (ISCs) that are scattered along the epithelial basement membrane maintain tissue homeostasis by their ability to steadily produce daughters that differentiate into either enterocytes or enteroendocrine cells, depending on the levels of Notch activity. However, the mechanisms controlling ISC self-renewal remain elusive. Here we show that a canonical Wnt signalling pathway controls ISC self-renewal. The ligand Wingless (Wg) is specifically expressed in the circular muscles next to ISCs, separated by a thin layer of basement membrane. Reduced function of wg causes ISC quiescence and differentiation, whereas wg overexpression produces excessive ISC-like cells that express high levels of the Notch ligand, Delta. Clonal analysis shows that the main downstream components of the Wg pathway, including Frizzled, Dishevelled and Armadillo, are autonomously required for ISC self-renewal. Furthermore, epistatic analysis suggests that Notch acts downstream of the Wg pathway and a hierarchy of Wg/Notch signalling pathways controls the balance between self-renewal and differentiation of ISCs. These data suggest that the underlying circular muscle constitutes the ISC niche, which produce Wg signals that act directly on ISCs to promote ISC self-renewal. This study demonstrates markedly conserved mechanisms regulating ISCs from Drosophila to mammals. The identification of the Drosophila ISC niche and the principal self-renewal signal will facilitate further understanding of intestinal homeostasis control and tumorigenesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lin, Guonan -- Xu, Na -- Xi, Rongwen -- England -- Nature. 2008 Oct 23;455(7216):1119-23. doi: 10.1038/nature07329. Epub 2008 Sep 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Graduate program, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18806781" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Proliferation ; Drosophila Proteins/*metabolism ; Drosophila melanogaster/*cytology/metabolism ; Female ; Gene Expression Regulation ; Intestines/cytology ; Muscles/metabolism ; *Paracrine Communication ; Receptors, Notch/metabolism ; Signal Transduction ; Stem Cells/*cytology/*metabolism ; Wnt1 Protein/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Stem cell self-renewal controlled by chromatin remodeling factors (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-03
    Description: The self-renewing ability of a stem cell is controlled by its specialized micro-environment or niche, whereas epigenetic regulation of gene expression by chromatin remodeling factors underlies cell fate determination. Here we report that the adenosine triphosphate-dependent chromatin remodeling factors ISWI and DOM control germline stem cell and somatic stem cell self-renewal in the Drosophila ovary, respectively. The iswi mutant germline stem cells are lost rapidly because of defects in responding to bone morphogenetic protein niche signals and in repressing differentiation, whereas the dom mutant somatic stem cells are lost because of defective self-renewal. This work demonstrates that different stem cell types can use different chromatin remodeling factors to control cell self-renewal.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xi, Rongwen -- Xie, Ting -- 1R01 GM64428-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2005 Dec 2;310(5753):1487-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16322456" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*physiology ; Animals ; Bone Morphogenetic Proteins/metabolism ; Cell Division/physiology ; Chromatin Assembly and Disassembly/*physiology ; Drosophila/cytology/enzymology ; Drosophila Proteins/*physiology ; Female ; Gene Expression Regulation ; Mutagenesis ; Ovary/cytology ; Stem Cells/*physiology ; Transcription Factors/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Comprehensive analysis of the chromatin landscape in Drosophila melanogaster (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-12-24
    Description: Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109908/" 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/PMC3109908/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kharchenko, Peter V -- Alekseyenko, Artyom A -- Schwartz, Yuri B -- Minoda, Aki -- Riddle, Nicole C -- Ernst, Jason -- Sabo, Peter J -- Larschan, Erica -- Gorchakov, Andrey A -- Gu, Tingting -- Linder-Basso, Daniela -- Plachetka, Annette -- Shanower, Gregory -- Tolstorukov, Michael Y -- Luquette, Lovelace J -- Xi, Ruibin -- Jung, Youngsook L -- Park, Richard W -- Bishop, Eric P -- Canfield, Theresa K -- Sandstrom, Richard -- Thurman, Robert E -- MacAlpine, David M -- Stamatoyannopoulos, John A -- Kellis, Manolis -- Elgin, Sarah C R -- Kuroda, Mitzi I -- Pirrotta, Vincenzo -- Karpen, Gary H -- Park, Peter J -- R01 GM071923/GM/NIGMS NIH HHS/ -- R01 GM082798/GM/NIGMS NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- R37 GM45744/GM/NIGMS NIH HHS/ -- RC1 HG005334/HG/NHGRI NIH HHS/ -- RC2 HG005639/HG/NHGRI NIH HHS/ -- U01 HG004258/HG/NHGRI NIH HHS/ -- U01 HG004258-04/HG/NHGRI NIH HHS/ -- U01 HG004279/HG/NHGRI NIH HHS/ -- U01HG004258/HG/NHGRI NIH HHS/ -- U54 HG004592/HG/NHGRI NIH HHS/ -- England -- Nature. 2011 Mar 24;471(7339):480-5. doi: 10.1038/nature09725. Epub 2010 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21179089" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Chromatin/*genetics/*metabolism ; Chromatin Immunoprecipitation ; Chromosomal Proteins, Non-Histone/analysis/metabolism ; Deoxyribonuclease I/metabolism ; Drosophila Proteins/genetics ; Drosophila melanogaster/embryology/*genetics/growth & development ; Exons/genetics ; Gene Expression Regulation/genetics ; Genes, Insect/genetics ; Genome, Insect/genetics ; Histones/chemistry/metabolism ; Male ; Molecular Sequence Annotation ; Oligonucleotide Array Sequence Analysis ; Polycomb Repressive Complex 1 ; RNA/analysis/genetics ; Sequence Analysis ; Transcription, Genetic/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Corrigendum: Hallmarks of pluripotency (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-12-18
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉De Los Angeles, Alejandro -- Ferrari, Francesco -- Xi, Ruibin -- Fujiwara, Yuko -- Benvenisty, Nissim -- Deng, Hongkui -- Hochedlinger, Konrad -- Jaenisch, Rudolf -- Lee, Soohyun -- Leitch, Harry G -- Lensch, M William -- Lujan, Ernesto -- Pei, Duanqing -- Rossant, Janet -- Wernig, Marius -- Park, Peter J -- Daley, George Q -- Nature. 2015 Dec 16. doi: 10.1038/nature16470.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26675727" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 6
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    Hallmarks of pluripotency (2015)
    Nature Publishing Group (NPG)
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    Publication Date: 2015-09-25
    Description: Stem cells self-renew and generate specialized progeny through differentiation, but vary in the range of cells and tissues they generate, a property called developmental potency. Pluripotent stem cells produce all cells of an organism, while multipotent or unipotent stem cells regenerate only specific lineages or tissues. Defining stem-cell potency relies upon functional assays and diagnostic transcriptional, epigenetic and metabolic states. Here we describe functional and molecular hallmarks of pluripotent stem cells, propose a checklist for their evaluation, and illustrate how forensic genomics can validate their provenance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉De Los Angeles, Alejandro -- Ferrari, Francesco -- Xi, Ruibin -- Fujiwara, Yuko -- Benvenisty, Nissim -- Deng, Hongkui -- Hochedlinger, Konrad -- Jaenisch, Rudolf -- Lee, Soohyun -- Leitch, Harry G -- Lensch, M William -- Lujan, Ernesto -- Pei, Duanqing -- Rossant, Janet -- Wernig, Marius -- Park, Peter J -- Daley, George Q -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Sep 24;525(7570):469-78. doi: 10.1038/nature15515.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stem Cell Transplantation Program, Division of Pediatric Hematology Oncology, Children's Hospital Boston, and Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA. ; Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA. ; Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA. ; Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA. ; School of Mathematical Sciences and Center for Statistical Science, Peking University, Beijing 100871, China. ; Stem Cell Unit, Department of Genetics, Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel. ; College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. ; Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, Massachusetts 02114, USA. ; Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA. ; Medical Research Council Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom. ; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA. ; South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China. ; The Hospital for Sick Children Research Institute, Toronto, Ontario ON M5G 0A4, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26399828" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Differentiation ; Embryonic Stem Cells/cytology/metabolism ; Genomics ; Humans ; Pluripotent Stem Cells/*cytology/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Metal-free C60/CNTs/g-C3N4 ternary heterostructures: synthesis and enhanced visible-light-driven photocatalytic performance (2018)
    Royal Society
    Details
    Publication Date: 2018-05-17
    Description: A metal-free C 60 /CNTs/g-C 3 N 4 nanoheterostructure with excellent visible-light photocatalysis for rhodamine B (Rh B) degradation has been reported. Via a convenient low-temperature solution-phase method, g-C 3 N 4 nanosheets can serve as substrate for dispersion of C 60 /CNTs. The loading of C 60 /CNTs onto g-C 3 N 4 nanosheets surfaces significantly enhanced visible-light-driven photocatalytic activity of g-C 3 N 4 catalyst, for oxidation of organic pollutant (Rh B, 100%). Excellent photocatalytic properties of C 60 /CNTs/g-C 3 N 4 can be predominantly attributed to the intimate interfacial contact among constructing compounds, increased specific surface area and enhanced light adsorption efficiency resulted from C 60 /CNTs carbon materials. Particularly, the synergistic heterostructure interaction remarkably hinders the electron–hole pairs recombination, giving rise to significantly enhanced photocatalytic performance of C 60 /CNTs/g-C 3 N 4 in comparison with other counterparts.
    Keywords: nanotechnology, photochemistry
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 8
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    Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants (2016)
    Oxford University Press
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    Publication Date: 2016-07-28
    Description: Whole-genome sequencing data allow detection of copy number variation (CNV) at high resolution. However, estimation based on read coverage along the genome suffers from bias due to GC content and other factors. Here, we develop an algorithm called BIC-seq2 that combines normalization of the data at the nucleotide level and Bayesian information criterion-based segmentation to detect both somatic and germline CNVs accurately. Analysis of simulation data showed that this method outperforms existing methods. We apply this algorithm to low coverage whole-genome sequencing data from peripheral blood of nearly a thousand patients across eleven cancer types in The Cancer Genome Atlas (TCGA) to identify cancer-predisposing CNV regions. We confirm known regions and discover new ones including those covering KMT2C, GOLPH3, ERBB2 and PLAG1 . Analysis of colorectal cancer genomes in particular reveals novel recurrent CNVs including deletions at two chromatin-remodeling genes RERE and NPM2 . This method will be useful to many researchers interested in profiling CNVs from whole-genome sequencing data.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-11-07
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion [Biophysics and Computational Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-11-16
    Description: DNA copy number variations (CNVs) play an important role in the pathogenesis and progression of cancer and confer susceptibility to a variety of human disorders. Array comparative genomic hybridization has been used widely to identify CNVs genome wide, but the next-generation sequencing technology provides an opportunity to characterize CNVs genome wide with unprecedented resolution. In this study, we developed an algorithm to detect CNVs from whole-genome sequencing data and applied it to a newly sequenced glioblastoma genome with a matched control. This read-depth algorithm, called BIC-seq, can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion. Using BIC-seq, we identified hundreds of CNVs as small as 40 bp in the cancer genome sequenced at 10× coverage, whereas we could only detect large CNVs (〉 15 kb) in the array comparative genomic hybridization profiles for the same genome. Eighty percent (14/16) of the small variants tested (110 bp to 14 kb) were experimentally validated by quantitative PCR, demonstrating high sensitivity and true positive rate of the algorithm. We also extended the algorithm to detect recurrent CNVs in multiple samples as well as deriving error bars for breakpoints using a Gibbs sampling approach. We propose this statistical approach as a principled yet practical and efficient method to estimate CNVs in whole-genome sequencing data.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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