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  • 1
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    Normalization of metabolomics data with applications to correlation maps (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-19
    Description: Motivation: In metabolomics, the goal is to identify and measure the concentrations of different metabolites (small molecules) in a cell or a biological system. The metabolites form an important layer in the complex metabolic network, and the interactions between different metabolites are often of interest. It is crucial to perform proper normalization of metabolomics data, but current methods may not be applicable when estimating interactions in the form of correlations between metabolites. We propose a normalization approach based on a mixed model, with simultaneous estimation of a correlation matrix. We also investigate how the common use of a calibration standard in nuclear magnetic resonance (NMR) experiments affects the estimation of correlations. Results : We show with both real and simulated data that our proposed normalization method is robust and has good performance when discovering true correlations between metabolites. The standardization of NMR data is shown in simulation studies to affect our ability to discover true correlations to a small extent. However, comparing standardized and non-standardized real data does not result in any large differences in correlation estimates. Availability and implementation: Source code is freely available at https://sourceforge.net/projects/metabnorm/ Contact: alexandra.jauhiainen@ki.se Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Intermediate state during hiPSC generation [Cell Biology] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-07-24
    Description: Pluripotency can be induced in somatic cells by forced expression of POU domain, class 5, transcription factor 1 (OCT3/4), sex determining region Y-box 2 (SOX2), Kruppel-like factor 4 (KLF4), myelocytomatosis oncogene (c-MYC) (OSKM). However, factor-mediated direct reprogramming is generally regarded as an inefficient and stochastic event. Contrary to this notion,...
    Keywords: Inaugural Articles
    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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  • 3
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    Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1) [Biochemistry] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-06-01
    Description: Methylation of cytosine in DNA plays a crucial role in development through inheritable gene silencing. The DNA methyltransferase Dnmt1 is responsible for the propagation of methylation patterns to the next generation via its preferential methylation of hemimethylated CpG sites in the genome; however, how Dnmt1 maintains methylation patterns is not fully understood. Here we report the crystal structure of the large fragment (291–1620) of mouse Dnmt1 and its complexes with cofactor S-adenosyl-L-methionine and its product S-adenosyl-L-homocystein. Notably, in the absence of DNA, the N-terminal domain responsible for targeting Dnmt1 to replication foci is inserted into the DNA-binding pocket, indicating that this domain must be removed for methylation to occur. Upon binding of S-adenosyl-L-methionine, the catalytic cysteine residue undergoes a conformation transition to a catalytically competent position. For the recognition of hemimethylated DNA, Dnmt1 is expected to utilize a target recognition domain that overhangs the putative DNA-binding pocket. Taking into considerations the recent report of a shorter fragment structure of Dnmt1 that the CXXC motif positions itself in the catalytic pocket and prevents aberrant de novo methylation, we propose that maintenance methylation is a multistep process accompanied by structural changes.
    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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  • 4
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    Morphology and dynamics of Venus's middle clouds with Akatsuki/IR1. (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract The Venusian atmosphere is covered by clouds with super‐rotating winds whose accelerating mechanism is still not well understood. The fastest winds, occurring at the cloud tops (∼70 km height), have been studied for decades thanks to their visual contrast in dayside ultraviolet images. The middle clouds (∼50‐55 km) can be observed at near‐infrared wavelengths (800‐950 nm), although with very low contrast. Here we present the first extensive analysis of their morphology and motions at lower latitudes along 2016 with 900‐nm images from the IR1 camera onboard Akatsuki. The middle clouds exhibit hemispherical asymmetries every 4–5 days, sharp discontinuities in elongated ”hook‐like” stripes, and large contrasts (3‐21%) probably associated with large changes in the optical thickness. Zonal winds obtained with IR1 images and with ground‐based observations reveal mean zonal winds peaking at the equator, while their combination with Venus Express unveils long‐term variations of 20 m s−1 along 10 years.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
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    Spatial coupling of mTOR and autophagy augments secretory phenotypes (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-04-23
    Description: Protein synthesis and autophagic degradation are regulated in an opposite manner by mammalian target of rapamycin (mTOR), whereas under certain conditions it would be beneficial if they occurred in unison to handle rapid protein turnover. We observed a distinct cellular compartment at the trans side of the Golgi apparatus, the TOR-autophagy spatial coupling compartment (TASCC), where (auto)lysosomes and mTOR accumulated during Ras-induced senescence. mTOR recruitment to the TASCC was amino acid- and Rag guanosine triphosphatase-dependent, and disruption of mTOR localization to the TASCC suppressed interleukin-6/8 synthesis. TASCC formation was observed during macrophage differentiation and in glomerular podocytes; both displayed increased protein secretion. The spatial coupling of cells' catabolic and anabolic machinery could augment their respective functions and facilitate the mass synthesis of secretory proteins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426290/" 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/PMC3426290/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Narita, Masako -- Young, Andrew R J -- Arakawa, Satoko -- Samarajiwa, Shamith A -- Nakashima, Takayuki -- Yoshida, Sei -- Hong, Sungki -- Berry, Lorraine S -- Reichelt, Stefanie -- Ferreira, Manuela -- Tavare, Simon -- Inoki, Ken -- Shimizu, Shigeomi -- Narita, Masashi -- DK083491/DK/NIDDK NIH HHS/ -- R01 DK083491/DK/NIDDK NIH HHS/ -- R01 DK083491-03/DK/NIDDK NIH HHS/ -- Cancer Research UK/United Kingdom -- New York, N.Y. -- Science. 2011 May 20;332(6032):966-70. doi: 10.1126/science.1205407. Epub 2011 Apr 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK Cambridge Research Institute (CRI), Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21512002" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/metabolism ; Animals ; *Autophagy ; *Cell Aging ; Cell Line ; Cytoplasm/metabolism ; Cytoplasmic Vesicles/*metabolism/ultrastructure ; Endoplasmic Reticulum, Rough/ultrastructure ; Genes, ras ; Golgi Apparatus/ultrastructure ; HL-60 Cells ; Humans ; Interleukin-6/metabolism ; Interleukin-8/metabolism ; Lysosomes/metabolism/ultrastructure ; Mice ; Monomeric GTP-Binding Proteins/genetics/metabolism ; Nocodazole/pharmacology ; Phagosomes/metabolism/ultrastructure ; Phenotype ; Podocytes/metabolism/ultrastructure ; Protein Biosynthesis ; Proteins/*secretion ; TOR Serine-Threonine Kinases/*metabolism ; Vacuoles/ultrastructure ; trans-Golgi Network/metabolism/ultrastructure
    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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  • 6
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    CELL BIOLOGY. GATA get a hold on senescence (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-09-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cassidy, Liam D -- Narita, Masashi -- New York, N.Y. -- Science. 2015 Sep 25;349(6255):1448-9. doi: 10.1126/science.aad2501.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK. ; University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK. masashi.narita@cruk.cam.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26404812" target="_blank"〉PubMed〈/a〉
    Keywords: Aging/*genetics ; Animals ; Autophagy/*genetics ; Cell Aging/*genetics ; *DNA Damage ; GATA4 Transcription Factor/*metabolism ; Humans ; Inflammation/*genetics
    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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  • 7
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    Simultaneous detection and removal of organomercurial compounds by using the genetic expression system of an organomercury lyase from the transposon Tn MERI1 (2002)
    Springer
    Details
    Publication Date: 2002-06-01
    Print ISSN: 0175-7598
    Electronic ISSN: 1432-0614
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Springer
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  • 8
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    Quantum units from the topological engineering of molecular graphenoids (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Robustly coherent spin centers that can be integrated into devices are a key ingredient of quantum technologies. Vacancies in semiconductors are excellent candidates, and theory predicts that defects in conjugated carbon materials should also display long coherence times. However, the quantum performance of carbon nanostructures has remained stunted by an inability to alter the sp〈sup〉2〈/sup〉-carbon lattice with atomic precision. Here, we demonstrate that topological tailoring leads to superior quantum performance in molecular graphene nanostructures. We unravel the decoherence mechanisms, quantify nuclear and environmental effects, and observe spin-coherence times that outclass most nanomaterials. These results validate long-standing assumptions on the coherent behavior of topological defects in graphene and open up the possibility of introducing controlled quantum-coherent centers in the upcoming generation of carbon-based optoelectronic, electronic, and bioactive systems.〈/p〉
    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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  • 9
    Electronic Resource
    Electronic Resource
    Synthesis of Tetrathiafulvalene-Containing Polyamides (1976)
    s.l. : American Chemical Society
    Macromolecules 9 (1976), S. 360-361 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma60050a036
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    Paper (German National Licenses)
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  • 10
    Electronic Resource
    Electronic Resource
    Pharmacokinetics of an antifibrotic agent, pirfenidone, in haemodialysis patients (1997)
    Springer
    European journal of clinical pharmacology 52 (1997), S. 77-78 
    Details
    ISSN: 1432-1041
    Keywords: Key words Pirfenidone; peritoneal sclerosis ; haemo‐dialysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002280050252
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