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  • 1
    Publication Date: 2013-12-29
    Description: MicroRNAs (miRNAs) are small non-coding RNA molecules capable of negatively regulating gene expression to control many cellular mechanisms. The miRTarBase database ( http://mirtarbase.mbc.nctu.edu.tw/ ) provides the most current and comprehensive information of experimentally validated miRNA-target interactions. The database was launched in 2010 with data sources for 〉100 published studies in the identification of miRNA targets, molecular networks of miRNA targets and systems biology, and the current release (2013, version 4) includes significant expansions and enhancements over the initial release (2010, version 1). This article reports the current status of and recent improvements to the database, including (i) a 14-fold increase to miRNA-target interaction entries, (ii) a miRNA-target network, (iii) expression profile of miRNA and its target gene, (iv) miRNA target-associated diseases and (v) additional utilities including an upgrade reminder and an error reporting/user feedback system.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2015-01-16
    Description: We present MethHC ( http://MethHC.mbc.nctu.edu.tw ), a database comprising a systematic integration of a large collection of DNA methylation data and mRNA/microRNA expression profiles in human cancer. DNA methylation is an important epigenetic regulator of gene transcription, and genes with high levels of DNA methylation in their promoter regions are transcriptionally silent. Increasing numbers of DNA methylation and mRNA/microRNA expression profiles are being published in different public repositories. These data can help researchers to identify epigenetic patterns that are important for carcinogenesis. MethHC integrates data such as DNA methylation, mRNA expression, DNA methylation of microRNA gene and microRNA expression to identify correlations between DNA methylation and mRNA/microRNA expression from TCGA (The Cancer Genome Atlas), which includes 18 human cancers in more than 6000 samples, 6548 microarrays and 12 567 RNA sequencing data.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2015-07-23
    Description: Background Chidamide is a novel benzamide type of subtype-selective histone deacetylase (HDAC) inhibitor with unique mechanisms of action compared with marketed HDAC inhibitors. This phase II study was to evaluate the efficacy and safety of chidamide in relapsed or refractory peripheral T-cell lymphoma (PTCL) in Chinese population. Patients and methods Patients with relapsed or refractory PTCL of different subtypes received chidamide of 30 mg orally twice per week. The primary end point was overall response rate (ORR). Responding patients should be confirmed at least 4 weeks after the criteria of the response were first met, and were reviewed by an independent review committee. Results Eighty-three patients were enrolled and 79 patients with eligible PTCL histology were for efficacy assessments. Patients enrolled over 10% were with subtypes of PTCL not otherwise specified (34%), anaplastic large-cell lymphoma (22%), extranodal natural killer (NK)/T-cell lymphoma, nasal type (20%), or angioimmunoblastic T-cell lymphoma (AITL, 13%). The ORR was 28% (22 of 79) including 14% (11 of 79) with complete response/unconfirmed complete response (CR/CRu). Median progression-free survival and overall survival were 2.1 and 21.4 months, respectively. AITL patients tended to have higher ORR (50%) and CR/CRu rate (40%), as well as more durable responses, to chidamide treatment. Most adverse events (AEs) were grade 1 or 2, and AEs ≥grade 3 that occurred in ≥10% patients were thrombocytopenia (22%), leucopenia (13%) and neutropenia (11%), respectively. Conclusion Chidamide represents a novel oral benzamide class of HDAC inhibitor with significant single-agent activity and manageable toxicity in relapsed or refractory PTCL, and provides a much needed treatment option in this indication in China. Results led to China Food and Drug Administration approval of chidamide in this indication.
    Print ISSN: 0923-7534
    Electronic ISSN: 1569-8041
    Topics: Medicine
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  • 4
    Publication Date: 2016-01-07
    Description: MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase ( http://miRTarBase.mbc.nctu.edu.tw/ ) that provides information about experimentally validated miRNA-target interactions (MTIs). The latest update of the miRTarBase expanded it to identify systematically Argonaute-miRNA-RNA interactions from 138 crosslinking and immunoprecipitation sequencing (CLIP-seq) data sets that were generated by 21 independent studies. The database contains 4966 articles, 7439 strongly validated MTIs (using reporter assays or western blots) and 348 007 MTIs from CLIP-seq. The number of MTIs in the miRTarBase has increased around 7-fold since the 2014 miRTarBase update. The miRNA and gene expression profiles from The Cancer Genome Atlas (TCGA) are integrated to provide an effective overview of this exponential growth in the miRNA experimental data. These improvements make the miRTarBase one of the more comprehensively annotated, experimentally validated miRNA-target interactions databases and motivate additional miRNA research efforts.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
    Publication Date: 2021-03-22
    Description: Radiogenic lead (Pb) and neodymium (Nd) isotope compositions extracted from authigenic phases in marine sediments are sensitive tracers to reconstruct past ocean circulation and water mass mixing. Chemical reductive leaching of hydrogenetic ferromanganese oxyhydroxides from bulk sediments is the most practical way to recover past seawater Pb and Nd isotope signatures in the Southern Ocean, due to the scarcity of alternative archives. However, the leached signal could be compromised if substantial quantities of Pb and Nd were released from non-hydrogenetic sediment fractions during chemical extraction. Here we developed a very short 10-s leaching method to extract reliable seawater Pb and Nd isotope signals from sediments in the Atlantic sector of Southern Ocean. The effect of a previously recommended MgCl2 pre-wash, the role of chelate ligands in the leaching solution and length of leaching time were investigated. The results show that 10-s exposure time of sediments to reductive leaching extracted sufficient and more reliable hydrogenetic Pb and Nd compared with the commonly used 30-min leaching approaches. The robustness of our improved leaching method was validated via direct comparison of Pb and Nd isotope signatures with actual seawater, porewater, and corresponding sediment leachates from three stations in front of the Antarctic Filchner-Rønne Ice Shelf. Our findings also indicate that in contrast previously studied sites on the West Antarctic continental shelf, the bottom seawater Nd concentration is less elevated through benthic fluxes in the area of the southern Weddell Sea shelf.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 6
    Publication Date: 2021-07-21
    Description: Radiogenic lead (Pb) and neodymium (Nd) isotope compositions extracted from authigenic phases in marine sediments are sensitive tracers to reconstruct past ocean circulation and water mass mixing. Chemical reductive leaching of hydrogenetic ferromanganese oxyhydroxides from bulk sediments is the most practical way to recover past seawater Pb and Nd isotope signatures in the Southern Ocean, due to the scarcity of alternative archives. However, the leached signal could be compromised if substantial quantities of Pb and Nd were released from non‐hydrogenetic sediment fractions during chemical extraction. Here we developed a very short 10‐s leaching method to extract reliable seawater Pb and Nd isotope signals from sediments in the Atlantic sector of Southern Ocean. The effect of a previously recommended MgCl2 pre‐wash, the role of chelate ligands in the leaching solution and length of leaching time were investigated. The results show that 10‐s exposure time of sediments to reductive leaching extracted sufficient and more reliable hydrogenetic Pb and Nd compared with the commonly used 30‐min leaching approaches. The robustness of our improved leaching method was validated via direct comparison of Pb and Nd isotope signatures with actual seawater, porewater, and corresponding sediment leachates from three stations in front of the Antarctic Filchner‐Rønne Ice Shelf. Our findings also indicate that in contrast previously studied sites on the West Antarctic continental shelf, the bottom seawater Nd concentration is less elevated through benthic fluxes in the area of the southern Weddell Sea shelf.
    Description: Plain Language Summary: Individual modern ocean water masses can often be identified by the isotopic signature of dissolved trace metals lead (Pb) and neodymium (Nd) supplied from surrounding continents. By analyzing past seawater Pb and Nd isotope ratios preserved in the sedimentary archives, we can understand how the ocean circulation changed. In the Southern Ocean, archives preserving past seawater Pb and Nd isotope compositions are very scarce. Thus, the chemical extraction of Pb and Nd from seawater‐derived ferromanganese oxyhydroxides within deep marine sediments becomes the most practical way to recover past seawater signal. However, Southern Ocean sediments commonly contain substantial quantities of Antarctic continental fine‐grained sediment, which easily partially dissolve during extraction, thereby releasing Pb and Nd, which did not originate from past ambient seawater. Here we established a gentle and efficient extraction method to obtain reliable past Southern Ocean seawater signatures. In addition, via analysis of regional seawater‐derived Pb and Nd signatures in the Atlantic sector of Southern Ocean, we found that the sediments further away from Antarctica and volcanically active regions are better suited to preserve unaltered seawater Pb and Nd isotope signals, which strongly supports the unique possibility of tracing past water mass sourcing in the Southern Ocean with our analytical approach.
    Description: Key Points: 10‐s reductive leaching is capable of reliably extracting seawater Pb and Nd isotope signals from Southern Ocean sediments. Natural porewater Pb isotopic compositions are analyzed for the first time in front of the Antarctic Filchner‐Rønne Ice Shelf. Identify potential sites for extracting seawater Pb and Nd isotopic signatures from bulk sediments in the Atlantic sector of Southern Ocean.
    Description: China Scholarship Council (CSC)
    Keywords: 551.9 ; Fe‐Mn oxyhydroxides ; Nd isotopes ; Pb isotopes ; reductive leaching ; sediment ; Southern Ocean
    Type: article
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  • 7
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    Cambridge University Press
    In:  EPIC3Climate Change 2014: Impacts, Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, Cambridge, United Kingdom and New York, NY, USA, Cambridge University Press, pp. 35-94, ISBN: 9781107641655
    Publication Date: 2015-03-08
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
    Format: application/pdf
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  • 8
    Publication Date: 2021-05-19
    Description: The proximate composition, amino acids and fatty acids composition in the muscle of wild, inshore and offshore cage-cultured large yellow croaker, Pseudosciaena crocea (Richardson, 1846), were determined to identify nutritional differences. Wild fish groups showed highest content of moisture and crude protein, but the lowest lipid content. Offshore cage-cultured fish showed significantly higher content of moisture and crude protein content, but lower crude lipid content than inshore cage-cultured fish. The content of aspartic acid, glutamic acid, and alanine was higher in wild large yellow croaker than inshore cage-cultured groups, but similar to offshore cage-cultured fish. Significant lower contents of total amino acids, essential amino acids, non-essential amino acids and flavor-enhancing amino acids content were recorded in two cultured fish groups than those in wild group. While no major differences in fatty acids composition were found between wild and cage-cultured groups except for linoleic acid. The fish from offshore cages has much better nutrient profile than inshore cage-cultured fish, but was still inferior compared to wild fish.
    Description: Published
    Keywords: Pseudosciaena crocea ; Composition ; Culture ; Wild ; Inshore ; Offshore
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.497-506
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  • 9
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biogeosciences 11 (2014): 3685-3693, doi:10.5194/bg-11-3685-2014.
    Description: Increasing numbers of studies have suggested that a comprehensive assessment of the impacts of cropping practices on greenhouse gas (GHG) emissions per unit yield (yield-scaled), rather than by land area (area-scaled), is needed to inform trade-off decisions to increase yields and reduce GHG emissions. We conducted a meta-analysis to quantify impacts of rice varieties on the global warming potential (GWP) of GHG emissions at the yield scale in China. Our results showed that significantly higher yield-scaled GWP occurred with indica rice varieties (1101.72 kg CO2 equiv. Mg−1) than japonica rice varieties (711.38 kg CO2 equiv. Mg−1). Lower yield-scaled GHG emissions occurred within 120–130 days of growth duration after transplanting (GDAT; 613.66 kg CO2 equiv. Mg−1), followed by 90–100 days of GDAT (749.72 kg CO2 equiv. Mg−1, 100–110 days of GDAT (794.29 kg CO2 equiv. Mg−1), and 70–80 days of GDAT (800.85 kg CO2 equiv. Mg−1). The fertilizer rate of 150–200 kg N ha−1 resulted in the lowest yield-scaled GWP. Consequently, appropriate cultivar choice and pairs were of vital importance in the rice cropping system. A further life cycle assessment of GHG emissions among rice varieties at the yield scale is urgently needed to develop win–win policies for rice production to achieve higher yield with lower emissions.
    Description: This research was part of the National Programs for High-Yielding Rice Science and Technology (Grant no. 2013BAD07B11) and the Project for “12th 5-year plan” Agro-scientific Research in the Public Interest (Grant No. 201203081).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 10
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Journal of neurochemistry 50 (1988), S. 0 
    ISSN: 1471-4159
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: Incubation of rat brain synaptosomes prelabeled with [2-3H]inositol resulted in a time-dependent release of labeled inositol 1 -phosphate. This process was Ca2+ dependent, and ATP (1 mM) enhanced the inositol 1-phosphate formation three- to fivefold. Using [l-14C]arachidonoyl-phosphatidylinositol which was introduced into saponin-permeabilized synaptosomes, ATP (1 mM) and free Ca2+ (˜20 μM) enhanced the phospholipase C hydrolysis of this substrate to form labeled diacylglycerol. When the same permeabilized synaptosomal preparation was incubated with [2-3H]inositol-phosphatidylinositol, ATP not only enhanced the formation of labeled inositol 1-phosphate, but also inhibited the conversion of inositol 1-phosphate to inositol. Furthermore, ATP appeared to reduce the Ca2+ requirement of the phosphatidylinositol-phospholipase C. Inhibition of the conversion of inositol 1-phosphate to inositol could not be overcome by increasing the Mg2+ concentration in the incubation medium. Although the ATP effect is not viewed as a receptor-mediated event, it is possible that such an event may occur in synaptosomes under conditions in which intrasynaptic Ca2+ concentration becomes elevated.
    Type of Medium: Electronic Resource
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