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  • 1
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    An STM and atomic force microscopy study of the effects of 1.8 MeV electron bombardment on the surface of graphite (1998)
    Springer
    Details
    Publication Date: 1998-09-01
    Print ISSN: 0022-2461
    Electronic ISSN: 1573-4803
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Published by Springer
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  • 2
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    dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-16
    Description: Given the increasing number of proteins reported to be regulated by S -nitrosylation (SNO), it is considered to act, in a manner analogous to phosphorylation, as a pleiotropic regulator that elicits dual effects to regulate diverse pathophysiological processes by altering protein function, stability, and conformation change in various cancers and human disorders. Due to its importance in regulating protein functions and cell signaling, dbSNO ( http://dbSNO.mbc.nctu.edu.tw ) is extended as a resource for exploring structural environment of SNO substrate sites and regulatory networks of S -nitrosylated proteins. An increasing interest in the structural environment of PTM substrate sites motivated us to map all manually curated SNO peptides (4165 SNO sites within 2277 proteins) to PDB protein entries by sequence identity, which provides the information of spatial amino acid composition, solvent-accessible surface area, spatially neighboring amino acids, and side chain orientation for 298 substrate cysteine residues. Additionally, the annotations of protein molecular functions, biological processes, functional domains and human diseases are integrated to explore the functional and disease associations for S -nitrosoproteome. In this update, users are allowed to search a group of interested proteins/genes and the system reconstructs the SNO regulatory network based on the information of metabolic pathways and protein-protein interactions. Most importantly, an endogenous yet pathophysiological S -nitrosoproteomic dataset from colorectal cancer patients was adopted to demonstrate that dbSNO could discover potential SNO proteins involving in the regulation of NO signaling for cancer pathways.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-20
    Description: Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM ( http://dbPTM.mbc.nctu.edu.tw/ ) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, 〉60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein–protein interaction and domain–domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    dbSNO: a database of cysteine S-nitrosylation (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-25
    Description: : S -nitrosylation (SNO), a selective and reversible protein post-translational modification that involves the covalent attachment of nitric oxide (NO) to the sulfur atom of cysteine, critically regulates protein activity, localization and stability. Due to its importance in regulating protein functions and cell signaling, a mass spectrometry-based proteomics method rapidly evolved to increase the dataset of experimentally determined SNO sites. However, there is currently no database dedicated to the integration of all experimentally verified S -nitrosylation sites with their structural or functional information. Thus, the dbSNO database is created to integrate all available datasets and to provide their structural analysis. Up to April 15, 2012, the dbSNO has manually accumulated 〉3000 experimentally verified S -nitrosylated peptides from 219 research articles using a text mining approach. To solve the heterogeneity among the data collected from different sources, the sequence identity of these reported S -nitrosylated peptides are mapped to the UniProtKB protein entries. To delineate the structural correlation and consensus motif of these SNO sites, the dbSNO database also provides structural and functional analyses, including the motifs of substrate sites, solvent accessibility, protein secondary and tertiary structures, protein domains and gene ontology. Availability : The dbSNO is now freely accessible via http://dbSNO.mbc.nctu.edu.tw . The database content is regularly updated upon collecting new data obtained from continuously surveying research articles. Contacts: francis@saturn.yu.edu.tw or yujuchen@gate.sinica.edu.tw 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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  • 5
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    dbGSH: a database of S-glutathionylation (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-06
    Description: : S -glutathionylation, the reversible protein posttranslational modification (PTM) that generates a mixed disulfide bond between glutathione and cysteine residue, critically regulates protein activity, stability and redox regulation. Due to its importance in regulating oxidative/nitrosative stress and balance in cellular response, a number of methods have been rapidly developed to study S -glutathionylation, thus expanding the dataset of experimentally determined glutathionylation sites. However, there is currently no database dedicated to the integration of all experimentally verified S -glutathionylation sites along with their characteristics or structural or functional information. Thus, the dbGSH database has been created to integrate all available datasets and to provide the relevant structural analysis. As of January 31, 2014, dbGSH has manually collected 〉2200 experimentally verified S -glutathionylated peptides from 169 research articles using a text-mining approach. To solve the problem of heterogeneity of the data collected from different sources, the sequence identity of the reported S -glutathionylated peptides is mapped to UniProtKB protein entries. To delineate the structural correlations and consensus motifs of these S -glutathionylation sites, the dbGSH database also provides structural and functional analyses, including the motifs of substrate sites, solvent accessibility, protein secondary and tertiary structures, protein domains and gene ontology. Availability and implementation: dbGSH is now freely accessible at http://csb.cse.yzu.edu.tw/dbGSH/ . The database content is regularly updated with new data collected by the continuous survey of research articles. Contact: francis@saturn.yzu.edu.tw or yujuchen@gate.sinica.edu.tw 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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  • 6
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    Pollen morphology of Philippine species of Phyllanthus (Phyllanthaceae, Euphorbiaceae s.l.) (2009)
    In:  Blumea - Biodiversity, Evolution and Biogeography of Plants (0006-5196) vol.54 (2009) nr.1/3 p.47
    Details
    Publication Date: 2015-03-06
    Description: The pollen morphology of 21 Philippine Phyllanthus species belonging to five subgenera and eleven sections was studied using scanning electron microscopy. Eleven pollen types were recognized, of which seven were previously reported and four are newly described, i.e., the Phyllanthus erythrotrichus type, the P. glochidioides type, the P. securinegoides type and the Pilate type. The pollen morphology of the Philippine Phyllanthus species included in this study provides insight into the taxonomy as well as the phylogeny of these species.
    Keywords: Euphorbiaceae ; Philippines ; Phyllanthaceae ; Phyllanthus ; pollen morphology ; SEM ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
    Format: application/pdf
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  • 7
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    Pollen morphology of Philippine species of Phyllanthus (Phyllanthaceae,\nEuphorbiaceae s.l.) (2009)
    In:  Blumea: Biodiversity, Evolution and Biogeography of Plants vol. 54 no. 1/3, pp. 47-58
    Details
    Publication Date: 2024-01-12
    Description: The pollen morphology of 21 Philippine Phyllanthus species belonging to five subgenera and eleven sections was studied using scanning electron microscopy. Eleven pollen types were recognized, of which seven were previously reported and four are newly described, i.e., the Phyllanthus erythrotrichus type, the P. glochidioides type, the P. securinegoides type and the Pilate type. The pollen morphology of the Philippine Phyllanthus species included in this study provides insight into the taxonomy as well as the phylogeny of these species.
    Keywords: Euphorbiaceae ; Philippines ; Phyllanthaceae ; Phyllanthus ; pollen morphology ; SEM ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 8
    Electronic Resource
    Electronic Resource
    Perpendicular magnetic anisotropy of Co–Ag granular thin films (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 85 (1999), S. 5048-5050 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The perpendicular magnetic anisotropy constant in giant magnetoresistive granular Co22Ag78 thin films is found to increase and then decrease with annealing temperature, the maximum being about 5×105 ergs/cc at an annealing temperature of about 600 K. The observation of domain patterns by magnetic force microscopy is consistent with this result. The origin of the perpendicular magnetic anisotropy is not clear, but suggested to be in an anisotropic Co–Co particle distribution and also due to a surface anisotropy of Co particles. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.370087
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  • 9
    Electronic Resource
    Electronic Resource
    Magnetic properties and domains in Co–Ag granular thin films (2000)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 87 (2000), S. 4837-4839 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The intrinsic perpendicular magnetic anisotropy and the domain patterns in granular CoxAg1−x films with 17%≤x≤62% are studied. Magnetic stripe domains are found in samples with x≥45% and to change to in-plane domain patterns with increasing annealing temperature. This is consistent with the fact that perpendicular magnetic anisotropy becomes negative with annealing. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.373175
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  • 10
    Electronic Resource
    Electronic Resource
    Effects of Cr2O3 or Y2O3 doping in barium ferrite thin-film medium for high-density recording : The 40th annual conference on magnetism and magnetic materials (1996)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 79 (1996), S. 4878-4880 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The effects of Cr2O3 or Y2O3 doping on the surface morphology and magnetic properties in barium ferrite thin films have been studied. Thin films were deposited by co-sputtering a barium ferrite target with a Cr2O3 or Y2O3 target. The deposited amorphous films were homogenized at a temperature of 600 °C for over 10 h followed by annealing at 800 °C in a tube furnace. It was observed that, whereas stoichiometric barium ferrite shows 5000 A(ring)×500 A(ring) acicular grainlike features, films doped with Cr2O3 or Y2O3 had equiaxed topographic features with an average size of 500 A(ring). Magnetic studies showed that the coercivity of the doped films was over 3500 Oe and was larger than that of stoichiometric films. A weak magnetostatic interaction was found in all the films. Studies of the magnetic after effect indicated excellent thermal stability in all the films. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.361638
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