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  • 1
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    Rapid Nondestructive Analysis of Threading Dislocations in Wurtzite Materials Using the Scanning Electron Microscope (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-03-31
    Description: Author(s): G. Naresh-Kumar, B. Hourahine, P. R. Edwards, A. P. Day, A. Winkelmann, A. J. Wilkinson, P. J. Parbrook, G. England, and C. Trager-Cowan We describe the use of electron channeling contrast imaging in the scanning electron microscope to rapidly and reliably image and identify threading dislocations (TDs) in materials with the wurtzite crystal structure. In electron channeling contrast imaging, vertical TDs are revealed as spots with b... [Phys. Rev. Lett. 108, 135503] Published Fri Mar 30, 2012
    Keywords: Condensed Matter: Structure, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 2
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    Ore deposits in an evolving Earth: an introduction (2014)
    Geological Society (of London)
    Details
    Publication Date: 2014-09-06
    Description: Ore deposits form by a variety of natural processes that concentrate elements into a small volume that can be economically mined. Their type, character and abundance reflect the environment in which they formed and thus they preserve key evidence for the evolution of magmatic and tectonic processes, the state of the atmosphere and hydrosphere, and the evolution of life over geological time. This volume presents 13 papers on topical subjects in ore deposit research viewed in the context of Earth evolution. These diverse, yet interlinked, papers cover topics including: controls on the temporal and spatial distribution of ore deposits; the sources of fluid, gold and other components in orogenic gold deposits; the degree of oxygenation in the Neoproterozoic ocean; bacterial immobilization of gold in the semi-arid near-surface environment; and mineral resources for the future, including issues of resource estimation, sustainability of supply and the criticality of certain elements to society.
    Print ISSN: 0305-8719
    Electronic ISSN: 2041-4927
    Topics: Geosciences
    Published by Geological Society (of London)
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  • 3
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    N-myristoyltransferase inhibitors as new leads to treat sleeping sickness (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-04-03
    Description: African sleeping sickness or human African trypanosomiasis, caused by Trypanosoma brucei spp., is responsible for approximately 30,000 deaths each year. Available treatments for this disease are poor, with unacceptable efficacy and safety profiles, particularly in the late stage of the disease when the parasite has infected the central nervous system. Here we report the validation of a molecular target and the discovery of associated lead compounds with the potential to address this lack of suitable treatments. Inhibition of this target-T. brucei N-myristoyltransferase-leads to rapid killing of trypanosomes both in vitro and in vivo and cures trypanosomiasis in mice. These high-affinity inhibitors bind into the peptide substrate pocket of the enzyme and inhibit protein N-myristoylation in trypanosomes. The compounds identified have promising pharmaceutical properties and represent an opportunity to develop oral drugs to treat this devastating disease. Our studies validate T. brucei N-myristoyltransferase as a promising therapeutic target for human African trypanosomiasis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2917743/" 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/PMC2917743/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Frearson, Julie A -- Brand, Stephen -- McElroy, Stuart P -- Cleghorn, Laura A T -- Smid, Ondrej -- Stojanovski, Laste -- Price, Helen P -- Guther, M Lucia S -- Torrie, Leah S -- Robinson, David A -- Hallyburton, Irene -- Mpamhanga, Chidochangu P -- Brannigan, James A -- Wilkinson, Anthony J -- Hodgkinson, Michael -- Hui, Raymond -- Qiu, Wei -- Raimi, Olawale G -- van Aalten, Daan M F -- Brenk, Ruth -- Gilbert, Ian H -- Read, Kevin D -- Fairlamb, Alan H -- Ferguson, Michael A J -- Smith, Deborah F -- Wyatt, Paul G -- 077503/Wellcome Trust/United Kingdom -- 077705/Wellcome Trust/United Kingdom -- 085622/Wellcome Trust/United Kingdom -- 087590/Wellcome Trust/United Kingdom -- 1097737/Canadian Institutes of Health Research/Canada -- G0900138/Medical Research Council/United Kingdom -- G0900138(90614)/Medical Research Council/United Kingdom -- WT077503/Wellcome Trust/United Kingdom -- WT077705/Wellcome Trust/United Kingdom -- WT083481,/Wellcome Trust/United Kingdom -- WT085622/Wellcome Trust/United Kingdom -- England -- Nature. 2010 Apr 1;464(7289):728-32. doi: 10.1038/nature08893.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 5EH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360736" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/*antagonists & inhibitors/metabolism ; Aminopyridines/chemistry/metabolism/pharmacology/therapeutic use ; Animals ; Antiparasitic Agents/chemistry/metabolism/*pharmacology/*therapeutic use ; Enzyme Assays ; Enzyme Inhibitors/chemistry/metabolism/pharmacology/therapeutic use ; Female ; Humans ; Mice ; Molecular Structure ; Pyrazoles/chemistry/metabolism/pharmacology/therapeutic use ; Rats ; Sulfonamides/chemistry/metabolism/pharmacology/therapeutic use ; Time Factors ; Trypanosoma brucei brucei/*drug effects/*enzymology/growth & development ; Trypanosomiasis, African/*drug therapy/*parasitology
    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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  • 4
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    Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-03
    Description: Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional conditions that the organism might encounter in nature. We comprehensively mapped transcription units (TUs) and grouped 2935 promoters into regulons controlled by various RNA polymerase sigma factors, accounting for ~66% of the observed variance in transcriptional activity. This global classification of promoters and detailed description of TUs revealed that a large proportion of the detected antisense RNAs arose from potentially spurious transcription initiation by alternative sigma factors and from imperfect control of transcription termination.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nicolas, Pierre -- Mader, Ulrike -- Dervyn, Etienne -- Rochat, Tatiana -- Leduc, Aurelie -- Pigeonneau, Nathalie -- Bidnenko, Elena -- Marchadier, Elodie -- Hoebeke, Mark -- Aymerich, Stephane -- Becher, Dorte -- Bisicchia, Paola -- Botella, Eric -- Delumeau, Olivier -- Doherty, Geoff -- Denham, Emma L -- Fogg, Mark J -- Fromion, Vincent -- Goelzer, Anne -- Hansen, Annette -- Hartig, Elisabeth -- Harwood, Colin R -- Homuth, Georg -- Jarmer, Hanne -- Jules, Matthieu -- Klipp, Edda -- Le Chat, Ludovic -- Lecointe, Francois -- Lewis, Peter -- Liebermeister, Wolfram -- March, Anika -- Mars, Ruben A T -- Nannapaneni, Priyanka -- Noone, David -- Pohl, Susanne -- Rinn, Bernd -- Rugheimer, Frank -- Sappa, Praveen K -- Samson, Franck -- Schaffer, Marc -- Schwikowski, Benno -- Steil, Leif -- Stulke, Jorg -- Wiegert, Thomas -- Devine, Kevin M -- Wilkinson, Anthony J -- van Dijl, Jan Maarten -- Hecker, Michael -- Volker, Uwe -- Bessieres, Philippe -- Noirot, Philippe -- New York, N.Y. -- Science. 2012 Mar 2;335(6072):1103-6. doi: 10.1126/science.1206848.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉INRA, UR1077, Mathematique Informatique et Genome, Jouy-en-Josas, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22383849" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Algorithms ; Bacillus subtilis/*genetics/*physiology ; Binding Sites ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Gene Regulatory Networks ; Oligonucleotide Array Sequence Analysis ; *Promoter Regions, Genetic ; RNA, Antisense/genetics/metabolism ; RNA, Bacterial/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Regulon ; Sigma Factor/metabolism ; Terminator Regions, Genetic ; *Transcription, Genetic ; *Transcriptome
    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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  • 5
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    The structural basis of sequence-independent peptide binding by OppA protein (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-06-10
    Description: Specific protein-ligand interactions are critical for cellular function, and most proteins select their partners with sharp discrimination. However, the oligopeptide-binding protein of Salmonella typhimurium (OppA) binds peptides of two to five amino acid residues without regard to sequence. The crystal structure of OppA reveals a three-domain organization, unlike other periplasmic binding proteins. In OppA-peptide complexes, the ligands are completely enclosed in the protein interior, a mode of binding that normally imposes tight specificity. The protein fulfills the hydrogen bonding and electrostatic potential of the ligand main chain and accommodates the peptide side chains in voluminous hydrated cavities.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tame, J R -- Murshudov, G N -- Dodson, E J -- Neil, T K -- Dodson, G G -- Higgins, C F -- Wilkinson, A J -- New York, N.Y. -- Science. 1994 Jun 10;264(5165):1578-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of York, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8202710" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/*metabolism ; Binding Sites ; Carrier Proteins/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrogen Bonding ; Ligands ; Lipoproteins/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Oligopeptides/chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary
    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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    Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-03
    Description: Adaptation of cells to environmental changes requires dynamic interactions between metabolic and regulatory networks, but studies typically address only one or a few layers of regulation. For nutritional shifts between two preferred carbon sources of Bacillus subtilis, we combined statistical and model-based data analyses of dynamic transcript, protein, and metabolite abundances and promoter activities. Adaptation to malate was rapid and primarily controlled posttranscriptionally compared with the slow, mainly transcriptionally controlled adaptation to glucose that entailed nearly half of the known transcription regulation network. Interactions across multiple levels of regulation were involved in adaptive changes that could also be achieved by controlling single genes. Our analysis suggests that global trade-offs and evolutionary constraints provide incentives to favor complex control programs.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buescher, Joerg Martin -- Liebermeister, Wolfram -- Jules, Matthieu -- Uhr, Markus -- Muntel, Jan -- Botella, Eric -- Hessling, Bernd -- Kleijn, Roelco Jacobus -- Le Chat, Ludovic -- Lecointe, Francois -- Mader, Ulrike -- Nicolas, Pierre -- Piersma, Sjouke -- Rugheimer, Frank -- Becher, Dorte -- Bessieres, Philippe -- Bidnenko, Elena -- Denham, Emma L -- Dervyn, Etienne -- Devine, Kevin M -- Doherty, Geoff -- Drulhe, Samuel -- Felicori, Liza -- Fogg, Mark J -- Goelzer, Anne -- Hansen, Annette -- Harwood, Colin R -- Hecker, Michael -- Hubner, Sebastian -- Hultschig, Claus -- Jarmer, Hanne -- Klipp, Edda -- Leduc, Aurelie -- Lewis, Peter -- Molina, Frank -- Noirot, Philippe -- Peres, Sabine -- Pigeonneau, Nathalie -- Pohl, Susanne -- Rasmussen, Simon -- Rinn, Bernd -- Schaffer, Marc -- Schnidder, Julian -- Schwikowski, Benno -- Van Dijl, Jan Maarten -- Veiga, Patrick -- Walsh, Sean -- Wilkinson, Anthony J -- Stelling, Jorg -- Aymerich, Stephane -- Sauer, Uwe -- New York, N.Y. -- Science. 2012 Mar 2;335(6072):1099-103. doi: 10.1126/science.1206871.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22383848" target="_blank"〉PubMed〈/a〉
    Keywords: *Adaptation, Physiological ; Algorithms ; Bacillus subtilis/*genetics/*metabolism ; Bacterial Proteins/metabolism ; Computer Simulation ; Data Interpretation, Statistical ; Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Genome, Bacterial ; Glucose/*metabolism ; Malates/*metabolism ; Metabolic Networks and Pathways/*genetics ; Metabolome ; Metabolomics ; Models, Biological ; Operon ; Promoter Regions, Genetic ; Transcription Factors/metabolism ; Transcription, Genetic
    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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    A review of advances and challenges in EBSD strain mapping (2014)
    Institute of Physics (IOP)
    Details
    Publication Date: 2014-03-06
    Description: High sensitivity cross-correlation based analysis of EBSD patterns was introduced by Wilkinson, Meaden and Dingley in 2006 [1, 2]. This paper will describe the basis of the method and the various modifications and improvements that have been made to it over the past few years. Strain sensitivity of ~ 10 −4 is readily obtained and sensitivity to lower strains is achievable if signal to noise ratio in the patterns is improved by simple integration. The method allows maps of local stress and dislocation density distributions to be generated in parallel with information concerning grain orientation, grain boundary misorientation and the presence of other microstructural features. The method is illustrated by example maps from a Ni-based superalloy and deformed Cu.
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics (IOP)
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  • 8
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    High‐Angular Resolution Electron Backscatter Diffraction as a New Tool for Mapping Lattice Distortion in Geological Minerals (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract Analysis of distortions of the crystal lattice within individual mineral grains is central to the investigation of microscale processes that control and record tectonic events. These distortions are generally combinations of lattice rotations and elastic strains, but a lack of suitable observational techniques has prevented these components being mapped simultaneously and routinely in earth science laboratories. However, the technique of high‐angular resolution electron backscatter diffraction (HR‐EBSD) provides the opportunity to simultaneously map lattice rotation and elastic strain gradients with exceptional precision, on the order of 0.01° for rotations and 10−4 in strain, using a scanning electron microscope. Importantly, these rotations and lattice strains relate to densities of geometrically necessary dislocations and residual stresses. Recent works have begun to apply and adapt HR‐EBSD to geological minerals, highlighting the potential of the technique to provide new insights into the microphysics of rock deformation. Therefore, the purpose of this review is to provide a summary of the technique, to identify caveats and targets for further development, and to suggest areas where it offers potential for major advances. In particular, HR‐EBSD is well suited to characterizing the roles of different dislocation types during crystal plastic deformation and to mapping heterogeneous internal stress fields associated with specific deformation mechanisms/microstructures or changes in temperature, confining pressure, or macroscopic deviatoric stress. These capabilities make HR‐EBSD a particularly powerful new technique for analyzing the microstructures of deformed geological materials.
    Print ISSN: 2169-9313
    Electronic ISSN: 2169-9356
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 9
    Electronic Resource
    Electronic Resource
    Control of Terfenol-D under load : The 6th joint magnetism and magnetic materials (MMM)−intermag conference (1994)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 76 (1994), S. 7160-7162 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A vibration control case study is described which demonstrates the application of magnetostrictive (Terfenol-D) actuators. The magnetomechanical properties of the material suggests that when incorporated in devices for applications a nonlinear response will result. This case study compares the performance of two kinds of control strategy (both discrete), a conventional proportional and integral (PI) algorithm and a variable structure algorithm (DVSC) in both servo and cancellation/regulation roles. Both strategies were implemented on an INMOS transputer based microcontroller with a sampling period of 300 μs. The results presented show that the control behavior of the DVSC strategy offers significant advantages over the PI strategy when controlling actuators with nonlinear characteristics, i.e., the rejection of a 5 Hz disturbance with a gain of −36 dB compared to a gain of −15 dB when using the PI strategy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.357994
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  • 10
    Electronic Resource
    Electronic Resource
    THE STEREOCHEMICAL MECHANISM OF THE COOPERATIVE EFFECTS IN HEMOGLOBIN REVISITED (1998)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 27 (1998), S. 1-34 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract In 1970, Perutz tried to put the allosteric mechanism of hemoglobin, proposed by Monod, Wyman and Changeux in 1965, on a stereochemical basis. He interpreted their two-state model in terms of an equilibrium between two alternative structures, a tense one (T) with low oxygen affinity, constrained by salt-bridges between the C-termini of the four subunits, and a relaxed one (R) lacking these bridges. The equilibrium was thought to be governed primarily by the positions of the iron atoms relative to the porphyrin: out-of-plane in five-coordinated, high-spin deoxyhemoglobin, and in-plane in six-coordinated, low-spin oxyhemoglobin. The tension exercised by the salt-bridges in the T-structure was to be transmitted to the heme-linked histidines and to restrain the movement of the iron atoms into the porphyrin plane that is necessary for oxygen binding. At the beta-hemes, the distal valine and histidine block the oxygen-combining site in the T-structure; its tension was thought to strengthen that blockage. Finally, Perutz attributed the linearity of proton release with early oxygen uptake to the sequential rupture of salt-bridges in the T-structure and to the accompanying drop in pKa of the weak bases that form part of them. Almost every feature of this mechanism has been disputed, but evidence that has come to light more than 25 years later now shows it to have been substantially correct. That new evidence is reviewed below.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.27.1.1
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