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  • 1
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    Covalency in oxidized uranium (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-07-30
    Description: Author(s): J. G. Tobin, S.-W. Yu, R. Qiao, W. L. Yang, C. H. Booth, D. K. Shuh, A. M. Duffin, D. Sokaras, D. Nordlund, and T.-C. Weng Using x-ray emission spectroscopy and absorption spectroscopy, it has been possible to directly access the states in the unoccupied conduction bands that are involved with 5 f and 6 d covalency in oxidized uranium. By varying the oxidizing agent, the degree of 5 f covalency can be manipulated and monit… [Phys. Rev. B 92, 045130] Published Wed Jul 29, 2015
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 2
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    Probing 5f-state configurations in URu_{2} Si_{2} with U L_{III} -edge resonant x-ray emission spectroscopy (2016)
    American Physical Society (APS)
    Details
    Publication Date: 2016-07-16
    Description: Author(s): C. H. Booth, S. A. Medling, J. G. Tobin, R. E. Baumbach, E. D. Bauer, D. Sokaras, D. Nordlund, and T.-C. Weng URu 2 Si 2 undergoes a second-order phase transition at 17.5 K that has defied attempts to identify its order parameter despite a vast literature extending over the last 30 years. A wide variety of theories have been posed to explain this so-called “hidden order”, some with exotic ground states. An important dividing line between these theories is the character of the 5 f orbital: on one side sit theories that require a localized f 2 configuration ( f -manifold crystalline electric field effects, hastatic order, etc.), while on the other sit those that start from an itinerant, partially occupied f 3 orbital (band structure + hybridization). Unfortunately, the experimental measures remain muddy on this issue, with indications of both localized f 2 and itinerant f 3 behavior depending on the experiment. Here, the authors report U L I I I -edge absorption/ L α 1 emission resonant x-ray emission spectroscopy measurements comparing data from URu 2 Si 2 to UCd 11 , UF 4 , and UO 2 data to unravel the various roles of f -orbital occupation, delocalization, and ligand-field splitting of the d manifold. The data indicate a dominant delocalized f 3 configuration that is likely partially occupied, with no measurable change in occupancy to temperatures as low as 10 K. While these measurements do not rule out a minority localized f 2 configuration, any theory relying on such a configuration must account for its relatively small contribution to the Fermi surface. [Phys. Rev. B 94, 045121] Published Fri Jul 15, 2016
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
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    miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database (2016)
    Oxford University Press
    Details
    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
    Published by Oxford University Press
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  • 4
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    Tracking a Marine Ecotourism Star: Movements of the Short Ocean Sunfish Mola ramsayi in Nusa Penida, Bali, Indonesia (2016)
    Hindawi
    Details
    Publication Date: 2016-08-16
    Description: Ocean sunfishes, Molidae, comprise the world’s heaviest bony fishes. They include the short mola, Mola ramsayi (Giglioli 1883), an important tourist draw at Nusa Penida and Nusa Lembongan, Bali, where SCUBA divers can observe ectoparasite-laden individuals being cleaned by smaller reef fishes. Despite widespread appeal, little is known about these fishes relative to regional oceanography. We present the first behavioral information for this species anywhere in the world. Satellite tag data indicate a wide thermal range (10–27.5°C) with depth occupation mostly (95%) in the upper 250 m and habitat preference near the bottom of the warm surface layer. One tag popped off as scheduled after 6 months off Nusa Penida,
    Print ISSN: 1687-9481
    Electronic ISSN: 1687-949X
    Topics: Biology
    Published by Hindawi
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  • 5
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    Oxidation and crystal field effects in uranium (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-07-08
    Description: Author(s): J. G. Tobin, S.-W. Yu, C. H. Booth, T. Tyliszczak, D. K. Shuh, G. van der Laan, D. Sokaras, D. Nordlund, T.-C. Weng, and P. S. Bagus An extensive investigation of oxidation in uranium has been pursued. This includes the utilization of soft x-ray absorption spectroscopy, hard x-ray absorption near-edge structure, resonant (hard) x-ray emission spectroscopy, cluster calculations, and a branching ratio analysis founded on atomic the… [Phys. Rev. B 92, 035111] Published Mon Jul 06, 2015
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 6
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    Functional prokaryotic-eukaryotic chimera from the pentameric ligand-gated ion channel family [Pharmacology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-07-20
    Description: Pentameric ligand-gated ion channels (pLGICs), which mediate chemo-electric signal transduction in animals, have been recently found in bacteria. Despite clear sequence and 3D structure homology, the phylogenetic distance between prokaryotic and eukaryotic homologs suggests significant structural divergences, especially at the interface between the extracellular (ECD) and the transmembrane (TMD) domains. To challenge this possibility, we constructed a chimera in which the ECD of the bacterial protein GLIC is fused to the TMD of the human α1 glycine receptor (α1GlyR). Electrophysiology in Xenopus oocytes shows that it functions as a proton-gated ion channel, thereby locating the proton activation site(s) of GLIC in its ECD. Patch-clamp experiments in BHK cells show that the ion channel displays an anionic selectivity with a unitary conductance identical to that of the α1GlyR. In addition, pharmacological investigations result in transmembrane allosteric modulation similar to the one observed on α1GlyR. Indeed, the clinically active drugs propofol, four volatile general anesthetics, alcohols, and ivermectin all potentiate the chimera while they inhibit GLIC. Collectively, this work shows the compatibility between GLIC and α1GlyR domains and points to conservation of the ion channel and transmembrane allosteric regulatory sites in the chimera. This provides evidence that GLIC and α1GlyR share a highly homologous 3D structure. GLIC is thus a relevant model of eukaryotic pLGICs, at least from the anionic type. In addition, the chimera is a good candidate for mass production in Escherichia coli, opening the way for investigations of “druggable” eukaryotic allosteric sites by X-ray crystallography.
    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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  • 7
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    GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks (2014)
    Springer Nature
    Details
    Publication Date: 2014-03-27
    Description: Virtually all cellular functions involve protein-protein interactions (PPIs). As an increasing number of PPIs are identified and vast amount of information accumulated, researchers are finding different ways to interrogate the data and understand the interactions in context. However, it is widely recognized that a significant portion of the data is scattered, redundant, not considered high quality, and not readily accessible to researchers in a systematic fashion. In addition, it is challenging to identify the optimal protein targets in the current PPI networks. The GeneSense server was developed to integrate gene annotation and PPI networks in an expandable architecture that incorporates selected databases with the aim to assemble, analyze, evaluate and disseminate protein-protein association information in a comprehensive and user-friendly manner. Three network models including nodenet, leafnet and loopnet are used to identify the optimal protein targets in the complex networks. GeneSense is freely available at www.biomedsense.org/genesense.php. Scientific Reports 4 doi: 10.1038/srep04474
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 8
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    Hobbes: optimized gram-based methods for efficient read alignment (2012)
    Oxford University Press
    Details
    Publication Date: 2012-03-29
    Description: Recent advances in sequencing technology have enabled the rapid generation of billions of bases at relatively low cost. A crucial first step in many sequencing applications is to map those reads to a reference genome. However, when the reference genome is large, finding accurate mappings poses a significant computational challenge due to the sheer amount of reads, and because many reads map to the reference sequence approximately but not exactly. We introduce Hobbes, a new gram-based program for aligning short reads, supporting Hamming and edit distance. Hobbes implements two novel techniques, which yield substantial performance improvements: an optimized gram-selection procedure for reads, and a cache-efficient filter for pruning candidate mappings. We systematically tested the performance of Hobbes on both real and simulated data with read lengths varying from 35 to 100 bp, and compared its performance with several state-of-the-art read-mapping programs, including Bowtie, BWA, mrsFast and RazerS. Hobbes is faster than all other read mapping programs we have tested while maintaining high mapping quality. Hobbes is about five times faster than Bowtie and about 2–10 times faster than BWA, depending on read length and error rate, when asked to find all mapping locations of a read in the human genome within a given Hamming or edit distance, respectively. Hobbes supports the SAM output format and is publicly available at http://hobbes.ics.uci.edu .
    Keywords: Computational Methods, Massively Parallel (Deep) Sequencing
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    High-resolution x-ray-emission study of 1s4p and 1s3d two-electron photoexcitations in Kr (2014)
    American Physical Society (APS)
    Details
    Publication Date: 2014-08-22
    Description: Author(s): M. Kavčič, M. Žitnik, D. Sokaras, T.-C. Weng, R. Alonso-Mori, D. Nordlund, J.-Cl. Dousse, and J. Hoszowska High-energy-resolution photoexcited KN2,3 x-ray-emission measurements were carried out on krypton with the excitation energy tuned around the 1s4p and 1s3d double-excitation thresholds. Comprehensive two-dimensional resonant inelastic x-ray-scattering maps were recorded for the range of excitation a... [Phys. Rev. A 90, 022513] Published Thu Aug 21, 2014
    Keywords: Atomic and molecular structure and dynamics
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
    Published by American Physical Society (APS)
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  • 10
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    Protein competition switches the function of COP9 from self-renewal to differentiation (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-08-15
    Description: The balance between stem cell self-renewal and differentiation is controlled by intrinsic factors and niche signals. In the Drosophila melanogaster ovary, some intrinsic factors promote germline stem cell (GSC) self-renewal, whereas others stimulate differentiation. However, it remains poorly understood how the balance between self-renewal and differentiation is controlled. Here we use D. melanogaster ovarian GSCs to demonstrate that the differentiation factor Bam controls the functional switch of the COP9 complex from self-renewal to differentiation via protein competition. The COP9 complex is composed of eight Csn subunits, Csn1-8, and removes Nedd8 modifications from target proteins. Genetic results indicated that the COP9 complex is required intrinsically for GSC self-renewal, whereas other Csn proteins, with the exception of Csn4, were also required for GSC progeny differentiation. Bam-mediated Csn4 sequestration from the COP9 complex via protein competition inactivated the self-renewing function of COP9 and allowed other Csn proteins to promote GSC differentiation. Therefore, this study reveals a protein-competition-based mechanism for controlling the balance between stem cell self-renewal and differentiation. Because numerous self-renewal factors are ubiquitously expressed throughout the stem cell lineage in various systems, protein competition may function as an important mechanism for controlling the self-renewal-to-differentiation switch.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pan, Lei -- Wang, Su -- Lu, Tinglin -- Weng, Changjiang -- Song, Xiaoqing -- Park, Joseph K -- Sun, Jin -- Yang, Zhi-Hao -- Yu, Junjing -- Tang, Hong -- McKearin, Dennis M -- Chamovitz, Daniel A -- Ni, Jianquan -- Xie, Ting -- GM64428/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2014 Oct 9;514(7521):233-6. doi: 10.1038/nature13562.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA [2] Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, 15 Da Tun Road, Beijing 100101, China [3]. ; 1] Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA [2] Department of Cell Biology and Anatomy, University of Kansas School of Medicine, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA [3]. ; 1] Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China [2]. ; Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA. ; 1] Department of Molecular Biology and Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9148, USA [2] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA. ; Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China. ; 1] Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA [2] Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, 15 Da Tun Road, Beijing 100101, China. ; Chinese Academy of Sciences Key Laboratory of Infection and Immunity, Institute of Biophysics, 15 Da Tun Road, Beijing 100101, China. ; Department of Plant Sciences, Tel Aviv University, Tel Aviv 69978, Israel. ; 1] Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA [2] Department of Cell Biology and Anatomy, University of Kansas School of Medicine, 3901 Rainbow Boulevard, Kansas City, Kansas 66160, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25119050" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Binding, Competitive ; *Cell Differentiation ; Cell Proliferation ; DNA Helicases/metabolism ; Drosophila Proteins/metabolism ; Drosophila melanogaster/*cytology/*metabolism ; Female ; Intracellular Signaling Peptides and Proteins/metabolism ; Male ; Multiprotein Complexes/*chemistry/*metabolism ; Ovary/cytology ; Peptide Hydrolases/*chemistry/*metabolism ; Protein Binding ; Stem Cells/*cytology/*metabolism ; Ubiquitins/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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