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  • 1
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    TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information (2014)
    Oxford University Press
    Details
    Publication Date: 2014-08-27
    Description: Motivation: Time-evolving differential protein–protein interaction (PPI) networks are essential to understand serial activation of differentially regulated (up- or downregulated) cellular processes (DRPs) and their interplays over time. Despite developments in the network inference, current methods are still limited in identifying temporal transition of structures of PPI networks, DRPs associated with the structural transition and the interplays among the DRPs over time. Results: Here, we present a probabilistic model for estimating Time-Evolving differential PPI networks with MultiPle Information (TEMPI). This model describes probabilistic relationships among network structures, time-course gene expression data and Gene Ontology biological processes (GOBPs). By maximizing the likelihood of the probabilistic model, TEMPI estimates jointly the time-evolving differential PPI networks (TDNs) describing temporal transition of PPI network structures together with serial activation of DRPs associated with transiting networks. This joint estimation enables us to interpret the TDNs in terms of temporal transition of the DRPs. To demonstrate the utility of TEMPI, we applied it to two time-course datasets. TEMPI identified the TDNs that correctly delineated temporal transition of DRPs and time-dependent associations between the DRPs. These TDNs provide hypotheses for mechanisms underlying serial activation of key DRPs and their temporal associations. Availability and implementation: Source code and sample data files are available at http://sbm.postech.ac.kr/tempi/sources.zip . Contact: seungjin@postech.ac.kr or dhwang@dgist.ac.kr 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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    MEIS2 is essential for neuroblastoma cell survival and proliferation by transcriptional control of M-phase progression (2014)
    Springer Nature
    Details
    Publication Date: 2014-09-12
    Description: MEIS2 is essential for neuroblastoma cell survival and proliferation by transcriptional control of M-phase progression Cell Death and Disease 5, e1417 (September 2014). doi:10.1038/cddis.2014.370 Authors: Y Zha, Y Xia, J Ding, J-H Choi, L Yang, Z Dong, C Yan, S Huang & H-F Ding
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 3
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    MAVS, cGAS, and endogenous retroviruses in T-independent B cell responses (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-12-20
    Description: Multivalent molecules with repetitive structures including bacterial capsular polysaccharides and viral capsids elicit antibody responses through B cell receptor (BCR) crosslinking in the absence of T cell help. We report that immunization with these T cell-independent type 2 (TI-2) antigens causes up-regulation of endogenous retrovirus (ERV) RNAs in antigen-specific mouse B cells. These RNAs are detected via a mitochondrial antiviral signaling protein (MAVS)-dependent RNA sensing pathway or reverse-transcribed and detected via the cGAS-cGAMP-STING pathway, triggering a second, sustained wave of signaling that promotes specific immunoglobulin M production. Deficiency of both MAVS and cGAS, or treatment of MAVS-deficient mice with reverse transcriptase inhibitors, dramatically inhibits TI-2 antibody responses. These findings suggest that ERV and two innate sensing pathways that detect them are integral components of the TI-2 B cell signaling apparatus.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391621/" 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/PMC4391621/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zeng, Ming -- Hu, Zeping -- Shi, Xiaolei -- Li, Xiaohong -- Zhan, Xiaoming -- Li, Xiao-Dong -- Wang, Jianhui -- Choi, Jin Huk -- Wang, Kuan-wen -- Purrington, Tiana -- Tang, Miao -- Fina, Maggy -- DeBerardinis, Ralph J -- Moresco, Eva Marie Y -- Pedersen, Gabriel -- McInerney, Gerald M -- Karlsson Hedestam, Gunilla B -- Chen, Zhijian J -- Beutler, Bruce -- P01 AI070167/AI/NIAID NIH HHS/ -- R01 AI093967/AI/NIAID NIH HHS/ -- R01 CA157996/CA/NCI NIH HHS/ -- U19 AI100627/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Dec 19;346(6216):1486-92. doi: 10.1126/science.346.6216.1486.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA. ; Department of Pediatrics and Children's Medical Center Research Institute, and McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA. ; Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA. Howard Hughes Medical Institute, Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9148, USA. ; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels vag 16, SE-171 77 Stockholm, Sweden. ; Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8502, USA. Bruce.Beutler@UTSouthwestern.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25525240" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/genetics/*immunology ; Animals ; Antibody Formation ; Antigens, T-Independent/*immunology ; B-Lymphocytes/*immunology ; Cytosol/immunology ; DNA/immunology ; Endogenous Retroviruses/genetics/*immunology ; Lymphocyte Activation ; Membrane Proteins/immunology ; Mice ; Mice, Inbred C57BL ; NF-kappa B/metabolism ; Nucleotides, Cyclic/immunology ; Nucleotidyltransferases/genetics/*immunology ; RNA, Viral/genetics/*immunology ; 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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  • 4
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    Search for low-mass dark matter with CsI(Tl) crystal detectors (2014)
    American Physical Society
    Details
    Publication Date: 2014-09-23
    Print ISSN: 1550-7998
    Electronic ISSN: 1550-2368
    Topics: Physics
    Published by American Physical Society
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  • 5
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    Highly specific and sensitive method for measuring nucleotide excision repair kinetics of ultraviolet photoproducts in human cells (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-28
    Description: The nucleotide excision repair pathway removes ultraviolet (UV) photoproducts from the human genome in the form of short oligonucleotides ~30 nt in length. Because there are limitations to many of the currently available methods for investigating UV photoproduct repair in vivo , we developed a convenient non-radioisotopic method to directly detect DNA excision repair events in human cells. The approach involves extraction of oligonucleotides from UV-irradiated cells, DNA end-labeling with biotin and streptavidin-mediated chemiluminescent detection of the excised UV photoproduct-containing oligonucleotides that are released from the genome during excision repair. Our novel approach is robust, with essentially no signal in the absence of UV or a functional excision repair system. Furthermore, our non-radioisotopic methodology allows for the sensitive detection of excision products within minutes following UV irradiation and does not require additional enrichment steps such as immunoprecipitation. Finally, this technique allows for quantitative measurements of excision repair in human cells. We suggest that the new techniques presented here will be a useful and powerful approach for studying the mechanism of human nucleotide excision repair in vivo .
    Keywords: Repair
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Dust properties of Lyman-break galaxies in cosmological simulations (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-21
    Description: Recent observations have indicated the existence of dust in high-redshift galaxies, however, the dust properties in them are still unknown. Here we present theoretical constraints on dust properties in Lyman-break galaxies (LBGs) at z  = 3 by post-processing a cosmological smoothed particle hydrodynamics simulation with radiative transfer calculations. We calculate the dust extinction in 2800 dark matter haloes using the metallicity information of individual gas particles in our simulation. We use only bright galaxies with rest-frame ultraviolet (UV) magnitude M 1700  〈 –20 mag, and study the dust size, dust-to-metal mass ratio, and dust composition. From the comparison of calculated colour excess between B and V band [i.e. E ( B  –  V )] and the observations, we constrain the typical dust size, and show that the best-fitting dust grain size is ~ 0.05 μm, which is consistent with the results of theoretical dust models for Type II supernova. Our simulation with the dust extinction effect can naturally reproduce the observed rest-frame UV luminosity function of LBGs at z  = 3 without assuming an ad hoc constant extinction value. In addition, in order to reproduce the observed mean E ( B  –  V ), we find that the dust-to-metal mass ratio needs to be similar to that of the local galaxies, and that the graphite dust is dominant or at least occupy half of dust mass.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 7
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    AUF1 contributes to Cryptochrome1 mRNA degradation and rhythmic translation (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-03
    Description: In the present study, we investigated the 3' untranslated region (UTR) of the mouse core clock gene cryptochrome 1 ( Cry1 ) at the post-transcriptional level, particularly its translational regulation. Interestingly, the 3'UTR of Cry1 mRNA decreased its mRNA levels but increased protein amounts. The 3'UTR is widely known to function as a cis -acting element of mRNA degradation. The 3'UTR also provides a binding site for microRNA and mainly suppresses translation of target mRNAs. We found that AU-rich element RNA binding protein 1 (AUF1) directly binds to the Cry1 3'UTR and regulates translation of Cry1 mRNA. AUF1 interacted with eukaryotic translation initiation factor 3 subunit B and also directly associated with ribosomal protein S3 or ribosomal protein S14, resulting in translation of Cry1 mRNA in a 3'UTR-dependent manner. Expression of cytoplasmic AUF1 and binding of AUF1 to the Cry1 3'UTR were parallel to the circadian CRY1 protein profile. Our results suggest that the 3'UTR of Cry1 is important for its rhythmic translation, and AUF1 bound to the 3'UTR facilitates interaction with the 5' end of mRNA by interacting with translation initiation factors and recruiting the 40S ribosomal subunit to initiate translation of Cry1 mRNA.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Parametric performance evaluation of a hydraulic centrifugal pump (2014)
    Institute of Physics (IOP)
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    Publication Date: 2014-12-11
    Description: Parametric study of a hydraulic centrifugal pump with backward curved blades has been performed numerically using three-dimensional Reynolds-averaged Navier-Stokes equations. The shear stress transport turbulence model was used for analysis of turbulence. The finite volume method and an unstructured grid system were used for the numerical solution. The optimal grid system in the computational domain was selected through a grid dependency test. Tested parameters were related to the geometry of the impeller and volute: seven variables defining the hub and shroud contours and the blades angle of impeller, and two variables defining the inlet width and expansion angle of volute. The effects of these parameters on the hydrodynamic performance of the centrifugal pump have been investigated. It was found that the centrifugal water pump with the twisted blades has the enhancing efficiency compared to the straight blades pump.
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
    Published by Institute of Physics (IOP)
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  • 9
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    Deleterious CHD7 alleles in human GnRH deficiency [Genetics] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-12-17
    Description: Inactivating mutations in chromodomain helicase DNA binding protein 7 (CHD7) cause CHARGE syndrome, a severe multiorgan system disorder of which Isolated gonadotropin-releasing hormone (GnRH) deficiency (IGD) is a minor feature. Recent reports have described predominantly missense CHD7 alleles in IGD patients, but it is unclear if these alleles are relevant...
    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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  • 10
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    Identification of Creb3l4 as an essential negative regulator of adipogenesis (2014)
    Springer Nature
    Details
    Publication Date: 2014-11-21
    Description: Identification of Creb3l4 as an essential negative regulator of adipogenesis Cell Death and Disease 5, e1527 (November 2014). doi:10.1038/cddis.2014.490 Authors: T-H Kim, S-H Jo, H Choi, J-M Park, M-Y Kim, H Nojima, J-W Kim & Y-H Ahn
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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