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  • Oxford University Press  (7)
  • Institute of Physics (IOP)  (2)
  • Sage  (1)
  • 2010-2014  (10)
  • 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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    Reconstruction of Holocene coastal progradation on the east coast of Korea based on OSL dating and GPR surveys of beach-foredune ridges (2013)
    Sage
    In: Holocene
    Details
    Publication Date: 2013-12-24
    Description: Coastal dunefields along the east coast of Korea have long been thought to have originated from beach ridges that prograded during the Holocene, but there has been little chronological evidence based on absolute dating. In this paper, we use optically stimulated luminescence (OSL) dating and ground-penetrating radar (GPR) surveys to reconstruct the coastal progradation of Anin dunefield in the Gangneung area on the east coast of Korea. GPR profiles and sedimentological analyses of four beach-foredune ridges reveal that the ridges are composed mainly of beach deposits showing seaward-dipping and horizontal laminae, capped by eolian sands with landward-dipping laminae. The beach deposits are, in places, underlain by fluvial sands with gravels. Coupled with data from OSL dating, we interpret these results to mean that the fluvial sands and rounded cobbles were deposited in the study area, during the last glacial period. Between the mid-Holocene (~6.5 kyr) and c. 3.5–3.0 kyr, the transgression rate of the sea decreased and coastal progradation occurred. Between c. 3.5 and 3.0 kyr, foreshore sediments, including granules and pebbles, accumulated over the older beach deposits, indicating erosional events. Progradation resumed at ~3.0 kyr and continues to the present. During the past 3 kyr, there has been an average rate of progradation of ~0.14 m/yr. The beach-foredune ridges in the Gangneung area represent the evolution of coastal progradation on the east coast of Korea during the Holocene.
    Print ISSN: 0959-6836
    Electronic ISSN: 1477-0911
    Topics: Geography , Geosciences
    Published by Sage
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  • 3
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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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  • 4
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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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  • 5
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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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  • 6
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    Effect of PAHM (Poly-acrylonitrile Hollow Microsphere) addition on the Lightweight and Firing Behavior of Whiteware (2011)
    Institute of Physics (IOP)
    Details
    Publication Date: 2011-09-17
    Description: The pore generation technology using PAHM (Poly-acrylonitrile Hollow Microsphere) was studied in order to reduce the weights of tableware. In this study, we verify the property of modified slurry and plasticity of green body by adding PAHM. The modified slurry was prepared by adding 25~55vol% of PAHM to the slurry for whiteware. The viscosity of slurry was controlled to be low value (25~45vol%). However, the viscosity of modified slurry increased and the plasticity of modified green body decreased inside the 45~55vol% range. The formed specimen by slip casting was fired at 1225 °C, 1240°C. As the amount of PAHM content increased, the weight decreased and the addition of 45vol/% of PAHM resulted in a weight drop of 39%. However, when the PAHM content increased, the strength decreases over 50%. This is caused by the presence of a large volume of surface defects (pores) and defects from the agglomeration of PAHM.
    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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  • 7
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    Parametric performance evaluation of a hydraulic centrifugal pump (2014)
    Institute of Physics (IOP)
    Details
    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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  • 8
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    GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis (2012)
    Oxford University Press
    Details
    Publication Date: 2012-05-22
    Description: Motivation: Gene clusters are arrangements of functionally related genes on a chromosome. In bacteria, it is expected that evolutionary pressures would conserve these arrangements due to the functional advantages they provide. Visualization of conserved gene clusters across multiple genomes provides key insights into their evolutionary histories. Therefore, a software tool that enables visualization and functional analyses of gene clusters would be a great asset to the biological research community. Results: We have developed GeneclusterViz, a Java-based tool that allows for the visualization, exploration and downstream analyses of conserved gene clusters across multiple genomes. GeneclusterViz combines an easy-to-use exploration interface for gene clusters with a host of other analysis features such as multiple sequence alignments, phylogenetic analyses and integration with the KEGG pathway database. Availability: http://biohealth.snu.ac.kr/GeneclusterViz/ ; http://microbial.informatics.indiana.edu/GeneclusterViz/ Contact: sunkim.bioinfo@snu.ac.kr ; ybrun@indiana.edu 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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  • 9
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    GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis (2012)
    Oxford University Press
    Details
    Publication Date: 2012-04-11
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    Effect of radiative transfer on damped Ly  and Lyman limit systems in cosmological SPH simulations (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-21
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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