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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Algorithmica 19 (1997), S. 354-368 
    ISSN: 1432-0541
    Keywords: Key words. Parallel algorithms, Maximal acyclic sets, Planar graphs.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science , Mathematics
    Notes: Abstract. Given a graph G=(V,E), the well-known spanning forest problem of G can be viewed as the problem of finding a maximal subset F of edges in G such that the subgraph induced by F is acyclic. Although this problem has well-known efficient NC algorithms, its vertex counterpart, the problem of finding a maximal subset U of vertices in G such that the subgraph induced by U is acyclic, has not been shown to be in NC (or even in RNC) and is not believed to be parallelizable in general. In this paper we present NC algorithms for solving the latter problem for two special cases. First, we show that, for a planar graph with n vertices, the problem can be solved in $O(\log^3 n)$ time with O(n) processors on an EREW PRAM. Second, we show that the problem is solvable in NC if the input graph G has only vertex-induced paths of length polylogarithmic in the number of vertices of G. As a consequence of this result, we show that certain natural extensions of the well-studied maximal independent set problem remain solvable in NC. Moreover, we show that, for a constant-degree graph with n vertices, the problem can be solved in $O(\sqrt{n}\log^3n)$ time with O(n 2 ) processors on an EREW PRAM.
    Type of Medium: Electronic Resource
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  • 2
    Publication Date: 2016-09-20
    Description: The compaction of nucleosomal structures creates a barrier for DNA-binding transcription factors (TFs) to access their cognate cis -regulatory elements. Pioneer factors (PFs) such as FOXA1 are able to directly access these cis -targets within compact chromatin. However, how these PFs interplay with nucleosomes remains to be elucidated, and is critical for us to understand the underlying mechanism of gene regulation. Here, we have conducted a computational analysis on a strand-specific paired-end ChIP-exo (termed as ChIP-ePENS) data of FOXA1 in LNCaP cells by our novel algorithm ePEST. We find that FOXA1 chromatin binding occurs via four distinct border modes (or footprint boundary patterns), with a preferential footprint boundary patterns relative to FOXA1 motif orientation. In addition, from this analysis three fundamental nucleotide positions ( oG, oS and oH ) emerged as major determinants for blocking exo-digestion and forming these four distinct border modes. By integrating histone MNase-seq data, we found an astonishingly consistent, ‘well-positioned’ configuration occurs between FOXA1 motifs and dyads of nucleosomes genome-wide. We further performed ChIP-seq of eight chromatin remodelers and found an increased occupancy of these remodelers on FOXA1 motifs for all four border modes (or footprint boundary patterns), indicating the full occupancy of FOXA1 complex on the three blocking sites ( oG, oS and oH ) likely produces an active regulatory status with well-positioned phasing for protein binding events. Together, our results suggest a positional-nucleosome-oriented accessing model for PFs seeking target motifs, in which FOXA1 can examine each underlying DNA nucleotide and is able to sense all potential motifs regardless of whether they face inward or outward from histone octamers along the DNA helix axis.
    Keywords: Protein-nucleic acid interaction, Computational Methods, Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2015-01-23
    Description: DAC can restore expression of NALP1 to suppress tumor growth in colon cancer Cell Death and Disease 6, e1602 (January 2015). doi:10.1038/cddis.2014.532 Authors: C Chen, B Wang, J Sun, H Na, Z Chen, Z Zhu, L Yan, S Ren & Y Zuo
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 4
    Publication Date: 2012-05-09
    Description: Previous studies have suggested that, over the course of the Neolithic period, settlements in the Yangtze coastal plain gradually moved seawards and concentrated to the east of Lake Taihu, probably responding to the effects of sea-level change during the middle to late Holocene. To test this hypothesis, sediment cores adjacent to six Neolithic settlement sites across the study area were collected and analyzed for pollen and other microfossils. These records reveal details of the environmental conditions before, during and after the Neolithic occupation at each site. Results show that a freshwater marsh environment became established before each human occupation and persisted throughout and after it. There is no evidence at any site of a sudden or drastic change in environmental conditions towards the end of human settlement. After c . 7000 cal. yr BP the study area had become a wetland enclosed by Chenier ridges on the east (the southern shore of the Yangtze) and the south (the northern shore of Hangzhou Bay). During the Neolithic period ( c . 7000-3000 cal. yr BP) sea level rose slowly by c . 2 m, and elevated water-tables saw the inland Taihu area become lacustrine, while to seaward on slightly higher ground enhanced sedimentation maintained freshwater marshes, fens and swamp-woodland, particularly near the Chenier ridges. These wetland-fringed coastal areas provided resources, including shellfish, deer, boar and migratory birds, that might have attracted the Neolithic communities that were abandoning their former settlement sites in the lower-lying inland area, flooded by the expanded lakes around Taihu, after c . 4200 cal. BP.
    Print ISSN: 0959-6836
    Electronic ISSN: 1477-0911
    Topics: Geography , Geosciences
    Published by Sage
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  • 5
    Publication Date: 2014-03-13
    Description: Alternative splicing (AS), in higher eukaryotes, is one of the mechanisms of post-transcriptional regulation that generate multiple transcripts from the same gene. One particular mode of AS is the skipping event where an exon may be alternatively excluded or constitutively included in the resulting mature mRNA. Both transcript isoforms from this skipping event site, i.e . in which the exon is either included (inclusion isoform) or excluded (skipping isoform), are typically present in one cell, and maintain a subtle balance that is vital to cellular function and dynamics. However, how the prevailing conditions dictate which isoform is expressed and what biological factors might influence the regulation of this process remain areas requiring further exploration. In this study, we have developed a novel computational method, graph-based exon-skipping scanner (GESS), for de novo detection of skipping event sites from raw RNA-seq reads without prior knowledge of gene annotations, as well as for determining the dominant isoform generated from such sites. We have applied our method to publicly available RNA-seq data in GM12878 and K562 cells from the ENCODE consortium and experimentally validated several skipping site predictions by RT-PCR. Furthermore, we integrated other sequencing-based genomic data to investigate the impact of splicing activities, transcription factors (TFs) and epigenetic histone modifications on splicing outcomes. Our computational analysis found that splice sites within the skipping-isoform-dominated group (SIDG) tended to exhibit weaker MaxEntScan-calculated splice site strength around middle, ‘skipping’, exons compared to those in the inclusion-isoform-dominated group (IIDG). We further showed the positional preference pattern of splicing factors, characterized by enrichment in the intronic splice sites immediately bordering middle exons. Finally, our analysis suggested that different epigenetic factors may introduce a variable obstacle in the process of exon–intron boundary establishment leading to skipping events.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 6
    Publication Date: 2018-06-29
    Description: The ultrafast laser excitation of matters leads to nonequilibrium states with complex solid-liquid phase-transition dynamics. We used electron diffraction at mega–electron volt energies to visualize the ultrafast melting of gold on the atomic scale length. For energy densities approaching the irreversible melting regime, we first observed heterogeneous melting on time scales of 100 to 1000 picoseconds, transitioning to homogeneous melting that occurs catastrophically within 10 to 20 picoseconds at higher energy densities. We showed evidence for the heterogeneous coexistence of solid and liquid. We determined the ion and electron temperature evolution and found superheated conditions. Our results constrain the electron-ion coupling rate, determine the Debye temperature, and reveal the melting sensitivity to nucleation seeds.
    Keywords: Physics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2018-09-20
    Description: Coxsackievirus A10 (CVA10) recently emerged as a major pathogen of hand, foot, and mouth disease and herpangina in children worldwide, and lack of a vaccine or a cure against CVA10 infections has made therapeutic antibody identification a public health priority. By targeting a local isolate, CVA10-FJ-01, we obtained a potent antibody, 2G8, against all three capsid forms of CVA10. We show that 2G8 exhibited both 100% preventive and 100% therapeutic efficacy against CVA10 infection in mice. Comparisons of the near-atomic cryo–electron microscopy structures of the three forms of CVA10 capsid and their complexes with 2G8 Fab reveal that a single Fab binds a border region across the three capsid proteins (VP1 to VP3) and explain 2G8’s remarkable cross-reactivities against all three capsid forms. The atomic structures of this first neutralizing antibody of CVA10 should inform strategies for designing vaccines and therapeutics against CVA10 infections.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 8
    Publication Date: 2013-07-09
    Description: Author(s): Y. Gao, Z. Chen, Z. Bond, A. Loether, L. E. Howard, S. LeMar, S. White, A. Watts, B. C. Walker, and M. F. DeCamp Time-resolved x-ray diffraction is a very powerful tool for visualizing transient one-dimensional crystalline strains, ranging from crystal growth to shockwave production. In this work, we use picosecond x-ray diffraction to visualize transient strain formation from nanometer-scaled laser-excited go... [Phys. Rev. B 88, 014302] Published Mon Jul 08, 2013
    Keywords: Dynamics, dynamical systems, lattice effects
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 9
    Publication Date: 2013-03-26
    Description: Author(s): Z. Chen, Z. Wei, Y. Chen, and C. Dames Most standard models for the thermal boundary conductance (TBC) assume isotropic properties and thus are inappropriate for layered and chainlike materials such as graphite, Bi 2 Te 3 , and high-density polyethylene (HDPE). To model such anisotropic materials, here a framework is introduced whereby the f... [Phys. Rev. B 87, 125426] Published Mon Mar 25, 2013
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 10
    Publication Date: 1997-11-01
    Print ISSN: 0178-4617
    Electronic ISSN: 1432-0541
    Topics: Computer Science , Mathematics
    Published by Springer
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