Nucleation in scale-free networks

We have studied nucleation dynamics of the Ising model in scale-free networks with degree distribution $P(k)\sim k^{-\gamma}$ by using forward flux sampling method, focusing on how the network topology would influence the nucleation rate and pathway. For homogeneous nucleation, the new phase clusters grow from those nodes with smaller degree, while the cluster sizes follow a power-law distribution. Interestingly, we find that the nucleation rate $R_{Hom}$ decays exponentially with the network size $N$, and accordingly the critical nucleus size increases linearly with $N$, implying that homogeneous nucleation is not relevant in the thermodynamic limit. These observations are robust to the change of $\gamma$ and also present in random networks. In addition, we have also studied the dynamics of heterogeneous nucleation, wherein $w$ impurities are initially added, either to randomly selected nodes or to targeted ones with largest degrees. We find that targeted impurities can enhance the nucleation rate $R_{Het}$ much more sharply than random ones. Moreover, $\ln (R_{Het}/R_{Hom})$ scales as $w^{\gamma-2/\gamma-1}$ and $w$ for targeted and random impurities, respectively. A simple mean field analysis is also present to qualitatively illustrate above simulation results.Comment: 7 pages, 5 figure

Searching for Ground Truth: a stepping stone in automating genre classification

This paper examines genre classification of documents and its role in enabling the effective automated management of digital documents by digital libraries and other repositories. We have previously presented genre classification as a valuable step toward achieving automated extraction of descriptive metadata for digital material. Here, we present results from experiments using human labellers, conducted to assist in genre characterisation and the prediction of obstacles which need to be overcome by an automated system, and to contribute to the process of creating a solid testbed corpus for extending automated genre classification and testing metadata extraction tools across genres. We also describe the performance of two classifiers based on image and stylistic modeling features in labelling the data resulting from the agreement of three human labellers across fifteen genre classes.

Zika Virus Attenuation by Codon Pair Deoptimization Induces Sterilizing Immunity in Mouse Models.

Zika virus (ZIKV) infection during the large epidemics in the Americas is related to congenital abnormities or fetal demise. To date, there is no vaccine, antiviral drug, or other modality available to prevent or treat Zika virus infection. Here we designed novel live attenuated ZIKV vaccine candidates using a codon pair deoptimization strategy. Three codon pair-deoptimized ZIKVs (Min E, Min NS1, and Min E+NS1) were de novo synthesized and recovered by reverse genetics and contained large amounts of underrepresented codon pairs in the E gene and/or NS1 gene. The amino acid sequence was 100% unchanged. The codon pair-deoptimized variants had decreased replication fitness in Vero cells (Min NS1 ≫ Min E > Min E+NS1), replicated more efficiently in insect cells than in mammalian cells, and demonstrated diminished virulence in a mouse model. In particular, Min E+NS1, the most restrictive variant, induced sterilizing immunity with a robust neutralizing antibody titer, and a single immunization achieved complete protection against lethal challenge and vertical ZIKV transmission during pregnancy. More importantly, due to the numerous synonymous substitutions in the codon pair-deoptimized strains, reversion to wild-type virulence through gradual nucleotide sequence mutations is unlikely. Our results collectively demonstrate that ZIKV can be effectively attenuated by codon pair deoptimization, highlighting the potential of Min E+NS1 as a safe vaccine candidate to prevent ZIKV infections.IMPORTANCE Due to unprecedented epidemics of Zika virus (ZIKV) across the Americas and the unexpected clinical symptoms, including Guillain-Barré syndrome, microcephaly, and other birth defects in humans, there is an urgent need for ZIKV vaccine development. Here we provided the first attenuated versions of ZIKV with two important genes (E and/or NS1) that were subjected to codon pair deoptimization. Compared to parental ZIKV, the codon pair-deoptimized ZIKVs were mammal attenuated and preferred insect to mammalian cells. Min E+NS1, the most restrictive variant, induced sterilizing immunity with a robust neutralizing antibody titer and achieved complete protection against lethal challenge and vertical virus transmission during pregnancy. More importantly, the massive synonymous mutational approach made it impossible for the variant to revert to wild-type virulence. Our results have proven the feasibility of codon pair deoptimization as a strategy to develop live attenuated vaccine candidates against flaviviruses such as ZIKV, Japanese encephalitis virus, and West Nile virus

In vivo imaging of Zika virus reveals dynamics of viral invasion in immune-sheltered tissues and vertical propagation during pregnancy

Rationale: Zika virus (ZIKV) is a pathogenic virus known to cause a wide range of congenital abnormalities, including microcephaly, Guillain-Barre syndrome, meningoencephalitis, and other neurological complications, in humans. This study investigated the noninvasive detection of ZIKV infection in vivo, which is necessary for elucidating the virus's mechanisms of viral replication and pathogenesis, as well as to accelerate the development of anti-ZIKV therapeutic strategies. Methods: In this study, a recombinant ZIKV harbouring Nluc gene (ZIKV-Nluc) was designed, recovered, and purified. The levels of bioluminescence were directly correlated with viral loads in vitro and in vivo. The dynamics of ZIKV infection in A129 (interferon (IFN)-α/β receptor deficient), AG6 (IFN-α/β and IFN-γ receptor deficient), and C57BL/6 mice were characterized. Pregnant dams were infected with ZIKV-Nluc at E10 via intra footpad injection. Then, the pooled immune sera (anti-ZIKV neutralizing antibodies) #22-1 in ZIKV-Nluc virus-infected mice were visualized. Results: ZIKV-Nluc showed a high genetic stability and replicated well in cells with similar properties to the wild-type ZIKV (ZIKVwt). Striking bioluminescence signals were consistently observed in animal organs, including spleen, intestine, testis, uterus/ovary, and kidney. The ileocecal junction was found to be the crucial visceral target. Infection of pregnant dams with ZIKV-Nluc showed that ZIKV was capable of crossing the maternal-fetal barrier to infect the fetuses via vertical transmission. Furthermore, it was visualized that treatment with the pooled immune sera was found to greatly restrict the spread of the ZIKV-Nluc virus in mice. Conclusions: This study is the first to report the real-time noninvasive tracking of the progression of ZIKV invading immune-sheltered tissues and propagating vertically during pregnancy. The results demonstrate that ZIKV-Nluc represents a powerful tool for the study of the replication, dissemination, pathogenesis, and treatment of ZIKV in vitro and in vivo

The Euler-Lagrange Cohomology and General Volume-Preserving Systems

We briefly introduce the conception on Euler-Lagrange cohomology groups on a symplectic manifold $(\mathcal{M}^{2n}, \omega)$ and systematically present the general form of volume-preserving equations on the manifold from the cohomological point of view. It is shown that for every volume-preserving flow generated by these equations there is an important 2-form that plays the analog role with the Hamiltonian in the Hamilton mechanics. In addition, the ordinary canonical equations with Hamiltonian $H$ are included as a special case with the 2-form $\frac{1}{n-1} H \omega$. It is studied the other volume preserving systems on $({\cal M}^{2n}, \omega)$. It is also explored the relations between our approach and Feng-Shang's volume-preserving systems as well as the Nambu mechanics.Comment: Plain LaTeX, use packages amssymb and amscd, 15 pages, no figure

Systematic Identification of the Influencing Factors for the Digital Transformation of the Construction Industry Based on LDA-DEMATEL-ANP

There is an urgent need to improve our understanding of the digital transformation of the construction in order to leverage the benefits of the wider adoption of the Industry 4.0 paradigm. However, there is a lack of systematic research on the digital transformation pathway of the construction industry. In view of this, this study uses the LDA theme model to explore the key influencing factors for the digital transformation of the construction industry and builds a digital comprehensive evaluation system of the construction industry with DEMATEL-ANP. The findings are as follows: Firstly, five elements of the construction industry, such as enterprise resources, enterprise capabilities, enterprise spirit, macro environment and industry environment, have an important impact on the digital transformation of the construction industry. Secondly, the ability of construction enterprises has the most significant influence on the digital transformation of the construction industry. This empirical study provides policy suggestions and an implementation framework for realizing high-quality development of the construction industry based on digital technological innovation. The study helps construction enterprises to understand the necessity of digital transformation and provides a theoretical basis and practical ideas for construction enterprises to formulate their own digital transformation strategies

Edge Shear Flows and Particle Transport near the Density Limit in the HL-2A Tokamak

Edge shear flow and its effect on regulating turbulent transport have long been suspected to play an important role in plasmas operating near the Greenwald density limit $n_G$. In this study, equilibrium profiles as well as the turbulent particle flux and Reynolds stress across the separatrix in the HL-2A tokamak are examined as $n_G$ is approached in ohmic L-mode discharges. As the normalized line-averaged density $\bar{n}_e/n_G$ is raised, the shearing rate of the mean poloidal flow $\omega_{\rm sh}$ drops, and the turbulent drive for the low-frequency zonal flow (the Reynolds power $\mathcal{P}_{Re}$) collapses. Correspondingly, the turbulent particle transport increases drastically with increasing collision rates. The geodesic acoustic modes (GAMs) gain more energy from the ambient turbulence at higher densities, but have smaller shearing rate than low-frequency zonal flows. The increased density also introduces decreased adiabaticity which not only enhances the particle transport but is also related to a reduction in the eddy-tilting and the Reynolds power. Both effects may lead to the cooling of edge plasmas and therefore the onset of MHD instabilities that limit the plasma density

Signal Transmission Across Tile Assemblies: 3D Static Tiles Simulate Active Self-Assembly by 2D Signal-Passing Tiles

The 2-Handed Assembly Model (2HAM) is a tile-based self-assembly model in which, typically beginning from single tiles, arbitrarily large aggregations of static tiles combine in pairs to form structures. The Signal-passing Tile Assembly Model (STAM) is an extension of the 2HAM in which the tiles are dynamically changing components which are able to alter their binding domains as they bind together. For our first result, we demonstrate useful techniques and transformations for converting an arbitrarily complex STAM$^+$ tile set into an STAM$^+$ tile set where every tile has a constant, low amount of complexity, in terms of the number and types of ``signals'' they can send, with a trade off in scale factor. Using these simplifications, we prove that for each temperature $\tau>1$ there exists a 3D tile set in the 2HAM which is intrinsically universal for the class of all 2D STAM$^+$ systems at temperature $\tau$ (where the STAM$^+$ does not make use of the STAM's power of glue deactivation and assembly breaking, as the tile components of the 2HAM are static and unable to change or break bonds). This means that there is a single tile set $U$ in the 3D 2HAM which can, for an arbitrarily complex STAM$^+$ system $S$, be configured with a single input configuration which causes $U$ to exactly simulate $S$ at a scale factor dependent upon $S$. Furthermore, this simulation uses only two planes of the third dimension. This implies that there exists a 3D tile set at temperature $2$ in the 2HAM which is intrinsically universal for the class of all 2D STAM$^+$ systems at temperature $1$. Moreover, we show that for each temperature $\tau>1$ there exists an STAM$^+$ tile set which is intrinsically universal for the class of all 2D STAM$^+$ systems at temperature $\tau$, including the case where $\tau = 1$.Comment: A condensed version of this paper will appear in a special issue of Natural Computing for papers from DNA 19. This full version contains proofs not seen in the published versio