Fast micro-differential evolution for topological active net optimization

This paper studies the optimization problem of topological active net (TAN), which is often seen in image segmentation and shape modeling. A TAN is a topological structure containing many nodes, whose positions must be optimized while a predefined topology needs to be maintained. TAN optimization is often time-consuming and even constructing a single solution is hard to do. Such a problem is usually approached by a ``best improvement local search'' (BILS) algorithm based on deterministic search (DS), which is inefficient because it spends too much efforts in nonpromising probing. In this paper, we propose the use of micro-differential evolution (DE) to replace DS in BILS for improved directional guidance. The resultant algorithm is termed deBILS. Its micro-population efficiently utilizes historical information for potentially promising search directions and hence improves efficiency in probing. Results show that deBILS can probe promising neighborhoods for each node of a TAN. Experimental tests verify that deBILS offers substantially higher search speed and solution quality not only than ordinary BILS, but also the genetic algorithm and scatter search algorithm

A general study on the volume dependence of spectral weights in lattice field theory

It has been suggested that the volume dependence of the spectral weight could be utilized to distinguish single and multi-particle states in Monte Carlo simulations. In a recent study using a solvable model, the Lee model, we found that this criteria is applicable only for stable particles and narrow resonances, not for the broad resonances. In this paper, the same question is addressed within the finite size formalism outlined by L\"uscher. Using a quantum mechanical scattering model, the conclusion that was found in previous Lee model study is recovered. Then, following similar arguments as in L\"uscher's, it is argued that the result is valid for a general massive quantum field theory under the same conditions as the L\"uscher's formulae. Using the spectral weight function, a possibility of extracting resonance parameters is also pointed out.Comment: 18 pages, no figure

Differential evolution with an evolution path: a DEEP evolutionary algorithm

Utilizing cumulative correlation information already existing in an evolutionary process, this paper proposes a predictive approach to the reproduction mechanism of new individuals for differential evolution (DE) algorithms. DE uses a distributed model (DM) to generate new individuals, which is relatively explorative, whilst evolution strategy (ES) uses a centralized model (CM) to generate offspring, which through adaptation retains a convergence momentum. This paper adopts a key feature in the CM of a covariance matrix adaptation ES, the cumulatively learned evolution path (EP), to formulate a new evolutionary algorithm (EA) framework, termed DEEP, standing for DE with an EP. Without mechanistically combining two CM and DM based algorithms together, the DEEP framework offers advantages of both a DM and a CM and hence substantially enhances performance. Under this architecture, a self-adaptation mechanism can be built inherently in a DEEP algorithm, easing the task of predetermining algorithm control parameters. Two DEEP variants are developed and illustrated in the paper. Experiments on the CEC'13 test suites and two practical problems demonstrate that the DEEP algorithms offer promising results, compared with the original DEs and other relevant state-of-the-art EAs

Directional Enhanced Probe for Side-Illumination Tip Enhanced Spectroscopy

We demonstrate a high-performance apertureless near-field probe made of a tapered metal tip with a set of periodic shallow grooves near the apex. The spontaneous emission from a single emitter near the tip is investigated systematically for the side-illumination tip enhanced spectroscopy (TES). In contrast with the bare tapered metal tip in conventional side-illumination TES, the corrugated probe not only enhances strongly local excitation field but also concentrates the emission directivity, which leads to high collection efficiency and signal-to-noise ratio. In particular, we propose an asymmetric TES tip based on two coupling nanorods with different length at the apex to realize unidirectional enhanced emission rate from a single emitter. Interestingly, we find that the radiation pattern is sensitive to the emission wavelength and the emitter positions respective to the apex, which can result in an increase of signal-to-noise ratio by suppressing undesired signal. The proposed asymmetrical corrugated probe opens up a broad range of practical applications, e.g. increasing the detection efficiency of tip enhanced spectroscopy at the single-molecule level

Mapping quantitative trait loci for T lymphocyte subpopulations in peripheral blood in swine

<p>Abstract</p> <p>Background</p> <p>Increased disease resistance through improved general immune capacity would be beneficial for the welfare and productivity of farm animals. T lymphocyte subpopulations in peripheral blood play an important role in immune capacity and disease resistance in animals. However, very little research to date has focused on quantitative trait loci (QTL) for T lymphocyte subpopulations in peripheral blood in swine.</p> <p>Results</p> <p>In the study, experimental animals consist of 446 piglets from three different breed populations. To identify QTL for T lymphocyte subpopulations in peripheral blood in swine, the proportions of CD4+, CD8+, CD4+CD8+, CD4+CD8-, CD4-CD8+, and CD4-CD8- T cells and the ratio of CD4+:CD8+ T cells were measured for all individuals before and after challenge with modified live CSF (classical swine fever) vaccine. Based on the combined data of individuals from three breed populations, genome-wide scanning of QTL for these traits was performed based on a variance component model, and the genome wide significance level for declaring QTL was determined via permutation tests as well as FDR (false discovery rate) correction. A total of 27 QTL (two for CD4+CD8+, one for CD4+CD8-, three for CD4-CD8+, two for CD4-CD8-, nine for CD4+, two for CD8+, and eight for CD4+:CD8+ ratio) were identified with significance level of <it>FDR </it>< 0.10, of which 11 were significant at the level of <it>FDR </it>< 0.05, including the five significant at <it>FDR </it>< 0.01.</p> <p>Conclusions</p> <p>Within these QTL regions, a number of known genes having potential relationships with the studied traits may serve as candidate genes for these traits. Our findings herein are helpful for identification of the causal genes underlying these immune-related trait and selection for immune capacity of individuals in swine breeding in the future.</p

Gap-free X and Y chromosome assemblies of Salix arbutifolia reveal an evolutionary change from male to female heterogamety in willows, without a change in the position of the sex-determining locus

Summary In the Vetrix clade of Salix, a genus of woody flowering plants, sex determination involves chromosome 15, but an XY system has changed to a ZW system. We studied the detailed genetic changes involved. We used genome sequencing, with chromosome conformation capture (Hi-C) and PacBio HiFi reads to assemble chromosome level gap-free X and Y of Salix arbutifolia, and distinguished the haplotypes in the 15X- and 15Y-linked regions, to study the evolutionary history of the sex-linked regions (SLRs). Our sequencing revealed heteromorphism of the X and Y haplotypes of the SLR, with the X-linked region being considerably larger than the corresponding Y region, mainly due to accumulated repetitive sequences and gene duplications. The phylogenies of single-copy orthogroups within the SLRs indicate that S. arbutifolia and Salix purpurea share an ancestral SLR within a repeat-rich region near the chromosome 15 centromere. During the change in heterogamety, the X-linked region changed to a W-linked one, while the Z was derived from the Y

MicroRNA-203 inhibits cell proliferation by repressing ΔNp63 expression in human esophageal squamous cell carcinoma

<p>Abstract</p> <p>Background</p> <p>This study was performed to investigate the effect of microRNA-203 (miR-203) and ΔNp63 on cell proliferation and the functional connection between miR-203 and ΔNp63 in ESCC.</p> <p>Methods</p> <p>We employed 2 human ESCC cell lines, Eca109 and TE-1, as the model system. The effect of miR-203 and ΔNp63 on cell proliferation was determined in cells transfected with miR-203 mimic and ΔNp63 small interfering RNA (siRNA), respectively. The regulation of ΔNp63 expression in ESCC cells by miR-203 was studied by luciferase reporter assay, RT-PCR and western blot analysis in cells transfected with miR-203. The effect of ΔNp63 re-expression on miR-203 induced inhibition of cell proliferation was studied by cell proliferation assay in cells cotransfected with miR-203 and pcDNA-ΔNp63 plasmid (without the 3'-UTR of <it>ΔNp63</it>).</p> <p>Results</p> <p>We found that both miR-203 and ΔNp63 siRNA signicantly inhibited cell proliferation in ESCC. MiR-203 could down-regulate endogenous ΔNp63 expression at the posttranscriptional level. Moreover, re-expression of ΔNp63 in cells transfected with miR-203 significantly attenuated the miR-203 induced inhibition of cell proliferation.</p> <p>Conclusions</p> <p>Our data implied that miR-203 could inhibit cell proliferation in human ESCC through ΔNp63-mediated signal pathway. Therefore, we propose that miR-203 might be used as a therapeutic agent for human ESCC.</p