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Lirex： A Package for Identification of LongInverted Repeats in Genomes

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Genomics, Proteomics & Bioinformatics 2017年第2期15卷 141-146页

作者： Yong Wang jiao-Mei huang Institute of Deep-Sea Science and Engineering Chinese Academy of Sciences Sanya 572000 China

Long inverted repeats(LIRs) are evolutionarily and functionally important structures in genomes because of their involvement in RNA interference, DNA recombination, and gene duplication. Identification of LIRs is highly complicated when mismatches and indels between the repeats are permitted. Long inverted repeat explorer(Lirex) was developed and introduced in this report. Written in Java, Lirex provides a user-friendly interface and allows users to specify LIR searching criteria, such as length of the region, as well as pattern and size of the repeats. Recombinogenic LIRs can be selected on the basis of mismatch rate and internal spacer size from identified LIRs. Lirex, as a cross-platform tool to identify LIRs in a genome, may assist in designing following experiments to explore the function of LIRs. Our tool can identify more LIRs than other LIR searching tools. Lirex is publicly available at http://124.***.219.129/Lirex.

关键词： Lirex Inverted repeats Recombination Stem-loop Mismatch rate

Gene engineering in swine for agriculture

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Journal of Integrative Agriculture 2017年第12期16卷 2792-2804页

作者： WANG Yan-fang huang jiao-jiao ZHAO Jian-guo Institute of Animal Science Chinese Academy of Agricultural Sciences Beijing 100193 P.R. China Institute of Zoology Chinese Academy of Sciences Beijing 100101 P.R.China University of Chinese Academy of Sciences Beijing 100049 P.R. China

Domestic pigs are the second most important source of meat world-wide, and the genetic improvement of economic traits, such as meat production, growth, and disease resistance, is a critical point for efficient production in pigs. Through conventional breeding and selection programs in pigs, which are painstakingly slow processes, some economic traits, such as growth and backfat, have been greatly improved over the past several decades. However, the improvement of many polygenetic traits is still very slow and challenging to be improved by conventional breeding strategies. The development of reproductive knowledge and a variety of techniques, including foreign gene transfer strategies, somatic cell nuclear transfer（SCNT） and particularly, recently developed nuclease-mediated genome editing tools, has provided efficient ways to produce genetically modified（GM） pigs for the dramatic improvement of economic traits. In this review, we briefly discuss the progress of genomic markers used in pig breeding program, trace the history of genetic engineering, mainly focusing on the progress of recently developed genome editing tools, and summarize the GM pigs which have been generated to aim at the agricultural purposes. We also discuss the specific challenges facing application of gene engineering in pig breeding, and future prospects.

关键词： gene engineering genome editing pig agricultural application

Novel Localized Excitations of Nonlinear Coupled Scalar Fields

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Communications in Theoretical Physics 2008年第6期49卷 1365-1372页

作者： LI Jin-Hua WU huang-jiao Department of Physics and Center of Nonlinear Science Ningbo University Ningbo 315211 China

Some extended solution mapping relations of the nonlinear coupled scalar field and the well-known φ^4 model are presented. Simultaneously, inspired by the new solutions of the famous φ^4 model recently proposed by Jia, huang and Lou, five kinds of new localized excitations of the nonlinear coupled scaiar field （NCSF） system are obtained.

关键词： nonlinear coupled scalar field solitary wave structure mapping and deformation approach

Neuroendocrine cells of prostate cancer: biologic functions and molecular mechanisms

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Asian Journal of Andrology 2019年第3期21卷 291-295页

作者： Yu-Hua huang Ya-Qun Zhang jiao-Ti huang Department of Urology The First Affiliated Hospital of Soochow University Suzhou 215006 China Department of Urology Beijing Hospital National Center of Gerontology Beijing 100730 China Department of Pathology Duke University School of Medicine Durham NC 27514 USA

Prostate cancer (PCa) is a major health risk for older men worldwide. Existing systemic therapies mostly target androgen receptor (AR). Although treatments are initially effective, the disease always recurs. A potential mechanism for the treatment failure is that PCa contains, in addition to the AR-positive luminal type tumor cells, a small component of neuroendocrine (NE) cells. The function of NE cells in PCa remains poorly understood, and one important characteristic of these cells is their lack of expression of AR and resistance to hormonal therapy. In addition, many patients develop the more aggressive small-cell neuroendocrine carcinoma (SCNC) after hormonal therapy. Although this clinical phenomenon of disease transformation from adenocarcinoma to SCNC is well established, the cell of origin for SCNC remains unclear. Recently, loss of function of Rb and TP53 and amplification and overexpression of MYCN and Aurora A kinase have been identified as important biomarkers and potential disease drivers. In this article, we systematically review the histology of normal prostate and prostate cancer including the main histologic types: adenocarcinoma and SCNC. We also review the findings from many studies using cellular and animal models as well as human specimens that attempt to understand the molecular mechanisms of treatment failure, disease progression, and tumor transformation from adenocarcinoma to SCNC.

关键词： adenocarcinoma neuroendocrine prostate small-cell carcinoma

Effect of Surface State on Nodular Corrosion Resistance of Zircaloy-4 Alloy

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Acta Metallurgica Sinica(English Letters) 2015年第2期28卷 254-260页

作者： Chuan-Ming Chen Bang-Xin Zhou Shao-Qiu Gou jiao huang Mei-Yi Yao Laboratory for Microstructures Shanghai University Institute of Materials Shanghai University

The effect of surface state on the nodular corrosion resistance of Zircaloy-4 alloy was investigated in super- heated steam at 500 ℃/10.3 MPa by autoclave tests. The microstructures of oxide films on the corroded specimens were observed by TEM and SEM. The results indicate that surface strained layer delays the appearance of nodular spots on the specimen surfaces and improves the nodular corrosion resistance. The columnar grains orientation of the oxide films formed on the specimens with surface strained layer was more consistent than that on the specimens without surface strained layer when a comparison was made on the same orientation of the grain surfaces. Such a kind of oxide micro- structure formed on the specimens with surface strained layer can hinder the diffusion of oxygen ions along the grain boundaries and delay the growth of oxide films, therefore retard the formation process of nodular spots. This indicates that the microstructure of the initial oxide films has an important influence on the subsequent growth of the oxide films.

关键词： Zircaloy-4 Surface strained layer Nodular corrosion resistance Microstructures

Atom Probe Tomography Study of Fe Segregation at Phase Interface in Zr–2.5Nb Alloy

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Acta Metallurgica Sinica(English Letters) 2019年第10期32卷 1281-1286页

作者： Xue Liang Qiang Li jiao huang Mei-Yi Yao Hui Li Qing-Dong Liu Institute of Materials Shanghai University Shanghai 200072 China Laboratory for Microstructures Shanghai University Shanghai 200444 China School of Materials Science and Engineering Inner Mongolia University of Technology Hohhot 010051. China School of Nuclear Science and Engineering Shanghai Jiaotong University Shanghai 200240 China

β-Nb is a typical second phase in Zr-Nb-based alloys used as fuel claddings in water-cooled nuclear reactors. The segregation of alloying element Fe may affect the corrosion resistance of Zr-Nb-based alloys. In this work, the Fe segregation at the interface between β-Nb phase and a-Zr matrix in Zr-2.5Nb alloy was studied using atom probe tomography and focused ion beam. The results suggested that the Fe concentration was much lower than Nb concentration in a-Zr matrix, while Fe selectively segregated at the β-Nb/a-Zr phase interface, leading to a Fe concentration peak at some interfaces. The peak Fe concentration varied from 0.4 to 1.2 at.% and appeared at the position where Zr concentration was approximately equal to Nb concentration. The selective segregation of Fe should be affected by the heat treatment and structure defects induced by cold rolling.

关键词： Zr-Nb alloy β-Nb phase Phase interface Segregation Atom probe tomography

Systemic lupus erythematosus presenting with progressive massive ascites and CA-125 elevation indicating Tjalma syndrome?A case report

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World Journal of Clinical Cases 2022年第26期10卷 9447-9453页

作者： Jun-Di Wang Yan-Fei Yang Xian-Feng Zhang jiao huang Department of Rheumatic Disease Affiliated Hangzhou First People’s HospitalZhejiang University School of MedicineHangzhou 310000Zhejiang ProvinceChina Department of Respiratory Disease Hangzhou Hospital of Traditional Chinese MedicineHangzhou 310000Zhejiang ProvinceChina

BACKGROUND Ascites,pleural effusion and raised CA-125 in the absence of malignancy in systemic lupus erythematosus is known as Tjalma *** SUMMARY We report a special case of a systemic lupus erythematosus patient presenting with Tjalma *** presented with ascites and elevated CA-125 in the absence of benign or malignant ovarian tumor and no pleural effusions,which is an unusual presentation for this rare *** Tjalma syndrome can present with massive ascites alone without pleural or pericardial effusions.

关键词： Tjalma syndrome Pseudo–pseudo Meigs’syndrome Systemic lupus erythematosus Ascites CA-125 Case report

Coexistence and local Mittag–Leffler stability of fractional-order recurrent neural networks with discontinuous activation functions

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Chinese Physics B 2019年第4期28卷 131-140页

作者： Yu-jiao huang Shi-Jun Chen Xu-Hua Yang Jie Xiao College of Computer Science and Technology Zhejiang University of Technology

In this paper, coexistence and local Mittag–Leffler stability of fractional-order recurrent neural networks with discontinuous activation functions are addressed. Because of the discontinuity of the activation function, Filippov solution of the neural network is defined. Based on Brouwer's fixed point theorem and definition of Mittag–Leffler stability, sufficient criteria are established to ensure the existence of (2k + 3)~n (k ≥ 1) equilibrium points, among which (k + 2)~n equilibrium points are locally Mittag–Leffler stable. Compared with the existing results, the derived results cover local Mittag–Leffler stability of both fractional-order and integral-order recurrent neural networks. Meanwhile discontinuous networks might have higher storage capacity than the continuous ones. Two numerical examples are elaborated to substantiate the effective of the theoretical results.

关键词： fractional-order recurrent neural network local Mittag–Leffler stability discontinuous activation function

Microstructure of Bi-containing zirconium alloys

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Rare Metals 2022年第10期41卷 3566-3573页

作者： Han-Pei Zhao Mei-Yi Yao jiao huang Jin-Long Zhang Jian-Chao Peng Bang-Xin Zhou Laboratory for Microstructure Shanghai UniversityShanghai200444China Institute of Materials Shanghai UniversityShanghai200072China

The effect of Bi addition(0.05 wt%-0.50 wt%)on the microstructure of zirconium alloys,including T5(Zr-0.7 S n-1.0 Nb-0.3 Fe-0.1 Cr),S5(Zr-0.8 Sn-0.35 Nb-0.4 Fe-0.1 Cr),Zr-4(Zr-1.5 Sn-0.2 Fe-0.1 Cr) and Zr-1 Nb,was investigated by transmission electron microscopy(TEM),energy-dispersive spectroscopy(EDS) and selected area electron diffraction(SAED).Results show that with the increase in Bi content,h-Zr(Fe,Cr,Nb)2,o-Zr(Fe,Sn,Bi)_(2) and Zr-Fe-Cr-Nb-Sn-Bi second-phase particles(SPPs) precipitate successively in the T5+xBi and S5+xBi alloys;in the Zr-4+xBi alloys,h-Zr(Fe,Cr)2,o-Zr(Fe,Sn,Bi)2,Zr-Fe-Cr-Sn-Bi and Zr-Fe-Cr-Bi SPPs are detected *** as for Zr-1 Nb+xBi alloys,Bi-free SPPs *** addition of Bi promotes the precipitation of SPPs with Sn in the *** concentration of Bi dissolved in α-Zr matrix increases with the decrease in Sn content in the *** reasonable Bi has little influence on the solid solution content of Nb in α-Zr matrix.

关键词： Zirconium alloy Bismuth Second-phase particles Microstructure