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Xi, Hong,Park, Jongsun,Ding, Guohui,Lee, Yong-Hwan,Li, Yixue Oxford University Press 2009 Nucleic acids research Vol.37 No.1
<P>Some mutations resulting in protein sequence change might be tightly related to certain human diseases by affecting its roles, such as sickle cell anemia. Until now several databases, such as PMD, OMIM and HGMD, have been developed, providing useful information about human disease-related mutation. Tandem mass spectrometry (MS) has been used for characterizing proteins in various conditions; however, there is no system in place for finding disease-related mutated proteins within the MS results. Here, a Systematical Platform for Identifying Mutated Proteins (SysPIMP; http://pimp.starflr.info/) was developed to efficiently identify human disease-related mutated proteins within MS results. SysPIMP comprises of three layers: (i) a standardized data warehouse, (ii) a pipeline layer for maintaining human disease databases and X!Tandem and BLAST and (iii) a web-based interface. From OMIM AV part, PMD and SwissProt databases, 35 497 non-redundant human disease-related mutated sequences were collected with disease information described by OMIM terms. With the interfaces to browse sequences archived in SysPIMP, X!Tandem, an open source database-search engine used to identify proteins within MS data, was integrated into SysPIMP to help support the detection of potential human disease-related mutants in MS results. In addition, together with non-redundant disease-related mutated sequences, original non-mutated sequences are also provided in SysPIMP for comparative research. Based on this system, SysPIMP will be the platform for efficiently and intensively studying human diseases caused by mutation.</P>
Xihong Zhao,Li Wang,Jin Chu,Yanyan Li,Yanmei Li,Lin Li,Mark E. Shirtliff,Xiaowei He,Yao Liu,Jihua Wang,Liansheng Yang,Zhenbo Xu 한국식품과학회 2010 Food Science and Biotechnology Vol.19 No.5
A loop-mediated isothermal amplification (LAMP) method for rapid detection of the foodborne Vibrio parahaemolyticus strains and related virulent factors had been developed and evaluated in this study. Six primers, including outer primers, inner primers, and loop primers, were specially designed for recognizing 8 distinct sequences on 3 target genes, which were tlh, tdh, and trh. The detection limits were found to be 100, 100 fg, and 1 pg DNA/tube for tlh, tdh, and trh, respectively. Application of LAMP assays were performed on 368 foodborne V. parahaemolyticus strains, the sensitivities of LAMP assays for the tlh, tdh, and trh were 100, 95.6, and 96.4%, and the negative predictive values (NPV) were 100, 84.7, and 93.1%, respectively; with a 100% specificity and positive predictive value (PPV) for all 3 target genes.
Xihong Zhao,Li Wang,Jin Chu,Yanmei Li,Yanyan Li,Zhenbo Xu,Lin Li,Mark E. Shirtliff,Xiaowei He,Yao Liu,Jihua Wang,Liansheng Yang 한국식품과학회 2010 Food Science and Biotechnology Vol.19 No.6
A loop-mediated isothermal amplification (LAMP) method for rapid detection of the food-borne Salmonella strains had been developed and evaluated in this study. The optimal reaction condition was found to be 65℃ for 45 min, with the detection limit as 1 pg DNA/tube and 100 CFU/reaction. Application of LAMP assays was performed on 214 food-borne Salmonella strains using a rapid procedure and easy result confirmation, where the specificity of LAMP and polymerase chain reaction (PCR)assays was 97.7% (209/214) and 91.6% (196/214),respectively; with a 100% specificity for both assays.
( Xihong Zhao ),( Jun Wang ),( Fereidoun Forghani ),( Joong Hyun Park ),( Myoung Su Park ),( Kun Ho Seo ),( Deog Hwan Oh ) 한국미생물 · 생명공학회 2013 Journal of microbiology and biotechnology Vol.23 No.12
Conventional molecular detection methods cannot distinguish between viable and dead Escherichia coli O157 cells. In this study, the loop-mediated isothermal amplification (LAMP) method combined with propidium monoazide (PMA) treatment was developed to selectively detect viable E. coli O157 cells. Four primers, including outer primers and inner primers, were specially designed for the recognition of six distinct sequences on the serogroups (O157) of the specific rfbE gene of the E. coli O157 genome. PMA selectively penetrated through the compromised cell membranes and intercalated into DNA. Amplification of DNA from dead cells was completely inhibited by 3.0 μg/ml PMA, whereas the DNA derived from viable cells was amplified remarkably within 1 h by PMA-LAMP. Exhibiting high sensitivity and specificity, PMA-LAMP is a suitable method for evaluating the inactivation efficacy of slightly acidic electrolyzed water in broth. PMA-LAMP can selectively detect viable E. coli O157 cells. This study offers a novel molecular detection method to distinguish between viable and dead E. coli O157 cells.
The complete chloroplast genome of Campsis grandiflora (Bignoniaceae)
박종선,XIHONG 한국식물분류학회 2022 식물 분류학회지 Vol.52 No.3
Campsis grandiflora (Thunb.) K. Schum is an ornamental species with various useful biological effects. The chloroplast genome of C. grandiflora isolated in Korea is 154,293 bp long (GC ratio: 38.1%) and has four subregions: 84,121 bp of large single-copy (36.2%) and 18,521 bp of small single-copy (30.0%) regions are separated by 24,332 bp of inverted repeat (42.9%) regions including 132 genes (87 protein-coding genes, eight rRNAs, and 37 tRNAs). One single-nucleotide polymorphism and five insertion and deletion (INDEL) regions (40-bp in total) were identified, indicating a low level of intraspecific variation in the chloroplast genome. All five INDEL regions were linked to the repetitive sequences. Seventy-two normal simple sequence repeats (SSRs) and 47 extended SSRs were identified to develop molecular markers. The phylogenetic trees of 29 representative Bignoniaceae chloroplast genomes indicate that the tribe-level phylogenic relationship is congruent with the findings of previous studies.
Field Testing and Analysis During Top-down Construction of Super-tall Buildings in Shanghai
Yongjing Tang,Xihong Zhao 대한토목학회 2016 KSCE JOURNAL OF CIVIL ENGINEERING Vol.20 No.2
Although certain measurements regarding super-tall buildings constructed using the top-down method have been published, new advances in top-down construction have been developed with the construction of super-tall buildings in China. This paper presents the theory of soil-structure interactions in pile foundations and extends it to the top-down construction method. Based on this theory, the forces and the deformation of the diaphragm wall, slab and soldier piles at various stages of construction can be computed. Two typical tall buildings of 60 and 37 stories with deeply embedded 4-level and 5-level basements located in Shanghai were used as case studies of the vertical displacements of their diaphragm walls and soldier piles, the deflections of the diaphragm walls, the earth pressures, and the rebar stresses during top-down construction. The values measured in the field agree well with the predicted values from soilstructure interactions theory and statistical-empirical formulas. Two additional super-tall buildings of 101 and 121 stories, in which the 4- level and 5-level basements and the main buildings are round, are discussed regarding their unique deformational characteristics. In addition, the diaphragm wall can serve a load-sharing function. These engineering case studies, including the comprehensive predictions of deformation based on field tests and estimates using statistical formulas, can improve tall building design.
Joint Channel Estimation and Equalization for MIMO-SCFDE Systems over Doubly Selective Channels
Zedong Xie,Xihong Chen,Xiaopeng Liu 한국통신학회 2017 Journal of communications and networks Vol.19 No.6
This paper considers a novel joint channel estimationand equalization (JCEE) algorithm for multiple-input-multipleoutputsingle-carrier frequency-domain-equalization (MIMOSCFDE)system over doubly selective channels for the first time. Given that the doubly selective channels can no longer support theassumption that the channel frequency-domain response remainsinvariant for the duration of one block, most of the channel estimationmethods cannot be applied directly in it. And the lack of theinformation interaction between channel estimation and channelequalization degrades the overall performance. We put forward anoise-eliminated minimum-mean-square-error channel estimation(MMSE-CE) algorithm for the initialization, which is then utilizedfor iterative processing using the ordered successive interferencecancellation (OSIC) technique. Analysis and simulation results validatethe improved performance of the proposed JCEE algorithmfor MIMO-SCFDE systems over doubly selective channels.
Extension of phase-isometries between the unit spheres of atomic $L_p$-spaces for $p>0$
Xujian Huang,Xihong Jin 대한수학회 2019 대한수학회보 Vol.56 No.6
In this paper, we prove that for every surjective phase-iso\-metry between the unit spheres of real atomic $L_p$-spaces for $p>0$, its positive homogeneous extension is a phase-isometry which is phase equivalent to a linear isometry.