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Search Results: 1 - 10 of 6403 matches for " GuangZhi Tong "
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Ensemble-based active learning for class imbalance problem  [PDF]
Yanping Yang, Guangzhi Ma
Journal of Biomedical Science and Engineering (JBiSE) , 2010, DOI: 10.4236/jbise.2010.310133
Abstract: In medical diagnosis, the problem of class imbalance is popular. Though there are abundant unlabeled data, it is very difficult and expensive to get labeled ones. In this paper, an ensemble-based active learning algorithm is proposed to address the class imbalance problem. The artificial data are created according to the distribution of the training dataset to make the ensemble diverse, and the random subspace re-sampling method is used to reduce the data dimension. In selecting member classifiers based on misclassification cost estimation, the minority class is assigned with higher weights for misclassification costs, while each testing sample has a variable penalty factor to induce the ensemble to correct current error. In our experiments with UCI disease datasets, instead of classification accuracy, F-value and G-means are used as the evaluation rule. Compared with other ensemble methods, our method shows best performance, and needs less labeled samples.
Generation of an infectious clone of HuN4-F112, an attenuated live vaccine strain of porcine reproductive and respiratory syndrome virus
Shanrui Zhang, Yanjun Zhou, Yifeng Jiang, Guoxin Li, Liping Yan, Hai Yu, Guangzhi Tong
Virology Journal , 2011, DOI: 10.1186/1743-422x-8-410
Abstract: In the study, genomic sequence of HuN4-F112, an attenuated vaccine virus derived from the highly pathogenic porcine reproductive and respiratory syndrome virus (PRRSV) HuN4 strain, was determined and its full-length cDNA was cloned. Capped RNA was transcribed in vitro from the cDNA clone and transfected into BHK-21 cells. The supernatant from transfected monolayers were serially passaged in Marc-145 cells. The rescued virus exhibited a similar growth pattern to its parental virus in Marc-145 cells with peak titers at 48 h post-infection.In conclusion, we rescued virus from an infectious cDNA clone of attenuated vaccine. It is possible in the future that a new attenuated PRRSV vaccine with broader specificity and good immunogenicity can be designed in vitro via an infectious cDNA clone platform coupled with validated information on virulence determinants.Porcine reproductive and respiratory syndrome (PRRS) was first reported in late 1980s in North America and shortly thereafter in Europe. The disease is characterized by reproductive failure in late gestation in sows and respiratory symptoms in pigs of all ages [1-3]. Nowadays, PRRS has become one of the most economically important infectious diseases of pig worldwide [4,5]. The PRRS virus (PRRSV) is a small enveloped positive-strand RNA virus belonging to the family Arteriviridae in the order Nidovirales together with equine arteritis virus (EAV), simian hemorrhagic fever virus, and lactate dehydrogenase-elevating virus (LDV) of mice[6,7]. PRRSV is further classified into two distinct genotypes, the North American type and the European type [8,9].Since May 2006, an atypical PRRS (also known as porcine high fever syndrome) has been pandemic in China. Several studies have confirmed that the causative agent of the outbreaks was highly pathogenic PRRSV (HP-PRRSV) and several HP-PRRSV strains were isolated [10-12]. The genome sequences of several strains representing PRRSV have been determined and infectious cDNA clones w
Co-expression of Ubiquitin gene and capsid protein gene enhances the potency of DNA immunization of PCV2 in mice
Fang Fu, Xuesong Li, Yuekun Lang, Yuju Yang, Guangzhi Tong, Guoxin Li, Yanjun Zhou, Xi Li
Virology Journal , 2011, DOI: 10.1186/1743-422x-8-264
Abstract: Porcine circovirus type 2 (PCV2) is a small, non-enveloped, single-stranded, circular DNA virus with a 1767 nt or 1768 nt ambisense genome [1] that contains at least two major open reading frames (ORFs). ORF1 encodes the replication proteins (Rep and Rep') involved in virus replication and ORF2 encodes the capsid protein (Cap) [2,3]. Cap, a protein associated with the development of neutralizing antibodies and antibody protection [4,5], has been a leading target for designing new vaccines against PCV2 infection.Immunologic potential of a DNA vaccine encoding the PCV2 Cap in mice was first investigated by Kamstrup, et al. [6]. DNA vaccines may be capable of inducing immunity regardless of maternally derived antibodies [7-9] and they have induced protective cellular and humoral immunity in preclinical models of infectious diseases. However, DNA vaccine applications are limited due to problems related to delivery, species of the immunized animals and degradation of plasmid DNA [10], resulting in modest cellular and humoral immune responses [11]. To compensate for these limitations, numerous studies have explored methods to improve immune responses induced by DNA immunization by optimizing plasmid design, vaccine delivery systems and adjuvants [12]. Adjuvants are of particular interest because they may enhance DNA delivery and increase the magnitude and duration of plasmid DNA expression [13]. Molecular adjuvants, such as co-stimulatory chemokines and cytokines, have been used previously in conjunction with DNA vaccines and have served as immune modulators [14].Ubiquitin, a 76-amino-acid peptide found in the cytoplasm of eukaryotic cells, is normally involved in controlling intracellular protein turnover [15] and was reported to enhance DNA vaccine responses against antigens in the adjuvant setting. Ubiquitinated proteins targeted to the proteasome system [16] are processed and presented through the major histocompatibility complex (MHC) class I pathway to stimulate dif
Proviral genomic sequence analysis of Chinese donkey leukocyte attenuated equine infectious anemia virus vaccine and its parental virus strain Liaoning
Liu Wang,Guangzhi Tong,Hongquan Liu,Zhibiao Yang,Huaji Qiu,Xiangang Kong,Mei Wang
Science China Life Sciences , 2002, DOI: 10.1360/02yc9007
Abstract: Proviral DNA was extracted from donkey leukocyte infected with Chinese donkey leukocyte attenuated equine infectious anemia virus (DLA-EIAV), and peripheral blood lymphocytes (PBL) from a horse infected with the virulent EIAV strain Liaoning (EIAV L). The entire proviral DNA from both viruses was cloned and sequenced. The lengths of complete genomic sequences of DLA-EIAV and EIAV L provirus were 8266 bp and 8235 bp, respectively. Sequence comparison indicated that DLA-EIAV shares 97.0% and 97.5% in sequence homology with EIAV L and donkey-adapted EIAV (DA-EIAV), respectively. Lots of variations occurred in long terminal repeat (LTR, consisting of U3, R, U5), ORF S2, and env regions between DLA-EIAV and EIAV L. The nucleotide sequence differences of the two viruses in U3, R, U5, ORF S2, and env are 13.2%, 7.5%, 5.1%, 3.9%, and 2.7%, respectively, and predicted amino acid sequence differences in env and S2 coding regions are 4.4% and 8.8%, respectively. Six conserved regions are characterized in Gp90. There is a cis-activating GATA motif in ENH of DLA-EIAV and EIAV L. Two N-linked glycosylation sites disappeared in DLA-EIAV Gp90 in comparison with that of EIAV L. A bHLH transcription factor binding consensus sequence was found in LTR of DLA-EIAV but not in EIAV L. Furthermore, there is a mutation in the stem of DLA-EIAV TAR resulting in formation of a uridine tuber. Further study is needed to uncover the relationship between sequence changes and their biological functions of DLA-EIAV and L.
Characterization of nonstructural protein 3 of a neurovirulent Japanese encephalitis virus strain isolated from a pig
Xufang Deng, Zixue Shi, Shuqing Li, Xiaodu Wang, Yafeng Qiu, Donghua Shao, Jianchao Wei, Guangzhi Tong, Zhiyong Ma
Virology Journal , 2011, DOI: 10.1186/1743-422x-8-209
Abstract: We characterized the NS3 protein of a neurovirulent strain of JEV (SH-JEV01) isolated from a field-infected pig. The NS3 gene of the JEV SH-JEV01 strain is 1857 bp in length and encodes protein of approximately 72 kDa with 99% amino acid sequence identity to that of the representative immunotype strain JaGAr 01. The NS3 protein was detectable 12 h post-infection in a mouse neuroblastoma cell line, Neuro-2a, and was distributed in the cytoplasm of cells infected with the SH-JEV01 strain of JEV. In the brain of mice infected with the SH-JEV01 strain of JEV, NS3 was detected in the cytoplasm of neuronal cells, including pyramidal neurons of the cerebrum, granule cells, small cells and Purkinje cells of the cerebellum.The NS3 protein of a neurovirulent strain of JEV isolated from a pig was characterized. It is an approximately 72 kDa protein and distributed in the cytoplasm of infected cells. The Purkinje cell of the cerebellum is one of the target cells of JEV infection. Our data should provide some basic information for the study of the role of NS3 in the pathogenesis of JEV and the immune response.Japanese encephalitis (JE), known previously as Japanese B encephalitis, is caused by Japanese encephalitis virus (JEV). JE is most prevalent in Southeast Asia and the Far East, and causes 10,000-15,000 human deaths from encephalitis in the world each year [1]. JEV is a mosquito-borne virus of the Flavivirus genus in the family Flaviviridae. Its genome is positive-sense single-stranded RNA, approximately 11 kb in length, which encodes a precursor polyprotein consisting of three structural proteins (C, prM and E) and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5) [2].The nonstructural protein 3 (NS3) of JEV is a multifunctional protein of 619 amino acid residues. It possesses enzymatic activities of serine protease, helicase and nucleoside 5'-triphosphatase, and plays important roles in the processing of the viral precursor polyprotein and the replic
Nonstructural Protein 1 of Influenza A Virus Interacts with Human Guanylate-Binding Protein 1 to Antagonize Antiviral Activity
Zixiang Zhu, Zixue Shi, Wenjun Yan, Jianchao Wei, Donghua Shao, Xufang Deng, Shaohui Wang, Beibei Li, Guangzhi Tong, Zhiyong Ma
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0055920
Abstract: Human guanylate-binding protein 1 (hGBP1) is an interferon-inducible protein involved in the host immune response against viral infection. In response to infection by influenza A virus (IAV), hGBP1 transcript and protein were significantly upregulated. Overexpression of hGBP1 inhibited IAV replication in a dose-dependent manner in vitro. The lysine residue at position 51 (K51) of hGBP1 was essential for inhibition of IAV replication. Mutation of K51 resulted in an hGBP1 that was unable to inhibit IAV replication. The viral nonstructural protein 1 (NS1) was found to interact directly with hGBP1. K51 of hGBP1 and a region between residues 123 and 144 in NS1 were demonstrated to be essential for the interaction between NS1 and hGBP1. Binding of NS1 to hGBP1 resulted in a significant reduction in both GTPase activity and the anti-IAV activity of hGBP1. These findings indicated that hGBP1 contributed to the host immune response against IAV replication and that hGBP1-mediated antiviral activity was antagonized by NS1 via binding to hGBP1.
Identification of CD8+ cytotoxic T lymphocyte epitopes from porcine reproductive and respiratory syndrome virus matrix protein in BALB/c mice
Weijun Zhang, Yan Lin, Yu Bai, Tiegang Tong, Qun Wang, Nihong Liu, Guangliang Liu, Yihong Xiao, Tao Yang, Zhigao Bu, Guangzhi Tong, Donglai Wu
Virology Journal , 2011, DOI: 10.1186/1743-422x-8-263
Abstract: Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important swine viral pathogens, and has caused significant economic losses to the swine industry worldwide. Characterization of field isolates suggested that PRRSV are genetically diverse, and this genetic variation increases the difficulty of developing effective vaccines. Based on significant sequence differencesPRRS viruses are grouped into two distinct genotypes, European isolate (Lelystad virus, LV) and North American isolate (VR-2332) [1]PRRSV has two major structural proteins, GP5 and M, encoded by ORFs 5 and 6, respectively. GP5, the most important neutralizing antigen of PRRSV, has the highest genetic diversity among isolates [2]. And, recent studies in Yorkshire × Landrace crossed and outbred pigs, showed that there are two immuno-dominant T-cell epitopes derived from the GP5 protein: L117AALICFVIRLAKNC and K149GRLYRWRSPVII/VEK [3]. The M protein, which contains highly conserved amino acid sequences, also has very good immunogenicity and is associated with protection against PRRSV infection. DNA vaccinations have also revealed that M is the most potent inducer of T lymphocyte proliferation [4].At present, effective vaccination strategies for the prevention and control of PRRSV infection are not available. Vaccines based on inactivated PRRSV virus have been ineffective at inducing protective immune responses. Live-attenuated PRRSV vaccines can provide protection against this pathogen, but have been observed to revert to virulence [5], restricting the application of this vaccination approach. The rational development of future PRRSV vaccines will necessitate a systematic understanding of the protective humoral and cellular immune responses that occur during PRRSV infection, and should aim to induce a broad immune responses that accommodates the plasticity of the major antigenic sites. Recent research has indicated that cell-mediated immunity may play a very important role in the
An Expandable Local and Parallel Two-Grid Finite Element Scheme
Yanren Hou,Guangzhi Du
Mathematics , 2015,
Abstract: An expandable local and parallel two-grid finite element scheme based on superposition principle for elliptic problems is proposed and analyzed in this paper by taking example of Poisson equation. Compared with the usual local and parallel finite element schemes, the scheme proposed in this paper can be easily implemented in a large parallel computer system that has a lot of CPUs. Convergence results base on $H^1$ and $L^2$ a priori error estimation of the scheme are obtained, which show that the scheme can reach the optimal convergence orders within $|\ln H|^2$ or $|\ln H|$ two-grid iterations if the coarse mesh size $H$ and the fine mesh size $h$ are properly configured in 2-D or 3-D case, respectively. Some numerical results are presented at the end of the paper to support our analysis.
Reconstituting turkey herpesvirus with bacterial artificial chromosome clones

Desong Lan,Xingming Shi,Yunfeng Wang,Hongyu Cui,Changjun Liu,Mei Wang,Wenwei Hu,Guangzhi Tong,

微生物学报 , 2008,
Abstract: Herpesvirus of turkey (HVT) is an alpherpesvirus and widely used as a live vaccine against Marek's disease (MD) because of its antigenic relationship with Marek's disease virus (MDV). OBJECTIVE: The aim of this study was to construct Herpesvirus of turkey Fc126 strain as an infectious bacterial artificial chromosome (BAC). METHODS: Using the selection marker Eco-gpt (Xanthine-guanine phosphoribosyl transferase)(1.3 kb) and BAC vector pBeloBAC11(7.4 kb), we constructed the transfer plasmid pGAB-gpt-BAC11. Then, the transfer plasmid and HVT-infected cells' total DNA were cotransfected into primary chicken embryo fibroblasts (CEFs). After six rounds of selection in medium containing mycophenolic acid, xanthine and hypoxanthine, we obtained purified recombinant viruses. Genomic DNA was extracted and electroporated into Escherichia coli DH10B competent cells. BAC clones were identified by restriction enzyme digestion and PCR analysis, and then tested for infectivity after transfection into CEFs using calcium phosphate. RESULTS: We obtained 25 BAC clones, and reconstituted recombinant viruses by transfection of HVT-BAC6 DNA, HVT-BAC8 DNA and HVT-BAC10 DNA into CEFs respectively. CONCLUSION: In this study, we cloned the complete genome of HVT Fc126 strain as an infectious bacterial artificial chromosome.
Effect of Modified NDV F48E9 Strain HN Gene and in vitro Expression of Its DNA Vaccine

Sun He,Xingming Shi,Yunfeng Wang,Mei Wang,Duoliang Ran,Guangzhi Tong,
贺 笋
,石星明,王云峰,王 玫,冉多良,童光志

微生物学报 , 2008,
Abstract: Improving expression of antigen is critical to the immunogenicity of DNA vaccines. To achieve this goal, we modified the NDV F48E9 strain HN gene by optimizing the condon usage and inserting the secretary leader sequence A/Goose/Guangdong/ 1/96 (H5N1) HA gene, Accession No. AF144305]. The HN gene modified and knocked the signal peptide off were named SoptiHN and optiHN. The three sequence: SoptiHN, optiHN and the NDV F48E9 strain HN gene were inserted into the vector pVAX1 and vector pVAX1-CpG including CpG-ODN sequence respectively. Then we got six recombinant plasmids: pV-SoptiHN, pVC-SoptiHN, pV-optiHN, pVC-optiHN, pV-HN and pVC-HN. By optimizing condon usage in transiently transfected 293T cells, expression levels of HN gene were higher from the codon-optimized gene than the counterpart. Moreover, both optimization of condon usage and addition of signal peptide could improve expression of HN gene in vitro.
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