Comparison of methods for library construction and short read annotation of shellfish viral metagenomes

Hong‑Ying Wei,Sheng Huang,Jiang‑Yong Wang,Fang Gao,Jing‑Zhe Jiang 한국유전학회 2018 Genes & Genomics Vol.40 No.3

The emergence and widespread use of high-throughput sequencing technologies have promoted metagenomic studies on environmental or animal samples. Library construction for metagenome sequencing and annotation of the produced sequence reads are important steps in such studies and influence the quality of metagenomic data. In this study, we collected some marine mollusk samples, such as Crassostrea hongkongensis, Chlamys farreri, and Ruditapes philippinarum, from coastal areas in South China. These samples were divided into two batches to compare two library construction methods for shellfish viral metagenome. Our analysis showed that reverse-transcribing RNA into cDNA and then amplifying it simultaneously with DNA by whole genome amplification (WGA) yielded a larger amount of DNA compared to using only WGA or WTA (whole transcriptome amplification). Moreover, higher quality libraries were obtained by agarose gel extraction rather than with AMPure bead size selection. However, the latter can also provide good results if combined with the adjustment of the filter parameters. This, together with its simplicity, makes it a viable alternative. Finally, we compared three annotation tools (BLAST, DIAMOND, and Taxonomer) and two reference databases (NCBI’s NR and Uniprot’s Uniref). Considering the limitations of computing resources and data transfer speed, we propose the use of DIAMOND with Uniref for annotating metagenomic short reads as its running speed can guarantee a good annotation rate. This study may serve as a useful reference for selecting methods for Shellfish viral metagenome library construction and read annotation.

Radiofrequency Ablation Combined with Transcatheter Arterial Chemoembolization Therapy Versus Surgical Resection for Hepatocellular Carcinoma within the Milan Criteria: A Meta-Analysis

Wei-dong Wang,Li-hua Zhang,Jia-Yan Ni,Xiong-ying Jiang,Dong Chen,Yao-ting Chen,Hong-liang Sun,Jiang-hong Luo,Lin-feng Xu 대한영상의학회 2018 Korean Journal of Radiology Vol.19 No.4

Objective: To meta-analytically compare combined transarterial chemoembolization (TACE) plus radiofrequency ablation (RFA) and surgical resection (SR) for the treatment of hepatocellular carcinoma (HCC) within the Milan criteria. Materials and Methods: PubMed, Medline, Embase, and Cochrane Library were searched for studies comparing these two therapies that were published between January 2006 and August 2017. Overall survival rate (OS), recurrence-free survival rate (RFS), major complications and the average length of hospital stay were compared between these two therapies. Metaanalytic pooled odds ratio (OR) was calculated using TACE plus RFA as the base category. Results: Seven case-control studies and one randomized trial were identified. Meta-analytic results revealed that, compared with SR, TACE plus RFA had significantly higher 1-year OS (OR for survival = 0.50, p = 0.009) and lower major complications (OR = 1.88, p = 0.02) after therapy. Three studies reported on the length of hospital stay. The average length ± standard deviation reported in individual studies for SR and TACE plus RFA groups was 19.8 ± 8.4 days and 7.4 ± 2.2 days, respectively; 18.7 ± 4.9 days and 11.5 ± 6.9 days, respectively; and 16.6 ± 6.7 days and 8.5 ± 4.1 days, respectively (p < 0.0001 for all studies). Three or 5-year OS and 1-, 3-, or 5-year RFS did not significantly differ between the two therapies. Conclusion: Combined TACE plus RFA may be an alternative to SR for the treatment of patients with HCC within Milan the criteria. Non-randomized design in most of the original studies was a limitation.

The infection status of anisakid larvae in marine fish and cephalopods from the Bohai Sea, China and their taxonomical consideration

Hong-Wei MA,Tai-Jing JIANG,Fu-Shi QUAN,Xiao-Guang CHEN,Hui-dong WANG,Yun-Shu ZHANG,Ming-Shan CUI,Wen-Yan ZHI,Dian-Chen JIANG 대한기생충학열대의학회 1997 The Korean Journal of Parasitology Vol.35 No.1

Detection of gas-solid flow faults of a circulating fluidized bed using pressure fluctuations in wind caps

Hua-wei Jiang,Jian-qiang Gao,Hong-wei Chen,Jun-fu Lu,Fu-mao Wang,Yang Wang,Zhen-xin Wu 한국화학공학회 2016 Korean Journal of Chemical Engineering Vol.33 No.7

Wind cap partial blockages and agglomeration are two of the most common gas-solid flow faults that occur under the actual operations of circulating fluidized bed boilers. Using the method of measuring pressure fluctuations, for the characterization of fluid dynamics in fluidized beds, has a great advantage, due to its flexible adaptation to any operating conditions to monitor fluidization. This paper presents research into the use of measuring and analyzing pressure fluctuations in wind caps, for the analysis of the gas-solid fluidization characteristics in a fluidized bed with wind cap partial blockages or agglomeration fault. Partial blockages in a wind cap near feeding side and partial blockages in another wind cap near recycling side as well as agglomeration of different extents were simulated in a cold circulating fluidized bed. Pressure fluctuations in the inlets of several wind caps were measured at different primary air velocities under different fault conditions. They were then analyzed with the methods of statistical average, standard deviation, wavelet analysis and homogeneous index. Based on the calculated characteristic parameters, the effects of gas-solid flow faults on the gas-solid fluidization characteristics were analyzed. Results showed that variations of characteristic parameters of pressure fluctuations were related to variations of the gas-solid flow condition, which were caused by wind cap partial blockages or agglomerations. It is shown that the proposed method is practical.

Twenty Years Development of Soilless Culture in Mainland China

Wei-Jie Jiang,Hong-jun Yu 한국원예학회 2006 한국원예학회 기타간행물 Vol.- No.-

Present Situation and Development of Countermeasures for Protected Horticulture in China

Wei-Jie Jiang,Hong-Jun Yu 한국원예학회 2006 한국원예학회 기타간행물 Vol.- No.-

Ischemic postconditioning protects cardiomyocytes against ischemia/reperfusion injury by inducing MIP2

Hong-Lin Zhu,Kang-Kai Wang,Xing Wei,Shun-Lin Qu,Chi Zhang,Xiao-Xia Zuo,Yan-Sheng Feng,Qi Luo,Guang-Wen Chen,Mei-Dong Liu,Lei Jiang,Xian-Zhong Xiao 생화학분자생물학회 2011 Experimental and molecular medicine Vol.43 No.8

Cardiomyocytes can resist ischemia/reperfusion (I/R)injury through ischemic postconditioning (IPoC)which is repetitive ischemia induced during the onset of reperfusion. Myocardial ischemic preconditioning up-regulated protein 2 (MIP2) is a member of the WD-40family proteins, we previously showed that MIP2 was up-regulated during ischemic preconditioning (IPC). As IPC and IPoC engaged similar molecular mechanisms in cardioprotection, this study aimed to elucidate whether MIP2 was up-regulated during IPoC and contributed to IPoC-mediated protection against I/R injury. The experiment was conducted on two models,an in vivo open chest rat coronary artery occlusion model and an in vitro model with H9c2 myogenic cells. In both models, 3 groups were constituted and randomly designated as the sham, I/R and IPoC/hypoxia postconditioning (HPoC) groups. In the IPoC group, after 45 min of ischemia, hearts were allowed three cycles of reperfusion/ischemia phases (each of 30 s duration)followed by reperfusion. In the HPoC group, after 6 h of hypoxia, H9c2 cells were subjected to three cycles of 10 minute reoxygenation and 10 minute hypoxia followed by reoxygenation. IPoC significantly reduced the infarct size, plasma level of Lactate dehydrogenase and creatine kinase MB in rats. 12 h after the reperfusion,MIP2 mRNA levels in the IPoC group were 10 folds that of the sham group and 1.4 folds that of the I/R group. Increased expression of MIP2 mRNA and attenuation of apoptosis were similarly observed in the HPoC group in the in vitro model. These effects were blunted by transfection with MIP2 siRNA in the H9c2cells. This study demonstrated that IPoC induced protection was associated with increased expression of MIP2. Both MIP2 overexpression and MIP2 suppression can influence the IPoC induced protection.

A Scheme to Improve SOS Security against DDoS Attack Using Active Network Technology

( Jiang Wei ),( Choong Seon Hong ) 한국정보처리학회 2004 한국정보처리학회 학술대회논문집 Vol.11 No.2

Secure overlay services (SOS) architecture has been proposed to provide reliable communication between clients and a target under DDoS attacks. The SOS architecture employs a set of overlay nodes arranged in three hierarchical layers that controls access to the target. Although the architecture is novel and works well under simple congestion based attacks, we observe that when the attacker uses same malicious traffic raid the SOS nodes, the SOS system can not responses this kind of repeating action, and wastes the chance to collect the information of attacker. We propose a scheme to improve the secure overlay services (SOS) against the DDoS attack.

Research on Transaction Security Mechanism of Mobile Commerce in Mobile Internet based on MAS

Jiang Wei-Jin,Xu Yu-Sheng,Guo Hong,Zhang Lian-Mei 보안공학연구지원센터 2015 International Journal of Security and Its Applicat Vol.9 No.12

In Mobile Internet (MI), existing uncertain factors, such as randomness, fuzziness and unpredictability, brought many security issues to on-line transactions. In on-line transactions of the mobile commerce based on mobile Internet, the trust is the premise and key which makes transactions smoothly.. Trust measurement between entities involves in trading volume, transaction time, personal income of consumer entity and its risk attitude to trust, and so on, which is difficult to be given accurately quantitative calculation. To find out the essential features of this kind of trust relationship, combined with cognitive theory and methods of social network in real life, in the research background of mobile commerce in Mobile Internet, by the research on problems in MI, such as trust, influencing factors to trust and trust mechanism, based on multi-Agent system coordination theory, a dynamic trust calculation model based on mobile Agent is given. The model can achieve the qualitative and quantitative conversion of trust. In order to effectively prevent credit speculation and fraud of malicious user, the paper presents evaluation methods of special attributes and punishment methods of. trust. To implement incentive mechanism for achieving credibility, the paper defines the time-sensitive functions, which makes dynamic attenuation of the trust. The existing trust assignment methods of new users are improved, and a new method is proposed which sets dynamically initial trust of new users based on minimum trust of the previous system, and effectively resists moral hazard of discarding reputation information. Through leading the evaluation system of trading and weighting system into the multi-factor mechanism, the model reflects better the impact of subjective factors on trust calculation, such as individual preferences, risk attitudes, enhances the sensitivity of the trust algorithm on single property of transaction. The detailed theoretical analysis and simulation results show that the mechanism can effectively reveal and resolve the trust computing problem of mobile network transactions and provides a valuable new idea to transaction security in MI.

Molecular characterization and expression profiles of IscA1 gene in a longdistance migrant, Agrotis segetum

Hong Chang,Jiang Long Guo,Xiao Wei Fu,Xiu Jing Shen,Youming Hou,Kongming Wu 한국응용곤충학회 2018 Journal of Asia-Pacific Entomology Vol.21 No.4

Cryptochrome (CRYs) proteins have been elucidated as the molecular basis for magnetoreception in Drosophila, and a putative magnetic receptor (named IscA1) protein may aslo be involved in sensing magnetic fields in Drosophila. However, whether IscA1 has a conserved role in diverse animals and functions in orientation during animal migration is unknown. Here we report on the cloning and sequencing of the IscA1 gene from Agrotis segetum, which encodes a predicted protein IscA1 that has 131 amino acids and two conserved iron-sulphur cluster binding domains. Multiple sequence alignment and phylogenetic analysis were used to show that IscA1 had a relatively high homology from species of Noctuoidea. Quantitative polymerase chain reaction showed that IscA1 was ubiquitously expressed in adult organs and, among all developmental stages, expression was higher in adults. When Agrotis segetum was exposed to 14 h light/10 h dark, IscA1 expression also showed daily oscillations, and constant light or dark disturbed these oscillations. IscA1 expression levels in a migratory population were higher than in a reared population and higher in a southward migratory population than in a northward. These findings suggest that the IscA1 gene in A. segetum might be associated with migration and provide a molecular basis for further study on the functions of IscA1 gene in magnetoreception and potential control of the turnip moth.