A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

Li, Meijing,Munkhdalai, Tsendsuren,Yu, Xiuming,Ryu, Keun Ho Hindawi Limited 2015 Mathematical problems in engineering Vol.2015 No.-

<P>Many researchers focus on developing protein-named entity recognition (Protein-NER) or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM) and parsing tree. PPIMiner consists of three main models: natural language processing (NLP) model, Protein-NER model, and PPI discovery model. The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method. ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems. The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods. In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools. PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction. We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER.</P>

MapReduce-based web mining for prediction of web-user navigation

Li, Meijing,Yu, Xiuming,Ryu, Keun Ho SAGE Publications 2014 JOURNAL OF INFORMATION SCIENCE Vol.40 No.5

<P>Predicting web user behaviour is typically an application for finding frequent sequence patterns. With the rapid growth of the Internet, a large amount of information is stored in web logs. Traditional frequent-sequence-pattern-mining algorithms are hard pressed to analyse information from within big datasets. In this paper, we propose an efficient way to predict navigation patterns of web users by improving frequent-sequence-pattern-mining algorithms based on the programming model of MapReduce, which can handle huge datasets efficiently. During the experiments, we show that our proposed MapReduce-based algorithm is more efficient than traditional frequent-sequence-pattern-mining algorithms, and by comparing our proposed algorithms with current existed algorithms in web-usage mining, we also prove that using the MapReduce programming model saves time.</P>

Fatigue Limit of Shot Peened LC9 Aluminum Alloy

WANG, Shengping,Yongjun, LI Xiuming, CHANG,YANG, Yuhui,YAO, Mei,WANG, Renzhi 대한금속재료학회(대한금속학회) 1996 METALS AND MATERIALS International Vol.2 No.2

The effects of shot peening on the three-point bending fatigue limit are described for LC9 aluminum alloy. Examination of the fatigue fracture surfaces revealed that the fatigue cracks were initiated under the hardened layer, depending upon the compressive residual stress (CRS) distribution. In this case, the local fatigue limit at the fatigue source is about 1.38 times of that of unstrengthened ones. An explanation is given with reference to the. concept of internal fatigue limit σ_(wi), which is regarded as the critical stress to initiate propagative fatigue microcrack in the interior of metal, and an intrinsic property of metal

A transcriptome analysis uncovers Panax notoginseng resistance to Fusarium solani induced by methyl jasmonate

Diqiu Liu,Qin Zhao,Xiuming Cui,Rui Chen,Xin Li,Bingling Qiu,Feng Ge 한국유전학회 2019 Genes & Genomics Vol.41 No.12

Background Panax notoginseng is a famous Chinese herbal medicine, but the root rot disease mainly caused by Fusarium solani severely reduces the yield and quality of its medicinal materials. Objective The defense priming in P. notoginseng through exogenous application of signaling molecule will supply theoretical support for the exogenous regulation of disease resistance in P. notoginseng. Methods In this study, the exogenous application of methyl jasmonate (MeJA) increased P. notoginseng’s resistance to F. solani. Furthermore, the P. notoginseng transcriptome during F. solani infection was investigated through next-generation sequencing to uncover the resistance mechanism of P. notogingseng induced by MeJA. Results The de novo assembly of transcriptome sequences produced 80,551 unigenes, and 36,771 of these unigenes were annotated by at least one database. A differentially expressed gene analysis revealed that a large number of genes related to terpenoid backbone biosynthesis, phenylalanine metabolism, and plant–pathogen interactions were predominantly upregulated by MeJA. Moreover, jasmonic acid (JA) biosynthesis-related genes and the JA signaling pathway genes, such as linoleate 13S-lipoxygenase, allene oxide cyclase, allene oxide synthase, TIFY, defensin, and pathogenesis-related proteins, showed increased transcriptional levels after inoculation with F. solani. Notably, according to the gene expression analysis, JA and ethylene signaling pathways may act synergistically to positively regulate the defense responses of P. notoginseng to F. solani. Conclusion JA signaling appears to play a vital role in P. notoginseng responses to F. solani infection, which will be helpful in improving the disease resistance of P. notoginseng cultivars as well as in developing an environmentally friendly biological control method for root rot disease.

DsbM, a Novel Disulfide Oxidoreductase Affects Aminoglycoside Resistance in Pseudomonas aeruginosa by OxyR-Regulated Response

Xuehan Wang,Mingxuan Li,Liwei Liu,Rui Mou,Xiuming Zhang,Yanling Bai,Haijin Xu,Mingqiang Qiao 한국미생물학회 2012 The journal of microbiology Vol.50 No.6

A Pseudomonas aeruginosa mutant strain M122 was isolated from a Mu transposon insertion mutant library. In our prophase research, we have found that PA0058, a novel gene encodes a 234-residue conserved protein, was disrupted in the M122 mutant. In this study, the bacteriostatic experiment in vitro indicates that M122 has abnormally high aminoglycoside resistance. We expressed PA0058 in E. coli and found that PA0058 oxidizes and reduces disulfide. This biochemical characterization suggests that PA0058 is a novel disulfide oxidoreductase. Hence, the protein was designated as DsbM. Microarray analysis of the M122 mutant showed its unusual phenotype might be related to the bacterial antioxidant defense system mediated by the oxyR regulon. Meanwhile, we detected –SH content in the periplasm of M122 and wild strain and found a lower –SH/S–S ratio in M122. Therefore, we consider that the loss of dsbM function decreased the –SH/S–S ratio, which then prolongs the OxyR-regulated response, thereby conferring high aminoglycoside resistance to the M122 mutant strain. Our findings have important implications for understanding the mechanisms underlying aminoglycoside resistance in P. aeruginosa.

Cloning and structure of a histocompatibility class IIA gene (Lelo-DAA) in Chinese longsnout catfish (Leiocassis longirostris)

Tong Shen,Jianming Li,Xiaoshun He,Meiling Lei,Jingru Wang,Xiuming Li 한국유전학회 2014 Genes & Genomics Vol.36 No.6

Here, the major histocompatibility complex(MHC) class II alpha chain gene in the Chinese longsnoutcatfish (Leiocassis longirostris) was characterized throughcloning, sequencing, polymorphism analysis, and expressionpatterns in various tissues. The full-length LeloDAAcDNA comprises 1,114 bp with a 50-UTR region of 79 bp,an open reading frame of 714 bp and a 30-UTR of 302 bp. The deduced protein sequence shows the followingimportant features: leader peptide, a1, a2, and CP/TM/CYT regions. Using long PCR techniques, the genomicsequence was further identified to be 2,093 bp in length,containing four exons and three introns. Three class IIAalleles were identified from four individuals. Two differentalleles observed (at most) in each individual suggest theexistence of a single locus of class IIA gene in the Chineselongsnout catfish genome. This locus is polymorphic andmost of the amino acidic changes occurred in the a1domain containing the peptide-binding region. Lelo-DAAmRNA expression was mainly found in the intestine, gills,spleen, head kidney and liver; minor expression wasdetected in the stomach, skin, heart and muscle. Our resultsyield insight into Chinese longsnout catfish T cell immuneresponses and will aid future work on the genetic status ofthis economically important species.