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Search Results: 1 - 10 of 61044 matches for " Lezheng Yu "
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An Improved Approach for Rapidly Identifying Different Types of Gram-Negative Bacterial Secreted Proteins  [PDF]
Lezheng Yu, Fengjuan Liu, Lixiao Du, Yizhou Li
Natural Science (NS) , 2018, DOI: 10.4236/ns.2018.105018
Abstract: Protein secretion plays an important role in bacterial lifestyles. In Gram-negative bacteria, a wide range of proteins are secreted to modulate the interactions of bacteria with their environments and other bacteria via various secretion systems. These proteins are essential for the virulence of bacteria, so it is crucial to study them for the pathogenesis of diseases and the development of drugs. Using amino acid composition (AAC), position-specific scoring matrix (PSSM) and N-terminal signal peptides, two different substitution models are firstly constructed to transform protein sequences into numerical vectors. Then, based on support vector machine (SVM) and the “one to one”?algorithm, a hybrid multi-classifier named SecretP v.2.2 is proposed to rapidly and accurately?distinguish different types of Gram-negative?bacterial secreted proteins. When performed on the same test set for a comparison with other methods, SecretP v.2.2 gets the highest total sensitivity of 93.60%. A public independent dataset is used to further test the power of SecretP v.2.2 for predicting NCSPs, it also yields satisfactory results.
Using the improved position specific scoring matrix and ensemble learning method to predict drug-binding residues from protein sequences  [PDF]
Juan Li, Yongqing Zhang, Wenli Qin, Yanzhi Guo, Lezheng Yu, Xuemei Pu, Menglong Li, Jing Sun
Natural Science (NS) , 2012, DOI: 10.4236/ns.2012.45043
Abstract: Identification of the drug-binding residues on the surface of proteins is a vital step in drug discovery and it is important for understanding protein function. Most previous researches are based on the structural information of proteins, but the structures of most proteins are not available. So in this article, a sequence-based method was proposed by combining the support vector machine (SVM)-based ensemble learning and the improved position specific scoring matrix (PSSM). In order to take the local environment information of a drug-binding site into account, an improved PSSM profile scaled by the sliding window and smoothing window was used to improve the prediction result. In addition, a new SVM-based ensemble learning method was developed to deal with the imbalanced data classification problem that commonly exists in the binding site predictions. When performed on the dataset of 985 drug-binding residues, the method achieved a very promising prediction result with the area under the curve (AUC) of 0.9264. Furthermore, an independent dataset of 349 drug- binding residues was used to evaluate the pre- diction model and the prediction accuracy is 84.68%. These results suggest that our method is effective for predicting the drug-binding sites in proteins. The code and all datasets used in this article are freely available at http://cic.scu.edu.cn/bioinformatics/Ensem_DBS.zip.
Predicting disease-associated substitution of a single amino acid by analyzing residue interactions
Yizhou Li, Zhining Wen, Jiamin Xiao, Hui Yin, Lezheng Yu, Li Yang, Menglong Li
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-14
Abstract: We found that SAPs can be well characterized by network topological features. Mutations are probably disease-associated when they occur at a site with a high centrality value and/or high degree value in a protein structure network. We also discovered that study of the neighboring residues around a mutation site can help to determine whether the mutation is disease-related or not. We compiled a dataset from the Swiss-Prot variant pages and constructed a model to predict disease-associated SAPs based on the random forest algorithm. The values of total accuracy and MCC were 83.0% and 0.64, respectively, as determined by 5-fold cross-validation. With an independent dataset, our model achieved a total accuracy of 80.8% and MCC of 0.59, respectively.The satisfactory performance suggests that network topological features can be used as quantification measures to determine the importance of a site on a protein, and this approach can complement existing methods for prediction of disease-associated SAPs. Moreover, the use of this method in SAP studies would help to determine the underlying linkage between SAPs and diseases through extensive investigation of mutual interactions between residues.Genetic variation is a major driving force in the evolution of organism. In individuals, specific genetic mutations such as SNPs can be deleterious and cause disease. The human genome project has yielded massive amounts of data on human SNPs, and this information can be used to further investigate human diseases. It is estimated that the human genome contains 10 million SNP sites [1]. As a major repository of human SNPs, the NCBI dbSNP database [2] contains ~25 million human entries in the release of build 130. The annotation of single nucleotide polymorphisms (SNPs) is attracting a great deal of attention. Non-synonymous SNPs (nsSNPs), also referred to as single amino acid polymorphisms (SAPs), are SNPs that cause amino acid substitutions, and these are believed to be directly related
Convergence Hypothesis: Evidence from Panel Unit Root Test with Spatial Dependence
Lezheng Liu,Isabel Ruiz
Ecos de Economía , 2006,
Abstract: In this paper we test the convergence hypothesis by using a revised 4- step procedure of panel unit root test suggested by Evans and Karras (1996). We use data on output for 24 OECD countries over 40 years long. Whether the convergence, if any, is conditional or absolute is also examined. According to a proposition by Baltagi, Bresson, and Pirotte (2005), we incorporate spatial autoregressive error into a fixedeffect panel model to account for not only the heterogeneous panel structure, but also spatial dependence, which might induce lower statistical power of conventional panel unit root test. Our empirical results indicate that output is converging among OECD countries. However, convergence is characterized as conditional. The results also report a relatively lower convergent speed compared to conventional panel studies.
Occurrence of sulfonamide antibiotics in sewage treatment plants
Hong Chang,JianYing Hu,LeZheng Wang,Bing Shao
Chinese Science Bulletin , 2008, DOI: 10.1007/s11434-008-0123-x
Abstract: The occurrence of sulfonamide antibiotics (SAs) was investigated in the six sewage treatment plants (STPs) of Beijing, China. Of the 13 objective antibiotics, sulfamethoxazole, sulfapyridine, sulfamerazine, sulfadiazine and sulfamethizol were detected in the influents with the average concentrations of 1.2 ± 0.45, 0.29 ± 0.25, 0.048 ± 0.012, 0.35 ± 0.52 and 0.33 ± 0.21 μg·L 1, respectively, and those in the effluents were 1.4 ± 0.74, 0.22 ± 0.19, 0.021 ± 0.008, 0.22 ± 0.21and 0.01 ± 0 μg·L 1, respectively. Sulfamethoxazole was the predominant compound detected, and was found in all wastewater samples with the other two compounds sulfapyridine and sulfamerazine. It should be noted that sulfadiazine was first reported in wastewaters, and the concentration levels of all detected compounds except for sulfamethizol (detected once in the effluent samples) in the influents were observed to be similar to those in the effluents. From the data in this study, it can be found that sulfamethoxazole, sulfapyridine, sulfamerazine and sulfadiazine could be partly removed in anoxic and aerobic treatment unit and vice versa in anaerobic process, which led to their low or even negative removal rates in the effluents. The increase on the concentrations of sulfamethoxazole and sulfapyridine in the effluents was found probably due to the biotransformation of their acetylated forms in anaerobic treatment unit. In addition, it was observed that the biodegradation of sulfamethoxazole and sulfapyridine could partly occur during the anoxic and aerobic process, while sulfamerazine was partly eliminated in the anaerobic and anoxic units.
Occurrence of sulfonamide antibiotics in sewage treatment plants
CHANG Hong,HU JianYing,WANG LeZheng,SHAO Bing,

科学通报(英文版) , 2008,
Abstract: The occurrence of sulfonamide antibiotics (SAs) was investigated in the six sewage treatment plants (STPs) of Beijing, China. Of the 13 objective antibiotics, sulfamethoxazole, sulfapyridine, sulfamerazine, sulfadiazine and sulfamethizol were detected in the influents with the average concentrations of 1.2 ± 0.45, 0.29 ± 0.25, 0.048 ± 0.012, 0.35 ± 0.52 and 0.33 ± 0.21 μg·L 1, respectively, and those in the effluents were 1.4 ± 0.74, 0.22 ± 0.19, 0.021 ± 0.008, 0.22 ± 0.21and 0.01 ± 0 μg·L 1, respectively. Sulfamethoxazole was the predominant compound detected, and was found in all wastewater samples with the other two compounds sulfapyridine and sulfamerazine. It should be noted that sulfadiazine was first reported in wastewaters, and the concentration levels of all detected compounds except for sulfamethizol (detected once in the effluent samples) in the influents were observed to be similar to those in the effluents. From the data in this study, it can be found that sulfamethoxazole, sulfapyridine, sulfamerazine and sulfadiazine could be partly removed in anoxic and aerobic treatment unit and vice versa in anaerobic process, which led to their low or even negative removal rates in the effluents. The increase on the concentrations of sulfamethoxazole and sulfapyridine in the effluents was found probably due to the biotransformation of their acetylated forms in anaerobic treatment unit. In addition, it was observed that the biodegradation of sulfamethoxazole and sulfapyridine could partly occur during the anoxic and aerobic process, while sulfamerazine was partly eliminated in the anaerobic and anoxic units. Supported by the National Natural Science Foundation of China (Grant No. 20610103) and the Ministry of Science and Technology of China (Grant No. 2006DFA91130)
STUDY ON THE PONTENTIAL EVOKED BY STEREOPSIS
与立体视觉相关的视诱发电位研究

Lei Jingjiang,Wu Lezheng,Wu Dezheng,Liang Jiongji,
雷静江
,吴乐正,吴德正,梁炯基

心理学报 , 1995,
Abstract: 在微机上编制能产生动态随机点立体图(DRDS),亮暗类棋盘格和随机点背景三种图形刺激的软件.记录了34例正常人在这三种刺激下的VBP.其结果为:(1)DRDS刺激下的VEPN1波潜伏期为265±25ms,基波能量占总交流能量的63.2±18.9%.(2)亮暗类棋盘格刺激下的VEPN1波的潜伏期为190±22ms,基波能量占总交流能量的39.2±19.6%.(3)随机点背景刺激下的VEP波则为一些杂乱的小波.结果提示:动态RDS刺激下的VEP除在潜伏期方面具有特异性外,并在谐波的能量分布上也具有特异性,且客观性更强.根据这些特征有助于对立体视觉功能进行客观性评价.
On the road: Clinical trials with stem cell extended to non-hematologic disease  [PDF]
Jinyang Yu, Yanqiu Yu
Advances in Bioscience and Biotechnology (ABB) , 2013, DOI: 10.4236/abb.2013.42031
Abstract:
Increasing evidence in scientific journals declares that stem cell can be used in human medicine for therapeutic purposes. We reviewed the lated literature on clinical trials conducted with stem cells. The main information was offered by
http://www.ClinicalTrials.gov. These clinical trials cover almost all human diseases, from hematologic diseases to non-hematologic diseases including Interventional trials and observational trials. In conclusion, at present, the clinical trials with stem cells have been extending to almost all human diseases. Optimal medicinal effect reported in some non-hematologic diseases is pushing the advance of stem cells therapy
Comparison of the Water Quality between the Surface Microlayer and Subsurface Water in Typical Water Bodies in Sichuan  [PDF]
Jiang Yu
Journal of Water Resource and Protection (JWARP) , 2010, DOI: 10.4236/jwarp.2010.210101
Abstract: Investigation and assessment of water quality status in the surface microlayer (SML) and subsurface water (SSW) in several kinds of typical water bodies in Sichuan were carried out from May to June 2010.The results showed that N, P were enriched to some extent at SML in Xichi pool, Funan River and Longquan reservoir, which made concentrations of the indexes such as total nitrogen (TN), total phosphorus (TP), chemical oxygen demand (COD)of SML be much higher than those of SSW (P<0.05), and the exceeding rates were up to 100%. The contents of TN,TP,COD of SML and SSW in Xichi pool, and Funan River exceeded III even Ⅳlevel of water quality standard, while these indexes in Longquan reservoir were lower than Ⅲ or Ⅱlevel of water quality standard. Though Chl. a mass concentration at SML and SSW in Funan River was prominently lower than those in Xichi pool and Longquan reservoir, according to the eutrophic evaluation standard, the water bodies of SML and SSW in Funan River and Xichi pool were in middle eutrophication, the highest index of eutrophication (E value) was up to 66.78, while there was light entuophic in Longquan reservoir, and there had obvious difference with E value and COD, TP, TN (P<0.05). This research shows that the water quality of Longquan reservoir is generally well. While Funan River is a middle eutrophication, and its pollution is more serious than Xichi pool, the two waters belong to national III even IV level, and SML has the capability of enrichment to the pollutants such as N, P.
Career Success of Knowledge workers: The Effects of Perceived Organizational Support and Person-Job Fit  [PDF]
Yu Chen
iBusiness (IB) , 2010, DOI: 10.4236/ib.2010.24051
Abstract: The purpose of this paper is to review relevant literatures on career success and develop a theoretical framework and testable propositions concerning how person-job ?t and perceived organizational support relate to career success.
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