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Articles by Jie Zhang
Total Records ( 13 ) for Jie Zhang
  Jie Zhang , Shaoquan Ni , Lulu Ge and Yuanyuan Wang
  Locomotive scheduling problem is to assign locomotive to all the trains on the train working diagram with the fewest costs. Locomotive operation optimization is of great significance to the benefits of railway transportation. The study proves that the a feasible solution of locomotive scheduling can be transformed into the form of the locomotive routing’s sequential connection by analyzing its characteristics. Accordingly, a two-stage heuristic algorithm is designed. The first stage is to solve the optimum locomotive routing connection on one station and the second stage to deal with locomotive deadheading and optimize the locomotive routing on all the stations synthetically. Compared with the actual locomotive scheduling in the railway operation practice, the results point out that the two-stage heuristic algorithm is an effective and efficient method to solve the locomotive scheduling problem.
  Zong-Liang Gao , Yuan-Xing Gu , Jian-Hua Zhou , Yao-Zhong Ding , Jie Zhang , Hao-Tai Chen , Li-Na Ma and Yong-Sheng Liu
  The cleavage at 2A/2B junction of Foot and Mouth Disease Virus (FMDV) is mediated by the 2A sequence. Here researchers calculate some data of the 2A sequence including the nucleotide usage bias (R-value), the Authentic Codon Bias (ACB value) and accumulation of Codon Bias (CUB2A value) to estimate potential effects of nucleotide and codon bias on the auto-cleavage of this junction. Researchers find that a high nucleotide usage bias exists in the 2A sequence (R-value = 0.856±0.113), ten positions 3, 5, 8, 9, 11, 14-18 show a stable codon usage tendency in the 2A sequence across all serotype while the accumulation of Codon Bias (CUB2A = 0.293±0.043) is low. It is interesting that an obvious downward trend of accumulation of codon bias in C-termini is present in the 2A sequence. These phenomena suggest that the nucleotide and codon usage models play potential roles in impairing the formation of the peptide bond linking the 2A/2B junction during co-translation by affecting conformation changes of A and P sites in the ribosome.
  Jun-Jun Ma , Feng Zhao , Jie Zhang , Jian-Hua Zhou , Li-Na Ma , Yao-Zhong Ding , Hao-Tai Chen , Yuan-Xing Gu and Yong-Sheng Liu
  Dengue Viruses (DENV) are the most common arboviral pathogens in tropical and subtropical regions of the world. Analysis of codon usage patterns of DENV can reveal much about the molecular evolution of the viruses. The codon usage patterns of 119 samples of DENV were analysed including the Relative Synonymous Codon Usage (RSCU) and Codon Usage Bias (CUB). The overall extent of codon usage bias is low in DENV. The codon usage patterns of the 4 serotypes of DENV are significant different indicating that the evolutionary genetics of them are independent. Compositional constraint is a significant factor that affects codon usage variation. Mutation pressure is the main factor in codon usage variation of these viruses. Furthermore, natural selection may play a role in codon usage pattern of DENV as well. However, more comprehensive analysis is needed for show the deeper characteristic of synonymous codon usage and other responsible factors of codon usage bias in DENV.
  Mohd. Yusri Mohd. Yunus and Jie Zhang
  A new Multivariate Statistical Process Monitoring (MSPM) framework is proposed, in which the correlation among of the samples are determined by using dissimilarity scale structure. The typical MSPM system adopts linear-based Principal Component Analysis (cPCA) as the multivariate data compression method. Recently however, Classical Scaling-based (CMDS) technique has been proposed as an alternative for reducing the multivariate space, nonetheless, it demands new sets of monitoring schemes as well as statistics. This proposed approach still retains the conventional PCA as the main data compression technique as well as employs the original Hotelling’sT2 and SPE statistics for charting the monitoring status via Shewhart control chart. Therefore, the original conceptual applications of MSPM are greatly preserved to certain extent, without heavily focusing on new terminologies as can be experienced in the previous CMDS systems. There are twenty different cases of Tennessee Eastman Process (TEP) have been chosen for demonstration and the fault detection results of the proposed approach were comparatively analyzed to the outcomes of conventional MSPM based on two performance factors-total number of detected cases and also total number of fastest detection cases. The last two measures are determined through fault detection time. The overall outcomes show that the new technique produces almost comparable performances to the conventional MSPM based monitoring system in terms of number of cases detected, whereas, the City-block scale has been found the most efficient detection scheme among of all. More importantly, these effective monitoring outcomes can be performed based on lower number of PCS models.
  Yanping Chen , Jatinder N.D. Gupta and Jie Zhang
  With the rapid development of economy and society in China, water shortage and water pollution have become more serious. As a result, water resource conflicts have become prominent problems in water resources management of China. The water resource conflicts are caused by such factors as inadequate water quantity, poor water quality and improper timing of water usage. This study firstly points out that neglecting to protect the interests of the vulnerable groups often aggravates water resource conflicts. Then, the characteristics of vulnerable groups in water resource conflicts and their harm to the society are illustrated and the current research on vulnerable groups in various fields is briefly reviewed. Finally, a framework to protect vulnerable groups in water resource conflicts is proposed. This proposed framework combines economic compensation and capacity building to prevent water resource conflicts from their source.
  Jungang Yang , Jie Zhang , Yihua Ma and Zhiyu Wang
  The objective of this research was to investigate the process features of etchers and automatically provide mass multi-characteristics data for fault detection test. Before applying a fault detection system in a modern semiconductor wafer fabrication system, a great number of experiments and tests must be carried out to ensure the effectiveness and efficiency of the system. However, it is difficult to collect and storage different types of data with different characteristics for testing. This study proposed a Markov Property considered data generation approach based on analysis of the process state changes in etchers. The markov property of etcher’s state changes was demonstrated and a data generation model was built. Comparing with the existed historical data based data generation method and random data generation method, the proposed method considered not only statistical information from historical data but also the impact of the etchers' state changes. Experiments and industrial examples were used to measure the performance of the proposed method and results show that it has advantages such as simple expression, rapid and automatic data generation and easy reconfiguration, therefore is especially useful for the Fault Detection system test and simulation.
  Zhiyong Fu , Jie Zhang , Yi Tan , Desheng Song , Changchun Liu and Jiaqi Wu
  A two-dimensional zinc phosphite-phosphate [C3H6(OH)NH3][Zn2(HPO3)(PO4)] (1) was hydrothermally synthesized with 2-hydroxypropylammonium cation as the structure-directing agent. This compound has been characterized by single-crystal X-ray diffraction, IR spectroscopy, and powder X-ray diffraction (XRD). Its microporous framework is constructed by ZnO4, PO4, and HPO3 tetrahedral building blocks with 3, 4, and 6-ring channels. With 1 as base catalytic support, the Knoevenagel condensation reaction of benzaldehyde and ethyl cyanoacetate gives a yield of 59%.
  Zainal Ahmad and Jie Zhang
  Combining multiple neural networks appears to be a very promising approach in improving neural network generalisation since it is very difficult, if not impossible, to develop a perfect single neural network. In the building of an aggregated neural network model, a number of individual networks are developed from different data sets and/or different training algorithms. In this paper, individual networks are developed from bootstrap re-samples of the original training and testing data sets. Instead of combining all the developed networks, this paper proposes two selective combination techniques: forward selection and backward elimination. These two techniques essentially combine those individual networks that, when combined, can significantly improve model generalisation. In forward selection, individual networks are gradually added into the aggregated network until the aggregated network error on the original training and testing data sets cannot be further reduced. In backward elimination, all the individual networks are initially aggregated and some of the individual networks are then gradually eliminated until the aggregated network error on the original training and testing data sets cannot be further reduced. The proposed techniques are applied to dynamic nonlinear process modelling and classification of diabetes database. Application results demonstrate that the proposed techniques can significantly improve model generalisation and perform better than aggregating all the individual networks and the heuristic selective combination method where networks with better performance on the training and testing data are selected.
  Ting-Ting Xi , Xin Lu and Jie Zhang
  Numerical simulations are performed to investigate the third harmonic emission from femtosecond laser filament, center of which is blocked by a droplet. It is shown that sudden stop of fundamental laser filament induced by the droplet leads to the enhancement of third harmonic emission. The diffraction on droplet leads to the increase of third harmonic energy in background reservoir which can be survived after the dissipation of filament.
  Jianqing Wang , Kaili Ren , Chunjie Bai , Lihua Teng , Jie Zhang and Pingsha Huang
  In order to elaborate the relationship between the plankton community and the water environment factors in Yongjiang River, the gray correlation analysis on the plankton community structure and the main water environmental factors was conducted. The results showed that Total Nitrogen (TN) had the maximum effect on phytoplankton abundance; Dissolve Oxygen (DO) has the minimum effect. The impacts from CODCr and BOD5 to all groups of plankton abundance were also significant. In addition, the study showed that TN and BOD5 were the main factors to affect the plankton community diversity index in Yongjiang River. By means of the grey relational grades, sequences and the measured data analysis, it is determined that TN and BOD5 were the two factors with more obvious effects on the plankton community in the Yongjiang River. Their variation resulted in significant changes in the plankton community structure.
  Jie Zhang , Michael L. Goodson , Yiling Hong and Kevin D. Sarge
  In a previous study we found that sumoylation of the DNA-binding protein heat shock factor 2 (HSF2) is up-regulated during mitosis, but the mechanism that mediates this regulation was unknown. Here we show that HSF2 interacts with the polycomb protein MEL-18, that this interaction decreases during mitosis, and that overexpression and RNA interference-mediated reduction of MEL-18 result in decreased and increased HSF2 sumoylation, respectively. Other results suggest that MEL-18 may also function to inhibit the sumoylation of other cellular proteins. The results also show that MEL-18 is able to interact with the small ubiquitin-like modifier (SUMO) ubiquitin carrier protein (E2) enzyme UBC9 and that MEL-18 inhibits the ability of UBC9 to transfer the SUMO protein to target proteins. Together, the results in this work suggest a mechanism in which MEL-18 bound to HSF2 inhibits its sumoylation by binding to and inhibiting the activity of UBC9 enzymes in the vicinity of HSF2. These results provide an explanation for how mitotic HSF2 sumoylation is regulated and suggest that MEL-18, in contrast to the sumoylation-stimulating activities of the polycomb protein PC2, actually functions like an anti-SUMO ubiquitin-protein isopeptide ligase (E3), interacting both with HSF2 and the SUMO E2 UBC9 but acting to inhibit UBC9 activity to decrease sumoylation of a target protein, in this case that of HSF2.
  Irina Borodina , Jeroen Siebring , Jie Zhang , Colin P. Smith , Geertje van Keulen , Lubbert Dijkhuizen and Jens Nielsen
  Streptomycetes are exploited for production of a wide range of secondary metabolites, and there is much interest in enhancing the level of production of these metabolites. Secondary metabolites are synthesized in dedicated biosynthetic routes, but precursors and co-factors are derived from the primary metabolism. High level production of antibiotics in streptomycetes therefore requires engineering of the primary metabolism. Here we demonstrate this by targeting a key enzyme in glycolysis, phosphofructokinase, leading to improved antibiotic production in Streptomyces coelicolor A3(2). Deletion of pfkA2 (SCO5426), one of three annotated pfkA homologues in S. coelicolor A3(2), resulted in a higher production of the pigmented antibiotics actinorhodin and undecylprodigiosin. The pfkA2 deletion strain had an increased carbon flux through the pentose phosphate pathway, as measured by 13C metabolic flux analysis, establishing the ATP-dependent PfkA2 as a key player in determining the carbon flux distribution. The increased pentose phosphate pathway flux appeared largely because of accumulation of glucose 6-phosphate and fructose 6-phosphate, as experimentally observed in the mutant strain. Through genome-scale metabolic model simulations, we predicted that decreased phosphofructokinase activity leads to an increase in pentose phosphate pathway flux and in flux to pigmented antibiotics and pyruvate. Integrated analysis of gene expression data using a genome-scale metabolic model further revealed transcriptional changes in genes encoding redox co-factor-dependent enzymes as well as those encoding pentose phosphate pathway enzymes and enzymes involved in storage carbohydrate biosynthesis.
  Manjot Bal , Jie Zhang , Oleg Zaika , Ciria C. Hernandez and Mark S. Shapiro
  M-type K+ channels, consisting of KCNQ1–5 (Kv7.1–7.5) subunits, form a variety of homomeric and heteromeric channels. Whereas all the subunits can assemble into homomeric channels, the ability of the subunits to assemble into heteromultimers is highly variable. KCNQ3 is widely thought to co-assemble with several other KCNQ subtypes, whereas KCNQ1 and KCNQ2 do not. However, the existence of other subunit assemblies is not well studied. To systematically explore the heteromeric assembly of KCNQ channels in individual living cells, we performed fluorescence resonance energy transfer (FRET) between cyan fluorescent protein- and yellow fluorescent protein-tagged KCNQ subunits expressed in Chinese hamster ovary cells under total internal reflection fluorescence microscopy in which excitation light only penetrates several hundred nanometers into the cell, thus isolating membrane events. We found significant FRET between homomeric subunits as expected from their functional expression in heterologous expression systems. Also as expected from previous work, robust FRET was observed between KCNQ2 and KCNQ3. KCNQ3 and KCNQ4 also showed substantial FRET as did KCNQ4 and KCNQ5. To determine functional assembly of KCNQ4/KCNQ5 heteromers, we performed two types of experiments. In the first, we constructed a mutant tetraethylammonium ion-sensitive KCNQ4 subunit and tested its assembly with KCNQ5 by patch clamp analysis of the tetraethylammonium ion sensitivity of the resulting current; however, those data were not conclusive. In the second, we co-expressed a KCNQ4 (G285S) pore mutant with KCNQ5 and found the former to act as a dominant negative, suggesting co-assembly of the two types of subunits. These data confirm that among the allowed assembly conformations are KCNQ3/4 and KCNQ4/5 heteromers.
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