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Search Results: 1 - 10 of 104257 matches for " ZHANG Dongxiao "
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Identification of hybrid node and link communities in complex networks
Dongxiao He,Di Jin,Weixiong Zhang
Computer Science , 2013,
Abstract: Identification of communities in complex networks has become an effective means to analysis of complex systems. It has broad applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of nodes and finding communities of links are two popular schemes for network structure analysis. These schemes, however, have inherent drawbacks and are often inadequate to properly capture complex organizational structures in real networks. We introduce a new scheme and effective approach for identifying complex network structures using a mixture of node and link communities, called hybrid node-link communities. A central piece of our approach is a probabilistic model that accommodates node, link and hybrid node-link communities. Our extensive experiments on various real-world networks, including a large protein-protein interaction network and a large semantic association network of commonly used words, illustrated that the scheme for hybrid communities is superior in revealing network characteristics. Moreover, the new approach outperformed the existing methods for finding node or link communities separately.
svdPPCS: an effective singular value decomposition-based method for conserved and divergent co-expression gene module identification
Wensheng Zhang, Andrea Edwards, Wei Fan, Dongxiao Zhu, Kun Zhang
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-338
Abstract: Using the singular value decomposition (SVD) technique, we developed a new computational tool, named svdPPCS (SVD-based Pattern Pairing and Chart Splitting), to identify conserved and divergent co-expression modules of two sets of microarray experiments. In the proposed methods, gene modules are identified by splitting the two-way chart coordinated with a pair of left singular vectors factorized from the gene expression matrices of the two biological categories. Importantly, the cutoffs are determined by a data-driven algorithm using the well-defined statistic, SVD-p. The implementation was illustrated on two time series microarray data sets generated from the samples of accessory gland (ACG) and malpighian tubule (MT) tissues of the line W118 of M. drosophila. Two conserved modules and six divergent modules, each of which has a unique characteristic profile across tissue kinds and aging processes, were identified. The number of genes contained in these models ranged from five to a few hundred. Three to over a hundred GO terms were over-represented in individual modules with FDR < 0.1. One divergent module suggested the tissue-specific relationship between the expressions of mitochondrion-related genes and the aging process. This finding, together with others, may be of biological significance. The validity of the proposed SVD-based method was further verified by a simulation study, as well as the comparisons with regression analysis and cubic spline regression analysis plus PAM based clustering.svdPPCS is a novel computational tool for the comparative analysis of transcriptional profiling. It especially fits the comparison of time series data of related organisms or different tissues of the same organism under equivalent or similar experimental conditions. The general scheme can be directly extended to the comparisons of multiple data sets. It also can be applied to the integration of data sets from different platforms and of different sources.Comparative analysis
Estimation of Economic Values for Production and Functional Traits in Chinese Holstein
Jun Chen,Yachun Wang,Yi Zhang,Dongxiao Sun,Yuan Zhang
Journal of Animal and Veterinary Advances , 2012,
Abstract: Bio-economic profit models were used on Chinese Holstein production system to evaluate economic values for production traits Milk Yield (MY), Fat Percentage (FP), Protein Percentage (PP)) growth traits Mature Live Weight (LW) and functional traits Age at First Calving (AFC), Calving Interval (CI), Production Lifetime (PL) and Somatic Cell Count (SCC) traits. Economic and production parameters were derived from large scale dairy farms located in Beijing in 2008 to characterize Chinese Holstein production system, which were described according to their growth stage and levels of feed and management environment. Revenue and cost were calculated according to different age group in dairy production. With a fixed number of cows per herd as a basis of evaluation, two milk payment systems were considered. Under payment system based on milk volume, estimated economic values were RMB 1.99 (MY, kg),-4.72 (PP, %), -8.00 (FP,%), 0 (SCC), -4.96 (AFC, days), 1.71 (CI, days), -2.73 (LW, kg) and 1.58 (PL, days), respectively. Under payment system based on milk composition and quality (fat percentage, Protein Percentage, SCC), changes in the economic values were only observed for PP (64.21), FP (41.24), SCC (-393.88), respectively. Sensitivity of economic values was studied, factors considered included the price of milk, price of beef, price of feed and other production variables. Economic values of MY, PP and FP increased significantly with higher price of milk and the beef price had no effect on the economic values of milk production traits. With higher feed price, the economic value for the grow traits and functional traits increased, but that for milk production traits decreased. In summary, evaluated economical value for different traits showed that production and functional traits would have a positive effect, while growth traits would have a negative effect on profitability of Chinese Holstein production system and price of milk and feed were identified as the main factors influencing profit. The bio-economic profit model constructed for Chinese Holstein breeding system could provide general ideas for breeding goals setting in Chinese dairy breeding system in the future.
The U/Θ effect of electricity parameters of the lotus root silk in the liquor with different pH values
Min Nie,TianPeng Zhang,ChangXing Pei,DongXiao Quan,Nan Chen
Chinese Science Bulletin , 2008, DOI: 10.1007/s11434-008-0260-2
Abstract: The silk of lotus root is a kind of natural biomaterial with the advantages of easy absorbing and dissolving and poisonless. It may become a new engineering material for clinic and tissue engineering. However, the relationship between its electricity parameters and the pH values of the liquor that the silk is dipped in is unknown presently. The electricity parameters of inductance, capacitance and impedance of the silk were measured in the environment with the temperature ranging from 23°C to 25°C and the humidity ranging from 45% to 55% when it was dipped in the liquor with different pH values for 24 h. The results show that the inductance and impedance vary in U shape curves with the liquor pH value, and the capacitance varies in Θ shape curve. The minimal value of the U curves and the maximal value of the Θ curve appear at the point where the pH value equals to 7. The phenomena are called the U/Θ effect. It means that the silk has perfect biocompatibility with human tissues. The study results may imply that the silk have broader potential applications in biomedicine, tissue engineering and bioelectronics.
Preliminary results of a new global ocean reanalysis
DongXiao Wang,YingHao Qin,XianJun Xiao,ZuQiang Zhang,FengMin Wu
Chinese Science Bulletin , 2012, DOI: 10.1007/s11434-012-5232-x
Abstract: Using a new global ocean reanalysis of the second generation Global Ocean Data Assimilation System of the Beijing Climate Center (BCC_GODAS2.0) spanning the period 1990–2009, we firstly quantify the accuracy of BCC_GODAS2.0 in representing the temperature and salinity by comparing with OISST and SODA data. The results show that the assimilation system may effectively improve the estimations of temperature and salinity by assimilating all kinds of observations, especially in the equatorial eastern Pacific. Moreover, the root mean square errors of monthly temperature and salinity are respectively reduced by 0.53°C and 0.28 psu, compared with the model control simulation results. Then, the applicability of this ocean reanalysis for sea surface temperature (SST) anomaly variability in the tropical Pacific is evaluated with the observational HadISST data. The NINO3 index of the new reanalysis shows a good agreement with that of HadISST, with a correlation of 93.6%. Variations in SST from BCC_GODAS2.0 are similar to those obtained from HadISST data along the equator, showing the major large zonal-scale features such as the strong magnitude of seasonal cycle. The amplitude of SST anomaly standard deviation in the equatorial eastern Pacific is also closer to observations (HadISST) than NCEP GODAS does. Besides, the first two leading empirical orthogonal function (EOF) modes of the monthly SST anomalies over the tropical Pacific region are explored. The EOF1 pattern of BCC_GODAS2.0 captures a traditional El Ni o pattern, which improves magnitudes of the positive SST anomaly in the cold tongue of the eastern Pacific. The EOF2 pattern exhibits a El Ni o Modoki pattern. Comparatively, the EOF2 pattern of BCC_GODAS2.0 extends more strongly toward the subtropics. It also overcomes the problem that negative loadings are confined in the narrow equatorial eastern Pacific. Consequently, the magnitude and spatial distribution of the leading EOF patterns of BCC_GODAS2.0 are well consistent with those of HadISST.
Marine Meteorology Research Progress of China from 2003 to 2006

WANG Dongxiao,ZHANG Yan,ZENG Lili,LUO Lin,

大气科学进展 , 2009,
Abstract: The progress in marine meteorology research achieved by scientists in China during the four-year period from 2003 to 2006 is summarized under four categories: marine disaster study, typhoon over the ocean, ocean-atmosphere monitoring technology, and ocean-atmosphere forecasting technology. Compared to the previous four years, many more first-hand datasets have been obtained and more scientific issues have been addressed. In particular, many contributions have been made by young scientists. A brief statement on the research strategy of marine meteorology in China for the coming years is given at the end.
Detection of genetic association and functional polymorphisms of UGDH affecting milk production trait in Chinese Holstein cattle
Xu Qing,Mei Gui,Sun Dongxiao,Zhang Qin
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-590
Abstract: Background We previously localized a quantitative trait locus (QTL) on bovine chromosome 6 affecting milk production traits to a 1.5-Mb region between BMS483 and MNB-209 via genome scanning followed by fine mapping. Results Totally 15 genes were mapped within such linkage region through bioinformatic analysis of the cattle-human comparative map and bovine genome assembly. Of them, the UDP-glucose dehydrogenase (UGDH) was suggested as a potential positional candidate gene for milk production traits based on its corresponding physiological and biochemical functions and genetic effects. By sequencing all the coding exons and the untranslated regions in UGDH with pooled DNA of 8 sires represented the separated families detected in our previous studies, a total of ten SNPs were identified and genotyped in 1417 Holstein cows of 8 separation families. Individual SNP-based association analysis revealed 4 significant associations of SNP Ex1-1, SNP Int3-1, SNP Int5-1, and SNP Ex12-3 with milk yield (P < 0.05), and 2 significant associations of SNP Ex1-1 and SNP Ex12-3 with protein yield (P < 0.05). Furthermore, our haplotype-based association analyses indicated that haplotypes G-C-C, formed by SNP Ex12-2-SNP Int11-1-SNP Ex11-1, T-G, formed by SNP Int9-3-SNP Int9-2, and C-C, formed by SNP Int5-1-SNP Int3-1, are significantly associated with protein percentage (F=4.15; P=0.0418) and fat percentage (F=5.18~7.25; P=0.0072~0.0231). Finally, by using an in vitro expression assay, we demonstrated that the A allele of SNP Ex1-1 and T allele of SNP Ex11-1of UGDH significantly decreases the expression of UGDH by 68.0% at the RNA, and 50.1% at the protein level, suggesting that SNP Ex1-1 and Ex11-1 represent two functional polymorphisms affecting expression of UGDH and may partly contributed to the observed association of the gene with milk production traits in our samples. Conclusions Taken together, our findings strongly indicate that UGDH gene could be involved in genetic variation underlying the QTL for milk production traits.
Thermal properties of carbon black aqueous nanofluids for solar absorption
Han Dongxiao,Meng Zhaoguo,Wu Daxiong,Zhang Canying
Nanoscale Research Letters , 2011,
Abstract: In this article, carbon black nanofluids were prepared by dispersing the pretreated carbon black powder into distilled water. The size and morphology of the nanoparticles were explored. The photothermal properties, optical properties, rheological behaviors, and thermal conductivities of the nanofluids were also investigated. The results showed that the nanofluids of high-volume fraction had better photothermal properties. Both carbon black powder and nanofluids had good absorption in the whole wavelength ranging from 200 to 2,500 nm. The nanofluids exhibited a shear thinning behavior. The shear viscosity increased with the increasing volume fraction and decreased with the increasing temperature at the same shear rate. The thermal conductivity of carbon black nanofluids increased with the increase of volume fraction and temperature. Carbon black nanofluids had good absorption ability of solar energy and can effectively enhance the solar absorption efficiency.
A novel method for rapid and reliable detection of complex vertebral malformation and bovine leukocyte adhesion deficiency in Holstein cattle
Zhang Yi,Fan Xuehua,Sun Dongxiao,Wang Yachun
Journal of Animal Science and Biotechnology , 2012, DOI: 10.1186/2049-1891-3-24
Abstract: Background Complex vertebral malformation (CVM) and bovine leukocyte adhesion deficiency (BLAD) are two autosomal recessive lethal genetic defects frequently occurring in Holstein cattle, identifiable by single nucleotide polymorphisms. The objective of this study is to develop a rapid and reliable genotyping assay to screen the active Holstein sires and determine the carrier frequency of CVM and BLAD in Chinese dairy cattle population. Results We developed real-time PCR-based assays for discrimination of wild-type and defective alleles, so that carriers can be detected. Only one step was required after the DNA extraction from the sample and time consumption was about 2 hours. A total of 587 Chinese Holstein bulls were assayed, and fifty-six CVM-carriers and eight BLAD-carriers were identified, corresponding to heterozygote carrier frequencies of 9.54% and 1.36%, respectively. The pedigree analysis showed that most of the carriers could be traced back to the common ancestry, Osborndale Ivanhoe for BLAD and Pennstate Ivanhoe Star for CVM. Conclusions These results demonstrate that real-time PCR is a simple, rapid and reliable assay for BLAD and CVM defective allele detection. The high frequency of the CVM allele suggests that implementing a routine testing system is necessary to gradually eradicate the deleterious gene from the Chinese Holstein population.
Sybil-proof Mechanisms in Query Incentive Networks
Wei Chen,Yajun Wang,Dongxiao Yu,Li Zhang
Computer Science , 2013,
Abstract: In this paper, we study incentive mechanisms for retrieving information from networked agents. Following the model in [Kleinberg and Raghavan 2005], the agents are represented as nodes in an infinite tree, which is generated by a random branching process. A query is issued by the root, and each node possesses an answer with an independent probability $p=1/n$. Further, each node in the tree acts strategically to maximize its own payoff. In order to encourage the agents to participate in the information acquisition process, an incentive mechanism is needed to reward agents who provide the information as well as agents who help to facilitate such acquisition. We focus on designing efficient sybil-proof incentive mechanisms, i.e., which are robust to fake identity attacks. %We consider incentive mechanisms which are sybil-proof, i.e., robust to fake identity attacks. We propose a family of mechanisms, called the direct referral (DR) mechanisms, which allocate most reward to the information holder as well as its direct parent (or direct referral). We show that, when designed properly, the direct referral mechanism is sybil-proof and efficient. In particular, we show that we may achieve an expected cost of $O(h^2)$ for propagating the query down $h$ levels for any branching factor $b>1$. This result exponentially improves on previous work when requiring to find an answer with high probability. When the underlying network is a deterministic chain, our mechanism is optimal under some mild assumptions. In addition, due to its simple reward structure, the DR mechanism might have good chance to be adopted in practice.
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