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Molecular Phylogeny and Biogeography of Percocypris (Cyprinidae, Teleostei)
Mo Wang, Jun-Xing Yang, Xiao-Yong Chen
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0061827
Abstract: Fierce predatory freshwater fishes, the species of Percocypris (Cyprinidae, Teleostei) inhabit large rivers or lakes, and have a specific distribution pattern. Only a single species or subspecies occurs in each large-scale drainage basin of the Southeastern Tibetan Plateau. In this study, the molecular phylogenetic relationships for all but one of the described subspecies/species of Percocypris were investigated based on three mitochondrial genes (16S; COI; Cyt b) and one nuclear marker (Rag2). The results of Maximum Likelihood and Bayesian Inference analyses show that Percocypris is a strongly supported monophyletic group and that it is the sister group of Schizothorax. Combined with analyses of morphological characters, our results suggest that Percocypris needs to be reclassified, and we propose that six species be recognized, with corresponding distributions in five main drainages (including one lake). In addition, based on the results of the estimation of divergence times and ancestral drainages, we hypothesize that Percocypris likely originated in the early Miocene from a paleo-connected drainage system containing the contemporary main drainages of the Southeastern Tibetan Plateau. This study suggests that vicariance (due to the uplift of the Tibetan Plateau modifying the large-scale morphologies of drainage basins in the Southeastern Tibetan Plateau) has played an important role in the speciation of the genus. Furthermore, external morphological characters (such as the length of the fins) and an internal trait (the position of pterygiophore) appear to be correlated with different habitats in rivers and the lake.
2DCMA: An Effective Maintenance Algorithm of Materialized Views in Peer Data Management Systems
Biao Qin,Shan Wang,Xiao-Yong Du,
Biao Qin,Shan Wang,and Xiao-Yong Du
计算机科学技术学报 , 2006,
Abstract: Update management is very important for data integration systems. So update management in peer data management systems (PDMSs) is a hot research area. This paper researches on view maintenance in PDMSs. First, the definition of view is extended and the peer view, local view and global view are proposed according to the requirements of applications. There are two main factors to influence materialized views in PDMSs. One is that schema mappings between peers are changed, and the other is that peers update their data. Based on the requirements, this paper proposes an algorithm called 2DCMA, which includes two sub-algorithms: data and definition consistency maintenance algorithms, to effectively maintain views. For data consistency maintenance, Mork's rules are extended for governing the use of updategrams and boosters. The new rule system can be used to optimize the execution plan. And are extended for the data consistency maintenance algorithm is based on the new rule system. Furthermore, an ECA rule is adopted for definition consistency maintenance. Finally, extensive simulation experiments are conducted in SPDMS. The simulation results show that the 2DCMA algorithm has better performance than that of Mork's when maintaining data consistency. And the 2DCMA algorithm has better performance than that of centralized view maintenance algorithm when maintaining definition consistency.
Database Research: Achievements and Challenges
Shan Wang,Xiao-Yong Du,Xiao-Feng Meng,Hong Chen,
Shan Wang,Xiao-Yong Du,Xiao-Feng Meng,and Hong Chen
计算机科学技术学报 , 2006,
Abstract: Database system is the infrastructure of the modern information system. The R&D in the database system and its technologies is one of the important research topics in the field. The database R&D in China took off later but it moves along by giant steps. This report presents the achievements Renmin University of China (RUC) has made in the past 25 years and at the same time addresses some of the research projects we, RUC, are currently working on. The National Natural Science Foundation of China supports and initiates most of our research projects and these successfully conducted projects have produced fruitful results.
Predicting RNA Secondary Structure Using Profile Stochastic Context-Free Grammars and Phylogenic Analysis
Xiao-Yong Fang,Zhi-Gang Luo,Zheng-Hua Wang,
Xiao-Yong Fang,Zhi-Gang Luo,and Zheng-Hua Wang
计算机科学技术学报 , 2008,
Abstract: Stochastic context-free grammars (SCFGs) have been applied to predicting RNA secondary structure. The prediction of RNA secondary structure can be facilitated by incorporating with comparative sequence analysis. However, most of existing SCFG-based methods lack explicit phylogenic analysis of homologous RNA sequences, which is probably the reason why these methods are not ideal in practical application. Hence, we present a new SCFG-based method by integrating phylogenic analysis with the newly defined profile SCFG. The method can be summarized as: 1) we define a new profile SCFG, M, to depict consensus secondary structure of multiple RNA sequence alignment; 2) we introduce two distinct hidden Markov models, λ and λ′, to perform phylogenic analysis of homologous RNA sequences. Here, λ is for non-structural regions of the sequence and λ′ is for structural regions of the sequence; 3) we merge λ and λ′ into M to devise a combined model for prediction of RNA secondary structure. We tested our method on data sets constructed from the Rfam database. The sensitivity and specificity of our method are more accurate than those of the predictions by Pfold. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Supported by the National Natural Science Foundation of China under Grant No. 60673018.
Cascading Walks Model for Human Mobility Patterns
Xiao-Pu Han,Xiang-Wen Wang,Xiao-Yong Yan,Bing-Hong Wang
Physics , 2013,
Abstract: Uncovering the mechanism behind the scaling law in human trajectories is of fundamental significance in understanding many spatio-temporal phenomena. In combination of the exploration and the preferential returns, we propose a simple dynamical model mainly based on the cascading processes to capture the human mobility patterns. By the numerical simulations and analytical studies, we show more than five statistical characters that are well consistent with the empirical observations, including several type of scaling anomalies, and the ultraslow diffusion property, implying the cascading processes associated with the other two mechanisms are indeed a key in the understanding of human mobility activities. Moreover, both of the diverse individual mobility and aggregated scaling move-lengths, bridging the micro and macro patterns in human mobility. Our model provides deeper understandings on the emergence of human mobility patterns.
Four New Species Records of Umbelopsis (Mucoromycotina) from China
Ya-ning Wang,Xiao-yong Liu,Ru-yong Zheng
Journal of Mycology , 2013, DOI: 10.1155/2013/970216
Abstract: Four species of Umbelopsis newly found in China, that is, U. angularis, U. dimorpha, U. nana, and U. versiformis, are reported in this paper. Descriptions and illustrations are provided for each of them. 1. Introduction The genus Umbelopsis Amos and H. L. Barnett, typified by U. versiformis Amos and H. L. Barnett, was placed in Deuteromycetes by Amos and Barnett in 1966 [1]. Von Arx [2] proposed that this genus should be classified in Zygomycetes in 1982. Meyer and Gams [3] erected the family Umbelopsidaceae of Mucorales to accommodate it in 2003. This family occupies a basal phylogenetic position within the Mucorales [4]. Members of this genus grow slowly and form a velvety layer; sporangiophores typically arise from vesicles on substrates, cymosely or umbellately branched; sporangia are uni- and/or multispored and ochraceous, reddish, or hyaline; columellae are usually small or absent; sporangiospores are variously shaped and have the same color as the sporangia; chlamydospores, if present, are often abundant and mostly intercalary on mycelia [3, 5–8]. So far, 15 species have been described in this genus, 13 of which are accepted by Meyer and Gams [3] and Mahoney et al. [8]. Three species have been recorded from China by Chen [9]: U. isabellina (Oudem.) W. Gams (as Mortierella isabellina Oudem.), U. ramanniana (M？ller) W. Gams (as M. ramanniana (M？ller) Linnem.), and U. vinacea (Dixon-Stew.) Arx (as M. vinacea Dixon-Stew.). In this paper, four species newly recorded from soil and plant residues in China are described and illustrated. 2. Materials and Methods Details of materials studied are presented under the description of each taxon. Strains found in China were isolated using the method of Zheng et al. [10]. For morphological observations, fungi grew at 20°C or 25°C for 6–10 days under natural light on malt extract agar ((MEA) 2% malt extract, 2% glucose, 0.1% peptone, and 2% agar), cornmeal agar ((CMA) 2% cornmeal and 2% agar), and potato dextrose agar ((PDA) 20% potato, 2% glucose, and 2% agar). Maximum growth temperatures were tested twice on PDA. For inducing the formation of zygospores, 0.1% lecithin was added to PDA [10]. Capitalized color designations refer to the Color Standards and Color Nomenclature published by Ridgway [11]. 3. Taxonomy 3.1. Umbelopsis angularis W. Gams & M. Sugiy., in Sugiyama et al., Mycoscience 44: 221, 2003. (Figure 1). Figure 1: Umbelopsis angularis. (a) Sporangiophores with various types of branching. (b) Branching pattern of lower parts of sporangiophores. (c) Sporangiophores with different sizes and shapes of
Exact Solution of the Gyration Radius of an Individual's Trajectory for a Simplified Human Regular Mobility Model
YAN Xiao-Yong,HAN Xiao-Pu,ZHOU Tao,WANG Bing-Hong,
中国物理快报 , 2011,
Abstract:
Exact solution of gyration radius of individual's trajectory for a simplified human mobility model
Xiao-Yong Yan,Xiao-Pu Han,Tao Zhou,Bing-Hong Wang
Physics , 2010, DOI: 10.1088/0256-307X/28/12/120506
Abstract: Gyration radius of individual's trajectory plays a key role in quantifying human mobility patterns. Of particular interests, empirical analyses suggest that the growth of gyration radius is slow versus time except the very early stage and may eventually arrive to a steady value. However, up to now, the underlying mechanism leading to such a possibly steady value has not been well understood. In this Letter, we propose a simplified human mobility model to simulate individual's daily travel with three sequential activities: commuting to workplace, going to do leisure activities and returning home. With the assumption that individual has constant travel speed and inferior limit of time at home and work, we prove that the daily moving area of an individual is an ellipse, and finally get an exact solution of the gyration radius. The analytical solution well captures the empirical observation reported in [M. C. Gonz`alez et al., Nature, 453 (2008) 779]. We also find that, in spite of the heterogeneous displacement distribution in the population level, individuals in our model have characteristic displacements, indicating a completely different mechanism to the one proposed by Song et al. [Nat. Phys. 6 (2010) 818].
Diversity of individual mobility patterns and emergence of aggregated scaling laws
Xiao-Yong Yan,Xiao-Pu Han,Bing-Hong Wang,Tao Zhou
Computer Science , 2012, DOI: 10.1038/srep02678
Abstract: Uncovering human mobility patterns is of fundamental importance to the understanding of epidemic spreading, urban transportation and other socioeconomic dynamics embodying spatiality and human travel. According to the direct travel diaries of volunteers, we show the absence of scaling properties in the displacement distribution at the individual level,while the aggregated displacement distribution follows a power law with an exponential cutoff. Given the constraint on total travelling cost, this aggregated scaling law can be analytically predicted by the mixture nature of human travel under the principle of maximum entropy. A direct corollary of such theory is that the displacement distribution of a single mode of transportation should follow an exponential law, which also gets supportive evidences in known data. We thus conclude that the travelling cost shapes the displacement distribution at the aggregated level.
Progesterone Administration Modulates Cortical TLR4/NF-κB Signaling Pathway after Subarachnoid Hemorrhage in Male Rats
Zhong Wang,Gang Zuo,Xiao-Yong Shi,Jian Zhang,Qi Fang,Gang Chen
Mediators of Inflammation , 2011, DOI: 10.1155/2011/848309
Abstract: Our previous study concerning brain trauma has shown that progesterone could regulate toll-like receptor 4 (TLR4) and nuclear factor-kappa B (NF-κB) signaling pathway in the brain, which also has been proved to play important roles in early brain injury (EBI) after subarachnoid hemorrhage (SAH). The aim of the current study was to investigate whether progesterone administration modulated TLR4/NF-κB pathway signaling pathway in the brain at the early stage of SAH. All SAH animals were subjected to injection of 0.3？ml fresh arterial, non-heparinized blood into prechiasmatic cistern in 20 seconds. Male rats were given 0 or 16？mg/kg injections of progesterone at post-SAH hours 1, 6, and 24. Brain samples were extracted at 48？h after SAH. As a result, SAH could induce a strong up-regulation of TLR4, NF-κB, pro-inflammatory cytokines, MCP-1, and ICAM-1 in the cortex. Administration of progesterone following SAH could down-regulate the cortical levels of these agents related to TLR4/NF-κB signaling pathway. Post-SAH progesterone treatment significantly ameliorated the EBI, such as the clinical behavior scale, brain edema, and blood-brain barrier (BBB) impairment. It was concluded that post-SAH progesterone administration may attenuate TLR4/NF-κB signaling pathway in the rat brain following SAH. 1. Introduction Early brain injury (EBI) is the most common cause of disability and death in patients suffering from aneurysmal subarachnoid hemorrhage (SAH) [1]. Treatment of EBI is considered as a major goal in the management of patients surviving SAH. However, the exact molecular mechanism of EBI still remains obscure, which has hindered the development of effective and specific treatment paradigms for EBI. The term EBI refers to the immediate injury to the brain as a whole, within the first 48？h of the ictus, secondary to SAH [2]. Previous reports [3, 4] have demonstrated that inflammatory responses mediated mainly by the activation of toll-like receptor 4 and nuclear factor-kappa B (TLR4/NF-κB) signaling pathway played an important role in the pathogenesis of EBI following SAH. In their study, the authors mentioned that E5564 (TLR4 inhibitor) could correct the neurological deficits and down-regulate inflammation by inhibiting activation of the TLR4/NF- B signaling in prechiasmatic blood injection model. There are now 10 mammalian toll-like receptors (TRLs) identified by sequence analysis. Among them, TRL4, which was widely expressed in brain, can detect endogenous agonists, such as the degradation products of macromolecules, heat shock protein 60 and 70, products
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