Transmission of HIV in sexual networks in sub-Saharan Africa and Europe

We are reviewing the literature regarding sexual networks and HIV transmission in sub-Saharan Africa and Europe. On Likoma Island in Malawi, a sexual network was reconstructed using a sociometric survey in which individuals named their sexual partners. The sexual network identified one giant component including half of all sexually active individuals. More than 25% of respondents were linked through independent chains of sexual relations. HIV was more common in the sparser regions of the network due to over-representation of groups with higher HIV prevalence. A study from KwaZulu-Natal in South-Africa collected egocentric data about sexual partners and found that new infections in women in a particular area was associated with the number of life-time partners in men. Data about sexual networks and HIV transmission are not reported in Europe. It is, however, found that the annual number of sexual partners follows a scale-free network. Phylogenetic studies that determine genetic relatedness between HIV isolates obtained from infected individuals, found that patients in the early stages of infections explain a high number of new infections. In conclusion, the limited information that is available suggest that sexual networks play a role in spread of HIV. Obtaining more information about sexual networks can be of benefit for modeling studies on HIV transmission and prevention.     

Duplication： a Mechanism Producing Disassortative Mixing Networks in Biology

Assortative/disassortative mixing is an important topological property of a network. A network is called assortative mixing if the nodes in the network tend to connect to their connectivity peers, or disassortative mixing if nodes with low degrees are more likely to connect with high-degree nodes. We have known that biological networks such as protein-protein interaction networks （PPI）, gene regulatory networks, and metabolic networks tend to be disassortative. On the other hand, in biological evolution, duplication and divergence are two fundamental processes. In order to make the relationship between the property of disassortative mixing and the two basic biological principles clear and to study the cause of the disassortative mixing property in biological networks, we present a random duplication model and an anti-preference duplication model. Our results show that disassortative mixing networks can be obtained by both kinds of models from uncorrelated initial networks. Moreover, with the growth of the network size, the disassortative mixing property becomes more obvious.     

Inferring epidemiological parameters from phylogenetic information for the HIV-1 epidemic among MSM

The HIV-1 epidemic in Europe is primarily sustained by a dynamic topology of sexual interactions among MSM who have individual immune systems and behavior. This epidemiological process shapes the phylogeny of the virus population. Both fields of epidemic modeling and phylogenetics have a long history, however it remains difficult to use phylogenetic data to infer epidemiological parameters such as the structure of the sexual network and the per-act infectiousness. This is because phylogenetic data is necessarily incomplete and ambiguous. Here we show that the cluster-size distribution indeed contains information about epidemiological parameters using detailed numberical experiments. We simulate the HIV epidemic among MSM many times using the Monte Carlo method with all parameter values and their ranges taken from literature. For each simulation and the corresponding set of parameter values we calculate the likelihood of reproducing an observed cluster-size distribution. The result is an estimated likelihood distribution of all parameters from the phylogenetic data, in particular the structure of the sexual network, the per-act infectiousness, and the risk behavior reduction upon diagnosis. These likelihood distributions encode the knowledge provided by the observed cluster-size distrbution, which we quantify using information theory. Our work suggests that the growing body of genetic data of patients can be exploited to understand the underlying epidemiological process.     

Modeling network growth with assortative mixing

We propose a model of an underlying mechanism responsible for the formation of assortative mixing in networks between “similar” nodes or vertices based on generic vertex properties. Existing models focus on a particular type of assortative mixing, such as mixing by vertex degree, or present methods of generating a network with certain properties, rather than modeling a mechanism driving assortative mixing during network growth. The motivation is to model assortative mixing by non-topological vertex properties, and the influence of these non-topological properties on network topology. The model is studied in detail for discrete and hierarchical vertex properties, and we use simulations to study the topology of resulting networks. We show that assortative mixing by generic properties directly drives the formation of community structure beyond a threshold assortativity of r ∼0.5, which in turn influences other topological properties. This direct relationship is demonstrated by introducing a new measure to characterise the correlation between assortative mixing and community structure in a network. Additionally, we introduce a novel type of assortative mixing in systems with hierarchical vertex properties, from which a hierarchical community structure is found to result. Electronic supplementary material Supplementary Online Material     

Detecting and describing the modular structures of weighted networks

In the functional properties of complex networks, modules play a central role. In this paper, we propose a new method to detect and describe the modular structures of weighted networks. In order to test the proposed method, as an example, we use our method to analyse the structural properties of the Chinese railway network. Here, the stations are regarded as the nodes and the track sections are regarded as the links. Rigorous analysis of the existing data shows that using the proposed algorithm, the nodes of network can be classified naturally. Moreover, there are several core nodes in each module. Remarkably, we introduce the correlation function $G_{rs}$, and use it to distinguish the different modules in weighted networks.     

Wide-band optical fibre local distribution systems

The concept of a wide-band optical local network is presented and the technical aspects are discussed in detail. The types of service are outlined and grouped according to the requirements for transmission capacity. The components available and their characteristics are presented. The modulation characteristics of the semiconductor laser are scrutinized and show that the laser is unfit for high-quality analogue intensity modulation. The aspects of digital and analogue transmission of television are examined and compared. Analogue transmission can provide transmission of only a few TV channels at the present level of quality whereas digital transmission can provide improved quality with a comfortable system margin. However, none of the schemes are suited for simultaneous transmission of many TV channels, which shows that the direct optical equivalent of a conventional CATV network cannot yet be constructed. The concepts of central switching and customer switching are outlined together with the options for multiplexing and network structure. Finally a review is made of known activities. The review covers eleven studied, planned and implemented experimental networks. Nearly all of the networks employ central switching. The older experiments use exclusively analogue transmission whereas there is a growing tendency to use digital transmission in recently planned networks.     

Spreading processes on dynamically changing contact networks

We develop and analyze an agent-based model for the study of information propagation in dynamic contact networks. We represent information as a state of a node in a network that can be probabilistically transferred to an adjacent node within a single time step. The model is based on a closed (yet sufficiently large) population that can support processes of link generation and annihilation using different contact regimes. Our study is confined to the case of homogeneous contacts, where each agent establishes and breaks contacts in the same way. We consider information to be available for spreading in a fixed time window (i.e. finite memory). We find, surprisingly, that information transmission (measured as the proportion of informed nodes after a fixed number of time steps) is identical for dynamic preferential and random networks, but radically different for the associate mixing contact regime. We also find that the probability of transmission is, similarly counterintuitively, not a main driver of the process as opposed the the main network par maters determining contact lifetime and the turnover rate on connections. We discuss the explanation and the significance of these results in the light of the fundamental difference between dynamic and static (cumulative) networks.     

Systematic series expansions for processes on networks

We use series expansions to study dynamics of equilibrium and nonequilibrium systems on networks. This analytical method enables us to include detailed nonuniversal effects of the network structure. We show that even low order calculations produce results which compare accurately to numerical simulation, while the results can be systematically improved. We show that certain commonly accepted analytical results for the critical point on networks with a broad degree distribution need to be modified in certain cases due to disassortativity; the present method is able to take into account the assortativity at sufficiently high order, while previous results correspond to leading and second order approximations in this method. Finally, we apply this method to real-world data.     

Eigenstates of the linearlized Ginzburg–Landau equation for mesoscopic multiply-connected superconductor

Multiply-connected mesoscopic superconductors have rich structures of vortex systems that result from interference of order parameter. We studied magnetic field dependence of transition temperatures and vortex arrangements of finite sized honeycomb superconducting networks with 6-fold rotational symmetries. Near and above the lower critical field, vortices locate at center of the network. As increasing the field, vortices form a hexagon or hexagonal multi-shell structure. In higher field, order parameter damps exponentially from the central point of the network to the edge of the network.     

Self-sustained oscillations of complex genomic regulatory networks

Recently, self-sustained oscillations in complex networks consisting of non-oscillatory nodes have attracted great interest in diverse natural and social fields. Oscillatory genomic regulatory networks are one of the most typical examples of this kind. Given an oscillatory genomic network, it is important to reveal the central structure generating the oscillation. However, if the network consists of large numbers of genes and interactions, the oscillation generator is deeply hidden in the complicated interactions. We apply the dominant phase-advanced driving path method proposed in Qian et al. (2010) [1] to reduce complex genomic regulatory networks to one-dimensional and unidirectionally linked network graphs where negative regulatory loops are explored to play as the central generators of the oscillations, and oscillation propagation pathways in the complex networks are clearly shown by tree branches radiating from the loops. Based on the above understanding we can control oscillations of genomic networks with high efficiency.     

Adaptive multimode transmission in wireless sensor networks with energy harvesting

Limited energy has always been an important factor restricting the development of wireless sensor networks. The unbalanced energy consumption of nodes will accelerate the death of some nodes. To solve the above problems, an adaptive routing algorithm for energy collection sensor networks based on distributed energy saving clustering (DEEC) is proposed. In each hop of data transmission, the optimal mode is adaptively selected from four transmission modes: single-hop cooperative, multi-hop cooperative, single-hop non-cooperative and multi-hop non-cooperative, so as to reduce and balance the energy consumption of nodes. The performance of the proposed adaptive multi-mode transmission method and several benchmark schemes are evaluated and compared by computer simulation, where a few performance metrics such as the network lifetime and throughput are adopted. The results show that, the proposed method can effectively reduce the energy consumption of the network and prolong the network lifetime; it is superior to various benchmark schemes.     

Communication on the structure of biological networks

Networks are widely used to represent interaction pattern among the components in complex systems. Structures of real networks from different domains may vary quite significantly. As there is an interplay between network architecture and dynamics, structure plays an important role in communication and spreading of information in a network. Here we investigate the underlying undirected topology of different biological networks which support faster spreading of information and are better in communication. We analyse the good expansion property by using the spectral gap and communicability between nodes. Different epidemic models are also used to study the transmission of information in terms of spreading of disease through individuals (nodes) in those networks. Moreover, we explore the structural conformation and properties which may be responsible for better communication. Among all biological networks studied here, the undirected structure of neuronal networks not only possesses the small-world property but the same is also expressed remarkably to a higher degree compared to any randomly generated network which possesses the same degree sequence. A relatively high percentage of nodes, in neuronal networks, form a higher core in their structure. Our study shows that the underlying undirected topology in neuronal networks, in a significant way, is qualitatively different from the same in other biological networks and that they may have evolved in such a way that they inherit a (undirected) structure which is excellent and robust in communication.     

Statistical analysis of gene regulatory networks reconstructed from gene expression data of lung cancer

Recently, inferring gene regulatory network from large-scale gene expression data has been considered as an important effort to understand the life system in whole. In this paper, for the purpose of getting further information about lung cancer, a gene regulatory network of lung cancer is reconstructed from gene expression data. In this network, vertices represent genes and edges between any two vertices represent their co-regulatory relationships. It is found that this network has some characteristics which are shared by most cellular networks of health lives, such as power-law, small-world behaviors. On the other hand, it also presents some features which are obviously different from other networks, such as assortative mixing. In the last section of this paper, the significance of these findings in the context of biological processes of lung cancer is discussed.     

Soliton propagation and collision in a variable-coefficient coupled Korteweg-de Vries equation

In complex networks it is common to model a network or generate a surrogate network based on the conservation of the number of connections of individual nodes. In this paper we analyse the ensemble of random networks that are defined by the conservation of the rich-club coefficient, which measures the density of connections among a group of nodes. We also present a method to generate such surrogate networks for a given network. We show that by choosing a suitable local linking term, the random networks not only preserve the rich-club coefficient but also closely approximate the degree distribution and the mixing pattern of real networks. Our work provides a different and complementary perspective to the network randomisation problem.     

Conserved Control Path in Multilayer Networks

The determination of directed control paths in complex networks is important because control paths indicate the structure of the propagation of control signals through edges. A challenging problem is to identify them in complex networked systems characterized by different types of interactions that form multilayer networks. In this study, we describe a graph pattern called the conserved control path, which allows us to model a common control structure among different types of relations. We present a practical conserved control path detection method (CoPath), which is based on a maximum-weighted matching, to determine the paths that play the most consistent roles in controlling signal transmission in multilayer networks. As a pragmatic application, we demonstrate that the control paths detected in a multilayered pan-cancer network are statistically more consistent. Additionally, they lead to the effective identification of drug targets, thereby demonstrating their power in predicting key pathways that influence multiple cancers.     

邻域搜索蚁群算法在无线传感器网络数据融合中的应用

为了减少网络中的数据传输量,提高数据融合率,降低网络延时,针对无线传感器网络数据融合问题的研究,提出了一种邻域搜索蚁群算法。首先利用蚁群算法寻找最短路径的优势,构造最短路径。为了避免蚁群算法的早熟收敛和收敛速度慢的问题,当达到一定的迭代次数后,运用具有可变邻域搜索的变异算子对搜索结果进行优化。算法不但考虑了无线传感器网络节点能量消耗也考虑了数据传输的网络延时问题。实验结果表明,该算法减少了网络能耗,降低了网络延时,稳定性更好,性能更优。     

CEAR: A cooperation based energy aware reward scheme for next generation green cognitive radio networks

Cognitive Radio (CR) networks are envisioned as a key empowering technology of the fifth-generation (5G) wireless communication networks, which solves the major issues of 5G, like high-speed data transmission, seamless connectivity, and increased demand for mobile data. Another significant characteristic of the 5G network is green communications, as energy consumption from the communication field is predicted to rise remarkably by the year 2030. In this work, we are concerned about energy-related issues and propose a cooperation-based energy-aware reward scheme (CEAR) for next-generation green CR networks. The proposed CEAR scheme is based on the antenna and temporal diversity of the primary users (PUs). For providing the service to the PUs, the users of another network called cognitive users (CUs) work as a cooperative relay node, and, in return, they get more spectrum access opportunities as a reward from the primary network. The CUs with delay-tolerant data packets take a cooperative decision by recognizing the availability and traffic load of PUs, channel state information, and data transmission requirements. We utilize the optimal stopping protocol for solving the decision-making problem and use the backward induction method to obtain the optimal cooperative solution. The simulation results reveal notable enhancements in energy efficiency (EE) of CUs compared with other cooperative schemes. The proposed CEAR scheme is more energy-efficient for ultra-dense network deployment because results show that the CU’s EE, spectral efficiency (SE), and throughput improved with the increase of PUs.     

一种改进的基于信息传播率的复杂网络影响力评估算法

评价网络中节点的信息传播影响力对于理解网络结构与网络功能具有重要意义.目前,许多基于最短路径的指标,如接近中心性、介数中心性以及半局部(SP)指标等相继用于评价节点传播影响力.最短路径表示节点间信息传播途径始终选择最优方式,然而实际上网络间的信息传播过程更类似于随机游走,信息的传播途径可以是节点间的任一可达路径,在集聚系数高的网络中,节点的局部高聚簇性有利于信息的有效扩散,若只考虑信息按最优传播方式即最短路径传播,则会低估节点信息传播的能力,从而降低节点影响力的排序精度.综合考虑节点与三步内邻居间的有效可达路径以及信息传播率,提出了一种SP指标的改进算法,即ASP算法.在多个经典的实际网络和人工网络上利用SIR模型对传播过程进行仿真,结果表明ASP指标与度指标、核数指标、接近中心性指标、介数中心性指标以及SP指标相比,可以更精确地对节点传播影响力进行排序.     

Hierarchical Structure, Disassortativity and Information Measures of the US Flight Network

We investigate the mixing structure of directed and evolutionary US flight network. It is shown that such a network is a hierarchical network, with average assortativity coefficient-0.37. Application of the informationbased method that can give the same result provides a way to explore the structure of complex networks.