抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such clusters, or communities, can be considered as fairly independent compartments of a graph, playing a similar role like, e. g., the tissues or the organs in the human body. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. This problem is very hard and not yet satisfactorily solved, despite the huge effort of a large interdisciplinary community of scientists working on it over the past few years. We will attempt a thorough exposition of the topic, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists, from the discussion of crucial issues like the significance of clustering and how methods should be tested and compared against each other, to the description of applications to real networks.

/pdf/community-detection-in-graphs-34rogm3r6p.pdf

Community detection in graphs

Networks have proved to be useful representations of complex systems. Within these networks, there are typically a number of subsystems defined by only a subset of nodes and edges. Detecting these structures often provides important information about the organization and functioning of the overall network. Here, progress towards quantifying medium- and large-scale structures within complex networks is reviewed.

/pdf/communities-modules-and-large-scale-structure-in-networks-4dmkk9s9td.pdf

Communities, modules and large-scale structure in networks

The field of complex network clustering has been very active in the past several years. In this paper, a discrete framework of the particle swarm optimization algorithm is proposed. Based on the proposed discrete framework, a multiobjective discrete particle swarm optimization algorithm is proposed to solve the network clustering problem. The decomposition mechanism is adopted. A problem-specific population initialization method based on label propagation and a turbulence operator are introduced. In the proposed method, two evaluation objectives termed as kernel k-means and ratio cut are to be minimized. However, the two objectives can only be used to handle unsigned networks. In order to deal with signed networks, they have been extended to the signed version. The clustering performances of the proposed algorithm have been validated on signed networks and unsigned networks. Extensive experimental studies compared with ten state-of-the-art approaches prove that the proposed algorithm is effective and promising.

https://see.xidian.edu.cn/iiip/mggong/down/TEC2013Gong.pdf

Complex Network Clustering by Multiobjective Discrete Particle Swarm Optimization Based on Decomposition

Detecting and analyzing dense groups or communities from social and information networks has attracted immense attention over the last decade due to its enormous applicability in different domains. Community detection is an ill-defined problem, as the nature of the communities is not known in advance. The problem has turned even more complicated due to the fact that communities emerge in the network in various forms such as disjoint, overlapping, and hierarchical. Various heuristics have been proposed to address these challenges, depending on the application in hand. All these heuristics have been materialized in the form of new metrics, which in most cases are used as optimization functions for detecting the community structure, or provide an indication of the goodness of detected communities during evaluation. Over the last decade, a large number of such metrics have been proposed. Thus, there arises a need for an organized and detailed survey of the metrics proposed for community detection and evaluation. Here, we present a survey of the start-of-the-art metrics used for the detection and the evaluation of community structure. We also conduct experiments on synthetic and real networks to present a comparative analysis of these metrics in measuring the goodness of the underlying community structure.

Metrics for Community Analysis: A Survey

Detecting and characterizing the community structure of complex network is fundamental. We compare the classical optimization indexes of modularity and modularity density, which are quality indexes for a partition of a network into communities. Based on this, we propose a quantitative function for community partition, named communitarity or C value. We demonstrate that the quantitative is superior to modularity Q and modularity density D. Both theoretical and numerical results show that optimizing the new index not only can resolve small modules, but also can correctly identify the number of communities.

Quantitative Function for Community Detection

Unveiling the mechanism of miR-122-5p in the mediation of forkhead box O3 (FOXO3) in regards to cochlear hair cell damage provides an effective solution for the treatment of ear hearing disorders. An oxidative stress model using a mouse cochlear hair cell line (HEI-OC1) was established via hydrogen peroxide (H2O2). Then HEI-OC1 cells were transfected with miR-122-5p mimic, miR-122-5p inhibitor, and lentiviral vector FOXO3-WT/MUT. Cell viability and apoptosis rate were determined by MTT assay and flow cytometry. Reactive oxygen species (ROS) were observed by confocal laser scanning microscopy. Bcl-2, Bax, capase-3 and c-caspase-9 levels were quantified by western blot analysis and quantitative reverse transcription polymerase chain reaction (RT-qPCR). Enzyme-linked immunosorbent assay (ELISA) was used to detect superoxide dismutase (SOD) and malondialdehyde (MDA) levels, and flow cytometry was performed to measure the mitochondrial membrane potential levels. In the HEI-OC1 oxidative stress model after transfection, the miR-122-5p level was decreased, whereas the FOXO3 level was increased, Moreover, the increased FOXO3 level diminished the cell viability, but promoted cell apoptosis. Apart from this, the Bcl-2 level was downregulated, while levels of Bax, c-caspase-3, c-caspase-9, ROS and MDA were upregulated. Meanwhile, the mitochondrial membrane potential level was also elevated. Overexpression of miR-122-5p was able to partially offset the effects of FOXO3 in the H2O2-treated HEI-OC1 cells. Collectively, miR-122-5p restrained the decrease in HEI-OC1 cell viability and apoptosis induced by treatment with H2O2.

/pdf/elucidation-of-the-mechanism-of-mir-122-5p-in-mediating-26lhsuwd.pdf

Elucidation of the mechanism of miR-122-5p in mediating FOXO3 injury and apoptosis of mouse cochlear hair cells induced by hydrogen peroxide

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Quantitative Function for Community Detection

Elucidation of the mechanism of miR-122-5p in mediating FOXO3 injury and apoptosis of mouse cochlear hair cells induced by hydrogen peroxide