Networks of coupled dynamical systems have been used to model biological oscillators, Josephson junction arrays, excitable media, neural networks, spatial games, genetic control networks and many other self-organizing systems. Ordinarily, the connection topology is assumed to be either completely regular or completely random. But many biological, technological and social networks lie somewhere between these two extremes. Here we explore simple models of networks that can be tuned through this middle ground: regular networks 'rewired' to introduce increasing amounts of disorder. We find that these systems can be highly clustered, like regular lattices, yet have small characteristic path lengths, like random graphs. We call them 'small-world' networks, by analogy with the small-world phenomenon (popularly known as six degrees of separation. The neural network of the worm Caenorhabditis elegans, the power grid of the western United States, and the collaboration graph of film actors are shown to be small-world networks. Models of dynamical systems with small-world coupling display enhanced signal-propagation speed, computational power, and synchronizability. In particular, infectious diseases spread more easily in small-world networks than in regular lattices.

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Collective dynamics of small-world networks

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 emergence of order in natural systems is a constant source of inspiration for both physical and biological sciences. While the spatial order characterizing for example the crystals has been the basis of many advances in contemporary physics, most complex systems in nature do not offer such high degree of order. Many of these systems form complex networks whose nodes are the elements of the system and edges represent the interactions between them. 
Traditionally complex networks have been described by the random graph theory founded in 1959 by Paul Erdohs and Alfred Renyi. One of the defining features of random graphs is that they are statistically homogeneous, and their degree distribution (characterizing the spread in the number of edges starting from a node) is a Poisson distribution. In contrast, recent empirical studies, including the work of our group, indicate that the topology of real networks is much richer than that of random graphs. In particular, the degree distribution of real networks is a power-law, indicating a heterogeneous topology in which the majority of the nodes have a small degree, but there is a significant fraction of highly connected nodes that play an important role in the connectivity of the network. 
The scale-free topology of real networks has very important consequences on their functioning. For example, we have discovered that scale-free networks are extremely resilient to the random disruption of their nodes. On the other hand, the selective removal of the nodes with highest degree induces a rapid breakdown of the network to isolated subparts that cannot communicate with each other. 
The non-trivial scaling of the degree distribution of real networks is also an indication of their assembly and evolution. Indeed, our modeling studies have shown us that there are general principles governing the evolution of networks. Most networks start from a small seed and grow by the addition of new nodes which attach to the nodes already in the system. This process obeys preferential attachment: the new nodes are more likely to connect to nodes with already high degree. We have proposed a simple model based on these two principles wich was able to reproduce the power-law degree distribution of real networks. Perhaps even more importantly, this model paved the way to a new paradigm of network modeling, trying to capture the evolution of networks, not just their static topology.

/pdf/statistical-mechanics-of-complex-networks-1zfjpvxipu.pdf

Statistical mechanics of complex networks

Imagined communities: Reflections on the origin and spread of nationalism

https://www.thelancet.com/pdfs/journals/lancet/PIIS0140-6736(12)61766-8.pdf

A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990-2010: a systematic analysis for the Global Burden of Disease Study 2010

OBJECTIVE We report the results of our angiosarcoma of the liver (ASL) registry to assess the occurrence, the impact of exposures to vinyl chloride, and to quantify latency. METHODS We examined more than 73,000 death certificates of North American workers employed between 1940 and 2008. RESULTS We found 13 deaths of ASL among workers with vinyl chloride exposure. All 13 occurred at single plant among workers with high vinyl chloride exposure. The mean latency after first exposure was 36.5 years ranging from 24 to 56 years. No ASL deaths occurred among workers with vinyl chloride exposures after 1974, when exposures were reduced. CONCLUSIONS We may have seen the last case of ASL among workers exposed to vinyl chloride. Nevertheless, given the long latency of this cancer, continued surveillance seems prudent.

Surveillance for angiosarcoma of the liver among vinyl chloride workers.

Genetic manipulation of microorganisms has been crucial in understanding their biology, yet for many microbial species, robust tools for comprehensive genetic analysis were lacking until the advent of CRISPR–Cas-based gene editing techniques. In this Progress article, we discuss advances in CRISPR-based techniques for the genetic analysis of genetically intractable microorganisms, with an emphasis on mycobacteria, fungi and parasites. We discuss how CRISPR-based analyses in these organisms have enabled the discovery of novel gene functions, the investigation of genetic interaction networks and the identification of virulence factors. In this Progress article, Collins and colleagues discuss how CRISPR-based analyses in genetically intractable microorganisms, including mycobacteria, fungi and parasites, have enabled the discovery of novel gene functions, the investigation of genetic interaction networks and the identification of virulence factors.

CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms

The gastrointestinal microbiome plays an important role in limiting susceptibility to infection with Clostridioides difficile. To better understand the ecology of bacteria important for C. difficile colonization resistance, we developed an experimental platform to simplify complex communities of fecal bacteria through dilution and rapidly screen for their ability to inhibit C. difficile. We simplified complex communities from six fecal donors and found that 17% of simplified communities inhibited C. difficile growth when initially isolated and when re-cultured from frozen stocks. Composition varied between simplified communities based upon fecal donor used for dilution; complexity ranged from 19-67 OTUs. One simplified community could be further simplified through dilution and retain the ability to inhibit C. difficile. We tested efficacy of seven simplified communities in a humanized microbiota mouse model and found that four communities were able to significantly reduce the severity of the initial C. difficile infection and limit susceptibility to disease relapse. Analysis of fecal microbiomes from treated mice demonstrated that simplified communities accelerated recovery of endogenous bacteria and led to stable engraftment of at least 20% of bacteria from simplified communities. Overall, the insights gained through the identification and characterization of these simplified communities increase our understanding of the microbial dynamics of C. difficile infection and recovery.

https://biorxiv.org/content/10.1101/2020.04.23.058867v1.full.pdf

James J. Collins

Papers

Surveillance for angiosarcoma of the liver among vinyl chloride workers.

CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms

Identification of simplified microbial communities that inhibit Clostridioides difficile infection through dilution/extinction

Language, Subjectivity, and Social Dynamics in the Writings of Pierre Bourdieu

Literacy and Literacies: Literacy, power, and identity: colonial legacies and indigenous transformations