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.

/pdf/collective-dynamics-of-small-world-networks-205zhem3gm.pdf

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

Recent findings indicate that fibrillating cardiac tissue arises from spiral wave chaos. Here we show that spiral wave chaos can be suppressed in a cardiac model by pacing the system with low-amplitude, high-frequency current pulses. This overdrive pacing technique is analyzed using a one-dimensional chain and a two-dimensional lattice of coupled, excitable elements with the kinetics described by the Luo-Rudy action potential model (1991). When two-dimensional media were excited with frequencies from 1:1 synchronization region, we found that spiral wave chaos could be suppressed in a limited number of cases. However, when used in conjunction with calcium channel blockers, high-frequency pacing suppressed spiral wave chaos in all episodes. These findings suggest that low-amplitude overdrive pacing in combination with class IV antiarrhythmic drugs, inhibitors of calcium channels, may be useful for eliminating fibrillation in cardiac tissue.

Suppressing arrhythmias in cardiac models with overdrive pacing

The Ethnography of Reading

When we view the verb classifier prefixes from the perspective of comparative subject (actor)2properties, and from the perspective of discourse structure, we see the interplay of Person and Anaphora on two levels of historical grammar. Comparative subject (actor) properties, indefiniteness and depersonalization, figure importantly in the constitution of the morphological set known in the Athapaskan literature as "classifiers." In particular, we find that depersonalization via pluralization of first person subject (actor) plays a major role in the regularization of this paradigm. Additionally, deictic elements employed in discourse coreference and deference behaviors intersect the Proto-Athapaskan person system at first person plural.

https://journals.linguisticsociety.org/proceedings/index.php/BLS/article/download/3254/2952

Athapaskan Classifiers, Person, and Deference

Die antibakterielle Therapie wird immer schwieriger, vor allem gramnegative Erreger zeigen zunehmend Resistenzen auch gegen Reserveantibiotika: Ihre ausere Lipopolysaccharid-Zellmembran schutzt sie vor auseren Einflussen und damit auch vor dem Eindringen von Medikamenten Eine quasi „antike“ Strategie, die schon Hippokrates beschrieben hat, zieht in diesem Zusammenhang neue Aufmerksamkeit auf sich: Silber kann bei topischer Anwendung die Wundheilung verbessern und Wundinfektionen vermindern Wie genau das aber funktioniert, war bis jetzt nicht bekannt

Edelmetall mit edler Wirkung: Silber unterstützt Antibiotika

To unravel the mechanism of human cellular reprogramming process at single-cell resolution, we performed parallel scRNA-Seq and scATAC-Seq analysis. Our analysis reveals that the cells undergoing reprogramming proceed in an asynchronous trajectory and diversify into heterogeneous sub-populations. BDD2-C8 fluorescent probe staining and negative staining for CD13, CD44 and CD201 markers, could enrich for the GDF3+ early reprogrammed cells. Combinatory usage of the surface markers enables the fine segregation of the early-intermediate cells with diverse reprogramming propensities. scATAC-Seq analysis further uncovered the genomic partitions and transcription factors responsible for the regulatory phasing of reprogramming process. Binary choice between a FOSL1 or a TEAD4-centric regulatory network determines the outcome of a successful reprogramming. Altogether, our study illuminates the multitude of diverse routes transversed by individual reprogramming cells and presents an integrative roadmap for identifying the mechanistic part-list of the reprogramming machinery.

https://www.biorxiv.org/content/biorxiv/early/2019/11/04/829853.full.pdf

James J. Collins

Papers

Suppressing arrhythmias in cardiac models with overdrive pacing

The Ethnography of Reading

Athapaskan Classifiers, Person, and Deference

Edelmetall mit edler Wirkung: Silber unterstützt Antibiotika

Diversification of Reprogramming Trajectories Revealed by Parallel Single-cell Transcriptome and Chromatin Accessibility Sequencing