scholarly journals RISE: a database of RNA interactome from sequencing experiments

2017 ◽  
Vol 46 (D1) ◽  
pp. D194-D201 ◽  
Author(s):  
Jing Gong ◽  
Di Shao ◽  
Kui Xu ◽  
Zhipeng Lu ◽  
Zhi John Lu ◽  
...  
Keyword(s):  
Small World ◽  
Rna Regulation ◽  
Scale Free ◽  
Functional Annotations ◽  
Comprehensive Collection ◽  
Non Coding Rnas ◽  
Basic Features ◽  
And Function ◽  
Integrative Visualization ◽  
Human And Mouse

Abstract We present RISE (http://rise.zhanglab.net), a database of RNA Interactome from Sequencing Experiments. RNA-RNA interactions (RRIs) are essential for RNA regulation and function. RISE provides a comprehensive collection of RRIs that mainly come from recent transcriptome-wide sequencing-based experiments like PARIS, SPLASH, LIGR-seq, and MARIO, as well as targeted studies like RIA-seq, RAP-RNA and CLASH. It also includes interactions aggregated from other primary databases and publications. The RISE database currently contains 328,811 RNA-RNA interactions mainly in human, mouse and yeast. While most existing RNA databases mainly contain interactions of miRNA targeting, notably, more than half of the RRIs in RISE are among mRNA and long non-coding RNAs. We compared different RRI datasets in RISE and found limited overlaps in interactions resolved by different techniques and in different cell lines. It may suggest technology preference and also dynamic natures of RRIs. We also analyzed the basic features of the human and mouse RRI networks and found that they tend to be scale-free, small-world, hierarchical and modular. The analysis may nominate important RNAs or RRIs for further investigation. Finally, RISE provides a Circos plot and several table views for integrative visualization, with extensive molecular and functional annotations to facilitate exploration of biological functions for any RRI of interest.

Resilience of Metrorail Networks: Quantification With Washington, DC as a Case Study

2019 ◽  
Vol 5 (4) ◽  
Author(s):  
Yalda Saadat ◽  
Bilal M. Ayyub ◽  
Yanjie Zhang ◽  
Dongming Zhang ◽  
Hongwei Huang
Keyword(s):  
Urban Areas ◽  
Small World ◽  
Washington Dc ◽  
Metro Station ◽  
Infrastructure Systems ◽  
Scale Free ◽  
Analytical Work ◽  
Basic Features ◽  
High Level

Abstract According to the United Nation's Department of Economic and Social Affairs Population Division, 66% of the world's population will reside in urban areas by 2050, a boost from 30% in 1950. Urbanization has indeed triumphed and has increased the demand for infrastructure systems including metrorail networks, one of the most tangible examples of complex transportation infrastructure systems. A synergistic rapid growth of urban population concurrent with great increases in metrorail use may lead to perturbations in the state of such a system. Taking into consideration of such perturbations and developing appropriate resilience measurements are paramount to the design of sustainable, robust, and resilient systems capable of performing satisfactorily through intentional and/or stochastic disruptions. As such, developing resilience metrics in a structured and appropriate manner is necessary. Using Washington, DC Metro as a case study, this paper examines metrorail network resilience and associated metrics with well-defined relationships to vulnerability and tied to efficiency. This examination includes developing a metro rail model in a graph form and obtaining its basic features by network topology analysis. The analytical work demonstrates that the Washington, DC Metro with its 91 stations and 140 links is a small-world network with the presence of a scale-free phenomenon and of a high level of vulnerability in the case of disruptive events. Evaluation of the efficiency and vulnerability of a metrorail network after disruption requires the consideration of two primary failure events, i.e., the failure of a metro station and the failure of a metro segment between stations. Vulnerability evaluation identifies the most critical stations and rail segments as illustrated using the Washington, DC Metro network. Such an assessment offers a logical basis to enhance system resilience and develop postfailure recovery strategies.

scholarly journals Minimal physicalism as a scale-free substrate for cognition and consciousness

2021 ◽  
Vol 2021 (2) ◽  
Author(s):  
Chris Fields ◽  
James F Glazebrook ◽  
Michael Levin
Keyword(s):  
Small World ◽  
Coarse Graining ◽  
Experimental Manipulation ◽  
Attention Switching ◽  
Scale Free ◽  
Basic Functions ◽  
Hierarchical Bayesian Inference ◽  
And Function ◽  
Minimal Physicalism

Abstract Theories of consciousness and cognition that assume a neural substrate automatically regard phylogenetically basal, nonneural systems as nonconscious and noncognitive. Here, we advance a scale-free characterization of consciousness and cognition that regards basal systems, including synthetic constructs, as not only informative about the structure and function of experience in more complex systems but also as offering distinct advantages for experimental manipulation. Our “minimal physicalist” approach makes no assumptions beyond those of quantum information theory, and hence is applicable from the molecular scale upwards. We show that standard concepts including integrated information, state broadcasting via small-world networks, and hierarchical Bayesian inference emerge naturally in this setting, and that common phenomena including stigmergic memory, perceptual coarse-graining, and attention switching follow directly from the thermodynamic requirements of classical computation. We show that the self-representation that lies at the heart of human autonoetic awareness can be traced as far back as, and serves the same basic functions as, the stress response in bacteria and other basal systems.

scholarly journals Emerging Data on the Diversity of Molecular Mechanisms Involving C/D snoRNAs

2021 ◽  
Vol 7 (2) ◽  
pp. 30
Author(s):  
Laeya Baldini ◽  
Bruno Charpentier ◽  
Stéphane Labialle
Keyword(s):  
Ribosomal Rna ◽  
Molecular Mechanisms ◽  
Molecular Level ◽  
Accurate Description ◽  
Small Nucleolar Rnas ◽  
Age Of Maturity ◽  
Non Coding Rnas ◽  
And Function ◽  
Nucleolar Rnas

Box C/D small nucleolar RNAs (C/D snoRNAs) represent an ancient family of small non-coding RNAs that are classically viewed as housekeeping guides for the 2′-O-methylation of ribosomal RNA in Archaea and Eukaryotes. However, an extensive set of studies now argues that they are involved in mechanisms that go well beyond this function. Here, we present these pieces of evidence in light of the current comprehension of the molecular mechanisms that control C/D snoRNA expression and function. From this inventory emerges that an accurate description of these activities at a molecular level is required to let the snoRNA field enter in a second age of maturity.

Form and function of eukaryotic unstable non-coding RNAs

2012 ◽  
Vol 40 (4) ◽  
pp. 836-841 ◽  
Author(s):  
Jonathan Houseley
Keyword(s):  
Unknown Function ◽  
Budding Yeast ◽  
Rna Degradation ◽  
Present Review ◽  
Form And Function ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Higher Eukaryotes ◽  
And Function

Unstable non-coding RNAs are produced from thousands of loci in all studied eukaryotes (and also prokaryotes), but remain of largely unknown function. The present review summarizes the mechanisms of eukaryotic non-coding RNA degradation and highlights recent findings regarding function. The focus is primarily on budding yeast where the bulk of this research has been performed, but includes results from higher eukaryotes where available.

Top Museums on Instagram

2019 ◽  
Vol 3 (2) ◽  
pp. 18-42 ◽  
Author(s):  
Vasiliki G. Vrana ◽  
Dimitrios A. Kydros ◽  
Evangelos C. Kehris ◽  
Anastasios-Ioannis T. Theocharidis ◽  
George I. Kavavasilis
Keyword(s):  
Social Network ◽  
Network Analysis ◽  
Small World ◽  
Marketing Strategies ◽  
The Other ◽  
Small World Network ◽  
Scale Free ◽  
Centrality Metrics ◽  
Photo Sharing ◽  
Visualization Algorithms

Pictures speak louder than words. In this fast-moving world where people hardly have time to read anything, photo-sharing sites become more and more popular. Instagram is being used by millions of people and has created a “sharing ecosystem” that also encourages curation, expression, and produces feedback. Museums are moving quickly to integrate Instagram into their marketing strategies, provide information, engage with audience and connect to other museums Instagram accounts. Taking into consideration that people may not see museum accounts in the same way that the other museum accounts do, the article first describes accounts' performance of the top, most visited museums worldwide and next investigates their interconnection. The analysis uses techniques from social network analysis, including visualization algorithms and calculations of well-established metrics. The research reveals the most important modes of the network by calculating the appropriate centrality metrics and shows that the network formed by the museum Instagram accounts is a scale–free small world network.

STABILITY OF TWO TYPICAL COMPLEX DYNAMICAL NETWORKS

2008 ◽  
Vol 22 (05) ◽  
pp. 553-560 ◽  
Author(s):  
WU-JIE YUAN ◽  
XIAO-SHU LUO ◽  
PIN-QUN JIANG ◽  
BING-HONG WANG ◽  
JIN-QING FANG
Keyword(s):  
Numerical Simulation ◽  
Dissipative System ◽  
Small World ◽  
Complex Dynamical Networks ◽  
Dynamical Networks ◽  
Scale Free ◽  
Scale Free Networks ◽  
General Complex ◽  
The Stability ◽  
Theoretical Results

When being constructed, complex dynamical networks can lose stability in the sense of Lyapunov (i. s. L.) due to positive feedback. Thus, there is much important worthiness in the theory and applications of complex dynamical networks to study the stability. In this paper, according to dissipative system criteria, we give the stability condition in general complex dynamical networks, especially, in NW small-world and BA scale-free networks. The results of theoretical analysis and numerical simulation show that the stability i. s. L. depends on the maximal connectivity of the network. Finally, we show a numerical example to verify our theoretical results.

Independence polynomial and matching polynomial of the Koch network

2015 ◽  
Vol 29 (32) ◽  
pp. 1550234
Author(s):  
Yunhua Liao ◽  
Xiaoliang Xie
Keyword(s):  
Lattice Gas ◽  
Small World ◽  
Partition Functions ◽  
Complete Class ◽  
Dimer Model ◽  
Scale Free ◽  
Matching Polynomial ◽  
Independence Polynomial ◽  
Classical Models ◽  
Explicit Formulae

The lattice gas model and the monomer-dimer model are two classical models in statistical mechanics. It is well known that the partition functions of these two models are associated with the independence polynomial and the matching polynomial in graph theory, respectively. Both polynomials have been shown to belong to the “[Formula: see text]-complete” class, which indicate the problems are computationally “intractable”. We consider these two polynomials of the Koch networks which are scale-free with small-world effects. Explicit recurrences are derived, and explicit formulae are presented for the number of independent sets of a certain type.

scholarly journals Analysis on Invulnerability of Wireless Sensor Network towards Cascading Failures Based on Coupled Map Lattice

Complexity ◽  
2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Xiuwen Fu ◽  
Yongsheng Yang ◽  
Haiqing Yao
Keyword(s):  
Random Network ◽  
Small World ◽  
Coupled Map Lattice ◽  
Wireless Sensor ◽  
Cascading Failures ◽  
Scale Free Network ◽  
Scale Free ◽  
Network Topologies ◽  
Free Network ◽  
Entire Network

Previous research of wireless sensor networks (WSNs) invulnerability mainly focuses on the static topology, while ignoring the cascading process of the network caused by the dynamic changes of load. Therefore, given the realistic features of WSNs, in this paper we research the invulnerability of WSNs with respect to cascading failures based on the coupled map lattice (CML). The invulnerability and the cascading process of four types of network topologies (i.e., random network, small-world network, homogenous scale-free network, and heterogeneous scale-free network) under various attack schemes (i.e., random attack, max-degree attack, and max-status attack) are investigated, respectively. The simulation results demonstrate that the rise of interference R and coupling coefficient ε will increase the risks of cascading failures. Cascading threshold values Rc and εc exist, where cascading failures will spread to the entire network when R>Rc or ε>εc. When facing a random attack or max-status attack, the network with higher heterogeneity tends to have a stronger invulnerability towards cascading failures. Conversely, when facing a max-degree attack, the network with higher uniformity tends to have a better performance. Besides that, we have also proved that the spreading speed of cascading failures is inversely proportional to the average path length of the network and the increase of average degree k can improve the network invulnerability.

Beyond Scale-Free Small-World Networks: Cortical Columns for Quick Brains

2013 ◽  
Vol 110 (10) ◽  
Author(s):  
Ralph Stoop ◽  
Victor Saase ◽  
Clemens Wagner ◽  
Britta Stoop ◽  
Ruedi Stoop
Keyword(s):  
Small World ◽  
Small World Networks ◽  
Scale Free ◽  
Cortical Columns

scholarly journals Non-Coding RNA in Pancreas and β-Cell Development

2018 ◽  
Vol 4 (4) ◽  
pp. 41 ◽  
Author(s):  
Wilson K. M. Wong ◽  
Anja E. Sørensen ◽  
Mugdha V. Joglekar ◽  
Anand A. Hardikar ◽  
Louise T. Dalgaard
Keyword(s):  
Cell Function ◽  
Islet Cells ◽  
Current Knowledge ◽  
Cell Development ◽  
Pancreas Development ◽  
Β Cell ◽  
Neighboring Gene ◽  
Non Coding Rnas ◽  
And Function

In this review, we provide an overview of the current knowledge on the role of different classes of non-coding RNAs for islet and β-cell development, maturation and function. MicroRNAs (miRNAs), a prominent class of small RNAs, have been investigated for more than two decades and patterns of the roles of different miRNAs in pancreatic fetal development, islet and β-cell maturation and function are now emerging. Specific miRNAs are dynamically regulated throughout the period of pancreas development, during islet and β-cell differentiation as well as in the perinatal period, where a burst of β-cell replication takes place. The role of long non-coding RNAs (lncRNA) in islet and β-cells is less investigated than for miRNAs, but knowledge is increasing rapidly. The advent of ultra-deep RNA sequencing has enabled the identification of highly islet- or β-cell-selective lncRNA transcripts expressed at low levels. Their roles in islet cells are currently only characterized for a few of these lncRNAs, and these are often associated with β-cell super-enhancers and regulate neighboring gene activity. Moreover, ncRNAs present in imprinted regions are involved in pancreas development and β-cell function. Altogether, these observations support significant and important actions of ncRNAs in β-cell development and function.

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