The impact of sources and sinks on the dynamics of homogeneous and heterogeneous boolean networks

The Other ◽

Structural Elements ◽

Sources And Sinks ◽

Random Boolean Networks ◽

Dynamical Behaviors ◽

Other Hand ◽

Random Boolean networks, originally introduced as simplified models for the genetic regulatory networks, are abstract models widely applied for the study of the dynamical behaviors of self-organizing complex systems. In these networks, connectivity and the bias of the Boolean functions are the most important factors that can determine the behavioral regime of the systems. On the other hand, it has been found that topology and some structural elements of the networks such as the reciprocity, self-loops and source nodes, can have relevant effects on the dynamical properties of critical Boolean networks. In this paper, we study the impact of source and sink nodes on the dynamics of homogeneous and heterogeneous Boolean networks. Our research shows that an increase of the source nodes causes an exponentially growing of the different behaviors that the system can exhibit regardless of the network topology, while the amount of order seems to undergo modifications depending on the topology of the system. Indeed, with the increase of the source nodes the orderliness of the heterogeneous networks also increases, whereas it diminishes in the homogeneous ones. On the other hand, although the sink nodes seem not to have effects on the dynamic of the homogeneous networks, for the heterogeneous ones we have found that an increase of the sinks gives rise to an increasing of the order, although the different potential behaviors of the system remains approximately the same.

Effects of Antimodularity and Multiscale Influence in Random Boolean Networks

Complexity ◽

10.1155/2019/8209146 ◽

2019 ◽

Vol 2019 ◽

pp. 1-14

Author(s):

Luis A. Escobar ◽

Hyobin Kim ◽

Carlos Gershenson

Keyword(s):

Complex Dynamics ◽

Boolean Networks ◽

Downward Causation ◽

Statistical Properties ◽

The Other ◽

Random Boolean Networks ◽

Dynamical Behaviors ◽

Modular Networks ◽

Other Hand ◽

The One

We investigate the effects of modularity, antimodularity, and multiscale influence on random Boolean networks (RBNs). On the one hand, we produced modular, antimodular, and standard RBNs and compared them to identify how antimodularity affects the dynamical behaviors of RBNs. We found that the antimodular networks showed similar dynamics to the standard networks. Confirming previous results, modular networks had more complex dynamics. On the other hand, we generated multilayer RBNs where there are different RBNs in the nodes of a higher scale RBN. We observed the dynamics of micro- and macronetworks by adjusting parameters at each scale to reveal how the behavior of lower layers affects the behavior of higher layers and vice versa. We found that the statistical properties of macro-RBNs were changed by the parameters of micro-RBNs, but not the other way around. However, the precise patterns of networks were dominated by the macro-RBNs. In other words, for statistical properties only upward causation was relevant, while for the detailed dynamics downward causation was prevalent.

The Robustness and Mutual Information Entropy of Random Modular Boolean Networks

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.989-994.4417 ◽

2014 ◽

Vol 989-994 ◽

pp. 4417-4420 ◽

Cited By ~ 1

Author(s):

Nan Zhao ◽

Bing Hui Guo ◽

Fan Chao Meng

Keyword(s):

Mutual Information ◽

Regulatory Networks ◽

Boolean Networks ◽

Information Propagation ◽

Entropy Analysis ◽

Random Boolean Networks ◽

Basic Model ◽

Different Types

Random Boolean networks have been proposed as a basic model of genetic regulatory networks for more than four decades. Attractors have been considered as the best way to represent the long-term behaviors of random Boolean networks. Most studies on attractors are made with random topologies. However, the real regulatory networks have been found to be modular or more complex topologies. In this work, we extend classical robustness and entropy analysis of random Boolean networks to random modular Boolean networks. We firstly focus on the robustness of the attractor to perturbations with different parameters. Then, we investigate and calculate how the amount of information propagated between the nodes when on an attractor, as quantified by the average pairwise mutual information. The results can be used to study the capability of genetic information propagation of different types of genetic regulatory networks.

Modular Random Boolean Networks

Artificial Life ◽

10.1162/artl_a_00042 ◽

2011 ◽

Vol 17 (4) ◽

pp. 331-351 ◽

Cited By ~ 18

Author(s):

Rodrigo Poblanno-Balp ◽

Carlos Gershenson

Keyword(s):

Chaotic Dynamics ◽

Regulatory Networks ◽

Boolean Networks ◽

Random Boolean Networks ◽

Analytical Results ◽

Statistical Experiments

Random Boolean networks (RBNs) have been a popular model of genetic regulatory networks for more than four decades. However, most RBN studies have been made with random topologies, while real regulatory networks have been found to be modular. In this work, we extend classical RBNs to define modular RBNs. Statistical experiments and analytical results show that modularity has a strong effect on the properties of RBNs. In particular, modular RBNs have more attractors, and are closer to criticality when chaotic dynamics would be expected, than classical RBNs.

Dynamical Criticality in Gene Regulatory Networks

Complexity ◽

10.1155/2018/5980636 ◽

2018 ◽

Vol 2018 ◽

pp. 1-14 ◽

Cited By ~ 9

Author(s):

Marco Villani ◽

Luca La Rocca ◽

Stuart Alan Kauffman ◽

Roberto Serra

Keyword(s):

Regulatory Networks ◽

Single Gene ◽

Biological Evolution ◽

Boolean Networks ◽

Dynamical Regime ◽

Random Boolean Networks ◽

Statistical Framework ◽

Gene Regulatory ◽

The Relationship

A well-known hypothesis, with far-reaching implications, is that biological evolution should preferentially lead to states that are dynamically critical. In previous papers, we showed that a well-known model of genetic regulatory networks, namely, that of random Boolean networks, allows one to study in depth the relationship between the dynamical regime of a living being’s gene network and its response to permanent perturbations. In this paper, we analyze a huge set of new experimental data on single gene knockouts in S. cerevisiae, laying down a statistical framework to determine its dynamical regime. We find that the S. cerevisiae network appears to be slightly ordered, but close to the critical region. Since our analysis relies on dichotomizing continuous data, we carefully consider the issue of an optimal threshold choice.

Understanding genetic regulatory networks

International Journal of Astrobiology ◽

10.1017/s147355040300154x ◽

2003 ◽

Vol 2 (2) ◽

pp. 131-139 ◽

Cited By ~ 12

Author(s):

Stuart Kauffman

Keyword(s):

Power Law ◽

Regulatory Networks ◽

Single Gene ◽

Chaotic Regime ◽

Boolean Networks ◽

Power Law Distribution ◽

Generic Properties ◽

Wiring Diagram ◽

Random Boolean Networks

Random Boolean networks (RBM) were introduced about 35 years ago as first crude models of genetic regulatory networks. RBNs are comprised of N on–off genes, connected by a randomly assigned regulatory wiring diagram where each gene has K inputs, and each gene is controlled by a randomly assigned Boolean function. This procedure samples at random from the ensemble of all possible NK Boolean networks. The central ideas are to study the typical, or generic properties of this ensemble, and see 1) whether characteristic differences appear as K and biases in Boolean functions are introducted, and 2) whether a subclass of this ensemble has properties matching real cells.Such networks behave in an ordered or a chaotic regime, with a phase transition, ‘the edge of chaos’ between the two regimes. Networks with continuous variables exhibit the same two regimes. Substantial evidence suggests that real cells are in the ordered regime. A key concept is that of an attractor. This is a reentrant trajectory of states of the network, called a state cycle. The central biological interpretation is that cell types are attractors. A number of properties differentiate the ordered and chaotic regimes. These include the size and number of attractors, the existence in the ordered regime of a percolating ‘sea’ of genes frozen in the on or off state, with a remainder of isolated twinkling islands of genes, a power law distribution of avalanches of gene activity changes following perturbation to a single gene in the ordered regime versus a similar power law distribution plus a spike of enormous avalanches of gene changes in the chaotic regime, and the existence of branching pathway of ‘differentiation’ between attractors induced by perturbations in the ordered regime.Noise is serious issue, since noise disrupts attractors. But numerical evidence suggests that attractors can be made very stable to noise, and meanwhile, metaplasias may be a biological manifestation of noise. As we learn more about the wiring diagram and constraints on rules controlling real genes, we can build refined ensembles reflecting these properties, study the generic properties of the refined ensembles, and hope to gain insight into the dynamics of real cells.

Proceedings of International Conference "Managinag risks to coastal regions and communities in a changinag world" (EMECS'11 - SeaCoasts XXVI) ◽

SCENARIOS FOR AN EXPANDING DEMAND OF TOURISM ON THE COASTS OF CUBA

10.21610/conferencearticle_58b43153a41e9 ◽

2017 ◽

Author(s):

Oscar Gutiérrez-Bolívar ◽

Pedro Fernández Carrasco ◽

Pedro Fernández Carrasco

Keyword(s):

United States ◽

The Other ◽

Sudden Increase ◽

Tourist Destination ◽

Other Hand ◽

The Usa ◽

The opening of relationships between United States and Cuba could be a drive for a huge increase in the affluence of tourism to Cuba and especially to the coast areas. Cuba has been for many years an important tourist destination for people from many countries, but almost forbidden for US citizens. The proximity of the USA, its amount of population as well as their great acquisition power will increase in a very substantial way the demand for accommodation and other uses in the proximity of the coasts. There will be a need to implement a package of measures that reduce the impact of such sudden increase in the coastal line. On the other hand that augment in tourism could be an opportunity to improve the standard of life of Cubans. The consideration of different possibilities of such development, the analysis of the damages that each one could cause as well as the measures that could avoid, ameliorate or compensate such effects are the goals that are going to be presented in this paper.

Laughter on the Fringes

10.1093/oso/9780190697099.001.0001 ◽

2019 ◽

Cited By ~ 2

Author(s):

Anna Peterson

Keyword(s):

The Other ◽

Literary Canon ◽

Autobiographical Writing ◽

Treasure Trove ◽

Old Comedy ◽

Other Hand ◽

Aggressive Humor ◽

The One ◽

The Individual ◽

This book examines the impact that Athenian Old Comedy had on Greek writers of the Imperial era. It is generally acknowledged that Imperial-era Greeks responded to Athenian Old Comedy in one of two ways: either as a treasure trove of Atticisms, or as a genre defined by and repudiated for its aggressive humor. Worthy of further consideration, however, is how both approaches, and particularly the latter one that relegated Old Comedy to the fringes of the literary canon, led authors to engage with the ironic and self-reflexive humor of Aristophanes, Eupolis, and Cratinus. Authors ranging from serious moralizers (Plutarch and Aelius Aristides) to comic writers in their own right (Lucian, Alciphron), to other figures not often associated with Old Comedy (Libanius) adopted aspects of the genre to negotiate power struggles, facilitate literary and sophistic rivalries, and provide a model for autobiographical writing. To varying degrees, these writers wove recognizable features of the genre (e.g., the parabasis, its agonistic language, the stage biographies of the individual poets) into their writings. The image of Old Comedy that emerges from this time is that of a genre in transition. It was, on the one hand, with the exception of Aristophanes’s extant plays, on the verge of being almost completely lost; on the other hand, its reputation and several of its most characteristic elements were being renegotiated and reinvented.

Application of Plant Extracts in Micropropagation and Cryopreservation of Bleeding Heart: An Ornamental-Medicinal Plant Species

Agriculture ◽

10.3390/agriculture11060542 ◽

2021 ◽

Vol 11 (6) ◽

pp. 542

Author(s):

Dariusz Kulus ◽

Natalia Miler

Keyword(s):

Tissue Culture ◽

Plant Growth ◽

Plant Growth Regulators ◽

Growth Regulators ◽

Plant Extracts ◽

The Other ◽

White Gold ◽

Natural Extracts ◽

Other Hand ◽

Lamprocapnos spectabilis (L.) Fukuhara (bleeding heart) is valued both in the horticultural and pharmaceutical markets. Despite its great popularity, information on the in vitro tissue culture technology in this species is limited. There is also little knowledge on the application of plant extracts in the tissue culture systems of plants other than orchids. The aim of this study is to compare the utility of traditional plant growth regulators (PGRs) and natural extracts—obtained from the coconut shreds, as well as oat, rice, and sesame seeds—in the micropropagation and cryopreservation of L. spectabilis ‘Gold Heart’ and ‘White Gold’. The biochemical analysis of extracts composition is also included. In the first experiment related to micropropagation via axillary buds activation, the single-node explants were cultured for a 10-week-long propagation cycle in the modified Murashige and Skoog medium fortified either with 1.11 µM benzyladenine (BA) and 1.23 µM indole-3-butritic acid (IBA) or with 10% (v/v) plant extracts. A PGRs- and extract-free control was also considered. In the cryopreservation experiment, the same 10% (v/v) extracts were added into the medium during a seven-day preculture in the encapsulation-vitrification cryopreservation protocol. It was found that the impact of natural additives was cultivar- and trait-specific. In the first experiment, the addition of coconut extract favoured the proliferation of shoots and propagation ratio in bleeding heart ‘Gold Heart’. Rice extract, on the other hand, promoted callus formation in ‘White Gold’ cultivar and was more effective in increasing the propagation ratio in this cultivar than the conventional plant growth regulators (4.1 and 2.6, respectively). Sesame extract suppressed the development of the explants in both cultivars analysed, probably due to the high content of polyphenols. As for the second experiment, the addition of plant extracts into the preculture medium did not increase the survival level of the cryopreserved shoot tips (sesame and oat extracts even decreased this parameter). On the other hand, coconut extract, abundant in simple sugars and endogenous cytokinins, stimulated a more intensive proliferation and growth of shoots after rewarming of samples. Analysing the synergistic effect of conventional plant growth regulators and natural extracts should be considered in future studies related to L. spectabilis.

Education and Learning at a Medieval English Cathedral: Exeter 1380–1548

The Journal of Ecclesiastical History ◽

10.1017/s0022046900031419 ◽

1981 ◽

Vol 32 (3) ◽

pp. 265-283 ◽

Cited By ~ 4

Author(s):

Nicholas Orme

Keyword(s):

Sixteenth Century ◽

Good Deal ◽

The Other ◽

Educational Institutions ◽

Medieval England ◽

Literary Education ◽

Other Hand ◽

The People ◽

During the last hundred years our knowledge of the educational institutions of medieval England has steadily increased, both of schools and universities. We know a good deal about what they taught, how they were organised and where they were sited. The next stage is to identify their relationship with the society which they existed to serve. Whom did they train, to what standards and for what ends? These questions pose problems. They cannot be answered from the constitutional and curricular records which tell us about the structure of educational institutions. Instead, they require a knowledge of the people—the pupils and scholars—who went to the medieval schools and universities. We need to recover their names, to compile their biographies and thereby to establish their origins, careers and attainments. If this can be done on a large enough scale, the impact of education on society will become clearer. In the case of the universities, the materials for this task are available and well known. Thanks to the late Dr A. B. Emden, most of the surviving names of the alumni of Oxford and Cambridge have been collected and published, together with a great many biographical records about them. For the schools, on the other hand, where most boys had their literary education if they had one at all, such data are not available. Except for Winchester and Eton, we do not possess lists of the pupils of schools until the middle of the sixteenth century, and there is no way to remedy the deficiency.

Most Often Motivated by Social Media: The Who, the What, and the How Much—Experience from Poland

Sustainability ◽

10.3390/su132011193 ◽

2021 ◽

Vol 13 (20) ◽

pp. 11193

Author(s):

Karol Król ◽

Dariusz Zdonek

Keyword(s):

Social Media ◽

Intrinsic Motivation ◽

Statistical Methods ◽

The Other ◽

Public Expression ◽

Other Hand ◽

The Impact ◽

The Way

Content published in social media (SM) can be motivating. It can induce action, stimulate demand, and shape opinions. On the other hand, it can demotivate, cause helplessness, or overwhelm with information. Still, the impact of SM is not always the same. The paper aims to analyse the relations between sex, personality, and the way social media is used and motivation to take specific actions. The conclusions are founded on a survey (n = 462). The data were analysed with statistical methods. The study revealed that the use of SM has a significant impact on the motivation to act. Browsing through descriptions and photographs of various achievements posted by others in SM increased the intrinsic motivation of the respondents. Positive comments and emojis had a similar effect. Moreover, women and extraverts noted a significantly greater impact of SM on their intrinsic motivation concerning health and beauty effort, travel, hobby, and public expression of opinions than men and introverts. The results can be useful to recruiters. Extravert women that are open to cooperation, thorough, and well-organised are more likely to be active in SM.