scholarly journals Determination and Identification of Important and Influential Nodes Involved in the Pathology of Escherichia Coli Using Improved TOPSIS Method

2019 ◽  
Author(s):  
zohreh minaei
Keyword(s):  
Escherichia Coli ◽  
Hybrid System ◽  
Biological Networks ◽  
Promising Method ◽  
Topsis Method ◽  
Influential Nodes ◽  
Important Nodes ◽  
Primary Index

Abstract Various disciplines are trying to solve one of the most noteworthy queries and broadly used concepts in biology, essentiality. Centrality is a primary index and a promising method for identifying essential nodes, particularly in biological networks. Thus, important nodes of the network can be identified by analyzing some of the centrality extracted from the network. In this paper, we aim to identify the important proteins in the Escherichia Coli (E.Coli) network based on extraction of centralities. During these operations, centralities such as degree of centrality, betweeness, laplacian and closeness, are considered as node's important indicators. Finally the important nodes will be determined based on the centrality and Technique for order performance by similarity (TOPSIS) method. After performing the weighted TOPSIS simulation and obtaining the output result, it was found that the proposed hybrid system is able to place 74 and 99 important nodes between the top 100 and 150 nodes, respectively. Finally, the results of this study are compared with other similar studies.

scholarly journals Controlling COVID-19 Propagation with Quarantine of Influential Nodes

2021 ◽  
Author(s):  
Sarkhosh S. Chaharborj ◽  
Shahriar S. Chaharborj ◽  
Phang Pei See
Keyword(s):  
Complex Network ◽  
Structural Organization ◽  
Centrality Measures ◽  
Topsis Method ◽  
Epidemic Disease ◽  
Dependability Analysis ◽  
Order Preference ◽  
Si Model ◽  
Influential Nodes ◽  
Important Nodes

Abstract We study importance of influential nodes in spreading of epidemic COVID-19 in a complex network. We will show that quarantine of important and influential nodes or consider of health protocols by efficient nodes is very helpful and effective in the controlling of spreading epidemic COVID-19 in a complex network. Therefore, identifying influential nodes in complex networks is the very significant part of dependability analysis, which has been a clue matter in analyzing the structural organization of a network. The important nodes can be considered as a person or as an organization. To find the influential nodes we use the technique for order preference by similarity to ideal solution (TOPSIS) method with new proposed formula to obtain the efficient weights. We use various centrality measures as the multi-attribute of complex network in the TOPSIS method. We define a formula for spreading probability of epidemic disease in a complex network to study the power of infection spreading with quarantine of important nodes. In the following, we use the Susceptible–Infected (SI) model to figure out the performance and efficiency of the proposed methods. The proposed method has been examined for efficiency and practicality using numerical examples.

scholarly journals Identification of Important Nodes in Directed Biological Networks: A Network Motif Approach

PLoS ONE ◽  
2014 ◽  
Vol 9 (8) ◽  
pp. e106132 ◽  
Author(s):  
Pei Wang ◽  
Jinhu Lü ◽  
Xinghuo Yu
Keyword(s):  
Biological Networks ◽  
Network Motif ◽  
Important Nodes

A dynamic weighted TOPSIS method for identifying influential nodes in complex networks

2018 ◽  
Vol 32 (19) ◽  
pp. 1850216 ◽  
Author(s):  
Pingle Yang ◽  
Xin Liu ◽  
Guiqiong Xu
Keyword(s):  
Complex Networks ◽  
Centrality Measures ◽  
Topsis Method ◽  
Decision Making Problem ◽  
Significant Research ◽  
Order Preference ◽  
Multi Attribute Decision Making ◽  
Influential Nodes ◽  
Influential Node ◽  
Grey Relational

Identifying the influential nodes in complex networks is a challenging and significant research topic. Though various centrality measures of complex networks have been developed for addressing the problem, they all have some disadvantages and limitations. To make use of the advantages of different centrality measures, one can regard influential node identification as a multi-attribute decision-making problem. In this paper, a dynamic weighted Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) is developed. The key idea is to assign the appropriate weight to each attribute dynamically, based on the grey relational analysis method and the Susceptible–Infected–Recovered (SIR) model. The effectiveness of the proposed method is demonstrated by applications to three actual networks, which indicates that our method has better performance than single indicator methods and the original weighted TOPSIS method.

scholarly journals In vivo evaluation of the interaction between the Escherichia coli IGP synthase subunits using the Bacterial Two-Hybrid system

2020 ◽  
Vol 367 (14) ◽  
Author(s):  
Sofia Chioccioli ◽  
Patrizia Bogani ◽  
Sara Del Duca ◽  
Lara Mitia Castronovo ◽  
Alberto Vassallo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Hybrid System ◽  
De Novo ◽  
Glycerol Phosphate ◽  
In Vivo Evaluation ◽  
Igp Synthase ◽  
Imidazole Glycerol Phosphate ◽  
Two Hybrid

ABSTRACT Histidine biosynthesis is one of the most characterized metabolic routes for its antiquity and its central role in cellular metabolism; indeed, it represents a cross-road between nitrogen metabolism and de novo synthesis of purines. This interconnection is due to the activity of imidazole glycerol phosphate synthase, a heterodimeric enzyme constituted by the products of two his genes, hisH and hisF, encoding a glutamine amidotransferase and a cyclase, respectively. Despite their interaction was suggested by several in vitro experiments, their in vivo complex formation has not been demonstrated. On the contrary, the analysis of the entire Escherichia coli interactome performed using the yeast two hybrid system did not suggest the in vivo interaction of the two IGP synthase subunits. The aim of this study was to demonstrate the interaction of the two proteins using the Bacterial Adenylate Cyclase Two-Hybrid (BACTH) system. Data obtained demonstrated the in vivo interaction occurring between the proteins encoded by the E. coli hisH and hisF genes; this finding might also open the way to pharmaceutical applications through the design of selective drugs toward this enzyme.

scholarly journals Influential Performance of Nodes Identified by Relative Entropy in Dynamic Networks

2020 ◽  
Vol 08 (01) ◽  
pp. 93-112
Author(s):  
Péter Marjai ◽  
Attila Kiss
Keyword(s):  
Diffusion Process ◽  
Complex Networks ◽  
Relative Entropy ◽  
Information Diffusion ◽  
Dynamic Networks ◽  
Centrality Measures ◽  
Topsis Method ◽  
Cover Time ◽  
Influential Nodes ◽  
Different Characteristics

For decades, centrality has been one of the most studied concepts in the case of complex networks. It addresses the problem of identification of the most influential nodes in the network. Despite the large number of the proposed methods for measuring centrality, each method takes different characteristics of the networks into account while identifying the “vital” nodes, and for the same reason, each has its advantages and drawbacks. To resolve this problem, the TOPSIS method combined with relative entropy can be used. Several of the already existing centrality measures have been developed to be effective in the case of static networks, however, there is an ever-increasing interest to determine crucial nodes in dynamic networks. In this paper, we are investigating the performance of a new method that identifies influential nodes based on relative entropy, in the case of dynamic networks. To classify the effectiveness, the Suspected-Infected model is used as an information diffusion process. We are investigating the average infection capacity of ranked nodes, the Time-Constrained Coverage as well as the Cover Time.

scholarly journals Interaction Network among Escherichia coli Membrane Proteins Involved in Cell Division as Revealed by Bacterial Two-Hybrid Analysis

2005 ◽  
Vol 187 (7) ◽  
pp. 2233-2243 ◽  
Author(s):  
Gouzel Karimova ◽  
Nathalie Dautin ◽  
Daniel Ladant
Keyword(s):  
Escherichia Coli ◽  
Cell Division ◽  
Membrane Proteins ◽  
Hybrid System ◽  
Molecular Interactions ◽  
Interaction Network ◽  
Deletion Mapping ◽  
Division Site ◽  
Cooperative Association ◽  
Two Hybrid

ABSTRACT Formation of the Escherichia coli division septum is catalyzed by a number of essential proteins (named Fts) that assemble into a ring-like structure at the future division site. Several of these Fts proteins are intrinsic transmembrane proteins whose functions are largely unknown. Although these proteins appear to be recruited to the division site in a hierarchical order, the molecular interactions underlying the assembly of the cell division machinery remain mostly unspecified. In the present study, we used a bacterial two-hybrid system based on interaction-mediated reconstitution of a cyclic AMP (cAMP) signaling cascade to unravel the molecular basis of septum assembly by analyzing the protein interaction network among E. coli cell division proteins. Our results indicate that the Fts proteins are connected to one another through multiple interactions. A deletion mapping analysis carried out with two of these proteins, FtsQ and FtsI, revealed that different regions of the polypeptides are involved in their associations with their partners. Furthermore, we showed that the association between two Fts hybrid proteins could be modulated by the coexpression of a third Fts partner. Altogether, these data suggest that the cell division machinery assembly is driven by the cooperative association among the different Fts proteins to form a dynamic multiprotein structure at the septum site. In addition, our study shows that the cAMP-based two-hybrid system is particularly appropriate for analyzing molecular interactions between membrane proteins.

scholarly journals Cadmium sulfide net framework nanoparticles for photo-catalyzed cell redox

RSC Advances ◽  
2020 ◽  
Vol 10 (62) ◽  
pp. 37820-37825
Author(s):  
Zhaoyu Chang ◽  
Jian Zhang ◽  
Wanyuan Dong ◽  
Xiangqi Meng ◽  
Hualei Wang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cadmium Sulfide ◽  
Hybrid System ◽  
Redox Reaction ◽  
Reaction Conditions ◽  
Nadh Regeneration ◽  
Net Framework

CdS net framework (CdS-NF) nanoparticles were synthesized under mild reaction conditions and used to construct an Escherichia coli–CdS-NF hybrid system which used NADH regeneration to promote the redox reaction.

scholarly journals A transferable heterogeneous two-hybrid system in Escherichia coli based on polyhydroxyalkanoates synthesis regulatory protein PhaR

2011 ◽  
Vol 10 (1) ◽  
pp. 21 ◽  
Author(s):  
Zhi-Hui Wang ◽  
Ping Ma ◽  
Jiong Chen ◽  
Jing Zhang ◽  
Chong-Bo Chen ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Hybrid System ◽  
Regulatory Protein ◽  
Two Hybrid
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