scholarly journals A scale-free, fully connected global transition network underlies known microbiome diversity

2020 ◽  
Author(s):  
Gongchao Jing ◽  
Yufeng Zhang ◽  
Lu Liu ◽  
Zengbin Wang ◽  
Zheng Sun ◽  
...  
Keyword(s):  
Minimum Spanning Tree ◽  
Structural Similarity ◽  
Global Scale ◽  
Global Features ◽  
Origin And Evolution ◽  
Scale Free ◽  
Microbiome Diversity ◽  
Transition Network ◽  
Fully Connected ◽  
High Degree

AbstractMicrobiomes are inherently linked by their structural similarity, yet the global features of such similarity are not clear. Here we propose as solution a search-based microbiome transition network. By traversing a composition-similarity based network of 177,022 microbiomes, we show that although the compositions are distinct by habitat, each microbiome is on-average only seven neighbors from any other microbiome on Earth, indicating the inherent homology of microbiome at the global scale. This network is scale-free, suggesting a high degree of stability and robustness in microbiome transition. By tracking the minimum spanning tree in this network, a global roadmap of microbiome dispersal was derived that tracks the potential paths of formulating and propagating microbiome diversity. Such search-based global microbiome networks, reconstructed within hours on just one computing node, provide a readily expanded reference for tracing the origin and evolution of existing or new microbiomes.

scholarly journals A Scale-Free, Fully Connected Global Transition Network Underlies Known Microbiome Diversity

mSystems ◽  
2021 ◽  
Author(s):  
Gongchao Jing ◽  
Yufeng Zhang ◽  
Lu Liu ◽  
Zengbin Wang ◽  
Zheng Sun ◽  
...  
Keyword(s):  
Structural Similarity ◽  
Global Features ◽  
Scale Free ◽  
Microbiome Diversity ◽  
Transition Network ◽  
Fully Connected ◽  
Global Transition

Microbiomes are inherently linked by their structural similarity, yet the global features of such similarity are not clear. Here, we propose as a solution a search-based microbiome transition network.

scholarly journals Quantitative method for resilience assessment framework of airport network during COVID-19

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260940
Author(s):  
Jiuxia Guo ◽  
Yang Li ◽  
Zongxin Yang ◽  
Xinping Zhu
Keyword(s):  
Complex Network ◽  
Small World ◽  
Global Scale ◽  
Assessment Framework ◽  
Small World Networks ◽  
Scale Free ◽  
Global Pandemic ◽  
Network Metrics ◽  
Resilience Assessment

The resilience and vulnerability of airport networks are significant challenges during the COVID-19 global pandemic. Previous studies considered node failure of networks under natural disasters and extreme weather. Herein, we propose a complex network methodology combined with data-driven to assess the resilience of airport networks toward global-scale disturbance using the Chinese airport network (CAN) and the European airport network (EAN) as a case study. The assessment framework includes vulnerability and resilience analyses from the network- and node-level perspectives. Subsequently, we apply the framework to analyze the airport networks in China and Europe. Specifically, real air traffic data for 232 airports in China and 82 airports in Europe are selected to form the CAN and EAN, respectively. The complex network analysis reveals that the CAN and the EAN are scale-free small-world networks, that are resilient to random attacks. However, the connectivity and vulnerability of the CAN are inferior to those of the EAN. In addition, we select the passenger throughput from the top-50 airports in China and Europe to perform a comparative analysis. By comparing the resilience evaluation of individual airports, we discovered that the factors of resilience assessment of an airport network for global disturbance considers the network metrics and the effect of government policy in actual operations. Additionally, this study also proves that a country’s emergency response-ability towards the COVID-19 has a significantly affectes the recovery of its airport network.

scholarly journals The structure of the sedimentary complex of the Middle and South Caspian depressions (Azerbaijan sector)

2021 ◽  
Vol 43 (4) ◽  
pp. 199-216
Author(s):  
N.P. Yusubov ◽  
I.S. Guliyev
Keyword(s):  
Seismic Data ◽  
Oil And Gas ◽  
Sedimentary Cover ◽  
Clay Content ◽  
Geological Structure ◽  
Point Of View ◽  
South Caspian Basin ◽  
Origin And Evolution ◽  
Geological Interpretation ◽  
High Degree

The high degree of knowledge of the upper horizons of the sedimentary cover of the Middle and South Caspian depressions, given an insufficient increase in hydrocarbon reserves, leads to the need for a detailed approach to the search for oil and gas deposits in deep-seated sediments (over 6 km). During the geological interpretation of new highly informative seismic data, as well as data of deep drilling and petrological core studies, there were revealed obvious shortcomings in the concepts of the origin and evolution of the Middle and South Caspian depressions. These ideas misinterpret evolution, especially the South Caspian Basin, which is characterized by a number of unique features: very thick sedimentary cover (up to 22 km), extremely high sedimentation rate, low heat flow and reservoir temperatures, abnormally high pore and reservoir pressures, high clay content of the section, etc. The main purpose of the study was to elucidate the regional structure and features of the dissection of the sedimentary cover of the Middle and South Caspian depressions, the conditions of occurrence and distribution of facies and thicknesses of individual complexes of deposits. The paper analyzes the results of some previous studies of the geological structure of the Middle and South Caspian depressions based on the data of deep seismic sounding, seismological and gravimetric observations. We consider the main conclusions of these studies, about the geological structure of the sedimentary complex of the region’s, very outdated and subject to revision. The results of seismic stratigraphic analysis of seismic data allowed the authors to identify new data about the tectonic structure and express a completely different point of view regarding the structure of the sedimentary cover in the region. The work also touches on the issue associated with the tectonics of the region and the alleged subduction zone here.

scholarly journals Brain Networks Maintain a Scale-free Organization across Consciousness, Anesthesia, and Recovery

2010 ◽  
Vol 113 (5) ◽  
pp. 1081-1091 ◽  
Author(s):  
UnCheol Lee ◽  
GabJin Oh ◽  
Seunghwan Kim ◽  
GyuJung Noh ◽  
ByungMoon Choi ◽  
...  
Keyword(s):  
General Anesthesia ◽  
Minimum Spanning Tree ◽  
Essential Feature ◽  
Fundamental Principle ◽  
Temporal Organization ◽  
Cumulative Distribution ◽  
Connection Matrix ◽  
Scale Free ◽  
States Of Consciousness ◽  
Network Connections

Background Loss of consciousness is an essential feature of general anesthesia. Although alterations of neural networks during anesthesia have been identified in the spatial domain, there has been relatively little study of temporal organization. Methods Ten healthy male volunteers were anesthetized with an induction dose of propofol on two separate occasions. The duration of network connections in the brain was analyzed by multichannel electroencephalography and the minimum spanning tree method. Entropy of the connections was calculated based on Shannon entropy. The global temporal configuration of networks was investigated by constructing the cumulative distribution function of connection times in different frequency bands and different states of consciousness. Results General anesthesia was associated with a significant reduction in the number of network connections, as well as significant alterations of their duration. These changes were most prominent in the δ bandwidth and were also associated with a significant reduction in entropy of the connection matrix. Despite these and other changes, a global "scale-free" organization was consistently preserved across multiple subjects, anesthetic exposures, states of consciousness, and electroencephalogram frequencies. Conclusions Our data suggest a fundamental principle of temporal organization of network connectivity that is maintained during consciousness and anesthesia, despite local changes. These findings are consistent with a process of adaptive reconfiguration during general anesthesia.

scholarly journals Studies on the Decrease Mechanisms of Typical Complex Networks

2021 ◽  
Author(s):  
Yuhu Qiu ◽  
Tianyang Lyu ◽  
Xizhe Zhang ◽  
Ruozhou Wang
Keyword(s):  
Average Length ◽  
Shortest Paths ◽  
Real Life ◽  
Network Models ◽  
Small World ◽  
Clustering Coefficient ◽  
Network Growth ◽  
Scale Free ◽  
Complex Network Models ◽  
High Degree

Network decrease caused by the removal of nodes is an important evolution process that is paralleled with network growth. However, many complex network models usually lacked a sound decrease mechanism. Thus, they failed to capture how to cope with decreases in real life. The paper proposed decrease mechanisms for three typical types of networks, including the ER networks, the WS small-world networks and the BA scale-free networks. The proposed mechanisms maintained their key features in continuous and independent decrease processes, such as the random connections of ER networks, the long-range connections based on nearest-coupled network of WS networks and the tendency connections and the scale-free feature of BA networks. Experimental results showed that these mechanisms also maintained other topology characteristics including the degree distribution, clustering coefficient, average length of shortest-paths and diameter during decreases. Our studies also showed that it was quite difficult to find an efficient decrease mechanism for BA networks to withstand the continuous attacks at the high-degree nodes, because of the unequal status of nodes.

Data Integration Through Protein Ontology

2011 ◽  
pp. 106-122
Author(s):  
Amandeep S. Sidhu ◽  
Tharam S. Dillon ◽  
Elizabeth Chang
Keyword(s):  
Hierarchical Classification ◽  
Structural Similarity ◽  
Protein Annotation ◽  
Functional Identification ◽  
Sequence Identity ◽  
Alternative Protein ◽  
Traditional Approaches ◽  
High Degree ◽  
Keyword Searches

Traditional approaches to integrate protein data generally involved keyword searches, which immediately excludes unannotated or poorly annotated data. An alternative protein annotation approach is to rely on sequence identity, or structural similarity, or functional identification. Some proteins have high degree of sequence identity, or structural similarity, or similarity in functions that are unique to members of that family alone. Consequently, this approach can’t be generalized to integrate the protein data. Clearly, these traditional approaches have limitations in capturing and integrating data for Protein Annotation. For these reasons, we have adopted an alternative method that does not rely on keywords or similarity metrics, but instead uses ontology. In this chapter we discuss conceptual framework of Protein Ontology that has a hierarchical classification of concepts represented as classes, from general to specific; a list of attributes related to each concept, for each class; a set of relations between classes to link concepts in ontology in more complicated ways then implied by the hierarchy, to promote reuse of concepts in the ontology; and a set of algebraic operators for querying protein ontology instances.

Subunit δ of Chloroplast F0F1 ATPase and OSCP of Mitochondrial F0F1 ATPase: a Comparison by CD-Spectroscopy

1991 ◽  
Vol 46 (9-10) ◽  
pp. 759-764 ◽  
Author(s):  
Siegfried Engelbrecht ◽  
Jennifer Reed ◽  
François Penin ◽  
Danièle C. Gautheron ◽  
Wolfgang Junge
Keyword(s):  
Primary Structure ◽  
Tertiary Structure ◽  
Atp Synthesis ◽  
Structural Similarity ◽  
Cd Spectroscopy ◽  
Α Helix ◽  
And Function ◽  
High Degree ◽  
Very High ◽  
Secondary And Tertiary Structure

Abstract CD spectra have been recorded with subunit δ from chloroplast CF0CF1 and with OSCP from mitochondrial MF0MF1. These subunits are supposed to act similarly at the interface between proton transport through the F0-portion and ATP-synthesis in the F1-portion of their respective F0F1-ATPase. Evaluation of the data for both proteins revealed a very high α-helix content of -85% and practically no β-sheets. Despite their low homology on the primary structure level (23% identity) and their different electrostatic properties (pl-values differ by 3 units), spinach δ and porcine OSCP are indistinguishable with respect to their secondary structure as measured by CD. Prediction and analysis of consensual a-helices even in poorly conserved regions indicate α high degree of structural similarity between chloroplast δ and OSCP. In view of the topology and function of δ and OSCP in intact F0F1 these findings are interpreted to indicate the dominance of secondary and tertiary structure over the primary structure in their supposed function between proton flow and ATP-synthesis.

scholarly journals Quantum-Like Interdependence Theory Advances Autonomous Human–Machine Teams (A-HMTs)

Entropy ◽  
2020 ◽  
Vol 22 (11) ◽  
pp. 1227
Author(s):  
William F. Lawless
Keyword(s):  
Autonomous Systems ◽  
Quantum Decoherence ◽  
Multi Agent Systems ◽  
Scale Free ◽  
Weapon Systems ◽  
Interdependence Theory ◽  
Human Autonomy ◽  
Degree Of Certainty ◽  
Human Operators ◽  
High Degree

As humanity grapples with the concept of autonomy for human–machine teams (A-HMTs), unresolved is the necessity for the control of autonomy that instills trust. For non-autonomous systems in states with a high degree of certainty, rational approaches exist to solve, model or control stable interactions; e.g., game theory, scale-free network theory, multi-agent systems, drone swarms. As an example, guided by artificial intelligence (AI, including machine learning, ML) or by human operators, swarms of drones have made spectacular gains in applications too numerous to list (e.g., crop management; mapping, surveillance and fire-fighting systems; weapon systems). But under states of uncertainty or where conflict exists, rational models fail, exactly where interdependence theory thrives. Large, coupled physical or information systems can also experience synergism or dysergism from interdependence. Synergistically, the best human teams are not only highly interdependent, but they also exploit interdependence to reduce uncertainty, the focus of this work-in-progress and roadmap. We have long argued that interdependence is fundamental to human autonomy in teams. But for A-HMTs, no mathematics exists to build from rational theory or social science for their design nor safe or effective operation, a severe weakness. Compared to the rational and traditional social theory, we hope to advance interdependence theory first by mapping similarities between quantum theory and our prior findings; e.g., to maintain interdependence, we previously established that boundaries reduce dysergic effects to allow teams to function (akin to blocking interference to prevent quantum decoherence). Second, we extend our prior findings with case studies to predict with interdependence theory that as uncertainty increases in non-factorable situations for humans, the duality in two-sided beliefs serves debaters who explore alternatives with tradeoffs in the search for the best path going forward. Third, applied to autonomous teams, we conclude that a machine in an A-HMT must be able to express itself to its human teammates in causal language however imperfectly.

scholarly journals A Key Motif in the Cholesterol-Dependent Cytolysins Reveals a Large Family of Related Proteins

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Jordan C. Evans ◽  
Bronte A. Johnstone ◽  
Sara L. Lawrence ◽  
Craig J. Morton ◽  
Michelle P. Christie ◽  
...  
Keyword(s):  
Large Family ◽  
Structural Similarity ◽  
Particle Analysis ◽  
Critical Component ◽  
Content Type ◽  
Conserved Motif ◽  
Forming Mechanism ◽  
Terrestrial Environments ◽  
Pore Complexes ◽  
High Degree

ABSTRACT The cholesterol-dependent cytolysins (CDCs) are bacterial, β-barrel, pore-forming toxins. A central enigma of the pore-forming mechanism is how completion of the prepore is sensed to initiate its conversion to the pore. We identified a motif that is conserved between the CDCs and a diverse family of nearly 300 uncharacterized proteins present in over 220 species that span at least 10 bacterial and 2 eukaryotic phyla. Except for this motif, these proteins exhibit little similarity to the CDCs at the primary structure level. Studies herein show this motif is a critical component of the sensor that initiates the prepore-to-pore transition in the CDCs. We further show by crystallography, single particle analysis, and biochemical studies of one of these CDC-like (CDCL) proteins from Elizabethkingia anophelis, a commensal of the malarial mosquito midgut, that a high degree of structural similarity exists between the CDC and CDCL monomer structures and both form large oligomeric pore complexes. Furthermore, the conserved motif in the E. anophelis CDCL crystal structure occupies a nearly identical position and makes similar contacts to those observed in the structure of the archetype CDC, perfringolysin O (PFO). This suggests a common function in the CDCs and CDCLs and may explain why only this motif is conserved in the CDCLs. Hence, these studies identify a critical component of the sensor involved in initiating the prepore-to-pore transition in the CDCs, which is conserved in a large and diverse group of distant relatives of the CDCs. IMPORTANCE The cholesterol-dependent cytolysins’ pore-forming mechanism relies on the ability to sense the completion of the oligomeric prepore structure and initiate the insertion of the β-barrel pore from the assembled prepore structure. These studies show that a conserved motif is an important component of the sensor that triggers the prepore-to-pore transition and that it is conserved in a large family of previously unidentified CDC-like proteins, the genes for which are present in a vast array of microbial species that span most terrestrial environments, as well as most animal and human microbiomes. These studies establish the foundation for future investigations that will probe the contribution of this large family of CDC-like proteins to microbial survival and human disease.

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