scholarly journals MicNet Toolbox: visualizing and deconstructing a microbial network

2021 ◽  
Author(s):  
Natalia Favila ◽  
David Madrigal-Trejo ◽  
Daniel Legorreta ◽  
Jazmín Sánchez-Pérez ◽  
Laura Espinosa-Asuar ◽  
...  
Keyword(s):  
Network Theory ◽  
Biological Network ◽  
Ecological Research ◽  
Straightforward Manner ◽  
Large Dataset ◽  
Microbial Network ◽  
Dimensionality Reduction Technique ◽  
Network Topologies ◽  
Local Patterns ◽  
Global And Local

Understanding both global and local patterns in the structure and interplay of microbial communities has been a fundamental question in ecological research. In this paper, we present a python toolbox that combines two emerging techniques that have been proposed as useful when analyzing compositional microbial data. On one hand, we introduce a visualization module that incorporates the use of UMAP, a recent dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density. On the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple this with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) using simulated community networks with known topologies to show that we are able to discern between network topologies. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data.

scholarly journals The spatial pattern of forest cover changes in Lithuania during the second half of the twentieth century

2015 ◽  
Vol 22 (4) ◽  
Author(s):  
Daiva Juknelienė ◽  
Gintautas Mozgeris
Keyword(s):  
World War Ii ◽  
Forest Cover ◽  
Agricultural Land ◽  
Moran’S I ◽  
Sources Of Information ◽  
Forest Cover Change ◽  
Moran's I ◽  
Local Patterns ◽  
Forest Cover Changes ◽  
Global And Local

The trends of forest cover change in Lithuanian municipalities are introduced in the current paper. Two sources of information on the forest cover in 1950s and today (2013) were used in this study: (i) a geographic forest cover database developed using historical orthophotomaps based on aerial photography, which was carried out in the period just after the World War II, and (ii) the information originating from the State Forest Cadaster and referring to the year 2013. These two layers were compared using GIS overlay techniques. The data was made available for the analyses aggregated up to the municipality level. The Global Moran’s I statistic and Anselin Local Moran’s I were used to identify global and local patterns in the distribution of forest cover characteristics in Lithuanian municipalities, respectively. The  main finding of this study was that the  proportion of the  forest cover in 1950 was 26.5%, i. e. notably differing from the official statistics – 19.7%. The proportion of the forest cover increased in all municipalities during the period 1950–2013. The largest increase in forest cover proportion was in the areas less suitable for agriculture. The relatively largest areas of new forests were identified in the south-eastern part of Lithuania, the deforestation was relatively slowest around less forested municipalities, while the afforestation was relatively slowest around the agricultural Pakruojis municipality. Deforestation was most commonly associated with the forest transformation into agricultural land, less often into scrublands or waters.

scholarly journals Promoting Metro Operation Safety by Exploring Metro Operation Accident Network

2021 ◽  
Vol 9 (4) ◽  
pp. 455-468
Author(s):  
Qi Suo ◽  
Liyuan Wang ◽  
Tianzi Yao ◽  
Zihao Wang
Keyword(s):  
Network Theory ◽  
Operation System ◽  
Causal Factors ◽  
Cascading Effects ◽  
Complex Network Theory ◽  
Facility Type ◽  
Safety Studies ◽  
Topological Characteristics ◽  
Event Chains ◽  
Global And Local

Abstract Understanding the causation of accidents is essential to promote metro operation safety. In terms of 243 reported metro operation accident cases in China, a directed weighted network was constructed based on complex network theory, where nodes and directed edges denotes factors and event chains respectively. To reveal the key causal factors, the topological characteristics of metro operation accident network (MOAN) were analyzed from both global and local views. The results show that facility-type factors are more closely related to the occurrence of the accidents from the perspectives of average path length and cascading effects. Accident types like train delay and train suspension are the great risk recipients. Key causal factors with large out-degree, out-strength, betweenness centrality and cluster coefficient, such as communication and signal failure, vehicle failure and piling into the train should be noticed. The research framework proposed in the paper is not only applicable to China’s metro operation system, but also appropriate for other transportation system safety studies.

scholarly journals A fresh look at the biodiversity lexicon for fiddler crabs (Decapoda: Brachyura: Ocypodidae). Part 2: Biogeography

2020 ◽  
Vol 40 (4) ◽  
pp. 364-383 ◽  
Author(s):  
Michael S Rosenberg
Keyword(s):  
Climate Change ◽  
Keystone Species ◽  
Species Assemblages ◽  
Fiddler Crabs ◽  
Species Ranges ◽  
Number Of Species ◽  
Coastal Species ◽  
As Species ◽  
Local Patterns ◽  
Global And Local

Abstract Fiddler crabs (Ocypodidae Rafinesque, 1815) occupy most tropical and semitropical coastlines worldwide where they are keystone species and ecosystem engineers. I present updated ranges for all 105 species and explore both global and local patterns to establish a baseline distribution as species ranges begin to shift with climate change. Globally, the average number of species per occupied coastline is five, with only limited allopatry observed within the group. Cohesive species assemblages were used to define four zoogeographic fiddler realms containing 24 provinces and transitional zones. These regions can serve as units of study when trying to explore which factors influence the distribution of coastal species.

scholarly journals Correlation and network topologies in global and local stock indices

2014 ◽  
Vol 378 (34) ◽  
pp. 2482-2489 ◽  
Author(s):  
Ashadun Nobi ◽  
Sungmin Lee ◽  
Doo Hwan Kim ◽  
Jae Woo Lee
Keyword(s):  
Stock Indices ◽  
Network Topologies ◽  
Global And Local ◽  
Local Stock

Networks, Agents and Models

2012 ◽  
Vol 4 (1) ◽  
pp. 13-23
Author(s):  
Fabian Muniesa ◽  
Ivan Tchalakov
Keyword(s):  
Network Theory ◽  
Quantitative Research ◽  
Computational Modelling ◽  
Actor Network Theory ◽  
Point Of View ◽  
Actor Network ◽  
The Social ◽  
Network Topologies ◽  
Critical Problems ◽  
Operational Models

Actor-Network Theory proves particularly inspiring in reconsidering the tenets of quantitative research and computational methods in the social sciences. However, translating insights from this perspective into operational models is problematic. The paper examines, in the form of a dialogue, critical problems of the computational modelling of network topologies considered from the point of view of Actor-Network Theory. In particular, the paper discusses the impetus of simulation and the inappropriateness of the distinction between agents and links.

Sound and Musics in the Global Village: On landscapes in sound and soundscapes in culture

2008 ◽  
Vol 13 (2) ◽  
pp. 153-160
Author(s):  
Tatjana Böhme-Mehner
Keyword(s):  
System Theory ◽  
Social Environment ◽  
Network Theory ◽  
Electroacoustic Music ◽  
The Self ◽  
The Other ◽  
Social Constructions ◽  
Central Theme ◽  
Global Village ◽  
Global And Local

AbstractFollowing Marshall McLuhan's concept of a global village as a form of universal organisation in a technically dominated world, terms of globality and locality, and the concepts of world and village as social constructions in order to organise perception in an enhanced social environment are discussed in matters of their relevance in the context of electroacoustic music and especially its studies. In relation to historical as well as to more theoretical examples from the field of electroacoustic music, problems of perceiving spaces, places and locations are introduced. The solutions proposed here are primarily based on system theory approaches (as for instance Luhmann and Bühl) and newer network theory concepts (as for example Castells and Nowotny). The network is proposed as a kind of explanatory model in today's media-dominated world. Focusing on a model oriented to difference, ‘global’ and ‘local’ are regarded as categories guiding perception in matters of equality and difference. In this way the problem of listening to the other in opposition to the self is introduced. Thus it is demonstrated that there can never be a global sound or even a sounding globality. The phenomenon of soundscapes is discussed as a central theme in relation to its role as a listening strategy, its appearance in music and its own musicality.

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