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Detecting the small island effect and nestedness of herpetofauna of the West Indies

De Gao, Gad Perry
2016 Ecology and Evolution  
To detect the small island effect (SIE) and nestedness patterns of herpetofauna of the West Indies, we derived and updated data on the presence/absence of herpetofauna in this region from recently published  ...  Antinestedness occurred in the entire system, whereas high degree of nestedness could still occur in portions within the region.  ...  Piecewise regressions with three segments were always better than those with two segments, suggesting the existence of two break points (T 1 and T 2 ) in the data sets.  ... 
doi:10.1002/ece3.2289 pmid:27551391 pmcid:PMC4984512 fatcat:kdwmjfrnxbaxrmh2vtyagc6k2m

Finding banded patternsin large data set using segmentation

F.B. Abdullahi, F. Coenen
2021 Bayero Journal of Pure and Applied Sciences  
Mannila and Terzi proposed nestedness and segmented nestedness of binary matrix; they defined the concept of k-nestedness, as a matrix is (almost) k-nestedness if the sets of columns can be partition into  ...  data segments to find banded patterns in N-D data.  ...  The paper address situations where we seek to establish sequentially bandings in large datasets using sequences of data segments.  ... 
doi:10.4314/bajopas.v13i1.13 fatcat:l7za727hrnaupoqp4fcqc5xbnq


Werner Ulrich, Nicholas J. Gotelli
2007 Ecology  
However, the detection of nestedness in binary presence-absence matrices will be affected by both the metric used to quantify nestedness and the reference null distribution.  ...  Nestedness is a common biogeographic pattern in which small communities form proper subsets of large communities.  ...  In an ordered binary presence-absence matrix, nestedness leads to a maximally ''packed'' pattern of ones and zeroes.  ... 
doi:10.1890/06-1208.1 pmid:17645028 fatcat:66iq7yctvjamlpkbkdgxlspexa

Learning to Detect Cells Using Non-overlapping Extremal Regions [chapter]

Carlos Arteta, Victor Lempitsky, J. Alison Noble, Andrew Zisserman
2012 Lecture Notes in Computer Science  
Cell detection in microscopy images is an important step in the automation of cell based-experiments. We propose a machine learning-based cell detection method applicable to different modalities.  ...  In the reported experiments, state-of-the-art cell detection accuracy is achieved for H&Estained histology, fluorescence, and phase-contrast images.  ...  Flaccavento for providing cell data sets. Financial support was provided by the RCUK Centre for Doctoral Training in Healthcare Innovation (EP/G036861/1) and ERC grant VisRec no. 228180.  ... 
doi:10.1007/978-3-642-33415-3_43 fatcat:s6m36yb2njc5zb54jc5ztggzoe

Assembly of complex plant–fungus networks

Hirokazu Toju, Paulo R. Guimarães, Jens M. Olesen, John N. Thompson
2014 Nature Communications  
Species in ecological communities build complex webs of interaction.  ...  Although revealing the architecture of these networks is fundamental to understanding ecological and evolutionary dynamics in nature, it has been difficult to characterize the structure of most species-rich  ...  The NODF index was originally proposed to evaluate the nestedness of 'binary' network matrices, in which the absence/presence of interactions between pairs of species are represented in a binary (0/1)  ... 
doi:10.1038/ncomms6273 pmid:25327887 pmcid:PMC4218951 fatcat:6xunm4endjhk7g5yl5cocgsyii

β-diversity of deep-sea holothurians and asteroids along a bathymetric gradient (NE Atlantic)

MC Wagstaff, KL Howell, BJ Bett, DSM Billett, S Brault, CT Stuart, MA Rex
2014 Marine Ecology Progress Series  
Here, we present the first evidence for turnover and nestedness along a bathymetric gradient in 2 major megafaunal taxa, holothurians and asteroids.  ...  This pattern differs fundamentally from those in some macrofaunal groups in low-energy environments where abyssal nestedness is high and diversity low, with diversity maintained partly by source-sink dynamics  ...  We thank Werner Ulrich, Andrés Baselga and Miguel Rodríguez-Gironés for use of their computer programs to calculate nestedness, and for much useful advice.  ... 
doi:10.3354/meps10877 fatcat:e65lwgd3oncerl4cg3k7ctc55y

Quantifying Loopy Network Architectures

Eleni Katifori, Marcelo O. Magnasco, Jérémie Bourdon
2012 PLoS ONE  
We present an algorithmic framework, the hierarchical loop decomposition, that allows mapping loopy networks to binary trees, preserving in the connectivity of the trees the architecture of the original  ...  Blinder and the Kleinfeld group at University of California San Diego, for making available the rat neocortex vasculature data to us.  ...  perform data cleaning post the digitization stage.  ... 
doi:10.1371/journal.pone.0037994 pmid:22701593 pmcid:PMC3368948 fatcat:tlqnosqooneklkifs2ylozj54i

A-expansion for multiple "hedgehog" shapes [article]

Hossam Isack, Yuri Boykov, Olga Veksler
2016 arXiv   pre-print
For example, in medical data we can separate multiple non-star organs with similar appearances and weak or noisy edges.  ...  Our general method has significantly more applications than standard one-star segmentation.  ...  In this case, we interpolate the vector field's orientation for every neighboring pixels and eliminate their edge constraint(s) if it were not consistent with the interpolated orientation, as shown in  ... 
arXiv:1602.01006v1 fatcat:aqsgrteznzauxlqecdmqf4llga

The Nested Structure of Emergent Supply Networks

Alexandra Brintrup, Jose Barros, Ashutosh Tiwari
2018 IEEE Systems Journal  
Inspired by studies in ecological networks, we look for a nested pattern in a large-scale data set describing the global automotive industry, including more than 18 000 firms, their clients, and products  ...  In addition, the manufacturers that procure from few suppliers procure from those that supply to most other manufacturers in the network.  ...  We investigate nestedness in supply networks by collecting large-scale data from the automotive industry.  ... 
doi:10.1109/jsyst.2015.2493345 fatcat:3aogtpgqovdk5j7px4svkn3cau

A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C

Ji Hyun Bak, Min Hyeok Kim, Lei Liu, Changbong Hyeon, Alexandre V. Morozov
2021 PLoS Computational Biology  
Despite the strong cell-to-cell heterogeneity, the cell-type specific pattern demonstrated in high-throughput chromosome conformation capture (Hi-C) data hints at a valuable link between structure and  ...  Here we present a unified method for analyzing Hi-C data to determine spatial organization of CDs over multiple genomic scales.  ...  We thank the Center for Advanced Computation in KIAS for providing computing resources.  ... 
doi:10.1371/journal.pcbi.1008834 pmid:33724986 fatcat:dfim4cziajedlb4v2mne6grnlu

Topological Phenotypes Constitute a New Dimension in the Phenotypic Space of Leaf Venation Networks

Henrik Ronellenfitsch, Jana Lasser, Douglas C. Daly, Eleni Katifori, Enrico Scarpella
2015 PLoS Computational Biology  
This phenotypic trait encodes information orthogonal to widely used geometric phenotypic traits, and thus constitutes a new dimension in the leaf venation phenotypic space.  ...  quantitative identification techniques for leaves which go beyond simple geometric traits such as vein density and is directly applicable to other planar or sub-planar networks such as blood vessels in  ...  much of the observed data.  ... 
doi:10.1371/journal.pcbi.1004680 pmid:26700471 pmcid:PMC4699199 fatcat:nnc3udcnxjdftibpot4quzyfle

Contrasting altitudinal variation of alpine plant communities along the Swedish mountains

Johannes Måsviken, Fredrik Dalerum, Sara A. O. Cousins
2020 Ecology and Evolution  
In this study, we investigate alpha, beta, and gamma diversity, as well as community structure, of vascular plant communities along altitudinal gradients at three latitudes in the Swedish mountains.  ...  Changes in abiotic factors along altitudinal and latitudinal gradients cause powerful environmental gradients.  ...  We calculated nestedness and modularity using binary matri- (Fortunato & Hric, 2016) .  ... 
doi:10.1002/ece3.6237 pmid:32551065 pmcid:PMC7297753 fatcat:e4qipqhynzaxneycnopjzegczm

Nestedness in complex networks: Observation, emergence, and implications [article]

Manuel Sebastian Mariani, Zhuo-Ming Ren, Jordi Bascompte, Claudio Juan Tessone
2019 arXiv   pre-print
This review article focuses on three main pillars: the existing methodologies to observe nestedness in networks; the main theoretical mechanisms conceived to explain the emergence of nestedness in ecological  ...  Known since more than 80 years in biogeography, nestedness has been found in systems as diverse as ecological mutualistic organizations, world trade, inter-organizational relations, among many others.  ...  Acknowledgements We wish to thank Javier Borge-Holthoefer, Matúš Medo, Albert Solé-Ribalta for the many inspiring discussions on nestedness and the detection of structural patterns in networks.  ... 
arXiv:1905.07593v1 fatcat:tfz6qucb45eoddfex5dh5oieou

Diatom Cooccurrence Shows Less Segregation than Predicted from Niche Modeling

Marius Bottin, Janne Soininen, Didier Alard, Juliette Rosebery, Paulo De Marco Júnior
2016 PLoS ONE  
In order to test the relative influence of environmental, biotic and spatial constraints on species' incidence distribution, cooccurrence and nestedness patterns of real communities were compared with  ...  Aggregations of species cooccurrences were associated with the high levels of nestedness.  ...  We would like to acknowledge Michel Coste, Luc Ector and the French "Agences de l'Eau" for providing data, and Peter Winterton for English editing.  ... 
doi:10.1371/journal.pone.0154581 pmid:27128737 pmcid:PMC4851409 fatcat:vzjzoicikngu3ju4uwtuecxuz4

Sampling completeness in seed dispersal networks: When enough is enough

José M. Costa, Luís P. da Silva, Jaime A. Ramos, Ruben H. Heleno
2016 Basic and Applied Ecology  
Nestedness was the only exception, as it never departed from the null models.  ...  We retrieved seeds from the droppings of 936 mist-netted birds captured during five days in seven sites in Portugal and estimated sampling completeness as the diversity of seed species, disperser species  ...  input data (binary/weighted).  ... 
doi:10.1016/j.baae.2015.09.008 fatcat:4iawkwnoe5gutmdmojrczogquq
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