Search results for "network science"

Gauging scale effects and biogeographical signals in similarity distance decay analyses: an Early Jurassic ammonite case study.

2016

17 pages; International audience; In biogeography, the similarity distance decay (SDD) relationship refers to the decrease in compositional similarity between communities with geographical distance. Although representing one of the most widely used relationships in biogeography, a review of the literature reveals that: (1) SDD is influenced by both spatial extent and sample size; (2) the potential effect of the phylogenetic level has yet to be tested; (3) the effect of a marked biogeographical structuring upon SDD patterns is largely unknown; and (4) the SDD relationship is usually explored with modern, mainly terrestrial organisms, whereas fossil taxa are seldom used in that perspective. U…

Distance decay 2.0 – a global synthesis of taxonomic and functional turnover in ecological communities

2021

AbstractUnderstanding the variation in community composition and species abundances, i.e., β-diversity, is at the heart of community ecology. A common approach to examine β-diversity is to evaluate directional turnover in community composition by measuring the decay in the similarity among pairs of communities along spatial or environmental distances. We provide the first global synthesis of taxonomic and functional distance decay along spatial and environmental distance by analysing 149 datasets comprising different types of organisms and environments. We modelled an exponential distance decay for each dataset using generalized linear models and extracted r2 and slope to analyse the streng…

Robust link prediction in criminal networks: A case study of the Sicilian Mafia

2020

Abstract Link prediction exercises may prove particularly challenging with noisy and incomplete networks, such as criminal networks. Also, the link prediction effectiveness may vary across different relations within a social group. We address these issues by assessing the performance of different link prediction algorithms on a mafia organization. The analysis relies on an original dataset manually extracted from the judicial documents of operation “Montagna”, conducted by the Italian law enforcement agencies against individuals affiliated with the Sicilian Mafia. To run our analysis, we extracted two networks: one including meetings and one recording telephone calls among suspects, respect…

Graph Theoretical Framework of Brain Networks in Multiple Sclerosis: A Review of Concepts.

2019

Abstract Network science provides powerful access to essential organizational principles of the human brain. It has been applied in combination with graph theory to characterize brain connectivity patterns. In multiple sclerosis (MS), analysis of the brain networks derived from either structural or functional imaging provides new insights into pathological processes within the gray and white matter. Beyond focal lesions and diffuse tissue damage, network connectivity patterns could be important for closely tracking and predicting the disease course. In this review, we describe concepts of graph theory, highlight novel issues of tissue reorganization in acute and chronic neuroinflammation an…

Alignment Free Dissimilarities for Nucleosome Classification

2016

Epigenetic mechanisms such as nucleosome positioning, histone modifications and DNA methylation play an important role in the regulation of cell type-specific gene activities, yet how epigenetic patterns are established and maintained remains poorly understood. Recent studies have shown a role of DNA sequences in recruitment of epigenetic regulators. For this reason, the use of more suitable similarities or dissimilarity between DNA sequences could help in the context of epigenetic studies. In particular, alignment-free dissimilarities have already been successfully applied to identify distinct sequence features that are associated with epigenetic patterns and to predict epigenomic profiles…

Modeling Chronic Toxicity: A Comparison of Experimental Variability With (Q)SAR/Read-Across Predictions

2018

This study compares the accuracy of (Q)SAR/read-across predictions with the experimental variability of chronic lowest-observed-adverse-effect levels (LOAELs) from in vivo experiments. We could demonstrate that predictions of the lazy structure-activity relationships (lazar) algorithm within the applicability domain of the training data have the same variability as the experimental training data. Predictions with a lower similarity threshold (i.e., a larger distance from the applicability domain) are also significantly better than random guessing, but the errors to be expected are higher and a manual inspection of prediction results is highly recommended.

2019

Background: Network science provides powerful access to essential organizational principles of the brain. The aim of this study was to investigate longitudinal evolution of gray matter networks in early relapsing–remitting MS (RRMS) compared with healthy controls (HCs) and contrast network dynamics with conventional atrophy measurements. Methods: For our longitudinal study, we investigated structural cortical networks over 1 year derived from 3T MRI in 203 individuals (92 early RRMS patients with mean disease duration of 12.1 ± 14.5 months and 101 HCs). Brain networks were computed based on cortical thickness inter-regional correlations and fed into graph theoretical analysis. Network conne…

FastaHerder2: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases.

2016

The accelerated growth of protein databases offers great possibilities for the study of protein function using sequence similarity and conservation. However, the huge number of sequences deposited in these databases requires new ways of analyzing and organizing the data. It is necessary to group the many very similar sequences, creating clusters with automated derived annotations useful to understand their function, evolution, and level of experimental evidence. We developed an algorithm called FastaHerder2, which can cluster any protein database, putting together very similar protein sequences based on near-full-length similarity and/or high threshold of sequence identity. We compressed 50…

A comparison between nine laboratories performing triangle tests

2012

WOS: 000299451400001; International audience; Fifteen groups of participants in nine laboratories performed triangle tests with two pairs of soft drinks. Groups differed in practice level with triangle tests: eight groups of 60 consumers who were not used to triangle test, three groups of qualified assessors who have already performed a few triangle tests, and four groups of trained assessors with a more extensive practice of triangle tests; qualified and trained groups included 9 or 18 assessors. The soft drinks were made from syrups at two levels of dilution in order to achieve about 55% of correct responses to test for difference and about 40% of correct responses to test for similarity.…

Perceived similarity between written Estonian and Finnish : Strings of letters or morphological units?

2017

The distance or similarity between two languages can be objective or actual, i.e. discoverable by the tools and methods of linguists, or perceived by users of the languages. In this article two methods, the Levenshtein Distance (LD), which purports to measure the objective distance, and the Index of Perceived Similarity (IPS), which quantifies language users’ perceptions, are compared. The data are the quantitative results of a test measuring conscious perceptions of similarity between Estonian and Finnish inflectional morphology by Finnish and Estonian native speakers (‘Finns’ and ‘Estonians’) with no knowledge of and exposure to the other (‘target’) language. The results show that Finns s…