An Information-Theoretic Approach to Detect the Associations of GPS-Tracked Heifers in Pasture

Sensor technologies, such as the Global Navigation Satellite System (GNSS), produce huge amounts of data by tracking animal locations with high temporal resolution. Due to this high resolution, all animals show at least some co-occurrences, and the pure presence or absence of co-occurrences is not satisfactory for social network construction. Further, tracked animal contacts contain noise due to measurement errors or random co-occurrences. To identify significant associations, null models are commonly used, but the determination of an appropriate null model for GNSS data by maintaining the autocorrelation of tracks is challenging, and the construction is time and memory consuming. Bioinformaticians encounter phylogenetic background and random noise on sequencing data. They estimate this noise directly on the data by using the average product correction procedure, a method applied to information-theoretic measures. Using Global Positioning System (GPS) data of heifers in a pasture, we performed a proof of concept that this approach can be transferred to animal science for social network construction. The approach outputs stable results for up to 30% missing data points, and the predicted associations were in line with those of the null models. The effect of different distance thresholds for contact definition was marginal, but animal activity strongly affected the network structure.

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An information-theoretic approach for measuring the distance of organ tissue samples using their transcriptomic signatures

10.1101/2020.01.23.917245 ◽

2020 ◽

Author(s):

Dimitris V. Manatakis ◽

Aaron VanDevender ◽

Elias S. Manolakos

Keyword(s):

Ex Vivo ◽

Practical Importance ◽

Supplementary Information ◽

Next Generation Sequencing Data ◽

Theoretic Approach ◽

Sequencing Data ◽

Tissue Samples ◽

Human Organ ◽

Information Theoretic ◽

Organ Models

AbstractMotivationRecapitulating aspects of human organ functions using in-vitro (e.g., plates, transwells, etc.), in-vivo (e.g., mouse, rat, etc.), or ex-vivo (e.g., organ chips, 3D systems, etc.) organ models are of paramount importance for precision medicine and drug discovery. It will allow us to identify potential side effects and test the effectiveness of therapeutic approaches early in their design phase and will inform the development of accurate disease models. Developing mathematical methods to reliably compare the “distance/similarity” of organ models from/to the real human organ they represent is an understudied problem with important applications in biomedicine and tissue engineering.ResultsWe introduce the Transctiptomic Signature Distance, TSD, an information-theoretic distance for assessing the transcriptomic similarity of two tissue samples, or two groups of tissue samples. In developing TSD, we are leveraging next-generation sequencing data and information retrieved from well-curated databases providing signature gene sets characteristic for human organs. We present the justification and mathematical development of the new distance and demonstrate its effectiveness in different scenarios of practical importance using several publicly available RNA-seq [email protected] informationSupplementary data are available at bioRxiv.

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An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data

BMC Bioinformatics ◽

10.1186/s12859-018-2086-5 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 9

Author(s):

Garrett Jenkinson ◽

Jordi Abante ◽

Andrew P. Feinberg ◽

John Goutsias

Keyword(s):

Bisulfite Sequencing ◽

Whole Genome ◽

Theoretic Approach ◽

Sequencing Data ◽

Modeling And Analysis ◽

Information Theoretic ◽

Whole Genome Bisulfite Sequencing ◽

Genome Bisulfite Sequencing ◽

Bisulfite Sequencing Data ◽

Information Theoretic Approach

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Why do some primate mothers carry their infant’s corpse? A cross-species comparative study

10.1101/2021.01.12.426348 ◽

2021 ◽

Author(s):

Elisa Fernández-Fueyo ◽

Yukimaru Sugiyama ◽

Takeshi Matsui ◽

Alecia J. Carter

Keyword(s):

Comparative Study ◽

Null Model ◽

Primate Species ◽

Species Variation ◽

Theoretic Approach ◽

Information Theoretic ◽

Quantitative Analyses ◽

Information Theoretic Approach ◽

Better Than

AbstractNon-human primates respond to the death of a conspecific in diverse ways, some which may present phylogenetic continuity with human thanatological behaviours. Of these responses, infant corpse carrying by mothers (ICC) is the most-frequently reported. Despite its prevalence, quantitative analyses of this behaviour are scarce and inconclusive. We compiled a database of 409 published cases across 50 different primate species of mothers’ responses to their infants’ deaths to test hypotheses proposed to explain between- and within-species variation in corpse carrying. Using Bayesian phylogenetic regressions, we preliminarily identified three factors as possible predictors of ICC occurrence. However, using an information-theoretic approach, no combination of these predictors performed better than the null model, offering no support for any of the hypotheses we tested. In contrast, for those cases in which infant corpses were carried, infant age affected ICC duration, with longer ICC observed for younger infants. This result may provide support for hypotheses that suggest that ICC is a by-product of a strong mother-infant bond. The results are discussed in the context of the evolution of emotion and their implications for evolutionary thanatology are considered.

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