Design and validation of a virtual player for studying interpersonal coordination in the mirror game

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.The mirror game has been recently proposed as a simple, yet powerful paradigm for studying interpersonal interactions. It has been suggested that a virtual partner able to play the game with human subjects can be an effective tool to affect the underlying neural processes needed to establish the necessary connections between the players, and also to provide new clinical interventions for rehabilitation of patients suffering from social disorders. Inspired by the motor processes of the central nervous system (CNS) and the musculoskeletal system in the human body, in this paper we develop a novel interactive cognitive architecture based on nonlinear control theory to drive a virtual player (VP) to play the mirror game with a human player (HP) in different configurations. Specifically, we consider two cases: the former where the VP acts as leader and the latter where it acts as follower. The crucial problem is to design a feedback control architecture capable of imitating and following or leading a human player in a joint action task. Movement of the end-effector of the VP is modeled by means of a feedback controlled Haken-Kelso-Bunz (HKB) oscillator, which is coupled with the observed motion of the HP measured in real time. To this aim, two types of control algorithms (adaptive control and optimal control) are used and implemented on the HKB model so that the VP can generate a human-like motion while satisfying certain kinematic constraints. A proof of convergence of the control algorithms is presented in the paper together with an extensive numerical and experimental validation of their effectiveness. A comparison with other existing designs is also discussed, showing the flexibility and the advantages of our control-based approach.This work was funded by the European Project AlterEgo FP7 ICT 2.9 - Cognitive Sciences and Robotics, Grant Number 600610

GeTallele: A Method for Analysis of DNA and RNA Allele Frequency Distributions

This is the final version. Available on open access from Frontiers Media via the DOI in this recordData Availability Statement: The data analyzed in this study is subject to the following licenses/restrictions: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. Requests to access these datasets should be directed to [email protected] allele frequencies (VAF) are an important measure of genetic variation that can be estimated at single-nucleotide variant (SNV) sites. RNA and DNA VAFs are used as indicators of a wide-range of biological traits, including tumor purity and ploidy changes, allele-specific expression and gene-dosage transcriptional response. Here we present a novel methodology to assess gene and chromosomal allele asymmetries and to aid in identifying genomic alterations in RNA and DNA datasets. Our approach is based on analysis of the VAF distributions in chromosomal segments (continuous multi-SNV genomic regions). In each segment we estimate variant probability, a parameter of a random process that can generate synthetic VAF samples that closely resemble the observed data. We show that variant probability is a biologically interpretable quantitative descriptor of the VAF distribution in chromosomal segments which is consistent with other approaches. To this end, we apply the proposed methodology on data from 72 samples obtained from patients with breast invasive carcinoma (BRCA) from The Cancer Genome Atlas (TCGA). We compare DNA and RNA VAF distributions from matched RNA and whole exome sequencing (WES) datasets and find that both genomic signals give very similar segmentation and estimated variant probability profiles. We also find a correlation between variant probability with copy number alterations (CNA). Finally, to demonstrate a practical application of variant probabilities, we use them to estimate tumor purity. Tumor purity estimates based on variant probabilities demonstrate good concordance with other approaches (Pearson's correlation between 0.44 and 0.76). Our evaluation suggests that variant probabilities can serve as a dependable descriptor of VAF distribution, further enabling the statistical comparison of matched DNA and RNA datasets. Finally, they provide conceptual and mechanistic insights into relations between structure of VAF distributions and genetic events. The methodology is implemented in a Matlab toolbox that provides a suite of functions for analysis, statistical assessment and visualization of Genome and Transcriptome allele frequencies distributions. GeTallele is available at: https://github.com/SlowinskiPiotr/GeTalleleMcCormick Genomic and Proteomic Center (MGPC)George Washington UniversityWellcome TrustEngineering and Physical Sciences Research Council (EPSRC

Always on the tipping point : A search for signals of past societies and related peatland ecosystem critical transitions during the last 6500 years in Poland

The research was funded by a grant from the National Science Centre (Poland) (No 2015/17/B/ST10/01656). The work was also made in the framework of the National Programme of Development of Humanities project (No 2bH15015483) as well as budgetary sources for scientific activity in 2016–2019, project number 0342/IP1/2016/74. V.E.J.J. was supported by the French National Research Agency (MIXOPEAT project, grant number ANR-17-CE01–0007). We thank Julie Loisel help with the calculation of the peat carbon accumulation rates. We thank also Jerzy Sikora and Paweł Zawilski for defining the chronology of the potsherd found during field surveys in the Głęboczek vicinity, and Sambor Czerwiński for constructing the lidar terrain map of the study area.Peer reviewedPublisher PD

ReQTL: Identifying correlations between expressed SNVs and gene expression using RNA-sequencing data

This is the author accepted manuscript. The final version is available on open access from OUP via the DOI in this recordBy testing for associations between DNA genotypes and gene expression levels, expression quantitative trait locus (eQTL) analyses have been instrumental in understanding how thousands of single nucleotide variants (SNVs) may affect gene expression. As compared to DNA genotypes, RNA genetic variation represents a phenotypic trait that reflects the actual allele content of the studied system. RNA genetic variation at expressed SNV loci can be estimated using the proportion of alleles bearing the variant nucleotide (variant allele fraction, VAFRNA). VAFRNA is a continuous measure which allows for precise allele quantitation in loci where the RNA alleles do not scale with the genotype count. We describe a method to correlate VAFRNA to gene expression, and assess its ability to identify genetically regulated expression solely from RNA-sequencing (RNA-seq) datasets.We introduce ReQTL, an eQTL modification which substitutes the DNA allele count for the variant allele fraction at expressed SNV loci in the transcriptome (VAFRNA). We exemplify the method on sets of RNA-seq data from human tissues obtained though the Genotype-Tissue Expression Project (GTEx) and demonstrate that ReQTL analyses are computationally feasible and can identify a subset of expressed eQTL loci.A toolkit to perform ReQTL analyses is available at https://github.com/HorvathLab/ReQTL.Re_QTL_Supplementary_Data.zipMcCormick Genomic and Proteomic Center (MGPC), The George Washington UniversityNIH National Center for Advancing Translational Scienc

Combining short-term manipulative experiments with long-term palaeoecological investigations at high resolution to assess the response of Sphagnum peatlands to drought, fire and warming

International audienceNorthern hemisphere peatlands are substantial carbon stores. However, recent climate change and human impacts (e.g., drainage and atmospheric nutrient deposition) may trigger the emission of their stored carbon to the atmosphere. Biodiversity losses are also an important consequence of those changes. Therefore, there is a need to recognise these processes in space and time. Global change experiments are often conducted to improve our understanding of the potential responses of various ecosystems to global warming and drought. Most of the experiments carried out in peatlands are focused on carbon balance and nitrogen deposition. Nevertheless, it is still unclear how fast peatlands respond to temperature changes and water-table lowering in the continental climate setting. This is important because continental regions account for a significant proportion of all northern hemisphere peatlands. A combination of short-term and long-term approaches in a single research project is especially helpful because it facilitates the correct interpretation of experimental data. Here we describe the CLIMPEAT project-a manipulative field experiment in a Sphagnum-dominated peatland supported by a high-resolution multi-proxy palaeoecological study. The design of the field experiment (e.g., treatments), methodology and biogeographical setting are presented. We suggest it is beneficial to support field experiments with an investigation of past environmental changes in the studied ecosystem, as human impacts during the past 300 years have already caused substantial changes in ecosystem functioning which may condition the response in experimental studies

Decoding identity from motion: how motor similarities colour our perception of self and others

This is the final version. Available on open access from Springer Verlag via the DOI in this record.For more than 4 decades, it has been shown that humans are particularly sensitive to biological motion and extract socially relevant information from it such as gender, intentions, emotions or a person’s identity. A growing number of findings, however, indicate that identity perception is not always highly accurate, especially due to large inter-individual differences and a fuzzy self-recognition advantage compared to the recognition of others. Here, we investigated the self-other identification performance and sought to relate this performance to the metric properties of perceptual/physical representations of individual motor signatures. We show that identity perception ability varies substantially across individuals and is associated to the perceptual/physical motor similarities between self and other stimuli. Specifically, we found that the perceptual representations of postural signatures are veridical in the sense that closely reflects the physical postural trajectories and those similarities between people’ actions elicit numerous misattributions. While, on average, people can well recognize their self-generated actions, they more frequently attribute to themselves the actions of those acting in a similar way. These findings are consistent with the common coding theory and support that perception and action are tightly linked and may modulate each other by virtue of similarity.European CommissionWellcome TrustEPSR

scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets

This is the final version. Available from BMC via the DOI in this record. All data generated or analyzed during this study are included in this published article and its supplementary information files.Background: Recently, pioneering expression quantitative trait loci (eQTL) studies on single cell RNA sequencing (scRNA-seq) data have revealed new and cell-specific regulatory single nucleotide variants (SNVs). Here, we present an alternative QTL-related approach applicable to transcribed SNV loci from scRNA-seq data: scReQTL. ScReQTL uses Variant Allele Fraction (VAFRNA) at expressed biallelic loci, and corelates it to gene expression from the corresponding cell. Results: Our approach employs the advantage that, when estimated from multiple cells, VAFRNA can be used to assess effects of SNVs in a single sample or individual. In this setting scReQTL operates in the context of identical genotypes, where it is likely to capture RNA-mediated genetic interactions with cell-specific and transient effects. Applying scReQTL on scRNA-seq data generated on the 10 × Genomics Chromium platform using 26,640 mesenchymal cells derived from adipose tissue obtained from three healthy female donors, we identified 1272 unique scReQTLs. ScReQTLs common between individuals or cell types were consistent in terms of the directionality of the relationship and the effect size. Comparative assessment with eQTLs from bulk sequencing data showed that scReQTL analysis identifies a distinct set of SNV-gene correlations, that are substantially enriched in known gene-gene interactions and significant genome-wide association studies (GWAS) loci. Conclusion: ScReQTL is relevant to the rapidly growing source of scRNA-seq data and can be applied to outline SNVs potentially contributing to cell type-specific and/or dynamic genetic interactions from an individual scRNA-seq dataset. Availability: https://github.com/HorvathLab/NGS/tree/master/scReQTLMcCormick Genomic and Proteomic Center (MGPC), The George Washington Universit

Anthropogenic- and natural sources of dust in peatland during the Anthropocene

As human impact have been increasing strongly over the last decades, it is crucial to distinguish human-induced dust sources from natural ones in order to define the boundary of a newly proposed epoch - the Anthropocene. Here, we track anthropogenic signatures and natural geochemical anomalies in the Mukhrino peatland, Western Siberia. Human activity was recorded there from cal AD 1958 (±6). Anthropogenic spheroidal aluminosilicates clearly identify the beginning of industrial development and are proposed as a new indicator of the Anthropocene. In cal AD 1963 (±5), greatly elevated dust deposition and an increase in REE serve to show that the geochemistry of elements in the peat can be evidence of nuclear weapon testing; such constituted an enormous force blowing soil dust into the atmosphere. Among the natural dust sources, minor signals of dryness and of the Tunguska cosmic body (TCB) impact were noted. The TCB impact was indirectly confirmed by an unusual occurrence of mullite in the pea

ECOLOGICAL CHARACTERISTICS OF GREAT SERTEYA PALEOLAKE BASED ON PALEOECOLOGICAL RESEARCH AT THE SERTEYA II SITE IN WESTERN RUSSIA

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Beyond in-phase and anti-phase coordination in a model of joint action

In 1985, Haken, Kelso and Bunz proposed a system of coupled nonlinear oscillators as a model of rhythmic movement patterns in human bimanual coordination. Since then, the Haken–Kelso–Bunz (HKB) model has become a modelling paradigm applied extensively in all areas of movement science, including interpersonal motor coordination. However, all previous studies have followed a line of analysis based on slowly varying amplitudes and rotating wave approximations. These approximations lead to a reduced system, consisting of a single differential equation representing the evolution of the relative phase of the two coupled oscillators: the HKB model of the relative phase. Here we take a different approach and systematically investigate the behaviour of the HKB model in the full four-dimensional state space and for general coupling strengths. We perform detailed numerical bifurcation analyses and reveal that the HKB model supports previously unreported dynamical regimes as well as bistability between a variety of coordination patterns. Furthermore, we identify the stability boundaries of distinct coordination regimes in the model and discuss the applicability of our findings to interpersonal coordination and other joint action tasks