Some operations preserving primitivity of words

We investigate some operations where essentially, from a given word w, the word ww′ is constructed where w′ is a modified copy of w or a modified mirror image of w. We study whether ww′ is a primitive word provided that w is primitive. For instance, we determine all cases with an edit distance of w and w′ at most 2 such that the primitivity of w implies the primitivity of ww′. The operations are chosen in such a way that in the case of a two-letter alphabet, all primitive words of length ≤11 can be obtained from single letters

Emergent diversity in an open-ended evolving virtual community

Understanding the dynamics of biodiversity has become an important line of research in theoretical ecology and, in particular, conservation biology. However, studying the evolution of ecological communities under traditional modeling approaches based on differential calculus requires speciesʼ characteristics to be predefined, which limits the generality of the results. An alternative but less standardized methodology relies on intensive computer simulation of evolving communities made of simple, explicitly described individuals. We study here the formation, evolution, and diversity dynamics of a community of virtual plants with a novel individual-centered model involving three different scales: the genetic, the developmental, and the physiological scales. It constitutes an original attempt at combining development, evolution, and population dynamics (based on multi-agent interactions) into one comprehensive, yet simple model. In this world, we observe that our simulated plants evolve increasingly elaborate canopies, which are capable of intercepting ever greater amounts of light. Generated morphologies vary from the simplest one-branch structure of promoter plants to a complex arborization of several hundred thousand branches in highly evolved variants. On the population scale, the heterogeneous spatial structuration of the plant community at each generation depends solely on the evolution of its component plants. Using this virtual data, the morphologies and the dynamics of diversity production were analyzed by various statistical methods, based on genotypic and phenotypic distance metrics. The results demonstrate that diversity can spontaneously emerge in a community of mutually interacting individuals under the influence of specific environmental conditions.This research was partially supported by a grant for the GENEX project (P09-TIC-5123) from the Consejería de Innovación y Ciencia de Andalucía. J.D.F. was supported by a FPU grant from the Spanish Ministerio de Educación. R.D. wishes to thank the Région Ile-de-France for supporting his research position at the Complex Systems Institute, Paris Ile-de-France

Graph grammars with string-regulated rewriting

Multicellular organisms undergo a complex developmental process, orchestrated by the genetic information in their cells, in order to form a newborn individual from a fertilized egg. This complex process, not completely understood yet, is believed to have a key role in generating the impressive biotic diversity of organisms found on earth. Inspired by mechanisms of Eukaryotic genetic expression, we propose and analyse graph grammars with string-regulated rewriting. In these grammatical systems a genome sequence is represented by a regulatory string, a graph corresponds to an organism, and a set of graph grammar rules represents different forms of implementing cell division. Accordingly, a graph derivation by the graph grammar resembles the developmental process of an organism. We give examples of the concept and compare its generative power to the power of the traditional context-free graph grammars. We demonstrate that the power of expression increases when genetic regulation is included in the model, as compared to non-regulated grammars. Additionally, we propose a hierarchy of string-regulated graph grammars, arranged by expressive power. These results highlight the key role that the transmission of regulatory information during development has in the emergence of biological diversity.D.L. was supported in part by a research stay fellowship at Otto-von-Guericke-Universität Magdeburg from the Spanish Ministerio de Educación

A graph-theoretical approach in brain functional networks. Possible implications in EEG studies

Abstract\ud \ud \ud \ud Background\ud \ud Recently, it was realized that the functional connectivity networks estimated from actual brain-imaging technologies (MEG, fMRI and EEG) can be analyzed by means of the graph theory, that is a mathematical representation of a network, which is essentially reduced to nodes and connections between them.\ud \ud \ud \ud Methods\ud \ud We used high-resolution EEG technology to enhance the poor spatial information of the EEG activity on the scalp and it gives a measure of the electrical activity on the cortical surface. Afterwards, we used the Directed Transfer Function (DTF) that is a multivariate spectral measure for the estimation of the directional influences between any given pair of channels in a multivariate dataset. Finally, a graph theoretical approach was used to model the brain networks as graphs. These methods were used to analyze the structure of cortical connectivity during the attempt to move a paralyzed limb in a group (N=5) of spinal cord injured patients and during the movement execution in a group (N=5) of healthy subjects.\ud \ud \ud \ud Results\ud \ud Analysis performed on the cortical networks estimated from the group of normal and SCI patients revealed that both groups present few nodes with a high out-degree value (i.e. outgoing links). This property is valid in the networks estimated for all the frequency bands investigated. In particular, cingulate motor areas (CMAs) ROIs act as ‘‘hubs’’ for the outflow of information in both groups, SCI and healthy. Results also suggest that spinal cord injuries affect the functional architecture of the cortical network sub-serving the volition of motor acts mainly in its local feature property.\ud In particular, a higher local efficiency El can be observed in the SCI patients for three frequency bands, theta (3-6 Hz), alpha (7-12 Hz) and beta (13-29 Hz).\ud By taking into account all the possible pathways between different ROI couples, we were able to separate clearly the network properties of the SCI group from the CTRL group. In particular, we report a sort of compensatory mechanism in the SCI patients for the Theta (3-6 Hz) frequency band, indicating a higher level of “activation” Ω within the cortical network during the motor task. The activation index is directly related to diffusion, a type of dynamics that underlies several biological systems including possible spreading of neuronal activation across several cortical regions.\ud \ud \ud \ud Conclusions\ud \ud The present study aims at demonstrating the possible applications of graph theoretical approaches in the analyses of brain functional connectivity from EEG signals. In particular, the methodological aspects of the i) cortical activity from scalp EEG signals, ii) functional connectivity estimations iii) graph theoretical indexes are emphasized in the present paper to show their impact in a real application.This study was performed with support of the European Union, through the COST program NEUROMATH (BM0601). This paper only reflects the authors’ views and funding agency is not liable for any use that may be made of the information contained herein.This study was performed with support of the European Union, through the COST program NEUROMATH (BM0601). This paper only reflects the authors’ views and funding agency is not liable for any use that may be made of the information contained herein.This article has been published as part of Nonlinear Biomedical Physics Volume 4 Supplement 1, 2010: Consciousness and its Measures: Joint Workshop for COST Actions Neuromath and Consciousness. The full contents of the supplement are available online at http://www.nonlinearbiomedphys.com/supplements/4/S1.This article has been published as part of Nonlinear Biomedical Physics Volume 4 Supplement 1, 2010: Consciousness and its Measures: Joint Workshop for COST Actions Neuromath and Consciousness. The full contents of the supplement are available online at http://www.nonlinearbiomedphys.com/supplements/4/S1

Evolutionary development of tensegrity structures

Contributions from the emerging fields of molecular genetics and evo-devo (evolutionary developmental biology) are greatly benefiting the field of evolutionary computation, initiating a promise of renewal in the traditional methodology. While direct encoding has constituted a dominant paradigm, indirect ways to encode the solutions have been reported, yet little attention has been paid to the benefits of the proposed methods to real problems. In this work, we study the biological properties that emerge by means of using indirect encodings in the context of form-finding problems. A novel indirect encoding model for artificial development has been defined and applied to an engineering structural-design problem, specifically to the discovery of tensegrity structures. This model has been compared with a direct encoding scheme. While the direct encoding performs similarly well to the proposed method, indirect-based results typically outperform the direct-based results in aspects not directly linked to the nature of the problem itself, but to the emergence of properties found in biological organisms, like organicity, generalization capacity, or modularity aspects which are highly valuable in engineering

Automating the search of molecular motor templates by evolutionary methods

The first author is supported by a FPU grant (AP2007-03704) from the Ministerio de Educación of the Spanish Government, and has been supported by the BioEmergences project (code 28892) of the Sixth Framework Programme of the European Union. Our research group has been partially supported by the local government (Junta de Andalucía) through a grant for the GENEX project (P09-TIC-5123).Biological molecular motors are nanoscale devices capable of transforming chemical energy into mechanical work, which are being researched in many scientific disciplines. From a computational point of view, the characteristics and dynamics of these motors are studied at multiple time scales, ranging from very detailed and complex molecular dynamics simulations spanning a few microseconds, to extremely simple and coarse-grained theoretical models of their working cycles. However, this research is performed only in the (relatively few) instances known from molecular biology. In this work, results from elastic network analysis and behaviour-finding methods are applied to explore a subset of the configuration space of template molecular structures that are able to transform chemical energy into directed movement, for a fixed instance of working cycle. While using methods based on elastic networks limits the scope of our results, it enables the implementation of computationally lightweight methods, in a way that evolutionary search techniques can be applied to discover novel molecular motor templates. The results show that molecular motion can be attained from a variety of structural configurations, when a functional working cycle is provided. Additionally, these methods enable a new computational way to test hypotheses about molecular motors

Robust Off- and Online Separation of Intracellularly Recorded Up and Down Cortical States

BACKGROUND: The neuronal cortical network generates slow (<1 Hz) spontaneous rhythmic activity that emerges from the recurrent connectivity. This activity occurs during slow wave sleep or anesthesia and also in cortical slices, consisting of alternating up (active, depolarized) and down (silent, hyperpolarized) states. The search for the underlying mechanisms and the possibility of analyzing network dynamics in vitro has been subject of numerous studies. This exposes the need for a detailed quantitative analysis of the membrane fluctuating behavior and computerized tools to automatically characterize the occurrence of up and down states. METHODOLOGY/PRINCIPAL FINDINGS: Intracellular recordings from different areas of the cerebral cortex were obtained from both in vitro and in vivo preparations during slow oscillations. A method that separates up and down states recorded intracellularly is defined and analyzed here. The method exploits the crossover of moving averages, such that transitions between up and down membrane regimes can be anticipated based on recent and past voltage dynamics. We demonstrate experimentally the utility and performance of this method both offline and online, the online use allowing to trigger stimulation or other events in the desired period of the rhythm. This technique is compared with a histogram-based approach that separates the states by establishing one or two discriminating membrane potential levels. The robustness of the method presented here is tested on data that departs from highly regular alternating up and down states. CONCLUSIONS/SIGNIFICANCE: We define a simple method to detect cortical states that can be applied in real time for offline processing of large amounts of recorded data on conventional computers. Also, the online detection of up and down states will facilitate the study of cortical dynamics. An open-source MATLAB toolbox, and Spike 2-compatible version are made freely available

Increasing crop rotational diversity can enhance cereal yields

9 Pág.Diversifying agriculture by rotating a greater number of crop species in sequence is a promising practice to reduce negative impacts of crop production on the environment and maintain yields. However, it is unclear to what extent cereal yields change with crop rotation diversity and external nitrogen fertilization level over time, and which functional groups of crops provide the most yield benefit. Here, using grain yield data of small grain cereals and maize from 32 long-term (10–63 years) experiments across Europe and North America, we show that crop rotational diversity, measured as crop species diversity and functional richness, enhanced grain yields. This yield benefit increased over time. Only the yields of winter-sown small grain cereals showed a decline at the highest level of species diversity. Diversification was beneficial to all cereals with a low external nitrogen input, particularly maize, enabling a lower dependence on nitrogen fertilisers and ultimately reducing greenhouse gas emissions and nitrogen pollution. The results suggest that increasing crop functional richness rather than species diversity can be a strategy for supporting grain yields across many environments.G.V., R.B. and S.H. acknowledge FORMAS grants 2018-02872 and 2018-02321. TMB acknowledges USDA AFRI grant 2017-67013-26254. LTEs managed by SRUC were supported by the Scottish Government RESAS Strategic Research Programme under project D3-, Healthy Soils for a Green Recovery. Swedish LTEs were funded by the Swedish University of Agricultural Sciences (SLU). We thank the Lawes Agricultural Trust and Rothamsted Research for data from the e-RA database. The Rothamsted Long-term Experiments National Capability (LTE-NC) was supported by the UK BBSRC (Biotechnology and Biological Sciences Research Council, BBS/E/C/000J0300) and the Lawes Agricultural Trust. The Woodslee site was supported by the Agro-Ecosystem Resilience Program (Agriculture & Agri-Food Canada) and field management provided by field crews over 6 decades is appreciated. La Canaleja LTE (Spain) was supported by RTA2017-00006-C03-01 project (Ministry of Science and Innovation. El Encín LTEs were supported by Spanish Ministry of Economy and Competitiveness funds (projects AGL2002-04186-C03-01.03, AGL2007-65698-C03-01.03, AGL2012-39929-C03-01 of which L. Navarrete was the P.I). R.A., A.G.D. and E.H.P. are also grateful to all members of the Weed Science Group from El Encín Experimental Station for their technical assistance in managing the experiments. The Brody/Poznan University of Life Sciences long-term experiments were funded by the Polish Ministry of Education and Science. We acknowledge the E-Obs dataset from the EU-FP6 project UERRA (http://www.uerra.eu) and the Copernicus Climate Change Service, and the data providers in the ECA&D project (https://www.ecad.eu/).Peer reviewe

Increasing crop rotational diversity can enhance cereal yields

Diversifying agriculture by rotating a greater number of crop species in sequence is a promising practice to reduce negative impacts of crop production on the environment and maintain yields. However, it is unclear to what extent cereal yields change with crop rotation diversity and external nitrogen fertilization level over time, and which functional groups of crops provide the most yield benefit. Here, using grain yield data of small grain cereals and maize from 32 long-term (10–63 years) experiments across Europe and North America, we show that crop rotational diversity, measured as crop species diversity and functional richness, enhanced grain yields. This yield benefit increased over time. Only the yields of winter-sown small grain cereals showed a decline at the highest level of species diversity. Diversification was beneficial to all cereals with a low external nitrogen input, particularly maize, enabling a lower dependence on nitrogen fertilisers and ultimately reducing greenhouse gas emissions and nitrogen pollution. The results suggest that increasing crop functional richness rather than species diversity can be a strategy for supporting grain yields across many environments

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London