Gene regulated car driving: using a gene regulatory network to drive a virtual car

This paper presents a virtual racing car controller based on an artificial gene regulatory network. Usually used to control virtual cells in developmental models, recent works showed that gene regulatory networks are also capable to control various kinds of agents such as foraging agents, pole cart, swarm robots, etc. This paper details how a gene regulatory network is evolved to drive on any track through a three-stages incremental evolution. To do so, the inputs and outputs of the network are directly mapped to the car sensors and actuators. To make this controller a competitive racer, we have distorted its inputs online to make it drive faster and to avoid opponents. Another interesting property emerges from this approach: the regulatory network is naturally resistant to noise. To evaluate this approach, we participated in the 2013 simulated racing car competition against eight other evolutionary and scripted approaches. After its first participation, this approach finished in third place in the competition

HLA DNA Sequence Variation among Human Populations: Molecular Signatures of Demographic and Selective Events

Molecular differences between HLA alleles vary up to 57 nucleotides within the peptide binding coding region of human Major Histocompatibility Complex (MHC) genes, but it is still unclear whether this variation results from a stochastic process or from selective constraints related to functional differences among HLA molecules. Although HLA alleles are generally treated as equidistant molecular units in population genetic studies, DNA sequence diversity among populations is also crucial to interpret the observed HLA polymorphism. In this study, we used a large dataset of 2,062 DNA sequences defined for the different HLA alleles to analyze nucleotide diversity of seven HLA genes in 23,500 individuals of about 200 populations spread worldwide. We first analyzed the HLA molecular structure and diversity of these populations in relation to geographic variation and we further investigated possible departures from selective neutrality through Tajima's tests and mismatch distributions. All results were compared to those obtained by classical approaches applied to HLA allele frequencies

Identification of proteins involved in the functioning of Riftia pachyptila symbiosis by Subtractive Suppression Hybridization

<p>Abstract</p> <p>Background</p> <p>Since its discovery around deep sea hydrothermal vents of the Galapagos Rift about 30 years ago, the chemoautotrophic symbiosis between the vestimentiferan tubeworm <it>Riftia pachyptila </it>and its symbiotic sulfide-oxidizing γ-proteobacteria has been extensively studied. However, studies on the tubeworm host were essentially targeted, biochemical approaches. We decided to use a global molecular approach to identify new proteins involved in metabolite exchanges and assimilation by the host. We used a Subtractive Suppression Hybridization approach (SSH) in an unusual way, by comparing pairs of tissues from a single individual. We chose to identify the sequences preferentially expressed in the branchial plume tissue (the only organ in contact with the sea water) and in the trophosome (the organ housing the symbiotic bacteria) using the body wall as a reference tissue because it is supposedly not involved in metabolite exchanges in this species.</p> <p>Results</p> <p>We produced four cDNA libraries: i) body wall-subtracted branchial plume library (BR-BW), ii) and its reverse library, branchial plume-subtracted body wall library (BW-BR), iii) body wall-subtracted trophosome library (TR-BW), iv) and its reverse library, trophosome-subtracted body wall library (BW-TR). For each library, we sequenced about 200 clones resulting in 45 different sequences on average in each library (58 and 59 cDNAs for BR-BW and TR-BW libraries respectively). Overall, half of the contigs matched records found in the databases with good E-values. After quantitative PCR analysis, it resulted that 16S, Major Vault Protein, carbonic anhydrase (RpCAbr), cathepsin and chitinase precursor transcripts were highly represented in the branchial plume tissue compared to the trophosome and the body wall tissues, whereas carbonic anhydrase (RpCAtr), myohemerythrin, a putative T-Cell receptor and one non identified transcript were highly specific of the trophosome tissue.</p> <p>Conclusion</p> <p>Quantitative PCR analyses were congruent with our libraries results thereby confirming the existence of tissue-specific transcripts identified by SSH. We focused our study on the transcripts we identified as the most interesting ones based on the BLAST results. Some of the keys to understanding metabolite exchanges may remain in the sequences we could not identify (hypothetical proteins and no similarity found). These sequences will have to be better studied by a longer -or complete- sequencing to check their identity, and then by verifying the expression level of the transcripts in different parts of the worm.</p

Constraining Non-Standard Interactions with Coherent Elastic Neutrino-Nucleus Scattering at the European Spallation Source

The European Spallation Source (ESS), currently under construction in Sweden, will provide an intense pulsed neutrino flux allowing for high-statistics measurements of coherent elastic neutrino-nucleus scattering (CE{\nu}NS) with advanced nuclear recoil detectors. In this paper, we investigate in detail the possibility of constraining non-standard neutrino interactions (NSIs) through such precision CE{\nu}NS measurements at the ESS, considering the different proposed detection technologies, either alone or in combination. We first study the sensitivity to neutral-current NSI parameters that each detector can reach in 3 years of data taking. We then show that operating two detectors simultaneously can significantly improve the expected sensitivity on flavor-diagonal NSI parameters. Combining the results of two detectors turns out to be even more useful when two NSI parameters are assumed to be nonvanishing at a time. In this case, suitably chosen detector combinations can reduce the degeneracies between some pairs of NSI parameters to a small region of the parameter space.Comment: 25 pages, 9 figure

Liver antioxidant and plasmatic immune responses in juvenile golden grey mullet (Liza aurata) exposed to dispersed crude oil

International audienceDispersant application is an oil spill response technique. To evaluate the environmental cost of this operation in nearshore habitats, the experimental approach conducted in this study exposed juvenile golden grey mullets (Liza aurata) for 48 hours to chemically dispersed oil (simulating, in vivo, dispersant application), to dispersant alone in sea water (as an internal control of chemically dispersed oil), to mechanically dispersed oil (simulating, in vivo, natural dispersion), to the water-soluble fraction of oil (simulating, in vivo, an oil slick confinement response technique) and to sea water alone (control condition). Biomarkers such as fluorescence of biliary polycyclic aromatic hydrocarbon (PAH) metabolites, total glutathione liver content, EROD (7-ethoxy-resorufin-O-deethylase) activity, liver antioxidant enzyme activity, liver lipid peroxidation and an innate immune parameter (haemolytic activity of the alternative complement pathway) were measured to assess the toxicity of dispersant application. Significant responses of PAH metabolites and total glutathione liver content to chemically dispersed oil were found, when compared to water-soluble fraction of oil. As it was suggested in other studies, these results highlight that priority must be given to oil slick confinement instead of dispersant application. However, since the same patterns of biomarkers responses were observed for both chemically and mechanically dispersed oil, the results also suggest that dispersant application is no more toxic than the natural dispersion occurring in nearshore areas (e.g. waves). The results of this study must, nevertheless, be interpreted cautiously since other components of nearshore habitats must be considered to establish a framework for dispersant use in nearshore areas

Gene regulated car driving: using a gene regulatory network to drive a virtual car

This paper presents a virtual racing car controller based on an artificial gene regulatory network. Usually used to control virtual cells in developmental models, recent works showed that gene regulatory networks are also capable to control various kinds of agents such as foraging agents, pole cart, swarm robots, etc. This paper details how a gene regulatory network is evolved to drive on any track through a three-stages incremental evolution. To do so, the inputs and outputs of the network are directly mapped to the car sensors and actuators. To make this controller a competitive racer, we have distorted its inputs online to make it drive faster and to avoid opponents. Another interesting property emerges from this approach: the regulatory network is naturally resistant to noise. To evaluate this approach, we participated in the 2013 simulated racing car competition against eight other evolutionary and scripted approaches. After its first participation, this approach finished in third place in the competition

Effectiveness of non-pharmacological interventions for irritable bowel syndrome : a systematic review

Introduction. Given the complexity of the therapeutic management of irritable bowel syndrome (IBS), alternative non-pharmacological therapies are frequently offered to patients. The aim of this study was to conduct a systematic review in order to establish the current evidence base for non-pharmacological interventions (body-directed and mind-body therapies) in the management of IBS. Materials and Methods. The literature was searched in several electronic databases (PubMed (including Medline), Web of Science (Clarivate Analytics), Scopus (Elsevier), ScienceDirect (Elsevier), Cochrane Library (Wiley), and Wiley Online Library (Wiley)) for randomized controlled trials (RCTs) published in the English language from 1990 to 2020. Effectiveness outcomes were examined through the change in overall IBS symptoms or abdominal pain up to 12 months after treatment. Results. 11 studies (parallel-group RCTs) were identified that enrolled 1590 participants in total. Body-directed therapies (acupuncture and osteopathic medicine) showed a beneficial effect compared with standard medical treatment for overall IBS symptoms at 6 months follow-up, while no study found any difference between body-directed and sham therapies for abdominal pain or overall IBS symptoms. It was not possible to conclude whether hypnotherapy was superior to standard medical treatment or supportive therapy for overall IBS symptoms or abdominal pain due to discordant results. Conclusions. Although body-directed therapies such as acupuncture and osteopathic medicine may be beneficial for overall IBS symptoms, higher-quality RCTs are needed to establish the clinical benefit of non-pharmacological interventions for IBS. An important challenge will be the definition of the optimal control groups to be used in non-pharmacological trials

Cyber Chronix, Participatory Research Approach to Develop and Evaluate a Storytelling Game on Personal Data Protection Rights and Privacy Risks

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