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Evaluation of head-free eye tracking as an input device for air traffic control
2013
Ergonomics
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The purpose of this study was to investigate the possibility to integrate a free head motion eye-tracking system as input device in air traffic control (ATC) activity. Sixteen participants used an eye tracker to select targets displayed on a screen as quickly and accurately as possible. We assessed the impact of the presence of visual feedback about gaze position and the method of target selection on selection performance under different difficulty levels induced by variations in target size
doi:10.1080/00140139.2012.744473
pmid:23231634
fatcat:w6yvcneqfzfk7kklt2jx5puhum
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... target-to-target separation. We tend to consider that the combined use of gaze dwell-time selection and continuous eye-gaze feedback was the best condition as it suits naturally with gaze displacement over the ATC display and free the hands of the controller, despite a small cost in terms of selection speed. In addition, target size had a greater impact on accuracy and selection time than target distance. These findings provide guidelines on possible further implementation of eye tracking in ATC everyday activity. Practitioner Summary: We investigated the possibility to integrate a free head motion eye-tracking system as input device in air traffic control (ATC). We found that the combined use of gaze dwell-time selection and continuous eye-gaze feedback allowed the best performance and that target size had a greater impact on performance than target distance.
Affective decision making under uncertainty during a plausible aviation task: An fMRI study
2013
NeuroImage
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While several cognitive theories have been proposed to explain this result (Causse, Dehais, Arexis, & Pastor, 2011; Goh & Wiegmann, 2002) , it may be that PCE is favored by strong negative emotions associated ...
measurements obtained in a separate experiment using the same task, where the mean heart rate was significantly higher during task performance in comparison to the resting state (Causse, Baracat, Pastor, & Dehais ...
doi:10.1016/j.neuroimage.2012.12.060
pmid:23313780
fatcat:num4cqlmkfejhcdhysdackakri
The effects of emotion on pilot decision-making: A neuroergonomic approach to aviation safety
2013
Transportation Research Part C: Emerging Technologies
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., 2007) , task commitment issues and psychological stress (Dehais et al., 2011 (Dehais et al., , 2012 or poor risk assessment (O' Hare and Smitheram, 1995; Wiegmann et al., 2002; Wiggins and O'Hare ...
doi:10.1016/j.trc.2012.04.005
fatcat:ip353e76kza5blpm6k4guyps4a
Molecular signatures of muscle growth and composition deciphered by the meta-analysis of age-related public transcriptomics data
2020
Physiological Genomics
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The lean-to-fat ratio is a major issue in beef meat industry both for carcass and meat production perspectives. This industrial perspective has motivated meat physiologists to use transcriptomics technologies to decipher mechanisms behind fat deposition within muscle during the time course of muscle growth. However, synthetic biological information from this volume of data remains to be produced to identify mechanisms found in various breeds and rearing practices. We conducted a meta-analysis
doi:10.1152/physiolgenomics.00020.2020
pmid:32657225
fatcat:xtxxmbce4nep7cvx36jwkft67i
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... 10 transcriptomic datasets stored in public databases, from the Longissimus thoracis of five different bovine breeds divergent by the age. We updated gene identifiers on the last version of the bovine genome (UCD1.2) and the 715 genes common to the 10 studies were subjected to the meta-analysis. Of the 238 genes differentially expressed (DEG), we identified a transcriptional signature of the dynamic regulation of glycolytic and oxidative metabolisms that agrees with a known shift between those two pathways from the animal puberty. We proposed some master genes of the myogenesis, namely MYOG and MAPK14, as probable regulators of the glycolytic and oxidative metabolisms. We also identified overexpressed genes related to lipid metabolism (APOE, LDLR, MXRA8 and HSP90AA1) that may contribute to the expected enhanced marbling as the age increases. Lastly, we proposed a transcriptional signature related to the induction (YBX1) or repression (MAPK14, YWAH, ERBB2) of the commitment of myogenic progenitors into the adipogenic lineage. The relationships between the abundance of the identified mRNA and marbling values remain to be analyzed in a marbling biomarkers discovery perspectives.
GWAS analyses reveal QTL in egg layers that differ in response to diet differences
2015
Genetics Selection Evolution
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The genetic architecture of egg production and egg quality traits, i.e. the quantitative trait loci (QTL) that influence these traits, is still poorly known. To date, 33 studies have focused on the detection of QTL for laying traits in chickens, but less than 10 genes have been identified. The availability of a high-density SNP (single nucleotide polymorphism) chicken array developed by Affymetrix, i.e. the 600K Affymetrix ® Axiom ® HD genotyping array offers the possibility to narrow down the
doi:10.1186/s12711-015-0160-2
pmid:26482360
pmcid:PMC4617898
fatcat:abaepemiczc27abpgdbvnx24zi
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... ocalization of previously detected QTL and to detect new QTL. This high-density array is also anticipated to take research beyond the classical hypothesis of additivity of QTL effects or of QTL and environmental effects. The aim of our study was to search for QTL that influence laying traits using the 600K SNP chip and to investigate whether the effects of these QTL differed between diets and age at egg collection. Results: One hundred and thirty-one QTL were detected for 16 laying traits and were spread across all marked chromosomes, except chromosomes 16 and 25. The percentage of variance explained by a QTL varied from 2 to 10 % for the various traits, depending on diet and age at egg collection. Chromosomes 3, 9, 10 and Z were overrepresented, with more than eight QTL on each one. Among the 131 QTL, 60 had a significantly different effect, depending on diet or age at egg collection. For egg production traits, when the QTL × environment interaction was significant, numerous inversions of sign of the SNP effects were observed, whereas for egg quality traits, the QTL × environment interaction was mostly due to a difference of magnitude of the SNP effects. Conclusions: Our results show that numerous QTL influence egg production and egg quality traits and that the genomic regions, which are involved in shaping the ability of layer chickens to adapt to their environment for egg production, vary depending on the environmental conditions. The next question will be to address what the impact of these genotype × environment interactions is on selection.
Genome-Wide Characterization of RNA Editing in Chicken Embryos Reveals Common Features among Vertebrates
2015
PLoS ONE
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RNA editing results in a post-transcriptional nucleotide change in the RNA sequence that creates an alternative nucleotide not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is described in more details in mammals, notably since the availability of next generation
doi:10.1371/journal.pone.0126776
pmid:26024316
pmcid:PMC4449034
fatcat:emjojzdqfvavpbxjjhjne7v7vi
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... uencing technologies allowing whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken is still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, and to extend the knowledge of its conservation among vertebrates. We performed sequencing of RNA and DNA from 8 embryos. Being aware of common pitfalls inherent to sequence analyses that lead to false positive discovery, we stringently filtered our datasets and found fewer than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual increase of editing level with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, attest to its tissue and stage specificity and provide support of the absence of non A-to-I events from the chicken transcriptome. A fascinating reality of the genome, with more and more empirical evidence, is that its biology is far more complex than previously thought. The rule "one gene has one DNA sequence leading to one mRNA translated into one protein", even if not (yet) an exception, is now wellknown to have evolved in a vast field of other possibilities. Taking the example of the human genome, the number of genes, the percentage of the genome that is transcribed, the alternative transcripts count per gene, or the way their expression is regulated, are all characteristics for which knowledge is moving with an extraordinary pace. The ENCODE project brought a lot of data and analyses in this area [1] . Among transformations that RNA transcripts undergo during maturation, RNA editing is a phenomenon leading to differences between the final RNA sequence and the DNA region it was transcribed from. The term was first used by Benne et al in 1986 [2], and can now be defined, in a broad sense, as a nucleotide insertion, deletion or substitution in the RNA sequence, occurring in various types of RNA, from tRNA to mRNA, whether coding or not [3] . Substitutions comprise several types of modifications, the most common in vertebrates being the A-to-I conversion, catalyzed by the ADAR family enzymes (Adenosine Desaminase that Acts on RNA) [4] and leading to an A-to-G reading of the cDNA molecule [5, 6] and C-to-U conversion, catalyzed by the APOBEC enzyme [7, 8] . RNA editing is limited to eukaryotes, with a few exceptions (see [9] for review). It is observed in chloroplasts, widespread in mitochondria, and also found as a nuclear phenomenon in animals. It seems to have arisen through different mechanisms in different lineages, rather than being inherited from a common ancestor, and whether natural selection was involved in its evolution is still debated [9] [10] [11] . While RNA editing is more widely characterized in mammals, especially in human, mouse and rat [12] [13] [14] [15] [16] [17] [18] , only a few studies have been performed in birds and these were targeting specific genes. The apolipoprotein B (APOB) RNA editing mechanism, well-known in mammals, seems to be absent from chicken [19] and zebra finch [20], which constitutes an argument in favor of the absence of the C-to-U editing phenomenon in these species. In chicken, the CYFIP2 (cytoplasmic FMR1 interacting protein 2) and FLNA (filamin A) genes are edited in brain and liver [21] , the splicing regulator NOVA1 (Neuro-Oncological Ventral Antigen 1) is edited in the brain [22] and the GABA A (gamma-Aminobutyric Acid Type A) Receptor, alpha3 subunit (GABRA3) is edited in the brain and the retina [23, 24] . But no genomewide study in chicken is available. High-throughput RNA sequencing allows a deeper transcriptome analysis than previous technologies, including RNA editing through a genome-wide approach [25] . This has been performed on several species, including human and mouse [12, 13, 15, 26, 27] but never in avian species. The number of editing sites (detected as RDD: RNA-DNA Differences) observed in mammals varies widely between studies, even in the same tissues of the same species, and an increasing number of analyses point to the requirement of very careful bioinformatics procedures to limit technical artifacts [14, 15, [28] [29] [30] [31] [32] . To improve the available knowledge about the extent of RNA editing in chicken, we chose an approach without a priori knowledge by using DNA and RNA sequencing on the same samples through Next Generation Sequencing (NGS) technology of whole embryos. Our results support the fact that RNA editing seems to be limited to A-to-I conversions in chicken, shows strong tissueand developmental-specificities and is conserved among vertebrates at specific coding sites.
Missing Critical Auditory Alarms in Aeronautics: Evidence for Inattentional Deafness?
2012
Proceedings of the Human Factors and Ergonomics Society Annual Meeting
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et al., 2012; Dehais et al. , 2011) . ...
Some experiments conducted in realistic flight simulators (Dehais et al., 2012; Dehais et al., 2010; Dehais et al., 2014) and in actual flight conditions confirmed that inattentional deafness could ...
doi:10.1177/1071181312561328
fatcat:pdgqydkfwbghlentc3fua4kixm
Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes
2011
BMC Genomics
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Transcriptome-wide investigation of genomic imprinting in chicken
2014
Nucleic Acids Research
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Genomic imprinting is an epigenetic mechanism by which alleles of some specific genes are expressed in a parent-of-origin manner. It has been observed in mammals and marsupials, but not in birds. Until now, only a few genes orthologous to mammalian imprinted ones have been analyzed in chicken and did not demonstrate any evidence of imprinting in this species. However, several published observations such as imprinted-like QTL in poultry or reciprocal effects keep the question open. Our main
doi:10.1093/nar/gkt1390
pmid:24452801
pmcid:PMC3973300
fatcat:ynfw7devsvfz3fzxjn3vs6r6cq
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... tive was thus to screen the entire chicken genome for parental-allele-specific differential expression on whole embryonic transcriptomes, using high-throughput sequencing. To identify the parental origin of each observed haplotype, two chicken experimental populations were used, as inbred and as genetically distant as possible. Two families were produced from two reciprocal crosses. Transcripts from 20 embryos were sequenced using NGS technology, producing $200 Gb of sequences. This allowed the detection of 79 potentially imprinted SNPs, through an analysis method that we validated by detecting imprinting from mouse data already published. However, out of 23 candidates tested by pyrosequencing, none could be confirmed. These results come together, without a priori, with previous statements and phylogenetic considerations assessing the absence of genomic imprinting in chicken.
Sequence analysis of a 24-kb contiguous genomic region at theArabidopsis thaliana PFLlocus on chromosome 11
1997
FEBS Letters
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As part of the European Union program of European Scientist Sequencing Arabidopsis (ESSA), the DNA sequence of a 24.053-bp insert of cosmid clone CC17J13 was determined. The cosmid is located on chromosome 1 at the PFL locus (position 30 cM). Analysis of the sequence and comparison to public databases predicts seven genes in this area, thus approximately one gene every 3.3 kb. Three cDNAs corresponding to genes in this region were also sequenced. The homologies and/or possible functions of the
doi:10.1016/s0014-5793(97)01190-3
pmid:9369203
fatcat:dorcqnylfrcyfcndh4j24lezki
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... putative) genes are discussed. Proteins encoded by genes in this region include a polyadenylatebinding protein (PAB-3) and a GTP-binding protein (Rab7) as well as a novel protein, possibly involved in double-stranded RNA unwinding and apoptosis. Intriguingly, the gene encoding the PAB-3 protein, which is very specifically expressed, is flanked by putative matrix attachment regions. © 1997 Federation of European Biochemical Societies.
A medium density genetic map and QTL for behavioral and production traits in Japanese quail
2015
BMC Genomics
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Behavioral traits such as sociability, emotional reactivity and aggressiveness are major factors in animal adaptation to breeding conditions. In order to investigate the genetic control of these traits as well as their relationships with production traits, a study was undertaken on a large second generation cross (F2) between two lines of Japanese Quail divergently selected on their social reinstatement behavior. All the birds were measured for several social behaviors (social reinstatement,
doi:10.1186/s12864-014-1210-9
pmid:25609057
pmcid:PMC4307178
fatcat:m7e5qkf35rhsplr5efr73oqdwq
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... ponse to social isolation, sexual motivation, aggression), behaviors measuring the emotional reactivity of the birds (reaction to an unknown object, tonic immobility reaction), and production traits (body weight and egg production).
Use of a proteome strategy for tagging proteins present at the plasma membrane
1998
The Plant Journal
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A plasma membrane (PM) fraction was purified from Arabidopsis thaliana using a standard procedure and analyzed by two-dimensional (2D) gel electrophoresis. The proteins were classified according to their relative abundance in PM or cell membrane supernatant fractions. Eightytwo of the 700 spots detected on the PM 2D gels were microsequenced. More than half showed sequence similarity to proteins of known function. Of these, all the spots in the PM-specific and PM-enriched fractions, together
doi:10.1046/j.1365-313x.1998.00335.x
pmid:10036779
fatcat:jpw3aqjhnvhqvnmi4gpgqsn3wu
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... half of the spots with similar abundance in PM fraction and supernatant, have previously been found at the PM, supporting the validity of this approach. Extrapolation from this analysis indicates that (i) approximately 550 polypeptides found at the PM could be resolved on 2D gels; (ii) that numerous proteins with multiple locations are found at the PM; and (iii) that approximately 80% of PM-specific spots correspond to proteins with unknown function. Among the latter, half are represented by ESTs or cDNAs in databases. In this way, several unknown gene products were potentially localized to the PM. These data are discussed with respect to the efficiency of organelle proteome approaches to link systematically genomic data 633 to genome expression. It is concluded that generalized proteomes can constitute a powerful resource, with future completion of Arabidopsis genome sequencing, for genome-wide exploration of plant function.
Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach
2017
Molecular Ecology
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A New Local Score Based Method Applied to Behavior-divergent Quail Lines Sequenced in Pools Precisely Detects Selection Signatures on Genes Related to Autism
[article]
2015
arXiv
pre-print
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Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans allows increasing the detection power, but haplotype-based methods require individual genotypes and are not applicable on pool-sequenced samples. We propose to take advantage of the local score approach to account for linkage disequilibrium, accumulating (possibly small) signals from single markers over a genomic segment, to clearly pinpoint a
arXiv:1507.06433v1
fatcat:73fcyv7yyvbflm7jljyfws6a7u
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... lection signal, avoiding windowing methods. This method provided results similar to haplotype-based methods on two benchmark data sets with individual genotypes. Results obtained for a divergent selection experiment on behavior in quail, where two lines were sequenced in pools, are precise and biologically coherent, while competing methods failed: our approach led to the detection of signals involving genes known to act on social responsiveness or autistic traits. This local score approach is general and can be applied to other genome-wide analyzes such as GWAS or genome scans for selection.
A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality
2014
Genetics Selection Evolution
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