REY Amandine

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Genome-wide analyses estimate that more than 90% of multi exonic human genes produce at least two transcripts through alternative splicing (AS). Various bioinformatics methods are available to analyze AS from RNAseq data. Most methods start by mapping the reads to an annotated reference genome, but some start by a de novo assembly of the reads. In this paper, we present a systematic comparison of a mapping-first approach (FARLINE) and an assembly-first approach (KISSPLICE). We applied these methods to two independent RNAseq datasets and found that the predictions of the two pipelines overlapped (70% of exon skipping events were common), but with noticeable differences. The assembly-first approach allowed to find more novel variants, including novel unannotated exons and splice sites. It also predicted AS in recently duplicated genes. The mapping-first approach allowed to find more lowly expressed splicing variants, and splice variants overlapping repeats. This work demonstrates that annotating AS with a single approach leads to missing out a large number of candidates, many of which are differentially regulated across conditions and can be validated experimentally. We therefore advocate for the combined use of both mapping-first and assembly-first approaches for the annotation and differential analysis of AS from RNAseq datasets.

In the last decade, research has shown that word processing is influenced by the lexical and semantic features of words. However, norms for a crucial semantic variable—that is, conceptual familiarity—have not been available for a sizeable French database. We thus developed French Canadian conceptual familiarity norms for 3,596 nouns. This enriches Desrochers and Thompson’s (2009) database, in which subjective frequency and imageability values are already available for the same words. We collected online data from 313 Canadian French speakers. The full database of conceptual familiarity ratings is freely available at http://lingualab.ca/fr/projets/normes-de-familiarite-conceptuelle. We then demonstrated the utility of these new conceptual familiarity norms by assessing their contribution to lexical decision times. We conducted a stepwise regression model with conceptual familiarity in the last step. This allowed us to assess the independent contribution of conceptual familiarity beyond the contributions of other well-known psycholinguistic variables, such as frequency, imageability, and age of acquisition. The results showed that conceptual familiarity facilitated lexical decision latencies. In sum, these ratings will help researchers select French stimuli for experiments in which conceptual familiarity must be taken into account.

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Chronic pain patients often complain of their "poor memory" and numerous studies objectively confirmed such difficulties in reporting working memory (WM) and long-term memory (LTM) dysfunctions. This paper provides a comprehensive review of the literature on memory impairment in chronic pain (CP) patients. Twenty-four observational studies evaluating WM or/and LTM in a chronic pain group and a control group were included in this review. Results showed that studies consistently reported a moderate decline, in both WM and LTM performances in CP patients. Even if CP patients complained about forgetfulness, objective measurements did not permit to conclude to a long-term storage impairment. CP patients exhibited more specifically encoding or retrieving difficulties compared to controls. Results showed that chronic pain selectively impacted the most attention-demanding memory processes, such as working memory and recollection in long-term memory. Results also demonstrated that CP patients exhibited a memory bias directed towards painful events compared to control subjects. Several authors have suggested that CP could be a maladaptive consequence of memory mechanisms. The long-lasting presence of pain continuously reinforces aversive emotional associations with incidental events. The inability to extinguish this painful memory trace could explain the chronic persistence of pain even when the original injury has disappeared. A major concern is the need to extricate pain-related cognitive effects from those resulting from all the co-morbidities associated with CP which both have a deleterious effect on cognitive function.

Numerous studies have explored the effect of sleep on memory. It is well known that a period of sleep, compared to a similar period of wakefulness, protects memories from interference, improves performance, and might also reorganize memory traces in a way that encourages creativity and rule extraction. It is assumed that these benefits come from the reactivation of brain networks, mainly involving the hippocampal structure, as well as from their synchronization with neocortical networks during sleep, thereby underpinning sleep-dependent memory consolidation and reorganization. However, this memory reorganization is difficult to explain within classical memory models. The present paper aims to describe whether the influence of sleep on memory could be explained using a multiple trace memory model that is consistent with the concept of embodied cognition: the Act–In (activation–integration) memory model. We propose an original approach to the results observed in sleep research on the basis of two simple mechanisms, namely activation and integration.

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Genome-wide analyses reveal that more than 90% of multi exonic human genes produce at least two transcripts through alternative splicing (AS). Various bioinformatics methods are available to analyze AS from RNAseq data. Most methods start by mapping the reads to an annotated reference genome, but some start by a de novo assembly of the reads. In this paper, we present a systematic comparison of a mapping-first approach ( FaRLine ) and an assembly-first approach ( KisSplice ). These two approaches are event-based, as they focus on the regions of the transcripts that vary in their exon content. We applied these methods to an RNAseq dataset from a neuroblastoma SK-N-SH cell line (ENCODE) differentiated or not using retinoic acid. We found that the predictions of the two pipelines overlapped (70% of exon skipping events were common), but with noticeable differences. The assembly-first approach allowed to find more novel variants, including novel unannotated exons and splice sites. It also predicted AS in families of paralog genes. The mapping-first approach allowed to find more lowly expressed splicing variants, and was better in predicting exons overlapping repeated elements. This work demonstrates that annotating AS with a single approach leads to missing a large number of candidates. We further show that these candidates cannot be neglected, since many of them are differentially regulated across conditions, and can be validated experimentally. We therefore advocate for the combine use of both mapping-first and assembly-first approaches for the annotation and differential analysis of AS from RNAseq data.

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There is much behavioral and neurophysiological evidence in support of the idea that seeing a tool activates motor components of action related to the perceived object (e.g., grasping, use manipulation). However, the question remains as to whether the processing of the motor components associated with the tool is automatic or depends on the situation, including the task and the modality of tool presentation. The present study investigated whether the activation of motor components involved in tool use in response to the simple perception of a tool is influenced by the link between prime and target tools, as well as by the modality of presentation, in perceptual or motor tasks. To explore this issue, we manipulated the similarity of gesture involved in the use of the prime and target (identical, similar, different) with two tool presentation modalities of the presentation tool (visual or auditory) in perceptual and motor tasks. Across the experiments, we also manipulated the relevance of the prime (i.e., associated or not with the current task). The participants saw a first tool (or heard the sound it makes), which was immediately followed by a second tool on which they had to perform a perceptual task (i.e., indicate whether the second tool was identical to or different from the first tool) or a motor task (i.e., manipulate the second tool as if it were the first tool). In both tasks, the similarity between the gestures employed for the first and the second tool was manipulated (Identical, Similar or Different gestures). The results showed that responses were faster when the manipulation gestures for the two tools were identical or similar, but only in the motor task. This effect was observed irrespective of the modality of presentation of the first tool, i.e. visual or auditory. We suggest that the influence of manipulation gesture on response time depends on the relevance of the first tool in motor tasks.

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According to grounded theories of cognition, knowledge is grounded in its sensory-motor features. Therefore, perceptual and conceptual processing should be based on the same distributed system so that conceptual and perceptual processes should interact. The present study assesses whether gustatory stimulation (participants tasted a sweet or a nonsweet yoghurt) could influence performance on a categorization task that involves the reactivation of the same sensory dimension. The results indicate that participants were slower (Experiment 1) or faster (Experiment 2), respectively, at categorizing pictures as representing edible sweet stimuli when they either simultaneously or had previously tasted a sweet yoghurt as compared to a nonsweet yoghurt. These results confirm the significant overlap between perceptual and memory mechanisms and suggest the functional equivalence between perceptually present and perceptually absent (memory reactivated) dimensions.

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In our daily lives, we constantly collect and integrate a large amount of sensory information (Calvert & Thesen, 2004). Throughout our perceptual activities, the knowledge we have about the environment is continuously "retrieved" into memory. The framework of embodied and situated cognition proposes that cognitive processes (i.e., mnemonic processes, language processes) are rooted in the same sensorimotor systems as those engaged in perceptual-motor processes (Glenberg, 1997 . Slotnick, 2004 . Pecher & Zwaan, 2005).Memory contains sensory-motor traces encoded during the individual's multiple experiences in his or her environment (Versace, Labeye, Badard, & Rose, 2009). Numerous works in cognitive psychology and neuroscience demonstrate that knowledge is constructed and (re)emerges from the activation of neural systems typically associated with perceptual-motor mechanisms. The content and functioning of our memory are intrinsically linked to our past and present sensory-motor activities. To be effective, the knowledge involved in our cognitive activities must be closely related to the present situation. This ability to adapt to specific situations would not be possible unless knowledge, including conceptual knowledge, is derived from the reactivation of memory traces of past experiences (Barsalou, 2008 . Versace et al., 2014). Conversely, sensory-motor activities are completely dependent on the memory traces of past sensory-motor experiences. Thus, the difference between perception and memory lies in the fact that, in the first case, properties are perceptually present, whereas, in the second case, they are absent but reactivated.The aim of this thesis was to study the links between memory and perception and, more precisely, to provide arguments in favor of the similarity between memetic and perceptual processes resulting from the activation of components of the same sensorimotor nature.We tested the hypothesis that perceptual effects should be obtainable with components reactivated in memory. To this end, we used perceptual effects - such as the masking effect or perceptual judgment biases - to explore the possibility of replicating this type of effect with the intervention of memetic dimensions.

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Abstract The n -3 polyunsaturated fatty acid, docosahexaenoic acid (DHA), displays anti-inflammatory properties that may prevent atherosclerosis progression. Exposure of apolipoprotein-E deficient (ApoE −/− ) mice to chronic intermittent hypoxia (CIH) accelerates atherosclerosis progression. Our aim was to assess DHA-supplementation influence on fatty acid incorporation in different tissues/organs and on atherosclerosis progression in ApoE −/− mice exposed to CIH. ApoE −/− mice were exposed to CIH or normoxia (N) and randomized to four groups (N control, CIH control, N+DHA, and CIH+DHA). DHA-supplementation enhanced DHA and reduced arachidonic acid (AA) contents in tissues/organs. CIH control mice exhibited increased atherosclerosis lesion sizes compared to N control mice. DHA prevented CIH induced atherosclerosis but did not improve atherosclerosis burden in N mice. Aortic matrix metalloproteinase-2 (MMP-2) expression was decreased in CIH+DHA mice ( p =0.007). DHA-supplementation prevented CIH-induced atherosclerosis acceleration. This was associated with a decrease of AA incorporation and of aortic MMP-2 gene expression.

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