SYNPHONI: scale-free and phylogeny-aware reconstruction of synteny conservation and transformation across animal genomes.

SUMMARY: Current approaches detect conserved genomic order either at chromosomal (macrosynteny) or at subchromosomal scales (microsynteny). The latter generally requires collinearity and hard thresholds on syntenic region size, thus excluding a major proportion of syntenies with recent expansions or minor rearrangements. 'SYNPHONI' bridges the gap between micro- and macrosynteny detection, providing detailed information on both synteny conservation and transformation throughout the evolutionary history of animal genomes. AVAILABILITY AND IMPLEMENTATION: Source code is freely available at https://github.com/nsmro/SYNPHONI, implemented in Python 3.9. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

How rich are false memories in a naturalistic context in healthy aging?

The recall of factual and contextual information is a core characteristic of episodic memory sensitive to aging effects. The innovative aim of the present study was to assess in a naturalistic context the quantity and quality of correct and false free recalls among younger and older adults considering feature binding (What-Where-When-Details) and recollection (Remembering vs. Knowing). Thanks to virtual reality, we designed a multimodal environment simulating a lively town in which we implemented a variant of a DRM task rich in sets of semantically related items (e.g., fruits on a market stall). We asked 30 young and 30 older participants to navigate in the virtual environment, paying attention to the items, and then recall as many items and as much contextual information as possible and indicate the presence of recollection. As expected, older adults produced fewer correct recall but more intrusions than younger adults, and their correct recall was more deficient in binding and recollection. In both age groups, false recall was associated with the correct context inferred from a related set of items. However, the intrusions produced by older adults were highly recollected compared to those of the younger adults, and they were associated with false item-related contextual information.

The production of false recognition and the associated state of consciousness following encoding in a naturalistic context in aging.

Using virtual reality, we implemented a naturalistic variant of the DRM paradigm in young and older adults to evaluate false recall and false recognition. We distinguished false recognition related to the highest semantic association (the critical lures), semantic similarity (i.e. items that belong to the same semantic category), and perceptual similarity (i.e. items that are similar, but not identical in terms of shape or color). The data revealed that younger adults recalled and recognized more correct elements than older adults did while the older adults intruded more critical items than younger adults. Both age groups produced false recognition related to the critical items, followed by perceptually and then semantically related items. False recognitions were highly recollective as they were mainly associated with a sense of remembering, even more so in older adults than in young adults. The decline of executive functions and working memory predicted age-related increases in false memories.

"Walk this way": specific contributions of active walking to the encoding of metric properties during spatial learning.

The effect of body-based information on spatial memory has been traditionally described as a facilitating factor for large-scale spatial learning in the field of active learning research (Chrastil & Warren, Psychonomic Bulletin and Review, 19(1):1-23; 2012). The specific contribution of body-based information to spatial representation properties is however not yet well defined and the mechanisms through which body-based information contributes to spatial learning are not clear enough. To disambiguate the effect of active spatial learning on the quality of spatial representations from the beneficial effect of physiological arousal, we compared four experimental conditions (walking on a unidirectional treadmill during learning, retrieval, both phases or no walking). Results showed no effect of the walking condition for a route perspective task, but a significant effect on a survey perspective task (landmark positioning on a map): participants who walked during encoding (encoding group and encoding + retrieval group) obtained better results than those who did not walk or walked only during retrieval. Geometrical analysis of spatial positions on maps revealed that the activity of walking during encoding improves the correlation between participants' coordinates and actual coordinates through better distance estimations and angular accuracy, even though the optic flow was not matched with individual walking speed. Control group variance in all measures was higher than that of the walking groups (regardless of the moment of walking). Taken together, these results provide arguments for the multimodal nature of spatial representations, where body-related information derived from walking is involved in metric properties accuracy and perspective switching.

Phenomenal, bodily and brain correlates of fictional reappraisal as an implicit emotion regulation strategy.

The ability to modulate our emotional experience, depending on our current goal and context, is of critical importance for adaptive behavior. This ability encompasses various emotion regulation strategies, such as fictional reappraisal, at stake whenever one engages in fictional works (e.g., movies, books, video games, virtual environments). Neuroscientific studies investigating the distinction between the processing of real and fictional entities have reported the involvement of brain structures related to self-relevance and emotion regulation, suggesting a threefold interaction between the appraisal of reality, aspects of the Self, and emotions. The main aim of this study is to investigate the effect of implicit fictional reappraisal on different components of emotion, as well as on the modulatory role of autobiographical and conceptual self-relevance. While recording electrodermal, cardiac, and brain activity (EEG), we presented negative and neutral pictures to 33 participants, describing them as either real or fictional. After each stimulus, the participants reported their subjective emotional experience, self-relevance of the stimuli, as well as their agreement with their description. Using the Bayesian mixed-modeling framework, we showed that stimuli presented as fictional, compared with real, were subjectively appraised as less intense and less negative, and elicited lower skin conductance response, stronger heart-rate deceleration, and lower late positive potential amplitudes. Finally, these phenomenal and physiological changes did, to a moderate extent, rely on variations of specific aspects of self-relevance. Implications for the neuroscientific study of implicit emotion regulation are discussed.

Dispositional mindfulness attenuates the emotional attentional blink.

Emotional stimuli have been shown to automatically hijack attention, hindering the detection of forthcoming targets. Mindfulness is defined as a present moment non-judgemental attentional stance that can be cultivated by meditation practices, but that may present interindividual variability in the general population. The mechanisms underlying modification in emotional reactivity linked to mindfulness are still a matter of debate. In particular, it is not clear whether mindfulness is associated with a diminished emotional response, or with faster recovery. We presented participants with target pictures embedded in a rapid visual presentation stream. The targets could be preceded by negative, neutral or scrambled critical distractors. We showed that dispositional mindfulness, in particular the Non-reacting facet, was related to faster disengagement of attention from emotional stimuli. These results could have implications for mood disorders characterised by an exaggerated attentional bias toward emotional stimuli, such as anxiety and post-traumatic stress disorders.

"Being there" and remembering it: Presence improves memory encoding.

Few studies have investigated the link between episodic memory and presence: the feeling of "being there" and reacting to a stimulus as if it were real. We collected data from 244 participants after they had watched the movie Avengers: Age of Ultron. They answered questions about factual (details of the movie) and temporal memory (order of the scenes) about the movie, as well as their emotion experience and their sense of presence during the projection. Both higher emotion experience and sense of presence were related to better factual memory, but not to temporal order memory. Crucially, the link between emotion and factual memory was mediated by the sense of presence. We interpreted the role of presence as an external absorption of the attentional focus toward the stimulus, thus enhancing memory encoding. Our findings could shed light on the cognitive processes underlying memory impairments in psychiatric conditions characterized by an altered sense of reality.

Secondary distinctiveness effects: Orthographic distinctiveness and bizarreness effects make independent contributions to memory performance.

The secondary distinctiveness effect means that items that are unusual compared to one's general knowledge stored in permanent memory are remembered better than common items. This research studied two forms of secondary-distinctiveness-based effects in conjunction: the bizarreness effect and the orthographic distinctiveness (OD) effect. More specifically, an experiment investigated in young adults a possible additive effect of bizarreness and OD effects in free recall performance. Results revealed that in young adults these two secondary-distinctiveness-based effects appear to be largely independent and can complement each other to enhance performance. Findings are discussed in light of current distinctiveness theory.

THE IMPORTANCE OF INSTRUMENT MAKERS FOR THE DEVELOPMENT OF EXPERIMENTAL PSYCHOLOGY: THE CASE OF ALFRED BINET AT THE SORBONNE LABORATORY.

The importance of instrument firms in the development of psychology, and science in general, should not be underestimated since it would not have been possible for various leading psychologists at the turn of the twentieth century to conduct certain experiments without the assistance of instrument makers, as is often the case today. To illustrate the historical perspective introduced here, the example of Alfred Binet is taken, as he is an interesting case of a psychologist working in close collaboration with various French instrument designers of the time. The objective of this article is twofold: (1) to show the considerable activity carried out by early psychologists to finalize new laboratory instruments in order to develop their research projects; (2) to reassess the work of a major figure in French psychology through his activity as a designer of precision instruments. The development of these new instruments would certainly have been difficult without the presence in Paris of numerous precision instrument manufacturers such as Charles Verdin, Otto Lund, Henri Collin, and Lucien Korsten, on whom Binet successively called in order to develop his projects in the field of experimental psychology.

A French description of German psychology laboratories in 1893 by Victor Henri, a collaborator of Binet.

There is a rich tradition of writings about the foundation of psychology laboratories, particularly in the United States but also in France. Various documents exist concerning former German laboratories in American and French literature. But the most interesting French paper was certainly written by a young psychologist named Victor Henri (1872-1940) who was a close collaborator of Alfred Binet (1857-1911) in the 1890s. Visiting various psychology laboratories, he wrote, in 1893, a clear description of the laboratories of Wundt, G. E. Müller, Martius and Ebbinghaus. An English translation is given of Henri's paper and the historical importance of his contribution is here expounded by contrasting the German and French psychologies of the time.

Investigating secondary-distinctiveness-based effects in aging and Alzheimer's disease patients.

The aim of the present study was 2-fold. First, two experiments were devised to further investigate secondary distinctiveness-based effects in relation to aging. By using a repeated study-test procedure, it aimed at restoring the bizarreness effect (Experiment 1) or at amplifying the orthographic distinctiveness (OD) effect in older adults (Experiment 2). Second, by including Alzheimer's disease patients (AD patients) in both experiments, it also aimed at instigating research on secondary distinctiveness-based effects in relation to Alzheimer disease. The results of Experiment 1 revealed that a repeated study-test procedure may to some extent facilitate the free recalling of bizarre images in older adults. However, the benefit of such procedure does not seem to be durable in older adults (no bizarreness effect for the last study-test cycle) and is inefficient in AD patients. Surprisingly, for both older adults and AD patients, results of Experiment 2 revealed a similar OD effect across all study-test cycles. The findings of both experiments were related to previous work suggesting that the bizarreness effect and the OD effect are mediated by different processing.

Hearing the inaudible experimental subject: Echoes of Inaudi, Binet's calculating prodigy.

Historians of psychology have traditionally focused on ideas (intellectual history), the "great men" who produced them (an older style of biography sometimes called "hagiography"), or-more recently-the influence of the contexts that shaped them (social and cultural history). A still more recent approach is to bring in those invisible subjects whose experiences have previously been ignored, most often through histories focusing on the discipline's forgotten women or minority contributors: "history from below" (subaltern history). A variation on this was popularized in the history of psychiatry (viz., "patient voices") and has since been carried into the history of psychology (e.g., "feminist voices"). The latest innovation is to focus on what Jill Morawski has referred to as "the discipline's experimental subjects." (These are the collective done-to, rather than the doers, of psychological research.) This history is one of those: an attempt to look behind Alfred Binet to find an influence that shaped his work. The purpose is thus to "give voice" to this unheard-from subject-the until-now inaudible Jacques Inaudi (including excerpts from newspaper interviews and translations from his recently discovered autobiography)-and at the same time advance Morawski's historiographical project. We then get a glimpse of what it was like to be a child prodigy in France in the 1880s, as well as what securing scientific patrons could do for one's prospects. By focusing specifically on Binet's unheard-from experimental subject, we are also afforded new perspectives of the history of late-19th century French psychology (reflecting another emerging interest, "international history"), and we gain new insights into the prehistory of contemporary Binet-style intelligence testing.

PSYCHOLOGY IN FRENCH ACADEMIC PUBLISHING IN THE LATE NINETEENTH CENTURY: ALFRED BINET, EDITORIAL DIRECTOR AT THE SCHLEICHER PUBLISHING HOUSE.

To date, historians of psychology have largely ignored the role of academic publishing and the editorial policies of the late nineteenth century. This paper analyzes the role played by academic publishing in the history of psychology in the specific case of France, a country that provides a very interesting and unique model. Up until the middle of the 1890s, there was no collection specifically dedicated to psychology. Alfred Binet was the first to found, in 1897, a collection of works specifically dedicated to scientific psychology. He chose to work with Reinwald-Schleicher. However, Binet was soon confronted with (1) competition from other French publishing houses, and (2) Schleicher's management and editorial problems that were to sound the death knell for Binet's emerging editorial ambitions. The intention of this paper is to encourage the efforts of the pioneers of modern psychology to have their work published and disseminated.

Jean-Martin Charcot's role in the 19th century study of music aphasia.

Jean-Martin Charcot (1825-93) was a well-known French neurologist. Although he is widely recognized for his discovery of several neurological disorders and his research into aphasia, Charcot's ideas about how the brain processes music are less well known. Charcot discussed the music abilities of several patients in the context of his 'Friday Lessons' on aphasia, which took place at the Salpêtrière Hospital in Paris in 1883-84. In his most comprehensive discussion about music, Charcot described a professional trombone player who developed difficulty copying music notation and playing his instrument, thereby identifying a new isolated syndrome of music agraphia without aphasia. Because the description of this case was published only in Italian by one of his students, Domenico Miliotti, there has been considerable confusion and under-acknowledgement of Charcot's ideas about music and the brain. In this paper, we describe Charcot's ideas regarding music and place them within the historical context of the growing interest in the neurological underpinnings of music abilities that took place in the 1880s.

A French description of the Psychology Laboratory of G. S. Hall at Clark University in 1893.

There is a rich tradition of writings about the foundation of psychology laboratories, particularly in the United States and in France. Like their German counterparts, American laboratories of psychology were described by several scholars in French journals. These descriptions stimulated the establishment of laboratories in France and provided templates for laboratory designs. We introduce here an article written by Marcel Baudouin (1860-1941), who visited and subsequently described the psychology laboratory of Granville Stanley Hall (1844-1924) at Clark University in Worcester, Massachusetts. The English translation of Baudouin's paper, provided here, constitutes an interesting new document on Hall's laboratory at Clark University as it stood in 1893. From the French perspective, the Clark laboratory provided an ideal model for the experimental psychology laboratory.

The effect of long-term working memory through personalization applied to free recall: uncurbing the primacy-effect enthusiasm.

In this study, a personalization method (Guida, Tardieu, & Nicolas, European Journal of Cognitive Psychology, 21: 862-896 2009) was applied to a free-recall task. Fifteen pairs of words, composed of an object and a location, were presented to 93 participants, who had to mentally associate each pair and subsequently recall the objects. A 30-s delay was introduced on half of the trials, the presentation rate was manipulated (5 or 10 s per item), and verbal and visuospatial working memory tests were administered to test for their effects on the serial curve. Two groups were constituted: a personalized group, for whom the locations were well-known places on their university campus, and a nonpersonalized group, for whom the locations did not refer to known places. Since personalization putatively operationalizes long-term working memory (Ericsson & Kintsch, Psychological Review, 102: 211-245 1995)-namely, the capacity to store information reliably and rapidly in long-term memory-and if we take a dual-store approach to memory, the personalization advantage would be expected to be greater for pre-recency than for recency items. Overall, the results were compatible with long-term working memory theory. They contribute to validating the personalization method as a methodology to characterize the contribution of long-term memory storage to performance in working memory tasks.

"A big piece of news": Théodule Ribot and the founding of the Revue Philosophique de la France et de l'Etranger.

This paper describes the founding of the Revue Philosophique de la France et de l'Étranger by Théodule Ribot (1839-1916) in 1876. Like the English journal Mind, which was launched the same year, this journal introduced the new scientific psychology to France. Its founding increased Ribot's scientific credibility in psychology and led him to be regarded as the most distinguished French specialist in the field. First, we review the state of French philosophy at the time of the journal's founding, focusing on the three main French schools of thought in philosophy and on their relations with psychology. Second, after analyzing the preface written by Ribot in the first issue of the Revue Philosophique, we examine how the journal was received in French philosophical circles. Finally, we discuss its subsequent history, highlighting its founder's promotion of new ideas in psychology.

How chunks, long-term working memory and templates offer a cognitive explanation for neuroimaging data on expertise acquisition: a two-stage framework.

Our review of research on PET and fMRI neuroimaging of experts and expertise acquisition reveals two apparently discordant patterns in working-memory-related tasks. When experts are involved, studies show activations in brain regions typically activated during long-term memory tasks that are not observed with novices, a result that is compatible with functional brain reorganization. By contrast, when involving novices and training programs, studies show a decrease in brain regions typically activated during working memory tasks, with no functional reorganization. We suggest that the latter result is a consequence of practice periods that do not allow important structures to be completely acquired: knowledge structures (i.e., Ericsson and Kintsch's retrieval structures; Gobet and Simon's templates) and in a lesser way, chunks. These structures allow individuals to improve performance on working-memory tasks, by enabling them to use part of long-term memory as working memory, causing a cerebral functional reorganization. Our hypothesis is that the two brain activation patterns observed in the literature are not discordant, but involve the same process of expertise acquisition in two stages: from decreased activation to brain functional reorganization. The dynamic of these two physiological stages depend on the two above-mentioned psychological constructs: chunks and knowledge structures.

The impact of processing time on the bizarreness and orthographic distinctiveness effects.

The bizarreness effect and the orthographic distinctiveness effect (OD effect) are typical cases of secondary-distinctiveness-based effects. This study tested the simple attentional account or processing time hypothesis as a possible explanation of the bizarreness effect and the OD effect. In the bizarreness effect literature, this hypothesis gained support by some studies but was also discredited by other research. In light of these conflicting results, Experiment 1 was devised to test the processing time hypothesis in the bizarreness effect by using black-and-white concrete images and manipulating the time allotted for processing the stimuli (500 ms, 1000 ms, 3000 ms). Concerning the OD effect, no research has directly investigated the impact of processing time by examining the effect under varying amounts of study time. Experiment 2 was thus devised to investigate this same hypothesis in the OD effect and time allotted for processing the stimuli was manipulated (250 ms, 500 ms, 1000 ms, 3000 ms). Results did not support the processing time hypothesis since the magnitude of the bizarreness effect and of the OD effect was not modulated by the amount of time allotted for processing the stimuli. We refer to alternative explanations to account for these two secondary-distinctiveness-based effects.

Repetition and spacing effects on true and false recognition in the DRM paradigm.

With the Deese-Roediger-McDermott (DRM) paradigm, the repetition effect on false memory had never been clarified. More importantly, the spacing effect on false memory was never directly investigated. So, we carried out two experiments to examine these effects on true and false recognition. In experiment 1, participants studied DRM lists which were presented one, three or five times. In experiment 2, we manipulated the repetition mode (massed vs. spaced with a short interval or a long interval) to explore the spacing effect. The results showed that true recognition increased monotonically with list repetition (experiment 1) and repetition spacing (experiment 2). The most striking finding was a similar spacing effect but no repetition effect on false recognition. Thus, these results were principally discussed in the light of the activation-monitoring framework.