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.

"Run to the hills": Specific contributions of anticipated energy expenditure during active spatial learning.

Grounded views of cognition consider that space perception is shaped by the body and its potential for action. These views are substantiated by observations such as the distance-on-hill effect, described as the overestimation of visually perceived uphill distances. An interpretation of this phenomenon is that slanted distances are overestimated because of the integration of energy expenditure cues. The visual perceptual processes involved are, however, usually tackled through explicit estimation tasks in passive situations. The goal of this study was to consider instead more ecological active spatial processing. Using immersive virtual reality and an omnidirectional treadmill, we investigated the effect of anticipated implicit physical locomotion cost by comparing spatial learning for uphill and downhill routes, while maintaining actual physical cost and walking speed constant. In the first experiment, participants learnt city layouts by exploring uphill or downhill routes. They were then tested using a landmark positioning task on a map. In the second experiment, the same protocol was used with participants who wore loaded ankle weights. The results from the first experiment showed that walking uphill routes led to a global underestimation of distances compared with downhill routes. This inverted distance-of-hill effect was not observed in the second experiment, where an additional effort was applied. These results suggest that the underestimation of distances observed in Experiment 1 emerged from recalibration processes whose function was to solve the transgression of proprioceptive predictions linked with uphill energy expenditure. The results are discussed in relation to constructivist approaches on spatial representations and predictive coding theories.

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.

Aging and posture in the memory of manipulable objects.

Thirty healthy elderly participants (mean age = 77.3) learned the names of manipulable and nonmanipulable objects while adopting a control posture (hands in front of them) or an interfering posture (holding their hands behind their back). Results on a recall task showed a postural interference (PI) effect, with the interfering posture reducing the memory of manipulable objects, but not of nonmanipulable ones. The effect was similar to the Postural Interference effect previously observed in young adults, although with a lower performance. These results call into question the embodied theory hypothesis that the deterioration of memory in aging is related to the decline of the sensorimotor system.

"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.

False memory in normal ageing: empirical data from the DRM paradigm and theoretical perspectives.

False memories refer to falsely remembering something that did not happen or that happened differently. The effects of age on episodic memory underlie both the decline in real memories and the increase in false memories. But, what is the richness and what is the feeling of reality of false memories in the elderly? This mini-review on false memory in young and older adults presents the results from the literature using one of the most used paradigms in the laboratory to study false memories - the Deese-Roediger-McDermott paradigm. This paradigm generally consists in the presentation of semantically associated items-lists (words or images) related to a non-presented critical lure (e.g., bed, rest, awake …, the critical lure is sleep). During free recall or recognition tests, the participants regularly produce false memories (intrusions or false recognitions of the critical lures), increasingly with aging. We specifically ask the question of the richness of the false memory trace in young and older adults in terms of contextual associations (What-Where-When-Details binding) and phenomenological characteristics (remembering, knowing, guessing). We propose to examine this issue using a naturalistic episodic memory task via navigation in a virtual environment enriched with series of associated elements (e.g., vegetables stand) linked to non-presented critical lures (e.g., carrots). Based on preliminary results, we propose an integrative model of memory trace which can explain the differences observed between young and old people on the richness of their false memories.

[False memory in normal aging: empirical data from the DRM paradigm and theoretical perspectives]. / Les faux souvenirs dans le vieillissement normal : données empiriques du paradigme DRM et perspectives théoriques.

False memories refer to falsely remembering something that did not happen or that happened differently. The effects of age on episodic memory underlie both the decline in real memories and the increase in false memories. But, what is the richness and what is the feeling of reality of false memories in the elderly? This mini-review on false memory in young and older adults presents the results from the literature using one of the most used paradigms in the laboratory to study false memories - the Deese-Roediger-McDermott paradigm. This paradigm generally consists in the presentation of semantically associated items-lists (words or images) related to a non-presented critical lure (e.g., bed, rest, awake …, the critical lure is sleep). During free recall or recognition tests, the participants regularly produce false memories (intrusions or false recognitions of the critical lures), increasingly with aging. We specifically ask the question of the richness of the false memory trace in young and older adults in terms of contextual associations (What-Where-When-Details binding) and phenomenological characteristics (remembering, knowing, guessing). We propose to examine this issue using a naturalistic episodic memory task via navigation in a virtual environment enriched with series of associated elements (e.g., vegetables stand) linked to non-presented critical lures (e.g., carrots). Based on preliminary results, we propose an integrative model of memory trace which can explain the differences observed between young and old people on the richness of their false memories.

The heart of cognitive control: Cardiac phase modulates processing speed and inhibition.

Bodily states are heavily intertwined with cognitive processes. A prominent communication channel between bodily signals and brain structures is provided by baroreceptors. Their phasic activity associated with the cardiac phase has been shown to modulate cognitive control in socio-emotional contexts. However, whether this effect is specific to the affective dimension or impacts general cognitive control processes remains controversial. The aim of the present study is to investigate the effect of cardiac phase on different facets of cognitive control. We built a nonemotional cognitive control task to delineate mechanisms such as processing speed, response selection, response inhibition, and conflict monitoring. We showed that the systole (after the blood is ejected from the heart), compared to the diastole, was related to faster responses. Moreover, the cardiac phase dynamics also impacted response inhibition, with an increased probability of failure toward the middle of the course of systole. Although the reported effects were small in terms of magnitude, they highlight the influence of bodily states on abstract cognitive processes.

Young and Older Adults Benefit From Sleep, but Not From Active Wakefulness for Memory Consolidation of What-Where-When Naturalistic Events.

An extensive psychological literature shows that sleep actively promotes human episodic memory (EM) consolidation in younger adults. However, evidence for the benefit of sleep for EM consolidation in aging is still elusive. In addition, most of the previous studies used EM assessments that are very different from everyday life conditions and are far from considering all the hallmarks of this memory system. In this study, the effect of an extended period of sleep was compared to the effect of an extended period of active wakefulness on the EM consolidation of naturalistic events, using a novel (What-Where-When) EM task, rich in perceptual details and spatio-temporal context, presented in a virtual environment. We investigated the long-term What-Where-When and Details binding performances of young and elderly people before and after an interval of sleep or active wakefulness. Although we found a noticeable age-related decline in EM, both age groups benefited from sleep, but not from active wakefulness. In younger adults, only the period of sleep significantly enhanced the capacity to associate different components of EM (binding performance) and more specifically the free recall of what-when information. Interestingly, in the elderly, sleep significantly enhanced not only the recall of factual elements but also associated details and contextual information as well as the amount of high feature binding (i.e., What-Where-When and Details). Thus, this study evidences the benefit of sleep, and the detrimental effect of active wakefulness, on long-term feature binding, which is one of the core characteristics of EM, and its effectiveness in normal aging. However, further research should investigate whether this benefit is specific to sleep or more generally results from the effect of a post-learning period of reduced interference, which could also concern quiet wakefulness.

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.

The Hipp chronoscope versus the d'Arsonval chronometer: laboratory instruments measuring reaction times that distinguish German and French orientations of psychology.

Chronoscopes and chronographs were commonly used instruments that measured reaction times (RTs) in the first psychology laboratories. The Hipp chronoscope is commonly associated with the emergence of psychological laboratories in the late 19th century. This instrument is considered the key apparatus for the study of scientific psychology. Although German and American psychologists preferred the Hipp chronoscope, French psychologists of late 19th century favored another chronometer built by Jacques Arsène d'Arsonval (1851-1940). Unlike German and American psychologists, French psychologists demanded less precision in most experimental situations because they claimed that individual differences are very pronounced in a variety of situations. The advantage of the d'Arsonval chronometer was its portability and its simplicity. This article presents this chronometer and its advantages and drawbacks. The Hipp chronoscope and the d'Arsonval chronometer were the most commonly used apparatuses in Europe for the measurement of RTs until World War II, as is demonstrated by the catalogues of the time (Zimmermann and Boulitte).

[Emotion regulation and the cognitive decline in aging: beyond the paradox]. / Régulation émotionnelle face au déclin cognitif dans le vieillissement : un faux paradoxe ?

Aging is usually associated with cognitive decline, specifically of the executive functions supported by the frontal lobe. However, in line with observations about the preservation or even the increase of well-being with age, it has been suggested that emotion regulation efficiency follows the same developmental trajectory, remaining stable over time, or even increasing. Emotion regulation refers to a family of strategies aiming at modifying the nature, the intensity, the duration or the expression of emotions. These various strategies rely on different neurocognitive processes in order to be efficient. As these processes are differently affected by aging, some of those strategies appear more affected than others. Thus, elderly people tend to use more frequently situation selection strategies, such as avoiding potentially negative situations, while their ability to regulate an emotion using cognitive reappraisal (i.e., changing the meaning of the situation), a strategy drawing heavily on executive resources, appears less efficient than in younger people.

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.

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.