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Ancestral sequence reconstruction (ASR) is typically performed using homogeneous evolutionary models, which assume that the same substitution propensities affect all sites and lineages. These assumptions are routinely violated: heterogeneous structural and functional constraints favor different amino acid states at different sites, and these constraints often change among lineages as epistatic substitutions accrue at other sites. To evaluate how realistic violations of the homogeneity assumption affect ASR, we developed site-specific substitution models and parameterized them using data from deep mutational scanning experiments on three protein families; we then used these models to perform ASR on the empirical alignments and on alignments simulated under heterogeneous conditions derived from the experiments.
View Article and Find Full Text PDFCreativity and Body: Living Metaphors in the Context of People Undergoing Heart Transplantation.
Integr Psychol Behav Sci
January 2025
Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
This article explores the embodied dimension of authoring life trajectories for individuals who have undergone heart transplantation. Confronting the radical otherness of existential finitude can create a rich context for examining the relationships between authorship, corporeality, and creative processes. By integrating Merleau-Ponty's phenomenology of the body with Susanne Langer's theory of affective semiosis and presentational signs, this work aims to foster a productive dialogue between these perspectives, grounded in Semiotic Cultural Psychology, which meta-theoretically synthesizes a diverse range of knowledge on the transformative interaction between individuals and culture.
View Article and Find Full Text PDFScene categorization by Hessian-regularized active perceptual feature selection.
Sci Rep
January 2025
College of Computer Sciences, Anhui University, Hefei, 230039, China.
Decoding the semantic categories of complex sceneries is fundamental to numerous artificial intelligence (AI) infrastructures. This work presents an advanced selection of multi-channel perceptual visual features for recognizing scenic images with elaborate spatial structures, focusing on developing a deep hierarchical model dedicated to learning human gaze behavior. Utilizing the BING objectness measure, we efficiently localize objects or their details across varying scales within scenes.
View Article and Find Full Text PDFCreating a culture, not just a space-A qualitative investigation into reflective practice groups in inpatient mental health settings from the perspectives of facilitators and attendees.
PLoS One
January 2025
Division of Psychiatry, University College London, London, United Kingdom.
Article Synopsis
- The study investigates the role of reflective practice groups in inpatient mental health settings, focusing on their impact on staff well-being and clinical practice amidst staff shortages.
- Interviews with fifteen participants revealed that these groups can enhance staff reflection and team cohesion, while factors like group composition and support for facilitators can influence engagement.
- The findings suggest actionable changes to improve staff participation in these groups and emphasize the need for further research on their effectiveness in mental health care.
The Replicability Crisis and Human Agency in the Neo-Structured World.
Integr Psychol Behav Sci
January 2025
Department of Psychology, St. Petersburg State University, St. Petersburg, Russian Federation.
The paper analyzes current discussions concerning the so called "replicability crisis" - a notion describing difficulties in attempts to confirm existing research findings by their additional scrutiny or by new empirical studies. We propose interpretation that this "crisis" may be seen as a manifestation of the increasing inconsistency between, on the one hand, the outdated views on a human being and social structures dominating in the academic mainstream across various disciplines, including psychology and sociology, and, on the other hand, the reality of the emerging new stage of societal evolution, neo-structuration, which brings to the forefront individual agency. Our analysis suggests the possibilities for the future inter-disciplinary paradigmatic shift, which implies putting in the center of research not the idea of a constant or predictably developing individual in the context of solid external structures operating in line with a presumably sustainable "progress".
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