Biology subjects

Afyouni, A.

Publications and source records attributed to Afyouni, A..

3 recordsLinked to original sources

bioRxiv2026

Agent-optimized GPU polygenic scoring at cohort scale

A polygenic score (PGS) is a unitless weighted sum of allele dosages, interpretable only as a percentile within a reference distribution. Evaluating risk across models requires scoring each individual against a whole reference panel, but current CPU pipelines process targets or models sequentially, making full cross-product calculations prohibitively expensive. We reformulated PGS calculation as a cohort-wide sparse matrix product on a GPU and optimized it via an autonomous coding agent under read-only inputs, cold starts, and strict numerical validation against pgsc_calc. The scorer was "trained" by the agent accessing synthetic data and real 1000 Genomes data. On a synthetic benchmark, the scorer achieved a 10.6-fold speedup during the training course (184.9 s to 17.4 s) and ran 71-fold faster than pgsc_calc. However, on held-out real genomes, the synthetic-trained scorer was 15.3-fold slower than the real-data-trained version and diverged significantly from pgsc_calc (maximum absolute difference of 3.7x10-1 vs. 3.1x10-4). Three replications of the synthetic loop from an identical prompt showed that agent optimization trajectory variance explains 91 to 96% of total wall-clock variance, against 0 to 2.6% for the data sampled and 0.2 to 3.3% for repeated execution. A memory-bounded rebuild then scored all the 3,202 1000 Genome genotypes against all 5,385 models in 6.5 h within a 72 GB memory cap, released here as a frozen scoring manifest with ancestry-stratified reference distributions for the whole PGS Catalog

bioinformatics↗

bioRxiv2020

Action Observation Network activity related to object-directed and socially directed actions in Adolescents

The Action Observation Network (AON) encompasses brain areas consistently engaged when we observe others actions. Although the core nodes of the AON are present from childhood, it is not known to what extent they are sensitive to different action features during development. As social cognitive abilities continue to mature during adolescence, the AON response to socially-oriented actions, but not to object-related actions, may differ in adolescents and adults. To test this hypothesis, we scanned with functional magnetic resonance imaging (fMRI) 28 typically-developing teenagers and 25 adults while they passively watched videos of hand actions varying along two dimensions: sociality (i.e. directed towards another person or not) and transitivity (i.e. involving an object or not). We found that observing actions recruited the same fronto-parietal and occipito-temporal regions in adults and adolescents. The modulation of voxelwise activity by the social or transitive nature of the action was similar in both groups of participants. Multivariate pattern analysis, however, revealed that the accuracy in decoding the social dimension from the brain activity patterns, increased with age in lateral occipital and parietal regions, known to be involved in semantic representations of actions, as well as in posterior superior temporal sulcus, a region commonly associated with perception of high level features necessary for social perception. Change in decoding the transitive dimension was observed only in the latter region. These findings indicate that the representation of others actions, and in particular their social dimensions, in the adolescent AON is still not as robust as in adults. Significance statementThe activity of the action observation network in the human brain is modulated according to the purpose of the observed action, in particular the extent to which it involves interaction with an object or another person. How this conceptual representation of actions is implemented during development is largely unknown. Here, using multivoxel pattern analysis of fMRI data, we discovered that, while the action observation network is in place in adolescence, the fine-grain organization of its posterior regions is less robust than in adults to decode the social or transitive dimensions of an action. This finding highlights the late maturation of social processing in the human brain.

neuroscience↗

bioRxiv2018

Imposing a curfew on the use of screen electronic devices improves sleep and daytime vigilance in adolescents.

The use of screen electronic devices (SED) in the evening negatively affects sleep. Yet, sleep is known to be essential for brain maturation and a key factor for good academic performance, and thus is particularly critical during childhood and adolescence. While previous studies reported correlations between SED use and sleep impairments, the causal relationship between SED use and sleep in adolescents remains unclear. Using actigraphy and daily questionnaires in a large sample of students (12 to 19 years old), we assessed SED use and sleep habits over one month, including a two-week baseline phase and a two-week interventional phase, where participants were asked to stop screen use after 9 pm during pre-school nights. During the interventional phase, we found that reduction in time spent on SED after 9 pm correlated with earlier sleep onset time and increased total sleep duration. The latter led to improved daytime vigilance. We also observed that the beneficial impact of the intervention on sleep was influenced by catechol-O-methyltransferase gene (COMT) Val158Met polymorphism, which is implicated in the dopaminergic modulation of human behaviors, including wake and sleep regulation. These findings provide evidence that restricting SED use in the evening represents a valid and promising approach for improving sleep duration in adolescents, with potential implications for daytime functioning and health.\n\nSTATEMENT OF SIGNIFICANCEWith the emergence of smartphones and other connected devices, adolescents spend a lot of time on screen electronic devices (SED), especially during the evening. We report that time spent on SED after 9 pm negatively correlates with sleep onset time, sleep duration as well as mood, body weight, and academic performance. Such observable correlations urge for educational strategies to address the chronic lack of sleep observed in todays adolescent populations. Here we also show that limiting the use of SED after 9 pm improves sleep duration and daytime vigilance in most adolescents. This simple education recommendation pertaining to sleep hygiene can be implemented by every household, yielding direct positive effects on sleep, and presumed benefits for health and daytime functioning.

neuroscience↗