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Ahuja, R.

Publications and source records attributed to Ahuja, R..

3 recordsLinked to original sources

Distinct contributions of memorability and object recognition to the representational goals of the macaque inferior temporal cortex

The primate inferior temporal (IT) cortex, at the apex of the ventral visual stream, encodes information that supports diverse representational goals--from recognizing objects to determining which images are likely to be remembered. Specific artificial neural networks (ANNs), that currently serve as the leading computational hypotheses of ventral stream processing, are typically trained exclusively for object recognition. We asked whether incorporating image memorability as an additional optimization objective could improve ANN-brain alignment. Models optimized for memorability explained additional, non-overlapping variance in IT responses beyond that captured by recognition-optimized networks, indicating that memorability and recognition rely on partly independent dimensions of IT representation. Notably, these models also exhibited fewer non-brain-like units, bringing their representational geometry closer to that of IT. Furthermore, networks jointly optimized for both objectives were more predictive of human memorability than memorability-only models, while maintaining their alignment with human object recognition performance patterns. Together, these findings suggest that IT encodes multiple representational goals and that models trained solely for recognition provide an incomplete account of ventral stream computation. SignificanceBrain regions often serve multiple representational goals, and identifying those goals is critical because they provide the key to building better encoding models of the system. The primate ventral visual stream has traditionally been understood as a pathway for object recognition, with the inferior temporal (IT) cortex regarded as its core substrate. However, IT responses also predict image memorability--a robust phenomenon whereby some images are consistently remembered better than others. Here we show that memorability constitutes a separable representational goal of IT. ANNs optimized for memorability explained neural variance not captured by recognition models, and the two objectives produced distinct representational geometries. Critically, models jointly optimized for both recognition and memorability provided the best match to IT responses, improved prediction of human memorability, and preserved recognition performance. These findings highlight memorability as an organizing principle of IT and demonstrate that multi-goal optimization yields more brain-like computational models of vision.

neuroscience↗

Cis-regulatory variation in ISOCHORISMATE SYNTHASE 1 modulates systemic salicylic acid biosynthesis and systemic acquired resistance in plants

Systemic acquired resistance (SAR) is a long-distance immune response that protects uninfected plant tissues following a localized pathogen attack. In the model plant Arabidopsis thaliana, SAR depends on the systemic accumulation of salicylic acid (SA), mediated by the transcription factor CCA1 HIKING EXPEDITION (CHE), which activates the SA biosynthetic gene ISOCHORISMATE SYNTHASE1 (ICS1). However, the conservation and functional significance of the CHE-ICS1 regulatory module across plant species remain poorly understood, particularly in the Brassicaceae, where ICS1 is the major contributor to SA biosynthesis among two known pathways: the ICS1 and PHENYLALANINE AMMONIA-LYASE (PAL) routes. Here, we identify natural variation in cis-regulatory elements within the ICS1 promoter that affects CHE binding across species. In multiple Brassicaceae species with divergent cis-element sequences, CHE fails to regulate ICS1, leading to the absence of systemic ICS1 induction and SA accumulation following pathogen infection. Despite this deficiency, SAR still occurs in these species, albeit to a lesser extent than in species with successful systemic induction of SA mediated by an intact CHE-ICS1 regulatory module. Interestingly, introducing the CHE-ICS1 module into species lacking this interaction confers systemic SA accumulation, highlighting the potential to enhance systemic immunity through cis-element modification. Our findings demonstrate that sequence variation in a cis-regulatory element underlies the interspecies diversification of SAR regulatory mechanisms and highlight the evolutionary plasticity of plant immune signaling. This study provides a molecular framework for engineering enhanced systemic immunity in crops, particularly within the Brassicaceae, through the targeted modification of cis-regulatory elements that regulate SA biosynthesis.

plant biology↗

AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes

Focal amplifications in the cancer genome, particularly extrachromosomal DNA (ecDNA) amplifications, are emerging as a pivotal event in cancer progression across diverse cancer contexts, presenting a paradigm shift in our understanding of tumor dynamics. Simultaneously, identification of the various modes of focal amplifications is bioinformatically challenging. We present AmpliconSuite, a collection of tools that enables robust identification of focal amplifications from whole-genome sequencing data. AmpliconSuite includes AmpliconSuite- pipeline; utilizing the AmpliconArchitect (AA) method, and AmpliconRepository.org; a community- editable website for the sharing of focal amplification calls. We also describe improvements made to AA since its initial release that improve its accuracy and speed. As a proof of principle, we utilized publicly available pan-cancer datasets encompassing 2,525 tumor samples hosted on AmpliconRepository.org to illustrate important properties of focal amplifications, showing ecDNA has higher copy number, and stronger oncogene enrichment, compared to other classes of focal amplifications. Finally, we illustrate how AmpliconSuite-pipeline enables delineation of the various mechanisms by which ecDNA forms.

bioinformatics↗