Biology subjects

Karami, A.

Publications and source records attributed to Karami, A..

8 recordsLinked to original sources

bioRxiv2026

Cortical localization and dynamics of elementary mathematical concepts

How the brain encodes abstract concepts remains poorly understood. Current theories propose that, in brains and computers alike, word meanings are represented by vectors of neural activation whose similarities reflect semantic relationships. Here, we tested whether this hypothesis also applies to abstract concepts of elementary mathematics. We collected behavioral, 7 Tesla functional MRI and magneto-encephalography (MEG) data and used representational similarity analysis to ask where, when and how fifteen concepts of integers, fractions, and geometric shapes are encoded in the adult brain. Behavioral similarity ratings revealed a rich conceptual structure characterized by both categorical distinctions (numbers vs shapes, integers vs fractions), a numerical distance effect for integers, and systematic correspondences between items involving the same number (e.g. three, third, triangle). Functional MRI identified a bilateral cortical network whose neural encodings of concepts correlated with their semantic similarity, overlapping with classic math-responsive regions and encompassing IPS and ITG as well as dorsolateral prefrontal cortex (dlPFC). A double dissociation was observed, with a preference for arithmetic in the right anterior intraparietal sulcus (IPS), and for geometry in left inferior temporal gyrus (ITG) and bilateral posterior IPS. MEG revealed that a semantic neural code common to written words and symbols is activated by about 230 ms, again primarily distinguishing integers, fractions and geometry concepts. Together, these findings suggest that mathematical concepts are organized in the brain along both categorical and numerical dimensions, with overlapping but partially distinct sites supporting arithmetic and geometry domains.

neuroscience↗

bioRxiv2026

A cortical semantic space integrating fractions and integers

How does the human brain represent the meaning of abstract symbols? Some theories postulate the existence of semantic spaces where concepts occupy positions that reflect their conceptual relationships. In the number domain, psychological evidence suggests that integers are represented along a mental number line which, with education, integrates higher-level number concepts such as fractions. To test this hypothesis, we recorded whole-brain 7T fMRI responses to integer and fraction symbols during a magnitude comparison task. Consistent with predictions, we found both behavioral and neural numerical distance effects. Activation vectors in intraparietal, inferior temporal, prefrontal, hippocampal, and parahippocampal cortices formed a two-dimensional semantic space organized by numerical magnitude and domain (fractions versus integers). Gaussian fits revealed a topographic map of numerical preferences in the anterior inferior parietal cortex, common to both domains. Our results suggest that, in educated adults, a joint semantic map integrates fractions and integers and supports symbolic magnitude representation and comparison.

neuroscience↗

bioRxiv2026

Reassessing Number-Detector Units in Convolutional Neural Networks

Convolutional neural networks (CNNs) have become essential models for predicting neural activity and behavior in visual tasks. However, their ability to capture higher-level cognitive functions, such as numerosity discrimination, remains debated. Numerosity, the ability to perceive and estimate the number of items in a visual scene, is often proposed to rely on specialized number-detector units within CNNs, analogous to number-selective neurons observed in the brain. In this study, we use CORnet, a biologically inspired CNN architecture inspired by the organization of the primate visual system. To address a limitation of classical Representational Similarity Analysis (RSA)--its assumption that all units contribute equally--we apply pruning, a feature selection approach that identifies the units most relevant for explaining behavioral similarity structure. Our results show that number-detector units are not critical for population-level representations of numerosity, challenging their proposed role in previous studies.

neuroscience↗

bioRxiv2025

Cell cycle- and EMT-dependent expression of Filip1L controls invadopodia in breast cancer cells

Invadopodia are actin- and protease-rich membrane structures that enable cancer cells to degrade extracellular matrix (ECM). Invadopodia activity is cell cycle-dependent, but how their regulation across the cell cycle is influenced by epithelial-to-mesenchymal transition (EMT) remains unclear. We show that as the EMT progresses, cell engagement in invadopodia-mediated ECM degradation shits from G2 phase in Early E/M cells to G1 phase in Late E/M or M cells. Using bulk mRNA sequencing of Early- versus Late- E/M cells sorted by cell cycle phase, we identified FILIP1L as an EMT- and cell cycle-regulated candidate whose expression peaks in the invasive phase of each cell state: G2 in Early E/M cells and G1 in Late E/M cells. We next demonstrated that FILIP1L is a novel invadopodia component, whose loss increases ECM degradation while impairing migration and 3D invasion. In mouse models, FILIP1L KD tumors develop fewer metastatic colonies, suggesting that FILIP1L supports productive invasion by coordinating between invadopodia and migratory cell states. FILIP1L expression increases with EMT progression and correlates with poor outcomes in breast cancer patients. Together, these findings identify a previously unrecognized link between EMT, cell cycle and invadopodia and establish FILIP1L as the key regulator of this process.

cancer biology↗

bioRxiv2025

Numerosity Is Directly Sensed and Dynamically Transformed in the Human Brain: Evidence from MEG-MRI Fusion

Humans can estimate the number of objects in a scene within a fraction of a second, suggesting that numerosity is encoded rapidly and directly by the visual system. Yet how this encoding unfolds over time and interacts with other visual features remains unclear. Here, we combined magnetoencephalography (MEG) with time-resolved representational similarity analysis (RSA) and MEG-fMRI fusion to track how numerosity is represented in the brain over time. We also used multidimensional scaling (MDS) to visualize the evolving patterns of neural activity. Two main findings emerged. First, numerosity exhibited the hallmarks of a primary perceptual attribute: its neural signature appeared rapidly after stimulus onset, preceding the encoding of non-numeric features that could otherwise define number. Second, Visualization of the neural patterns using MDS suggested a temporal transformation in representational geometry, reflecting the engagement of two distinct coding schemes- an early, linear number line, consistent with a "summation code", dominating activity in occipital regions, and a later, curved number line, consistent with "numerosity-tuned code", emerging more strongly in associative areas along the dorsal stream. Together, these findings demonstrate that numerosity processing is encoded directly from the visual image and unfolds through a rapid hierarchical transformation, from a broad quantity signal to a finely tuned, number-specific code, linking perceptual encoding to higher-level numerical abstraction.

neuroscience↗

bioRxiv2023

Neural codes for visual numerosity independent of other quantities are present both in the dorsal and in the ventral stream of the human brain

Visual numerosity, a feature of visual sets traditionally associated with the parietal cortex, has recently been suggested to be encoded in a broader range of cortical regions, including early visual and associative cortices of both streams. However, a clear picture of how numerosity information is represented alongside other non-numeric features across the cortex is still lacking. To address this, we conducted a whole-brain 3T fMRI study with thirty-one adult subjects (eighteen females) engaged in a numerosity estimation task involving visual sets varying in number, item size, total item area, total field area, and density, thus allowing us to perform a tight control of the stimulus properties. Using model-based semipartial correlation representational similarity analyses, we found that numerosity is represented independently of other visual properties already in early visual areas and amplified in both retinotopic and non-retinotopic associative areas along both the dorsal and ventral streams. Dimensionality reduction analyses of BOLD activity patterns revealed clearly distinct neural representational geometries of numerosity across brain regions: a one-dimensional representation of numerical rank in early visual and in associative retinotopic regions of the ventral stream, and a curved structure encoding rank-order together with distance to end-point in associative regions of both the dorsal and ventral stream. These findings indicate that numerosity is represented over and above other visual features broadly in the brain but with substantially different neural coding schemes across regions, and are discussed in light of two non necessarily exclusive interpretations.

neuroscience↗

bioRxiv2023

Fragrance and color production by corona and perianth tissues of Iranian narcissus genotypes (Narcissus tazetta L.)

Flower color, shape and scent are the most attracting factors for consumers in the floriculture industry. The most fragrant Iranian narcissi (Narcissus tazetta L.) grown in natural habitats are Shahla, Meskinak, and Porpar genotypes. The present study was conducted to evaluate the color, scent, and also their interaction separately in corona and perianth of eleven Iranian narcissus accessions, for a better understanding of the bio-physiological differences in these tissues. For this purpose, the volatile organic compounds (VOCs) were analyzed using Headspace GCMS (gas chromatography/mass spectrometry); and total carotenoid, color values, and tissue thickness were measured in both perianth and corona tissues. Sensory analysis for corona and perianth was also conducted to evaluate scent perception. Besides, the expression of genes related to scent and color in corona and perianth was evaluated. Moreover, epidermal cells of perianth and corona were assessed by polarized light and SEM microscopy. The two most abundant compounds in both tissues were E-{beta}-ocimene and benzyl acetate, respectively; among which the first compound was higher in perianth, while the second one was higher in corona. Among identified VOCs, -terpineol, acetic acid, 2-phenylethyl ester, -pinene, {beta}-myrcene, and limonene were detected in corona of all genotypes of N. tazetta; however, these compounds were not identified in perianth of every genotypes. In corona, the negative correlations between the measured values of E-{beta}-ocimene and carotenoid and also, between the expression level of ocimene synthase and PSY (Phytoene synthase) with DXR (1-Deoxy-D-xylulose 5-phosphate reductoisomerase) suggested that there might be a competition between carotenoids and monoterpenes precursors in the MEP (methyl-D-erythritol phosphate) pathway. Volatile organic compound, color, scent emission, fresh weight and thickness of tissue were different in perianth and corona; while the surface coverage (with epidermal conical cells) were similar in these tissues. The findings of this research illustrated clearly for the first time that while both perianth and corona play important roles in scent production, corona has a more distinguished role in greater production of scent and color in Iranian narcissus flowers.

plant biology↗

bioRxiv2021

Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium and age-associated mitochondrial dysfunction

Stratified squamous epithelium of the esophagus is comprised of basal keratinocytes that execute a terminal differentiation program in overlying suprabasal and superficial cell layers. Although morphologic progression coupled with expression of specific molecular markers has been characterized along the esophageal epithelial differentiation gradient, the molecular heterogeneity within the cell types along this trajectory has yet to be classified at the level of single cell resolution. To explore the molecular characteristics of esophageal keratinocytes along the squamous differentiation continuum, we performed single cell RNA-Sequencing transcriptomic profiling of 7,972 cells from murine esophageal epithelial sheets. We identified 8 distinct cell clusters in esophageal epithelium, unveiling an unexpected level of diversity, particularly among basal cells. We further mapped the cellular pathways and lineage trajectories within basal, suprabasal, and superficial clusters as well as within the heterogeneous basal cell populations, providing a comprehensive molecular view of esophageal epithelial cells in the context of squamous differentiation. Finally, we explored the impact of tissue aging upon esophageal epithelial cell clusters and demonstrated that mitochondrial dysfunction is a feature of aging in normal esophageal epithelium. These studies provide an unparalleled molecular perspective on murine esophageal keratinocytes that will serve as a valuable resource for dissecting cell type-specific roles in esophageal biology under conditions of homeostasis, aging, and tissue pathology.

molecular biology↗