Biology subjects

Yazdani, Z.

Publications and source records attributed to Yazdani, Z..

4 recordsLinked to original sources

bioRxiv2026

Graph-based characterization of in vitro neuronal network maturation using machine learning and digital holographic microscopy

SignificanceDigital Holographic Microscopy (DHM) provides label-free quantitative phase images (QPIs) of living cells and has become a powerful tool for studying cellular morphology and dynamics. While most DHM studies have focused on cell-level analysis, the quantitative characterization of neuronal network organization and maturation from DHM images remains largely unexplored, highlighting the need for dedicated computational approaches. AimWe aimed to develop an automated framework combining deep-learning-based image analysis and graph theory to quantitatively characterize the organization, connectivity, and maturation of neuronal networks in primary rat cortical cultures imaged by DHM. ApproachTwo U-Net convolutional neural networks were trained on manually annotated DHM phase images to segment neuronal cell bodies and neurites. The resulting segmentation maps were used to infer putative morphological connections between neurons and generate graph representations of neuronal networks, referred to as graph fingerprints. A panel of 18 connectomics-inspired graph features was then computed to characterize local and global properties of network organization across four stages of culture maturation. ResultsThe mean area under the receiver operating characteristic curves was 0.98 for cell-body and 0.91 for neurite segmentation, indicating near-perfect identification. Graph-theoretical analysis revealed reproducible topological changes during network maturation in vitro, including increased density, reduced modularity, and progressive network integration. Correlation analysis showed that the 18 graph features grouped into two highly correlated families. A Random Forest classifier identified density and modularity as the most informative descriptors, achieving an accuracy of 87% in classifying maturation stages of neuronal cultures. ConclusionsOur results demonstrate that combining DHM, deep-learning-based segmentation, and graphtheoretical analysis enables quantitative characterization of neuronal network organization and maturation from label-free phase images. This framework provides a foundation for future studies of pharmacological experiments, neuronal network phenotyping, and human induced pluripotent stem cell (hiPSC)-derived neuronal cultures, where quantitative assessment of network organization remains a major challenge.

neuroscience↗

bioRxiv2026

Protracted functional and structural reorganization of human prefrontal cortex supports lateralized category geometries

Despite being visually responsive, how prefrontal cortex represents visual categories across development and how this compares to posterior visual cortex remains unknown. Here, we show that ventrolateral prefrontal cortex (VLPFC) follows a fundamentally distinct developmental trajectory. Using functional and quantitative MRI in children and adults, we demonstrate that VLPFC exhibits reliable and structured category-selective responses in childhood that undergo prolonged reorganization into mature, hemisphere-specific representational geometries. Right VLPFC progressively organizes categories along an animate-inanimate axis, while left VLPFC consolidates a word-selective organization, a lateralization that strengthens across development. This restructuring contrasts sharply with ventral temporal cortex (VTC), which exhibits bilaterally organized, adult-like category structure in childhood. Critically, prefrontal representational structure emerges in alignment with conserved folding patterns of the precentral and inferior frontal sulci, suggesting that cortical anatomy provides a stable scaffold for the maturation of abstract representations. Quantitative MRI further reveals a non-linear trajectory of tissue development in right VLPFC, marked by adolescent reductions in macromolecular content and increased microstructural heterogeneity in adulthood, a pattern not observed in VTC. Together, these findings demonstrate that VLPFC undergoes prolonged, anatomically constrained refinement of category-related geometry characterized by hemisphere-specific taxonomies, rather than simply inheriting representational structure from sensory cortex. O_LIUnlike VTC (which shows early, bilateral, and stable category organization), VLPFC contains reliable, category-selective representations from childhood that undergo prolonged, hemisphere-specific developmental refinement rather than simple amplification C_LIO_LIRight VLPFC progressively consolidates an animate-inanimate representational axis across development, while left VLPFC establishes an early, stable word-selective organization consistent with language network maturation C_LIO_LIFunctional boundaries in VLPFC align with conserved intrasulcal folding motifs (plis de passage), demonstrating that anatomical scaffolding of category-selective responses extends beyond sensory cortex to prefrontal association cortex C_LIO_LIRight VLPFC undergoes adolescent pruning of cortical tissue microstructure diverging sharply from the continuous tissue proliferation observed in ventral temporal cortex C_LI

neuroscience↗

bioRxiv2024

Microstructural pruning in human prefrontal cortex scaffolds its functional reorganization across development

Neural representations in occipitotemporal cortex emerge during development in response to visual experience with ecological stimulus categories, such as faces or words. While similar category-selective representations have also been observed in the frontal lobe, how they emerge across development, whether current models of brain development extend to prefrontal cortex, and the extent to which such high-level representations are anatomically consistent across the lifespan is unknown. Through a combination of functional and quantitative MRI scans, we observe previously undescribed cortical folding patterns in human-specific inferior frontal cortex whose consistency reveals that childhood representations for visual object categories rearrange into stable adulthood patterns. This functional restructuring was distinct from occipitotemporal cortex where adult-like response patterns only scale in magnitude across development. The unique form of functional development in prefrontal cortex was accompanied by restructuring of cortical tissue properties: macromolecules are pruned across adolescence in prefrontal cortex while they proliferate in temporal cortex. These results suggest visual representations in distinct cortical lobes undergo distinct developmental trajectories, and that human-specific prefrontal cortex shows an especially protracted maturational process that necessitates late-stage tissue restructuring detectable in the living brain.

neuroscience↗

bioRxiv2020

Design an efficient multi-epitope peptide vaccine candidate against SARS-CoV-2: An in silico analysis

BackgroundTo date, no specific vaccine or drug has been proven to be effective for SARS-CoV-2 infection. Therefore, we implemented immunoinformatics approach to design an efficient multi-epitopes vaccine against SARS-CoV-2. ResultsThe designed vaccine construct has several immunodominant epitopes from structural proteins of Spike, Nucleocapsid, Membrane and Envelope. These peptides promote cellular and humoral immunity and Interferon gamma responses. In addition, these epitopes have antigenicity ability and no allergenicity probability. To enhance the vaccine immunogenicity, we used three potent adjuvants; Flagellin, a driven peptide from high mobility group box 1 as HP-91 and human beta defensin 3 protein. The physicochemical and immunological properties of the vaccine structure were evaluated. Tertiary structure of the vaccine protein was predicted and refined by I-Tasser and galaxi refine and validated using Rampage and ERRAT. Results of Ellipro showed 242 residues from vaccine might be conformational B cell epitopes. Docking of vaccine with Toll-Like Receptors 3, 5 and 8 proved an appropriate interaction between the vaccine and receptor proteins. In silico cloning demonstrated that the vaccine can be efficiently expressed in Escherichia coli. ConclusionsThe designed multi epitope vaccine is potentially antigenic in nature and has the ability to induce humoral and cellular immune responses against SARS-CoV-2. This vaccine can interact appropriately with the TLR3, 5, and 8. Also, this vaccine has high quality structure and suitable characteristics such as high stability and potential for expression in Escherichia coli.

immunology↗