Biology subjects

Shafi, M.

Publications and source records attributed to Shafi, M..

3 recordsLinked to original sources

bioRxiv2025

GRAYU: Graph-based Database integrating Ayurvedic formulations, medicinal plants, phytochemicals and diseases

The translation of Indias extensive traditional knowledge on indigenous medicinal plants into modern therapeutic solutions is contingent upon a systematic framework. While traditional Indian medicine offers a rich source of therapeutic leads, this knowledge is often not structured for modern computational analysis, creating a barrier to systematic drug discovery. To this end, we present GRAYU, a curated and comprehensive online database that integrates data across multiple categories, connecting 1039 traditional formulations to 12,949 indigenous plants, 129,542 phytochemicals, and 13,480 indicated diseases. It also provides insights into 1,382,362 plant-phytochemical, 116,824 plant-disease, 2,405 plant-formulation, and 4,087 formulation-disease associations. Case studies on phytochemical analogs, sustainable plant substitution, and disease-network pharmacology showcased the potential of integrative graphs to decode shared molecular signatures and therapeutic networks across traditional Ayurvedic formulations. GRAYU represents a user-friendly resource for researchers to investigate complex bio-associations and formulate novel therapeutic hypotheses, with insights from traditional Indian medicine. GRAYU is available at https://caps.ncbs.res.in/GRAYU/.

bioinformatics↗

bioRxiv2024

Neurophysiological signatures of default mode network dysfunction and cognitive decline in Alzheimer disease.

Neural hyper-excitability and network dysfunction are neurophysiological hallmarks of Alzheimers disease (AD) in animal studies, but their presence and clinical relevance in humans remain poorly understood. We introduce a novel perturbation-based approach combining transcranial magnetic stimulation and electroencephalography (TMS-EEG), alongside resting-state EEG (rsEEG), to investigate neurophysiological basis of default mode network (DMN) dysfunction in early AD. While rsEEG revealed global neural slowing and disrupted synchrony, these measures reflected widespread changes in brain neurophysiology without network-specific insights. In contrast, TMS-EEG identified network-specific local hyper-excitability in the parietal DMN and disrupted connectivity with frontal DMN regions, which uniquely predicted distinct cognitive impairments and mediated the link between structural brain integrity and cognition. Our findings provide mechanistic insights into how network-specific neurophysiological disruptions contribute to AD-related cognitive dysfunction. Perturbation-based assessments hold promise as novel markers of early detection, disease progression, and target engagement for disease-modifying therapies aiming to restore abnormal neurophysiology in AD.

neuroscience↗

bioRxiv2020

Greater TMS-evoked frontoparietal effective connectivity is correlated with better cognitive performance

Fronto-parietal activity has been related to fluid intelligence and flexible cognitive control. However, causal insights on this relation are lacking. We used real-time integration of MRI-guided TMS and EEG to characterize the spatial and temporal properties of signal propagation between these two regions and relate them to cognitive performance. 31 healthy adults (55 {+/-}6 years, 20 female) underwent TMS-EEG and a full cognitive assessment. Local and propagated current from 5 source space-reconstructed scouts ipsilateral to two stimulation sites (pre frontal cortex (PFC) and inferior parietal lobule (IPL)) was quantified in two-time windows (15-40ms and 40-80ms) and related to domain-general (global cognition) and domain-specific (memory, working memory, reasoning, flexibility, lexical access and visuo-spatial) cognitive functions. TMS-evoked activity from stimulation of the PFC and the IPL resulted in local and distributed activity across frontoparietal regions. TMS-evoked activity in local regions was not correlated with cognitive functions. In response to TMS of the PFC, propagated current to the distal superior parietal scout in the first 15-40ms was significantly associated with global cognition ({beta} = 2.63, SE = .898, p = .008, R2 = .31). Similarly, following TMS of the IPL, propagation to the middle prefrontal gyrus scout (15-40ms) was significantly associated with global cognition ({beta} = 2.67, SE = 1.289, p = .025, R2 = .27). In an exploratory step, domain-specific correlations were seen in the PFC condition. Locally evoked activity measured via source space reconstruction from TMS of two association hubs is not associated with cognitive functions. However, the propagation of the TMS pulse through frontoparietal connections is associated with overall cognitive ability. These associations are driven by a number of cognitive domains in the PFC stimulation condition.

neuroscience↗