Biology subjects

Habes, M.

Publications and source records attributed to Habes, M..

5 recordsLinked to original sources

bioRxiv2025

An extended structure of the intracellular domain of the Torpedo nicotinic acetylcholine receptor and its proposed interactions with rapsyn

To gain insight into the interactions between rapsyn and the nAChR that induce clustering at the post-synaptic membrane, we refined a cryo-EM dataset using an intracellular domain focused strategy to obtain a 3.0 [A] map with the most extensive density yet for the intracellular domain of the Torpedo nAChR. The improved map allowed us to extend the structure beyond the MX -helix and prior to the MA -helix of the intracellular domain. The new structure defines a sharp N-terminal boundary of each MA -helix to place agrin-dependent phosphorylated tyrosines unambiguously within the flexible regions of the MX-MA loops. Two distinct conformations of the {delta} M4 -helix were also resolved, indicating that M4 conformational heterogeneity reflects intrinsic flexibility rather than a change in gating state. The new structural constraints defined for the MX-MA loop were then used to evaluate AlphaFold3-predicted full-length models of the nAChR, rapsyn, and various rapsyn-nAChR complexes, identifying a consistent, asymmetric 3:1 binding architecture where each rapsyn is always sandwiched between the MX-MA loops from two subunits and where each phospho-tyrosine is lodged in a cationic pocket formed by conserved residues implicated in congenital myasthenic syndromes. The defined architecture fits published cryo-ET maps of Torpedo post-synaptic membranes and explains how both phosphorylated tyrosines and myasthenic syndrome-causing rapsyn mutations modulate receptor clustering.

neuroscience↗

bioRxiv2025

Advancing Fair and Explainable Machine Learning for Neuroimaging Dementia Pattern Classification in Multi-Ethnic Populations

Dementia, a degenerative disease affecting millions globally, is projected to triple by 2050. Early and precise diagnosis is essential for effective treatment and improved quality of life. However, current diagnostic approaches frequently demonstrate inconsistent precision and impartiality, particularly among diverse cultural groups. This study investigates performance discrepancies in dementia classification among White American, African American, and Hispanic populations. We reveal significant cross-group bias, particularly when models trained on one group are tested on another. To address this, we introduce a novel combination of few-shot learning and domain alignment to improve model adaptability across underrepresented populations. Our results show that these techniques substantially reduce inter-group performance gaps, especially between White American and Hispanic cohorts. This finding highlights the crucial need for fairness-aware strategies and the inclusion of diverse populations in training data to ensure accurate and equitable dementia diagnoses.

neuroscience↗

bioRxiv2024

A New Halogenated Solvent For Ex Vivo Magnetic Resonance Imaging

Magnetic Resonance Imaging (MRI) is a prominent non-invasive imaging technique. Structural MRI, the most common MRI modality, interacts with the hydrogen nuclei in samples, also called protons. When using structural MRI to scan ex vivo tissues, the biological samples are often placed in proton-free liquids containing no hydrogen atoms to obtain clean images that do not require background removal. Several proton-free liquids have been used during the last two decades, but they are all per- and polyfluoroalkyl substances (PFAS), and PFAS have recently been recognized as a significant environmental concern. To find replacement solutions, new families of proton-free liquids without fluorine atoms will need to be investigated for stability and safety and to check potential effects on subsequent tissue staining. The present work is a preliminary step in that direction. We validate the MRI properties of a broadly used, affordable, non-PFAS, proton-free solvent that has, as far as we know, never been considered for ex vivo MRI scanning.

neuroscience↗

bioRxiv2019

Disconnectome Associated with Progressive Ischemic Periventricular White Matter Lesions

Periventricular white matter (PVWM) hyperintensities on T2-weighted MRI are ubiquitous in older adults and associated with dementia. Efforts to determine how PVWM lesions impact structural connectivity to impinge on brain function remain challenging in part because white matter tractography algorithms for diffusion tensor imaging (DTI) may lose fidelity in the presence of lesions. We used a "virtual lesion" approach to characterize the "disconnectome" associated with periventricular white matter (PVWM) lesions. We simulated progressive ischemic PVWM lesions using sub-threshold cerebral blood flow (CBF) masks derived from a previously published group-averaged map acquired from N=436 middle aged subjects in which the lowest CBF values were seen in PVWM and morphologically recapitulated the spatial pattern of PVWM hyperintensities seen in typical aging. We mimicked the age-dependent evolution of PVWM lesion burden by varying the threshold applied to the CBF map. We found that the optic radiations, inferior fronto-occipital fasciculus, inferior longitudinal fasciculus, corpus callosum, temporopontine tract and fornix were affected in early simulated PVWM lesion burdens, and that the connectivity of subcortical, cerebellar, and visual regions were significantly disrupted with increasing simulated PVWM lesion burdens. We also validated the use of virtual lesions to simulate the disconnectome due to WM hyperintensities in a cognitively normal elderly cohort (N=46) by evaluating correlations between structural and functional connectomes. The virtual lesion approach provides new insights into the spatial-temporal changes of the brain structural connectome under progressive PVWM burdens during normal aging. Significance StatementWe determined the disconnectomes caused by periventricular white matter (PVWM) lesions using the "virtual lesion" approach. We validated the approach using lesions, DTI and resting-state fMRI data from elderly subjects. We simulated disconnectome of progressive PVWM lesions using cerebral blood flow (CBF) masks in PVWM region with normative DTI data, which provides specificity for an ischemic mechanism and begins to address the possibility that connectivity may be affected by reduced CBF prior to the development of overt lesions on T2-weighted FLAIR MRI. The current study presented new insights into the spatial-temporal evolutions of the brain structural connectome under progressive PVWM burdens under normal aging.

neuroscience↗

bioRxiv2019

Harmonization of large multi-site imaging datasets: Application to 10,232 MRIs for the analysis of imaging patterns of structural brain change throughout the lifespan

As medical imaging enters its information era and presents rapidly increasing needs for big data analytics, robust pooling and harmonization of imaging data across diverse cohorts with varying acquisition protocols have become critical. We describe a comprehensive effort that merges and harmonizes a large-scale dataset of 10,232 structural brain MRI scans from participants without known neuropsychiatric disorder from 18 different studies that represent geographic diversity. We use this dataset and multi-atlas-based image processing methods to obtain a hierarchical partition of the brain from larger anatomical regions to individual cortical and deep structures and derive normative age trends of brain structure through the lifespan (3 to 96 years old). Critically, we present and validate a methodology for harmonizing this pooled dataset in the presence of nonlinear age trends. We provide a web-based visualization interface to generate and present the resulting age trends, enabling future studies of brain structure to compare their data with this normative reference of brain development and aging, and to examine deviations from normative ranges, potentially related to disease.

bioinformatics↗