bioRxiv Preprints

{
  "doi": "10.64898/2026.03.16.712233",
  "url": "https://www.biorxiv.org/content/10.64898/2026.03.16.712233v4",
  "title": "EEG-based classification models reveal differential neural processing of words and images",
  "source": "biorxiv",
  "authors": "Morakabati, N. R.; Thiha, A. S.; Schechtman, E.",
  "version": "4",
  "abstract": "Background: Machine learning methods employing neuroimaging data are useful for monitoring the activation of neural representations. Specifically, they can be used to discern the brain networks engaged in processing specific categories of items. This approach has been employed on neuroimaging data, including functional magnetic resonance imaging data and electroencephalography (EEG) data. New method: Here, we present a task and an analytical pipeline for investigating category representations using EEG. Participants (N = 30) viewed a series of images and words of objects belonging to five categories (Animals, Tools, Food, Scenes, and Vehicles) and responded when items from the same category were presented consecutively. Results: We trained support vector machines on EEG data within participants and found that both image trials and word trials yielded significant category classification accuracy, with image trials achieving higher accuracy than word trials. When comparing categories in a pair-wise fashion, all pairs were statistically distinguishable for image trials, whereas only one pair was distinguishable for word trials. Parietal and Left Temporal electrodes contributed more to",
  "category": "neuroscience",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Eitan Schechtman",
  "journal_published_doi": null,
  "corresponding_institution": "University of California Irvine"
}

{
  "doi": "10.64898/2026.07.21.739325",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.21.739325v2",
  "title": "Numerosity adaptation reflects multiple levels of sensory processing",
  "source": "biorxiv",
  "authors": "Takahashi, T. J.; Roach, N. W.; Hayashi, M. J.",
  "version": "2",
  "abstract": "Psychophysical and neuroimaging studies have repeatedly suggested that perceived numerosity is susceptible to adaptation, involving high-level number representations. However, whether adaptation to low-level visual features contributes to numerosity adaptation remains unclear. Here, we provide evidence that numerosity adaptation involves not only high- but also low-level visual processing stages. Through a series of psychophysical experiments, we found that the effect of numerosity adaptation was significantly reduced, but not eliminated, when the contrast polarity of stimuli was inverted relative to the preceding adaptor. Follow-up experiments confirmed that the persistence of the aftereffects was not due to retinal adaptation or top-down decision bias. Finally, a computational model incorporating both high- and low- level adaptation successfully reproduced the behavioral pattern. These findings suggest that numerosity adaptation involves at least two stages of visual processing: adaptation to low-level visual features at early sensory stages and to numerosity at higher levels of the visual processing hierarchy. HighlightsO_LINumber adaptation is sensitive to mismatches in contras",
  "category": "neuroscience",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Masamichi J Hayashi",
  "journal_published_doi": null,
  "corresponding_institution": "National Institute of Information and Communications Technology"
}

{
  "doi": "10.64898/2026.06.04.729642",
  "url": "https://www.biorxiv.org/content/10.64898/2026.06.04.729642v2",
  "title": "Falls Induced by Optogenetic Inhibition of Basal Forebrain Cholinergic Projections after Dorsomedial Striatal Dopamine Depletion in a Dual Disruption Model of Falling Vulnerability in Parkinson Disease",
  "source": "biorxiv",
  "authors": "Kucinski, A.",
  "version": "2",
  "abstract": "Falls are a common and debilitating feature of Parkinson's Disease (PD) patients. Prefrontal acetylcholine (ACh) deficits, as well as nigrostriatal dopamine deficits, are implicated in vulnerability to falls. PD patients with loss of cortical ACh and associated cognitive dysfunction experience a higher rate of falls than PD patients without cortical ACh loss. In addition, chemogenetic inhibition of basal forebrain (BF) neurons in rats increases the vulnerability to falls on a balance beam task. Here, the impact of transient optogenetic inhibition specifically of BF cholinergic neurons was assessed in rats with dorsomedial striatal dopamine lesions during traversal of straight or zig-zag balance beams using the Michigan Complex Movement Control Task (MCMCT). Adding transient optogenetic inhibition of BF cholinergic neurons with striatal dopamine lesions elevated falls above the level produced by striatal dopamine lesions or BF ACh inhibition alone, especially on the challenging zig-zag task. These results support the critical role of BF-cortical cholinergic circuits in alleviating vulnerability to falls in PD patients with striatal dopamine loss, suggesting that it is combined loss ",
  "category": "neuroscience",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Aaron Kucinski",
  "journal_published_doi": null,
  "corresponding_institution": "University of Michigan"
}

{
  "doi": "10.64898/2026.05.22.727188",
  "url": "https://www.biorxiv.org/content/10.64898/2026.05.22.727188v2",
  "title": "Occurrence of Biased mTOR Signaling in Hepatocellular Carcinoma",
  "source": "biorxiv",
  "authors": "Singh, R.; Patel, N.; Singh, N.; Mourya, P.; Shingade, A.; Mange, A.; Kaur, J.; Beloshe, S.; Dudhalkar, A.; Chavan, P.; Yengkhom, G. D.; Patkar, S.; Goel, M.; Ingle, A.; Tripathy, S. R.; Epari, S.; Arandkar, S.; Thorat, R.; Shetty, S.",
  "version": "2",
  "abstract": "Background: mTOR signaling promotes cell growth and anabolic processes in all eukaryotes. Hyperactivation of mTOR signaling is associated with various cancers along with hepatocellular carcinoma (HCC). HCC is a highly lethal malignancy with multiple aetiologies such as viral infection, alcohol abuse, and metabolic dysfunction. Therapeutic options for HCC remain limited due to an incomplete understanding of oncogenic drivers and poorly characterized mechanisms of disease progression. Methods: Various regimens of DEN and CCl4 carcinogen dosage were investigated on C57BL/6J mice to induce HCC. The histological analysis for fibrosis and serum markers for liver function were performed. Molecular analyses of oncogenic drivers were performed in the HCC tissues obtained from mice and HCC patients. The impact of inhibition of mTOR signaling was assessed on HCC progression. Results: We established a rapid DEN+CCl4 induced (DCI) HCC model in C57BL/6 mice to study disease progression longitudinally. The molecular analysis revealed upregulation of MAPK and downregulation of mTORC1-S6K-S6 signaling in HCC. However, other branches of mTOR such as mTORC1-ULK1, mTORC1-4EBP1, and mTORC2-PKC were upr",
  "category": "cancer biology",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Sunil Shetty",
  "journal_published_doi": null,
  "corresponding_institution": "Advanced Centre for Treatment Research and Education in Cancer (ACTREC)-Tata Memorial Centre"
}

{
  "doi": "10.1101/2025.02.25.639997",
  "url": "https://www.biorxiv.org/content/10.1101/2025.02.25.639997v3",
  "title": "deepthought: the microscopy acquisition stack as an object of study",
  "source": "biorxiv",
  "authors": "Kesavan, P. S.; Devadasan, S.; Bohra, D.",
  "version": "3",
  "abstract": "Analysis-in-the-loop microscopy has been demonstrated many times, but it is rarely used outside the laboratories that build it. Each demonstration constructs its own acquisition infrastructure, so little transfers between them, and it has remained unclear which parts of the problem are already solved. In this work, the microscopy acquisition stack was itself treated as the object of study, and was investigated by construction. A minimal stack was built end to end, and four applications were then driven through it as test conditions. These were fixed-cell high-throughput immunofluorescence, live time-lapse imaging of an unsynchronized population, fluorescence anisotropy imaging, and autonomous focus and exposure. Each element of the stack was then classified by how it varied across these applications. Device access, sequencing, data storage and viewing held constant, and mature implementations of each were adopted unchanged. Interpretation, or how an image becomes a set of entities, differed with the application and belongs behind an interface. Two elements had nothing available to adopt and were therefore built. These are a geometric representation of the sample that a plan can tra",
  "category": "bioinformatics",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Kesavan Paruthi Subburam",
  "journal_published_doi": null,
  "corresponding_institution": "NDimensional Systems"
}

{
  "doi": "10.64898/2026.05.29.728838",
  "url": "https://www.biorxiv.org/content/10.64898/2026.05.29.728838v2",
  "title": "An integrated resource for systems-level analysis of aging hallmarks and associated genes",
  "source": "biorxiv",
  "authors": "Tiwari, R.; Balaji, M.; Chivukula, N.; Sil, P.; Samal, A.",
  "version": "2",
  "abstract": "Aging is a complex biological process involving progressive cellular dysfunction, tissue decline, and increased susceptibility to multiple chronic diseases. A systemic view of aging through its established hallmarks provides a structured framework to understand this complexity and drive therapeutic discovery. To this end, we present AgingHallmarksDB, an interactive web platform that enables systems-level analysis of hallmark-associated gene sets. Aging-related genes were first curated from seven established resources, and those present in at least two of these resources were considered as consensus aging-related genes. Using functional annotations derived from GO, KEGG, and Reactome, a total of 3111 genes were mapped to the 11 aging hallmarks, of which 2593 were supported by additional experimental or manually curated evidence, with 1089 of these forming the consensus set. Further, AgingHallmarksDB supplements hallmarks and gene annotations with tissue or cell-type class specificity, exosomal profiles, and regulatory interactions, enabling users to perform hallmark enrichment, protein-protein and regulatory interaction-based analysis. To elucidate the interconnectedness of hallmark",
  "category": "bioinformatics",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Areejit Samal",
  "journal_published_doi": null,
  "corresponding_institution": "The Institute of Mathematical Sciences (IMSc), Chennai 600113, India; Homi Bhabha National Institute (HBNI), Mumbai 400094, India"
}

{
  "doi": "10.64898/2026.07.04.722344",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.04.722344v2",
  "title": "Negligible incorporation of lipophilic dyes into bona fide small extracellular vesicles",
  "source": "biorxiv",
  "authors": "Ji, Y.; Ji, Q.; Ji, J.; Shentu, Y.; Zhou, l.; Wu, J.; Shao, Q.; Xu, W.; Zhang, C.; Shen, M.; Xie, Q.",
  "version": "2",
  "abstract": "Lipophilic dyes are widely used to track extracellular vesicles (EVs), yet their labeling efficiency toward bona fide small EVs (sEVs) remains poorly defined. Using a serum-free HEK293F system that produces endogenously fluorescent protein-tagged sEVs (sEVs-FPT) as an unambiguous reference while minimizing interference from dye-binding non-vesicular particles, we reassessed this efficiency with two orthogonal methods: nanoflow cytometry and fluorescence microscopy. PKH26, PKH67, and DiD labeled less than 0.5% of sEVs-FPT, regardless of vesicle heterogeneity. In vivo, dye-derived signals were far less abundant than tag-derived signals and failed to colocalize with them. Mechanistic evidence indicates that this failure stems from the inability of sEVs, as acellular structures, to actively internalize dye aggregates. These findings reveal a fundamental limitation of lipophilic dye-based EV tracking and underscore the need for orthogonally validated labeling strategies.",
  "category": "bioengineering",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Yuhua Ji",
  "journal_published_doi": null,
  "corresponding_institution": "Jinan University"
}

{
  "doi": "10.64898/2026.01.27.701271",
  "url": "https://www.biorxiv.org/content/10.64898/2026.01.27.701271v2",
  "title": "Optimizing Network-Level TMS-fMRI: Benchmarking the TMS-Compatible Sushi MR Setup",
  "source": "biorxiv",
  "authors": "Xiong, Y.; Burke, M.; Melo, L.; Takahashi, K.; Lueckel, M.; Bergmann, T. O.; Nitsche, M. A.; Genc, E.; Chiappini, E.",
  "version": "2",
  "abstract": "Concurrent TMS-fMRI can map how stimulation affects both the targeted cortex and connected brain-wide networks, but this requires MR receive hardware that allows TMS coil placement while preserving reliable whole-brain BOLD sensitivity. We developed and benchmarked a practical TMS-compatible 'Sushi' MR receive setup assembled from two flexible 18-channel body arrays. Across six experiments, we tested functional readout validity, signal quality, and active TMS-fMRI compatibility. Resting-state fMRI (n = 12) and verbal N-back task-fMRI (n = 8) were acquired with Sushi, a commercially available 2x7-channel Surface setup, and a standard 64-channel head/neck array. Functional similarity to the 64-channel reference was quantified with spatial overlap, and multi-echo combination (MEcomb) was tested as a post-acquisition signal optimization strategy. Sushi recovered subject-specific resting-state networks that more closely matched the 64-channel reference than Surface, with no significant difference from the 64-channel test-retest reference. For task-fMRI, MEcomb increased task-map similarity for Sushi, whereas setup comparisons within each pipeline were not significant. MEcomb also improv",
  "category": "neuroscience",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Emilio Chiappini",
  "journal_published_doi": null,
  "corresponding_institution": "Leibniz Research Centre for Working Environment and Human Factors (IfADo)"
}

{
  "doi": "10.1101/2025.08.02.668261",
  "url": "https://www.biorxiv.org/content/10.1101/2025.08.02.668261v2",
  "title": "TICToK: A comprehensive knowledgebase of tattoo ink chemicals and investigation of their associated toxicities and regulations",
  "source": "biorxiv",
  "authors": "Chivukula, N.; Madgaonkar, S. R.; Marigoudar, S. R.; Sharma, K. V.; Kishore, V.; Singh, A. V.; Samal, A.",
  "version": "2",
  "abstract": "Tattoos and permanent make-up, involving dermal injection of chemicals, are increasingly popular, with 30-40% of young adults in North America and Europe having at least one tattoo. Recent studies have suggested a possible association between tattooing and health risks, including skin cancers and lymphomas, although no definitive link has yet been established. This study comprehensively catalogs tattoo ink chemicals and investigates their potential adverse effects, addressing the urgent need for greater understanding of tattoo-related health concerns. First, 364 unique tattoo chemicals were identified from various scientific and regulatory sources, with nearly half functioning as pigments. Hazardous chemicals were identified, revealing carcinogens, endocrine disruptors, neurotoxicants, and dermal toxicants. A regulatory analysis based on key EU regulations, including harmonised classifications under Classification, Labelling and Packaging (CLP) regulation, Restriction Entry 75 of the REACH regulation, Cosmetic Products Regulation (CPR), and SVHC candidate list, revealed existing regulatory coverage of tattoo ink chemicals. Curated chemical-disease associations highlighted that some",
  "category": "pharmacology and toxicology",
  "published_at": "2026-07-26T00:00:00.000Z",
  "corresponding_author": "Areejit Samal",
  "journal_published_doi": null,
  "corresponding_institution": "The Institute of Mathematical Sciences (IMSc), Chennai 600113, India; Homi Bhabha National Institute (HBNI), Mumbai 400094, India"
}

{
  "doi": "10.64898/2026.07.24.740456",
  "url": "https://www.biorxiv.org/content/10.64898/2026.07.24.740456v1",
  "title": "Microbial Metabolites Potentiate MAIT Cell Anti-Tumor Immunity Against Solid Tumors",
  "source": "biorxiv",
  "authors": "Zhu, Y.; Shen, X.; Chen, Y.; Ma, N.; Zhang, C.; Zhao, A. S.; Tian, Y.; Gumate, S.; Huang, J.; Lin, S.; Wang, A.; Agopian, V. G.; Li, Y.-R.; Yang, L.",
  "version": "1",
  "abstract": "Mucosal-associated invariant T (MAIT) cells sense riboflavin metabolites through the monomorphic antigen-presenting molecule MR1, providing a unique opportunity to therapeutically mobilize a broadly shared T cell population without genetic engineering. Here, we show that the highly potent microbial metabolites, 5-OP-RU and 5-OE-RU, can be exploited as pharmacologic precision immune activators to drive human MAIT cell responses against solid tumors. Ligand stimulation in human co-culture systems elicited robust MAIT cell cytotoxicity, inflammatory cytokine secretion, and transcriptional states transformation. In vivo administration of riboflavin ligands 5-OP-RU significantly suppressed tumor growth in xenograft liver cancer models. Metabolite-driven MAIT activation also reprogrammed the local immune landscape, enhancing effector function and overcoming features of the immunosuppressive niche by markedly eliminating tumor-associated macrophages (TAMs) and myeloid-derived suppressor cells (MDSCs) within the tumor microenvironment (TME). These findings reveal that microbial riboflavin metabolites can power and redirect MAIT cells to solid tumors, establishing MR1-metabolite signaling a",
  "category": "cancer biology",
  "published_at": "2026-07-25T00:00:00.000Z",
  "corresponding_author": "Yichen Zhu",
  "journal_published_doi": null,
  "corresponding_institution": "University of California, Los Angeles"
}