DOI: 10.5281/zenodo.15057423
title: From literature to predictive modelling: Insights and machine learning applications from in vitro comet assays related to the genotoxicity of titanium dioxide nanomaterials.

description: Input categories



Input features





Bibliographic information



Author(s), study title, and Digital Object Identifier (DOI)





Nanomaterial / (nanoparticle / nanoform)



Common names (e.g., Aeroxide P25) and standardized identifiers (e.g., JRC codes NM100, NM101), CAS number, supplier name, catalogue/batch number, and synthesis method (if synthesized de novo).





Pchem properties and characterization methods



Coating, morphology, crystallinity, particle core size (nm), hydrodynamic size (nm), specific surface area (m²/g), zeta potential (mV), polydispersity index (PDI), and purity (%). Characterization techniques (e.g., SEM, TEM, DLS). Hydrodynamic size, polydispersity index (PdI), and zeta potential noted with the measurement medium (e.g., water, cell culture medium).





Notes on pchem: For each row, pchem measurements (e.g., hydrodynamic size, zeta potential) were linked to relevant experimental conditions, such as the medium (e.g., water or culture medium), concentration (e.g., 10 µg/mL or 200 µg/mL), or exposure duration. For instance, hydrodynamic size was reported at multiple time points (e.g., 24 hours and 48 hours), the measurements were tied to the corresponding time point. Similarly, if specific treatments such as sonication were applied, p-chem property values were aligned with these conditions. This linking ensures that pchem properties are contextually accurate and condition-specific. 

-Missing pchem data for JRC NMs (e.g., NM100 -105) were supplemented from the JRC Report, which provided details such as coating, crystallinity, primary size, hydrodynamic size, PdI, specific surface area, and purity (all measured in water).

-Ghosh, Chakraborty reported an average hydrodynamic diameter of 6000 nm with a PdI of 1.53. As PdI > 1 is implausible, this value was assumed to be a typographical error and adjusted to 0.53





Sonication procedures



Medium used (e.g., Milli-Q water, BSA, culture medium). Parameters: frequency (kHz), power (W), amplitude (%), duration (total/pulsed/continuous mode). Instrumentation details and protocols.





Notes on sonication: Assumptions were made when the operational mode was not explicitly stated. For example, if an article reported "10 minutes of sonication" without further details, it was assumed to be continuous mode unless otherwise specified.





Aggregation, agglomeration



Assessment of aggregation/agglomeration during experiments (binary format)





Cellular conditions



Light conditions (e.g., experiments conducted in darkness to prevent photoactivation of TiO₂). Medium composition (e.g., DMEM, RPMI-1640, BEGM), including concentrations of FBS (%), glutamine (mM), penicillin (U/mL), and streptomycin (mg/mL).





Notes on Cellular conditions: To ensure consistency: i) the presence or absence of antibiotics (e.g., penicillin/streptomycin) was recorded, ii) If antibiotics were not mentioned, a value of 0 was assigned, indicating their absence, iii) if antibiotics were acknowledged but no concentrations provided, the value was recorded as NaN, signaling incomplete information.





Cell line information



Cell line (e.g., A549, SH-SY5Y, PBMC), type (e.g., neuroblast-like, epithelial, mononuclear), species (e.g., human, monkey, hamster), tissue (e.g., peripheral blood, brain, alveolar) and origin (e.g., immortalized, primary)





Enzyme treatment



For enzyme-modified comet assays, enzyme quantity, incubation time (min), temperature (°C), and buffer composition.





Cold lysis conditions



Incubation time (h), temperature (°C), buffer composition, and low-melting-point agarose concentration (%) in gels.





Electrophoresis conditions



Alkaline buffer composition, DNA unwinding duration (min), and temperature (°C). Electrophoresis parameters: duration (min), voltage (V), current (V/cm), and temperature (°C).





Notes on Electrophoresis: For studies lacking detailed descriptions of electrophoresis parameters, information was sourced from the referenced publications.





Statistical and imaging information



Image analysis software, magnification (x), and statistical evaluation parameters.





Cell seeding and preparation



Multiwell plate specifications, cell density per well/mL/cm², cells/comets scored per replicate, and staining compounds.





Assay details



Positive/negative controls, replication (duplicate/triplicate), assay type, and descriptions of the assays.





Exposure conditions



Exposure concentration (μg/mL) and duration (h) of TiO₂ treatement.










[1] https://products.evonik.com/assets/or/ld/AEROXIDE_TiO2_P_25_TDS_EN_EN_TDS_PV_52043891_en_GB_WORLD.pdf




[2] https://publications.jrc.ec.europa.eu/repository/handle/JRC86291