Digital Transformation in Toxicology: Improving Communication and Efficiency in Risk Assessment.

Toxicology is undergoing a digital revolution, with mobile apps, sensors, artificial intelligence (AI), and machine learning enabling better record-keeping, data analysis, and risk assessment. Additionally, computational toxicology and digital risk assessment have led to more accurate predictions of chemical hazards, reducing the burden of laboratory studies. Blockchain technology is emerging as a promising approach to increase transparency, particularly in the management and processing of genomic data related with food safety. Robotics, smart agriculture, and smart food and feedstock offer new opportunities for collecting, analyzing, and evaluating data, while wearable devices can predict toxicity and monitor health-related issues. The review article focuses on the potential of digital technologies to improve risk assessment and public health in the field of toxicology. By examining key topics such as blockchain technology, smoking toxicology, wearable sensors, and food security, this article provides an overview of how digitalization is influencing toxicology. As well as highlighting future directions for research, this article demonstrates how emerging technologies can enhance risk assessment communication and efficiency. The integration of digital technologies has revolutionized toxicology and has great potential for improving risk assessment and promoting public health.

Interfacial Water in the SARS Spike Protein: Investigating the Interaction with Human ACE2 Receptor and In Vitro Uptake in A549 Cells.

The severity of global pandemic due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has engaged the researchers and clinicians to find the key features triggering the viral infection to lung cells. By utilizing such crucial information, researchers and scientists try to combat the spread of the virus. Here, in this work, we performed in silico analysis of the protein-protein interactions between the receptor-binding domain (RBD) of the viral spike protein and the human angiotensin-converting enzyme 2 (hACE2) receptor to highlight the key alteration that happened from SARS-CoV to SARS-CoV-2. We analyzed and compared the molecular differences between spike proteins of the two viruses using various computational approaches such as binding affinity calculations, computational alanine, and molecular dynamics simulations. The binding affinity calculations showed that SARS-CoV-2 binds a little more firmly to the hACE2 receptor than SARS-CoV. The major finding obtained from molecular dynamics simulations was that the RBD-ACE2 interface is populated with water molecules and interacts strongly with both RBD and ACE2 interfacial residues during the simulation periods. The water-mediated hydrogen bond by the bridge water molecules is crucial for stabilizing the RBD and ACE2 domains. Near-ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) confirmed the presence of vapor and molecular water phases in the protein-protein interfacial domain, further validating the computationally predicted interfacial water molecules. In addition, we examined the role of interfacial water molecules in virus uptake by lung cell A549 by binding and maintaining the RBD/hACE2 complex at varying temperatures using nanourchins coated with spike proteins as pseudoviruses and fluorescence-activated cell sorting (FACS) as a quantitative approach. The structural and dynamical features presented here may serve as a guide for developing new drug molecules, vaccines, or antibodies to combat the COVID-19 pandemic.

In-depth analysis of iodine in artificial biofilm model layers by variable excitation energy XPS and argon gas cluster ion sputtering XPS.

Here, we present a study on agarose thin-film samples that represent a model system for the exopolysaccharide matrix of biofilms. Povidone-iodide (PVP-I) was selected as an antibacterial agent to evaluate our x-ray photoelectron spectroscopy (XPS)-based methodology to trace specific marker elements, here iodine, commonly found in organic matrices of antibiotics. The in-depth distribution of iodine was determined by XPS analyses with variable excitation energies and in combination with argon gas cluster ion beam sputter cycles. On mixed agarose/PVP-I nanometer-thin films, both methods were found to solve the analytical task and deliver independently comparable results. In the mixed agarose/PVP-I thin film, we found the outermost surface layer depleted in iodine, whereas the iodine is homogeneously distributed in the depth region between this outermost surface layer and the interface between the thin film and the substrate. Depletion of iodine from the uppermost surface in the thin-film samples is assumed to be caused by ultrahigh vacuum exposure resulting in a loss of molecular iodine (I2) as reported earlier for other iodine-doped polymers.

Emerging cold plasma treatment and machine learning prospects for seed priming: a step towards sustainable food production.

Seeds are vulnerable to physical and biological stresses during the germination process. Seed priming strategies can alleviate such stresses. Seed priming is a technique of treating and drying seeds prior to germination in order to accelerate the metabolic process of germination. Multiple benefits are offered by seed priming techniques, such as reducing fertilizer use, accelerating seed germination, and inducing systemic resistance in plants, which are both cost-effective and eco-friendly. For seed priming, cold plasma (CP)-mediated priming could be an innovative alternative to synthetic chemical treatments. CP priming is an eco-friendly, safe and economical, yet relatively less explored technique towards the development of seed priming. In this review, we discussed in detail the application of CP technology for seed priming to enhance germination, the quality of seeds, and the production of crops in a sustainable manner. Additionally, the combination treatment of CP with nanoparticle (NP) priming is also discussed. The large numbers of parameters need to be monitored and optimized during CP treatment to achieve the desired priming results. Here, we discussed a new perspective of machine learning for modeling plasma treatment parameters in agriculture for the development of synergistic protocols for different types of seed priming.

Comparative Study of NAP-XPS and Cryo-XPS for the Investigation of Surface Chemistry of the Bacterial Cell-Envelope.

Bacteria generally interact with the environment via processes involving their cell-envelope. Thus, techniques that may shed light on their surface chemistry are attractive tools for providing an understanding of bacterial interactions. One of these tools is Al Kα-excited photoelectron spectroscopy (XPS) with its estimated information depth of <10 nm. XPS-analyses of bacteria have been performed for several decades on freeze-dried specimens in order to be compatible with the vacuum in the analysis chamber of the spectrometer. A limitation of these studies has been that the freeze-drying method may collapse cell structure as well as introduce surface contaminants. However, recent developments in XPS allow for analysis of biological samples at near ambient pressure (NAP-XPS) or as frozen hydrated specimens (cryo-XPS) in vacuum. In this work, we have analyzed bacterial samples from a reference strain of the Gram-negative bacterium Pseudomonas fluorescens using both techniques. We compare the results obtained and, in general, observe good agreement between the two techniques. Furthermore, we discuss advantages and disadvantages with the two analysis approaches and the output data they provide. XPS reference data from the bacterial strain are provided, and we propose that planktonic cells of this strain (DSM 50090) are used as a reference material for surface chemical analysis of bacterial systems.

In situ monitoring of the influence of water on DNA radiation damage by near-ambient pressure X-ray photoelectron spectroscopy.

Ionizing radiation damage to DNA plays a fundamental role in cancer therapy. X-ray photoelectron-spectroscopy (XPS) allows simultaneous irradiation and damage monitoring. Although water radiolysis is essential for radiation damage, all previous XPS studies were performed in vacuum. Here we present near-ambient-pressure XPS experiments to directly measure DNA damage under water atmosphere. They permit in-situ monitoring of the effects of radicals on fully hydrated double-stranded DNA. The results allow us to distinguish direct damage, by photons and secondary low-energy electrons (LEE), from damage by hydroxyl radicals or hydration induced modifications of damage pathways. The exposure of dry DNA to x-rays leads to strand-breaks at the sugar-phosphate backbone, while deoxyribose and nucleobases are less affected. In contrast, a strong increase of DNA damage is observed in water, where OH-radicals are produced. In consequence, base damage and base release become predominant, even though the number of strand-breaks increases further.

Versailles Project on Advanced Materials and Standards interlaboratory study on intensity calibration for x-ray photoelectron spectroscopy instruments using low-density polyethylene.

We report the results of a Versailles Project on Advanced Materials and Standards interlaboratory study on the intensity scale calibration of x-ray photoelectron spectrometers using low-density polyethylene (LDPE) as an alternative material to gold, silver, and copper. An improved set of LDPE reference spectra, corrected for different instrument geometries using a quartz-monochromated Al Kα x-ray source, was developed using data provided by participants in this study. Using these new reference spectra, a transmission function was calculated for each dataset that participants provided. When compared to a similar calibration procedure using the NPL reference spectra for gold, the LDPE intensity calibration method achieves an absolute offset of ∼3.0% and a systematic deviation of ±6.5% on average across all participants. For spectra recorded at high pass energies (≥90 eV), values of absolute offset and systematic deviation are ∼5.8% and ±5.7%, respectively, whereas for spectra collected at lower pass energies (<90 eV), values of absolute offset and systematic deviation are ∼4.9% and ±8.8%, respectively; low pass energy spectra perform worse than the global average, in terms of systematic deviations, due to diminished count rates and signal-to-noise ratio. Differences in absolute offset are attributed to the surface roughness of the LDPE induced by sample preparation. We further assess the usability of LDPE as a secondary reference material and comment on its performance in the presence of issues such as variable dark noise, x-ray warm up times, inaccuracy at low count rates, and underlying spectrometer problems. In response to participant feedback and the results of the study, we provide an updated LDPE intensity calibration protocol to address the issues highlighted in the interlaboratory study. We also comment on the lack of implementation of a consistent and traceable intensity calibration method across the community of x-ray photoelectron spectroscopy (XPS) users and, therefore, propose a route to achieving this with the assistance of instrument manufacturers, metrology laboratories, and experts leading to an international standard for XPS intensity scale calibration.

Role of Water in Phase Transformations and Crystallization of Ferrihydrite and Hematite.

The oxides, hydroxides, and oxo-hydroxides of iron belong to the most abundant materials on earth. They also feature a wide range of practical applications. In many environments, they can undergo facile phase transformations and crystallization processes. Water appears to play a critical role in many of these processes. Despite numerous attempts, the role of water has not been fully revealed yet. We present a new approach to study the influence of water in the crystallization and phase transformations of iron oxides. The approach employs model-type iron oxide films that comprise a defined homogeneous nanostructure. The films are exposed to air containing different amounts of water reaching up to pressures of 10 bar. Ex situ analysis via scanning electron microscopy, transmission electron microscopy, selected area electron diffraction, and X-ray diffraction is combined with operando near-ambient pressure X-ray photoelectron spectroscopy to follow water-induced changes in hematite and ferrihydrite. Water proves to be critical for the nucleation of hematite domains in ferrihydrite, the resulting crystallite orientation, and the underlying crystallization mechanism.

Bacterial cellulose films with ZnO nanoparticles and propolis extracts: Synergistic antimicrobial effect.

This study aimed to obtain possible materials for future antimicrobial food packaging applications based on biodegradable bacterial cellulose (BC). BC is a fermentation product obtained by Gluconacetobacter xylinum using food or agricultural wastes as substrate. In this work we investigated the synergistic effect of zinc oxide nanoparticles (ZnO NPs) and propolis extracts deposited on BC. ZnO NPs were generated in the presence of ultrasounds directly on the surface of BC films. The BC-ZnO composites were further impregnated with ethanolic propolis extracts (EEP) with different concentrations.The composition of raw propolis and EEP were previously determined by gas-chromatography mass-spectrometry (GC-MS), while the antioxidant activity was evaluated by TEAC (Trolox equivalent antioxidant capacity). The analysis methods performed on BC-ZnO composites such as scanning electron microscopy (SEM), thermo-gravimetrically analysis (TGA), and energy-dispersive X-ray spectroscopy (EDX) proved that ZnO NPs were formed and embedded in the whole structure of BC films. The BC-ZnO-propolis films were characterized by SEM and X-ray photon spectroscopy (XPS) in order to investigate the surface modifications. The antimicrobial synergistic effect of the BC-ZnO-propolis films were evaluated against Escherichia coli, Bacillus subtilis, and Candida albicans. The experimental results revealed that BC-ZnO had no influence on Gram-negative and eukaryotic cells.

Detection of suspended nanoparticles with near-ambient pressure x-ray photoelectron spectroscopy.

Two systems of suspended nanoparticles have been studied with near-ambient pressure x-ray photoelectron spectroscopy: silver nanoparticles in water and strontium fluoride-calcium fluoride core-shell nanoparticles in ethylene glycol. The corresponding dry samples were measured under ultra high vacuum for comparison. The results obtained under near-ambient pressure were overall comparable to those obtained under ultra high vacuum, although measuring silver nanoparticles in water requires a high pass energy and a long acquisition time. A shift towards higher binding energies was found for the silver nanoparticles in aqueous suspension compared to the corresponding dry sample, which can be assigned to a change of surface potential at the water-nanoparticle interface. The shell-thickness of the core-shell nanoparticles was estimated based on simulated spectra from the National Institute of Standards and Technology database for simulation of electron spectra for surface analysis. With the instrumental set-up presented in this paper, nanoparticle suspensions in a suitable container can be directly inserted into the analysis chamber and measured without prior sample preparation.

In Situ Industrial Bimetallic Catalyst Characterization using Scanning Transmission Electron Microscopy and X-ray Absorption Spectroscopy at One Atmosphere and Elevated Temperature.

We have developed a new experimental platform for in situ scanning transmission electron microscope (STEM) energy dispersive X-ray spectroscopy (EDS) which allows real time, nanoscale, elemental and structural changes to be studied at elevated temperature (up to 1000 °C) and pressure (up to 1 atm). Here we demonstrate the first application of this approach to understand complex structural changes occurring during reduction of a bimetallic catalyst, PdCu supported on TiO2 , synthesized by wet impregnation. We reveal a heterogeneous evolution of nanoparticle size, distribution, and composition with large differences in reduction behavior for the two metals. We show that the data obtained is complementary to in situ STEM electron energy loss spectroscopy (EELS) and when combined with in situ X-ray absorption spectroscopy (XAS) allows correlation of bulk chemical state with nanoscale changes in elemental distribution during reduction, facilitating new understanding of the catalytic behavior for this important class of materials.

Versailles Project on Advanced Materials and Standards Interlaboratory Study on Measuring the Thickness and Chemistry of Nanoparticle Coatings Using XPS and LEIS.

We report the results of a VAMAS (Versailles Project on Advanced Materials and Standards) inter-laboratory study on the measurement of the shell thickness and chemistry of nanoparticle coatings. Peptide-coated gold particles were supplied to laboratories in two forms: a colloidal suspension in pure water and; particles dried onto a silicon wafer. Participants prepared and analyzed these samples using either X-ray photoelectron spectroscopy (XPS) or low energy ion scattering (LEIS). Careful data analysis revealed some significant sources of discrepancy, particularly for XPS. Degradation during transportation, storage or sample preparation resulted in a variability in thickness of 53 %. The calculation method chosen by XPS participants contributed a variability of 67 %. However, variability of 12 % was achieved for the samples deposited using a single method and by choosing photoelectron peaks that were not adversely affected by instrumental transmission effects. The study identified a need for more consistency in instrumental transmission functions and relative sensitivity factors, since this contributed a variability of 33 %. The results from the LEIS participants were more consistent, with variability of less than 10 % in thickness and this is mostly due to a common method of data analysis. The calculation was performed using a model developed for uniform, flat films and some participants employed a correction factor to account for the sample geometry, which appears warranted based upon a simulation of LEIS data from one of the participants and comparison to the XPS results.

X-ray spectromicroscopy of nanoparticulate iron oxide phases.

Soft x-ray spectromicroscopy techniques have seen great amount of development in the recent years, and with the development of new diffraction limited synchrotron source, many new nanoscale and mesoscale characterization opportunities of applied materials are foreseen. In this perspective, the authors present some examples that illustrate the capabilities of spectromicroscopy techniques, namely, 2D and 3D spatially resolved chemical quantification, surface and bulk sensitive measurements, and polarization dependent measurements as applied to iron oxide nanoparticulate materials of biological, geological, and other origins.

XPS depth profiling of an ultrathin bioorganic film with an argon gas cluster ion beam.

The growing interest in artificial bioorganic interfaces as a platform for applications in emerging areas as personalized medicine, clinical diagnostics, biosensing, biofilms, prevention of biofouling, and other fields of bioengineering is the origin of a need for in detail multitechnique characterizations of such layers and interfaces. The in-depth analysis of biointerfaces is of special interest as the properties of functional bioorganic coatings can be dramatically affected by in-depth variations of composition. In worst cases, the functionality of a device produced using such coatings can be substantially reduced or even fully lost.

Synergistic Effects in Bimetallic Palladium-Copper Catalysts Improve Selectivity in Oxygenate Coupling Reactions.

Condensation reactions such as Guerbet and aldol are important since they allow for C-C bond formation and give higher molecular weight oxygenates. An initial study identified Pd-supported on hydrotalcite as an active catalyst for the transformation, although this catalyst showed extensive undesirable decarbonylation. A catalyst containing Pd and Cu in a 3:1 ratio dramatically decreased decarbonylation, while preserving the high catalytic rates seen with Pd-based catalysts. A combination of XRD, EXAFS, TEM, and CO chemisorption and TPD revealed the formation of CuPd bimetallic nanoparticles with a Cu-enriched surface. Finally, density functional theory studies suggest that the surface segregation of Cu atoms in the bimetallic alloy catalyst produces Cu sites with increased reactivity, while the Pd sites responsible for unselective decarbonylation pathways are selectively poisoned by CO.

Multimode Surface Functional Group Determination: Combining Steady-State and Time-Resolved Fluorescence with X-ray Photoelectron Spectroscopy and Absorption Measurements for Absolute Quantification.

The quantitative determination of surface functional groups is approached in a straightforward laboratory-based method with high reliability. The application of a multimode BODIPY-type fluorescence, photometry, and X-ray photoelectron spectroscopy (XPS) label allows estimation of the labeling ratio, i.e., the ratio of functional groups carrying a label after reaction, from the elemental ratios of nitrogen and fluorine. The amount of label on the surface is quantified with UV/vis spectrophotometry based on the molar absorption coefficient as molecular property. The investigated surfaces with varying density are prepared by codeposition of 3-(aminopropyl)triethoxysilane (APTES) and cyanoethyltriethoxysilane (CETES) from vapor. These surfaces show high functional group densities that result in significant fluorescence quenching of surface-bound labels. Since alternative quantification of the label on the surface is available through XPS and photometry, a novel method to quantitatively account for fluorescence quenching based on fluorescence lifetime (τ) measurements is shown. Due to the complex distribution of τ on high-density surfaces, the stretched exponential (or Kohlrausch) function is required to determine representative mean lifetimes. The approach is extended to a commercial Rhodamine B isothiocyanate (RITC) label, clearly revealing the problems that arise from such charged labels used in conjunction with silane surfaces.

En route to traceable reference standards for surface group quantifications by XPS, NMR and fluorescence spectroscopy.

The fluorine content of polymer particles labelled with 2,2,2-trifluoroethylamine was reliably quantified with overlapping sensitivity ranges by XPS and solid-state NMR. This provides a first step towards reference materials for the metrological traceability of surface group quantifications. The extension of this concept to fluorescence spectroscopy is illustrated.

Quantification of variable functional-group densities of mixed-silane monolayers on surfaces via a dual-mode fluorescence and XPS label.

The preparation of aminated monolayers with a controlled density of functional groups on silica surfaces through a simple vapor deposition process employing different ratios of two suitable monoalkoxysilanes, (3-aminopropyl)diisopropylethoxysilane (APDIPES) and (3-cyanopropyl)dimethylmethoxysilane (CPDMMS), and advances in the reliable quantification of such tailored surfaces are presented here. The one-step codeposition process was carried out with binary silane mixtures, rendering possible the control over a wide range of densities in a single step. In particular, APDIPES constitutes the functional silane and CPDMMS the inert component. The procedure requires only small amounts of silanes, several ratios can be produced in a single batch, the deposition can be carried out within a few hours and a dry atmosphere can easily be employed, limiting self-condensation of the silanes. Characterization of the ratio of silanes actually bound to the surface can then be performed in a facile manner through contact angle measurements using the Cassie equation. The reliable estimation of the number of surface functional groups was approached with a dual-mode BODIPY-type fluorescence label, which allows quantification by fluorescence and XPS on one and the same sample. We found that fluorescence and XPS signals correlate over at least 1 order of magnitude, allowing for a direct linking of quantitative fluorescence analysis to XPS quantification. Employment of synchrotron-based methods (XPS; reference-free total reflection X-ray fluorescence, TXRF) made the traceable quantification of surface functional groups possible, providing an absolute reference for quantitative fluorescence measurements through a traceable measurement chain.