Interpreting support vector machines applied in laser-induced breakdown spectroscopy.

Laser-induced breakdown spectroscopy is often combined with a multivariate black box model-such as support vector machines (SVMs)-to obtain desirable quantitative or qualitative results. This approach carries obvious risks when practiced in high-stakes applications. Moreover, the lack of understanding of a black-box model limits the user's ability to fine-tune the model. Thus, here we present four approaches to interpret SVMs through investigating which features the models consider important in the classification task of 19 algal and cyanobacterial species. The four feature importance metrics are compared with popular approaches to feature selection for optimal SVM performance. We report that the distinct feature importance metrics yield complementary and often comparable information. In addition, we identify our SVM model's bias towards features with a large variance, even though these features exhibit a significant overlap between classes. We also show that the linear and radial basis kernel SVMs weight the same features to the same degree.

Laser-induced breakdown spectroscopy as a readout method for immunocytochemistry with upconversion nanoparticles.

Immunohistochemistry (IHC) and immunocytochemistry (ICC) are widely used to identify cancerous cells within tissues and cell cultures. Even though the optical microscopy evaluation is considered the gold standard, the limited range of useful labels and narrow multiplexing capabilities create an imminent need for alternative readout techniques. Laser-induced breakdown spectroscopy (LIBS) enables large-scale multi-elemental analysis of the surface of biological samples, e.g., thin section or cell pellet. It is, therefore, a potential alternative for IHC and ICC readout of various labels or tags (Tag-LIBS approach). Here, we introduce Tag-LIBS as a method for the specific determination of HER2 biomarker. The cell pellets were labeled with streptavidin-conjugated upconversion nanoparticles (UCNP) through a primary anti-HER2 antibody and a biotinylated secondary antibody. The LIBS scanning enabled detecting the characteristic elemental signature of yttrium as a principal constituent of UCNP, thus indirectly providing a reliable way to differentiate between HER2-positive BT-474 cells and HER2-negative MDA-MB-231 cells. The comparison of results with upconversion optical microscopy and luminescence intensity scanning confirmed that LIBS is a promising alternative for the IHC and ICC readout.

Laser-induced breakdown spectroscopy as a straightforward bioimaging tool for plant biologists; the case study for assessment of photon-upconversion nanoparticles in Brassica oleracea L. plant.

The main purpose of this work is to thoroughly describe the implementation protocol of laser-induced breakdown spectroscopy (LIBS) method in the plant analysis. Numerous feasibility studies and recent progress in instrumentation and trends in chemical analysis make LIBS an established method in plant bioimaging. In this work, we present an easy and straightforward phytotoxicity case study with a focus on LIBS method. We intend to demonstrate in detail how to manipulate with plants after exposures and how to prepare them for analyses. Moreover, we aim to achieve 2D maps of spatial element distribution with a good resolution without any loss of sensitivity. The benefits of rapid, low-cost bioimaging are highlighted. In this study, cabbage (Brassica oleracea L.) was treated with an aqueous dispersion of photon-upconversion nanoparticles (NaYF4 doped with Yb3+ and Tm3+ coated with carboxylated silica shell) in a hydroponic short-term toxicity test. After a 72-hour plant exposure, several macroscopic toxicity end-points were monitored. The translocation of Y, Yb, and Tm across the whole plant was set by employing LIBS with a lateral resolution 100 µm. The LIBS maps of rare-earth elements in B.oleracea plant grown with 50 µg/mL nanoparticle-treated and ion-treated exposures showed the root as the main storage, while the transfer via stem into leaves was minimal. On the contrary, the LIBS maps of plants exposed to the 500 µg/mL nanoparticle-treated and ion-treated uncover slightly different trends, nanoparticles as well as ions were transferred through the stem into leaves. However, the main storage organ was a root as well.

Methodology for the Implementation of Internal Standard to Laser-Induced Breakdown Spectroscopy Analysis of Soft Tissues.

The improving performance of the laser-induced breakdown spectroscopy (LIBS) triggered its utilization in the challenging topic of soft tissue analysis. Alterations of elemental content within soft tissues are commonly assessed and provide further insights in biological research. However, the laser ablation of soft tissues is a complex issue and demands a priori optimization, which is not straightforward in respect to a typical LIBS experiment. Here, we focus on implementing an internal standard into the LIBS elemental analysis of soft tissue samples. We achieve this by extending routine methodology for optimization of soft tissues analysis with a standard spiking method. This step enables a robust optimization procedure of LIBS experimental settings. Considering the implementation of LIBS analysis to the histological routine, we avoid further alterations of the tissue structure. Therefore, we propose a unique methodology of sample preparation, analysis, and subsequent data treatment, which enables the comparison of signal response from heterogenous matrix for different LIBS parameters. Additionally, a brief step-by-step process of optimization to achieve the highest signal-to-noise ratio (SNR) is described. The quality of laser-tissue interaction is investigated on the basis of the zinc signal response, while selected experimental parameters (e.g., defocus, gate delay, laser energy, and ambient atmosphere) are systematically modified.

Preparation and Analysis of Quantum Dots: Applications of Capillary Electrophoresis.

The implementation of quantum dots in analytical chemistry has already advanced from basic research activities to routine applications of commercially available fluorescent agents present in sophisticated assays kits. Nevertheless, a further development of new preparation and characterization methods of nanoparticles is still required to increase the sensitivity of analytical methods substantially. Thus, in many bioanalytical applications, important molecules such as DNA, proteins, and antibodies are routinely conjugated with fluorescent tags to reach even the absolute sensitivity, that is, the capability to detect a single molecule in complex matrices. Semiconductor quantum dots have already proved to be suitable components of highly luminescent tags, probes, and sensors with broad applicability in analytical chemistry. Quantum dots provide high extinction coefficients together with wide ranges of excitation wavelengths, size- and composition-tunable emissions, narrow and symmetric emission spectra, good quantum yields, relatively long size-dependent luminescence lifetime, and low photobleaching. Most of these properties are superior when compared with conventional organic fluorescent dyes. In this chapter, optimized procedures for the preparation of water-dispersed CdTe quantum dots; their coatings and conjugation reactions with antibodies, DNA, and macrocycles; and their analyses by capillary electrophoresis are described. The potential of capillary electrophoresis for fast analyses of nanoparticles, their conjugates with antibodies and immunocomplexes with targeted antigens, is demonstrated as an example.

Detail investigation of toxicity, bioaccumulation, and translocation of Cd-based quantum dots and Cd salt in white mustard.

In this study, a model crop plant white mustard (Sinapis alba L.) was treated with an aqueous dispersion of silica-coated CdTe quantum dots (CdTe/SiO2 QDs) in a 72-h short-term toxicity test. The toxicity was established via measurements of (i) the root length and (ii) the chlorophyll fluorescence. These results were compared to two other sources of cadmium, free Cd ions (CdCl2) and prime un-shell nanoparticles CdTe QDs. Tested compounds were applied in concentrations representing 20 and 200 µM Cd. The uptake and translocation of Cd were investigated using inductively coupled plasma optical emission spectrometry (ICP-OES) and the spatial Cd distribution was investigated in detail applying laser induced breakdown spectroscopy (LIBS). The LIBS maps with a lateral resolution of 100 µm were constructed for the whole plants, and maps with a lateral resolution of 25 µm (micro-LIBS arrangement) were used to analyse only the most interesting parts of plants with Cd presence (e.g. root tips or a part crossing the root into the above-ground part). Our results show that the bioaccumulation patterns and spatial distribution of Cd in CdTe/SiO2 QDs-treated plants differ from the plants of positive control and CdTe QDs. Fluorescence microscopy photographs revealed that CdTe/SiO2 became adsorbed onto the plant surface in comparison to CdTe QDs. Further, a physico-chemical characterization of QDs before and after the test exposure showed only minor changes in the nanoparticle diameters and no tendencies of QDs for agglomeration or aggregation during the exposure.

Laser-induced breakdown spectroscopy as a novel readout method for nanoparticle-based immunoassays.

Laser-induced breakdown spectroscopy (LIBS) was examined as a novel method for readout of microtiter plate immunoassays involving nanoparticles (NP). The so-called Tag-LIBS technique is a sensitive method for the detection of specific biomarkers. It was applied to the determination of NP labels using nanosecond ablation sampling. The NP labels were examined from the bottom of a standard 96-well microtiter plate. Thanks to the flexibility of LIBS instrumentation, both the plasma emission collection and the focusing optics arrangements can be collinearly arranged. The experiments showed that silver NPs and gold NPs can be readily quantified on the bottom of the microtiter plate. Utilizing this technique, a sandwich immunoassay for human serum albumin using streptavidin-coated AgNP labels was developed. The assay has a 10 ng·mL-1 detection limit which is comparable to the sensitivity of fluorometric readout. The main advantage of this LIBS technique is its wide scope in which it enables a detection of almost any type of NP labels, irrespective to any fluorescence or catalytic properties. Owing to the immediate signal response, the relatively simple instrumentation also enables assay automation. The LIBS capability of multi-elemental analyses makes it a promising and fast alternative to other readout techniques, in particular with respect to multiplexed detection of biomarkers. Graphical abstract Laser-induced breakdown spectroscopy (LIBS) is used as a novel readout method of nanoparticle-based immunoassays in microtiter plates. After formation of sandwich immunocomplex, the analyte concentration is quantified as the signal of Ag nanoparticle labels determined by LIBS.

The effects of photon-upconversion nanoparticles on the growth of radish and duckweed: Bioaccumulation, imaging, and spectroscopic studies.

In this study, radish (Raphanus sativus L.) and common duckweed (Lemna minor L.) were treated with an aqueous dispersion of carboxylated silica-coated photon-upconversion nanoparticles containing rare-earth elements (Y, Yb, and Er). The total concentration of rare earths and their bioaccumulation factors were determined in root, hypocotyl, and leaves of R. sativus after 72 h, and in L. minor fronds after 168 h. In R. sativus, translocation factors were determined as the ratio of rare earths concentration in hypocotyl versus root and in leaves versus hypocotyl. The lengths of the root and hypocotyl in R. sativus, as well as the frond area in L. minor, were monitored as toxicity endpoints. To distinguish rare earth bioaccumulation patterns, two-dimensional maps of elemental distribution in the whole R. sativus plant and L. minor fronds were obtained by laser-induced breakdown spectroscopy with a lateral resolution of 100 µm. Moreover, the bioaccumulation was inspected using a photon-upconversion laser microscanner. The results revealed that the tested nanoparticles became adsorbed onto L. minor fronds and R. sativus roots, as well as transferred from roots through the hypocotyl and into leaves of R. sativus. The bioaccumulation patterns and spatial distribution of rare earths in nanoparticle-treated plants therefore differed from those of the positive control. Overall, carboxylated silica-coated photon-upconversion nanoparticles are stable, can easily translocate from roots to leaves, and are expected to become adsorbed onto the plant surface. They are also significantly toxic to the tested plants at nominal concentrations of 100 and 1000 µg/mL.

Feasibility of Nanoparticle-Enhanced Laser Ablation Inductively Coupled Plasma Mass Spectrometry.

Nanoparticles (NPs) applied to the surface of some solids can increase signals in inductively coupled plasma mass spectrometry (ICPMS). Drops containing 20 and/or 40 nm nanoparticles of Ag and/or Au were deposited on metallic and ceramic/glass samples, and after being dried, both the samples treated with NPs and plain targets were ablated by one pulse per spot. The laser ablation ICPMS (LA-ICPMS) signals were enhanced for metallic samples modified with NPs in comparison to signals produced at the plain, untreated surface. Maps of LA-ICPMS signals recorded for several laser fluences show that the NP-induced signal enhancement exceeds even 2 orders of magnitude for metallic samples. No enhancement was achieved for nonconductive samples. This enhancement is limited to the peripheral annular region of the dried droplet area where NPs are concentrated due to the "coffee stain" effect. Ablation crater profilometric inspection revealed a more uniform material rearrangement over the NP-treated surface compared with the ablated plain target. However, besides a smoother crater bottom, no other evidence of an NP-enhancing effect was noticed, although an increased ablation rate was anticipated. Limits of detection dropped by 1 order of magnitude for the minor elements in the presence of NPs. Observed phenomena depend only on the NP surface concentration but not on the material or size of the NPs. An electron microprobe study of the collected ablation aerosol has shown that aerosol particles consisting of target material are aggregated around the NPs. The hypothesis is that such aggregates exhibit better transport/vaporization efficiency, thus enhancing signals for metallic samples. A detailed study of the suggested mechanism will be continued in ongoing work.

Time-Dependent Growth of Silica Shells on CdTe Quantum Dots.

The purpose of this study is to investigate the time dependent growth of silica shells on CdTe quantum dots to get their optimum thicknesses for practical applications. The core/shell structured silica-coated CdTe quantum dots (CdTe/SiO2 QDs) were synthesized by the Ströber process, which used CdTe QDs co-stabilized by mercaptopropionic acid. The coating procedure used silane primer (3-mercaptopropyltrimethoxysilane) in order to make the quantum dots (QDs) surface vitreophilic. The total size of QDs was dependent on both the time of silica shell growth in the presence of sodium silicate, and on the presence of ethanol during this growth. The size of particles was monitored during the first 72 h using two principally different methods: Dynamic Light Scattering (DLS), and Scanning Electron Microscopy (SEM). The data obtained by both methods were compared and reasons for differences discussed. Without ethanol precipitation, the silica shell thickness grew slowly and increased the nanoparticle total size from approximately 23 nm up to almost 30 nm (DLS data), and up to almost 60 nm (SEM data) in three days. During the same time period but in the presence of ethanol, the size of CdTe/SiO2 QDs increased more significantly: up to 115 nm (DLS data) and up to 83 nm (SEM data). The variances occurring between silica shell thicknesses caused by different methods of silica growth, as well as by different evaluation methods, were discussed.

Short-term assessment of cadmium toxicity and uptake from different types of Cd-based Quantum Dots in the model plant Allium cepa L.

We report on the toxicity and bioaccumulation of three different types of Cd-based quantum dots (QDs), dispersed in aqueous medium, for a model plant Allium cepa L. It is believed that encapsulation of nanoparticles should reduce their toxicity and increase their stability in different environments; in this work we studied how QD encapsulation affects their phytotoxicity. Core, core/shell, and core/shell/shell QDs (CdTe, CdTe/ZnS, and CdTe/CdS/ZnS QDs capped by 2-mercaptopropionic acid) were tested and CdCl2 was used as a positive control. After 24-h and 72-h exposure, total Cd content (MCd) and bioaccumulation factors (BAFs) were determined in all parts of A. cepa plants (roots, bulb, shoot), and the total length of the root system was monitored as a toxicity end-point. Measurements of total Cd content versus free Cd2+ content (with Differential Pulse Voltammetry, DPV) in exposure media showed differences in chemical stability of the three QD types. Correspondingly, selected QDs showed different toxicity for A. cepa and different Cd bioaccumulation patterns. CdTe QDs were the most toxic; their effect was similar to CdCl2 due to the release of free Cd2+, which was confirmed by the DPV measurements. Plants exposed to CdTe QDs also bioaccumulated the most Cd among all QD exposure groups. CdTe/ZnS QDs showed no toxicity and very low bioaccumulation of Cd in A. cepa; the main source of measured Cd in the plants were QDs adsorbed on their roots, which was confirmed by fluorescence microscopy. On the contrary, CdTe/CdS/ZnS QD toxicity and bioaccumulation patterns were similar to those of CdTe QDs and pointed to unstable CdS/ZnS shells.

Comparative investigation of toxicity and bioaccumulation of Cd-based quantum dots and Cd salt in freshwater plant Lemna minor L.

The purpose of this study was to determine the toxicity of two different sources of cadmium, i.e. CdCl2 and Cd-based Quantum Dots (QDs), for freshwater model plant Lemna minor L. Cadmium telluride QDs were capped with two coating ligands: glutathione (GSH) or 3-mercaptopropionic acid (MPA). Growth rate inhibition and final biomass inhibition of L. minor after 168-h exposure were monitored as toxicity endpoints. Dose-response curves for Cd toxicity and EC50168h values were statistically evaluated for all sources of Cd to uncover possible differences among the toxicities of tested compounds. Total Cd content and its bioaccumulation factors (BAFs) in L. minor after the exposure period were also determined to distinguish Cd bioaccumulation patterns with respect to different test compounds. Laser-Induced Breakdown Spectroscopy (LIBS) with lateral resolution of 200µm was employed in order to obtain two-dimensional maps of Cd spatial distribution in L. minor fronds. Our results show that GSH- and MPA-capped Cd-based QDs have similar toxicity for L. minor, but are significantly less toxic than CdCl2. However, both sources of Cd lead to similar patterns of Cd bioaccumulation and distribution in L. minor fronds. Our results are in line with previous reports that the main mediators of Cd toxicity and bioaccumulation in aquatic plants are Cd2+ ions dissolved from Cd-based QDs.

Multivariate classification of echellograms: a new perspective in Laser-Induced Breakdown Spectroscopy analysis.

In this work, we proposed a new data acquisition approach that significantly improves the repetition rates of Laser-Induced Breakdown Spectroscopy (LIBS) experiments, where high-end echelle spectrometers and intensified detectors are commonly used. The moderate repetition rates of recent LIBS systems are caused by the utilization of intensified detectors and their slow full frame (i.e. echellogram) readout speeds with consequent necessity for echellogram-to-1D spectrum conversion (intensity vs. wavelength). Therefore, we investigated a new methodology where only the most effective pixels of the echellogram were selected and directly used in the LIBS experiments. Such data processing resulted in significant variable down-selection (more than four orders of magnitude). Samples of 50 sedimentary ores samples (distributed in 13 ore types) were analyzed by LIBS system and then classified by linear and non-linear Multivariate Data Analysis algorithms. The utilization of selected pixels from an echellogram yielded increased classification accuracy compared to the utilization of common 1D spectra.