Analyzing atomic force microscopy images of virus-like particles by expectation-maximization

Analysis of virus-like particles (VLPs) is an essential task in optimizing their implementation as vaccine antigens for virus-initiated diseases. Interrogating VLP collections for elasticity by probing with a rigid atomic force microscopy (AFM) tip is a potential method for determining VLP morphological changes. During VLP morphological change, it is not expected that all VLPs would be in the same state. This leads to the open question of whether VLPs may change in a continuous or stepwise fashion. For continuous change, the statistical distribution of observed VLP properties would be expected as a single distribution, while stepwise change would lead to a multimodal distribution of properties. This study presents the application of a Gaussian mixture model (GMM), fit by the Expectation-Maximization (EM) algorithm, to identify different states of VLP morphological change observed by AFM imaging.

Supervised discretization for decluttering classification models

Presented here is the first demonstration of supervised discretization to 'declutter' multivariate classification data in chemical sensor applications. The performance of multivariate classification models is often limited by the non-informative chemical variance within each target class; decluttering methods seek to reduce within-class variance while retaining between-class variance. Supervised discretization is shown to declutter classes in a manner that is superior to the state-of-the-art External Parameter Orthogonalization (EPO) by constructing a more parsimonious model with fewer parameters to optimize and is, consequently, less susceptible to overfitting and information loss. The comparison of supervised discretization and EPO is performed on three classification applications: X-ray fluorescence spectra of pine ash where the pine was grown in three distinct soil types, laser induced breakdown spectroscopy of colored artisanal glasses, and laser induced breakdown spectroscopy of exotic hardwood species.

Comparison of Spectroscopic Techniques for Determining the Peroxide Value of 19 Classes of Naturally Aged, Plant-Based Edible Oils

The peroxide value of edible oils is a measure of the degree of oxidation, which directly relates to the freshness of the oil sample. Several studies previously reported in the literature have paired various spectroscopic techniques with multivariate analyses to rapidly determine peroxide values using field portable and process instrumentation; those efforts presented "best-case scenarios" with oils from narrowly defined training and test sets. The purpose of this paper is to evaluate the use of near- and mid-infrared absorption and Raman scattering spectroscopies on oil samples from different oil classes, including seasonal and vendor variations, to determine which measurement technique or combination thereof is best for predicting peroxide values. Following peroxide value assays of each oil class using an established titration-based method, global and global-subset calibration models were constructed from spectroscopic data collected on the 19 oil classes used in this study. Spectra from each optical technique were used to create partial least squares regression calibration models to predict the peroxide value of unknown oil samples. A global peroxide value model based on near-infrared (8 mm optical path length) oil measurements produced the lowest RMSEP (4.9), followed by 24 mm optical path length near infrared (5.1), Raman (6.9) and 50 µm optical path length mid-infrared (7.3). However, it was determined that the Raman RMSEP resulted from chance correlations. Global peroxide value models based on low-level fusion of the NIR (8 and 24 mm optical path length) data and all infrared data produced the same RMSEP of 5.1. Global subset models, based on any of the spectroscopies and olive oil training sets from any class (pure, extra light, extra virgin), all failed to extrapolate to the non-olive oils. However, the near-infrared global subset model built on extra virgin olive oil could extrapolate to test samples from other olive oil classes. This work demonstrates the difficulty of developing a truly global method for determining peroxide value of oils.

Characterization of Green Paints in Ming and Qianlong Dynasties' Lin'xi Pavilion by Complimentary Techniques

During conservation of the painted ceiling decoration of Lin'xi Pavilion in the Forbidden City, two distinct paint campaigns were isolated as a unique case study into architectural paint materials during both the Ming and Qing dynasties. Paint samples and cross sections from both paint generations were analyzed with SEM-EDX, time of flight-secondary ion mass spectrometry (ToF-SIMS), XRD, FTIR, and Raman spectroscopies. Similar organic and inorganic materials characteristic of these time periods were identified. The pigments of interest found in both paint generations were botallackite and atacamite polymorphs. This suggests a shift from natural mineral sources to synthetic copper-based pigments for these larger architectural projects.

Raman hyperspectral imaging with multivariate analysis for investigating enzyme immobilization

Directed enzyme evolution has led to significant application of biocatalysis for improved chemical transformations throughout the scientific and industrial communities. Biocatalytic reactions utilizing evolved enzymes immobilized within microporous supports have realized unique advantages, including notably higher enzyme stability, higher enzyme load, enzyme reusability, and efficient product-enzyme separation. To date, limited analytical methodology is available to discern the spatial and chemical distribution of immobilized enzymes, in which techniques for surface visualization, enzyme stability, or activity are instead employed. New analytical tools to investigate enzyme immobilization are therefore needed. In this work, development, application, and evaluation of an analytical methodology to study enzyme immobilization is presented. Specifically, Raman hyperspectral imaging with principal component analysis, a multivariate method, is demonstrated for the first time to investigate evolved enzymes immobilized onto microporous supports for biocatalysis. Herein we demonstrate the ability to spatially and spectrally resolve evolved pantothenate kinase (PanK) immobilized onto two commercially-available, chemically-diverse porous resins. This analytical methodology is able to chemically distinguish evolved enzyme, resin, and chemical species pertinent to immobilization. As such, a new analytical approach to study immobilized biocatalysts is demonstrated, offering potential wide application for analysis of protein or biomolecule immobilization.

Multi-Analytical Study of Copper-Based Historic Pigments and their Alteration Products

Copper-containing materials such as verdigris are commonly found in historic and artistic works of art, often at advanced states of decay. Applied on paper as inks and watercolors, many of which needed a binder such as gum arabic, the intrinsic instability of this pigment was known since the medieval period. The decay of verdigris (a mixture of copper acetates) as a pigment, as watercolor, and as a dye, was studied using a combination of vibrational (Fourier transform infrared) and X-ray photoelectron spectroscopy (XPS) and X-ray diffraction (XRD) instrumental techniques. Changes in the copper oxidative states and the formation of copper oxide were monitored during accelerated degradation as powdered solids and applied on mockup samples (with and without binder). Accelerated aging of both commercially available and synthesized verdigris pigments showed the presence of an intermediate species, Cu(CH₃COO)₂•3Cu(OH)₂•2H₂O, which points to the beginning of the decay processes, that culminates in the formation of Cu(II) oxide. However, the presence of gum arabic seems to delay deterioration, by temporarily reducing Cu(II) to Cu(I), even when the final product includes Cu(II). This novel application of XPS and supporting techniques has significant implications in art conservation, as the identified behavior helps explain the better preservation state of some works of art.

A novel multivariate curve resolution-alternating least squares (MCR-ALS) methodology for application in hyperspectral Raman imaging analysis

Multivariate curve resolution-alternating least squares (MCR-ALS) applied to hyperspectral Raman imaging is extensively used to spatially and spectrally resolve the individual, pure chemical species within complex, heterogeneous samples. A critical aspect of performing MCR-ALS with hyperspectral Raman imaging is the selection of the number of chemical components within the experimental data. Several methods have previously been proposed to determine the number of chemical components, but it remains a challenging task that if done incorrectly, can lead to the loss of chemical information. In this work, we show that the choice of 'optimal' number of factors in the MCR-ALS model may vary depending on the relative contribution of the targeted species to the overall spectral intensity. In a data set consisting of 27 hyperspectral Raman images of TiO2 polymorphs, it was observed that the more dominant species were best resolved with a parsimonious model. However, species with intensities near the noise level often needed more factors to be resolved than was predicted by standard methods. Based on the observations in this data set, we propose a new method that employs approximate reference spectra for determining optimal model complexity for identifying minor constituents with MCR-ALS.

Assessing utility of handheld laser induced breakdown spectroscopy as a means of Dalbergia speciation

Many species of Dalbergia are prized hardwoods, generally referred to as 'Rosewood,' and used in high-end products due to their distinctive hue and scent. Despite more than 58 species of Dalbergia being listed as endangered in Appendix 1 of The Convention on International Trade in Endangered Species of Fauna and Flora (CITES), the illegal logging and trade of this timber is ongoing. In this work, a handheld laser induced breakdown spectrometer (LIBS) was used to analyze seven Dalbergia species and two other exotic hardwood species to evaluate the ability of handheld LIBS for rapid classification of Dalbergia in the field. The KNN model of the classification presented 80% to 90% sensitivity for discriminating between Dalbergia species in the training set. PLS-DA models were based on a binary decision tree structure. Cumulatively, the PLS-DA decision tree model showed greater than 97% sensitivity and 99% selectivity for prediction of Dalbergia species included in the training set. The data presented in the following study are promising for the use of handheld LIBS devices and both KNN and PLS-DA models for applications in customs screenings at the port of entry of hard woods, among others.

Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) with Raman Imaging Applied to Lunar Meteorites

Lunar meteorites provide a more random sampling of the surface of the Moon than do the returned lunar samples, and they provide valuable information to help estimate the chemical composition of the lunar crust, the lunar mantle, and the bulk Moon. As of July 2014, ∼96 lunar meteorites had been documented and ten of these are unbrecciated mare basalts. Using Raman imaging with multivariate curve resolution-alternating least squares (MCR-ALS), we investigated portions of polished thin sections of paired, unbrecciated, mare-basalt lunar meteorites that had been collected from the LaPaz Icefield (LAP) of Antarctica-LAP 02205 and LAP 04841. Polarized light microscopy displays that both meteorites are heterogeneous and consist of polydispersed sized and shaped particles of varying chemical composition. For two distinct probed areas within each meteorite, the individual chemical species and associated chemical maps were elucidated using MCR-ALS applied to Raman hyperspectral images. For LAP 02205, spatially and spectrally resolved clinopyroxene, ilmenite, substrate-adhesive epoxy, and diamond polish were observed within the probed areas. Similarly, for LAP 04841, spatially resolved chemical images with corresponding resolved Raman spectra of clinopyroxene, troilite, a high-temperature polymorph of anorthite, substrate-adhesive epoxy, and diamond polish were generated. In both LAP 02205 and LAP 04841, substrate-adhesive epoxy and diamond polish were more readily observed within fractures/veinlet features. Spectrally diverse clinopyroxenes were resolved in LAP 04841. Factors that allow these resolved clinopyroxenes to be differentiated include crystal orientation, spatially distinct chemical zoning of pyroxene crystals, and/or chemical and molecular composition. The minerals identified using this analytical methodology-clinopyroxene, anorthite, ilmenite, and troilite-are consistent with the results of previous studies of the two meteorites using electron microprobe analysis. To our knowledge, this is the first report of MCR-ALS with Raman imaging used for the investigation of both lunar and other types of meteorites. We have demonstrated the use of multivariate analysis methods, namely MCR-ALS, with Raman imaging to investigate heterogeneous lunar meteorites. Our analytical methodology can be used to elucidate the chemical, molecular, and structural characteristics of phases in a host of complex, heterogeneous geological, geochemical, and extraterrestrial materials.

Raman Microspectroscopic Mapping with Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) Applied to the High-Pressure Polymorph of Titanium Dioxide, TiO2-II

The high-pressure, α-PbO₂-structured polymorph of titanium dioxide (TiO₂-II) was recently identified in micrometer-sized grains recovered from four Neoarchean spherule layers deposited between ∼2.65 and ∼2.54 billion years ago. Several lines of evidence support the interpretation that these layers represent distal impact ejecta layers. The presence of shock-induced TiO₂-II provides physical evidence to further support an impact origin for these spherule layers. Detailed characterization of the distribution of TiO₂-II in these grains may be useful for correlating the layers, estimating the paleodistances of the layers from their source craters, and providing insight into the formation of the TiO₂-II. Here we report the investigation of TiO₂-II-bearing grains from these four spherule layers using multivariate curve resolution-alternating least squares (MCR-ALS) applied to Raman microspectroscopic mapping. Raman spectra provide evidence of grains consisting primarily of rutile (TiO₂) and TiO₂-II, as shown by Raman bands at 174 cm^-1 (TiO₂-II), 426 cm^-1 (TiO₂-II), 443 cm^-1 (rutile), and 610 cm^-1 (rutile). Principal component analysis (PCA) yielded a predominantly three-phase system comprised of rutile, TiO₂-II, and substrate-adhesive epoxy. Scanning electron microscopy (SEM) suggests heterogeneous grains containing polydispersed micrometer- and submicrometer-sized particles. Multivariate curve resolution-alternating least squares applied to the Raman microspectroscopic mapping yielded up to five distinct chemical components: three phases of TiO₂ (rutile, TiO₂-II, and anatase), quartz (SiO₂), and substrate-adhesive epoxy. Spectral profiles and spatially resolved chemical maps of the pure chemical components were generated using MCR-ALS applied to the Raman microspectroscopic maps. The spatial resolution of the Raman microspectroscopic maps was enhanced in comparable, cost-effective analysis times by limiting spectral resolution and optimizing spectral acquisition parameters. Using the resolved spectra of TiO₂-II generated from MCR-ALS analysis, a Raman spectrum for pure TiO₂-II was estimated to further facilitate its identification.

Spatial and spectral resolution of carbonaceous material from hematite (α-Fe2O3) using multivariate curve resolution-alternating least squares (MCR-ALS) with Raman microspectroscopic mapping: implications for the search for life on Mars

We report a novel application of multivariate analysis with Raman microspectroscopic mapping to enhance the search for life on Mars.

Omnidirectionally Stretchable High-Performance Supercapacitor Based on Isotropic Buckled Carbon Nanotube Films

The emergence of stretchable electronic devices has attracted intensive attention. However, most of the existing stretchable electronic devices can generally be stretched only in one specific direction and show limited specific capacitance and energy density. Here, we report a stretchable isotropic buckled carbon nanotube (CNT) film, which is used as electrodes for supercapacitors with low sheet resistance, high omnidirectional stretchability, and electro-mechanical stability under repeated stretching. After acid treatment of the CNT film followed by electrochemical deposition of polyaniline (PANI), the resulting isotropic buckled acid treated CNT@PANI electrode exhibits high specific capacitance of 1147.12 mF cm(-2) at 10 mV s(-1). The supercapacitor possesses high energy density from 31.56 to 50.98 μWh cm(-2) and corresponding power density changing from 2.294 to 28.404 mW cm(-2) at the scan rate from 10 to 200 mV s(-1). Also, the supercapacitor can sustain an omnidirectional strain of 200%, which is twice the maximum strain of biaxially stretchable supercapacitors based on CNT assemblies reported in the literature. Moreover, the capacitive performance is even enhanced to 1160.43-1230.61 mF cm(-2) during uniaxial, biaxial, and omnidirectional elongations.

Adaptable infrared surface plasmon resonance spectroscopy accessory

A second generation prototype enabling surface plasmon resonance spectroscopic measurements in the infrared (IR) range is described. The new design (v2) uses the optical train (optics and detector) within conventional FT-IR spectrometers by confining dimensions of the accessory to space available within the sample compartment of the spectrometer. The v2 accessory builds upon knowledge gained from a previous version that was based on a modified commercial variable angle spectroscopic accessory and addresses observed limitations of the original design-improved temporal stability and measurement acquisition speed, crucial to biomolecular binding studies, as well as optical flexibility, a requirement for investigations of novel plasmon-supporting materials. Different aspects of the accessory, including temporal stability, mechanical resilience, and sensitivity to changes in refractive index of a sample were evaluated and presented in this contribution.