Versatile Analytical Tool Research Articles

Exploiting the Surface-Enhanced IR Absorption Effect in the Photothermally Induced Resonance AFM-IR Technique toward Nanoscale Chemical Analysis.

The photothermally induced resonance AFM-IR technique (denoted as PTIR) is a promising and still developing analytical method that can provide nanoscale chemical and topographical information. Herein, by taking advantage of a customized PTIR system with either top-down or bottom-up incidence mode for a quantum cascade laser (QCL), we explore how the surface-enhanced IR absorption (SEIRA) effect due to the Au-coated AFM tip and/or substrate may affect the PTIR signals from 25 to 580 nm thick p-nitrobenzoic acid (PNBA) samples, as a function of sample thickness, incidence mode, laser polarization, and Au film morphology. By analysis of the νas(NO2) band intensity, it is revealed that the SEIRA effect may increase the PTIR signals by 1.5-8.3 times, with that from the Au-coated substrate being greater than that from the Au-coated tip. Nevertheless, the overall PTIR signal goes up monotonically over the entire thickness range for the top-down incidence mode, while it increases and then decreases with the sample thickness for the bottom-up incidence mode. The p-polarized laser enhances the PTIR signal more than does the s-polarized laser, especially on the Au-coated substrate. The significant loss of the PTIR signal of a PNBA sample corroborates the substantial loss of the SEIRA effect of an annealed Au film. The present work may promote the application of the SEIRA effect to the PTIR technique and provides hints for developing the PTIR technique into a more versatile analytical tool.

A review of the rheological properties of dilute and concentrated food emulsions.

Rheology is a powerful and versatile analytical tool for providing information about changes in the composition, structure, and interactions of food emulsions. Moreover, an understanding of emulsion rheology is essential for designing efficient food processing operations and emulsion-based foods with the desired physicochemical, sensory, and nutritional attributes, such as appearance, texture, flavor, shelf life, and bioavailability. This article provides a brief overview of the current understanding of food emulsions, with a focus on how their viscosity is related to the properties of the emulsion droplets present.

ATR-FTIR as a versatile analytical tool for the rapid determination of storage life of fresh Agaricus bisporus via its moisture content

Agaricus bisporus, an edible macroscopic fungus, is the most widely cultivated mushroom in the world. A. bisporus is highly susceptible to microbial attacks when stored in the refrigerator at 0 °C for more than 5 days. Hence, it is imperative to measure the freshness level of A. bisporus during its refrigeration to prevent any wastage of harvest. Herein, we propose a novel analytical technique of using Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy as a non-invasive inspection tool to assess the moisture content of A. bisporus samples. The score plot of Principal Component Analysis (PCA) shows that the proposed analytical method can effectively discriminate aged and fresh A. bisporus. Finally, the application of ATR-FTIR coupled PCA for determination of storage life of fresh A. bisporus is demonstrated. Non-destructive analysis, rapidity, simplicity and high accuracy are the attributes of this inspection tool that may popularize this versatile analytical technique for the rapid determination of storage life of fresh A. bisporus during cold storage.

A Multiplexed SERS-Active Microneedle for Simultaneous Redox Potential and pH Measurements in Rat Joints.

To detect redox potential and pH simultaneously in rat joints, a surface-enhanced Raman scattering (SERS)-active microneedle was structured with two separate grooves containing redox-sensitive and pH-sensitive SERS probes, respectively. The multiplexed SERS-active microneedles brought the two SERS probes into muscles with minimal invasion to sense their redox status and pH in 5 min, and they also detected the dynamical evolution of redox status and pH in muscles. The multiplexed SERS-active microneedles were also inserted into rat joints to sense their redox status and pH, which lack flowable fluids. The strategy of one SERS probe in one groove would allow SERS-active microneedles to become a multiplexed analytical tool for minimally invasive sampling in vivo and direct Raman detection ex vivo, and the multiplexed SERS-active microneedles would become a versatile analytical tool to promote research in biomedicines.

Hierarchical density-based cluster analysis framework for atom probe tomography data

Atom probe tomography (APT) has enabled the direct visualization of solute clusters. However one of the main analysis methods used by the APT community, i.e. the maximum separation method, often suffers from subjective parametric selection and limited applicability. To address the need for more robust and versatile analysis tools, a framework based on hierarchical density-based cluster analysis is implemented. Cluster analysis begins with the HDBSCAN algorithm to conservatively segment the datasets into regions containing clusters and a matrix or noise region. The stability of each cluster and the probability that an atom belongs to a cluster are quantified. Each clustered region is further analyzed by the DeBaCl algorithm to separate and refine clusters present in the sub-volumes. Finally, the k-nearest neighbor algorithm may be used to re-assign matrix atoms to clusters, based on their probability values. Four mandatory parameters are required for this cluster analysis approach. However, the selection of an appropriate value for only one of these parameters, i.e. a rough estimate of the minimum cluster size, is essential. The improved performance of the method was evaluated by analyzing four synthetic APT datasets and comparing the outcome with the commonly-used maximum separation method. Codes and data are made available through GitHub.

Enhancement of carbon detection sensitivity in laser induced breakdown spectroscopy with low pressure ambient helium gas

Carbon detection is usually difficult to carry out with high sensitivity and minimally destructive effect. While the conventional laser induced breakdown spectroscopy (LIBS) method operated with atmospheric ambient air is well known as a powerful and versatile analytical tool, it suffers nevertheless from the low sensitivity of C detection when measured in both atmospheric and low pressure ambient air with the more adverse effect found in the former case. This was shown to have its origin in the serious time mismatching effect between the formation of the shock wave plasma by the ablated major host elements and the premature fast passage of the much lighter ablated C atom. However, this study shows the result of high sensitivity C analysis of stone samples using LIBS technique with relatively low laser pulse energy of 60 mJ and low pressure He ambient gas without showing visible surface damage. The helium gas provides the additional delayed excitation by the He metastable excited states through the Penning-like ionization process. The C emission intensities measured from the jasper and black stone in 2.6 kPa He ambient gas are in general significantly higher than those measured in 0.5 kPa ambient air. The enhancement is shown to increase reaching an 8 fold enhancement with increased laser energy up to 60 mJ before undesirable surface damage is created. A further measurement of C emission using pelletized KBr mixtures with various CaCO3 concentrations reveals a straight calibration line of rather large slope with extrapolated zero intercept and estimated detection limit of around 0.6 ppm, demonstrating its potential application for highly sensitive quantitative analysis of C with minimal destructive effect.

Experimental and numerical analysis of strain gradient in tensile concrete prisms reinforced with multiple bars

This work is a continuation of the ongoing research on deformation behavior of reinforced concrete elements under tension. The previous studies have revealed that deformation behaviors of elements reinforced with multiple bars and the traditional prismatic members reinforced with a center bar are essentially different. The latter layout, though typical of laboratory specimens, could not represent the norm of structures in real-life. Thus, a new test methodology to investigate the strain distribution in concrete prismatic members reinforced with multiple bars subjected to axial tension is devised. Prismatic concrete specimens with different reinforcement configurations were fabricated and tested using the proposed setup. Deformation behavior of the specimens is modeled with a tailor-designed bond modeling approach for rigorous finite element analysis. It is revealed that the average deformations of the concrete could be different from the prevailing approach of average deformations of the steel, and are dependent on the reinforcement configurations. Therefore, the efficiency of concrete in tension should be carefully taken into account for rational design of structural elements. The study endorses promising abilities of finite element technique as a versatile analysis tool whose full potential is to be revealed with the advent of computer hardware.

BRepertoire: a user-friendly web server for analysing antibody repertoire data.

Antibody repertoire analysis by high throughput sequencing is now widely used, but a persisting challenge is enabling immunologists to explore their data to discover discriminating repertoire features for their own particular investigations. Computational methods are necessary for large-scale evaluation of antibody properties. We have developed BRepertoire, a suite of user-friendly web-based software tools for large-scale statistical analyses of repertoire data. The software is able to use data preprocessed by IMGT, and performs statistical and comparative analyses with versatile plotting options. BRepertoire has been designed to operate in various modes, for example analysing sequence-specific V(D)J gene usage, discerning physico-chemical properties of the CDR regions and clustering of clonotypes. Those analyses are performed on the fly by a number of R packages and are deployed by a shiny web platform. The user can download the analysed data in different table formats and save the generated plots as image files ready for publication. We believe BRepertoire to be a versatile analytical tool that complements experimental studies of immune repertoires. To illustrate the server’s functionality, we show use cases including differential gene usage in a vaccination dataset and analysis of CDR3H properties in old and young individuals. The server is accessible under http://mabra.biomed.kcl.ac.uk/BRepertoire.

The role of ionic liquids in the biocatalytic evaluation of bisphenol levels as contaminant: an automatic approach.

An automatic assay was developed that is intended to be a generic tool for evaluation of a horseradish peroxidase activity in different ionic liquids (ILs). Ionic liquids with different characteristics were used and their effects on the enzymatic reaction, were compared with those obtained with conventional organic solvents. In addition, ILs were tested as solvents for the enzyme substrate (bisphenol A (BPA)). ILs were shown to be a good alternative to conventional organic solvents from either the effect on enzymatic activity or the solubilization of bisphenol. Since bisphenol A is an endocrine disruptor frequently used in plastic industries, it was also applied the developed enzymatic methodology for quantification of this compound in real beverage samples. To increase the sensitivity (already increased by the use of an IL) and the selectivity of the methodology, a sample pre-treatment using a molecular recognition solid phase extraction was applied. Finally, the methodology presented detection and quantification limits of 7.73 × 10-4 and 1.29 × 10-3 mmol L-1 and a linear range up to 1.00 mmol L-1, allowing accurate and reliable quantifications of bisphenol in beer and cola drink samples. This work confirmed the potential of a sequential injection analysis (SIA) system as a simple, versatile, robust, and rapid analytical tool for automating enzymatic assays in ILs medium and, at the same time, showed it to be a relevant automatic alternative for routine determinations of bisphenol A in food samples.

Surface-enhanced Raman spectroscopy: bottlenecks and future directions.

In this feature article, we discuss in detail developmental bottleneck issues in Raman spectroscopy in its early stages and surface-enhanced Raman spectroscopy (SERS) in the past four decades. We divide SERS research into two different directions with different targets. Fundamental research is extending the limits of SERS to single-molecule, sub-nanometer resolution and femtosecond processes. In contrast, practical research is expanding the range of applications with the aim of providing versatile analytical tools for surface, materials, life, environmental, forensic and food sciences and also commercial instruments for use in daily life. In the second direction there have continually been many complex bottlenecks to be overcome. We attempt to enumerate the key issues in detail and also describe the achievements made to overcome the bottlenecks. In the last, but not least important part, we discuss the remaining bottlenecks and possible strategies for overcoming them to enable SERS to be an even more powerful and versatile technique.

Recent advances in interactive and automated analysis

Computers and distributed software applications are becoming nowadays ubiquitous, and therefore their safety and reliability have increasingly important societal impact. In this context, formal methods equipped with powerful and versatile analysis tools are more important than ever in the design process. Despite the relevant scientific results and well-established tools obtained in recent years, there is a constant need of enhancing the analysis capabilities in order to handle increasingly complex systems. We briefly discuss some recent advances in the field, introducing five papers selected from the 22th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (TACAS 2016).

Estimating the Learning Curve of a Novel Medical Device: Bipolar Sealer Use in Unilateral Total Knee Arthroplasties

BackgroundThe use of cost-effectiveness analysis for medical devices has proven to be challenging because of the existence of the learning effects in the device-operator interactions. The need for the relevant analytical framework for assessing the economic value of such technologies has been recognized. ObjectivesTo present a modified difference-in-differences (DID) cost-effectiveness methodology that facilitates visualization of a new health technology’s learning curve. MethodsUsing the Premier Perspective database (Premier Inc., Charlotte, NC), we examined the impact of physicians adopting a bipolar sealer (BPS) to control blood loss in primary unilateral total knee arthroplasties on hospital lengths of stay and total hospitalization costs when compared with two control groups. In our DID approach, we substituted month-from-adoption for the calendar-month-of-adoption in both graphical representations and ordinary least-squares regression results to estimate the effect of the BPS. ResultsThe results clearly demonstrated a learning curve associated with the adoption of the BPS technology. Although the reductions in length of stay were immediate, the first postadoption year costs increased by $1335 (extrahospital controls) to $1565 (within-hospital controls). Importantly, and also consistent with a learning curve hypothesis, these initial higher costs were offset by subsequent cost savings in the second and third years postadoption. ConclusionsThe presented modified DID approach is a suitable and versatile analytical tool for economic evaluation of a slowly diffusing medical device or health technology. It provides a better understanding of the potential learning effects associated with relevant interventions.

Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods.

Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.

Application of 1H NMR-based metabolomics for discrimination of different parts and development of a new processing workflow for Cistanche deserticola

Cistanche deserticola (CD) is one of the two authoritative source plants of Cistanches Herba, a well-known medicinal plant. Herein, 1H NMR spectroscopy was employed to characterize the chemical profile and to distinguish the different parts, as well as to propose a new processing workflow for CD. Signal assignment was achieved by multiple one and two dimensional NMR spectroscopic techniques in combination with available databases and authentic compounds. The upper parts of the plant were distinguished from the lower parts by combining 1H NMR spectroscopic dataset with multivariate statistical analysis. A new processing method that hyphenated steaming with freeze-drying, was demonstrated to be superior to either steaming coupled with oven-drying or direct freeze-drying via holistic 1H NMR-based metabolomic characterization. Phenylethanoid glycosides, mainly echinacoside and acteoside, were screened out and confirmed as the chemical markers responsible for exhibiting the superiority of the new processing workflow, whereas serial primary metabolites, especially carbohydrates and tricarboxylic acid cycle metabolites, were found as the primary molecules governing the discrimination between the upper and lower parts of the plant. Collectively, 1H NMR spectroscopy was demonstrated as a versatile analytical tool to characterize the chemical profile and to guide the in-depth exploitation of CD by providing comprehensive qualitative and quantitative information.

Secondary Ion Mass Spectrometry Analyses of Diamond and Moissanite in Ophiolite

The Cameca 1280‐HR large geometry SIMS instrument is a highly versatile analytical tool which can support a broad range of geochemical applications. Research using the Potsdam 1280 instrument focuses primarily on isotope ratio determinations in geomaterials. Optimized measurement protocols have already been established for δ18O determinations in zircon, and we are also working towards routine oxygen isotope determinations for quartz, calcite, mica, apatite and titanite. The primary challenge in developing such measurement systems are the identification and characterization of suitable reference materials (RMs), and this is made particularly challenging due to the matrix dependent ion yields of the SIMS ion source.Here we wish to report our progress towards establishing new analytical protocols for the determination of δ13C in both diamond and moissanite. In the case of diamond, our facility possesses three natural RMs with which we are able to produce data with a typical analytical repeatability of ∼0.15 ‰ (1sd). An inter‐comparison of our three diamond RMs demonstrates an overall data quality of better than 0.5‰ in terms of systematic offset between the various materials characterized using gas source mass spectrometry (Palot et al., 2012). A single such δ13C determination in diamond requires 80 s of data acquisition and involves a test portion mass of ∼400 pg of material. In‐house diamond reference materials for δ15N calibration allow us to measure this isotopic system to a total analytical uncertainty of ± 1.6 ‰ (1sd) at nitrogen concentrations reaching down to 250 μg/g. Due to the relatively low abundance of nitrogen in diamonds, such isotope ratio determinations require around 9 minutes of data collection.With respect to δ13C determinations in moissanite, we use a kimberlitic SiC as calibrant (Mathez et al., 1995), on which we achieve a repeatability of ∼0.2 ‰ (1sd) on a ∼350 pg test portion mass. Total data acquisition time for such measurements is 80 s. We are currently in the process of developing a second moissanite RM based on a synthetic, coarse‐grained powder. We will also investigate this new material for its δ30Si characteristics.

NMR-based Stable Isotope Resolved Metabolomics in systems biochemistry

Metabolism is the basic activity of live cells, and monitoring the metabolic state provides a dynamic picture of the cells or tissues, and how they respond to external changes, for in disease or treatment with drugs. NMR is an extremely versatile analytical tool that can be applied to a wide range of biochemical problems. Despite its modest sensitivity its versatility make it an ideal tool for analyzing biochemical dynamics both in vitro and in vivo, especially when coupled with its isotope editing capabilities, from which isotope distributions can be readily determined. These are critical for any analyses of flux in live organisms. This review focuses on the utility of NMR spectroscopy in metabolomics, with an emphasis on NMR applications in stable isotope-enriched tracer research for elucidating biochemical pathways and networks with examples from nucleotide biochemistry. The knowledge gained from this area of research provides a ready link to genomic, epigenomic, transcriptomic, and proteomic information to achieve systems biochemical understanding of living cells and organisms.

The Fractional Occupation Number Weighted Density as a Versatile Analysis Tool for Molecules with a Complicated Electronic Structure.

The fractional occupation number weighted density (FOD) analysis is explored as a general theoretical diagnostic for complicated electronic structures. Its main feature is to provide robustly and quickly the information on the localization of "hot" (strongly correlated and chemically active) electrons in a molecule. We demonstrate its usage in four different prototypical applications: 1) As a new and fast measure of the biradical character of polycyclic aromatic hydrocarbons, 2) for the selection of active orbital spaces in multiconfigurational or complete active space self consistent field (MCSCF/CASSCF) treatments, 3) as a possibility to describe molecular-energy landscapes consistently in regions with varying biradical character, as exemplified by partial double-bond torsions, and 4) as a powerful visualization method for static electron correlation effects in large biomolecules in connection with an efficient semi-empirical tight-binding molecular orbital scheme. The last application opens a full quantum-mechanical, unbiased route to the automatic detection of errors in experimental protein X-ray structures, such as false protonation states or misplaced atoms. In the first example, the complete (unfragmented) quantum-chemical calculation of the FOD for an entire metalloprotein with more than 7500 atoms is described.

Analytical verification and quality assessment of the Tosoh HLC-723GX HbA1c analyzer

ObjectivesIon-exchange high-performance liquid chromatography (IE-HPLC) has long been used as a reproducible and versatile analytical tool for HbA1c measurement.In this study, we performed analytical verification and quality assessment of the recently introduced small IE-HPLC Tosoh HLC-723GX HbA1c analyzer, and a comparison of results to immunoassay (IA) and capillary electrophoresis (CE). Design and methodsThe total imprecision of Tosoh HLC-723GX was verified according to CLSI EP15-A2 protocol using commercial control materials (C-QC) and pooled human whole blood samples (HWB). The Sigma metric was used for the evaluation of quality targets. HbA1c results were compared to automated CE (MiniCap Flex Piercing, Sebia, France) and IA (Tina-quant HbA1c Gen 2, Cobas Integra 400+, Roche Diagnostics, USA) procedures. ResultsThe total imprecision of Tosoh HLC-723GX-HbA1c for IFCC(mmol/mol) and NGSP(%) units was: 1.91/1.25% (HbA1c=31mmol/mol/5.0%) and 0.51/0.63% (HbA1c=84mmol/mol/9.8%) for C-QC, and 0.39/0.2% (HbA1c=47mmol/mol/6.5%) and 0.77/0.46% (HbA1c=94mmol/mol/10.8%) in HWB samples, respectively. Bland-Altman analysis did not reveal any deviation of the results between Tosoh HLC-723GX and CE: mean difference 0.0% (95%CI: −0.02927 to 0.02653%), while the mean HbA1c difference against IA was −0.07% (95%CI: −0.1039 to −0.02765). At the selected HbA1c clinical decision level (48mmol/mol/6,5%), six sigma analysis gave σ value of 3.91, within a desirable classification of performance. ConclusionThe analytical performance of the Tosoh HLC-723GX complies with the rigorous quality criteria for clinical use of HbA1c, with the results comparable to the CE procedure. Tosoh HLC-723GX provides a plausible analytical choice for reliable HbA1c measurement in low-volume laboratories.

Assessment of antibiotic residues in commercial and farm milk collected in the region of Guelma (Algeria)

In an attempt to enhance the quality and quantity of food production (especially milk) and in order to prevent, or treat,animal diseases, the use of antibiotics in Algeria follows an increasing trend. The increased use evidently contributes to the emergence of increased contamination levels of antibiotic residues. In this work, two methods were used to detect presence of antibiotic residues in raw and fermented cow’s milk collected in Guelma’s farms (in Algeria). The screening comprised different points of sale in Guelma province. In a first step a widely used prescreening method based on microbial inhibition assay; Delvotest SP-NT; was used to analyze 131 milk samples. In a second step a liquid chromatography coupled to mass spectrometry (LC-MS/MS) was used. The latter was first optimized for extraction of 36 veterinary drugs of penicillins, quinolones, macrolides, tetracyclines, sulfonamides, and trimethoprim from the collected milk. After simple extraction and dilution, the 194 samples, including those previously tested by the Delvotest SP-NT, were analyzed by LC-MS/MS. Results obtained by both methods were compared. Among the LC-MS/MS findings, 65.46 % of non-conform samples contained authorized residues at levels higher than the MRL, residues without set MRL, or non-authorized residues. The comparison of both methods showed that Delvotest SP-NT is less trustworthy due to number of false negative results. This was further confirmed by LC-MS/MS pointing out the traces of antibiotics in numerous samples. In 65.46 % of milk samples residues of antibiotics were found suggesting a lack of public health controls as well as an evidence of the negligent use of antibiotics in the livestock industry, which both form a risk to public health. This indication should be confirmed by a nationwide study with in-depth analyses of antibiotic’s presence in food chain originated from animals. The study offered an LC-MS/MS based analytical method ready to be used in Algerian National Residues Control Plan as a versatile analytical tool to monitor and determine the occurrence of antibiotic multi-residues in milk.

Measuring the Stiffness of Ex Vivo Mouse Aortas Using Atomic Force Microscopy.

Arterial stiffening is a significant risk factor and biomarker for cardiovascular disease and a hallmark of aging. Atomic force microscopy (AFM) is a versatile analytical tool for characterizing viscoelastic mechanical properties for a variety of materials ranging from hard (plastic, glass, metal, etc.) surfaces to cells on any substrate. It has been widely used to measure the stiffness of cells, but less frequently used to measure the stiffness of aortas. In this paper, we will describe the procedures for using AFM in contact mode to measure the ex vivo elastic modulus of unloaded mouse arteries. We describe our procedure for isolation of mouse aortas, and then provide detailed information for the AFM analysis. This includes step-by-step instructions for alignment of the laser beam, calibration of the spring constant and deflection sensitivity of the AFM probe, and acquisition of force curves. We also provide a detailed protocol for data analysis of the force curves.