A low-cost hyperspectral scanner for natural imaging and the study of animal colour vision above and under water.

Hyperspectral imaging is a widely used technology for industrial and scientific purposes, but the high cost and large size of commercial setups have made them impractical for most basic research. Here, we designed and implemented a fully open source and low-cost hyperspectral scanner based on a commercial spectrometer coupled to custom optical, mechanical and electronic components. We demonstrate our scanner's utility for natural imaging in both terrestrial and underwater environments. Our design provides sub-nm spectral resolution between 350-950 nm, including the UV part of the light spectrum which has been mostly absent from commercial solutions and previous natural imaging studies. By comparing the full light spectra from natural scenes to the spectral sensitivity of animals, we show how our system can be used to identify subtle variations in chromatic details detectable by different species. In addition, we have created an open access database for hyperspectral datasets collected from natural scenes in the UK and India. Together with comprehensive online build- and use-instructions, our setup provides an inexpensive and customisable solution to gather and share hyperspectral imaging data.

A laser-induced breakdown spectroscopy-integrated lateral flow strip (LIBS-LFS) sensor for rapid detection of pathogen.

Incorporation of new readout methods with established analytical devices allows methodological innovations in analytical sciences. Herein, we present a new sensing platform by combining an ultrasensitive element analyzer, namely the laser-induced breakdown spectroscopy (LIBS) and a lateral flow strip (LFS). AgxAuy bimetallic nanoparticles (AgxAuyBNPs) are selected as the labels to deliver the optimal quantitative performance by analyzing the Ag (I) signal from the test (T) line of LFS. For prototypical application in pathogen detection, the LIBS-LFS sensor can achieve a detection limit of 1.6 cfu mL-1 of Staphylococcus aureus (S. aureus) within 10 min, which is superior to conventional methods. Importantly, the signals of AgxAuyBNPs for visual and LIBS analysis are stable and still readable after the detection is finished and the test strip is stored for up to 13 days, suggesting a potential for long-term data preservation. This combination of LIBS with LFS provides a new concept toward integrated nano/analytical devices that can benefit various application scenarios.

Translating vibrational spectroscopy into clinical applications - vision or reality?

The Faraday Discussion meeting "Advanced Vibrational Spectroscopy for Biomedical Applications" provided an excellent opportunity to share and discuss recent research and applications on a highly interdisciplinary level. Spectral pathology, single cell analysis, data handling, clinical spectroscopy, and the spectral analysis of biofluids were among the topics covered during the meeting. The focus on discussion rather than "merely" presentation was highly appreciated and fruitful discussions evolved around the interpretation of the amide-bands, optical resolution, the role of diffraction and data analysis procedure, to name a few. The meeting made clear that the spectroscopy of molecular vibrations in biomolecules has evolved from a purely academic research tool to a technology used in clinical practice in some cases. In this sense, biomedical vibrational spectroscopy has reached a pivotal point at which questions like diagnostic value, therapeutic consequence and financial viability are gaining more and more importance.

A novel rapid quantitative analysis of drug migration on tablets using laser induced breakdown spectroscopy.

There have been few reports wherein drug migration from the interior to the surface of a tablet has been analyzed quantitatively until now. In this paper, we propose a novel, rapid, quantitative analysis of drug migration in tablets using laser induced breakdown spectroscopy (LIBS). To evaluate drug migration, model tablets containing nicardipine hydrochloride as active pharmaceutical ingredient (API) were prepared by a conventional wet granulation method. Since the color of this API is pale yellow and all excipients are white, we can observe the degree of drug migration by visual inspection in these model tablets. In order to prepare tablets with different degrees of drug migration, the temperature of the drying process after tableting was varied between 50 to 80 °C. Using these manifold tablets, visual inspection, Fourier transform (FT)-IR mapping and LIBS analysis were carried out to evaluate the drug migration in the tablets. While drug migration could be observed using all methods, only LIBS analysis could provide quantitative analysis wherein the average LIBS intensity was correlated with the degree of drug migration obtained from the drying temperature. Moreover, in this work, we compared the sample preparation, data analysis process and measurement time for visual inspection, FT-IR mapping and LIBS analysis. The results of the comparison between these methods demonstrated that LIBS analysis is the simplest and the fastest method for migration monitoring. From the results obtained, we conclude that LIBS analysis is one of most useful process analytical technology (PAT) tools to solve the universal migration problem.

A low-cost, portable, and quantitative spectral imaging system for application to biological tissues.

The ability of diffuse reflectance spectroscopy to extract quantitative biological composition of tissues has been used to discern tissue types in both pre-clinical and clinical cancer studies. Typically, diffuse reflectance spectroscopy systems are designed for single-point measurements. Clinically, an imaging system would provide valuable spatial information on tissue composition. While it is feasible to build a multiplexed fiber-optic probe based spectral imaging system, these systems suffer from drawbacks with respect to cost and size. To address these we developed a compact and low cost system using a broadband light source with an 8-slot filter wheel for illumination and silicon photodiodes for detection. The spectral imaging system was tested on a set of tissue mimicking liquid phantoms which yielded an optical property extraction accuracy of 6.40 +/- 7.78% for the absorption coefficient (micro(a)) and 11.37 +/- 19.62% for the wavelength-averaged reduced scattering coefficient (micro(s)').

Machine vision detection of bonemeal in animal feed samples.

There is growing public concern about contaminants in food and feed products, and reflection-based machine vision systems can be used to develop automated quality control systems. An important risk factor in animal feed products is the presence of prohibited ruminant-derived bonemeal that may contain the BSE (Bovine Spongiform Encephalopathy) prion. Animal feed products are highly complex in composition and texture (i.e., vegetable products, mineral supplements, fish and chicken meal), and current contaminant detection systems rely heavily on labor-intensive microscopy. In this study, we developed a training data set comprising 3.65 million hyperspectral profiles of which 1.15 million were from bonemeal samples, 2.31 million from twelve other feed materials, and 0.19 million denoting light green background (bottom of Petri dishes holding feed materials). Hyperspectral profiles in 150 spectral bands between 419 and 892 nm were analyzed. The classification approach was based on a sequence of linear discriminant analyses (LDA) to gradually improve the classification accuracy of hyperspectral profiles (reduce level of false positives), which had been classified as bonemeal in previous LDAs. That is, all hyperspectral profiles classified as bonemeal in an initial LDA (31% of these were false positives) were used as input data in a second LDA with new discriminant functions. Hyperspectral profiles classified as bonemeal in LDA2 (false positives were equivalent to 16%) were used as input data in a third LDA. This approach was repeated twelve times, in which at each step hyperspectral profiles were eliminated if they were classified as feed material (not bonemeal). Four independent feed materials were experimentally contaminated with 0-25% (by weight) bonemeal and used for validation. The analysis presented here provides support for development of an automated machine vision to detect bonemeal contamination around the 1% (by weight) level and therefore constitutes an important initial screening tool in comprehensive, rapid, and practically feasible quality control of feed materials.

Massively parallel single-molecule manipulation using centrifugal force.

Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology, and medicine. However, widespread adoption of single-molecule techniques has been impeded by equipment cost and the laborious nature of making measurements one molecule at a time. We have solved these issues by developing an approach that enables massively parallel single-molecule force measurements using centrifugal force. This approach is realized in an instrument that we call the centrifuge force microscope in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force-field while their micro-to-nanoscopic motions are observed. We demonstrate high-throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Additionally, we verify the force accuracy of the instrument by measuring the well-established DNA overstretching transition at 66 +/- 3 pN. With significant benefits in efficiency, cost, simplicity, and versatility, single-molecule centrifugation has the potential to expand single-molecule experimentation to a wider range of researchers and experimental systems.

Determination of phytoplankton composition using absorption spectra.

Characterisation of phytoplankton communities in aquatic ecosystems is a costly task in terms of time, material and human resources. The general objective of this paper is not to replace microscopic counts but to complement them, by fine-tuning a technique using absorption spectra measurements that reduces the above-mentioned costs. Therefore, the objective proposed in this paper is to assess the possibility of achieving a qualitative determination of phytoplankton communities by classes, and also a quantitative estimation of the number of phytoplankton cells within each of these classes, using spectrophotometric determination. Samples were taken in three areas of the Spanish Mediterranean coast. These areas correspond to estuary systems that are influenced by both continental waters and Mediterranean Sea waters. 139 Samples were taken in 7-8 stations per area, at different depths in each station. In each sample, the absorption spectrum and the phytoplankton classes (Bacyllariophyceae (diatoms), Cryptophyceae, Clorophyceae, Chrysophyceae, Prasynophyceae, Prymnesophyceae, Euglenophyceae, Cyanophyceae, Dynophyceae and the Synechococcus sp.) were determined. Data were analysed by means of the Partial Least Squares (PLS) multivariate statistical technique. The absorbances obtained between 400 and 750 nm were used as the independent variable and the cell/l of each phytoplankton class was used as the dependent variable, thereby obtaining models which relate the absorbance of the sample extract to the phytoplankton present in it. Good results were obtained for diatoms (Bacillarophyceae), Chlorophyceae and Cryptophyceae.

The use of tunable diode laser absorption spectroscopy for rapid measurements of the delta13C of animal breath for physiological and ecological studies.

In this study we introduce the use of tunable diode laser absorption spectroscopy (TDLAS) as a technique for making measurements of the delta13C of animal 'breath' in near real time. The carbon isotope ratios (delta13C) of breath CO2 trace the carbon source of the materials being metabolized, which can provide insight into the use of specific food resources, e.g. those derived from plants using C3 versus C4 or CAM photosynthetic pathways. For physiological studies, labeled substrates and breath analyses provide direct evidence of specific physiological (e.g. fermentative digestion) or enzymatic (e.g. sucrase activity) processes. Although potentially very informative, this approach has rarely been taken in animal physiological or ecological research. In this study we quantify the utilization of different plant resources (photosynthetic types--C3 or C4) in arthropod herbivores by measuring the delta13C of their 'breath' and comparing it with bulk tissue values. We show that breath delta13C values are highly correlated with bulk tissues and for insect herbivores reflect their dietary guild, in our case C3-specialists, C4-specialists, or generalists. TDLAS has a number of advantages that will make it an important tool for physiologists, ecologists and behaviorists: it is non-invasive, fast, very sensitive, accurate, works on animals of a wide range of body sizes, per-sample costs are small, and it is potentially field-deployable.

Cost-effective diffuse reflectance spectroscopy device for quantifying tissue absorption and scattering in vivo.

A hybrid optical device that uses a multimode fiber coupled to a tunable light source for illumination and a 2.4-mm photodiode for detection in contact with the tissue surface is developed as a first step toward our goal of developing a cost-effective, miniature spectral imaging device to map tissue optical properties in vivo. This device coupled with an inverse Monte Carlo model of reflectance is demonstrated to accurately quantify tissue absorption and scattering in tissue-like turbid synthetic phantoms with a wide range of optical properties. The overall errors for quantifying the absorption and scattering coefficients are 6.0+/-5.6 and 6.1+/-4.7%, respectively. Compared with fiber-based detection, having the detector right at the tissue surface can significantly improve light collection efficiency, thus reducing the requirement for sophisticated detectors with high sensitivity, and this design can be easily expanded into a quantitative spectral imaging system for mapping tissue optical properties in vivo.

Fast, sensitive, and inexpensive alternative to analytical pigment HPLC: quantification of chlorophylls and carotenoids in crude extracts by fitting with Gauss peak spectra.

Quantification of pigments in complex mixtures is an important task in the physiology of photosynthetic organisms, because pigment composition differs depending on the species, tissue, and physiological state. Currently available methods, however, are either limited to very few pigments (classical UV/vis spectroscopic methods), or they are time-consuming, labor intensive, or costly (e.g., HPLC). Here we describe a UV/vis spectrophotometric method that is capable of a rapid (approximately 1 min/sample) and inexpensive (<1 euro/sample) quantification of more than a dozen pigments in a crude extract, which means it is suitable for high-throughput screening applications. A detection limit of <1 pmol for each pigment allows for determining the pigment composition in only 0.5 microg of lyophilized leaves or algae. The method is based on the description of each pigment spectrum by a series of Gaussian peaks. A sample spectrum is then fitted by a linear combination of these "Gauss peak spectra" including an automatic correction of wavelength inaccuracy, baseline instability, sample turbidity, and effects of temperature/water content. Here we present the Gauss peak spectra from 350 to 750 nm for acetone solutions of all chlorophyll and carotenoid derivatives that are abundant (including conditions of Cd, Cu, or Zn stress) in leaves of higher plants, Euglena, brown algae, and various cyanobacteria like Anabaena and Trichodesmium: [Mg]-Chl a, b, c1, c2; pheophytin a, b; [Cd]-Chl a, b; [Cu]-Chl a, b; [Zn]-Chl a, b; antheraxanthin, aurochrome, beta-carotene, beta-cryptoxanthin, cis- and trans-canthaxanthin, diadinochrome (=diadinoxanthin 5,6-epoxide), cis- and trans-diadinoxanthin, diatoxanthin, cis- and trans-echinenone, fucoxanthin, lutein, myxoxanthophyll, neoxanthin, violaxanthin, and all three stereoisomers of zeaxanthin in acetone. We present extensive tests of our new quantification method for determining optimal and limiting conditions of its performance and for comparison with previous methods. Finally, we show application examples for Thlaspi fendleri (Chlorophyta), Euglena gracilisc (Euglenophyta), Ectocarpus siliculosus (Phaeophyta), and Trichodesmium erythraeum IMS101 (cyanobacteria).

Participant recruitment and motivation for participation in optical technology for cervical cancer screening research trials.

In order to improve recruitment for cervical cancer screening trials, it is necessary to analyze the effectiveness of recruitment strategies used in current trials. A trial to test optical spectroscopy for the diagnosis of cervical neoplasia recruited 1000 women from the community; the trial evaluated the emerging technology against Pap smears and colposcopically directed biopsies for cervical dysplasia. We have examined women's reasons for participating as well as the effectiveness and efficiency for each recruitment strategy. Reasons for participation were identified and compared between trials. The recruitment method that resulted in the most contacts was newspaper reportorial coverage and advertising, followed by family and friends, then television news coverage. The most cost-effective method for finding eligible women who attend the research appointment is word of mouth from a family member or friend. Recommendations are given for maximizing the efficiency of recruitment for cervical cancer screening trials.

Using a spectral reflectance technique to measure transcutaneous bilirubin in neonates: a new device.

Devices that use a spectral reflectance technique are used to non-invasively measure total bilirubin levels in neonates to monitor the development of hyperbilirubinemia. As a screening technique for the healthy neonate population, these devices provide instantaneous information, may reduce the need of heel-pricks on neonates, and indicate which neonates will need serum bilirubin measurement. Evidence from studies supported by the manufacturer of BiliChek (tm), the newest device using the spectral reflectance technique, suggests that there is a linear correlation between transcutaneous bilirubin measured by BiliChek (tm) and total serum bilirubin as measured by the gold standard technique (i.e. HPLC). The correlation, however, is limited by gestational age of the neonate, as well as certain pathological neonatal conditions. Prospective cohort studies on the effectiveness of the technology in the reduction of hospital readmission, and using the incidence of morbidity and mortality from kernicterus as clinical endpoints, would be useful.

A continuous spectrophotometric method based on enzymatic cycling for determining L-glutamate.

A continuous spectrophotometric assay for determining low levels of L-glutamate is described. The assay, which involves the enzymes L-glutamate oxidase and glutamic-pyruvic transaminase, is based on the recycling of L-glutamate into alpha-ketoglutarate, with the concomitant appearance of one molecule of hydrogen peroxide in each turn of the cycle. This is subsequently reduced by means of a peroxidase-coupled reaction, using 2, 2'-azinobis(3-ethylbenzthiazoline-6-sulfonic acid) as substrate. In this way the interference observed in the cyclic assay using glutamic-oxalacetic transaminase, which is due to the fact that L-aspartate is also a substrate of L-glutamate oxidase, is eliminated. A kinetic study of the system is presented, with the accumulation of chromophore being seen to undergo a transient phase, which is dependent both on the cycling rate and on the auxiliary enzyme concentration. The kinetic parameters characterizing the system have been determined, making it possible to optimize costs with respect to the enzymes involved in the cycle, since the minimum amount needed for a given rate constant of the cycle can be calculated.