Watson–Crick and Sugar-Edge Base Pairing of Cytosine in the Gas Phase: UV and Infrared Spectra of Cytosine·2-Pyridone

While keto-amino cytosine is the dominant species in aqueous solution, spectroscopic studies in molecular beams and in noble gas matrices show that other cytosine tautomers prevail in apolar environments. Each of these offers two or three H-bonding sites (Watson–Crick, wobble, sugar-edge). The mass- and isomer-specific S1 ← S0 vibronic spectra of cytosine·2-pyridone (Cyt·2PY) and 1-methylcytosine·2PY are measured using UV laser resonant two-photon ionization (R2PI), UV/UV depletion, and IR depletion spectroscopy. The UV spectra of the Watson–Crick and sugar-edge isomers of Cyt·2PY are separated using UV/UV spectral hole-burning. Five different isomers of Cyt·2PY are observed in a supersonic beam. We show that the Watson–Crick and sugar-edge dimers of keto-amino cytosine with 2PY are the most abundant in the beam, although keto-amino-cytosine is only the third most abundant tautomer in the gas phase. We identify the different isomers by combining three different diagnostic tools: (1) methylation of the cytosine N1–H group prevents formation of both the sugar-edge and wobble isomers and gives the Watson–Crick isomer exclusively. (2) The calculated ground state binding and dissociation energies, relative gas-phase abundances, excitation and the ionization energies are in agreement with the assignment of the dominant Cyt·2PY isomers to the Watson–Crick and sugar-edge complexes of keto-amino cytosine. (3) The comparison of calculated ground state vibrational frequencies to the experimental IR spectra in the carbonyl stretch and NH/OH/CH stretch ranges strengthen this identification.

End-tidal CO2 pressure: an important parameter for a correct interpretation of changes in cerebral hemodynamics and oxygenation measured with functional near infrared spectrophotometry (fNIRS)

The aim of the present study was to investigate the effects of different speech tasks (recitation of prose (PR), alliteration (AR) and hexameter (HR) verses) and a control task (mental arithmetic (MA) with voicing of the result) on endtidal CO2 (ET-CO2), cerebral hemodynamics; i.e. total hemoglobin (tHb) and tissue oxygen saturation (StO2). tHb and StO2 were measured with a frequency domain near infrared spectrophotometer (ISS Inc., USA) and ET-CO2 with a gas analyzer (Nellcor N1000). Measurements were performed in 24 adult volunteers (11 female, 13 male; age range 22 to 64 years) during task performance in a randomized order on 4 different days to avoid potential carry over effects. Statistical analysis was applied to test differences between baseline, 2 recitation and 5 recovery periods. The two brain hemispheres and 4 tasks were tested separately. Data analysis revealed that during the recitation tasks (PR, AR and HR) StO2 decreased statistically significant (p < 0.05) during PR and AR in the right prefrontal cortex (PFC) and during AR and HR in the left PFC. tHb showed a significant decrease during HR in the right PFC and during PR, AR and HR in the left PFC. During the MA task, StO2 increased significantly. A significant decrease in ET-CO2 was found during all 4 tasks with the smallest decrease during the MA task. In conclusion, we hypothesize that the observed changes in tHb and StO2 are mainly caused by an altered breathing during the tasks that led a lowering of the CO2 content in the blood provoked a cerebral CO2 reaction, i.e. a vasoconstriction of blood vessels due to decreased CO2 pressure and thereby decrease in cerebral blood volume. Therefore, breathing changes should be monitored during brain studies involving speech when using functional near infrared spectroscopy (fNIRS) to ensure a correct interpretation of changes in hemodynamics and oxygenation.

Independent measurement of biogenic silica in sediments by FTIR spectroscopy and PLS regression

We present an independent calibration model for the determination of biogenic silica (BSi) in sediments, developed from analysis of synthetic sediment mixtures and application of Fourier transform infrared spectroscopy (FTIRS) and partial least squares regression (PLSR) modeling. In contrast to current FTIRS applications for quantifying BSi, this new calibration is independent from conventional wet-chemical techniques and their associated measurement uncertainties. This approach also removes the need for developing internal calibrations between the two methods for individual sediments records. For the independent calibration, we produced six series of different synthetic sediment mixtures using two purified diatom extracts, with one extract mixed with quartz sand, calcite, 60/40 quartz/calcite and two different natural sediments, and a second extract mixed with one of the natural sediments. A total of 306 samples—51 samples per series—yielded BSi contents ranging from 0 to 100 %. The resulting PLSR calibration model between the FTIR spectral information and the defined BSi concentration of the synthetic sediment mixtures exhibits a strong cross-validated correlation ( R2cv = 0.97) and a low root-mean square error of cross-validation (RMSECV = 4.7 %). Application of the independent calibration to natural lacustrine and marine sediments yields robust BSi reconstructions. At present, the synthetic mixtures do not include the variation in organic matter that occurs in natural samples, which may explain the somewhat lower prediction accuracy of the calibration model for organic-rich samples.

Spectroscopy and detectability of liquid brines on mars

Recent geomorphological observations as well as chemical and thermodynamic studies demonstrate that liquid water should be stable today on the Martian surface at some times of the day. In Martian conditions, brines would be particularly more stable than pure water because salts can depress the freezing point and lower the evaporation rate of water. Despite this evidence, no clear spectral signature of liquid has been observed so far by the hyperspectral imaging spectrometers OMEGA and CRISM. However, past spectral analysis lacks a good characterization of brines׳ spectral signatures. This study thus aims to determine how liquid brines can be detected on Mars by spectroscopy. In this way, laboratory experiments were performed for reproducing hydration and dehydration cycles of various brines while measuring their spectral signatures. The resulting spectra first reveal a very similar spectral evolution for the various brine types and pure water, with the main difference observed at the end of the dehydration with the crystallization of various hydrated minerals from brines. The main characteristic of this spectral behavior is an important decoupling between the evolution of albedo and hydration bands depths. During most of the wetting/drying processes, spectra usually display a low albedo associated with shallow water absorption band depths. Strong water absorption band depth and high albedo are respectively only observed when the surface is very wet and when the surface is very dry. These experiments can thus explain why the currently active Martian features attributed to the action of a liquid are only associated with low albedo and very weak spectral signatures. Hydration experiments also reveal that deliquescence occurs easily even at low temperature and moderate soil water vapor pressure and could thus cause seasonal darkening on Mars. These experiments demonstrate that the absence of water absorptions in CRISM in the middle afternoon does not rule out water activity and suggest future spectral investigations to identify water on the Martian surface.

Real-Time In Vivo Characterization of Primary Liver Tumors With Diffuse Optical Spectroscopy During Percutaneous Needle Interventions: Feasibility Study in Woodchucks

OBJECTIVE This study presents the first in vivo real-time optical tissue characterization during image-guided percutaneous intervention using near-infrared diffuse optical spectroscopy sensing at the tip of a needle. The goal of this study was to indicate transition boundaries from healthy tissue to tumors, namely, hepatic carcinoma, based on the real-time feedback derived from the optical measurements. MATERIALS AND METHODS Five woodchucks with hepatic carcinoma were used for this study. The woodchucks were imaged with contrast-enhanced cone beam computed tomography with a flat panel detector C-arm system to visualize the carcinoma in the liver. In each animal, 3 insertions were performed, starting from the skin surface toward the hepatic carcinoma under image guidance. In 2 woodchucks, each end point of the insertion was confirmed with pathologic examination of a biopsy sample. While advancing the needle in the animals under image guidance such as fluoroscopy overlaid with cone beam computed tomography slice and ultrasound, optical spectra were acquired at the distal end of the needles. Optical tissue characterization was determined by translating the acquired optical spectra into clinical parameters such as blood, water, lipid, and bile fractions; tissue oxygenation levels; and scattering amplitude related to tissue density. The Kruskal-Wallis test was used to study the difference in the derived clinical parameters from the measurements performed within the healthy tissue and the hepatic carcinoma. Kurtoses were calculated to assess the dispersion of these parameters within the healthy and carcinoma tissues. RESULTS Blood and lipid volume fractions as well as tissue oxygenation and reduced scattering amplitude showed to be significantly different between the healthy part of the liver and the hepatic carcinoma (P < 0.05) being higher in normal liver tissue. A decrease in blood and lipid volume fractions and tissue oxygenation as well as an increase in scattering amplitude were observed when the tip of the needle crossed the margin from the healthy liver tissue to the carcinoma. The kurtosis for each derived clinical parameter was high in the hepatic tumor as compared with that in the healthy liver indicating intracarcinoma variability. CONCLUSIONS Tissue blood content, oxygenation level, lipid content, and tissue density all showed significant differences when the needle tip was guided from the healthy tissue to the carcinoma and can therefore be used to identify tissue boundaries during percutaneous image-guided interventions.

Real-time analysis of δ13C- and δD-CH4 in ambient air with laser spectroscopy: method development and first intercomparison results

In situ and simultaneous measurement of the three most abundant isotopologues of methane using mid-infrared laser absorption spectroscopy is demonstrated. A field-deployable, autonomous platform is realized by coupling a compact quantum cascade laser absorption spectrometer (QCLAS) to a preconcentration unit, called trace gas extractor (TREX). This unit enhances CH4 mole fractions by a factor of up to 500 above ambient levels and quantitatively separates interfering trace gases such as N2O and CO2. The analytical precision of the QCLAS isotope measurement on the preconcentrated (750 ppm, parts-per-million, µmole mole−1) methane is 0.1 and 0.5 ‰ for δ13C- and δD-CH4 at 10 min averaging time. Based on repeated measurements of compressed air during a 2-week intercomparison campaign, the repeatability of the TREX–QCLAS was determined to be 0.19 and 1.9 ‰ for δ13C and δD-CH4, respectively. In this intercomparison campaign the new in situ technique is compared to isotope-ratio mass spectrometry (IRMS) based on glass flask and bag sampling and real time CH4 isotope analysis by two commercially available laser spectrometers. Both laser-based analyzers were limited to methane mole fraction and δ13C-CH4 analysis, and only one of them, a cavity ring down spectrometer, was capable to deliver meaningful data for the isotopic composition. After correcting for scale offsets, the average difference between TREX–QCLAS data and bag/flask sampling–IRMS values are within the extended WMO compatibility goals of 0.2 and 5 ‰ for δ13C- and δD-CH4, respectively. This also displays the potential to improve the interlaboratory compatibility based on the analysis of a reference air sample with accurately determined isotopic composition.

Synchrotron X-ray photoabsorption spectroscopy of plasmas

Theoretical X-ray opacities are used in numerous radiative transfer simulations of plasmas at different temperatures and densities, for example astrophysics, fusion, metrology and EUV and X-rays radiation sources. However, there are only a reduced number of laboratories working on the validation of those theoretical results empirically, in particular for high temperature plasmas (mayor que 1eV). One of those limitations comes from the use of broad band EUV- X ray sources to illuminate the plasma which, among other issues, present low reproducibility and repetition rate [1]. Synchrotron radiation facilities are a more appropriate radiation source in that sense, since they provide tunable, reproducible and high resolution photons. Only their ?low? photon intensity for these experiments has prevented researchers to use it for this purpose. However, as new synchrotron facilities improve their photon fluxes, this limitation not longer holds [2]. This work evaluates the experimental requirements to use third generation synchrotron radiation sources for the empirical measurement of opacities of plasmas, proposing a pausible experimental set-up to carry them out. Properties of the laser or discharge generated plasmas to be studied with synchrotron radiation will be discussed in terms of their maximum temperatures, densities and temporal evolution. It will be concluded that there are encouraging reasons to pursue these kind of experiments which will provide with an appropriate benchmark for theoretical opacities

Degradation in seawater of structural adhesives for hybrid fibre-metal laminated materials

The adhesives used for applications in marine environments are subject to particular chemical conditions, which are mainly characterised by an elevated chlorine ion content and intermittent wetting/drying cycles, among others.These conditions can limit the use of adhesives due to the degradation processes that they experience. In this work, the chemical degradation of two different polymers, polyurethane and vinylester, was studied in natural seawater under immersion for different periods of time.The diffusion coefficients and concentration profiles of water throughout the thickness of the adhesiveswere obtained.Microstructural changes in the polymer due to the action of water were observed by SEM, and the chemical degradation of the polymer was monitored with the Fourier transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC). The degradation of the mechanical properties of the adhesive was determined by creep tests withMixed Cantilever Beam (MCB) specimens at different temperatures. After 180 days of immersion of the specimens, it was concluded that the J-integral value (depending on the strain) implies a loss of stiffness of 51% and a decrease in the failure load of 59% for the adhesive tested.

Raman and infrared spectra of dimethyl ether 13C-isotopologue (CH3O13CH3) from a CCSD(T) potential energy surface

So far, no experimental data of the infrared and Raman spectra of 13C isotopologue of dimethyl ether are available. With the aim of providing some clues of its low-lying vibrational bands and with the hope of contributing in a next spectral analysis, a number of vibrational transition frequencies below 300 cm−1 of the infrared spectrum and around 400 cm−1 of the Raman spectrum have been predicted and their assignments were proposed. Calculations were carried out through an ab initio three dimensional potential energy surface based on a previously reported one for the most abundant dimethyl ether isotopologue (M. Villa et al., J. Phys. Chem. A 115 (2011) 13573). The potential function was vibrationally corrected and computed with a highly correlated CCSD(T) method involving the COC bending angle and the two large amplitude CH3 internal rotation degrees of freedom. Also, the Hamiltonian parameters could represent a support for the spectral characterization of this species. Although the computed vibrational term values are expected to be very accurate, an empirical adjustment of the Hamiltonian has been performed with the purpose of anticipating some workable corrections to any possible divergence of the vibrational frequencies. Also, the symmetry breaking derived from the isotopic substitution of 13C in the dimethyl ether was taken into account when the symmetrization procedure was applied.

Nondestructive quantification of chemical and physical properties of fruits by time-resolved reflectance spectroscopy in the wavelength range 650-1000 nm

Time-resolved reflectance spectroscopy can be used to assess nondestructively the bulk (rather than the superficial) optical properties of highly diffusive media. A fully automated system for time-resolved reflectance spectroscopy was used to evaluate the absorption and the transport scattering spectra of fruits in the red and the near-infrared regions. In particular, data were collected in the range 650-1000 nm from three varieties of apples and from peaches, kiwifruits, and tomatoes. The absorption spectra were usually dominated by the water peak near 970 nm, whereas chlorophyll was detected at 675 nm. For ail species the scattering decreased progressively with increasing wavelength. A best fit to water and chlorophyll absorption line shapes and to Mie theory permitted the estimation of water and chlorophyll content and the average size of scattering centers in the bulls; of intact fruits.

On-line measurement of soil properties without direct spectral response in near infrared spectral range

So far, the majority of reports on on-line measurement considered soil properties with direct spectral responses in near infrared spectroscopy (NIRS). This work reports on the results of on-line measurement of soil properties with indirect spectral responses, e.g. pH, cation exchange capacity (CEC), exchangeable calcium (Caex) and exchangeable magnesium (Mgex) in one field in Bedfordshire in the UK. The on-line sensor consisted of a subsoiler coupled with an AgroSpec mobile, fibre type, visible and near infrared (vis–NIR) spectrophotometer (tec5 Technology for Spectroscopy, Germany), with a measurement range 305–2200 nm to acquire soil spectra in diffuse reflectance mode. General calibration models for the studied soil properties were developed with a partial least squares regression (PLSR) with one-leave-out cross validation, using spectra measured under non-mobile laboratory conditions of 160 soil samples collected from different fields in four farms in Europe, namely, Czech Republic, Denmark, Netherland and UK. A group of 25 samples independent from the calibration set was used as independent validation set. Higher accuracy was obtained for laboratory scanning as compared to on-line scanning of the 25 independent samples. The prediction accuracy for the laboratory and on-line measurements was classified as excellent/very good for pH (RPD = 2.69 and 2.14 and r2 = 0.86 and 0.78, respectively), and moderately good for CEC (RPD = 1.77 and 1.61 and r2 = 0.68 and 0.62, respectively) and Mgex (RPD = 1.72 and 1.49 and r2 = 0.66 and 0.67, respectively). For Caex, very good accuracy was calculated for laboratory method (RPD = 2.19 and r2 = 0.86), as compared to the poor accuracy reported for the on-line method (RPD = 1.30 and r2 = 0.61). The ability of collecting large number of data points per field area (about 12,800 point per 21 ha) and the simultaneous analysis of several soil properties without direct spectral response in the NIR range at relatively high operational speed and appreciable accuracy, encourage the recommendation of the on-line measurement system for site specific fertilisation.

Non-destructive optical characterisation of fruits with time-resolved reflectance spectroscopy.

Increasing attention is being paid to the possible development of non-invasive tests for the assessment of the quality of fruits We propose a novel non-destructive method for the measurement of the internal optical properties of fruits and vegetables by means of time resolved reflectance spectroscopy in the visible and NIR range. A fully automated instrumentation for time-resolved reflectance measurements was developed It is based on mode-locked laser sources and electronics for time-correlated single photon counting, and provides a time-resolution of 120-160 ps The system was used to probe the optical properties of several species and varieties of fruits and vegetables in the red and NIR range (650-1000 nm). In most fruits, the absorption line shape is dominated by the absorption peak of water, centred around 970 nm Generally, the absorption spectra also show the spectral features typical of chlorophyll, with maximum at 675 nm In particular, for what concerns apples, variations in peak intensity are observed depending on the variety, the degree of ripeness as well as the position on the apple. For all the species and varieties considered, the transport scattering coefficient decreases progressively upon increasing the wavelength.

Non-destructive optical characterization of fruits in the red and near infrared.

Increasing attention is being paid to the possible development of non-invasive tests for the assessment of the quality of Fruits. We propose a novel non-destructive method for the measurement of the internal optical properties of fruits and vegetables by means of lime-resolved reflectance spectroscopy in the visible and NIR range. A Fully automated instrumentation for time-resolved reflectance measurements was developed. It is based on mode-locked laser sources and electronics for time-correlated single photon counting, and provides a time-resolution of 120-160 ps. The system was used to probe the optical properties of several species and varieties of Fruits and vegetables in the red and NIR range (650-1000 nm). In most Fruits, the absorption line shape is dominated by the absorption peak of water, centred around 970 nm. Generally, the absorption spectra also show the spectral features typical of chlorophyll, with maximum at 675 nm. In particular, for what concerns apples, variations in peak intensity are observed depending on the variety, the degree of ripeness as well as the position on the apple. For all the species and varieties considered, the transport scattering coefficient decreases progressively upon increasing the wavelength.

Models for internal quality sorting of fruit, based on time-domain laser reflectance spectroscopy (TDRS).

Non-destructive measurement of fruit quality has been an important objective through recent years (Abbott, 1999). Near infrared spectroscopy (NIR) is applicable to the cuantification of chemicals in foods and NIK "laser spectroscopy" can be used to estimate the firmness of fruits. However, die main limitation of current optical techniques that measure light transmission is that they do not account for the coupling between absorption and scattering inside the tissue, when quantifying the intensity o f reemitted light. The solution o f this l i m i t a t i o n was the goal o f the present work.