Global analysis of steady-state polarized fluorescence spectra using trilinear curve resolution.

Global analysis using trilinear curve resolution is described and shown to be a powerful method for the resolution of polarized fluorescence data arrays, in which the measured fluorescence intensity is a separable function of polarization orientation, excitation wavelength, and emission wavelength. This methodology is applicable to mixtures the components of which have linearly independent excitation and emission spectra and distinct anisotropies. Normalized excitation and emission spectra of individual components can be uniquely determined without prior assumptions concerning spectral shapes (e.g., sum of Gaussians) and without the uncertainties inherent in bilinear techniques such as principal component analysis or factor analysis. The normalized excitation and emission vectors are combined with the total absorption spectrum of the multicomponent mixture to compute absolute absorption and emission spectra. The precision of this methodology is evaluated as a function of noise, overlap, relative intensity, and anisotropy difference between components using simulated mixtures of the DNA bases. The ability of this method to extract individual spectra from steady-state fluorescence data arrays is illustrated for mixtures containing two and three components.     

Determination of tyrosine and tryptophan in proteins by the absorption spectra of derivatives

The contents of tyrosine and tryptophan were determined by the method based on the first derivatives of the proteins absorption spectra within the alkali pH. The advantages of the method are as follows: a much better resolution of tyrosine and tryptophan spectral maxima located at 293 and 307 nm, respectively, which allows the precision of their assay to be increased, especially in case of a small amount of one amino acid and relative abundance of the other and high turbidity of the preparations; the account of the cystine absorption is not necessary; possibility to study proteins containing the chromophore prosthetic groups.     

Power spectra of extinction in the fossil record

Recent Fourier analyses of fossil extinction data have indicated that the power spectrum of extinction during the Phanerozoic may take the form of 1/f noise, a result which, it has been suggested, could be indicative of the presence of `critical dynamics'' in the processes giving rise to extinction. In this paper we examine extinction power spectra in some detail, using family-level data from two widely available compilations. We find that although the average form of the power spectrum roughly obeys the 1/f law, the spectrum can be represented more accurately by dividing it into two regimes: a low-frequency one which is well fit by an exponential, and a high-frequency one in which it follows a power law with a 1/f² form. We give explanations for the occurrence of each of these behaviours and for the position of the crossover between them.     

Analysis of the near-ultraviolet absorption and circular dichroic spectra of parsley plastocyanin for the effects of pH and copper center conformation changes

The absorption and circular dichroic (CD) spectra of parsley plastocyanin (PC) were measured in order to determine the effects of changes in primary amino acid sequence on both the copper center and protein components of the PC molecule. The near-ultraviolet (uv) absorption and CD spectra of parsley PC were found to be qualitatively similar to those of spinach, poplar, and lettuce PC, except for the near-uv CD spectrum of the reduced form at low pH (ca. pH 5.0). The CD spectrum of reduced parsley PC in the 250-265 nm wavelength region changes from positive to negative ellipticity upon reduction of pH, and is characterized by a pKa value of 5.7. This pKa value is the same as that for the protonation of the histidine 87 copper ligand, observed by NMR, and the change in conformation of the copper center. Similar processes are believed to occur in the other PC species at lower pH values. Thus, the pH-dependent perturbations of the near-uv CD spectra of reduced PC are interpreted as due to transitions in the reduced copper center. The increase in the near-uv absorption spectrum of reduced PC can be divided into pH-independent and pH-dependent portions. The pH-independent portion resembles the absorption spectrum of tetrahedral Cu(I) metallothionein, suggesting the presence of Cu(I)-Cys 84 and/or Cu(I)-Met 92 charge transfer transitions in the near-uv absorption spectra of reduced PC. The pH dependence of the absorption spectrum changes and the pH difference absorption spectrum indicate that tyrosine residues may contribute to at least a part of the pH-dependent portion of the absorption increase of reduced PC.     

Computer-assisted analysis of photoacoustic spectra of solid and solution state cyanide methemoglobin

A computer-assisted method for analyzing photoacoustic spectra has been developed. Using this analysis, the relative absorption spectrum and either the chromophore concentration or thermal diffusivity characteristic of a sample can be derived from its photoacoustic spectrum. We have demonstrated the accuracy of the method by analyzing photoacoustic spectra of solution and crystalline-phase bovine cyanide methemoglobin. BASIC and FORTRAN routines used to collect and to analyze photoacoustic spectra are described. Photoacoustic spectroscopy can be used in conjunction with the analytical method presented here to obtain accurate absorption spectra from a variety of solid, opaque, and/or turbid samples.     

Red spectra from white and blue noise

The value of maps of the interval in modelling population dynamics has recently been called into question because temporal variations from such maps have blue or white power spectra, whereas many observations of real populations show time-series with red spectra. One way to deal with this discrepancy is to introduce chaotic or stochastic fluctuations in the parameters of the map. This leads to on–off intermittency and can markedly redden the spectrum produced by a model that does not by itself have a red spectrum. The parameter fluctuations need not themselves have a red spectrum in order to achieve this effect. Because the power spectrum is not invariant under a change of variable, another way to redden the spectrum is by a suitable transformation of the variables used. The question this poses is whether spectra are the best means of characterizing a fluctuating variable.     

Computer-aided analysis of infrared, circular dichroism and absorption spectra

Marquardt and Powell optimization methods without constraintson the optimized spectral parameters were employed for decompositionof complex i.r., c.d. and absorption spectra into componentbands. The procedure resolved experimental spectra into eightcomponent bands and it can be easily adjusted for a larger setof component bands. The CPU time required for achievement ofsatisfactory convergence of parameters for eight component bandsis rather large even when using mainframe computers and thereforedivision of spectra into a few non-overlapped parts is advisable.The program also can be used for calculation of absorption,c.d. and difference spectra from formatted raw spectral data. Received on January 13, 1986; accepted on April 7, 1986     

Effects of phytoplankton species composition on absorption spectra and modeled hyperspectral reflectance

Understanding the spectral characteristics of remotely-sensed reflectance by different phytoplankton species can assist in the development of algorithms to identify various algal groups using satellite ocean color remote sensing. One of the main challenges is to separate the effect of species composition on the reflectance spectrum from other factors such as pigment concentration and particle size structure. Measuring the absorption spectra of nine different cultured algae, and estimating the reflectance of the different species, provides a useful approach to study the effects of species composition on the bio-optical properties. The results show that the absorption spectra of different species exhibit different spectral characteristics and that species composition can significantly change the absorption characteristics at four main peaks (438, 536, 600 and 650 nm). A ‘distance angle index’ was used to compare different phytoplankton species. Results indicate that this index can be used to identify species from the absorption spectra, using a database of standard absorption spectra of known species as reference. By taking into account the role of species composition in the phytoplankton absorption model, the performance of the model can be improved by up to 5%. A reflectance-species model is developed to estimate the remotely-sensed reflectance from the absorption spectra, and the reflectance of different phytoplankton species at the same chlorophyll-a concentration is compared, to understand effects of species composition on the reflectance spectra. Different phytoplankton species can cause up to 33% difference in the modeled reflectance at short wavelengths under the condition of the same chlorophyll-a concentration, and variations in the reflectance spectrum correspond to the colors of the algae. The standard deviation of the reflectance among different species shows that the variations from 400 to 450 nm are sensitive to species composition at low chlorophyll-a concentrations, whereas variations in the 510 to 550 nm range are more sensitive under high chlorophyll-a concentrations. For this reason, the green bands may be more suitable for estimating species composition from hyperspectral satellite data during bloom conditions, whereas the blue bands may be more helpful in detection of species under low chlorophyll-a concentrations. In this theoretical approach, variations in reflectance at the same chlorophyll-a concentration can be used to identify phytoplankton species. Another approach to identify phytoplankton species from remotely-sensed hyperspectral reflectance measurements would be to derive the absorption spectra of phytoplankton from the reflectance measurements, and compare these with a standard database of absorption spectra.     

Nonlinear Optical Properties of Large-Sized Gold Nanorods

The nonlinear optical properties of single gold nanorods (GNRs) with a large diameter of ～200 nm and a long length of ～800 nm were investigated by using a focused femtosecond (fs) laser light with tunable wavelength. While the linear and nonlinear optical properties of small-sized GNRs have been extensively studied, the nonlinear optical properties of large-sized GNRs and the effects of high-order surface plasmon resonances remain unexplored. Second harmonic generation (SHG) or/and two-photon-induced luminescence (TPL) were observed in the nonlinear response spectra, and their dependences on excitation wavelength and polarization were examined. The scattering and absorption spectra of the small- and large-sized GNRs were compared by using the discrete dipole approximation method. It was found that the extinction of large-sized GNRs is dominated by scattering rather than absorption, which is dominant in small-sized GNRs. In addition, it was revealed that the excitation wavelength-dependent SHG of a GNR is governed by the linear scattering of the GNR and the maximum SHG is achieved at the valley of the scattering spectrum. In comparison, the excitation wavelength dependence of TPL is determined by the absorption spectrum of the GNR. The polarization-dependent SHG of a GNR exhibits a strong dependence on the dimension of the GNR, and it may appear as bipolar distributions parallel or perpendicular to the long axis of the GNR or multipole distributions.     

A representation learning approach for recovering scatter-corrected spectra from Fourier-transform infrared spectra of tissue samples

Infrared spectra obtained from cell or tissue specimen have commonly been observed to involve a significant degree of scattering effects, often Mie scattering, which probably overshadows biochemically relevant spectral information by a nonlinear, nonadditive spectral component in Fourier transform infrared (FTIR) spectroscopic measurements. Correspondingly, many successful machine learning approaches for FTIR spectra have relied on preprocessing procedures that computationally remove the scattering components from an infrared spectrum. We propose an approach to approximate this complex preprocessing function using deep neural networks. As we demonstrate, the resulting model is not just several orders of magnitudes faster, which is important for real-time clinical applications, but also generalizes strongly across different tissue types. Using Bayesian machine learning approaches, our approach unveils model uncertainty that coincides with a band shift in the amide I region that occurs when scattering is removed computationally based on an established physical model. Furthermore, our proposed method overcomes the trade-off between computation time and the corrected spectrum being biased towards an artificial reference spectrum.     

An open‐source code for Mie extinction extended multiplicative signal correction for infrared microscopy spectra of cells and tissues

Infrared spectroscopy of single cells and tissue is affected by Mie scattering. During recent years, several methods have been proposed for retrieving pure absorbance spectra from such measurements, while currently no user‐friendly version of the state‐of‐the‐art algorithm is available. In this work, an open‐source code for correcting highly scatter‐distorted absorbance spectra of cells and tissues is presented, as well as several improvements of the latest version of the Mie correction algorithm based on extended multiplicative signal correction (EMSC) published by Konevskikh et al. In order to test the stability of the code, a set of apparent absorbance spectra was simulated. To this purpose, pure absorbance spectra based on a Matrigel spectrum are simulated. Scattering contributions where obtained by mimicking the scattering features observed in a set of experimentally obtained spectra . It can be concluded that the algorithm is not depending strongly on the reference spectrum used for initializing the algorithm and retrieves well the underlying pure absorbance spectrum. The calculation time of the algorithm is considerably improved with respect to the resonant Mie scattering EMSC algorithm used by the community today.      

Energy spectra of secondary electrons in water vapour

The purpose of this work is to present a method for the calculation of secondary electron spectra generated by photons in water vapour in the energy region from 10 eV to 10 MeV. The cross sections below and above 1 keV have been treated separately. Examples are given for secondary electron spectra for low-energy photons, <100 eV, in which all electrons are photoelectrons, and at higher energy regions, such as for ⁶⁰Co photons. The spectrum of the first generation of secondary electrons, produced by ⁶⁰Co photons, which are mainly due to incoherent scattering, was fitted with a set of polynomial functions which can be used as input for electron radiation action calculations.     

Partial analysis of the bands seen in circular dichroism spectra of green and blue-green algal cells and thylakoids

A comparison was made of the circular dichroism (C.D.) spectra of Chlorella, Euglena, and Anacystis cells and thylakoids. Analyses of the spectra reveal that these C.D. bands are similar to those observed previously in whole spinach choloroplasts and subchloroplast particles. C.D. spectra of Euglena chloroplasts show bands at longer wavelengths than previously reported. From comparisons of circular dichroism spectra and fine structure, it was concluded that: (a) bands seen in circular dichroism spectra were not the result of light scattering from thylakoid membranes; and (b) bands seen in the C.D. spectra of nonmembranous systems (previously reported) could account for circular dichroism of algae. We also concluded that comparisons would have to be made with model systems in order to correct for effects of absorption flattening, concentration obscuring, and differential light scattering of membranous systems.     

Method of decomposing spectra using the original spectrum and its derivatives

A method for the decomposition of optical spectra into bands was proposed, which is based on simultaneous approximation of the initial spectrum and its derivatives. The bands of the standard (gaussian) form were used in the decomposition procedure. A method for the selection of the optimal smoothing filter was described. The efficiency of the proposed method was demonstrated on model and experimental absorption spectra. It was shown that this method makes it possible to determine the number of bands and its parameters more exactly than the standard approach based on the analysis of one derivative of one power.     

Photosynthetic action spectra of marine algae

A polarographic oxygen determination, with tissue in direct contact with a stationary platinum electrode, has been used to measure the photosynthetic response of marine algae. These were exposed to monochromatic light, of equal energy, at some 35 points through the visible spectrum (derived from a monochromator). Ulva and Monostroma (green algae) show action spectra which correspond very closely to their absorption spectra. Coilodesme (a brown alga) shows almost as good correspondence, including the spectral region absorbed by the carotenoid, fucoxanthin. In green and brown algae, light absorbed by both chlorophyll and carotenoids seems photosynthetically effective, although some inactive absorption by carotenoids is indicated. Action spectra for a wide variety of red algae, however, show marked deviations from their corresponding absorption spectra. The photosynthetic rates are high in the spectral regions absorbed by the water-soluble "phycobilin" pigments (phycoerythrin and phycocyanin), while the light absorbed by chlorophyll and carotenoids is poorly utilized for oxygen production. In red algae containing chiefly phycoerythrin, the action spectrum closely resembles that of the water-extracted pigment, with peaks corresponding to its absorption maxima (495, 540, and 565 mµ). Such algae include Delesseria, Schizymenia, and Porphyrella. In the genus Porphyra, there is a series P. nereocystis, P. naiadum, and P. perforata, with increasingly more phycocyanin and less phycoerythrin: the action spectra reflect this, with increasing activity in the orange-red region (600 to 640 mµ) where phycocyanin absorbs. In all these red algae, photosynthesis is almost minimal at 435 mµ and 675 mµ, where chlorophyll shows maximum absorption. Although the chlorophylls (and carotenoids) are present in quantities comparable to the green algae, their function is apparently not that of a primary light absorber; this role is taken over by the phycobilins. In this respect the red algae (Rhodophyta) appear unique among photosynthetic plants.     

Selective absorption and scattering of light by solutions of macromolecules and by particulate suspensions

For particulate suspensions and for solutions that scatter light measurably the total absorbance A generally contains contributions due to specific absorption (Aa) and scattering of light (As). The quantity As is closely related to the turbidity tau. In general, spectrophotometry of such systems requires proper modification of the spectrophotometer used in order to permit accurate determination of the absorbance A and of the derived quantities Aa and As. Apparent deviation from Beer's law in such systems is often due to inappropriate experimental technique. After a discussion of the parameters that determine the intensity of light scattered by solutes, an account is given of the experimental precautions to be taken for determination of the absorbance of light scattering suspensions and solutions and of techniques for correcting absorbance spectra for scattering of light. Measurement of the turbidity is briefly confronted with determination of the scattering ratio i90 degrees/Io and the impact of erroneous turbidity measurements on derived molecular parameters is discussed.     

Delayed light action spectra of several algae in visible and ultraviolet light

Action spectra for delayed light production by several algae were determined from 250 to 750 mµ incident light. In the visible portion of the spectrum the action spectra resemble those reported by previous workers for photosynthesis and light emission. Blue-green algae had a maximum at 620 mµ, red algae at 550 mµ, whereas green and brown algae have action spectra corresponding to chlorophyll and carotenoid absorption. In the ultraviolet portion of the spectrum delayed light is emitted by algae down to 250 mµ incident light. The action spectra of the different algae are not alike in the ultraviolet portion of the spectrum. This indicates that pigments other than chlorophyll must be sensitizing or shielding the algae in the ultraviolet region.     

Theoretical study of the Raman optical activity spectra of with M = Co,Rh

Vibrational Raman optical activity (ROA) spectra were calculated under off-resonance, near-resonance, and at-resonance conditions for ( A ) and under off-resonance conditions for ( B ) using a new driver software for calculating the ROA intensities from complex (damped) time-dependent linear response Kohn-Sham theory. The off-resonance spectra of A and B show many similarities. At an incident laser wavelength of 532 nm, used in commercial ROA spectrometers, the spectrum of A is enhanced by near-resonance with the ligand-field transitions of the complex. The near-resonance spectrum exhibits many qualitative differences compared with the off-resonance case, but it remains bi-signate. Even under full resonance with the ligand-field electronic transitions, the ROA spectrum of A remains bi-signate when the electronic transitions are broadened such as to yield absorption line widths that are comparable with those in the experimental UV-vis absorption and electronic circular dichroism spectra.     

Effects of suspensoids (turbidity) on penetration of solar radiation in aquatic ecosystems

In mainland Australia and in southern Africa, the aridity of the climate and sparse vegetative cover increase the susceptibility of the soils to erosion, and as a consequence surface waters are usually turbid. The inanimate suspensoids in such waters, the tripton fraction of the limnologist, are responsible for virtually all the light scattering, and also, by virtue of the yellow-brown humic materials adsorbed on their surface, for a substantial part of the light absorption. Spectral absorption data for suspensoids in terms of theirin situ absorption coefficient values, and the contribution of suspensoids to absorption of photosynthetically available radiation (PAR) are given for certain Australian water bodies.To understand the effect of suspensoids on attenuation of the solar flux with depth, the scattering coefficient must also be known, and this can be determined from the nephelometric turbidity or from up- and down-welling irradiance measurements. The effect of particle size on scattering efficiency is discussed.An equation expressing the vertical attenuation coefficient for downward irradiance as a function of absorption coefficient, scattering coefficient and solar altitude is presented, and is used to explore the effects of absorption due to dissolved colour and suspensoids, and the effects of scattering by suspensoids, on the penetration of PAR.Suspensoids, by increasing the rate of attenuation of the solar flux with depth, can greatly diminish the euphotic depth of a water body, with a consequent decrease in the ratio of the euphotic to the mixed depth: thus turbidity can reduce productivity of a water body substantially below that which might be expected on the basis of nutrient availability. Shallow turbid waters of low intrinsic colour can, however, be highly productive. By diminishing the depth of the layer within which solar energy is dissipated as heat, suspensoids can greatly modify the hydrodynamic behaviour of water bodies, and this also has far-reaching ecological consequences.Suspensoids drastically impair the visual clarity of water, a fact of major significance for the aquatic fauna, as well of aesthetic significance for humanity. The reciprocal of the Secchi depth is more correctly thought of as a guide to the vertical contrast attenuation coefficient rather than to the vertical attenuation coefficient for irradiance. The reflectivity of a water body, being at any wavelength proportional to the backscattering coefficient divided by the absorption coefficient, is highly dependent on the concentration, and optical character, of the suspensoids present. This has implications not only for the appearance (colour, muddiness) of the water to an observer, but also for the remote sensing of water composition by air- or satellite-borne radiometric sensors.     

UV Spectral Properties of Phenylalanine Powder

A technique is described which makes it possible to measure the absorption spectrum of phenylalanine powder. Reflectance spectra are used to calculate the amount of light scattered from the samples; thus, the treatment of the data makes it unnecessary to normalize the absorbance to some value known from other work. Further, the unique scattering in the spectral region of an absorption band can be found. The fluorescence quantum yield of phenylalanine powder at 300K is calculated to be 1.0 ± 0.1, a sizeable increase over the value of 0.04 found for aqueous phenylalanine solutions.