Reflectance and transmittance spectra of leaves and shoots of 22 vascular plant species and reflectance spectra of trunks and branches of 12 tree species in Japan

This data paper reports spectral reflectance and transmittance data of leaves from 21 terrestrial vascular plant species (seven herbaceous, and 14 broadleaf and long-needle coniferous tree species) and of shoots from one short-needle coniferous tree species. The reflectance spectra of branches of one tree species, of the trunks of 12 tree species and ground surface of one deciduous broad-leaf forest are also reported. Optical measurements and leaf samplings were made at five sites on Honshu Island, Japan, which are typical vegetation types in East Asia, i.e., grassland, paddy field, and deciduous broad-leaf or coniferous forests. The collection and measurements were conducted for main species in each site. To include other common vegetation types in East Asia, such as evergreen broad-leaf or coniferous forests, the sample collection and the measurements were conducted at gardens and an experimental forest. Leaves of ten deciduous species were measured at different phenological stages from leaf expansion to senescence since those species shows significant seasonal changes in spectral reflectance and transmittance of leaves. Leaves at different position in a canopy (e.g., sunlit versus shaded leaves) were also measured for eight of 21 species. The spectral reflectance and transmittance from both adaxial and abaxial sides of the all leaves or needles, expect Picea abies needles. The measurements of the leaves were conducted with a spectroradiometer attached via an optical fiber to an integrating sphere. Two types of integrating spheres were used: a model LI-1800-12 (Li-Cor) and an RTS-3ZC integrating sphere (Analytical Spectral Devices). A leaf clip accessory was also used instead of an integrating sphere for measuring the leaves of two species. All data were measured within the 350–2,500-nm spectral range with 1-nm steps between measurements but the data obtained by LI-1800 is unavailable in 1,650–1,740, 1,890–1,950, and 2,050–2,500 nm because of a large amount of noise. These data are used as input parameters in a radiative transfer model designed to estimate the leaf area index from radiation reflected from a canopy surface.     

Determination of oxygen saturation and hematocrit of flowing human blood using two different spectrally resolving sensors.

The blood parameters oxygen saturation and hematocrit were determined by two different spectral sensors using reflectance spectra from 550 to 900 nm and partial transmission spectra centered at 660 nm. The spectra were analyzed by the method of partial least squares. One sensor consists of a miniature integrating sphere, while the other was fiber-guided. The results show that the geometry of the sensors and different blood flows do not influence the spectral analysis significantly. Independent of the sensor geometry, both hematocrit and oxygen saturation could be determined with an absolute predicted root mean square error of less than 3%. Furthermore, the analysis showed that hematocrit prediction requires eight wavelength regions and oxygen saturation prediction requires four wavelength regions using reflectance spectroscopy. This implies that if the measurement is restricted to reflectance, a spectrometer is indispensable for determining both blood parameters. Hematocrit determination could be improved using reflectance measurements in combination with transmission.     

Comparative study of integrating cavity absorption meters

Integrating spheres (IS) are widely used for recording spectra of scattering samples by placing the specimen inside or outside the sphere. An unusual application of integrating spheres has been also demonstrated earlier where the liquid sample completely filled the spherical cavity; such a device is often called an integrating cavity absorption meter (ICAM). In the present work, integrating cavities with different coatings are compared. The spheres were made of glass, covered by metal or white paint, and their surfaces were prepared for diffuse or specular reflectance. The spheres were evaluated by recording kinetic traces following a short light pulse with the aid of time-correlated single photon counting (TCSPC), and by recording steady-state spectra through single-photon counting (SPC) detection. The relative efficiencies of the spheres were determined by comparing the steady-state spectra. Possible reasons for differences in the performance are discussed.     

Accurate measurement of optical properties of narrow leaves and conifer needles with a typical integrating sphere and spectroradiometer

Accurate information on the optical properties (reflectance and transmittance spectra) of single leaves is important for an ecophysiological understanding of light use by leaves, radiative transfer models and remote sensing of terrestrial ecosystems. In general, leaf optical properties are measured with an integrating sphere and a spectroradiometer. However, this method is usually difficult to use with grass leaves and conifer needles because they are too narrow to cover the sample port of a typical integrating sphere. Although ways to measure the optical properties of narrow leaves have been suggested, they have problems. We propose a new measurement protocol and calculation algorithms. The protocol does not damage sample leaves and is valid for various types of leaves, including green and senescent. We tested our technique with leaves of Aucuba japonica, an evergreen broadleaved shrub, and compared the spectral data of whole leaves and narrow strips of the leaves. The reflectance and transmittance of the strips matched those of the whole leaves, indicating that our technique can accurately estimate the optical properties of narrow leaves. Tests of conifer needles confirmed the applicability.     

Microalgal fatty acid composition: rapid assessment using near-infrared spectroscopy

The feasibility of assessing microalgal fatty acid composition using near-infrared spectroscopy (NIRS) is described. The chlamydomonad microalga, Rhopalosolen saccatus (previously known as Characium saccatum), was isolated from the Fitzroy River, Central Queensland, Australia. R. saccatus was grown in batch culture with varying phosphorus nutrition and assessed for dry matter, total lipid and fatty acid composition using gas chromatography (GC). Transmission spectra (1100–2500 nm) were acquired of liquid culture, and reflectance spectra were acquired of wet and dry filtrates of cultures and of methyl esters. Partial least square (PLS) regression models were built on biomass, total lipid and a number of fatty acids. All sample presentation models supported PLS regression model with a cross validation correlation coefficient (R _cv) >0.87 for biomass and R _cv >0.68 for total lipid; however, the use of dry filtrates of culture is recommended as the sample presentation mode of choice. Models for fatty acids based on culture transmission spectra, reflectance spectra of wet and dry culture filtrates, or reflectance spectra of methyl esters in solvent were not acceptable. Dry extracts of methyl esters supported adequate models for fatty acids from C8:0 to C22:0, with the exception of capric and behenic acids, with an R _cv of 0.89–0.94; however, in practice, samples processed to this stage can be easily analyzed by GC. Near-infrared spectroscopy can be a potential choice for rapid estimation of biomass (dry matter) and lipid content and composition in microalgae, with further work required to demonstrate oping robustness of the calibration model in prediction of unknown samples.     

Sensing the Heat of Tomato Products Red: The New Approach to the Objective Assessment of their Color

The concept of optothermal window (OW) detection was used for the first time to assess the color of several products (juice, purée, paste) derived from thermally processed tomatoes. Unlike traditional techniques that operate either in the reflectance or transmission mode, the method proposed here actually relies on indirect measurement of absorbance in optically opaque and scattering samples. Very good correlation between the magnitude of the OW signal and the color-related parameters [colorimetric index L* and tomato paste index (TPI)] was observed.     

Discrimination of single‐porin Escherichia (E.) coli mutants by ATR and transmission mode FTIR spectroscopy

Vibrational spectroscopy has long been used in bacterial identification with different levels of taxonomic discrimination but its true potential for intra‐species differentiation remains poorly explored. Herein, both transmission Fourier‐transform infrared (FTIR) and attenuated total reflectance (ATR)‐FTIR spectroscopy are used to analyse E. coli strains that differ solely in their porin expression profile. In this previously unreported approach, the applicability of both FTIR‐spectroscopy techniques is compared with the same collection of unique strains. ATR‐FTIR spectroscopy proved to reliably distinguish between several E. coli porin mutants with an accuracy not replicated by FTIR in transmission mode (using previously optimized procedures). Further studies should allow the identification of the individual contribution of the single porin channel to the overall bacterial infrared spectrum and of molecular predictive patterns of porin alterations. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

The effect of colour of the substrate on the landing and oviposition behaviour of the cabbage root fly

Field and laboratory experiments were made in order to understand the relation between the spectral characteristic of a substrate and its attractiveness for Delia radicum (L.) (Diptera: Anthomyiidae) flies to land or oviposit. Landing females preferred substrates with high reflectance of green and particularly of yellow wavelengths, but substrates with a high proportion of the blue and green reflectance simultaneously (light blue and white) were also very attractive. Unattractive substrates had either low reflectance across the whole insect-visible spectrum (dark blue) or increased reflectance only in orange or red region of the spectrum (red) or a large proportion of UV reflectance (aluminium). Landing males were most attracted to the substrates with the highest total reflection. Oviposition attractiveness of a substrate grew with an increase in the proportion of reflectance in the blue and a decrease in the green regions of the spectrum. In addition, the oviposition attractiveness increased with increasing total reflection and contrast with the background, and decreased with a high proportion of UV reflectance.     

Multispectral fluorescence and reflectance imaging at the leaf level and its possible applications

Images taken at different spectral bands are increasingly used for characterizing plants and their health status. In contrast to conventional point measurements, imaging detects the distribution and quantity of signals and thus improves the interpretation of fluorescence and reflectance signatures. In multispectral fluorescence and reflectance set-ups, images are separately acquired for the fluorescence in the blue, green, red, and far red, as well as for the reflectance in the green and in the near infrared regions. In addition, 'reference' colour images are taken with an RGB (red, green, blue) camera. Examples of imaging for the detection of photosynthetic activity, UV screening caused by UV-absorbing substances, fruit quality, leaf tissue structure, and disease symptoms are introduced. Subsequently, the different instrumentations used for multispectral fluorescence and reflectance imaging of leaves and fruits are discussed. Various types of irradiation and excitation light sources, detectors, and components for image acquisition and image processing are outlined. The acquired images (or image sequences) can be analysed either directly for each spectral range (wherein they were captured) or after calculating ratios of the different spectral bands. This analysis can be carried out for different regions of interest selected manually or (semi)-automatically. Fluorescence and reflectance imaging in different spectral bands represents a promising tool for non-destructive plant monitoring and a 'road' to a broad range of identification tasks.     

Anthocyanin contribution to chlorophyll meter readings and its correction

Leaf chlorophyll content is an important physiological parameter which can serve as an indicator of nutritional status, plant stress or senescence. Signals proportional to the chlorophyll content can be measured non-destructively with instruments detecting leaf transmittance (e.g., SPAD-502) or reflectance (e.g., showing normalized differential vegetation index, NDVI) in red and near infrared spectral regions. The measurements are based on the assumption that only chlorophylls absorb in the examined red regions. However, there is a question whether accumulation of other pigments (e.g., anthocyanins) could in some cases affect the chlorophyll meter readings. To answer this question, we cultivated tomato plants (Solanum lycopersicum L.) for a long time under low light conditions and then exposed them for several weeks (4 h a day) to high sunlight containing the UV-A spectral region. The senescent leaves of these plants evolved a high relative content of anthocyanins and visually revealed a distinct blue color. The SPAD and NDVI data were collected and the spectra of diffusive transmittance and reflectance of the leaves were measured using an integration sphere. The content of anthocyanins and chlorophylls was measured analytically. Our results show that SPAD and NDVI measurement can be significantly affected by the accumulated anthocyanins in the leaves with relatively high anthocyanin content. To describe theoretically this effect of anthocyanins, concepts of a specific absorbance and a leaf spectral polarity were developed. Corrective procedures of the chlorophyll meter readings for the anthocyanin contribution are suggested both for the transmittance and reflectance mode.     

The physical mechanism of cuticular color in Phelotrupes auratus (Coleoptera,Geotrupidae)

The physical mechanism of cuticular color in Phelotrupes auratus was investigated by polarized inspection, spectrophotometry and transmission electron microscopy (TEM). No color change was observed when viewed through either a right‐ or left‐handed circular polarizer. Further, under the incidence of linearly polarized light, the reflected intensity was markedly reduced when observed through a linear polarizer set with its optical axis perpendicular to that of the incident light. These results indicate that P. auratus does not possess any circularly polarizing reflectors. TEM observations revealed a total of ten or twelve thin layers (about 60–120 nm in thickness) of two types of material (electron‐dense and electron‐lucent) alternately stacked in the epicuticle. The thickness of the layers in the different color forms of the beetle corresponded to the peak wavelengths in the reflectance spectra, λmax(α), with thicker layers found in beetles exhibiting reflectance peaks at longer wavelengths and vice versa. Based on these findings, we concluded that all the cuticular color forms of P. auratus were not produced by a circularly polarizing reflector but by a simple multilayer reflector.     

Effect of Light Incident Angle on Fano Resonance Loss Mediation in Silver Nanoparticles Integrated Thin Silicon Wafers

In this work, we have studied the role of light incidence angle in the suppression of Fano resonance loss for mediating broadband light incoupling. At light normal incidence angle, the transmission loss of silver nanoparticles (Ag NPs) integrated 100 μm silicon (Si) wafer is reduced to ~?4 from ~?11%, and total reflectance is reduced to 32.7 from 38.7%. The reduction in reflectance is observed only in surface plasmon off-resonance region of the NPs, but the reflectance is enhanced slightly in surface plasmon resonance (SPR) region. With the change in light incident angles, we have observed a reduction in reflectance from NPs integrated silicon wafer at SPR region. At 40° light incident angle, the reflectance is reduced to 21 from 38.7% due to minimization of the Fano resonance in SPR region of the NPs. The Fano resonance loss reduction is explained based on modification in NPs’ dipole and quadrupole modes hybridization at the silicon interface with different light incident angles instead of normal incidence. Experimental observations are validated by simulating Ag NPs’ near-fields and angular distribution of far-fields at the silicon interface, scattering efficiency spectra at different light incident angles by finite difference time domain calculations.     

Characterization of cotton fabric scouring by FT-IR ATR spectroscopy

FT-IR attenuated total reflectance (ATR) spectroscopy has been used for the fast characterization of cotton fabric scouring process. The greige and the scoured cotton fabrics showed very similar FT-IR spectrum in transmission mode because the bulk composition of the fabrics are similar. However, FT-IR ATR spectroscopy can provide information about the surface of a fabric. By examination of C–H stretching region at 2800–3000 cm⁻¹, the amount of waxes left on the fabric can be estimated. The presence of pectins and/or waxes can also be probed by observation of carbonyl peak induced by the HCl vapor treatment on the fabric. Based on these changes of FT-IR ATR spectra, the scouring process has been characterized.     

FTIR Spectroscopic Study of Biogenic Mn-Oxide Formation by Pseudomonas putida GB-1

Biomineralization in heterogeneous aqueous systems results from a complex association between pre-existing surfaces, bacterial cells, extracellular biomacromolecules, and neoformed precipitates. Fourier transform infrared (FTIR) spectroscopy was used in several complementary sample introduction modes (attenuated total reflectance [ATR], diffuse reflectance [DRIFT], and transmission) to investigate the processes of cell adhesion, biofilm growth, and biological Mn-oxidation by Pseudomonas putida strain GB-1. Distinct differences in the adhesive properties of GB-1 were observed upon Mn oxidation. No adhesion to the ZnSe crystal surface was observed for planktonic GB-1 cells coated with biogenic MnO _x , whereas cell adhesion was extensive and a GB-1 biofilm was readily grown on ZnSe, CdTe, and Ge crystals prior to Mn-oxidation. IR peak intensity ratios reveal changes in biomolecular (carbohydrate, phosphate, and protein) composition during biologically catalyzed Mn-oxidation. In situ monitoring via ATR-FTIR of an active GB-1 biofilm and DRIFT data revealed an increase in extracellular protein (amide I and II) during Mn(II) oxidation, whereas transmission mode measurements suggest an overall increase in carbohydrate and phosphate moieties. The FTIR spectrum of biogenic Mn oxide comprises Mn-O stretching vibrations characteristic of various known Mn oxides (e.g., “acid” birnessite, romanechite, todorokite), but it is not identical to known synthetic solids, possibly because of solid-phase incorporation of biomolecular constituents. The results suggest that, when biogenic MnO _x accumulates on the surfaces of planktonic cells, adhesion of the bacteria to other negatively charged surfaces is hindered via blocking of surficial proteins.     

Heterogeneity of genetic control of blood pressure in ethnically different populations.

We review the literature on statistical genetic analyses of blood pressure in samples from various ethnic backgrounds using different statistical methods and packages. We then provide the results of a complex segregation analysis performed on familial data on systolic and diastolic blood pressure in 2 ethnically different populations, Chuvashans and Turkmenians. Two types of major gene models were tested in the segregation analysis: Model type 1 tests for a Mendelian mode of transmission and estimates genotype-specific averages regardless of age and sex effect, and model type 2 estimates age and sex effects on each of 3 genotypes within the putative major genotype. In both total samples, by both types of segregation analysis, familial aggregation of both systolic and diastolic blood pressure was inconsistent with the Mendelian mode of inheritance. In the next step of analysis the pedigrees in both samples were sorted into 2 groups on the basis of 2 likelihoods as obtained under Mendelian and nontransmission models for each entire sample. This procedure resulted in the appearance of 2 subsamples (large and small) in each ethnic sample. The segregation analysis that was carried out then on the larger subsample provided consistent evidence to support the major gene effect on systolic and diastolic blood pressure in 2 ethnic groups. Interestingly, model type 2 showed that in both ethnically different large subsamples, for each sex the genotype predisposing to a larger mean value of systolic (or diastolic) blood pressure also displayed the highest rate of blood pressure increase with age. We discuss in detail possible sources of heterogeneity in familial transmission of blood pressure observed in our 2 samples, and we suggest a method to improve the analysis of heterogeneity for trait inheritance.     

Metal binding in amyloid β-peptides shows intra- and inter-peptide coordination modes

X-ray absorption spectroscopy data show different metal binding site structures in beta-amyloid peptides according to whether they are complexed with Cu(2+) or Zn(2+) ions. While the geometry around copper is stably consistent with an intra-peptide binding with three metal-coordinated Histidine residues, the zinc coordination mode depends on specific solution conditions. In particular, different sample preparations are seen to lead to different geometries around the absorber that are compatible with either an intra- or an inter-peptide coordination mode. This result reinforces the hypothesis that assigns different physiological roles to the two metals, with zinc favoring peptide aggregation and, as a consequence, plaque formation.     

Adult thermoregulatory behaviour does not provide,by itself,an adaptive explanation for the reflectance–climate relationship (Bogert's pattern) in Iberian butterflies

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Sibling correlations of skin pigmentation during growth

The present study is focused on the analysis of skin color correlations in a sample of 1039 siblings aged 4 to 20 years from the province of Biscay (Basque Country, Spain). Measurements were taken at the upper inner arm and forehead by means of an EEL DS29 Digital Unigalvo reflectance spectrophotometer fitted with filters 601, 605, and 609. The reflectance data were internally standardized according to sex and age of the individuals, and the analysis of the degree of similarity between siblings was based on the calculation of intraclass correlation coefficients. All 3 filters gave fairly high and statistically significant correlations regarding forehead skin color (between 0.28 and 0.45) for all types of siblings under consideration. However, with respect to filter 609 the arm reflectance values did not reveal correlation either between brothers (0.01) or between siblings (0.02), even though it did reveal correlation between sisters (0.29). When other filters or type of sibling were considered (also for arm), all coefficients happened to be statistically significant and relatively high (0.35-0.43). This study confirms that the degree of sibling resemblance with regard to skin pigmentation is influenced by growth factors and that the upper inner arm and the forehead skin patterns change with age in the sense that, during and especially after puberty, the coefficients of correlation are higher for arm reflectance than for forehead reflectance; the forehead is a site that is more influenced by environment.     

Preparation of soybean seed samples for FT-IR microspectroscopy

Typical preparation of seed samples for infrared (IR) microspectroscopy involves imbibition of the seed for varying time periods followed by cryosectioning. Imbibition, however, may initiate germination even at 4° C with associated changes in the chemistry of the sample. We have found that it is possible to section seeds that are sufficiently hard, such as soybeans, on a standard laboratory microtome without imbibition. The use of dry sectioning of unimbibed seeds is reported here, as well as a comparison of different mounting media and modes of analysis. Glycerol, Tissue-Tek, and ethanol were used as mounting media, and the quality of the resulting spectra was assessed. Ethanol was the preferred mountant, because it dried quickly with no residue and thus did not interfere with the spectrum of interest. Analysis in transmission mode using barium fluoride windows to hold the samples was compared with transmission-reflection analysis with sections mounted on special infrared-reflecting slides. The two modes of analysis performed well in different regions of the spectrum. The mode of analysis (transmission vs. transmission-reflection) should be based on the components of greatest interest in the sample.     

Time dependent rate of diffusion-influenced ligand binding to receptors on cell surfaces.

The theory of the kinetics of binding of ligands to a sphere partially covered by receptors is extended to provide the full time dependence of the reactive flux. The ligands diffuse to the receptors; the receptors are either fully or partially absorbing. The total flux into the sphere with many receptors is expressed analytically in terms of the flux into a single isolated receptor on the sphere. At steady state, the Berg-Purcell formula is generalized to the case where the binding to a single receptor is only partially diffusion controlled. At short times, the receptors behave independently and the total flux is the sum of the fluxes to the isolated receptors.