Retrieval of the photochemical reflectance index for assessing xanthophyll cycle activity: a comparison of near-surface optical sensors

Abstract. Unattended optical sensors are increasingly being deployed on eddy covariance flux towers and are often used to complement existing vegetation and micrometeorological measurements to enable assessment of biophysical states and biogeochemical processes over a range of spatial scales. Of particular interest are sensors that can measure the photochemical reflectance index (PRI), which can provide information pertaining to leaf pigments and photosynthetic activity. This interest has facilitated the production of a new range of lower-cost sensors specifically designed to measure temporal changes in the PRI signal. However, little is known about the characteristics (spectral, radiometric and temporal) of many of these PRI sensors, making it difficult to compare data obtained from these sensors across time, geographical locations and instruments. Furthermore, direct testing of the capability of these sensors to actually detect the conversion of the xanthophyll cycle, which is the original biological basis of the PRI diurnal signal, is largely absent, which often results in an unclear interpretation of the signal, particularly given the wide range of factors now known to influence PRI. Through a series of experiments, we assess the sensitivity of one of the leading brands of PRI sensor (Skye SKR 1800) to changes in vegetation photosynthetic activity in response to changing irradiance. We compare the results with those obtained using a more expensive industry-standard spectrometer (PP-systems UniSpec) and determine the radiometric compatibility of measurements made by the different instruments. Results suggest that the lower cost SKR 1800 instrument is able to track rapid (seconds to minutes) and more gradual diurnal changes in photosynthetic activity associated with xanthophyll cycle pigment conversion. Measurements obtained from both the high and lower cost instrument were significantly linearly correlated but were subject to a large systematic bias, illustrating that small differences in instrument configuration can have a large impact on the PRI measurement values obtained. Despite differences in absolute PRI values, significant correlations were observed between the PRI derived from the SKR 1800 and the epoxidation state of the xanthophyll cycle (r2 = 0.46, p < 0.05), although the dynamic range of the SKR 1800 PRI signal was often lower than more expensive instruments and thus the lower cost instrument may be less sensitive to pigment dynamics related to photosynthetic activity. Based on our findings, we make a series of recommendations for the effective use of such sensors under field conditions.

Download Full-text

Retrieval of the photochemical reflectance index for assessing xanthophyll cycle activity: a comparison of near-surface optical sensors

Biogeosciences ◽

10.5194/bg-11-6277-2014 ◽

2014 ◽

Vol 11 (22) ◽

pp. 6277-6292 ◽

Cited By ~ 25

Author(s):

A. Harris ◽

J. A. Gamon ◽

G. Z. Pastorello ◽

C. Y. S. Wong

Keyword(s):

Optical Sensors ◽

Xanthophyll Cycle ◽

Lower Cost ◽

Photosynthetic Activity ◽

Spectral Response ◽

Systematic Bias ◽

Diurnal Changes ◽

Near Surface ◽

Photochemical Reflectance Index ◽

Wide Range

Abstract. Unattended optical sensors are increasingly being deployed on eddy covariance flux towers and are often used to complement existing vegetation and micrometeorological measurements to enable assessment of biophysical states and biogeochemical processes over a range of spatial scales. Of particular interest are sensors that can measure the photochemical reflectance index (PRI), which can provide information pertaining to leaf pigments and photosynthetic activity. This interest has facilitated the production of a new range of lower-cost multispectral sensors specifically designed to measure temporal changes in the PRI signal. However, little is known about the characteristics (spectral, radiometric and temporal) of many of these PRI sensors, making it difficult to compare data obtained from these sensors across time, geographical locations and instruments. Furthermore, direct testing of the capability of these sensors to actually detect the conversion of the xanthophyll cycle, which is the original biological basis of the PRI diurnal signal, is largely absent, often resulting in an unclear interpretation of the signal, particularly given the wide range of factors now known to influence PRI. Through a series of experiments, we assess the sensitivity of one of the leading brands of PRI sensor (Skye SKR 1800) to changes in vegetation photosynthetic activity in response to changing irradiance. We compare the results with those obtained using a more expensive industry-standard visible to near-infrared hyperspectral spectrometer (PP Systems UniSpec) and determine the radiometric compatibility of measurements made by the different instruments. Results suggest that the SKR 1800 instrument is able to track rapid (seconds to minutes) and more gradual diurnal changes in photosynthetic activity associated with xanthophyll cycle pigment conversion. Measurements obtained from both the high and lower cost instrument were significantly linearly correlated but were subject to a large systematic bias, illustrating that differences in instrument configuration (e.g. spectral response functions and band positions) can have a large impact on the PRI measurement values obtained. Despite differences in absolute PRI values, significant correlations were observed between the canopy PRI derived from both the SKR 1800 and the UniSpec instruments, and the epoxidation state of the xanthophyll cycle (r2 = 0.46 p < 0.05 and r2 = 0.76 p < 0.01, respectively). However, the dynamic range of the SKR 1800 PRI signal was often lower than more expensive instruments and thus the lower cost multispectral instrument may be less sensitive to pigment dynamics related to photosynthetic activity. Based on our findings, we make a series of recommendations for the effective use of such sensors under field conditions and advocate that sensors should be fully characterized prior to their field deployment.

Download Full-text

A Short Review of Cavity-Enhanced Raman Spectroscopy for Gas Analysis

Sensors ◽

10.3390/s21051698 ◽

2021 ◽

Vol 21 (5) ◽

pp. 1698

Author(s):

Christian Niklas ◽

Hainer Wackerbarth ◽

Georgios Ctistis

Keyword(s):

Raman Spectroscopy ◽

Laser Beam ◽

Gas Sensors ◽

Optical Sensors ◽

Lower Cost ◽

Short Review ◽

Gas Analysis ◽

Beam Power ◽

Laser Beam Power ◽

Wide Range

The market of gas sensors is mainly governed by electrochemical, semiconductor, and non-dispersive infrared absorption (NDIR)-based optical sensors. Despite offering a wide range of detectable gases, unknown gas mixtures can be challenging to these sensor types, as appropriate combinations of sensors need to be chosen beforehand, also reducing cross-talk between them. As an optical alternative, Raman spectroscopy can be used, as, in principle, no prior knowledge is needed, covering nearly all gas compounds. Yet, it has the disadvantage of a low quantum yield through a low scattering cross section for gases. There have been various efforts to circumvent this issue by enhancing the Raman yield through different methods. For gases, in particular, cavity-enhanced Raman spectroscopy shows promising results. Here, cavities can be used to enhance the laser beam power, allowing higher laser beam-analyte interaction lengths, while also providing the opportunity to utilize lower cost equipment. In this work, we review cavity-enhanced Raman spectroscopy, particularly the general research interest into this topic, common setups, and already achieved resolutions.

Download Full-text

Revealing the role of missing scales in boundary layer observations in gravity wave propagation using the Flying Fiber Optic eXperiment (FlyFOX)

10.5194/egusphere-egu21-10672 ◽

2021 ◽

Author(s):

Karl Lapo ◽

Antonia Fritz ◽

Anita Freundorfer ◽

Shravan K. Muppa ◽

Christoph K. Thomas

Keyword(s):

Boundary Layer ◽

Stable Boundary Layer ◽

Fiber Optic ◽

Spatial Scales ◽

Horizontal Wind ◽

Neutral Stability ◽

Near Surface ◽

Stable Boundary ◽

Mountain Valley ◽

Wide Range

The stable boundary layer, especially the very stable boundary layer, (vSBL) is a fundamental challenge for boundary layer meteorology as assumptions such as ergodicity and local scaling do not apply. The violation of these commonly-employed theories is associated with the presence of submeso-scale structures, which span spatial scales between tens of meters and kilometers and temporal scales from tens of seconds up to an hour. The nature of these structures is largely unknown but they are suspected to encompass a wide-range of flow modes, including meandering of the horizontal wind direction, thermal submeso fronts, complex and unknown non-stationary modes, and relevant to this work, various wave modes. Progress on submeso-turbulence interactions requires distributed observations with fine enough resolution to separate between the submeso and turbulent scales.&#160;To that end we present results from FlyFOX in which fiber optic distributed sensing (FODS) was deployed along a tethered balloon. FODS yields spatially continuous observations of air temperature with fine spatial (0.25m &#8211; 0.5m) and temporal (1s-10s) resolutions along fiber optic cables that can span kilometers. In this case FlyFOX spanned between 0.5m and 200m height. FlyFOX was deployed in a broad mountain valley in the Ficthelgebirge mountains, Germany in which intense cold air pooling commonly occurs.&#160;Using FlyFOX we simultaneously characterize the spatial and temporal spectra of the boundary layer through morning transitions, revealing that the vSBL has a unique spectral enhancement between 80s-640s and 8m-64m relative to weakly-stable and neutral conditions. These scales correspond to a gap in the observational capabilities of existing methods, which FlyFOX fills.&#160;Corresponding to this observational gap, we demonstrate the existence of &#8220;sublayer striations&#8221;, thin (5m-20m) but persistent layers (duration up to an hour) of exceptionally stable air separated by layers of near-neutral stability. Using wavelet coherence for different time scales, gravity waves were found to be unable to penetrate into the sublayer striations and instead ducted in the neutral air between striations. During periods with overall lower static stability, these sublayer striations did not occur and waves acted across the entire depth of the SBL from ~120m down to ~0.5m and can be tracked propagating along the surface at 1m height using a near surface DTS array. These sublayer striations thereby acted to decouple the upper boundary layer from the surface layer in this mountain valley. FlyFOX and FODS provide an observational breakthrough for the study of vertical coupling and wave activity in the vSBL by closing an observational gap and facilitating observations of atmospheric properties from the turbulent to submeso scales.

Download Full-text

Gamma models for estimating the odds ratio for a skewed biomarker measured in pools and subject to errors

Biostatistics ◽

10.1093/biostatistics/kxz028 ◽

2019 ◽

Author(s):

Dane R Van Domelen ◽

Emily M Mitchell ◽

Neil J Perkins ◽

Enrique F Schisterman ◽

Amita K Manatunga ◽

...

Keyword(s):

Odds Ratio ◽

Adjusted Odds Ratio ◽

Lower Cost ◽

Cost Effective ◽

Ratio Estimation ◽

Statistical Efficiency ◽

Function Model ◽

Processing Error ◽

Wide Range ◽

Pooled Samples

SUMMARYMeasuring a biomarker in pooled samples from multiple cases or controls can lead to cost-effective estimation of a covariate-adjusted odds ratio, particularly for expensive assays. But pooled measurements may be affected by assay-related measurement error (ME) and/or pooling-related processing error (PE), which can induce bias if ignored. Building on recently developed methods for a normal biomarker subject to additive errors, we present two related estimators for a right-skewed biomarker subject to multiplicative errors: one based on logistic regression and the other based on a Gamma discriminant function model. Applied to a reproductive health dataset with a right-skewed cytokine measured in pools of size 1 and 2, both methods suggest no association with spontaneous abortion. The fitted models indicate little ME but fairly severe PE, the latter of which is much too large to ignore. Simulations mimicking these data with a non-unity odds ratio confirm validity of the estimators and illustrate how PE can detract from pooling-related gains in statistical efficiency. These methods address a key issue associated with the homogeneous pools study design and should facilitate valid odds ratio estimation at a lower cost in a wide range of scenarios.

Download Full-text

On the generation of internal waves by river plumes in subcritical initial conditions

Scientific Reports ◽

10.1038/s41598-021-81464-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

R. Mendes ◽

J. C. B. da Silva ◽

J. M. Magalhaes ◽

B. St-Denis ◽

D. Bourgault ◽

...

Keyword(s):

Numerical Modeling ◽

Internal Waves ◽

Coastal Waters ◽

Initial Conditions ◽

Spatial Scales ◽

River Plumes ◽

Wide Range ◽

Near Shore ◽

Generation Mechanisms ◽

Douro River

AbstractInternal waves (IWs) in the ocean span across a wide range of time and spatial scales and are now acknowledged as important sources of turbulence and mixing, with the largest observations having 200 m in amplitude and vertical velocities close to 0.5 m s−1. Their origin is mostly tidal, but an increasing number of non-tidal generation mechanisms have also been observed. For instance, river plumes provide horizontally propagating density fronts, which were observed to generate IWs when transitioning from supercritical to subcritical flow. In this study, satellite imagery and autonomous underwater measurements are combined with numerical modeling to investigate IW generation from an initial subcritical density front originating at the Douro River plume (western Iberian coast). These unprecedented results may have important implications in near-shore dynamics since that suggest that rivers of moderate flow may play an important role in IW generation between fresh riverine and coastal waters.

Download Full-text

Low-energy optical switching of SO2 linkage isomerisation in single crystals of a ruthenium-based coordination complex

RSC Advances ◽

10.1039/d1ra01696b ◽

2021 ◽

Vol 11 (22) ◽

pp. 13183-13192

Author(s):

Jacqueline M. Cole ◽

David J. Gosztola ◽

Sven O. Sylvester

Keyword(s):

Single Crystals ◽

Optical Sensors ◽

Optical Switching ◽

Optical Switches ◽

Low Energy ◽

Coordination Complex ◽

Wide Range

Single crystals that behave as optical switches are desirable for a wide range of applications, from optical sensors to read–write memory media.

Download Full-text

Triazole, Benzotriazole, and Naphthotriazole as Corrosion Inhibitors for Brass

CORROSION ◽

10.5006/0010-9312-32.10.414 ◽

1976 ◽

Vol 32 (10) ◽

pp. 414-417 ◽

Cited By ~ 15

Author(s):

R. WALKER

Keyword(s):

Corrosion Inhibitors ◽

Lower Cost ◽

Solution Ph ◽

Inhibitor Efficiency ◽

Wide Range ◽

Better Than

Abstract The use of triazole, benzotriazole, and naphthotriazole as corrosion inhibitors for brass is briefly reviewed. The corrosion of 70/30 brass immersed in a wide range of solutions is reported both with and without the inhibitors. The inhibitor efficiency of benzotriazole is given as a function of the solution pH and the concentration used. Triazole was only effective in mildly corrosive solutions and benzotriazole and naphthotriazole were much better. Generally naphthotriazole was better than benzotriazole but is much more expensive and a higher concentration of benzotriazole can give the same protection as naphthotriazole at a much lower cost.

Download Full-text

Future trends in diagnosis using laboratory-on-a-chip technologies

Parasitology ◽

10.1017/s0031182099004126 ◽

1999 ◽

Vol 117 (7) ◽

pp. 191-203 ◽

Cited By ~ 16

Author(s):

M. S. TALARY ◽

J. P. H. BURT ◽

R. PETHIG

Keyword(s):

Gene Expression ◽

Lower Cost ◽

Building Blocks ◽

Cancer Diagnostics ◽

Future Trends ◽

Biotechnological Applications ◽

Environmental Testing ◽

Current State ◽

Microelectronic Fabrication ◽

Wide Range

There has been an enormous growth in the development of biotechnological applications, where advances in the techniques of microelectronic fabrication and the technologies of miniaturization and integration in semiconductor industries are being applied to the production of Laboratory-on-a-Chip devices. The aim of this development is to create devices that will perform the same processes that are currently carried out in the laboratory in reduced timescales, at a lower cost, requiring less reagents, and with a greater resolution of detection and specificity. The expectations of this Laboratory-on-a-Chip revolution is that this technology will facilitate rapid advances in gene discovery, genetic mapping and gene expression with broader applications ranging from infectious diseases and cancer diagnostics to food quality and environmental testing. A review of the current state of development in this field reveals the scale of the ongoing revolution and serves to highlight the advances that can be perceived in the development of Laboratory-on-a-Chip technologies. Since miniaturization can be applied to such a wide range of laboratory processes, some of the sub-units that can be used as building blocks in these devices are described, with a brief description of some of the fabrication processes that can be used to create them.

Download Full-text

MAX-DOAS observations of aerosols, formaldehyde and nitrogen dioxide in the Beijing area: comparison of two profile retrieval approaches

Atmospheric Measurement Techniques ◽

10.5194/amt-8-941-2015 ◽

2015 ◽

Vol 8 (2) ◽

pp. 941-963 ◽

Cited By ~ 47

Author(s):

T. Vlemmix ◽

F. Hendrick ◽

G. Pinardi ◽

I. De Smedt ◽

C. Fayt ◽

...

Keyword(s):

Standard Deviation ◽

A Priori ◽

Systematic Bias ◽

Aerosol Extinction ◽

Data Set ◽

Near Surface ◽

Beijing Area ◽

Least Squares Fit ◽

Relative Differences ◽

Good Agreement

Abstract. A 4-year data set of MAX-DOAS observations in the Beijing area (2008–2012) is analysed with a focus on NO2, HCHO and aerosols. Two very different retrieval methods are applied. Method A describes the tropospheric profile with 13 layers and makes use of the optimal estimation method. Method B uses 2–4 parameters to describe the tropospheric profile and an inversion based on a least-squares fit. For each constituent (NO2, HCHO and aerosols) the retrieval outcomes are compared in terms of tropospheric column densities, surface concentrations and "characteristic profile heights" (i.e. the height below which 75% of the vertically integrated tropospheric column density resides). We find best agreement between the two methods for tropospheric NO2 column densities, with a standard deviation of relative differences below 10%, a correlation of 0.99 and a linear regression with a slope of 1.03. For tropospheric HCHO column densities we find a similar slope, but also a systematic bias of almost 10% which is likely related to differences in profile height. Aerosol optical depths (AODs) retrieved with method B are 20% high compared to method A. They are more in agreement with AERONET measurements, which are on average only 5% lower, however with considerable relative differences (standard deviation ~ 25%). With respect to near-surface volume mixing ratios and aerosol extinction we find considerably larger relative differences: 10 ± 30, −23 ± 28 and −8 ± 33% for aerosols, HCHO and NO2 respectively. The frequency distributions of these near-surface concentrations show however a quite good agreement, and this indicates that near-surface concentrations derived from MAX-DOAS are certainly useful in a climatological sense. A major difference between the two methods is the dynamic range of retrieved characteristic profile heights which is larger for method B than for method A. This effect is most pronounced for HCHO, where retrieved profile shapes with method A are very close to the a priori, and moderate for NO2 and aerosol extinction which on average show quite good agreement for characteristic profile heights below 1.5 km. One of the main advantages of method A is the stability, even under suboptimal conditions (e.g. in the presence of clouds). Method B is generally more unstable and this explains probably a substantial part of the quite large relative differences between the two methods. However, despite a relatively low precision for individual profile retrievals it appears as if seasonally averaged profile heights retrieved with method B are less biased towards a priori assumptions than those retrieved with method A. This gives confidence in the result obtained with method B, namely that aerosol extinction profiles tend on average to be higher than NO2 profiles in spring and summer, whereas they seem on average to be of the same height in winter, a result which is especially relevant in relation to the validation of satellite retrievals.

Download Full-text

Structural interpretation using refraction velocities from marine seismic surveys

Geophysics ◽

10.1190/1.1442026 ◽

1986 ◽

Vol 51 (1) ◽

pp. 12-19 ◽

Cited By ~ 3

Author(s):

James F. Mitchell ◽

Richard J. Bolander

Keyword(s):

Sedimentary Rock ◽

Seismic Energy ◽

Seismic Survey ◽

Subsurface Structure ◽

Seismic Reflection Data ◽

Near Surface ◽

Reflection Data ◽

Wide Range ◽

Streamer Length ◽

Set Up

Subsurface structure can be mapped using refraction information from marine multichannel seismic data. The method uses velocities and thicknesses of shallow sedimentary rock layers computed from refraction first arrivals recorded along the streamer. A two‐step exploration scheme is described which can be set up on a personal computer and used routinely in any office. It is straightforward and requires only a basic understanding of refraction principles. Two case histories from offshore Peru exploration demonstrate the scheme. The basic scheme is: step (1) shallow sedimentary rock velocities are computed and mapped over an area. Step (2) structure is interpreted from the contoured velocity patterns. Structural highs, for instance, exhibit relatively high velocities, “retained” by buried, compacted, sedimentary rocks that are uplifted to the near‐surface. This method requires that subsurface structure be relatively shallow because the refracted waves probe to depths of one hundred to over one thousand meters, depending upon the seismic energy source, streamer length, and the subsurface velocity distribution. With this one requirement met, we used the refraction method over a wide range of sedimentary rock velocities, water depths, and seismic survey types. The method is particularly valuable because it works well in areas with poor seismic reflection data.

Download Full-text