Rotation of reference frame dependent polarimetric variables for equidistant fisheye lens projections.

The effect of a linear polarizer is conventionally well defined when viewed along the axis normal to its face. However, even for ideal linear polarizers, the non-normal viewing geometries attainable with wide-angle lenses require further considerations. A method to describe the polarization state of light passed through a linear polarizer and observed with an equidistant fisheye lens is described.

Improved shadow correction for the marine optical buoy, MOBY.

A 3-D instrument self-shading correction has been developed for the MOBY upwelling radiance measurements. This correction was tested using the 23 year time series of MOBY measurements, at the Lanai, Hawaii site. The correction is small (less than 2%) except when the sun and collectors are aligned within 20° azimuth on opposite sides of the main MOBY structure. Estimates of the correction uncertainty were made with a Monte-Carlo method and the variation of the model input parameters at this site. The correction uncertainty was generally less than 1%, but increased to 30% of the correction in the strongest shadow region.

Deriving consistent ocean biological and biogeochemical products from multiple satellite ocean color sensors.

A methodology is developed for deriving consistent ocean biological and biogeochemical products from multiple satellite ocean color sensors that have slightly different sensor spectral characteristics. Specifically, the required coefficients for algorithm modifications are obtained using the hyperspectral in situ optical measurements from the Marine Optical Buoy (MOBY) in the water off Hawaii. It is demonstrated that using the proposed approach for modifying ocean biological and biogeochemical algorithms, satellite-derived ocean property data over the global open ocean are consistent from multiple satellite sensors, although their corresponding sensor-measured normalized water-leaving radiance spectra nLw(λ) are different. Therefore, the proposed approach allows satellite-derived ocean biological and biogeochemical products to be consistent and can therefore be routinely merged from various satellite ocean color sensors. The proposed approach can be applied to any satellite algorithms that use the input of sensor-measured nLw(λ) spectra.

Uncertainty in global downwelling plane irradiance estimates from sintered polytetrafluoroethylene plaque radiance measurements.

Global downwelling plane irradiance is a necessary variable to normalize water-leaving radiance measurements, reducing the magnitude and spectral variabilities introduced by the incident light field. As a result, the normalized measurements, known as remote sensing reflectance, have higher correlation with the inherent optical properties of the water body and so to the composition of optically active water components. For in situ measurements, the global downwelling plane irradiance can be estimated from the exitant radiance of sintered polytetrafluoroethylene plaques or other diffuse reflectance standards. This allows use of a single spectrometer to measure all necessary variables to estimate the remote sensing reflectance, reducing cost in acquisition and maintenance of instrumentation. However, despite being in use for more than 30 years, the uncertainty associated with the method has been only partially evaluated. In this study, we use a suite of sky radiance distributions for 24 atmospheres and nine solar zenith angles in combination with full bidirectional reflectance distribution function determinations of white and gray plaques to evaluate the uncertainties. The isolated and interactive effects of bidirectional reflectance distribution, shadowing, and tilt error sources are evaluated. We find that under the best-performing geometries of each plaque, and with appropriate estimation functions, average standard uncertainty ranges from 1% to 6.5%. The simulated errors are found to explain both previous empirical uncertainty estimates and new data collected during this study. Those errors are of the same magnitude as uncertainties of plane irradiance sensors (e.g., cosine collectors) and overlap with uncertainty requirements for different uses of in situ data, which supports the continued use of the plaque method in hydrologic optics research and monitoring. Recommendations are provided to improve the quality of measurements and assure that uncertainties will be in the range of those calculated here.

An Ocean-Colour Time Series for Use in Climate Studies: The Experience of the Ocean-Colour Climate Change Initiative (OC-CCI).

Ocean colour is recognised as an Essential Climate Variable (ECV) by the Global Climate Observing System (GCOS); and spectrally-resolved water-leaving radiances (or remote-sensing reflectances) in the visible domain, and chlorophyll-a concentration are identified as required ECV products. Time series of the products at the global scale and at high spatial resolution, derived from ocean-colour data, are key to studying the dynamics of phytoplankton at seasonal and inter-annual scales; their role in marine biogeochemistry; the global carbon cycle; the modulation of how phytoplankton distribute solar-induced heat in the upper layers of the ocean; and the response of the marine ecosystem to climate variability and change. However, generating a long time series of these products from ocean-colour data is not a trivial task: algorithms that are best suited for climate studies have to be selected from a number that are available for atmospheric correction of the satellite signal and for retrieval of chlorophyll-a concentration; since satellites have a finite life span, data from multiple sensors have to be merged to create a single time series, and any uncorrected inter-sensor biases could introduce artefacts in the series, e.g., different sensors monitor radiances at different wavebands such that producing a consistent time series of reflectances is not straightforward. Another requirement is that the products have to be validated against in situ observations. Furthermore, the uncertainties in the products have to be quantified, ideally on a pixel-by-pixel basis, to facilitate applications and interpretations that are consistent with the quality of the data. This paper outlines an approach that was adopted for generating an ocean-colour time series for climate studies, using data from the MERIS (MEdium spectral Resolution Imaging Spectrometer) sensor of the European Space Agency; the SeaWiFS (Sea-viewing Wide-Field-of-view Sensor) and MODIS-Aqua (Moderate-resolution Imaging Spectroradiometer-Aqua) sensors from the National Aeronautics and Space Administration (USA); and VIIRS (Visible and Infrared Imaging Radiometer Suite) from the National Oceanic and Atmospheric Administration (USA). The time series now covers the period from late 1997 to end of 2018. To ensure that the products meet, as well as possible, the requirements of the user community, marine-ecosystem modellers, and remote-sensing scientists were consulted at the outset on their immediate and longer-term requirements as well as on their expectations of ocean-colour data for use in climate research. Taking the user requirements into account, a series of objective criteria were established, against which available algorithms for processing ocean-colour data were evaluated and ranked. The algorithms that performed best with respect to the climate user requirements were selected to process data from the satellite sensors. Remote-sensing reflectance data from MODIS-Aqua, MERIS, and VIIRS were band-shifted to match the wavebands of SeaWiFS. Overlapping data were used to correct for mean biases between sensors at every pixel. The remote-sensing reflectance data derived from the sensors were merged, and the selected in-water algorithm was applied to the merged data to generate maps of chlorophyll concentration, inherent optical properties at SeaWiFS wavelengths, and the diffuse attenuation coefficient at 490 nm. The merged products were validated against in situ observations. The uncertainties established on the basis of comparisons with in situ data were combined with an optical classification of the remote-sensing reflectance data using a fuzzy-logic approach, and were used to generate uncertainties (root mean square difference and bias) for each product at each pixel.

New theoretical formulation for the determination of radiance transmittance at the water-air interface: comment.

We challenge a recent paper in this journal suggesting that the well-established formula governing the transmittance of radiance across a refracting interface needs revision [Optics Express, 25(22) 27086 (2017)]. We provide a simple example of radiative transfer across an interface showing that the accepted formula is correct.

Fusarium verticillioides: Advancements in Understanding the Toxicity, Virulence, and Niche Adaptations of a Model Mycotoxigenic Pathogen of Maize.

The importance of understanding the biology of the mycotoxigenic fungus Fusarium verticillioides and its various microbial and plant host interactions is critical given its threat to maize, one of the world's most valuable food crops. Disease outbreaks and mycotoxin contamination of grain threaten economic returns and have grave implications for human and animal health and food security. Furthermore, F. verticillioides is a member of a genus of significant phytopathogens and, thus, data regarding its host association, biosynthesis of secondary metabolites, and other metabolic (degradative) capabilities are consequential to both basic and applied research efforts across multiple pathosystems. Notorious among its secondary metabolites are the fumonisin mycotoxins, which cause severe animal diseases and are implicated in human disease. Additionally, studies of these mycotoxins have led to new understandings of F. verticillioides plant pathogenicity and provide tools for research into cellular processes and host-pathogen interaction strategies. This review presents current knowledge regarding several significant lines of F. verticillioides research, including facets of toxin production, virulence, and novel fitness strategies exhibited by this fungus across rhizosphere and plant environments.

Impact of spectral resolution of in situ ocean color radiometric data in satellite matchups analyses.

The spectral resolution requirements for in situ remote sensing reflectanceRRS measurements aiming at supporting satellite ocean color validation and System Vicarious Calibration (SVC) were investigated. The study, conducted using sample hyperspectral RRS from different water types, focused on the visible spectral bands of the ocean land color imager (OLCI) and of the Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) satellite sensors. Allowing for a ±0.5% maximum difference between in situ and satellite derived RRS solely due to the spectral band characteristics of the in situ radiometer, a spectral resolution of 1 nm for SVC of PACE is needed in oligotrophic waters. Requirements decrease to 3 nm for SVC of OLCI. In the case of validation activities, which exhibit less stringent uncertainty requirements with respect to SVC, a maximum difference of ±1% between in situ and satellite derived data indicates the need for a spectral resolution of 3 nm for both OLCI and PACE in oligotrophic waters. Conversely, spectral resolutions of 6 nm for PACE and 9 nm for OLCI appear to satisfy validation activities in optically complex waters.

Immersion Coefficient for the Marine Optical Buoy (MOBY) Radiance Collectors.

The immersion coefficient accounts for the difference in responsivity for a radiometer placed in the air versus water or another medium. In this study, the immersion coefficients for the radiance collectors on the Marine Optical Buoy (MOBY) were modeled and measured. The experiment showed that the immersion coefficient for the MOBY radiance collectors agreed with a simple model using only the index of refraction for water and fused silica. With the results of this experiment, we estimate that the uncertainty in the current value of the immersion coefficient used in the MOBY project is 0.05 % (k = 1).

NIR- and SWIR-based on-orbit vicarious calibrations for satellite ocean color sensors.

The near-infrared (NIR) and shortwave infrared (SWIR)-based atmospheric correction algorithms are used in satellite ocean color data processing, with the SWIR-based algorithm particularly useful for turbid coastal and inland waters. In this study, we describe the NIR- and two SWIR-based on-orbit vicarious calibration approaches for satellite ocean color sensors, and compare results from these three on-orbit vicarious calibrations using satellite measurements from the Visible Infrared Imaging Radiometer Suite (VIIRS) onboard the Suomi National Polar-orbiting Partnership (SNPP). Vicarious calibration gains for VIIRS spectral bands are derived using the in situ normalized water-leaving radiance nLw(λ) spectra from the Marine Optical Buoy (MOBY) in waters off Hawaii. The SWIR vicarious gains are determined using VIIRS measurements from the South Pacific Gyre region, where waters are the clearest and generally stable. Specifically, vicarious gain sets for VIIRS spectral bands of 410, 443, 486, 551, and 671 nm derived from the NIR method using the NIR 745 and 862 nm bands, the SWIR method using the SWIR 1238 and 1601 nm bands, and the SWIR method using the SWIR 1238 and 2257 nm bands are (0.979954, 0.974892, 0.974685, 0.965832, 0.979042), (0.980344, 0.975344, 0.975357, 0.965531, 0.979518), and (0.980820, 0.975609, 0.975761, 0.965888, 0.978576), respectively. Thus, the NIR-based vicarious calibration gains are consistent with those from the two SWIR-based approaches with discrepancies mostly within ~0.05% from three data processing methods. In addition, the NIR vicarious gains (745 and 862 nm) derived from the two SWIR methods are (0.982065, 1.00001) and (0.981811, 1.00000), respectively, with the difference ~0.03% at the NIR 745 nm band. This is the fundamental basis for the NIR-SWIR combined atmospheric correction algorithm, which has been used to derive improved satellite ocean color products over open oceans and turbid coastal/inland waters. Therefore, a unified vicarious gain set for VIIRS bands M1-M8 and M10-M11 has been implemented in the VIIRS ocean color data processing. Using the unified vicarious gain set, VIIRS mission-long ocean color data have been successfully reprocessed using the NIR-, SWIR-, and NIR-SWIR-based atmospheric correction algorithms.

Elevated nuclear sphingoid base-1-phosphates and decreased histone deacetylase activity after fumonisin B1 treatment in mouse embryonic fibroblasts.

Fumonisin B1 (FB1) is a mycotoxin produced by a common fungal contaminant of corn. Administration of FB1 to pregnant LM/Bc mice induces exencephaly in embryos, and ingestion of FB1-contaminated food during early pregnancy is associated with increased risk for neural tube defects (NTDs) in humans. FB1 inhibits ceramide synthase enzymes in sphingolipid biosynthesis, causing sphinganine (Sa) and bioactive sphinganine-1-phosphate (Sa1P) accumulation in blood, cells, and tissues. Sphingosine kinases (Sphk) phosphorylate Sa to form Sa1P. Upon activation, Sphk1 associates primarily with the plasma membrane, while Sphk2 is found predominantly in the nucleus. In cells over-expressing Sphk2, accumulation of Sa1P in the nuclear compartment inhibits histone deacetylase (HDAC) activity, causing increased acetylation of histone lysine residues. In this study, FB1 treatment in LM/Bc mouse embryonic fibroblasts (MEFs) resulted in significant accumulation of Sa1P in nuclear extracts relative to cytoplasmic extracts. Elevated nuclear Sa1P corresponded to decreased histone deacetylase (HDAC) activity and increased histone acetylation at H2BK12, H3K9, H3K18, and H3K23. Treatment of LM/Bc MEFs with a selective Sphk1 inhibitor, PF-543, or with ABC294640, a selective Sphk2 inhibitor, significantly reduced nuclear Sa1P accumulation after FB1, although Sa1P levels remained significantly increased relative to basal levels. Concurrent treatment with both PF-543 and ABC294640 prevented nuclear accumulation of Sa1P in response to FB1. Other HDAC inhibitors are known to cause NTDs, so these results suggest that FB1-induced disruption of sphingolipid metabolism leading to nuclear Sa1P accumulation, HDAC inhibition, and histone hyperacetylation is a potential mechanism for FB1-induced NTDs.

Polarization properties of FEL lamps as applied to radiometric calibration.

The polarization of the irradiance from several 1000 W FEL lamps was measured between 450 and 900 nm. These lamps are universally used as irradiance calibration standards in radiometric laboratories. The irradiance was polarized between 2.3% and 3.2%, with the polarization axis aligned with the coiled filament, nearly perpendicular to the lamp axis. We have presented a simple model of the filament that explains the degree of polarization and the plane of polarization, based on the polarized emissivity of tungsten, and gives an approximate value for this polarization. While the irradiance is polarized, this polarization does not significantly effect the polarization of the light when reflected from a Spectralon plaque (Labsphere, Inc.). The polarization of these lamps should be considered when these FEL lamps are used to characterize optical instruments, particularly grating spectrometers without polarization scrambling devices.

Neural network method to correct bidirectional effects in water-leaving radiance.

Ocean color algorithms that rely on "atmospherically corrected" nadir water-leaving radiances to infer information about marine constituents such as the chlorophyll concentration depend on a reliable method to convert the angle-dependent measured radiances from the observation direction to the nadir direction. It is also important to convert the measured radiances to the nadir direction when comparing and merging products from different satellite missions. The standard correction method developed by Morel and coworkers requires knowledge of the chlorophyll concentration. Also, the standard method was developed based on the Case 1 (open ocean) assumption, which makes it unsuitable for Case 2 situations such as turbid coastal waters. We introduce a neural network method to convert the angle-dependent water-leaving radiance (or the corresponding remote sensing reflectance) from the observation direction to the nadir direction. This method relies on neither an "atmospheric correction" nor prior knowledge of the water constituents or the inherent optical properties. It directly converts the remote sensing reflectance from an arbitrary slanted viewing direction to the nadir direction by using a trained neural network. This method is fast and accurate, and it can be easily adapted to different remote sensing instruments. Validation using NuRADS measurements in different types of water shows that this method is suitable for both Case 1 and Case 2 waters. In Case 1 or chlorophyll-dominated waters, our neural network method produces corrections similar to those of the standard method. In Case 2 waters, especially sediment-dominated waters, a significant improvement was obtained compared to the standard method.

Technique for monitoring performance of VIIRS reflective solar bands for ocean color data processing.

A technique for monitoring and evaluating the performance of on-orbit calibration for satellite ocean color sensors has been developed. The method is based on the sensor on-orbit vicarious calibration approach using in situ ocean optics measurements and radiative transfer simulations to predict (calculate) sensor-measured top-of-atmosphere spectral radiances. Using this monitoring method with in situ normalized water-leaving radiance nLw(λ) data from the Marine Optical Buoy (MOBY) in waters off Hawaii, we show that the root-cause for an abnormal inter-annual difference of chlorophyll-a data over global oligotrophic waters between 2012 and 2013 from the Visible Infrared Imaging Radiometer Suite (VIIRS) is primarily due to the VIIRS on-orbit calibration performance. In particular, VIIRS-produced Sensor Data Records (SDR) (or Level-1B data) are biased low by ~1% at the wavelength of 551 nm in 2013 compared with those in 2012. The VIIRS calibration uncertainty led to biased low chlorophyll-a data in 2013 by ~30-40% over global oligotrophic waters. The methodology developed in this study can be implemented for the routine monitoring of on-orbit satellite sensor performance (such as VIIRS). Particularly, long-term Chl-a data over open oceans can also be used as an additional source to evaluate ocean color satellite sensor performance. We show that accurate long-term and consistent MOBY in situ measurements can be used not only for the required system vicarious calibration for satellite ocean color data processing, but also can be used to characterize and monitor both the short-term and long-term sensor on-orbit performances.

A new instrument for measuring the high dynamic range radiance distribution in near-surface sea water.

A new instrument for measuring the full radiance distribution in the ocean interior is introduced. The system is based on CMOS technology to achieve intra-scene dynamic range of 6 decades and system dynamic range of more than 9 decades. The spatial resolution is nominally 0.5 degrees with a temporal frame rate between 1 and 15 frames per second. The general instrumentation, detailed calibration, and a characterization of the system are described. Validity of the camera systems is demonstrated by comparison of the radiance measurements with other classical oceanographic radiometers.

Detailed validation of the bidirectional effect in various Case I and Case II waters.

Simulated bidirectional reflectance distribution functions (BRDF) were compared with measurements made just beneath the water's surface. In Case I water, the set of simulations that varied the particle scattering phase function depending on chlorophyll concentration agreed more closely with the data than other models. In Case II water, however, the simulations using fixed phase functions agreed well with the data and were nearly indistinguishable from each other, on average. The results suggest that BRDF corrections in Case II water are feasible using single, average, particle scattering phase functions, but that the existing approach using variable particle scattering phase functions is still warranted in Case I water.

Increased sphingoid base-1-phosphates and failure of neural tube closure after exposure to fumonisin or FTY720.

BACKGROUND: Fumonisin B(1) (FB(1)) is a mycotoxin produced by a common fungal contaminant of corn. Ingestion of FB(1)-contaminated food is associated with increased risk for neural tube defects (NTDs). FB(1) induces NTDs in inbred LM/Bc mice. FB(1) inhibits ceramide synthase in de novo sphingolipid biosynthesis, resulting in accumulation of sphinganine and sphinganine-1-phosphate (Sa1P). Sa1P functions as a ligand for a family of G protein-coupled S1P receptors. METHODS: Pregnant SWV and LM/Bc mice were treated with FB(1) (20 mg/kg/day intraperitoneally on embryonic day (ED) 7.5-8.5) or the known S1P receptor agonist FTY720 (10 mg/kg/day oral gavage on ED 6.5-8.5). LC/MS was used to detect sphingoid base-1-phosphates in maternal blood spots, plasma, and embryonic tissue. Strain-specific SWV and LM/Bc mouse embryonic fibroblasts (MEFs) and serum free mouse embryo (SFME) neural progenitor cells were treated with FB(1) (40 µM for 24 hr) and LC/MS was used to detect sphingoid base-1-phosphates. RESULTS: FTY720 induced NTDs in both the SWV and the LM/Bc strains of mice. Sphinganine-1-P (Sa1P) and FTY720-P were elevated in the blood spots and plasma of mice treated with FB(1) or FTY720, respectively. FTY720-P was elevated in ED 9.5 exencephalic embryos. Sa1P was elevated in SFME and MEF cells treated with FB(1), and Sa1P was higher in MEFs generated from the FB(1)-NTD-susceptible LM/Bc strain. CONCLUSIONS: Elevated sphingoid base-1-P after FB(1) or FTY720 suggest a potential role for these bioactive lipid ligands and activation of S1P receptor signaling pathways in the failure of neural tube closure after FB(1) or FTY720. Sa1P may represent a biomarker for FB(1)-NTD risk assessment.

An instrument to measure the downwelling polarized radiance distribution in the ocean.

We have built a new camera system to measure the downwelling polarized radiance distribution in the ocean. This system uses 4 fisheye lenses and coherent fiber bundles behind each image to transmit all 4 fisheye images onto a single camera image. This allows simultaneous images to be collected with 4 unique polarization states, and thus the full Stokes vector of the rapidly changing downwelling light field.

Observation of non-principal plane neutral points in the in-water upwelling polarized light field.

Neutral points are specific directions in the light field where the three Stokes parameters Q, U, V, and thus the degree of polarization simultaneously go to zero. We have made the first measurement of non-principal-plane neutral points in the upwelling light field in natural waters. These neutral points are located at approximately 40°- 80° nadir angle and between 120° - 160° azimuth to the sun which is well off of the principal plane. Calculations show that the neutral point positions are very sensitive to the balance in the incident light between the partially polarized skylight and the direct solar beam.

Assessment of MERIS reflectance data as processed with SeaDAS over the European seas.

The uncertainties associated with MERIS remote sensing reflectance (RRS) data derived from the SeaWiFS Data Analysis System (SeaDAS) are assessed with field observations. In agreement with the strategy applied for other sensors, a vicarious calibration is conducted using in situ data from the Marine Optical BuoY offshore Hawaii, and leads to vicarious adjustment factors departing from 1 by 0.2% to 1.6%. The three field data sets used for validation have been collected at fixed stations in the northern Adriatic Sea and the Baltic Sea, and in a variety of European waters in the Baltic, Black, Mediterranean and North Seas. Excluding Baltic waters, the mean absolute relative difference |ψ| between satellite and field data is 10-14% for the spectral interval 490-560 nm, 16-18% at 443 nm, and 24-26% at 413 nm. In the Baltic Sea, the |ψ| values are much higher for the blue bands characterized by low RRS amplitudes, but similar or lower at 560 and 665 nm. For the three validation sets, the root-mean-square differences decrease from approximately 0.0013 sr-1 at 413 nm to 0.0002 sr-1 at 665 nm, and are found similar or lower than those obtained for SeaWiFS or MODIS-Aqua. As derived from SeaDAS, the RRS records associated with these three missions thus provide a multi-mission data stream of consistent accuracy.