Biooptical variability in the Greenland Sea observed with the Multispectral Airborne Radiometer System (MARS)

A site-specific ocean color remote sensing algorithm was developed and used to convert Multispectral Airborne Radiometer System (MARS) spectral radiance measurements to chlorophyll-a concentration profiles along aircraft tracklines in the Greenland Sea. The analysis is described and the results given in graphical or tabular form. Section 2 describes the salient characteristics and history of development of the MARS instrument. Section 3 describes the analyses of MARS flight segments over consolidated sea ice, resulting in a set of altitude dependent ratios used (over water) to estimate radiance reflected by the surface and atmosphere from total radiance measured. Section 4 presents optically weighted pigment concentrations calculated from profile data, and spectral reflectances measured in situ from the top meter of the water column; this data was analyzed to develop an algorithm relating chlorophyll-a concentrations to the ratio of radiance reflectances at 441 and 550 nm (with a selection of coefficients dependent upon whether significant gelvin presence is implied by a low ratio of reflectances at 410 and 550 nm). Section 5 describes the scaling adjustments which were derived to reconcile the MARS upwelled radiance ratios at 410:550 nm and 441:550 nm to in situ reflectance ratios measured simultaneously on the surface. Section 6 graphically presents the locations of MARS data tracklines and positions of the surface monitoring R/V. Section 7 presents stick-plots of MARS tracklines selected to illustrate two-dimensional spatial variability within the box covered by each day's flight. Section 8 presents curves of chlorophyll-a concentration profiles derived from MARS data along survey tracklines. Significant results are summarized in Section 1

Bio-Optical Properties of the Arabian Sea as Determined by In Situ and Sea WiFS Data

The overall objective of this work was to characterize optical and fluorescence properties in the euphotic zone during two British Ocean Flux Study (BOFS) Arabian Sea cruises. This was later expanded in 1995 to include three U.S. JGOFS Arabian Sea Cruises. The region was to be divided into one or more "bio-optical provinces," within each of which a single set of regression models was to be developed to relate the vertical distribution of irradiance attenuation and normalized fluorescence (SF and NF) to remote sensing reflectance and diffuse attenuation coefficient. The working hypothesis was that over relatively large spatial and temporal scales, the vertical profiles of bio-optical properties were predictable. The specific technical objectives were: (1) To characterize the vertical distribution of the inherent and apparent optical properties by measuring downwelling and upwelling irradiances, upwelling radiances, scalar irradiance of PAR, and beam transmissions at each station - from these data, spectral diffuse attenuation coefficients, irradiance reflectances, remote sensing reflectances, surface-leaving radiances and beam attenuation coefficients were determined; (2) To characterize the spectral absorption of total particulate, detrital, and dissolved organic material at each station from discrete water samples; (3) To describe the vertical distribution of photoadaptive properties in the water column by measuring profiles of stimulated (SF) and natural (NF) fluorescence and examining relationships between SF and NF as a function of diffuse optical depth, pigment biomass and primary productivity; and (4) To establish locally derived, in-water algorithms relating remote sensing reflectance spectra to diffuse attenuation coefficients, phytoplankton pigment concentrations and primary productivity, through intercomparisons with in situ measurements, for application to SeaWiFS data

SeaWiFS Technical Report Series

The Sea-viewing Wide Field-of-view Sensor (SeaWiFS) mission will provide operational ocean color that will be superior to the previous Coastal Zone Color Sensor (CZCS) proof-of-concept mission. An algorithm is needed that exploits the full functionality of SeaWiFS whilst remaining compatible in concept with algorithms used for the CZCS. This document describes the theoretical rationale of radiance band-ratio methods for determining chlorophyll-a and other important biogeochemical parameters, and their implementation for the SeaWIFS mission. Pigment interrelationships are examined to explain the success of the CZCS algorithms. In the context where chlorophyll-a absorbs only weakly at 520 nm, the success of the 520 nm to 550 nm CZCS band ratio needs to be explained. This is explained by showing that in pigment data from a range of oceanic provinces chlorophyll-a (absorbing at less than 490 nm), carotenoids (absorbing at greater than 460 nm), and total pigment are highly correlated. Correlations within pigment groups particularly photoprotectant and photosynthetic carotenoids are less robust. The sources of variability in optical data are examined using the NIMBUS Experiment Team (NET) bio-optical data set and bio-optical model. In both the model and NET data, the majority of the variance in the optical data is attributed to variability in pigment (chlorophyll-a), and total particulates, with less than 5% of the variability resulting from pigment assemblage. The relationships between band ratios and chlorophyll is examined analytically, and a new formulation based on a dual hyperbolic model is suggested which gives a better calibration curve than the conventional log-log linear regression fit. The new calibration curve shows the 490:555 ratio is the best single-band ratio and is the recommended CZCS-type pigment algorithm. Using both the model and NET data, a number of multiband algorithms are developed; the best of which is an algorithm based on the 443:555 and 490:555 ratios. From model data, the form of potential algorithms for other products, such as total particulates and dissolved organic matter (DOM), are suggested

SeaWiFS Technical Report Series. Volume 29: SeaWiFS CZCS-type pigment algorithm

The Sea-viewing Wide Field-of-view Sensor (SeaWiFS) mission will provide operational ocean color that will be superior to the previous Coastal Zone Color Sensor (CZCS) proof-of-concept mission. an algorithm is needed that exploits the full functionality of SeaWiFS whilst remaining compatible in concept with algorithms used for the CZCS. This document describes the theoretical rationale of radiance band-radio methods for determining chlorophyll alpha and other important biogeochemical parameters, and their implementation for the SeaWiFS mission. Pigment interrelationships are examined to explain the success of the CZCS algorithms. In the context where chlorophyll alpha absorbs only weakly at 520 nm, the success of the 520 nm to 550 nm CZCS band ratio needs to be explained. This is explained by showing that in pigment data from a range of oceanic provinces chlorophyll alpha (absorbing at less than 490 nm), carotenoids (absorbing at greater than 460 nm), and total pigment are highly correlated. Correlations within pigment groups particularly photoprotectant and photosynthetic carotenoids are less robust. The sources of variability in optical data re examined using the NIMBUS Experiment Team (NET) bio-optical data set and bio-optical model. In both the model and NET data, the majority of the variance in the optical data is attributed to variability in pigment (chlorophyll alpha, and total particulates, with less than 5% of the variability resulting from pigment assemblage. The relationships between band ratios and chlorophyll is examined analytically, and a new formulation based on a dual hyperbolic model is suggested which gives a better calibration curve than the conventional log-log linear regression fit. The new calibration curve shows that 490:555 ratio is the best single-band ratio and is the recommended CZCS-type pigment algorithm. Using both the model and NET data, a number of multiband algorithms are developed; the best of which is an algorithm based on the 443:555 and 490:555 ratios. From model data, the form of potential algorithms for other products, such as total particulates and dissolved organic matter (DOM), are suggested

Macronutrient uptake and carotenoid/chlorophyll a ratio in the dinoflagellate Amphidinium carteri Hulburt, cultured under different nutrient and light conditions

Population growth, macronutrient (NO3 -, PO4 3-) uptake and carotenoids/chlorophyll a ratio we determined in Amphidinium carteri Hulburt, cultured under conditions of continuous light (50, 150, 300 and 750 µmol quanta m-2 s-1 ) and three nutrient concentrations NaNO3/NaH2PO4 at 441.5/18.1 µM (low) 883/36.3 µM (medium) and 1766/72.6 µM (high). Both nutrient and irradiance had a significant effect (p < 0.05) on cellular abundance during the period of culture, except for the fourth and seventh day for nutrients (p > 0.05). In cultures under low nutrient condition, NO3 - and PO4 3- were almost depleted by the fifth day and in cultures with medium nutrient this condition occurred in the sixth day; whereas, at high nutrient condition the nutrients were not depleted. We concluded that A. carteri had higher growth rates and nutrient consumption at 300 µmol quanta m-2 s-1 during the first five days and in general the effect of nutrients on the pigment ratios was not significant (p > 0.05). However, the average peridinin/Chla ratio decreased up to 72% from the lowest and the highest irradiance. The opposite was observed for the average of diadinoxanthin/Chla ratio that increased almost two-fold, and the averages dinoxanthin and diatoxanthin to Chla ratios that increased from low to high irradiances. The average diatoxanthin/Chla ratio at 750 µmol quanta m-2 s-1 increased up to 2.7-fold from the exponential to the stationary phase only in the low and medium nutrient concentration. Likewise, the average peridinin, dinoxanthin and diatoxanthin to Chla ratios were not significantly different at 50 and 150 µmol quanta m-2 s-1 . These results indicate important changes in average carotenoids/Chla ratios in A. carteri cultured under different irradiances

SeaWiFS Technical Report Series

This document provides brief reports, or case studies, on a number of investigations sponsored by the Calibration and Validation Team (CVT) within the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) Project. Chapter I describes the calibration and characterization of the GSFC sphere, which was used in the recent recalibration of the SeaWiFS instrument. Chapter 2 presents a revision of the diffuse attenuation coefficient, K(490), algorithm based on the SeaWiFS wavelengths. Chapter 3 provides an implementation scheme for an algorithm to remove out-of-band radiance when using a sensor calibration based on a finite width (truncated) spectral response function, e.g., between the 1% transmission points. Chapter 4 describes the implementation schemes for the stray light quality flag (local area coverage [LAC] and global area coverage [GAC]) and the LAC stray light correction

Growth and accessory pigments to chlorophyll a ratios of Thalassiosira pseudonana (Bacillariophyceae) cultured under different irradiances.

This study investigated how different light conditions affect the growth and accessory pigment to chlorophyll a ratios in Thalassiosira pseudonana. The microalga was grown for five days under four irradiances (50, 150, 300 and 750 µmol quanta m-2 s-1) with f/2 medium. Daily growth and pigment composition were determined for each treatment. Initial mean cellular density for all treatment was 1.15 ± 0.057 × 105 cell ml-1, which increased the first two days of culture to 1.21 ± 0.012 x 106 cell ml-1 on average and did not show significant changes among irradiances. Growth rates decreased with the final cell numbers being similar among treatments except for the lowest irradiance, which increased their cellular density. Chlorophyll a and fucoxanthin concentrations showed statistically significant differences (p < 0.001) among the different levels of light. These concentrations were always higher at low than at high irradiances. For diadinoxanthin the concentrations decreased as the irradiance increased, which was contrary to what occurred with diatoxanthin. Fucoxanthin to chlorophyll a ratio was not significantly affected by the irradiance level (p = 0.444), but did change during time under culture (p = 0.003). Diatoxanthin to chlorophyll a ratios increased among different irradiances and with time, with higher values at high irradiances, whereas, diadinoxanthin to chlorophyll a ratios only increased at 750 µmol quanta m-2 s-1. It is concluded that variations in light intensity did not change the cellular densities of T. pseudonana but did have significant effects on accessory pigment to chlorophyll a ratios

A comparison of methods for the measurement of the absorption coefficient in natural waters

In the spring of 1992 an optical closure experiment was conducted at Lake Pend Oreille, Idaho. A primary objective of the experiment was to compare techniques for the measurement of the spectral absorption coefficient and other inherent optical properties of natural waters. Daily averages of absorption coefficients measured using six methods are compared at wavelengths of 456, 488, and 532 nm. Overall agreement was within 40% at 456 nm and improved with increasing wavelength to 25% at 532 nm. These absorption measurements were distributed over the final 9 days of the experiment, when bio-optical conditions in Lake Pend Oreille (as indexed by the beam attenuation coefficient cp(660) and chlorophyll a fluorescence profiles) were representative of those observed throughout the experiment. However, profiles of stimulated chlorophyll a fluorescence and beam transmission showed that bio-optical properties in the lake varied strongly on all time and space scales. Therefore environmental variability contributed significantly to deviations between daily mean absorption coefficients measured using the different techniques

Immunisation with a Multivalent, Subunit Vaccine Reduces Patent Infection in a Natural Bovine Model of Onchocerciasis during Intense Field Exposure

Human onchocerciasis, caused by the filarial nematode Onchocerca volvulus, is controlled almost exclusively by the drug ivermectin, which prevents pathology by targeting the microfilariae. However, this reliance on a single control tool has led to interest in vaccination as a potentially complementary strategy. Here, we describe the results of a trial in West Africa to evaluate a multivalent, subunit vaccine for onchocerciasis in the naturally evolved host-parasite relationship of Onchocerca ochengi in cattle. Naïve calves, reared in fly-proof accommodation, were immunised with eight recombinant antigens of O. ochengi, administered separately with either Freund's adjuvant or alum. The selected antigens were orthologues of O. volvulus recombinant proteins that had previously been shown to confer protection against filarial larvae in rodent models and, in some cases, were recognised by serum antibodies from putatively immune humans. The vaccine was highly immunogenic, eliciting a mixed IgG isotype response. Four weeks after the final immunisation, vaccinated and adjuvant-treated control calves were exposed to natural parasite transmission by the blackfly vectors in an area of Cameroon hyperendemic for O. ochengi. After 22 months, all the control animals had patent infections (i.e., microfilaridermia), compared with only 58% of vaccinated cattle (P = 0.015). This study indicates that vaccination to prevent patent infection may be an achievable goal in onchocerciasis, reducing both the pathology and transmissibility of the infection. The cattle model has also demonstrated its utility for preclinical vaccine discovery, although much research will be required to achieve the requisite target product profile of a clinical candidate

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe