316 research outputs found
Capturing optically important constituents and properties in a marine biogeochemical and ecosystem model
We present a numerical model of the ocean that couples a three-stream radiative transfer component with a marine biogeochemicalāecosystem component in a dynamic three-dimensional physical framework. The radiative transfer component resolves the penetration of spectral irradiance as it is absorbed and scattered within the water column. We explicitly include the effect of several optically important water constituents (different phytoplankton functional types; detrital particles; and coloured dissolved organic matter, CDOM). The model is evaluated against in situ-observed and satellite-derived products. In particular we compare to concurrently measured biogeochemical, ecosystem, and optical data along a meridional transect of the Atlantic Ocean. The simulation captures the patterns and magnitudes of these data, and estimates surface upwelling irradiance analogous to that observed by ocean colour satellite instruments. We find that incorporating the different optically important constituents explicitly and including spectral irradiance was crucial to capture the variability in the depth of the subsurface chlorophyll a (Chl a) maximum. We conduct a series of sensitivity experiments to demonstrate, globally, the relative importance of each of the water constituents, as well as the crucial feedbacks between the light field, the relative fitness of phytoplankton types, and the biogeochemistry of the ocean. CDOM has proportionally more importance at attenuating light at short wavelengths and in more productive waters, phytoplankton absorption is relatively more important at the subsurface Chl a maximum, and water molecules have the greatest contribution when concentrations of other constituents are low, such as in the oligotrophic gyres. Scattering had less effect on attenuation, but since it is important for the amount and type of upwelling irradiance, it is crucial for setting sea surface reflectance. Strikingly, sensitivity experiments in which absorption by any of the optical constituents was increased led to a decrease in the size of the oligotrophic regions of the subtropical gyres: lateral nutrient supplies were enhanced as a result of decreasing high-latitude productivity. This new model that captures bio-optical feedbacks will be important for improving our understanding of the role of light and optical constituents on ocean biogeochemistry, especially in a changing environment. Further, resolving surface upwelling irradiance will make it easier to connect to satellite-derived products in the future
Expanding understanding of optical variability in Lake Superior with a 4-year dataset
Lake Superior is one of the largest freshwater lakes on our planet,
but few optical observations have been made to allow for the development and
validation of visible spectral satellite remote sensing products. The dataset
described here focuses on coincidently observing inherent and apparent
optical properties along with biogeochemical parameters. Specifically, we
observe remote sensing reflectance, absorption, scattering, backscattering,
attenuation, chlorophyll concentration, and suspended particulate matter over
the ice-free months ofĀ 2013–2016. The dataset substantially increases the
optical knowledge of the lake. In addition to visible spectral satellite
algorithm development, the dataset is valuable for characterizing the
variable light field, particle, phytoplankton, and colored dissolved organic
matter distributions, and helpful in food web and carbon cycle
investigations. The compiled data can be freely accessed at
https://seabass.gsfc.nasa.gov/archive/URI/Mouw/LakeSuperior/
Application of the BeerāLambert Model to Attenuation of Photosynthetically Active Radiation in a Shallow, Eutrophic Lake
Models of primary production in aquatic systems must include a means to estimate subsurface light. Such models often use the BeerāLambert law, assuming exponential attenuation of light with depth. It is further assumed that the diffuse attenuation coefficient may be estimated as a summation of scattering/absorbing constituent concentrations multiplied by their respective specific attenuation coefficients. While theoretical deviations from these assumptions have been documented, it is useful to consider the empirical performance of this common approach. Photosynthetically active radiation (PAR) levels and water quality conditions were recorded weekly from six to eight monitoring stations in western Lake Erie between 2012 and 2016. Exponential PAR extinction models yielded a mean attenuation coefficient of 1.55Ā m (interquartile rangeĀ =Ā 0.74ā1.90Ā m). While more complex light attenuation models are available, analysis of residuals indicated that the simple BeerāLambert model is adequate for shallow, eutrophic waters similar to western Lake Erie (R2Ā >Ā 0.9 for 96% of samples). Three groups of water quality variables were predictive of PAR attenuation: total and nonvolatile suspended particles, dissolved organic substances (dissolved organic carbon and chromophoric dissolved organic matter), and organic solids (volatile suspended solids and chlorophyll). Multiple regression models using these variables predicted 3ā90% of the variability in PAR attenuation, with a median adjusted R2Ā =Ā 0.86. Explanatory variables within these groups may substitute for each other while maintaining similar model performance, indicating that various combinations of water quality variables may be useful to predict PAR attenuation, depending on availability within a model framework or monitoring program.Key PointsThe BeerāLambert law effectively models photosynthetically active radiation in western Lake Erie, despite some systematic deviationsFieldāobtained water quality parameters can predict photosynthetically active radiation attenuation with a high degree of confidenceSuspended particle concentration is most predictive of photosynthetically active radiation attenuation in this turbid, eutrophic basinPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147097/1/wrcr23654_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147097/2/wrcr23654-sup-0001-2018WR023024-SI.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147097/3/wrcr23654.pd
Impact of phytoplankton community size on a linked global ocean optical and ecosystem model
Author Posting. Ā© The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Journal of Marine Systems 89 (2012): 61-75, doi:10.1016/j.jmarsys.2011.08.002.We isolated the effect phytoplankton cell size has on varying remote sensing reflectance
spectra (Rrs(Ī»)) in the presence of optically active constituents by using optical and radiative
transfer models linked in an offline diagnostic calculation to a global
biogeochemical/ecosystem/circulation model with explicit phytoplankton size classes. Two case
studies were carried out, each with several scenarios to isolate the effects of chlorophyll
concentration, phytoplankton cell size, and size-varying phytoplankton absorption on Rrs(Ī»).
The goal of the study was to determine the relative contribution of phytoplankton cell size and chlorophyll to overall Rrs(Ī») and to understand where a standard band ratio algorithm (OC4) may
under/overestimate chlorophyll due to Rrs(Ī») being significantly affected by phytoplankton size.
Phytoplankton cell size was found to contribute secondarily to Rrs(Ī») variability and to amplify
or dampen the seasonal cycle in Rrs(Ī»), driven by chlorophyll. Size and chlorophyll were found
to change in phase at low to mid-latitudes, but were anti-correlated or poorly correlated at high
latitudes. Phytoplankton size effects increased model calculated Rrs(443) in the subtropical ocean during local spring through early fall months in both hemispheres and decreased Rrs(443)
in the Northern Hemisphere high latitude regions during local summer to fall months. This study
attempts to tease apart when/where variability about the OC4 relationship may be associated
with cell size variability. The OC4 algorithm may underestimate [Chl] when the fraction of
microplankton is elevated, which occurs in the model simulations during local spring/summer
months at high latitudes in both hemispheres.Funding for this study came from a NASA Earth and Space Science Fellowship and
University of Rhode Island Graduate School Oceanography Alumni Fellowship, both awarded to
C. Mouw. The CCSM-3 BEC simulations were generated with support from NASA Ocean
Biology and Biogeochemistry Program (NNX07AL80G) and the NSF Center for Microbial
Oceanography Research and Education (C-MORE, EF-0424599)
Phytoplankton functional types from Space.
The concept of phytoplankton functional types has emerged as a useful approach to
classifying phytoplankton. It finds many applications in addressing some serious
contemporary issues facing science and society. Its use is not without challenges,
however. As noted earlier, there is no universally-accepted set of functional types,
and the types used have to be carefully selected to suit the particular problem being
addressed. It is important that the sum total of all functional types matches all
phytoplankton under consideration. For example, if in a biogeochemical study,
we classify phytoplankton as silicifiers, calcifiers, DMS-producers and nitrogen fix-
ers, then there is danger that the study may neglect phytoplankton that do not
contribute in any significant way to those functions, but may nevertheless be a
significant contributor to, say primary production. Such considerations often lead
to the adoption of a category of āother phytoplanktonā in models, with no clear
defining traits assigned them, but that are nevertheless necessary to close budgets
on phytoplankton processes. Since this group is a collection of all phytoplankton
that defy classification according to a set of traits, it is difficult to model their physi-
ological processes. Our understanding of the diverse functions of phytoplankton is
still growing, and as we recognize more functions, there will be a need to balance the
desire to incorporate the increasing number of functional types in models against
observational challenges of identifying and mapping them adequately. Modelling
approaches to dealing with increasing functional diversity have been proposed,
for example, using the complex adaptive systems theory and system of infinite
diversity, as in the work of Bruggemann and Kooijman (2007). But it is unlikely that
remote-sensing approaches might be able to deal with anything but a few prominent
functional types. As long as these challenges are explicitly addressed, the functional-
type concept should continue to fill a real need to capture, in an economic fashion,
the diversity in phytoplankton, and remote sensing should continue to be a useful
tool to map them.
Remote sensing of phytoplankton functional types is an emerging field, whose
potential is not fully realised, nor its limitations clearly established. In this report,
we provide an overview of progress to date, examine the advantages and limitations
of various methods, and outline suggestions for further development. The overview
provided in this chapter is intended to set the stage for detailed considerations of
remote-sensing applications in later chapters.
In the next chapter, we examine various in situ methods that exist for observing
phytoplankton functional types, and how they relate to remote-sensing techniques.
In the subsequent chapters, we review the theoretical and empirical bases for the
existing and emerging remote-sensing approaches; assess knowledge about the
limitations, assumptions, and likely accuracy or predictive skill of the approaches;
provide some preliminary comparative analyses; and look towards future prospects
with respect to algorithm development, validation studies, and new satellite mis-
sions
Satellite sensor requirements for monitoring essential biodiversity variables of coastal ecosystems.
The biodiversity and high productivity of coastal terrestrial and aquatic habitats are the foundation for important benefits to human societies around the world. These globally distributed habitats need frequent and broad systematic assessments, but field surveys only cover a small fraction of these areas. Satellite-based sensors can repeatedly record the visible and near-infrared reflectance spectra that contain the absorption, scattering, and fluorescence signatures of functional phytoplankton groups, colored dissolved matter, and particulate matter near the surface ocean, and of biologically structured habitats (floating and emergent vegetation, benthic habitats like coral, seagrass, and algae). These measures can be incorporated into Essential Biodiversity Variables (EBVs), including the distribution, abundance, and traits of groups of species populations, and used to evaluate habitat fragmentation. However, current and planned satellites are not designed to observe the EBVs that change rapidly with extreme tides, salinity, temperatures, storms, pollution, or physical habitat destruction over scales relevant to human activity. Making these observations requires a new generation of satellite sensors able to sample with these combined characteristics: (1) spatial resolution on the order of 30 to 100-m pixels or smaller; (2) spectral resolution on the order of 5 nm in the visible and 10 nm in the short-wave infrared spectrum (or at least two or more bands at 1,030, 1,240, 1,630,
2,125, and/or 2,260 nm) for atmospheric correction and aquatic and vegetation assessments; (3) radiometric
quality with signal to noise ratios (SNR) above 800 (relative to signal levels typical of the open ocean), 14-bit digitization, absolute radiometric calibration <2%, relative calibration of 0.2%, polarization sensitivity <1%, high radiometric stability and linearity, and operations designed to minimize sunglint; and (4) temporal resolution of hours to days. We refer to these combined specifications as H4 imaging. Enabling H4 imaging is vital for the conservation and management of global biodiversity and ecosystem services, including food provisioning and water security. An agile satellite in a 3-d repeat low-Earth orbit could sample 30-km swath images of several hundred coastal habitats daily. Nine H4 satellites would provide weekly coverage of global coastal zones. Such satellite constellations are now feasible and are used in various applications
Borrelia burgdorferi EbfC defines a newly-identified, widespread family of bacterial DNA-binding proteins
The Lyme disease spirochete, Borrelia burgdorferi, encodes a novel type of DNA-binding protein named EbfC. Orthologs of EbfC are encoded by a wide range of bacterial species, so characterization of the borrelial protein has implications that span the eubacterial kingdom. The present work defines the DNA sequence required for high-affinity binding by EbfC to be the 4 bp broken palindrome GTnAC, where ānā can be any nucleotide. Two high-affinity EbfC-binding sites are located immediately 5ā² of B. burgdorferi erp transcriptional promoters, and binding of EbfC was found to alter the conformation of erp promoter DNA. Consensus EbfC-binding sites are abundantly distributed throughout the B. burgdorferi genome, occurring approximately once every 1 kb. These and other features of EbfC suggest that this small protein and its orthologs may represent a distinctive type of bacterial nucleoid-associated protein. EbfC was shown to bind DNA as a homodimer, and site-directed mutagenesis studies indicated that EbfC and its orthologs appear to bind DNA via a novel Ī±-helical ātweezerā-like structure
Mediterranean dietary pattern and cancer risk in the EPIC cohort
Background: Although several studies have investigated the association of the Mediterranean diet with overall mortality or risk of specific cancers, data on overall cancer risk are sparse. Methods: We examined the association between adherence to Mediterranean dietary pattern and overall cancer risk using data from the European Prospective Investigation Into Cancer and nutrition, a multi-centre prospective cohort study including 142 605 men and 335 873. Adherence to Mediterranean diet was examined using a score (range: 0ā9) considering the combined intake of fruits and nuts, vegetables, legumes, cereals, lipids, fish, dairy products, meat products, and alcohol. Association with cancer incidence was assessed through Cox regression modelling, controlling for potential confounders. Results: In all, 9669 incident cancers in men and 21 062 in women were identified. A lower overall cancer risk was found among individuals with greater adherence to Mediterranean diet (hazard ratio=0.96, 95% CI 0.95ā0.98) for a two-point increment of the Mediterranean diet score. The apparent inverse association was stronger for smoking-related cancers than for cancers not known to be related to tobacco (P (heterogeneity)=0.008). In all, 4.7% of cancers among men and 2.4% in women would be avoided in this population if study subjects had a greater adherence to Mediterranean dietary pattern. Conclusion: Greater adherence to a Mediterranean dietary pattern could reduce overall cancer risk
Missing Links: Referrer Behavior and Job Segregation
How does referral recruitment contribute to job segregation, and what can organizations do about it?
Current theory on network effects in the labor market emphasizes the job-seeker perspective, focusing on the
segregated nature of job-seekersā information and contact networks, and leaves little role for organizational
influence. But employee referrals are necessarily initiated from within a firm by referrers. We argue that
referrer behavior is the missing link that can help organizations manage the segregating effects of referring.
Adopting the referrerās perspective of the process, we develop a computational model which integrates a set
of empirically documented referrer behavior mechanisms gleaned from extant organizational case studies.
Using this model, we compare the segregating effects of referring when these behaviors are inactive to the
effects when the behaviors are active. We show that referrer behaviors substantially boost the segregating
effects of referring. This impact of referrer behavior presents an opportunity for organizations. Contrary to
popular wisdom, we show that organizational policies designed to influence referrer behaviors can mitigate
most if not all of the segregating effects of referring
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