Correction of profiles of in-situ chlorophyll fluorometry for the contribution of fluorescence originating from non-algal matter

In situ chlorophyll fluorometers have been widely employed for more than half a century, and to date, it still remains the most used instrument to estimate chlorophyll-a concentration in the field, especially for measurements onboard autonomous observation platforms, e.g., Bio-Argo floats and gliders. However, in deep waters (> 300 m) of some specific regions, e.g., subtropical gyres and the Black Sea, the chlorophyll fluorescence profiles frequently reveal “deep sea red fluorescence” features. In line with previous studies and through the analysis of a large data set (cruise transect in the South East Pacific and data acquired by 82 Bio- Argo floats), we show that the fluorescence signal measured by a humic-like DOM fluorometer is highly correlated to the “deep sea red fluorescence.” Both fluorescence signals are indeed linearly related in deep waters. To remove the contribution of non-algal organic matter from chlorophyll fluorescence profiles, we introduce a new correction. Rather that removing a constant value (generally the deepest chlorophyll a fluorescence value from the profile, i.e., so-called “deep-offset correction”), we propose a correction method which relies on DOM fluorometry and on its variation with depth. This new method is validated with chlorophyll concentration extracted from water samples and further applied on the Bio-Argo float data set. More generally, we discuss the potential of the proposed method to become a standard and routine procedure in quality-control and correction of chlorophyll a fluorescence originating from Bio-Argo network

Data-Model Comparison Search Analysis of Coincident PBO Balmer α, EURD Lyman β Geocoronal Measurements From March 2000

Recent Lyman series and Balmer series airglow measurements provide a fresh opportunity to investigate the density distribution and variability of atomic hydrogen in the upper atmosphere. Dedicated nightside Balmer α Fabry-Perot spectrometer measurements at the Pine Bluff Observatory (PBO), University of Wisconsin-Madison, have been acquired since late 1999 taking advantage of several technological advances. Extreme ultraviolet spectral radiance measurements by the Espectrógrafo Ultravioleta extremo para la Radiación Difusa (EURD) instrument on the Spanish MINISAT-1 satellite from October 1997 to December 2001 provide extensive sets of geocoronal Lyman β, Lyman γ and He 584 Å emission intensities. In this paper, coincident EURD Lyman β and PBO Balmer α radiance measurements from the early March 2000 new moon period are presented. In addition to serving as examples of the data sets now available, the data volume poses an analysis challenge not faced in prior geocoronal studies. A data-model comparison search procedure employing resonance radiation transport results for extensive sets of parametric density distribution models is being developed for use in analyses of multiple large data sets; this is described, and example results for the PBO and EURD March 2000 data sets are presented. The tightness of the constraints obtained for the solar line-center Lyman β irradiance and the atomic hydrogen column abundance is somewhat surprising, given the crudeness of the parameter binning in the search procedure and the fact that a small number of recognized corrections remain to be made to each data set

Identification, Genotyping and Antimicrobial Susceptibility Testing of Brucella spp. Isolated from Livestock in Egypt

Brucellosis is a highly contagious zoonosis worldwide with economic and public health impacts. The aim of the present study was to identify Brucella (B.) spp. isolated from animal populations located in different districts of Egypt and to determine their antimicrobial resistance. In total, 34-suspected Brucella isolates were recovered from lymph nodes, milk, and fetal abomasal contents of infected cattle, buffaloes, sheep, and goats from nine districts in Egypt. The isolates were identified by microbiological methods and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Differentiation and genotyping were confirmed using multiplex PCR for B. abortus, Brucella melitensis, Brucella ovis, and Brucella suis (AMOS) and Bruce-ladder PCR. Antimicrobial susceptibility testing against clinically used antimicrobial agents (chloramphenicol, ciprofloxacin, erythromycin, gentamicin, imipenem, rifampicin, streptomycin, and tetracycline) was performed using E-Test. The antimicrobial resistance-associated genes and mutations in Brucella isolates were confirmed using molecular tools. In total, 29 Brucella isolates (eight B. abortus biovar 1 and 21 B. melitensis biovar 3) were identified and typed. The resistance of B. melitensis to ciprofloxacin, erythromycin, imipenem, rifampicin, and streptomycin were 76.2%, 19.0%, 76.2%, 66.7%, and 4.8%, respectively. Whereas, 25.0%, 87.5%, 25.0%, and 37.5% of B. abortus were resistant to ciprofloxacin, erythromycin, imipenem, and rifampicin, respectively. Mutations in the rpoB gene associated with rifampicin resistance were identified in all phenotypically resistant isolates. Mutations in gyrA and gyrB genes associated with ciprofloxacin resistance were identified in four phenotypically resistant isolates of B. melitensis. This is the first study highlighting the antimicrobial resistance in Brucella isolated from different animal species in Egypt. Mutations detected in genes associated with antimicrobial resistance unravel the molecular mechanisms of resistance in Brucella isolates from Egypt. The mutations in the rpoB gene in phenotypically resistant B. abortus isolates in this study were reported for the first time in Egypt

Geocoronal Hydrogen Observations Spanning Three Solar Minima

The 11-year solar cycle is a dominant source of natural variability in the upper atmosphere, and its effect on atomic hydrogen distributions and emissions must be understood to investigate possible signs of longer-term climatic trends in this region. We present midlatitude geocoronal hydrogen Balmer α observations from solar cycle 23 (1997–2006) and three solar minimum periods, 1985, 1997, and 2006. The 1997 through 2006 observations were taken with the Wisconsin H-αMapper Fabry-Perot (WHAM), a ground-based CCD-annular summing instrument that began observations at the Kitt Peak Observatory in Arizona in 1997. The 1985 observations were made with a similarly designed “pre-WHAM” Fabry-Perot Interferometer utilizing photomultiplier detection and located in Wisconsin. WHAM has consistently observed higher column emission intensities during solar maximum periods than during solar minimum conditions, with the ratio dependent upon the viewing geometry. The observations from three solar minimum periods agree to within 18% uncertainties over most of the shadow altitude range. An analysis of recent Fabry-Perot observations of upper atmospheric hydrogen during solar cycle 23 and during three solar minima (1985, 1997, 2006) established a reference data set of highly precise, consistently calibrated, thermospheric plus exospheric hydrogen column emission observations from northern midlatitudes that can be used to compare with future observations

The Wisconsin Plasma Astrophysics Laboratory

The Wisconsin Plasma Astrophysics Laboratory (WiPAL) is a flexible user facility designed to study a range of astrophysically relevant plasma processes as well as novel geometries that mimic astrophysical systems. A multi-cusp magnetic bucket constructed from strong samarium cobalt permanent magnets now confines a 10 m$^3$, fully ionized, magnetic-field free plasma in a spherical geometry. Plasma parameters of $T_{e}\approx5$ to $20$ eV and $n_{e}\approx10^{11}$ to $5\times10^{12}$ cm$^{-3}$ provide an ideal testbed for a range of astrophysical experiments including self-exciting dynamos, collisionless magnetic reconnection, jet stability, stellar winds, and more. This article describes the capabilities of WiPAL along with several experiments, in both operating and planning stages, that illustrate the range of possibilities for future users.Comment: 21 pages, 12 figures, 2 table

Epitaxial and layer-by-layer growth of EuO thin films on yttria-stabilized cubic zirconia (001) using MBE distillation

We have succeeded in growing epitaxial and highly stoichiometric films of EuO on yttria-stabilized cubic zirconia (YSZ) (001). The use of the Eu-distillation process during the molecular beam epitaxy assisted growth enables the consistent achievement of stoichiometry. We have also succeeded in growing the films in a layer-by-layer fashion by fine tuning the Eu vs. oxygen deposition rates. The initial stages of growth involve the limited supply of oxygen from the YSZ substrate, but the EuO stoichiometry can still be well maintained. The films grown were sufficiently smooth so that the capping with a thin layer of aluminum was leak tight and enabled ex situ experiments free from trivalent Eu species. The findings were used to obtain recipes for better epitaxial growth of EuO on MgO (001).Comment: 10 pages, 15 figure

Recommendations for obtaining unbiased chlorophyll estimates from in situ chlorophyll fluorometers: A global analysis of WET Labs ECO sensors

Chlorophyll fluorometers provide the largest in situ global data set for estimating phytoplankton biomass because of their ease of use, size, power consumption, and relatively low price. While in situ chlorophyll a (Chl) fluorescence is proxy for Chl a concentration, and hence phytoplankton biomass, there exist large natural variations in the relationship between in situ fluorescence and extracted Chl a concentration. Despite this large natural variability, we present here a global validation data set for the WET Labs Environmental Characterization Optics (ECO) series chlorophyll fluorometers that suggests a factor of 2 overestimation in the factory calibrated Chl a estimates for this specific manufacturer and series of sensors. We base these results on paired High Pressure Liquid Chromatography (HPLC) and in situ fluorescence match ups for which non-photochemically quenched fluorescence observations were removed. Additionally, we examined matches between the factory-calibrated in situ fluorescence and estimates of chlorophyll concentration determined from in situ radiometry, absorption line height, NASA’s standard ocean color algorithm as well as laboratory calibrations with phytoplankton monocultures spanning diverse species that support the factor of 2 bias. We therefore recommend the factor of 2 global bias correction be applied for the WET Labs ECO sensors, at the user level, to improve the global accuracy of chlorophyll concentration estimates and products derived from them. We recommend that other fluorometer makes and models should likewise undergo global analyses to identify potential bias in factory calibration

Two databases derived from BGC-Argo float measurements for marine biogeochemical and bio-optical applications

Since 2012, an array of 105 Biogeochemical-Argo (BGC-Argo) floats has been deployed across the world’s oceans to assist in filling observational gaps that are required for characterizing open-ocean environments. Profiles of biogeochemical (chlorophyll and dissolved organic matter) and optical (single-wavelength particulate optical backscattering, downward irradiance at three wavelengths, and photosynthetically available radiation) variables are collected in the upper 1000m every 1 to 10 days. The database of 9837 vertical profiles collected up to January 2016 is presented and its spatial and temporal coverage is discussed. Each variable is quality controlled with specifically developed procedures and its time series is quality-assessed to identify issues related to biofouling and/or instrument drift. A second database of 5748 profile-derived products within the first optical depth (i.e., the layer of interest for satellite remote sensing) is also presented and its spatiotemporal distribution discussed. This database, devoted to field and remote ocean color applications, includes diffuse attenuation coefficients for downward irradiance at three narrow wavebands and one broad waveband (photosynthetically available radiation), calibrated chlorophyll and fluorescent dissolved organic matter concentrations, and single wavelength particulate optical backscattering. To demonstrate the applicability of these databases, data within the first optical depth are compared with previously established bio-optical models and used to validate remotely derived bio-optical products. The quality-controlled databases are publicly available from the SEANOE (SEA scieNtific Open data Edition) publisher at https://doi.org/10.17882/49388 and https://doi.org/10.17882/47142 for vertical profiles and products within the first optical depth, respectively