bluuebunny/crossref_metadata_2025 huggingface dataset:
A shipboard natural community continuous culture system for ecologically relevant low‐level nutrient enrichment experiments
Authors: Hutchins David A. , Pustizzi Frances , Hare Clinton E. , DiTullio Giacomo R.
Published: August 2016

Inputs of low concentrations of new and regenerated forms of nitrogen (≤1 µM) have large impacts on phytoplankton community structure and ocean biogeochemistry in the oligotrophic central gyres. However, current manipulative experimental methods cannot effectively simulate low‐level, continuous supplies of nitrate, such as those from upwelling or eddy events, or steady‐state inputs of regenerated ammonium and dissolved organic nitrogen from zooplankton grazing. Using a new shipboard continuous culture system based on laboratory chemostat methodology, we compared the effects of a continuous supply of 1 µM nitrate, ammonium, and urea‐N at a dilution rate of 0.5 d−1 on algal community composition in the North Atlantic. In the Gulf Stream, continuous inputs of 1 µM nitrate dramatically changed phytoplankton community structure from dominance by cyanobacteria to dominance by diatoms. Equimolar continuous supplies of ammonium resulted in much smaller increases in total phytoplankton biomass, and favored a community co‐dominated by diatoms and cyanobacteria, and promoted the growth of pelagophytes. In the Sargasso Sea, continuous 1 µM urea‐N inputs greatly increased the biomass and dominance of Synechococcus relative to the initial community and compared with control and 1 µM nitrate additions. The shipboard natural community continuous culture system is uniquely suited for realistically simulating inputs of low levels of limiting nutrients, allowing new types of prognostic enrichment experiments that give novel insights into the processes that control phytoplankton community structure in the ocean.
The use of quantitative polymerase chain reaction for the detection and enumeration of the harmful alga Aureococcus anophagefferens in environmental samples along the United States East Coast
Authors: Popels Linda C. , Cary S. Craig , Hutchins David A. , Forbes Rachel , Pustizzi Frances , Gobler Christopher J. , Coyne Kathryn J.
Published: August 2016

Aureococcus anophagefferens is a small pelagophyte that has caused harmful brown tide blooms in New York, New Jersey, Rhode Island, and Maryland. It is visually indistinguishable from other small algae in environmental samples using standard light microscopy, and current species‐specific immunofluorescent counting techniques are not sensitive enough to detect concentrations lower than approximately 5000 cells mL−1. A TaqMan molecular probe was developed that is specific for A. anophagefferens based on a unique 18S rDNA sequence to detect cells at low levels. Real‐time quantitative PCR (qPCR) on an ABI Prism 7700 Sequence Detection System was used to generate a standard curve of cycle thresholds (Ct) with known concentrations of A. anophagefferens (R2 = 0.98). Cell concentrations of A. anophagefferens in environmental samples are determined by linear regression analysis, with a sensitivity of approximately 1 cell mL−1. Estuarine and coastal water samples were collected along the U.S. East Coast from Florida to Delaware, and during a transect from the Delaware River to offshore mid‐Atlantic waters, then analyzed using qPCR. Aureococcus has a wide distribution at background concentrations as far south as Northern Florida, far outside the presently recognized range of the organism. It was also found in offshore Atlantic samples, suggesting a possible oceanic source for bloom inoculation. qPCR allows for detection of cells at prebloom levels, which is essential for effective management and prediction of brown tide blooms.
An automated pH‐controlled culture system for laboratory‐based ocean acidification experiments
Authors: McGraw Christina M. , Cornwall Christopher E. , Reid Malcolm R. , Currie Kim I. , Hepburn Christopher D. , Boyd Philip , Hurd Catriona L. , Hunter Keith A.
Published: August 2016

Using a spectrophotometric pH measurement system, an automated 12‐tank culture system was developed, which is capable of maintaining pH levels between 7.51 and 8.00 (local, in‐situ pH) within 0.02 pH units at 15.1°C. The precise control of pH in the individual culture tanks was achieved through the addition of CO2‐enriched seawater to unamended seawater. A feed‐back system, which automatically adjusted the mixing ratio of unamended and CO2‐enriched seawater, ensured that the pH in each tank was kept within 0.02 pH units of target values. After each tank adjustment, the spectrophotometric pH measurement was combined with a dissolved inorganic carbon measurement to automatically re‐calculate carbonate chemistry in each tank. The system was used to study the growth of the geniculate coralline alga Arthrocardia corymbosa at pH levels of 7.52, 7.76, and 7.98.
Vibrational sum‐frequency generation as a probe for composition, chemical reactivity, and film formation dynamics of the sea surface nanolayer
Authors: Laβ Kristian , Kleber Joscha , Friedrichs Gernot
Published: August 2016

Vibrational Sum Frequency Generation (VSFG) is a surface sensitive nonlinear laser spectroscopic technique, which has been widely used in physics and physical chemistry to investigate interface processes and heterogeneous chemistry. As the technique advances from basic to applied research, we have assessed its suitability for investigations of natural air‐water interfaces, which are typically covered with an organic nanolayer. Vibrational spectra of natural sea surface nanolayer samples are presented. Strong signals attributable to the alkyl chains of lipids and indications for more or less soluble carbohydrate material have been found. Furthermore, the use of VSFG spectroscopy as a time‐resolved detection tool for monitoring surface layer formation and its reactive decay is demonstrated. Ozone‐induced film oxidation served as an example. We successfully applied VSFG to characterize the efficiency of a surface water screen sampler as well. Overall, VSFG spectroscopy turns out to be a versatile tool that can provide valuable information about composition, structure, chemical reactivity, and film formation dynamics of the sea surface nanolayer.
Different fixatives and chloridric acid concentrations in microphytobenthic primary production estimates using radiolabeled carbon: their use and misuse
Authors: Cibic Tamara , Virgilio Damiano
Published: August 2016

In literature, different fixatives have been used to stop microphytobenthic photosynthetic activity estimated using the 14C technique, and different concentrations of HCl have been used to remove the excess labeled bicarbonate. To standardize these two steps of the 14C method, we designed a series of experiments using sublittoral muddy sediments colonized by microphytobenthos. The first aim was to identify which fixative among formaldehyde, glutaraldehyde, and HCl was most effective in arresting photosynthetic activity. Formaldehyde increases cell membrane permeability leading to a loss of assimilated carbon because an underestimate of disintegrations per minute (DPM) of up to 64% was obtained when compared with HCl values. Glutaraldehyde led to an overestimate of DPM due to its autofluorescence. We propose that the best way to stop photosynthetic activity is by using HCl. The second aim of the article was to define which HCl concentration from 0.1N to 5N was sufficient to remove the excess labeled bicarbonate. The residual inorganic 14C led to an overestimate of DPM values when mild acids were added. None of the acid treatments completely removed the inorganic labeled carbon because of the sediment matrix effect. However, a further pH decrease, caused by too strong acid normalities, could digest the organic carbon pool. Besides dark estimates, blank production estimates should be assessed before each primary production experiment to consider the sediment matrix effect.
An automated method to monitor lake ice phenology
Authors: Pierson D.C. , Weyhenmeyer G. A. , Arvola L. , Benson B. , Blenckner T. , Kratz T. , Livingstone D.M. , Markensten H. , Marzec G. , Pettersson K. , Weathers K.
Published: August 2016

A simple method to automatically measure the date of ice‐on, the date of ice‐off, and the duration of lake ice cover is described. The presence of ice cover is detected by recording water temperature just below the ice/water interface and just above the lake bottom using moored temperature sensors. The occurrence of ice‐on rapidly leads to detectible levels of inverse stratification, defined as existing when the upper sensor records a temperature at least 0.1°C below that of the bottom sensor, whereas the occurrence of ice‐off leads to the return of isothermal mixing. Based on data from 10 lakes over a total of 43 winter seasons, we found that the timing and duration of inverse stratification monitored by recording temperature sensors compares well with ice cover statistics based on human observation. The root mean square difference between the observer‐based and temperature‐based estimates was 7.1 d for ice‐on, 6.4 d for ice‐off, and 10.0 d for the duration of ice cover. The coefficient of determination between the two types of estimates was 0.93, 0.86, and 0.91, respectively. The availability of inexpensive self‐contained temperature loggers should allow expanded monitoring of ice cover in a large and diverse array of lakes. Such monitoring is needed to improve our ability to monitor the progression of global climate change, and to improve our understanding of the relationship between climate and ice cover over a wide range of temporal and spatial scales.
A mini‐electrodialysis system for desalting small volume saline samples for Fourier transform ion cyclotron resonance mass spectrometry
Authors: Chen Hongmei , Stubbins Aron , Hatcher Patrick G.
Published: August 2016

An affordable, commercially available mini‐electrodialysis (mini‐ED) system has been evaluated for the efficient desalting of small volume samples of seawater before analysis by electrospray Fourier transform ion cyclotron resonance mass spectrometry (ESI FT‐ICR MS). Mini‐ED FT‐ICR mass spectra were compared with spectra for samples that were treated by C18 solid phase extraction, a commonly used method for rapid sample preparation for this type of analysis. In this comparison, it is clear that mini‐ED provides more representative molecular information, compared with C18 isolation, and recovers the overwhelming majority of peaks from salt‐free samples, indicating that it adequately represents the DOM that can be ionized and analyzed by ESI FT‐ICR MS. The ED system produces a significant carbon blank. However, the substances contributing to this blank are not detectable by ESI FT‐ICR MS. Based on these findings mini‐ED is recommended as a promising method for the desalting of aqueous environmental samples before analysis by ESI FT‐ICR MS.
Quantification of toxic and toxin‐producing cyanobacterial cells by RING‐FISH in combination with flow cytometry
Authors: Dziallas Claudia , Pinnow Solvig , Grossart Hans‐Peter
Published: August 2016

Blooms of potential toxic cyanobacteria increased in number and extent during the last decades. Species like Microcystis aeruginosa—due to their ability to produce toxins—are a fundamental threat for human and animal lives in drinking and recreational waters. To prevent detrimental effects, it is vital to quantify cyanobacterial cells that are toxic (i.e., possess toxin genes) and toxin‐producing in these waters. Therefore, we applied and modified the method RING‐FISH (recognition of individual genes fluorescence in situ hybridization) targeting the microcystin‐ synthetase gene D or its transcript, respectively. Using two toxin‐producing cyanobacterial strains as well as two nontoxic controls, we compared RING‐FISH with real‐time quantitative PCR (qPCR), finding high agreement of both methods. RING‐FISH is easy to apply for epifluorescence microscopy and yields valuable information on the genetic toxic potential and toxicity of cyanobacteria populations. In combination with flow cytometry unicellular toxic and toxin‐producing cyanobacteria, e.g., M. aeruginosa, can be quantified by RING‐FISH in a high throughput manner. Complemented with fluorescence activated cell sorting (FACS) toxic and toxin‐producing cells can be retrieved from complex population for further molecular analyses. In contrast to qPCR, our RING‐FISH protocol largely circumvents PCR biases and quantifies cells possessing or expressing certain functions independent of the copy number of the targeted gene. Furthermore, RING‐FISH is easily adaptable for the detection and quantification of functional genes of other prokaryotic and eukaryotic cells.
Free‐rising, tethered CTD profiler: increased vertical resolution and near surface profiling
Authors: Maske Helmut , Ochoa José , Jáureguí César Almeda , Avendaño Andrés Carrasco
Published: August 2016

The formation of a diurnal thermocline at few meters depth is difficult to document because of the mixing induced by research platforms. We built a free‐rising CTD‐platform, including sensors for chlorophyll fluorescence, turbidity, and light, that profiles to ~0.4 m below the surface with better than 0.03 m resolution and at sufficient distance from the research platform to measure an undisturbed water column. The profiler, with a practical maximum depth of 100 m is controlled mechanically using sacrificial weights and a safety tether that assures easy recovery of the instrument. The design concept is easily adapted to many commercial CTD models. Off Baja California, most profiles showed temperature stratification near the surface and some profiles showed near surface chlorophyll fluorescence thin layers; these features would be difficult to observe with normal CTD profilers.
A novel, highly efficient method for the separation and quantification of plastic particles in sediments of aquatic environments
Authors: Imhof Hannes K. , Schmid Johannes , Niessner Reinhard , Ivleva Natalia P. , Laforsch Christian
Published: August 2016

Although plastic debris is constantly accumulating in aquatic environments, the impact on aquatic ecosystems is not yet fully understood. A first important step to assess the consequences of plastic debris in aquatic ecosystems is the establishment of a reliable, verified, and standardized method to quantify the amount of plastic particles in the environment. We improved the density separation approach by the construction of the so called Munich Plastic Sediment Separator (MPSS). It enables a reliable separation of different ecologically relevant size classes of plastic particles from sediment samples. A ZnCl2‐solution (1.6–1.7 kg/L) as separation fluid allows for an extraction of plastic particles ranging from large fragments to small microplastic particles (S‐MPP, <1 mm). Subsequent identification and quantification of the particles with spatial resolution down to 1 µm can be performed using Raman microspectroscopy. Our study is the first providing validated recovery rates of 100% for large microplastic particles (L‐MPP, 1–5 mm) and 95.5% for S‐MPP. The recovery rate for S‐MPP, using the MPSS, was significantly higher than the value obtained by application of classical density separation setup (39.8%). Moreover, our recovery rates were significantly higher than those based on froth flotation (55.0% for L‐MPP) commonly used in recycling industries. Hence, our improved method can be used for a reliable and time‐efficient separation, identification and quantification of plastic fragments down to S‐MPP. This will help foster studies quantifying the increasing contamination of aquatic environments with microplastic particles, which is a crucial prerequisite for future risk assessment and management strategies.
Polyp flats, a new system for experimenting with jellyfish polyps, with insights into the effects of ocean acidification
Authors: Olariaga Alejandro , Guallart Elisa F. , Fuentes Verónica , López‐Sanz Àngel , Canepa Antonio , Movilla Juancho , Bosch Mar , Calvo Eva , Pelejero Carles
Published: August 2016

Research interest on jellyfish has grown exponentially over the last years and studies focusing on the biology and ecology of the jellyfish polyp stage are being recognized as crucial in understanding jellyfish proliferations. Due to the difficulty of conducting in situ work with jellyfish polyps, laboratory experiments are the most used approach. Here, we describe the design and successful testing of a new system that allows continuous seawater renewal while keeping constant the selected physicochemical conditions of the water throughout the experiment in contrast to closed systems used previously. As a first test, we started an experiment to assess the effects of ocean acidification on the growth and development of jellyfish polyps of Aurelia sp. This new design demonstrated high precision in maintaining constant conditions (pH, temperature, and flow rates) among the replicates of each treatment, and ensured excellent conditions for jellyfish polyp survival. All together it has shown to be an effective platform to assess the effect of environmental variables on the growth and development of jellyfish polyps.
Improving automated phosphorus measurements in freshwater: an analytical approach to eliminating silica interference
Authors: Koenig Lauren E. , Baumann Adam J. , McDowell William H.
Published: August 2016

Phosphorus is a nutrient of particular interest in investigations of aquatic ecosystems due to its significance for water quality, biogeochemical cycles, and ecological stoichiometry. Two limitations to current methods hinder our ability to characterize freshwater phosphorus dynamics: inadequate detection limits and susceptibility to interference from silica. While the analytical constraints associated with detection limits are widely appreciated, the importance of silica interference is not. The magnitude of interference varies between analytical approaches used for colorimetric soluble reactive phosphorus (SRP) analysis because small variations in reagent chemistry, reaction time, temperature, and sample preservation affect the silica sensitivity. Variability in SRP methodology across individual laboratories makes it difficult to diagnose the severity of this issue in the literature. Here we show that standard methods (4500‐P.F., APHA 1992) adopted for one automated method of phosphorus analysis results in significant overestimation of SRP in oligotrophic waters of moderate silica concentration (3.9 µg P L−1 for 1 mg SiO2 L−1). We outline and apply modifications to this method to quantify low‐level SRP (<5 µg P L−1) while eliminating silica interference for application in fresh waters, particularly those with a high background Si:P ratio. We adopt a more acidic color reagent, lower the reaction temperature, and increase the reaction time for a continuous flow autoanalyzer that is commonly employed in many freshwater ecology laboratories. We report a method detection limit (MDL) of 0.6 µg P L−1 and show that the proposed method maintains sensitivity with negligible silica interference for investigators wishing to conduct low‐level phosphorus analysis.
Comparison of sandwich hybridization assay and quantitative PCR for the quantification of live and preserved cultures of Heterosigma akashiwo (Raphidophyceae)
Authors: Doll Cameron , Main Christopher R. , Bianco Colleen , Coyne Kathryn J. , Greenfield Dianne I.
Published: August 2016

In this study, we directly compared two molecular techniques, sandwich hybridization assay (SHA) and quantitative PCR (qPCR), for quantifying laboratory cultures of the ichthyotoxic raphidophyte Heterosigma akashiwo. To maximize comparisons, all experiments entailed raising H. akashiwo in the laboratory, generating cellular homogenates then splitting them such that for each sample, the same homogenate was analyzed using both SHA and qPCR. To verify molecular data, all experiments included cell counts using light microscopy and a Sedgewick Rafter chamber. Results of standard curves for several geographically distinct strains using SHA were similar to prior research whereas others exhibited significantly different slopes, suggesting physiological differences between isolates. Data generated by qPCR showed a high degree of correlation with SHA responses. We also investigated the use of each method for quantifying H. akashiwo samples preserved with Lugol's iodine solution. Neither SHA nor qPCR produced results that were significantly different from initial values for Lugol's preserved samples stored under refrigeration for up to 4 months. By comparison, samples stored at room temperature exhibited a highly significant decline in responses relative to controls after 4 months using both assays as well as a marked increase in ΔΔCt within 24 hours using qPCR followed by a decline and lack of signal after 1 month. To determine whether an environmental matrix would influence assay results, natural seawater samples were spiked with H. akashiwo culture. No significant differences between culture and spiked field samples were observed for either SHA or qPCR.
Application and assessment of a membrane‐based pCO2 sensor under field and laboratory conditions
Authors: Jiang Zong‐Pei , Hydes David J. , Hartman Sue E. , Hartman Mark C. , Campbell Jon M. , Johnson Bruce D. , Schofield Bryan , Turk Daniela , Wallace Douglas , Burt William J. , Thomas Helmuth , Cosca Cathy , Feely Richard
Published: August 2016

The principle, application, and assessment of the membrane‐based ProOceanus CO2‐Pro sensor for partial pressure of CO2 (pCO2) are presented. The performance of the sensor is evaluated extensively under field and laboratory conditions by comparing the sensor outputs with direct measurements from calibrated pCO2 measuring systems and the thermodynamic carbonate calculation of pCO2 from discrete samples. Under stable laboratory condition, the sensor agreed with a calibrated water‐air equilibrator system at −3.0 ± 4.4 µatm during a 2‐month intercomparison experiment. When applied in field deployments, the larger differences between measurements and the calculated pCO2 references (6.4 ± 12.3 µatm on a ship of opportunity and 8.7 ± 14.1 µatm on a mooring) are related not only to sensor error, but also to the uncertainties of the references and the comparison process, as well as changes in the working environments of the sensor. When corrected against references, the overall uncertainties of the sensor results are largely determined by those of the pCO2 references (± 2 and ± 8 µatm for direct measurements and calculated pCO2, respectively). Our study suggests accuracy of the sensor can be affected by temperature fluctuations of the detector optical cell and calibration error. These problems have been addressed in more recent models of the instrument through improving detector temperature control and through using more accurate standard gases. Another interesting result in our laboratory test is the unexpected change in alkalinity which results in significant underestimation in the pCO2 calculation as compared to the direct measurement (up to 90 µatm).
Quantifying lateral and intratidal variability in water level and velocity in a tide‐dominated river using combined RTK GPS and ADCP measurements
Authors: Matte Pascal , Secretan Yves , Morin Jean
Published: August 2016

Cross‐sectional gradients in water levels and velocities play a determining role in the circulation dynamics of tidal rivers and estuaries. Documenting and analyzing their variability throughout a tidal cycle require observations with high spatial and temporal resolution. A survey strategy and a data analysis procedure have been designed to obtain continuous and synoptic water level and velocity fields over a tidal cycle, along 13 cross‐sections of the St. Lawrence fluvial estuary dominated by large tidal ranges. The method combines both RTK GPS and ADCP technologies for the simultaneous measurement of water levels and velocities along repeated boat transects, allowing fast data acquisition over wide river sections and under rapidly changing conditions. The reconstruction of continuous and synoptic fields is made by interpolation. Simplifying assumptions about data stationarity and/or homogeneity are avoided by adapting the interpolation procedures to the shape and distribution of the underlying data in a space‐time reference frame, thus minimizing distortion in the reconstructed quantities. The capabilities and limitations of the method are assessed through error computations and comparisons with alternate data analysis methods and complementary data sets from tide gauges. With these latest observations, new insights into the tidal hydrodynamics of the St. Lawrence fluvial estuary are gained in regions of contrasting tidal and fluvial properties, specifically related to the effects of channel curvature and bathymetry on tidal propagation and cross‐channel flow properties at the intratidal scale.
Improving the precision of lake ecosystem metabolism estimates by identifying predictors of model uncertainty
Authors: Rose Kevin C. , Winslow Luke A. , Read Jordan S. , Read Emily K. , Solomon Christopher T. , Adrian Rita , Hanson Paul C.
Published: August 2016

Diel changes in dissolved oxygen are often used to estimate gross primary production (GPP) and ecosystem respiration (ER) in aquatic ecosystems. Despite the widespread use of this approach to understand ecosystem metabolism, we are only beginning to understand the degree and underlying causes of uncertainty for metabolism model parameter estimates. Here, we present a novel approach to improve the precision and accuracy of ecosystem metabolism estimates by identifying physical metrics that indicate when metabolism estimates are highly uncertain. Using datasets from seventeen instrumented GLEON (Global Lake Ecological Observatory Network) lakes, we discovered that many physical characteristics correlated with uncertainty, including PAR (photosynthetically active radiation, 400–700 nm), daily variance in Schmidt stability, and wind speed. Low PAR was a consistent predictor of high variance in GPP model parameters, but also corresponded with low ER model parameter variance. We identified a threshold (30% of clear sky PAR) below which GPP parameter variance increased rapidly and was significantly greater in nearly all lakes compared with variance on days with PAR levels above this threshold. The relationship between daily variance in Schmidt stability and GPP model parameter variance depended on trophic status, whereas daily variance in Schmidt stability was consistently positively related to ER model parameter variance. Wind speeds in the range of ~0.8‐3 m s−1 were consistent predictors of high variance for both GPP and ER model parameters, with greater uncertainty in eutrophic lakes. Our findings can be used to reduce ecosystem metabolism model parameter uncertainty and identify potential sources of that uncertainty.
Low‐cost, high‐flow mesocosm system for simulating ocean acidification with CO2 gas
Authors: Jokiel Paul L. , Bahr Keisha D. , Rodgers Ku'ulei S.
Published: August 2016

The high cost of building and operating open‐flow experimental systems for studies of biological response to ocean acidification (OA) has led to extensive use of short‐term incubations in closed‐flow systems that do not simulate natural conditions. An inexpensive, highly reliable, open‐system that tracks natural diurnal and seasonal changes in water chemistry is described. This approach is based on a gravity‐feed seawater supply system that uses a peristaltic pump to regulate CO2 injection rate and a power head that cavitates the injected CO2 into microscopic bubbles that are dissolved immediately. This report describes low‐cost methods applicable to small or very large experimental systems. This methodology permits long‐term experiments under full sunlight with rapid seawater turnover rate that assures realistic environmental conditions in the experimental chambers.
A new device to follow temporal variations of oxygen demand in deltaic sediments: the LSCE benthic station
Authors: Toussaint Flora , Rabouille Christophe , Cathalot Cécile , Bombled Bruno , Abchiche Abdel , Aouji Oualid , Buchholtz Gilles , Clemençon Aurélien , Geyskens Nicolas , Répécaud Michel , Pairaud Ivane , Verney Romaric , Tisnérat‐Laborde Nadine
Published: August 2016

A new benthic station equipped with oxygen microelectrodes and environmental sensors was developed by Laboratoire des Sciences du Climat et de L'Environnement (LSCE) and Division Technique of the Institut National des Sciences de L'Univers (DT‐ INSU) to perform in situ time series monitoring of sediment oxygen demand, linked to the mineralization of organic matter. The time series typically cover periods of 2‐ 3 months, with a base frequency of 1 set of oxygen profiles per day. The profiling head assessed the lateral heterogeneity of the sediment oxygen demand at the beginning of the time series over a 0.8‐ m long rectangle to discriminate spatial and temporal variability. A continuous recalibration is performed using a moored oxygen optode anchored to the benthic station together with a set of environmental sensors. These sensors (turbidity, temperature, salinity, and oxygen) can trigger a high‐ frequency profiling mode to investigate the fate of particulate organic matter delivered during floods, resuspension, and deposition events. Deployments of the benthic station were performed in the Rhone River subaqueous delta (Mediterranean Sea). We show that “stable” periods (when neither floods nor storms occur) were characterized by a stable oxygen demand. In the case of resuspension events, an increase of the sediment oxygen demand by a factor of 2‐ 3 with a relaxation time of 1 day was observed, indicating that the new benthic station can adequately capture the impact of resuspension events on the oxygen demand in deltaic sediments.
An automatic and quantitative approach to the detection and tracking of acoustic scattering layers
Authors: Cade David E. , Benoit‐Bird Kelly J.
Published: August 2016

Acoustic scattering layers are ubiquitous, horizontally extensive aggregations of both vertebrate and invertebrate organisms that play key roles in oceanic ecosystems. However, currently there are no conventions or widely adaptable automatic methods for identifying these often dynamic, spatially complex features, so it is difficult to consistently and efficiently describe and compare results. We developed an automatic scattering layer detection method that can be used to monitor changes in layer depth, width, and internal structure over time. Extensive, contiguous regions of the water column that have echo strengths above a threshold were identified as “background layers.” They correspond to regions of the water column that contain scattering from diffusely distributed organisms. Often, background layers contained contiguous, horizontally extensive features of concentrated acoustic scattering we identified as “strata.” These features were identified by fitting Gaussian curves to the echo envelope of each vertical profile of scattering, and their boundaries were identified as the endpoints of the region containing 95% of the area under the fitted curves. These endpoints were linked horizontally to make continuous tracks. Bottom and top tracks were paired to identify features that sometimes extended horizontally for tens of kilometers. This approach was effective in three disparate ecosystems (the Gulf of California, Monterey Bay, and the Bering Sea), and a sensitivity analysis showed its robustness to changes in input parameters. By allowing a comparable, automated approach to be used across environments, this method promotes the improved classification and characterization of acoustic scattering layers necessary for examining their role in oceanic ecosystems.
Imaging‐in‐Flow: Digital holographic microscopy as a novel tool to detect and classify nanoplanktonic organisms
Authors: Zetsche Eva‐Maria , El Mallahi Ahmed , Dubois Frank , Yourassowsky Catherine , Kromkamp Jacco C. , Meysman Filip J.R.
Published: August 2016

Traditional taxonomic identification of planktonic organisms is based on light microscopy, which is both time‐ consuming and tedious. In response, novel ways of automated (machine) identification, such as flow cytometry, have been investigated over the last two decades. To improve the taxonomic resolution of particle analysis, recent developments have focused on “imaging‐ in‐ flow,” i.e., the ability to acquire microscopic images of planktonic cells in a flow‐ through mode. Imaging‐ in‐ flow systems are traditionally based on classical brightfield microscopy and are faced with a number of issues that decrease the classification performance and accuracy (e.g., projection variance of cells, migration of cells out of the focus plane). Here, we demonstrate that a combination of digital holographic microscopy (DHM) with imaging‐ in‐ flow can improve the detection and classification of planktonic organisms. In addition to light intensity information, DHM provides quantitative phase information, which generates an additional and independent set of features that can be used in classification algorithms. Moreover, the capability of digitally refocusing greatly increases the depth of field, enables a more accurate focusing of cells, and reduces the effects of position variance. Nanoplanktonic organisms similar in shape were successfully classified from images captured with an off‐ axis DHM with partial coherence. Textural features based on DHM phase information proved more efficient in separating the three tested phytoplankton species compared with shape‐ based features or textural features based on light intensity. An overall classification score of 92.4% demonstrates the potential of holographic‐ based imaging‐ in‐ flow for similar looking organisms in the nanoplankton range.
Removing the light history signal from normalized variable fluorescence (Fv/Fm) measurements on marine phytoplankton
Authors: From Nikolaj , Richardson Katherine , Mousing Erik Askov , Jensen Poul Erik
Published: August 2016

Variable fluorescence normalized to maximal fluorescence, Fv/Fm, determined by Fast Repetition Rate Fluorometry (FRRF) is being increasingly used to compare photosynthetic electron transport capacity in natural phytoplankton communities. Interpreting results of such studies is, however, complicated by the fact that both nutrient status and light history (photoinhibition under in situ conditions) are known to influence Fv/Fm. Thus, the value of Fv/Fm measurements in the field would be greatly enhanced if the light history signal could be separated from other influences. Here, both field and laboratory studies demonstrate that dark treatment (30 min‐4 h) before FRRF measurement is not sufficient to remove a light history signal in Fv/Fm. The signal could, however, be essentially eliminated by incubation of samples in low light prior to Fv/Fm determination. For the study conditions tested, the most effective treatment for removal of the signal was 4 h at 50 µmol m‐2 s‐1. However, the effectiveness of the light treatment in removing the light history was influenced by temperature. Therefore, no universal protocol for eliminating the light history signal can be developed, but recommendations are given for developing site‐specific approaches for separating the light history signal from other factors influencing Fv/Fm. Carrying out light incubations before determining Fv/Fm not only provides the possibility for eliminating a light history signal in the measurements but the difference between Fv/Fm measured after light and dark incubations appears also to be a potentially useful indicator of the degree of photoinhibition experienced by phytoplankton under natural conditions.
An interlaboratory comparison for the quantification of aqueous dimethylsulfide
Authors: Swan Hilton B. , Armishaw Paul , Iavetz Raluca , Alamgir Mahiuddin , Davies Stephen R. , Bell Thomas G. , Jones Graham B.
Published: August 2016

An interlaboratory comparison (ILC) was conducted to evaluate the proficiency of multiple laboratories to quantify dimethylsulfide (DMS) in aqueous solution. Ten participating laboratories were each supplied with blind duplicate test solutions containing dimethylsulfoniopropionate hydrochloride (DMSP HCl) dissolved in acidified artificial seawater. The test solutions were prepared by the coordinating laboratory from a DMSP HCl reference material that was synthesized and purity certified for this purpose. A concentration range was specified for the test solutions and the participating laboratories were requested to dilute them as required for their analytical procedure, together with the addition of excess alkali under gas‐tight conditions to convert the DMSP to DMS. Twenty‐two DMS concentrations and their estimated expanded measurement uncertainties (95% confidence level) were received from the laboratories. With two exceptions, the within‐laboratory variability was 5% or less and the between‐laboratory variability was ~ 25%. The magnitude of expanded measurement uncertainties reported from all participants ranged from 1% to 33% relative to the result. The information gained from this pilot ILC indicated the need for further test sample distribution studies of this type so that participating laboratories can identify systematic errors in their analysis procedures and realistically evaluate their measurement uncertainty. The outcome of ILC studies provides insights into the comparability of data in the global surface seawater DMS database.
A new method for ecological surveying of the abyss using autonomous underwater vehicle photography
Authors: Morris Kirsty J. , Bett Brian J. , Durden Jennifer M. , Huvenne Veerle A. I. , Milligan Rosanna , Jones Daniel O. B. , McPhail Stephen , Robert Katleen , Bailey David M. , Ruhl Henry A.
Published: August 2016

The extent and speed of marine environmental mapping is increasing quickly with technological advances, particularly with optical imaging from autonomous underwater vehicles (AUVs). This contribution describes a new deep‐sea digital still camera system that takes high‐frequency (>1 Hz) color photographs of the seafloor, suitable for detailed biological and habitat assessment, and the means of efficient processing of this mass imagery, to allow assessment across a wide range of spatial scales from that of individual megabenthic organisms to landscape scales (>100 km2). As part of the Autonomous Ecological Surveying of the Abyss (AESA) project, the AUV Autosub6000 obtained > 150,000 seafloor images (~160 km total transect length) to investigate the distribution of megafauna on the Porcupine Abyssal Plain (4850 m; NE Atlantic). An automated workflow for image processing was developed that corrected nonuniform illumination and color, geo‐referenced the photographs, and produced 10‐image mosaics ('tiles,' each representing a continuous strip of 15‐20 m2 of seafloor), with overlap between consecutive images removed. These tiles were then manually annotated to generate biological data. This method was highly advantageous compared with alternative techniques, greatly increasing the rate of image acquisition and providing a 10‐50 fold increase in accuracy in comparison to trawling. The method also offers more precise density and biodiversity estimates [Coefficient of variation (CV) < 10%] than alternative techniques, with a 2‐fold improvement in density estimate precision compared with the WASP towed camera system. Ultimately, this novel system is expected to make valuable contributions to understanding human impact in the deep ocean.
Automation of 13C/12C ratio measurement for freshwater and seawater DOC using high temperature combustion
Authors: Lalonde Karine , Middlestead Paul , Gélinas Yves
Published: August 2016

We provide a detailed description of the hyphenation of an Aurora 1030C high temperature catalytic conversion DOC analyzer, a GD‐100 CO2 trap and a continuous flow IRMS, which has made possible the high‐throughput, automated measurements of 13C/12C ratios, and DOC concentrations for a wide range of aquatic samples. Precision of 13C/12C ratios increases exponentially with sample concentration, reaching 0.2‰ or better for high concentration samples (>5 mg L‐1), comparable to that obtained in a conventional elemental analyzer‐IRMS setup. The system blank contribution is the limiting factor in obtaining maximal performance; optimal system blanks values are on the order of 0.2 µg C with an isotopic signature varying from ‐20 to ‐12‰ during the lifetime of the combustion column. With appropriate blank correction procedures, accurate analyses (±0.5‰ or better) can be obtained on concentrations as low as 0.5 mg DOC L‐1, representing the lower limit typically observed in aquatic systems. Sample matrix does not affect reproducibility or accuracy; this method is amenable to both freshwater and seawater samples. Although no certified DOC standards exist for δ13C, our two laboratories analyzed a consensus reference material from a deep‐ocean environment (CRM Batch 13 Lot # 05‐13, Hansell 2013) and found δ13C values of ‐19.9 ± 0.5‰ (n = 4) and ‐20.6 ± 0.3‰ (n = 3), which corroborates previously reported values for similar samples (Bouillon et al. 2006; Lang et al. 2007; Panetta et al. 2008) and is consistent with its marine origin.
Considerations for the measurement of spectrophotometric pH for ocean acidification and other studies
Authors: DeGrandpre Mike D. , Spaulding Reggie S. , Newton Jenny O. , Jaqueth Emma J. , Hamblock Sarah E. , Umansky Andre A. , Harris Katherine E.
Published: August 2016

Indicator‐based spectrophotometric pH is commonly used for the analysis of seawater because of its high precision and long‐term reproducibility. Users come from an increasingly diverse range of disciplines, primarily motivated by studies focused on the causes and effects of ocean acidification. While the analysis is readily implemented and straightforward, there are many variables that must be predetermined or measured, all of which can contribute uncertainty to the measurement. The indicator equilibrium constant and molar absorption coefficient ratios are available in the literature, but for various reasons, the conditions of analysis can be different, creating errors. Most of the parameters are temperature, salinity, and pressure dependent, posing potential additional errors. Indicator impurities and indicator perturbation of the sample pH also create uncertainties. We systematically evaluate all of the sources of error and compute how the errors propagate into CO2 equilibrium calculations of the partial pressure of CO2 (pCO2) and calcium carbonate saturation states (Ω). The primary sources of uncertainty originate from wavelength and absorbance errors in low quality or poorly functioning spectrophotometers (0.007 to 0.020 pH units) and indicator impurities (0.000 to >0.040 pH units). These errors generate pCO2 and Ω uncertainties of 11‐200 µatm and 0.08‐0.38, respectively, depending upon the pH value and its uncertainty.
A new approach to δ15N compound‐specific amino acid trophic position measurements: preparative high pressure liquid chromatography technique for purifying underivatized amino acids for stable isotope analysis
Authors: Broek Taylor A. B. , McCarthy Matthew D.
Published: August 2016

Compound specific isotope analysis of amino acids (CSI‐AA) has emerged as an important new method for investigating trophic dynamics in both aquatic and terrestrial systems. Multiple studies have shown that δ15N values of glutamic acid (Glu) and phenylalanine (Phe) can be coupled to provide precise estimates of trophic position (TP), while simultaneously decoupling baseline δ15N values from the effects of trophic transfer. However, the current standard gas chromatography‐combustion‐isotope ratio mass spectrometry (GC‐C‐IRMS) approach is limited by high expense, limited availability, and relatively low precision. We present a new method for making TP estimates in biological samples by CSI‐AA (TPCSIA), based on a high‐pressure liquid chromatography (HPLC) purification of underivatized amino acids, followed by offline elemental analysis‐isotope ratio mass spectrometry (EA‐IRMS). We compare results from our new HPLC/EA‐IRMS method versus GC‐C‐IRMS in both standard and natural materials. Nitrogen isotopic values of purified Glu and Phe standards were identical within error for both methods. In five widely different marine organisms, the δ15N values of Glu and Phe were also indistinguishable within error between the two approaches; however, the δ15N values produced by the HPLC/EA‐IRMS approach had higher average precision (average SD = 0.3 ± 0.2 ‰) than the GC‐C‐IRMS measurements (average SD = 0.45 ± 0.15 ‰). The resulting TPCSIA estimates were statistically indistinguishable (t < 1.2, df = 6, P > 0.3) between the two methods for all organisms examined. Our HPLC/EA‐IRMS method may therefore allow significant expansion of TPCSIA applications, requiring only commonly available instrumentation to produce high precision TPCSIA values.
Spontaneous Hemoperitoneum: An Unusual Presentation of a Common Disease
Authors: Raghunath BV , Bhat Vishwanath
Published: August 2016

Intraluminal hemorrhage associated with ectopic gastric mucosa in a Meckel's diverticulum is a common presentation. However, intraperitoneal bleeding associated with Meckel's diverticulum, is considerably rare. Herein, we report a case of spontaneous intraperitoneal bleeding caused due to nonruptured, acutely inflammed Meckel's diverticulum causing erosion of one of the branches of ileocolic artery and presenting with peritonism.

How to cite this article

Raghunath BV, Bhat V. Spontaneous Hemoperitoneum: An Unusual Presentation of a Common Disease. J Med Sci 2015;1(2):36-37.
Uterine Necrosis following B-Lynch and Gunasheela's Global Stitch Sutures for Primary Postpartum Hemorrhage
Authors: Punya BS , Sailakshmi MPA , Akash Suhasini
Published: August 2016

Uterine atony causing postpartum hemorrhage (PPH) is one of the leading causes of maternal morbidity and mortality. Here by reporting a case of 22-year-old woman who underwent full-term vaginal delivery followed by atonic PPH, for which emergency laparotomy was done and stepwise devascularization along with B-Lynch and Gunasheela's global brace sutures over the uterus. On postoperative day 9, she developed features suggesting sepsis and magnetic resonance imaging (MRI) showed area of avascularity and features of abscess formation in the uterine wall. She underwent subtotal hysterectomy and histopathology showed uterine necrosis.

How to cite this article

Punya BS, Sailakshmi MPA, Akash S, Nagarathnamma R. Uterine Necrosis following B-Lynch and Gunasheela's Global Stitch Sutures for Primary Postpartum Hemorrhage. J Med Sci 2015;1(2):38-40.
Effectiveness and Utilization Pattern of Cognitive Behavior Therapy of Anxiety Disorders: Evidence from a Psychiatry Clinic
Authors: Hebbar Sudhir
Published: August 2016

Psychotherapy efficacy studies are conducted in highly controlled research settings. In contrast, effectiveness studies are done in routine clinical practice. In India, the literature on psychotherapy outcome is almost nonexistent.

Materials and methods

Here is a retrospective effectiveness study done by a psychiatrist in his clinic. A total of 67 patients visited for the treatment of anxiety disorders, whose data were available for analysis.

Results

Out of this sample, 44 patients opted for cognitive behavior therapy (CBT) of which 20 (45%) patients dropped out of therapy by the 3rd session. Male patients represented 4 times more than female patients. The average number of sessions attended was 5.4. Of the 24 patients who attended 4 and more number of sessions, on Clinical global impression scale, 10 (41%) improved very much, 11 (45%) improved much, 2 (8%) improved minimally, and 1 (4%) did not change.

Conclusion

This indicates CBT is quite effective for anxiety disorders in patients who attend 4 and more sessions. Early dropout is a significant obstacle to the effectiveness.

How to cite this article

Hebbar S. Effectiveness and Utilization Pattern of Cognitive Behavior Therapy of Anxiety Disorders: Evidence from a Psychiatry Clinic. J Med Sci 2015;1(3):52-54.