bluuebunny/crossref_metadata_2025 huggingface dataset:
The spectrum of coincident entities with small lymphocytic lymphoma/chronic lymphocytic leukemia (SLL/CLL) diagnosed by cytology
Authors: Kastenbaum Hannah A. , Khalbuss Walid E. , Felgar Raymond E. , Stoller Ronald , Monaco Sara E.
Published: October 2010

Background:

The cytologic diagnosis of Small lymphocytic lymphoma/chronic lymphocytic leukemia (SLL/CLL) often relies on finding a small lymphoid population with the characteristic immunoprofile by ancillary testing. There are only a few reports of other processes identified with SLL/CLL. The aim of this study was to review the fine needle aspiration (FNA) and touch prep (TP) diagnoses of SLL/CLL in order to identify any coincident entities.

Materials and Methods:

We retrospectively reviewed all FNA and TP cytology cases between January 2005 and May 2009 with a diagnosis of SLL/CLL to determine the presence of any coincident process.

Results:

We identified 29 cases, including 23 FNAs and six TPs, from 23 patients. Ancillary studies were utilized in 97% of the cases, including flow cytometry (FC, 79%), immunohistochemistry (IHC, 55%), fluorescent in situ hybridization studies (24%) and special stains (7%). Coincident entities were identified in nine cases (31%) and included seven (28%) neoplastic entities (Hodgkin lymphoma [HL], adenocarcinoma, squamous cell carcinoma, seminoma) and two (7%) non-neoplastic entities (infection and immunoglobulin containing cells). Six cases (21%) suspicious for large cell transformation were also identified.

Conclusion:

In our review of SLL/CLL, coincident entities were present in 31% of the cases and included a spectrum of non-neoplastic and neoplastic processes. FC was the most frequently utilized ancillary test, but IHC provided important information by excluding a mantle cell lymphoma or confirming a coincident process. Thus, cytomorphologic evaluation in these patients is important due to the high risk of a coincident process that may not be apparent by FC alone and may require clinical management.
Determination of HER-2 status on FNAC material from breast carcinomas usingin situhybridization with dual chromogen visualization with silver enhancement (dual SISH)
Authors: Beraki Elsa , Sauer Torill
Published: October 2010

During the last years, HER-2 status kits and protocols for chromogen visualization of hybridization signals have come on the market. The first generation using chromogen visualization used single color probes. The second generation, now emerging on the market, uses dual chromogen visualization. The aim of this study has been to test a new dual color chromogen kit (Ventana INFORM HER2 Dual Colour ISH Roche®) and compare the results with our in-house method(s). The material consisted primarily of cytological material from invasive breast carcinomas in 49 women. Dual SISH was done on all 49 cytological and histological specimens. The histological specimens were treated according to the manufacturer’s recommendations. The procedure was modified in several steps in order to adapt it to the cytological material. Hybridization failed in two cytological specimens. Dual SISH showed concordant results on cytological and histological material as to amplified/not amplified. The included cases had the same HER-2 expression in the invasive and thein situcomponents on histology. Four IDC showed HER-2 amplification (8.5%). Polysomy was found in two cases. All dual SISH results except for one concurred with the results of the in-house method(s) (1/47=2.1%). The dual SISH is suitable for cytological examination of HER-2 status. The protocol must be optimized for cytological material.
Source apportionment of PM2.5 in Cork Harbour, Ireland using a combination of single particle mass spectrometry and quantitative semi-continuous measurements
Authors: Healy R. M. , Hellebust S. , Kourtchev I. , Allanic A. , O'Connor I. P. , Bell J. M. , Healy D. A. , Sodeau J. R. , Wenger J. C.
Published: October 2010

Abstract. An aerosol time-of-flight mass spectrometer (ATOFMS) was deployed for the measurement of the size resolved chemical composition of single particles at a site in Cork Harbour, Ireland for three weeks in August 2008. The ATOFMS was co-located with a suite of semi-continuous instrumentation for the measurement of particle number, elemental carbon (EC), organic carbon (OC), sulfate and particulate matter smaller than 2.5 μm in diameter (PM2.5). The temporality of the ambient ATOFMS particle classes was subsequently used in conjunction with the semi-continuous measurements to apportion PM2.5 mass using positive matrix factorisation. The synergy of the single particle classification procedure and positive matrix factorisation allowed for the identification of six factors, corresponding to vehicular traffic, marine, long-range transport, various combustion, domestic solid fuel combustion and shipping traffic with estimated contributions to the measured PM2.5 mass of 23%, 14%, 13%, 11%, 5% and 1.5% respectively. Shipping traffic was found to contribute 18% of the measured particle number (20–600 nm mobility diameter), and thus may have important implications for human health considering the size and composition of ship exhaust particles. The positive matrix factorisation procedure enabled a more refined interpretation of the single particle results by providing source contributions to PM2.5 mass, while the single particle data enabled the identification of additional factors not possible with typical semi-continuous measurements, including local shipping traffic.
Ultrafine particle formation in the inland sea breeze airflow in Southwest Europe
Authors: Fernández-Camacho R. , Rodríguez S. , de la Rosa J. , Sánchez de la Campa A. M. , Viana M. , Alastuey A. , Querol X.
Published: October 2010

Abstract. Studies on ultrafine particles (diameter < 100nm) and air quality have mostly focused on vehicle exhaust emissions and on new particle formation in "clean" ambient air. Here we present a study focused on the processes contributing to ultrafine particle concentrations in a city (Huelva, SW Spain) placed close to a coastal area where significant anthropogenic emissions of aerosol precursors occur. The overall data analysis shows that two processes predominantly contribute to the number of particles coarser than 2.5 nm: vehicle exhaust emissions and new particle formation due to photo-chemical activity. As typically occurs in urban areas, vehicle exhaust emissions result in high concentrations of black carbon (BC) and particles coarser than 2.5 nm (N) during the morning rush hours. The highest N concentrations were recorded during the 11:00–17:00 h period, under the sea breeze regime, when low BC concentrations were registered and photochemical activity resulted in high O3 levels and in new particle formation in the aerosol precursors' rich inland airflow. In this period, it is estimated that about 80% of the number of particles are linked to sulfur dioxide emissions. The contributions to N of "carbonaceous material and those compounds nucleating/condensing immediately after emission" and of the "new particle formation processes in air masses rich gaseous precursors (e.g. SO2)" were estimated by means of a relatively novel method based on simultaneous measurements of BC and N. A comparison with two recent studies suggests that the daily cycles of "new particle formation" during the inland sea breeze is blowing period seem to be a feature of ultrafine particles in coastal areas of South-west Europe.
Updated African biomass burning emission inventories in the framework of the AMMA-IDAF program, with an evaluation of combustion aerosols
Authors: Liousse C. , Guillaume B. , Grégoire J. M. , Mallet M. , Galy C. , Pont V. , Akpo A. , Bedou M. , Castéra P. , Dungall L. , Gardrat E. , Granier C. , Konaré A. , Malavelle F. , Mariscal A. , Mieville A. , Rosset R. , Serça D. , Solmon F. , Tummon F. , Assamoi E. , Yoboué V. , Van Velthoven P.
Published: October 2010

Abstract. African biomass burning emission inventories for gaseous and particulate species have been constructed at a resolution of 1 km by 1km with daily coverage for the 2000–2007 period. These inventories are higher than the GFED2 inventories, which are currently widely in use. Evaluation specifically focusing on combustion aerosol has been carried out with the ORISAM-TM4 global chemistry transport model which includes a detailed aerosol module. This paper compares modeled results with measurements of surface BC concentrations and scattering coefficients from the AMMA Enhanced Observations period, aerosol optical depths and single scattering albedo from AERONET sunphotometers, LIDAR vertical distributions of extinction coefficients as well as satellite data. Aerosol seasonal and interannual evolutions over the 2004–2007 period observed at regional scale and more specifically at the Djougou (Benin) and Banizoumbou (Niger) AMMA/IDAF sites are well reproduced by our global model, indicating that our biomass burning emission inventory appears reasonable.
Will climate change increase ozone depletion from low-energy-electron precipitation?
Authors: Baumgaertner A. J. G. , Jöckel P. , Dameris M. , Crutzen P. J.
Published: October 2010

Abstract. We investigate the effects of a strengthened stratospheric/mesospheric residual circulation on the transport of nitric oxide (NO) produced by energetic particle precipitation. During periods of high geomagnetic activity, energetic electron precipitation (EEP) is responsible for winter time ozone loss in the polar middle atmosphere between 1 and 6 hPa. However, as climate change is expected to increase the strength of the Brewer-Dobson circulation including extratropical downwelling, the enhancements of EEP NOx concentrations are expected to be transported to lower altitudes in extratropical regions, becoming more significant in the ozone budget. Changes in the mesospheric residual circulation are also considered. We use simulations with the chemistry climate model system EMAC to compare present day effects of EEP NOx with expected effects in a climate change scenario for the year 2100. In years of strong geomagnetic activity, similar to that observed in 2003, an additional polar ozone loss of up to 0.4 μmol/mol at 5 hPa is found in the Southern Hemisphere. However, this would be approximately compensated by an ozone enhancement originating from a stronger poleward transport of ozone from lower latitudes caused by a strengthened Brewer-Dobson circulation, as well as by slower photochemical ozone loss reactions in a stratosphere cooled by risen greenhouse gas concentrations. In the Northern Hemisphere the EEP NOx effect appears to lose importance due to the different nature of the climate-change induced circulation changes.
The complex dynamics of the seasonal component of USA's surface temperature
Authors: Vecchio A. , Capparelli V. , Carbone V.
Published: October 2010

Abstract. The dynamics of the climate system has been investigated by analyzing the complex seasonal oscillation of monthly averaged temperatures recorded at 1167 stations covering the whole USA. We found the presence of an orbit-climate relationship on time scales remarkably shorter than the Milankovitch period {related to the nutational forcing}. The relationship manifests itself through occasional destabilization of the phase of the seasonal component due to the local changing of balance between direct insolation and the net energy received by the Earth. Quite surprisingly, we found that the local intermittent dynamics is modulated by a periodic component of about 18.6 yr due to the nutation of the Earth, which represents the main modulation of the Earth's precession. The global effect in the last century results in a cumulative phase-shift of about 1.74 days towards earlier seasons, in agreement with the phase shift expected from the Earth's precession. The climate dynamics of the seasonal cycle can be described through a nonlinear circle-map, indicating that the destabilization process can be associated to intermittent transitions from quasi-periodicity to chaos.
A upper limit for water dimer absorption in the 750 nm spectral region and a revised water line list
Authors: Shillings A. J. L. , Ball S. M. , Barber M. J. , Tennyson J. , Jones R. L.
Published: October 2010

Abstract. The absorption of solar radiation by water dimer molecules in the Earth's atmosphere can potentially act as a positive feedback effect for climate change. There seems little doubt from the results of previous laboratory and theoretical studies that significant concentrations of the water dimer should be present in the atmosphere, yet attempts to detect water dimer absorption signatures in atmospheric field studies have so far yielded inconclusive results. Here we report spectral measurements in the near-infrared in the expected region of the third overtone of the water dimer hydrogen-bonded OHb stretching vibration around 750 nm. The results were obtained using broadband cavity ringdown spectroscopy (BBCRDS), a methodology that allows absorption measurements to be made under controlled laboratory conditions but over absorption path lengths representative of atmospheric conditions. In order to account correctly and completely for overlapping absorption of monomer molecules in the same spectral region, we have also constructed a new list of spectral data (UCL08) for the water monomer in the 750–20 000 cm−1 (13 μm–500 nm) range. Our results show that the additional lines included in the UCL08 spectral database provide a substantially improved representation of the measured water monomer absorption in the 750 nm region, particularly at wavelengths dominated by weak monomer absorption features. No absorption features which could not be attributed to the water monomer were detected in the BBCRDS experiments up to water mixing ratios more than an order of magnitude greater than those in the ambient atmosphere. The absence of detectable water dimer features leads us to conclude that, in the absence of significant errors in calculated dimer oscillator strengths or monomer/dimer equilibrium constants, the widths of water dimer features present around 750 nm must be substantially greater (~100 cm−1 HWHM) than those reported at longer wavelengths.
The role of the QBO in the inter-hemispheric coupling of summer mesospheric temperatures
Authors: Espy P. J. , Ochoa Fernández S. , Forkman P. , Murtagh D. , Stegman J.
Published: October 2010

Abstract. Inter-hemispheric coupling between the polar summer mesosphere and planetary-wave activity in the extra-tropical winter stratosphere has recently been inferred using Polar Mesospheric Cloud (PMC) properties as a proxy for mesospheric temperature (Karlsson et al., 2007). Here we confirm these results using a ten-year time series of July mesospheric temperatures near 60° N derived from the hydroxyl (OH) nightglow. In addition, we show that the time/lagged correlation between these summer mesospheric temperatures and the ECMWF winter stratospheric temperatures displays a strong Quasi-Biennial Oscillation (QBO). The sign and phase of the correlation is consistent with the QBO modulation of the extra-tropical stratospheric dynamics in the Southern Hemisphere via the Holton-Tan mechanism (Holton and Tan, 1980). This lends strength to the identification of synoptic and planetary waves as the driver of the inter-hemispheric coupling, and results in a strong QBO modulation of the polar summer mesospheric temperatures.
Impact of organic nitrates on urban ozone production
Authors: Farmer D. K. , Perring A. E. , Wooldridge P. J. , Blake D. R. , Baker A. , Meinardi S. , Huey L. G. , Tanner D. , Vargas O. , Cohen R. C.
Published: October 2010

Abstract. Urban O3 is produced by photochemical chain reactions that amplify background O3 in mixtures of gaseous nitrogen oxides (NOx) and organic molecules. Current thinking treats NOx and organics as independent variables that limit O3 production depending on the NOx to organic ratio; in this paradigm, reducing organics either has no effect or reduces O3. We describe a theoretical counterexample where NOx and organics are strongly coupled and reducing organics increases O3 production, and illustrate the example with observations from Mexico City. This effect arises from chain termination in the HOx and NOx cycles via organic nitrate production. We show that emission reductions that inadvertently reduce organic nitrate production rates will be counterproductive without concurrent reductions in NOx or other organics.
Simulation of the aerosol effect on the microphysical properties of shallow stratocumulus clouds over East Asia using a bin-based meso-scale cloud model
Authors: Choi I.-J. , Iguchi T. , Kim S.-W. , Yoon S.-C. , Nakajima T.
Published: October 2010

Abstract. A bin-based meso-scale cloud model has been employed to explore the aerosol influence on the cloud microphysical properties and precipitation efficiency of shallow stratocumulus in East Asia in March 2005. We newly constructed aerosol size distributions and hygroscopicity parameters for five aerosol species that reproduced observed aerosol and cloud condensation nuclei (CCN) number concentrations in the target period, and thereby used in model simulation of the cloud microphysical properties and precipitation efficiency. It is found that the simulated results were satisfactorily close to the satellite-based observation. Significant effects of aerosols as well as of the meteorological condition were found in the simulated cloud properties and precipitation as confirmed by comparing maritime and polluted aerosol cases and by a sensitivity test with interchanging the aerosol conditions for two cases. Cloud droplets in the polluted condition tended to exhibit relatively narrower cloud drop spectral widths with a bias toward smaller droplet sizes than those in maritime condition, supporting the dispersion effect. The polluted aerosol condition also had a tendency of thinner and higher cloud layers than maritime aerosol condition under relatively humid meteorological condition, possibly due to enhanced updraft. In our cases, vertical structures of cloud droplet number and size were affected predominantly by the change in aerosol conditions, whereas in the structures of liquid water content and cloud fraction were influenced by both meteorological and aerosol conditions. Aerosol change made little differences in cloud liquid water, vertical cloud structure, and updraft/downdraft velocities between the maritime and polluted conditions under dry atmospheric condition. Quantitative evaluations of the sensitivity factor between aerosol and cloud parameters revealed a large sensitivity values in the target area compared to the previously reported values, indicating the strong aerosol-cloud interaction.
Evaluating the effects of microphysical complexity in idealised simulations of trade wind cumulus using the Factorial Method
Authors: Dearden C. , Connolly P. J. , Choularton T. W. , Field P. R.
Published: October 2010

Abstract. The effect of microphysical and environmental factors on the development of precipitation in warm idealised clouds are explored using an idealised process modelling framework. A simple one-dimensional column model is used to drive a suite of microphysics schemes including a flexible multi-moment bulk scheme (including both single and dual moment liquid water) and a state-of-the-art bin-resolved scheme with explicit treatments of liquid and aerosol. The Factorial Method is employed to quantify and compare the sensitivities of each scheme under a set of controlled conditions, in order to isolate the effect of additional microphysical complexity in terms of the impact on surface precipitation. For the schemes considered, and in the absence of entrainment, surface precipitation totals were found to depend increasingly on the meteorological conditions as the level of microphysical complexity is increased. The dual-moment liquid bulk scheme was shown to provide the best agreement with the bin scheme when the cloud base updraught speeds are relatively weak. At higher updraughts, all schemes show that the sensitivity to the magnitude of vertical velocity reduces dramatically, and any subsequent change in precipitation is governed almost entirely by the change in aerosol concentration. However the effect of changes in temperature were found to be underestimated in the bulk schemes compared to the bin scheme; this can be accounted for through differences in the depletion of rain below cloud base by evaporation. Collectively, these results demonstrate the usefulness of the Factorial Method as a model development tool for quantitatively comparing and contrasting the behaviour of microphysics schemes of differing levels of complexity within a specified parameter space.
Global distributions of acetone in the upper troposphere from MIPAS–E spectra
Authors: Moore D. P. , Remedios J. J. , Waterfall A. M.
Published: October 2010

Abstract. This study reports the first global measurements of acetone in the upper troposphere. Profiles are obtained between 6 and 15 km from measurements made by the Michelson Interferometer for Passive Atmospheric Sounding onboard Envisat (MIPAS–E) from August 2003. The best accuracy and precision is obtained at lower altitudes in the mid-latitudes and poles. We report a strong hemispheric difference in the acetone volume mixing ratios (vmrs) with the highest average concentrations in the Northern Hemisphere (NH) mid-latitude upper troposphere of between 2000 ppt and 3000 ppt. These high distributions are possibly linked to higher vegetative emissions during the NH summer season. Globally, concentrations range between 750 ppt and 3000 ppt in the middle troposphere (300 to 500 hPa) and between 50 ppt and 2000 ppt in the upper troposphere (120 to 200 hPa). The results show the likely strong influence of mid-latitude and boreal processes on the acetone summertime distribution. Zonal distributions of acetone show that vmrs of the gas decrease rapidly with increasing altitude (decreasing pressure) but there is reversible transport between the upper troposphere and the lowermost stratosphere. Acetone vmrs remain fairly constant poleward of 45° S with vmrs between 400 ppt and 500 ppt. Northern Hemisphere vmrs poleward of 45° N are consistently higher than this on a day-to-day basis by between 200 ppt and 1000 ppt on average.
A simple representation of surface active organic aerosol in cloud droplet formation
Authors: Prisle N. L. , Dal Maso M. , Kokkola H.
Published: October 2010

Abstract. Atmospheric aerosols often contain surface active organics. Surface activity can affect cloud droplet formation through both surface partitioning and surface tension reduction in activating droplets. However, a comprehensive thermodynamic account for these effects in Köhler modeling is computationally demanding and requires knowledge of both droplet composition and component molecular properties, which is generally unavailable. Here, a simple representation of activation properties for surface active organics is introduced and compared against detailed model predictions and laboratory measurements of CCN activity for mixed surfactant-salt particles from the literature. This simple organic representation is seen to work well for aerosol organic-inorganic composition ranges typically found in the atmosphere, and agreement with both experiments and detailed model predictions increases with surfactant strength. The simple representation does not require resolution of the organic aerosol composition and relies solely on properties of the organic fraction that can be measured directly with available techniques. Thus, it has high potential for application to complex and ambient aerosol. It is not computationally demanding, and therefore also has potential for implementation to atmospheric models accounting for cloud microphysics.
A new fully automated FTIR system for total column measurements of greenhouse gases
Authors: Geibel M. C. , Gerbig C. , Feist D. G.
Published: October 2010

Abstract. This article introduces a new fully automated FTIR system that is part of the Total Carbon Column Observing Network (TCCON). It will provide continuous ground-based measurements of column-averaged volume mixing ratio for CO2, CH4 and several other greenhouse gases in the tropics. Housed in a 20-foot shipping container it was developed as a transportable system that could be deployed almost anywhere in the world. We describe the automation concept which relies on three autonomous subsystems and their interaction. Crucial components like a sturdy and reliable solar tracker dome are described in detail. The automation software employs a new approach relying on multiple processes, database logging and web-based remote control. First results of total column measurements at Jena, Germany show that the instrument works well and can provide parts of the diurnal as well as seasonal cycle for CO2. Instrument line shape measurements with an HCl cell suggest that the instrument stays well-aligned over several months. After a short test campaign for side by side intercomaprison with an existing TCCON instrument in Australia, the system will be transported to its final destination Ascension Island.
CO2-gradient measurements using a parallel multi-analyzer setup
Authors: Siebicke L. , Steinfeld G. , Foken T.
Published: October 2010

Abstract. Accurate CO2 concentration gradient measurements are needed for the computation of advective flux terms, which are part of the full Net Ecosystem Exchange (NEE) budget equation. A typical draw back of current gradient measurement designs in advection research is the inadequate sampling of complex flow phenomena using too few observation points in space and time. To overcome this draw back, a new measurement design is presented which allows the parallel measurement of several sampling points at a high frequency. Due to the multi-analyzer nature of the design, inter-instrument bias becomes more of a concern compared to conventional setups. Therefore a statistical approach is presented which allows for accurate observations of concentration gradients, which are typically small in relation to analyzer accuracy, to be obtained. This bias correction approach applies a conditional, time dependent signal correction. The correction depends on a mixing index based on cross correlation analysis, which characterizes the degree of mixing of the atmosphere between individual sample points. The approach assumes statistical properties of probability density functions (pdf) of concentration differences between a sample point and the field average which are common to the pdf's from several sample points. The validity of the assumptions made was successfully verified by Large Eddy Simulation (LES) using the model PALM. The study presents concentration time series before and after correction, measured at a 2 m height in the sub-canopy at the FLUXNET spruce forest site Waldstein-Weiden\\-brunnen (DE-Bay), analyzes the dependence of statistical parameters of pdf's from atmospheric parameters such as stratification, quantifies the errors and evaluates the performance of the bias correction approach. The improvements that are achieved by applying the bias correction approach are one order of magnitude larger than possible errors associated with it, which is a strong incentive to use the correction approach. In conclusion, the presented bias correction approach is well suited for – but not limited to – horizontal gradient measurements in a multi-analyzer setup, which would not have been reliable without this approach. Finally, possible future improvements of the bias correction approach are outlined and further fields of application indicated.
The water column distribution of carbonate system variables at the ESTOC site from 1995 to 2004
Authors: González-Dávila M. , Santana-Casiano J. M. , Rueda M. J. , Llinás O.
Published: October 2010

Abstract. The accelerated rate of increase in atmospheric carbon dioxide and the substantial fraction of anthropogenic CO2 emissions absorbed by the oceans are affecting the anthropocenic signatures of seawater. Long-term time series are a powerful tool for investigating any change in ocean bio-geochemistry and its effects on the carbon cycle. We have evaluated the ESTOC (European Station for Time series in the Ocean at the Canary islands) observations of measured pH (total scale at 25 °C) and total alkalinity plus computed total dissolved inorganic carbon concentration (CT) from 1995 to 2004 for surface and deep waters, by following all changes in response to increasing atmospheric carbon dioxide. The observed values for the surface partial pressure of CO2 from 1995 to 2008 were also taken into consideration. The data were treated to better understand the fundamental processes controlling vertical distributions in the Eastern North Atlantic Ocean and the accumulation of anthropogenic CO2, CANT. CT at constant salinity, NCT, increased at a rate of 0.85 μmol kg−1 yr−1 in the mixed layer, linked to an fCO2 increase of 1.7±0.7 μatm yr−1 in both the atmosphere and the ocean. Consequently, the mixed layer at ESTOC site has also become more acidic, −0.0017±0.0003 units yr−1, whereas the carbonate ion concentrations and CaCO3 saturation states have also decreased over time. NCT increases at a rate of 0.53, 0.49 and 0.40 μmol kg−1 yr−1 at 300, 600, and 1000 m, respectively. The general processes controlling the vertical variations of alkalinity and the inorganic carbon distribution were computed by considering the pre-formed values, the production/decomposition of organic matter and the formation/dissolution of carbonates. At 3000 m, 30% of the inorganic carbon production is related to the dissolution of calcium carbonate, increasing to 35% at 3685 m. The total column inventory of anthropogenic CO2 for the decade was 66±3 mol m−2. A model fitting indicated that the column inventory of CANT increased from 61.7 mol m−2 in the year 1994 to 70.2 mol m−2 in 2004. The ESTOC site is presented as a reference site to follow CANT changes in the Northeast Atlantic Sub-tropical gyre.
Influence of bioturbation on the biogeochemistry of the sediment in the littoral zone of an acidic mine pit lake
Authors: Lagauzère S. , Moreira S. , Koschorreck M.
Published: October 2010

Abstract. In the last decades, the mining exploitation of large areas in Lusatia (South-eastern Germany) but also in other mining areas worldwide has led to the formation of hundreds of pit lakes. Pyrite oxidation in the surrounding dumps makes many such lakes extremely acidic (pH < 3). The biogeochemical functioning of these lakes is mainly governed by cycling of iron. This represents a relevant ecological problem and intensive research has been conducted to understand the involved biogeochemical processes and develop bioremediation strategies. Despite some studies reporting the presence of living organisms (mostly bacteria, algae, and macro-invertebrates) under such acidic conditions, and their trophic interactions, their potential impact on the ecosystem functioning was poorly investigated. The present study aimed to assess the influence of chironomid larvae on oxygen dynamics and iron cycle in the sediment of acidic pit lakes. In the Mining Lake 111, used as a study case since 1996, Chironomus crassimanus (Insecta, Diptera) is the dominant benthic macro-invertebrate species and occurs at relatively high abundances in shallow water. A 16-day laboratory experiment using microcosms combined with high resolution measurements (DET gel probes and O2 microsensors) was carried out. The burrowing activity of C. crassimanus larvae induced a 3-fold increase of the oxygen consumption by sediment, and stimulated the mineralization of organic matter in the upper layers of the sediment. The iron cycle was also impacted (e.g. lower rates of reduction and oxidation, increase of iron-oxidizing bacteria abundance, stimulation of mineral formation) but with no significant effect on the iron flux at the sediment-water interface, and thus on the water acidity budget. This work provides the first assessment of bioturbation in an acidic mining lake and shows that its influence on biogeochemistry cannot be neglected.
Distribution and host diversity of Amoebophryidae parasites across oligotrophic waters of the Mediterranean Sea
Authors: Siano R. , Alves-de-Souza C. , Foulon E. , Bendif El M. , Simon N. , Guillou L. , Not F.
Published: October 2010

Abstract. Sequences affiliated to Syndiniales (Marine alveolate, MALV) regularly dominate 18S rDNA genetic libraries of nearly all marine ecosystems investigated so far. Among them, Amoebophryidae (MALV group II) is composed of numerous and genetically distant environmental sequences, where Amoebophrya is the only known and formally described genus. Amoebophrya species include virulent pathogens for a wide range of dinoflagellate species. Beside their regular occurrence in marine ecosystems, their quantitative distribution and the environmental factors triggering host infection have barely been studied in open oligotrophic waters. In order to understand the functional role of these parasites in natural environments, we studied the distribution and contribution to the eukaryotic community of the small free-living stage of Amoebophryidae (the dinospores) along a transect in the Mediterranean Sea, as well as their host diversity at three oligotrophic stations. Dinospores were more abundant at a coastal station (max. 1.5 × 103 cells ml−1) than in oligotrophic waters (max. 51 ± 16.3 cells ml−1), where they represented 10.3 to 34.9% of the total eukaryotic community at 40 and 30 m depth, respectively and 21.2% on average along the water column. Positive correlation was found between dinospore occurrence and higher concentration of NO3 + NO2 at the coastal station. At selected stations, out of 38 different dinoflagellates taxa identified, 15 were infected, among which a majority were not recognized as Amoebophryidae host so far. Prevalences (percentage of infected cells) generally varied between 2% and 10%, with a notable exception for Blepharocysta paulsenii for which 25% of cells were infected at the station C. The present study shows that dinospores are able to thrive, infects and most probably exert a control on host populations both in coastal and ultra-oligotrophic open waters. Our results emphasize the role of parasitism in microbial food web dynamics and ultimately on biogeochemical cycles.
An improved Antarctic dataset for high resolution numerical ice sheet models (ALBMAP v1)
Authors: Le Brocq A. M. , Payne A. J. , Vieli A.
Published: October 2010

Abstract. The dataset described in this paper (ALBMAP) has been created for the purposes of high-resolution numerical ice sheet modelling of the Antarctic Ice Sheet. It brings together data on the ice sheet configuration (e.g. ice surface and ice thickness) and boundary conditions, such as the surface air temperature, accumulation and geothermal heat flux. The ice thickness and basal topography is based on the BEDMAP dataset (Lythe et al., 2001), however, there are a number of inconsistencies within BEDMAP and, since its release, more data has become available. The dataset described here addresses these inconsistencies, including some novel interpolation schemes for sub ice-shelf cavities, and incorporates some major new datasets. The inclusion of new datasets is not exhaustive, this considerable task is left for the next release of BEDMAP, however, the data and procedure documented here provides another step forward and demonstrates the issues that need addressing in a continental scale dataset useful for high resolution ice sheet modelling. The dataset provides an initial condition that is as close as possible to present-day ice sheet configuration, aiding modelling of the response of the Antarctic Ice Sheet to various forcings, which are, at present, not fully understood.
Climatology-based regional modelling of potential vegetation and average annual long-term runoff for Mesoamerica
Authors: Imbach P. , Molina L. , Locatelli B. , Roupsard O. , Ciais P. , Corrales L. , Mahé G.
Published: October 2010

Abstract. Mean annual cycles of runoff, evapotranspiration, leaf area index (LAI) and potential vegetation were modelled for Mesoamerica using the SVAT model MAPSS with different climatology datasets. We calibrated and validated the model after building a comprehensive database of regional runoff, climate, soils and LAI. The performance of several gridded precipitation climatology datasets (CRU, FCLIM, WorldClim, TRMM, WindPPT and TCMF) was evaluated and FCLIM produced the most realistic runoff. Annual runoff was successfully predicted (R2=0.84) for a set of 138 catchments, with a low runoff bias (12%) that might originate from an underestimation of the precipitation over cloud forests. The residuals were larger in small catchments but remained homogeneous across elevation, precipitation, and land-use gradients. Assuming a uniform distribution of parameters around literature values, and using a Monte Carlo-type approach, we estimated an average model uncertainty of 42% of the annual runoff. The MAPSS model was most sensitive to the parameterization of stomatal conductance. Monthly runoff seasonality was mimicked "fairly" in 78% of the catchments. Predicted LAI was consistent with MODIS collection 5 and GLOBCARBON remotely sensed global products. The simulated evapotranspiration:runoff ratio increased exponentially for low precipitation areas, highlighting the importance of accurately modelling evapotranspiration below 1500 mm of annual rainfall with the help of SVAT models such as MAPSS. We propose the first high-resolution (1 km2 pixel) maps combining average long-term runoff, evapotranspiration, leaf area index and potential vegetation types for Mesoamerica.
A multi basin SWAT model analysis of runoff and sedimentation in the Blue Nile, Ethiopia
Authors: Easton Z. M. , Fuka D. R. , White E. D. , Collick A. S. , Biruk Ashagre B. , McCartney M. , Awulachew S. B. , Ahmed A. A. , Steenhuis T. S.
Published: October 2010

Abstract. A multi basin analysis of runoff and erosion in the Blue Nile Basin, Ethiopia was conducted to elucidate sources of runoff and sediment. Erosion is arguably the most critical problem in the Blue Nile Basin, as it limits agricultural productivity in Ethiopia, degrades benthos in the Nile, and results in sedimentation of dams in downstream countries. A modified version of the Soil and Water Assessment Tool (SWAT) model was developed to predict runoff and sediment losses from the Ethiopian Blue Nile Basin. The model simulates saturation excess runoff from the landscape using a simple daily water balance coupled to a topographic wetness index in ways that are consistent with observed runoff processes in the basin. The spatial distribution of landscape erosion is thus simulated more correctly. The model was parameterized in a nested design for flow at eight and sediment at three locations in the basin. Subbasins ranged in size from 1.3 to 174 000 km2, and interestingly, the partitioning of runoff and infiltrating flow could be predicted by topographic information. Model predictions showed reasonable accuracy (Nash Sutcliffe Efficiencies ranged from 0.53–0.92) with measured data across all sites except Kessie, where the water budget could not be closed; however, the timing of flow was well captured. Runoff losses increased with rainfall during the monsoonal season and were greatest from areas with shallow soils and large contributing areas. Analysis of model results indicate that upland landscape erosion dominated sediment delivery to the main stem of the Blue Nile in the early part of the growing season when tillage occurs and before the soil was wetted up and plant cover was established. Once plant cover was established in mid August landscape erosion was negligible and sediment export was dominated by channel processes and re-suspension of landscape sediment deposited early in the growing season. These results imply that targeting small areas of the landscape where runoff is produced can be the most effective at controlling erosion and protecting water resources. However, it is not clear what can be done to manage channel erosion, particularly in first order streams in the basin.
Earth observation Water Cycle Multi-Mission Observation Strategy (WACMOS)
Authors: Su Z. , Dorigo W. , Fernández-Prieto D. , Van Helvoirt M. , Hungershoefer K. , de Jeu R. , Parinussa R. , Timmermans J. , Roebeling R. , Schröder M. , Schulz J. , Van der Tol C. , Stammes P. , Wagner W. , Wang L. , Wang P. , Wolters E.
Published: October 2010

Abstract. Observing and monitoring the different components of the global water cycle and their dynamics are essential steps to understand the climate of the Earth, forecast the weather, predict natural disasters like floods and droughts, and improve water resources management. Earth observation technology is a unique tool to provide a global understanding of many of the essential variables governing the water cycle and monitor their evolution over time from global to basin scales. In the coming years an increasing number of Earth observation missions will provide an unprecedented capacity to quantify several of these variables on a routine basis. In this context, the European Space Agency (ESA), in collaboration with the Global Energy and Water Cycle Experiment (GEWEX) of the World Climate Research Program (WCRP), launched the Water Cycle Multi-Mission Observation Strategy (WACMOS) project in 2009. The project aims at developing and validating a novel set of geo-information products relevant to the water cycle covering the following thematic areas: evapotranspiration, soil moisture, cloud characterization and water vapour. The generation of these products is based on a number of innovative techniques and methods aiming at exploiting the synergies of different types of Earth observation data available today to the science community. This paper provides an overview of the major findings of the project with the ultimate goal of demonstrating the potential of innovative multi-mission based strategies to improve current observations by maximizing the synergistic use of the different types of information provided by the currently available observation systems.
Influence of flood frequency on residential building losses
Authors: Elmer F. , Thieken A. H. , Pech I. , Kreibich H.
Published: October 2010

Abstract. For the purpose of flood risk analysis, reliable loss models are an indispensable need. The most common models use stage-damage functions relating damage to water depth. They are often derived from empirical flood loss data (i.e. loss data collected after a flood event). However, object specific loss data (e.g. losses of single residential buildings) from recent flood events in Germany showed higher average losses in less probable events, regardless of actual water level. Hence, models that were derived from such data tend to overestimate losses caused by more probable events. Therefore, it is the aim of the study to analyse the relation between flood damage and recurrence interval and to propose a method for considering recurrence interval in flood loss modelling. The survey was based on residential building loss data (n=2158) of recent flood events in 2002, 2005 and 2006 in Germany and on-site recurrence interval of the respective events. We discovered a highly significant positive correlation between loss extent and recurrence interval for classified water levels as well as increasing average losses for longer recurrence intervals within each class. The application of principal component analysis revealed the interrelation between factors that influence the damage extent directly or indirectly, and recurrence interval. No single factor or component could be identified that explained the influence of recurrence interval, which led to the conclusion that recurrence interval cannot substitute, but complement other damage influencing factors in flood loss modelling approaches. Finally, a method was developed to include recurrence interval in typical flood loss models and make them applicable to a wider range of flood events. Validation including statistical error analysis showed that the modified models improve loss estimates in comparison to traditional approaches. The proposed multi-parameter model FLEMOps+r performs particularly well.
Numerical simulations of spreading of the Persian Gulf outflow into the Oman Sea
Authors: Ezam M. , Bidokhti A. A. , Javid A. H.
Published: October 2010

Abstract. A three dimensional numerical model namely POM (Princeton Ocean Model) and observational data are used to study the Persian Gulf outflow structure and its spreading pathways during 1992. In the model, the monthly wind speed data were taken from ICOADS (International Comprehensive Ocean-Atmosphere Data Set) and the monthly SST (sea surface temperatures) were taken from AVHRR (Advanced Very High Resolution Radiometer) with the addition of monthly net shortwave radiations from NCEP (National Center for Environmental Prediction). The mean monthly precipitation rates from NCEP data and the calculated evaporation rates are used to impose the surface salinity fluxes. At the open boundaries the temperature and salinity were prescribed from the mean monthly climatological values from WOA05 (World Ocean Atlas 2005). Also the four major components of the tide were prescribed at the open boundaries. The results show that the outflow mainly originates from two branches at different depths in the Persian Gulf. The permanent branch exists during the whole year deeper than 40 m along the Gulf axis and originates from the inner parts of the Persian Gulf. The other seasonal branch forms in the vicinity of the shallow southern coasts due to high evaporation rates during winter. Near the Strait of Hormuz the two branches join and form the main outflow source water. The results of simulations reveal that during the winter the outflow boundary current mainly detaches from the coast well before Ras Al Hamra Cape, however during summer the outflow seems to follow the coast even after this Cape. This is due to a higher density of the colder outflow that leads to more sinking near the coast in winter. Thus, the outflow moves to a deeper depth of about 500 m (for which some explanations are given) while the main part detaches and spreads at a depth of about 300 m. However in summer it all moves at a depth of about 200–250 m. During winter, the deeper, stronger and wider outflow is more affected by the steep topography, leading to separation from the coast. While during summer, the weaker and shallower outflow is less influenced by bottom topography and so continues along the boundary.
Reflection seismic studies over the end-glacial Burträsk fault, Skellefteå, Sweden
Authors: Juhlin C. , Lund B.
Published: October 2010

Abstract. Reflection seismic data were acquired along a ca. 22 km long profile over the end-glacial Burträsk Fault with a nominal receiver and source spacing of 20 m. A steeply dipping reflection can be correlated to the Burträsk Fault, indicating that the fault dips at about 55° to the southeast near the surface. The reflection from the fault is rather poorly imaged, probably due to a jump in the fault and the crookedness of the seismic profile in the vicinity of the fault. A more pronounced steeply dipping reflection is observed about 4 km southeast of the Burträsk Fault. Based on its correlation with a topographic low at the surface this reflection is interpreted to originate from a fracture zone. There are no signs of large displacements along this fault as the glacial ice receded, but it may be active today. Other reflections on the processed seismic section may originate from changes in lithological variations in the supra-crustal rocks or from intrusions of more mafic rock. Constraints on the fault geometry provided by the reflection seismic data will help determine what stresses were required to activate the fault when the major rupture along it occurred.