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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Grillakis, Manolis G.; Koutroulis, Aristeidis G.; Daliakopoulos, Ioannis N.; Tsanis, Ioannis K.;

    Bias correction of climate variables is a standard practice in climate change impact (CCI) studies. Various methodologies have been developed within the framework of quantile mapping. However, it is well known that quantile mapping may significantly modify the long-term statistics due to the time dependency of the temperature bias. Here, a method to overcome this issue without compromising the day-to-day correction statistics is presented. The methodology separates the modeled temperature signal into a normalized and a residual component relative to the modeled reference period climatology, in order to adjust the biases only for the former and preserve the signal of the later. The results show that this method allows for the preservation of the originally modeled long-term signal in the mean, the standard deviation and higher and lower percentiles of temperature. To illustrate the improvements, the methodology is tested on daily time series obtained from five Euro CORDEX regional climate models (RCMs).

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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Earth System Dynamic...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Papadimitriou, Lamprini V.; Koutroulis, Aristeidis G.; Grillakis, Manolis G.; Tsanis, Ioannis K.;

    Global climate model (GCM) outputs feature systematic biases that render them unsuitable for direct use by impact models, especially for hydrological studies. To deal with this issue, many bias correction techniques have been developed to adjust the modelled variables against observations, focusing mainly on precipitation and temperature. However, most state-of-the-art hydrological models require more forcing variables, in addition to precipitation and temperature, such as radiation, humidity, air pressure, and wind speed. The biases in these additional variables can hinder hydrological simulations, but the effect of the bias of each variable is unexplored. Here we examine the effect of GCM biases on historical runoff simulations for each forcing variable individually, using the JULES land surface model set up at the global scale. Based on the quantified effect, we assess which variables should be included in bias correction procedures. To this end, a partial correction bias assessment experiment is conducted, to test the effect of the biases of six climate variables from a set of three GCMs. The effect of the bias of each climate variable individually is quantified by comparing the changes in simulated runoff that correspond to the bias of each tested variable. A methodology for the classification of the effect of biases in four effect categories (ECs), based on the magnitude and sensitivity of runoff changes, is developed and applied. Our results show that, while globally the largest changes in modelled runoff are caused by precipitation and temperature biases, there are regions where runoff is substantially affected by and/or more sensitive to radiation and humidity. Global maps of bias ECs reveal the regions mostly affected by the bias of each variable. Based on our findings, for global-scale applications, bias correction of radiation and humidity, in addition to that of precipitation and temperature, is advised. Finer spatial-scale information is also provided, to suggest bias correction of variables beyond precipitation and temperature for regional studies.

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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Hydrology and Earth ...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Storto, Andrea; Alvera-Azcárate, Aida; Balmaseda, Magdalena A.; Barth, Alexander; +19 Authors

    Ocean reanalyses combine ocean models, atmospheric forcing fluxes, and observations using data assimilation to give a four-dimensional description of the ocean. Metrics assessing their reliability have improved over time, allowing reanalyses to become an important tool in climate services that provide a more complete picture of the changing ocean to end users. Besides climate monitoring and research, ocean reanalyses are used to initialize sub-seasonal to multi-annual predictions, to support observational network monitoring, and to evaluate climate model simulations. These applications demand robust uncertainty estimates and fit-for-purpose assessments, achievable through sustained advances in data assimilation and coordinated inter-comparison activities. Ocean reanalyses face specific challenges: i) dealing with intermittent or discontinued observing networks, ii) reproducing inter-annual variability and trends of integrated diagnostics for climate monitoring, iii) accounting for drift and bias due e.g. to air-sea flux or ocean mixing errors, iv) optimizing initialization and improving performances during periods and in regions with sparse data. Other challenges such as multi-scale data assimilation to reconcile mesoscale and large-scale variability and flow-dependent error characterization for rapidly evolving processes, are amplified in long-term reanalyses. The demand to extend reanalyses backward in time requires tackling all these challenges, especially in the emerging context of earth system reanalyses and coupled data assimilation. This mini-review aims at documenting recent advances from the ocean reanalysis community, discussing unsolved challenges that require sustained activities for maximizing the utility of ocean observations, supporting data rescue and advancing specific research and development requirements for reanalyses. © 2019 Storto, Alvera Azcarate, Balmaseda, Barth, Chevallier, Counillon, Domingues, Drévillon, Drillet, Forget, Garric, Haines, Hernandez, Iovino, Jackson, Lellouche, Masina, Mayer, Oke, Penny, Peterson, Yang and Zuo.

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  • Authors: Canals, Rocío; Hammarlöf, Disa; Kröger, Carsten; Owen, Siân; +15 Authors

    Salmonella Typhimurium ST313 causes invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa, targeting susceptible HIV + , malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered the S. Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of the Salmonella expression compendium SalComD23580: bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl . We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Fernández, Alfonso; Muñoz, Ariel; González-Reyes, Álvaro; Aguilera-Betti, Isabella; +8 Authors

    Streamflow in south-central Chile (SCC, ∼ 37–42∘ S) is vital for agriculture, forestry production, hydroelectricity, and human consumption. Recent drought episodes have generated hydrological deficits with damaging effects on these activities. This region is projected to undergo major reductions in water availability, concomitant with projected increases in water demand. However, the lack of long-term records hampers the development of accurate estimations of natural variability and trends. In order to provide more information on long-term streamflow variability and trends in SCC, here we report findings of an analysis of instrumental records and a tree-ring reconstruction of the summer streamflow of the Río Imperial (∼ 37∘ 40′ S–38∘ 50′ S). This is the first reconstruction in Chile targeted at this season. Results from the instrumental streamflow record (∼ 1940 onwards) indicated that the hydrological regime is fundamentally pluvial with a small snowmelt contribution during spring, and evidenced a decreasing trend, both for the summer and the full annual record. The reconstruction showed that streamflow below the average characterized the post-1980 period, with more frequent, but not more intense, drought episodes. We additionally found that the recent positive phase of the Southern Annular Mode has significantly influenced streamflow. These findings agree with previous studies, suggesting a robust regional signal and a shift to a new hydrological scenario. In this paper, we also discuss implications of these results for water managers and stakeholders; we provide rationale and examples that support the need for the incorporation of tree-ring reconstructions into water resources management.

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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Hydrology and Earth ...arrow_drop_down
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Tirpitz, Jan-Lukas; Frieß, Udo; Hendrick, François; Alberti, Carlos; +61 Authors

    The second Cabauw Intercomparison of Nitrogen Dioxide measuring Instruments (CINDI-2) took place in Cabauw (the Netherlands) in September 2016 with the aim of assessing the consistency of multi-axis differential optical absorption spectroscopy (MAX-DOAS) measurements of tropospheric species (NO2, HCHO, O3, HONO, CHOCHO and O4). This was achieved through the coordinated operation of 36 spectrometers operated by 24 groups from all over the world, together with a wide range of supporting reference observations (in situ analysers, balloon sondes, lidars, long-path DOAS, direct-sun DOAS, Sun photometer and meteorological instruments). In the presented study, the retrieved CINDI-2 MAX-DOAS trace gas (NO2, HCHO) and aerosol vertical profiles of 15 participating groups using different inversion algorithms are compared and validated against the colocated supporting observations, with the focus on aerosol optical thicknesses (AOTs), trace gas vertical column densities (VCDs) and trace gas surface concentrations. The algorithms are based on three different techniques: six use the optimal estimation method, two use a parameterized approach and one algorithm relies on simplified radiative transport assumptions and analytical calculations. To assess the agreement among the inversion algorithms independent of inconsistencies in the trace gas slant column density acquisition, participants applied their inversion to a common set of slant columns. Further, important settings like the retrieval grid, profiles of O3, temperature and pressure as well as aerosol optical properties and a priori assumptions (for optimal estimation algorithms) have been prescribed to reduce possible sources of discrepancies. The profiling results were found to be in good qualitative agreement: most participants obtained the same features in the retrieved vertical trace gas and aerosol distributions; however, these are sometimes at different altitudes and of different magnitudes. Under clear-sky conditions, the root-mean-square differences (RMSDs) among the results of individual participants are in the range of 0.01–0.1 for AOTs, (1.5–15) ×1014molec.cm-2 for trace gas (NO2, HCHO) VCDs and (0.3–8)×1010molec.cm-3 for trace gas surface concentrations. These values compare to approximate average optical thicknesses of 0.3, trace gas vertical columns of 90×1014molec.cm-2 and trace gas surface concentrations of 11×1010molec.cm-3 observed over the campaign period. The discrepancies originate from differences in the applied techniques, the exact implementation of the algorithms and the user-defined settings that were not prescribed. For the comparison against supporting observations, the RMSDs increase to a range of 0.02–0.2 against AOTs from the Sun photometer, (11–55)×1014molec.cm-2 against trace gas VCDs from direct-sun DOAS observations and (0.8–9)×1010molec.cm-3 against surface concentrations from the long-path DOAS instrument. This increase in RMSDs is most likely caused by uncertainties in the supporting data, spatiotemporal mismatch among the observations and simplified assumptions particularly on aerosol optical properties made for the MAX-DOAS retrieval. As a side investigation, the comparison was repeated with the participants retrieving profiles from their own differential slant column densities (dSCDs) acquired during the campaign. In this case, the consistency among the participants degrades by about 30 % for AOTs, by 180 % (40 %) for HCHO (NO2) VCDs and by 90 % (20 %) for HCHO (NO2) surface concentrations. In former publications and also during this comparison study, it was found that MAX-DOAS vertically integrated aerosol extinction coefficient profiles systematically underestimate the AOT observed by the Sun photometer. For the first time, it is quantitatively shown that for optimal estimation algorithms this can be largely explained and compensated by considering biases arising from the reduced sensitivity of MAX-DOAS observations to higher altitudes and associated a priori assumptions.

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    Authors: Butchart, Neal; Anstey, James A.; Hamilton, Kevin; Osprey, Scott; +29 Authors

    The Stratosphere–troposphere Processes And their Role in Climate (SPARC) Quasi-Biennial Oscillation initiative (QBOi) aims to improve the fidelity of tropical stratospheric variability in general circulation and Earth system models by conducting coordinated numerical experiments and analysis. In the equatorial stratosphere, the QBO is the most conspicuous mode of variability. Five coordinated experiments have therefore been designed to (i) evaluate and compare the verisimilitude of modelled QBOs under present-day conditions, (ii) identify robustness (or alternatively the spread and uncertainty) in the simulated QBO response to commonly imposed changes in model climate forcings (e.g. a doubling of CO2 amounts), and (iii) examine model dependence of QBO predictability. This paper documents these experiments and the recommended output diagnostics. The rationale behind the experimental design and choice of diagnostics is presented. To facilitate scientific interpretation of the results in other planned QBOi studies, consistent descriptions of the models performing each experiment set are given, with those aspects particularly relevant for simulating the QBO tabulated for easy comparison.

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    Authors: Clyne, Margot; Lamarque, Jean-Francois; Mills, Michael J.; Khodri, Myriam; +19 Authors

    As part of the Model Intercomparison Project on the climatic response to Volcanic forcing (VolMIP), several climate modeling centers performed a coordinated pre-study experiment with interactive stratospheric aerosol models simulating the volcanic aerosol cloud from an eruption resembling the 1815 Mt. Tambora eruption (VolMIP-Tambora ISA ensemble). The pre-study provided the ancillary ability to assess intermodel diversity in the radiative forcing for a large stratospheric-injecting equatorial eruption when the volcanic aerosol cloud is simulated interactively. An initial analysis of the VolMIP-Tambora ISA ensemble showed large disparities between models in the stratospheric global mean aerosol optical depth (AOD). In this study, we now show that stratospheric global mean AOD differences among the participating models are primarily due to differences in aerosol size, which we track here by effective radius. We identify specific physical and chemical processes that are missing in some models and/or parameterized differently between models, which are together causing the differences in effective radius. In particular, our analysis indicates that interactively tracking hydroxyl radical (OH) chemistry following a large volcanic injection of sulfur dioxide (SO2) is an important factor in allowing for the timescale for sulfate formation to be properly simulated. In addition, depending on the timescale of sulfate formation, there can be a large difference in effective radius and subsequently AOD that results from whether the SO2 is injected in a single model grid cell near the location of the volcanic eruption, or whether it is injected as a longitudinally averaged band around the Earth.

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    Authors: Cameletti, Michela;
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    Authors: Schneider, Johannes; Weigel, Ralf; Klimach, Thomas; Dragoneas, Antonis; +23 Authors

    We analyse aerosol particle composition measurements from five research missions between 2014 and 2018 to assess the meridional extent of particles containing meteoric material in the upper troposphere and lower stratosphere (UTLS). Measurements from the Jungfraujoch mountaintop site and a low-altitude aircraft mission show that meteoric material is also present within middle- and lower-tropospheric aerosol but within only a very small proportion of particles. For both the UTLS campaigns and the lower- and mid-troposphere observations, the measurements were conducted with single-particle laser ablation mass spectrometers with bipolar-ion detection, which enabled us to measure the chemical composition of particles in a diameter range of approximately 150 nm to 3 µm. The five UTLS aircraft missions cover a latitude range from 15 to 68∘ N, altitudes up to 21 km, and a potential temperature range from 280 to 480 K. In total, 338 363 single particles were analysed, of which 147 338 were measured in the stratosphere. Of these total particles, 50 688 were characterized by high abundances of magnesium and iron, together with sulfuric ions, the vast majority (48 610) in the stratosphere, and are interpreted as meteoric material immersed or dissolved within sulfuric acid. It must be noted that the relative abundance of such meteoric particles may be overestimated by about 10 % to 30 % due to the presence of pure sulfuric acid particles in the stratosphere which are not detected by the instruments used here. Below the tropopause, the observed fraction of the meteoric particle type decreased sharply with 0.2 %–1 % abundance at Jungfraujoch, and smaller abundances (0.025 %–0.05 %) were observed during the lower-altitude Canadian Arctic aircraft measurements. The size distribution of the meteoric sulfuric particles measured in the UTLS campaigns is consistent with earlier aircraft-based mass-spectrometric measurements, with only 5 %–10 % fractions in the smallest particles detected (200–300 nm diameter) but with substantial (> 40 %) abundance fractions for particles from 300–350 up to 900 nm in diameter, suggesting sedimentation is the primary loss mechanism. In the tropical lower stratosphere, only a small fraction (< 10 %) of the analysed particles contained meteoric material. In contrast, in the extratropics the observed fraction of meteoric particles reached 20 %–40 % directly above the tropopause. At potential temperature levels of more than 40 K above the thermal tropopause, particles containing meteoric material were observed in much higher relative abundances than near the tropopause, and, at these altitudes, they occurred at a similar abundance fraction across all latitudes and seasons measured. Above 440 K, the observed fraction of meteoric particles is above 60 % at latitudes between 20 and 42∘ N. Meteoric smoke particles are transported from the mesosphere into the stratosphere within the winter polar vortex and are subsequently distributed towards low latitudes by isentropic mixing, typically below a potential temperature of 440 K. By contrast, the findings from the UTLS measurements show that meteoric material is found in stratospheric aerosol particles at all latitudes and seasons, which suggests that either isentropic mixing is effective also above 440 K or that meteoric fragments may be the source of a substantial proportion of the observed meteoric material.

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14 Research products
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Grillakis, Manolis G.; Koutroulis, Aristeidis G.; Daliakopoulos, Ioannis N.; Tsanis, Ioannis K.;

    Bias correction of climate variables is a standard practice in climate change impact (CCI) studies. Various methodologies have been developed within the framework of quantile mapping. However, it is well known that quantile mapping may significantly modify the long-term statistics due to the time dependency of the temperature bias. Here, a method to overcome this issue without compromising the day-to-day correction statistics is presented. The methodology separates the modeled temperature signal into a normalized and a residual component relative to the modeled reference period climatology, in order to adjust the biases only for the former and preserve the signal of the later. The results show that this method allows for the preservation of the originally modeled long-term signal in the mean, the standard deviation and higher and lower percentiles of temperature. To illustrate the improvements, the methodology is tested on daily time series obtained from five Euro CORDEX regional climate models (RCMs).

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    Authors: Papadimitriou, Lamprini V.; Koutroulis, Aristeidis G.; Grillakis, Manolis G.; Tsanis, Ioannis K.;

    Global climate model (GCM) outputs feature systematic biases that render them unsuitable for direct use by impact models, especially for hydrological studies. To deal with this issue, many bias correction techniques have been developed to adjust the modelled variables against observations, focusing mainly on precipitation and temperature. However, most state-of-the-art hydrological models require more forcing variables, in addition to precipitation and temperature, such as radiation, humidity, air pressure, and wind speed. The biases in these additional variables can hinder hydrological simulations, but the effect of the bias of each variable is unexplored. Here we examine the effect of GCM biases on historical runoff simulations for each forcing variable individually, using the JULES land surface model set up at the global scale. Based on the quantified effect, we assess which variables should be included in bias correction procedures. To this end, a partial correction bias assessment experiment is conducted, to test the effect of the biases of six climate variables from a set of three GCMs. The effect of the bias of each climate variable individually is quantified by comparing the changes in simulated runoff that correspond to the bias of each tested variable. A methodology for the classification of the effect of biases in four effect categories (ECs), based on the magnitude and sensitivity of runoff changes, is developed and applied. Our results show that, while globally the largest changes in modelled runoff are caused by precipitation and temperature biases, there are regions where runoff is substantially affected by and/or more sensitive to radiation and humidity. Global maps of bias ECs reveal the regions mostly affected by the bias of each variable. Based on our findings, for global-scale applications, bias correction of radiation and humidity, in addition to that of precipitation and temperature, is advised. Finer spatial-scale information is also provided, to suggest bias correction of variables beyond precipitation and temperature for regional studies.

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    Authors: Storto, Andrea; Alvera-Azcárate, Aida; Balmaseda, Magdalena A.; Barth, Alexander; +19 Authors

    Ocean reanalyses combine ocean models, atmospheric forcing fluxes, and observations using data assimilation to give a four-dimensional description of the ocean. Metrics assessing their reliability have improved over time, allowing reanalyses to become an important tool in climate services that provide a more complete picture of the changing ocean to end users. Besides climate monitoring and research, ocean reanalyses are used to initialize sub-seasonal to multi-annual predictions, to support observational network monitoring, and to evaluate climate model simulations. These applications demand robust uncertainty estimates and fit-for-purpose assessments, achievable through sustained advances in data assimilation and coordinated inter-comparison activities. Ocean reanalyses face specific challenges: i) dealing with intermittent or discontinued observing networks, ii) reproducing inter-annual variability and trends of integrated diagnostics for climate monitoring, iii) accounting for drift and bias due e.g. to air-sea flux or ocean mixing errors, iv) optimizing initialization and improving performances during periods and in regions with sparse data. Other challenges such as multi-scale data assimilation to reconcile mesoscale and large-scale variability and flow-dependent error characterization for rapidly evolving processes, are amplified in long-term reanalyses. The demand to extend reanalyses backward in time requires tackling all these challenges, especially in the emerging context of earth system reanalyses and coupled data assimilation. This mini-review aims at documenting recent advances from the ocean reanalysis community, discussing unsolved challenges that require sustained activities for maximizing the utility of ocean observations, supporting data rescue and advancing specific research and development requirements for reanalyses. © 2019 Storto, Alvera Azcarate, Balmaseda, Barth, Chevallier, Counillon, Domingues, Drévillon, Drillet, Forget, Garric, Haines, Hernandez, Iovino, Jackson, Lellouche, Masina, Mayer, Oke, Penny, Peterson, Yang and Zuo.

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  • Authors: Canals, Rocío; Hammarlöf, Disa; Kröger, Carsten; Owen, Siân; +15 Authors

    Salmonella Typhimurium ST313 causes invasive nontyphoidal Salmonella (iNTS) disease in sub-Saharan Africa, targeting susceptible HIV + , malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered the S. Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of the Salmonella expression compendium SalComD23580: bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl . We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.

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    Authors: Fernández, Alfonso; Muñoz, Ariel; González-Reyes, Álvaro; Aguilera-Betti, Isabella; +8 Authors

    Streamflow in south-central Chile (SCC, ∼ 37–42∘ S) is vital for agriculture, forestry production, hydroelectricity, and human consumption. Recent drought episodes have generated hydrological deficits with damaging effects on these activities. This region is projected to undergo major reductions in water availability, concomitant with projected increases in water demand. However, the lack of long-term records hampers the development of accurate estimations of natural variability and trends. In order to provide more information on long-term streamflow variability and trends in SCC, here we report findings of an analysis of instrumental records and a tree-ring reconstruction of the summer streamflow of the Río Imperial (∼ 37∘ 40′ S–38∘ 50′ S). This is the first reconstruction in Chile targeted at this season. Results from the instrumental streamflow record (∼ 1940 onwards) indicated that the hydrological regime is fundamentally pluvial with a small snowmelt contribution during spring, and evidenced a decreasing trend, both for the summer and the full annual record. The reconstruction showed that streamflow below the average characterized the post-1980 period, with more frequent, but not more intense, drought episodes. We additionally found that the recent positive phase of the Southern Annular Mode has significantly influenced streamflow. These findings agree with previous studies, suggesting a robust regional signal and a shift to a new hydrological scenario. In this paper, we also discuss implications of these results for water managers and stakeholders; we provide rationale and examples that support the need for the incorporation of tree-ring reconstructions into water resources management.

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    Authors: Tirpitz, Jan-Lukas; Frieß, Udo; Hendrick, François; Alberti, Carlos; +61 Authors

    The second Cabauw Intercomparison of Nitrogen Dioxide measuring Instruments (CINDI-2) took place in Cabauw (the Netherlands) in September 2016 with the aim of assessing the consistency of multi-axis differential optical absorption spectroscopy (MAX-DOAS) measurements of tropospheric species (NO2, HCHO, O3, HONO, CHOCHO and O4). This was achieved through the coordinated operation of 36 spectrometers operated by 24 groups from all over the world, together with a wide range of supporting reference observations (in situ analysers, balloon sondes, lidars, long-path DOAS, direct-sun DOAS, Sun photometer and meteorological instruments). In the presented study, the retrieved CINDI-2 MAX-DOAS trace gas (NO2, HCHO) and aerosol vertical profiles of 15 participating groups using different inversion algorithms are compared and validated against the colocated supporting observations, with the focus on aerosol optical thicknesses (AOTs), trace gas vertical column densities (VCDs) and trace gas surface concentrations. The algorithms are based on three different techniques: six use the optimal estimation method, two use a parameterized approach and one algorithm relies on simplified radiative transport assumptions and analytical calculations. To assess the agreement among the inversion algorithms independent of inconsistencies in the trace gas slant column density acquisition, participants applied their inversion to a common set of slant columns. Further, important settings like the retrieval grid, profiles of O3, temperature and pressure as well as aerosol optical properties and a priori assumptions (for optimal estimation algorithms) have been prescribed to reduce possible sources of discrepancies. The profiling results were found to be in good qualitative agreement: most participants obtained the same features in the retrieved vertical trace gas and aerosol distributions; however, these are sometimes at different altitudes and of different magnitudes. Under clear-sky conditions, the root-mean-square differences (RMSDs) among the results of individual participants are in the range of 0.01–0.1 for AOTs, (1.5–15) ×1014molec.cm-2 for trace gas (NO2, HCHO) VCDs and (0.3–8)×1010molec.cm-3 for trace gas surface concentrations. These values compare to approximate average optical thicknesses of 0.3, trace gas vertical columns of 90×1014molec.cm-2 and trace gas surface concentrations of 11×1010molec.cm-3 observed over the campaign period. The discrepancies originate from differences in the applied techniques, the exact implementation of the algorithms and the user-defined settings that were not prescribed. For the comparison against supporting observations, the RMSDs increase to a range of 0.02–0.2 against AOTs from the Sun photometer, (11–55)×1014molec.cm-2 against trace gas VCDs from direct-sun DOAS observations and (0.8–9)×1010molec.cm-3 against surface concentrations from the long-path DOAS instrument. This increase in RMSDs is most likely caused by uncertainties in the supporting data, spatiotemporal mismatch among the observations and simplified assumptions particularly on aerosol optical properties made for the MAX-DOAS retrieval. As a side investigation, the comparison was repeated with the participants retrieving profiles from their own differential slant column densities (dSCDs) acquired during the campaign. In this case, the consistency among the participants degrades by about 30 % for AOTs, by 180 % (40 %) for HCHO (NO2) VCDs and by 90 % (20 %) for HCHO (NO2) surface concentrations. In former publications and also during this comparison study, it was found that MAX-DOAS vertically integrated aerosol extinction coefficient profiles systematically underestimate the AOT observed by the Sun photometer. For the first time, it is quantitatively shown that for optimal estimation algorithms this can be largely explained and compensated by considering biases arising from the reduced sensitivity of MAX-DOAS observations to higher altitudes and associated a priori assumptions.

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    Authors: Butchart, Neal; Anstey, James A.; Hamilton, Kevin; Osprey, Scott; +29 Authors

    The Stratosphere–troposphere Processes And their Role in Climate (SPARC) Quasi-Biennial Oscillation initiative (QBOi) aims to improve the fidelity of tropical stratospheric variability in general circulation and Earth system models by conducting coordinated numerical experiments and analysis. In the equatorial stratosphere, the QBO is the most conspicuous mode of variability. Five coordinated experiments have therefore been designed to (i) evaluate and compare the verisimilitude of modelled QBOs under present-day conditions, (ii) identify robustness (or alternatively the spread and uncertainty) in the simulated QBO response to commonly imposed changes in model climate forcings (e.g. a doubling of CO2 amounts), and (iii) examine model dependence of QBO predictability. This paper documents these experiments and the recommended output diagnostics. The rationale behind the experimental design and choice of diagnostics is presented. To facilitate scientific interpretation of the results in other planned QBOi studies, consistent descriptions of the models performing each experiment set are given, with those aspects particularly relevant for simulating the QBO tabulated for easy comparison.

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    Authors: Clyne, Margot; Lamarque, Jean-Francois; Mills, Michael J.; Khodri, Myriam; +19 Authors

    As part of the Model Intercomparison Project on the climatic response to Volcanic forcing (VolMIP), several climate modeling centers performed a coordinated pre-study experiment with interactive stratospheric aerosol models simulating the volcanic aerosol cloud from an eruption resembling the 1815 Mt. Tambora eruption (VolMIP-Tambora ISA ensemble). The pre-study provided the ancillary ability to assess intermodel diversity in the radiative forcing for a large stratospheric-injecting equatorial eruption when the volcanic aerosol cloud is simulated interactively. An initial analysis of the VolMIP-Tambora ISA ensemble showed large disparities between models in the stratospheric global mean aerosol optical depth (AOD). In this study, we now show that stratospheric global mean AOD differences among the participating models are primarily due to differences in aerosol size, which we track here by effective radius. We identify specific physical and chemical processes that are missing in some models and/or parameterized differently between models, which are together causing the differences in effective radius. In particular, our analysis indicates that interactively tracking hydroxyl radical (OH) chemistry following a large volcanic injection of sulfur dioxide (SO2) is an important factor in allowing for the timescale for sulfate formation to be properly simulated. In addition, depending on the timescale of sulfate formation, there can be a large difference in effective radius and subsequently AOD that results from whether the SO2 is injected in a single model grid cell near the location of the volcanic eruption, or whether it is injected as a longitudinally averaged band around the Earth.

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    Authors: Cameletti, Michela;
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