bluuebunny/crossref_metadata_2025 huggingface dataset:
Using next generation sequencing to tackle non-typhoidal Salmonella infections
Authors: Wain John , Keddy Karen H , Hendriksen Rene S , Rubino Salvatore
Published: January 2013

The publication of studies using next generation sequencing to analyse large numbers of bacterial isolates from global epidemics is transforming microbiology, epidemiology and public health. The emergence of multidrug resistant Salmonella Typhimurium ST313 is one example. While the epidemiology in Africa appears to be human-to-human spread and the association with invasive disease almost absolute, more needs to be done to exclude the possibility of animal reservoirs and to transfer the ability to track all Salmonella infections to the laboratories in the front line. In this mini-review we summarise what is currently known about non-typhoidal Salmonella in sub-Saharan Africa and discuss some of the issues which remain.
West Nile Virus outbreak in Sardinia, Italy, in 2011
Authors: Spissu Nicoletta , Panichi Giovanni , Montisci Antonio , Fiore Filippo
Published: January 2013

West Nile Virus (WNV) is an enveloped, positive-sense RNA virus belonging to the genus Flavivirus, antigenically related to the Japanese encephalitis complex in the family Flaviviridae. The principal vectors are mosquitoes, in particular Culex spp, and virus amplification seems to occur in susceptible birds that are the principal vertebrate reservoir hosts, whereas humans, horses and other vertebrates are considered incidental or dead-end hosts. The first Italian equine outbreak was reported in late summer of 1998 in Tuscany, in the area surrounding the Fucecchio marshes, where 14 clinical cases of WND in housed equines were recorded. In 2011 WNV appeared for the first time in Sardinia, representing the first clinical cases in equines in Italy in 2011. The outbreak occurred both in humans and in equines. The serological survey performed on 253 equines living in the province of Oristano detected a total of 87 IgG-positive subjects. Among them, 46 horses showed neurological signs such as ataxia, paresis, paralysis, hyperesthesia, muscle fasciculations, seizures, or fever. Nine of them died or were euthanized. In forthcoming years, surveillance of wild birds and insects will be used to forecast the extension and spread of WNV. The information gathered will be used to direct or optimise strategies intended to prevent virus transmission.
Prolonged Apoptotic Cell Accumulation in Germinal Centers of Mer-Deficient Mice Causes Elevated B Cell and CD4+ Th Cell Responses Leading to Autoantibody Production
Authors: Khan Tahsin N. , Wong Eric B. , Soni Chetna , Rahman Ziaur S. M.
Published: January 2013

Mer receptor tyrosine kinase is a member of the Tyro-3/Axl/Mer (TAM) subfamily of receptor tyrosine kinases, and its expression on phagocytes facilitates their clearance of apoptotic cells (ACs). Mer expression in germinal centers (GCs) occurs predominantly on tingible body macrophages. B and T cells do not express Mer. In this study, we show that Mer deficiency ((Mer−/−) resulted in the long-term accumulation of ACs primarily in GCs and not in the T cell zone, marginal zone, or red pulp areas of the spleen. AC accumulation in GCs led to augmented Ab-forming cell, GC, and IgG2 Ab responses in Mer−/− mice, which were sustained for at least 80 d. Enhanced responses in Mer−/− mice were due to increased activation and proliferation of B cells and CD4+ Th cells, including follicular helper T cells, which resulted in high titers of anti-nuclear Abs in Mer−/− mice compared with wild-type controls. Secondary IgG-producing Ab-forming cell, total IgG, and IgG2 Ab responses were also increased in Mer−/− mice. Finally, compared with wild-type controls, Mer−/− mice had increased percentage of IFN-γ–producing CD4+ Th cells and elevated levels of Th1 (i.e., IL-2 and IFN-γ) and proinflammatory (i.e., TNF and IL-6) cytokines, consistent with elevated levels of Th1-biased IgG2 Abs in Mer−/− mice. Together, our results demonstrate that Mer deficiency induces prolonged accumulation of ACs in GCs, resulting in dysregulation of GC B cell and CD4+ Th cell responses and Th1 cytokine production, leading to alteration of B cell tolerance and the development of autoantibodies.
An Unbiased Genome-Wide Mycobacterium tuberculosis Gene Expression Approach To Discover Antigens Targeted by Human T Cells Expressed during Pulmonary Infection
Authors: Commandeur Susanna , van Meijgaarden Krista E. , Prins Corine , Pichugin Alexander V. , Dijkman Karin , van den Eeden Susan J. F. , Friggen Annemieke H. , Franken Kees L. M. C. , Dolganov Gregory , Kramnik Igor , Schoolnik Gary K. , Oftung Fredrik , Korsvold Gro Ellen , Geluk Annemieke , Ottenhoff Tom H. M.
Published: January 2013

Mycobacterium tuberculosis is responsible for almost 2 million deaths annually. Mycobacterium bovis bacillus Calmette-Guérin, the only vaccine available against tuberculosis (TB), induces highly variable protection against TB, and better TB vaccines are urgently needed. A prerequisite for candidate vaccine Ags is that they are immunogenic and expressed by M. tuberculosis during infection of the primary target organ, that is, the lungs of susceptible individuals. In search of new TB vaccine candidate Ags, we have used a genome-wide, unbiased Ag discovery approach to investigate the in vivo expression of 2170 M. tuberculosis genes during M. tuberculosis infection in the lungs of mice. Four genetically related but distinct mouse strains were studied, representing a spectrum of TB susceptibility controlled by the supersusceptibility to TB 1 locus. We used stringent selection approaches to select in vivo–expressed M. tuberculosis (IVE-TB) genes and analyzed their expression patterns in distinct disease phenotypes such as necrosis and granuloma formation. To study the vaccine potential of these proteins, we analyzed their immunogenicity. Several M. tuberculosis proteins were recognized by immune cells from tuberculin skin test-positive, ESAT6/CFP10-responsive individuals, indicating that these Ags are presented during natural M. tuberculosis infection. Furthermore, TB patients also showed responses toward IVE-TB Ags, albeit lower than tuberculin skin test-positive, ESAT6/CFP10-responsive individuals. Finally, IVE-TB Ags induced strong IFN-γ+/TNF-α+ CD8+ and TNF-α+/IL-2+ CD154+/CD4+ T cell responses in PBMC from long-term latently M. tuberculosis–infected individuals. In conclusion, these IVE-TB Ags are expressed during pulmonary infection in vivo, are immunogenic, induce strong T cell responses in long-term latently M. tuberculosis–infected individuals, and may therefore represent attractive Ags for new TB vaccines.
Organizational resilience: A conceptual integrative framework
Authors: Kantur Deniz , İşeri-Say Arzu
Published: January 2013

Increasingly chaotic business environments of today demand organizations to be more resilient. While the concept of resilience is widely discussed in disaster (e.g., Wildavsky, 1991) and crisis management literatures (e.g., Manyena, 2006), the literature on organizational resilience is developing disjointedly in organizational studies. The literature review suggests that some factors that are suggested in the literature as components of organizational resilience are sources contributing to the emergence of resilience in organizations. This study proposes an integrative framework for organizational resilience and introduces a new outcome concept of organizational evolvability, emphasizing the heightened sensitivity and increased wisdom of the post-event organization. In this model, sources of organizational resilience are categorized as perceptual stance, contextual integrity, strategic capacity and strategic acting, and organizational resilience leads to organizational evolvability as its outcome. The proposed organizational resilience framework attempts to provide a synthesis of the divergent literature on resilience and aims to strengthen organizational resilience research for richer theoretical and empirical progress.
Look up, look around: Is there anything different about team-level OCB in China?
Authors: Mo Shenjiang , Wang Zhongming , Akrivou Kleio , Booth Simon A
Published: January 2013

Ethical leadership has been widely identified as the key variable in enhancing team-level organizational citizenship behavior (team-level OCB) in western economic and business contexts. This is challenged by empirical evidence in China and findings of this study. Our study examined the relationship between ethical leadership, organizational ethical context (ethical culture and corporate ethical values) and team-level OCB. Team-level data has been collected from 57 functional teams in 57 firms operating in China. The findings suggest that although ethical leadership is positively associated with team-level OCB, ethical context positively moderates the relationship between ethical leadership and team-level OCB. The higher ethical context is found to be, the greater is the (positive) effects of ethical leadership on team-level OCB and the opposite holds true when ethical context is low. Key implications are discussed on the role of contextual ethics for team-level OCB, while managerial implications include how non-Chinese firms could improve team-level OCB in the Chinese business context.
The role of strategic alliances in complementing firm capabilities
Authors: Rice John , Liao Tung-Shan , Martin Nigel , Galvin Peter
Published: January 2013

Strategic alliance research emerged to explain alliance formation based upon transaction cost minimisation and opportunism reduction. Later research, and early research from Japan, emphasised the role of alliances in facilitating the transfer of knowledge between organisations. Most recently, alliance research has focussed on the development of shared, potentially idiosyncratic, resource stocks. This paper builds on this recent research, testing the proposition that alliances are important vehicles allowing firms to access or acquire external resources, hence shoring up capability gaps and building new capabilities as required during firm, product and industry life cycles. Using a sample from Australian manufacturing small-and-medium-sized enterprises, the paper reveals that alliances employed by firms can be viewed as initiatives to either fill a gap in the firm's resource stock or to exploit a perceived opportunity in its operational and strategic environment.
Regional and monthly and clear-sky aerosol direct radiative effect (and forcing) derived from the GlobAEROSOL-AATSR satellite aerosol product
Authors: Thomas G. E. , Chalmers N. , Harris B. , Grainger R. G. , Highwood E. J.
Published: January 2013

Abstract. Using the GlobAEROSOL-AATSR dataset, estimates of the instantaneous, clear-sky, direct aerosol radiative effect and radiative forcing have been produced for the year 2006. Aerosol Robotic Network sun-photometer measurements have been used to characterise the random and systematic error in the GlobAEROSOL product for 22 regions covering the globe. Representative aerosol properties for each region were derived from the results of a wide range of literature sources and, along with the de-biased GlobAEROSOL AODs, were used to drive an offline version of the Met Office unified model radiation scheme. In addition to the mean AOD, best-estimate run of the radiation scheme, a range of additional calculations were done to propagate uncertainty estimates in the AOD, optical properties, surface albedo and errors due to the temporal and spatial averaging of the AOD fields. This analysis produced monthly, regional estimates of the clear-sky aerosol radiative effect and its uncertainty, which were combined to produce annual, global mean values of (−6.7 ± 3.9) W m−2 at the top of atmosphere (TOA) and (−12 ± 6) W m−2 at the surface. These results were then used to give estimates of regional, clear-sky aerosol direct radiative forcing, using modelled pre-industrial AOD fields for the year 1750 calculated for the AEROCOM PRE experiment. However, as it was not possible to quantify the uncertainty in the pre-industrial aerosol loading, these figures can only be taken as indicative and their uncertainties as lower bounds on the likely errors. Although the uncertainty on aerosol radiative effect presented here is considerably larger than most previous estimates, the explicit inclusion of the major sources of error in the calculations suggest that they are closer to the true constraint on this figure from similar methodologies, and point to the need for more, improved estimates of both global aerosol loading and aerosol optical properties.
Atmospheric inorganic nitrogen input via dry, wet, and sea fog deposition to the subarctic western North Pacific Ocean
Authors: Jung J. , Furutani H. , Uematsu M. , Kim S. , Yoon S.
Published: January 2013

Abstract. Aerosol, rainwater, and sea fog water samples were collected during the cruise conducted over the subarctic western North Pacific Ocean in the summer of 2008, in order to estimate dry, wet, and sea fog deposition fluxes of atmospheric inorganic nitrogen (N). During sea fog events, mean number densities of particles with diameters larger than 0.5 μm decreased by 12–78%, suggesting that particles with diameters larger than 0.5 μm could act preferentially as condensation nuclei (CN) for sea fog droplets. Mean concentrations of nitrate (NO3−), methanesulfonic acid (MSA), and non sea-salt sulfate (nss-SO42−) in sea fog water were higher than those in rainwater, whereas those of ammonium (NH4+) in both sea fog water and rainwater were similar. These results reveal that sea fog scavenged NO3− and biogenic sulfur species more efficiently than rain. Mean dry, wet, and sea fog deposition fluxes for atmospheric total inorganic N (TIN; i.e. NH4+ + NO3−) over the subarctic western North Pacific Ocean were estimated to be 4.9 μmol m−2 d−1, 33 μmol m−2 d−1, and 7.8 μmol m−2 d−1, respectively. While NO3− was the dominant inorganic N species in dry and sea fog deposition, inorganic N supplied to surface waters by wet deposition was predominantly by NH4+. The contribution of dry, wet, and sea fog deposition to total deposition flux for TIN (46 μmol m−2 d−1) were 11%, 72%, and 17%, respectively, suggesting that ignoring sea fog deposition would lead to underestimate of the total influx of atmospheric inorganic N into the subarctic western North Pacific Ocean, especially in summer periods.
Comparison of global 3-D aviation emissions datasets
Authors: Olsen S. C. , Wuebbles D. J. , Owen B.
Published: January 2013

Abstract. Aviation emissions are unique from other transportation emissions, e.g., from road transportation and shipping, in that they occur at higher altitudes as well as at the surface. Aviation emissions of carbon dioxide, soot, and water vapor have direct radiative impacts on the Earth's climate system while emissions of nitrogen oxides (NOx), sulfur oxides, carbon monoxide (CO), and hydrocarbons (HC) impact air quality and climate through their effects on ozone, methane, and clouds. The most accurate estimates of the impact of aviation on air quality and climate utilize three-dimensional chemistry-climate models and gridded four dimensional (space and time) aviation emissions datasets. We compare five available aviation emissions datasets currently and historically used to evaluate the impact of aviation on climate and air quality: NASA-Boeing 1992, NASA-Boeing 1999, QUANTIFY 2000, Aero2k 2002, and AEDT 2006 and aviation fuel usage estimates from the International Energy Agency. Roughly 90% of all aviation emissions are in the Northern Hemisphere and nearly 60% of all fuelburn and NOx emissions occur at cruise altitudes in the Northern Hemisphere. While these datasets were created by independent methods and are thus not strictly suitable for analyzing trends they suggest that commercial aviation fuelburn and NOx emissions increased over the last two decades while HC emissions likely decreased and CO emissions did not change significantly. The bottom-up estimates compared here are consistently lower than International Energy Agency fuelburn statistics although the gap is significantly smaller in the more recent datasets. Overall the emissions distributions are quite similar for fuelburn and NOx with regional peaks over the populated land masses of North America, Europe, and East Asia. For CO and HC there are relatively larger differences. There are however some distinct differences in the altitude distribution of emissions in certain regions for the Aero2k dataset.
Idealized WRF model sensitivity simulations of sea breeze types and their effects on offshore windfields
Authors: Steele C. J. , Dorling S. R. , von Glasow R. , Bacon J.
Published: January 2013

Abstract. The behaviour and characteristics of the marine component of sea breeze cells have received little attention relative to their onshore counterparts. Yet there is a growing interest and dependence on the offshore wind climate from, for example, a wind energy perspective. Using idealized model experiments, we investigate the sea breeze circulation at scales which approximate to those of the southern North Sea, a region of major ongoing offshore wind farm development. We also contrast the scales and characteristics of the pure and the little known corkscrew and backdoor sea breeze types, where the type is pre-defined by the orientation of the synoptic scale flow relative to the shoreline. We find, crucially, that pure sea breezes, in contrast to corkscrew and backdoor types, can lead to substantial wind speed reductions offshore and that the addition of a second eastern coastline emphasises this effect through generation of offshore "calm zones". The offshore extent of all sea breeze types is found to be sensitive to both the influence of Coriolis acceleration and to the boundary layer scheme selected. These extents range, for example for a pure sea breeze produced in a 2 m s−1 offshore gradient wind, from 0 km to 21 km between the Mellor-Yamada-Nakanishi-Niino and the Yonsei State University schemes respectively. The corkscrew type restricts the development of a backdoor sea breeze on the opposite coast and is also capable of traversing a 100 km offshore domain even under high along-shore gradient wind speed (>15 m s−1) conditions. Realistic variations in sea surface skin temperature and initializing vertical thermodynamic profile do not significantly alter the resulting circulation, though the strengths of the simulated sea breezes are modulated if the effective land-sea thermal contrast is altered. We highlight how sea breeze impacts on circulation need to be considered in order to improve the accuracy of both assessments of the offshore wind energy climate and forecasts of wind energy output.
Using measurements of the aerosol charging state in determination of the particle growth rate and the proportion of ion-induced nucleation
Authors: Leppä J. , Gagné S. , Laakso L. , Manninen H. E. , Lehtinen K. E. J. , Kulmala M. , Kerminen V.-M.
Published: January 2013

Abstract. The fraction of charged nucleation mode particles as a function of particle diameter depends on the particle growth rate and the proportion of particles formed via ion-induced nucleation. In this study we have tested the applicability of recent data analysis methods to determine the growth rate and the proportion of ion-induced nucleation from the measured charged fractions. For this purpose we have conducted a series of aerosol dynamic simulations covering a wide range of atmospheric conditions. The growth rate and initial fraction of charged particles were estimated from simulated data using these methods and compared with the values obtained directly from the simulations. We found that the data analysis methods used in this study should not be used when the nuclei growth rate is less than ~3 nm h−1, or when charged particles grow much more rapidly than neutral ones. Furthermore, we found that the difference in removal rates of neutral and charged particles should be taken into account when estimating the proportion of ion-induced nucleation. Neglecting the higher removal rate of charged particles compared with that of neutral ones could result in an underestimation of the proportion of ion-induced nucleation by up to a factor of 2. This underestimation is further increased if charged particles grow more rapidly than neutral ones. We also provided a simple way of assessing whether these methods are suitable for analyzing data measured under specific conditions. The assessment procedure was illustrated using a few examples of actual measurement sites with a more detailed examination of the typical conditions observed at the SMEAR II station in Hyytiälä, Finland.
Modeling microphysical effects of entrainment in clouds observed during EUCAARI-IMPACT field campaign
Authors: Jarecka D. , Pawlowska H. , Grabowski W. W. , Wyszogrodzki A. A.
Published: January 2013

Abstract. This paper discusses aircraft observations and large-eddy simulation (LES) of the 15 May 2008, North Sea boundary-layer clouds from the EUCAARI-IMPACT field campaign. These clouds were advected from the north-east by the prevailing lower-tropspheric winds, and featured stratocumulus-over-cumulus cloud formations. Almost-solid stratocumulus deck in the upper part of the relatively deep weakly decoupled marine boundary layer overlaid a field of small cumuli with a cloud fraction of ~10%. The two cloud formations featured distinct microphysical characteristics that were in general agreement with numerous past observations of strongly-diluted shallow cumuli on the one hand and solid marine boundary-layer stratocumulus on the other. Macrophysical and microphysical cloud properties were reproduced well by the double-moment warm-rain microphysics large-eddy simulation. A novel feature of the model is its capability to locally predict homogeneity of the subgrid-scale mixing between the cloud and its cloud-free environment. In the double-moment warm-rain microphysics scheme, the homogeneity is controlled by a single parameter α, that ranges from 0 to 1 and limiting values representing the homogeneous and the extremely inhomogeneous mixing scenarios, respectively. Parameter α depends on the characteristic time scales of the droplet evaporation and of the turbulent homogenization. In the model, these scales are derived locally based on the subgrid-scale turbulent kinetic energy, spatial scale of cloudy filaments, the mean cloud droplet radius, and the humidity of the cloud-free air entrained into the cloud. Simulated mixing is on average quite inhomogeneous, with the mean parameter α around 0.7 across the entire depth of the cloud field, but with local variations across almost the entire range, especially near the base and the top of the cloud field.
Observations of peroxyacetyl nitrate (PAN) in the upper troposphere by the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS)
Authors: Tereszchuk K. A. , Moore D. P. , Harrison J. J. , Boone C. D. , Park M. , Remedios J. J. , Randel W. J. , Bernath P. F.
Published: January 2013

Abstract. Peroxyacetyl nitrate (CH3CO·O2NO2, abbreviated as PAN) is a trace molecular species present in the troposphere and lower stratosphere due primarily to pollution from fuel combustion and the pyrogenic outflows from biomass burning. In the lower troposphere, PAN has a relatively short life-time and is principally destroyed within a few hours through thermolysis, but it can act as a reservoir and carrier of NOx in the colder temperatures of the upper troposphere where UV photolysis becomes the dominant loss mechanism. Pyroconvective updrafts from large biomass burning events can inject PAN into the upper troposphere and lower stratosphere (UTLS), providing a means for the long-range transport of NOx. Given the extended lifetimes at these higher altitudes, PAN is readily detectable via satellite remote sensing. A new PAN data product is now available for the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS) Version 3.0 data set. We report measurements of PAN in Boreal biomass burning plumes recorded during the Quantifying the impact of BOReal forest fires on Tropospheric oxidants over the Atlantic using Aircraft and Satellites (BORTAS) campaign. The retrieval method employed and errors analysis are described in full detail. The retrieved volume mixing ratio (VMR) profiles are compared to coincident measurements made by the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) instrument on the European Space Agency (ESA) ENVIronmental SATellite (ENVISAT). Three ACE-FTS occultations containing measurements of Boreal biomass burning outflows, recorded during BORTAS, were identified as having coincident measurements with MIPAS. In each case, the MIPAS measurements demonstrated good agreement with the ACE-FTS VMR profiles for PAN. The ACE-FTS PAN data set is used to obtain zonal mean distributions of seasonal averages from ~5 to 20 km. A strong seasonality is clearly observed for PAN concentrations in the global UTLS. Since the principal source of PAN in the UTLS is due to lofted biomass burning emissions from the pyroconvective updrafts created by large fires, the observed seasonality in enhanced PAN coincides with fire activity in different geographical regions throughout the year. This work is part of an in-depth investigation that is being conducted in an effort to study the aging and chemical evolution of biomass burning emissions in the UTLS by remote, space-borne measurements made by ACE-FTS to further our understanding of the impact of pyrogenic emissions on atmospheric chemistry. Included in this study will be the addition of new, pyrogenic, volatile organic hydrocarbons (VOCs) and oxygenated volatile organic compounds (OVOCs) to expand upon the already extensive suite of molecules retrieved by ACE-FTS to aid in elucidating biomass burning plume chemistry in the free troposphere.
Constraints on emissions of carbon monoxide, methane, and a suite of hydrocarbons in the Colorado Front Range using observations of 14CO2
Authors: LaFranchi B. W. , Pétron G. , Miller J. B. , Lehman S. J. , Andrews A. E. , Dlugokencky E. J. , Miller B. R. , Montzka S. A. , Hall B. , Neff W. , Sweeney C. , Turnbull J. C. , Wolfe D. E. , Tans P. P. , Gurney K. R. , Guilderson T. P.
Published: January 2013

Abstract. Atmospheric radiocarbon (14CO) represents an important observational constraint on emissions of fossil-fuel derived carbon into the atmosphere due to the absence of 14CO in fossil fuel reservoirs. The high sensitivity and precision that accelerator mass spectrometry (AMS) affords in atmospheric 14CO analysis has greatly increased the potential for using such measurements to evaluate bottom-up emissions inventories of fossil fuel CO2 (CO2ff), as well as those for other co-emitted species. Here we use observations of 14CO2 and a series of hydrocarbons and combustion tracers from discrete air samples collected between June 2009 and September 2010 at the National Oceanic and Atmospheric Administration Boulder Atmospheric Observatory (BAO; Lat: 40.050° N, Lon: 105.004° W) to derive emission ratios of each species to CO2ff. From these emission ratios, we estimate emissions of these species by using the Vulcan CO2ff high resolution data product as a reference. The species considered in this analysis are carbon monoxide (CO), methane (CH4), acetylene (C2H2), benzene (C6H6), and C3–C5 alkanes. Comparisons of top-down emissions estimates are made to existing inventories of these species for Denver and adjacent counties, as well as to previous efforts to estimate emissions from atmospheric observations over the same area. We find that CO is overestimated in the 2008 National Emissions Inventory (NEI, 2008) by a factor of ~2. A close evaluation of the inventory suggests that the ratio of CO emitted per unit fuel burned from on-road gasoline vehicles is likely over-estimated by a factor of 2.5. The results also suggest that while the oil and gas sector is the largest contributor to the CH4 signal in air arriving from the north and east, it is very likely that other sources, including agricultural sources, contribute to this signal and must be accounted for when attributing these signals to oil and gas industry activity from a top-down perspective. Our results are consistent with ~60% of the total CH4 emissions from regions to the north and east of the BAO tower stemming from the oil and gas industry, equating to ~70 Gg yr−1 or ~1.7% of total natural gas production in the region.
Incorporating genomic information and predicting gene expression patterns in a simplified biogeochemical model
Authors: Wang P. , Burd A. B. , Moran M. A. , Hood R. R. , Coles V. J. , Yager P. L.
Published: January 2013

Abstract. We present results from a new marine plankton model that combines selective biogeochemical processes with genetic information. The model allows for phytoplankton to adapt to a changing environment by invoking different utilization pathways for acquisition of nutrients (nitrogen and phosphorus) in response to concentration changes. The simulations use simplified environmental conditions represented by a continuously stirred tank reactor, which is populated by 96 different types of phytoplankton that differ in their physiological characteristics and nutrient uptake/metabolism genes. The results show that the simulated phytoplankton community structure is conceptually consistent with observed regional and global phytoplankton biogeography, the genome content from the dominant types of phytoplankton reflects the imposed environmental constraints, and the transcription of the gene clusters is qualitatively simulated according to the environmental changes. The model shows the feasibility of including genomic knowledge into a biogeochemical model and is suited to understanding and predicting changes in marine microbial community structure and function, and to simulating the biological response to rapid environmental changes.
The Northern Circumpolar Soil Carbon Database: spatially distributed datasets of soil coverage and soil carbon storage in the northern permafrost regions
Authors: Hugelius G. , Tarnocai C. , Broll G. , Canadell J. G. , Kuhry P. , Swanson D. K.
Published: January 2013

Abstract. High-latitude terrestrial ecosystems are key components in the global carbon (C) cycle. Estimates of global soil organic carbon (SOC), however, do not include updated estimates of SOC storage in permafrost-affected soils or representation of the unique pedogenic processes that affect these soils. The Northern Circumpolar Soil Carbon Database (NCSCD) was developed to quantify the SOC stocks in the circumpolar permafrost region (18.7 × 106 km2). The NCSCD is a polygon-based digital database compiled from harmonized regional soil classification maps in which data on soil order coverage have been linked to pedon data (n = 1778) from the northern permafrost regions to calculate SOC content and mass. In addition, new gridded datasets at different spatial resolutions have been generated to facilitate research applications using the NCSCD (standard raster formats for use in geographic information systems and Network Common Data Form files common for applications in numerical models). This paper describes the compilation of the NCSCD spatial framework, the soil sampling and soil analytical procedures used to derive SOC content in pedons from North America and Eurasia and the formatting of the digital files that are available online. The potential applications and limitations of the NCSCD in spatial analyses are also discussed. The database has the doi:10.5879/ecds/00000001. An open access data portal with all the described GIS-datasets is available online at: http://www.bbcc.su.se/data/ncscd/.
Optimal depth-based regional frequency analysis
Authors: Wazneh H. , Chebana F. , Ouarda T. B. M. J.
Published: January 2013

Abstract. Classical methods of regional frequency analysis (RFA) of hydrological variables face two drawbacks: (1) the restriction to a particular region which can correspond to a loss of some information and (2) the definition of a region that generates a border effect. To reduce the impact of these drawbacks on regional modeling performance, an iterative method was proposed recently. The proposed method is based on the statistical notion of the depth function and a weight function φ. This depth-based RFA (DBRFA) approach was shown to be superior to traditional approaches in terms of flexibility, generality and performance. The main difficulty of the DBRFA approach is the optimal choice of the weight function φ (e.g. φ minimizing estimation errors). In order to avoid subjective choice and naïve selection procedures of φ, the aim of the present paper is to propose an algorithm-based procedure to optimize the DBRFA and automate the choice of φ according to objective performance criteria. This procedure is applied to estimate flood quantiles in three different regions in North America. One of the findings from the application is that the optimal weight function depends on the considered region and can also quantify the region homogeneity. By comparing the DBRFA to the canonical correlation analysis (CCA) method, results show that the DBRFA approach leads to better performances both in terms of relative bias and mean square error.
Bivariate return period based on copulas for hydrologic dam design: comparison of theoretical and empirical approach
Authors: Requena A. I. , Mediero L. , Garrote L.
Published: January 2013

Abstract. Hydrologic frequency analyses are usually focused on flood peaks. Multivariate analyses on flood variables have not been so exhaustively studied despite the fact that they are required to represent the full hydrograph, which is essential for designing some structures like dams. In this work, a bivariate copula model was used to obtain the bivariate joint distribution of flood peak and volume. An empirical bivariate return period was defined in terms of acceptable risk to the dam through the maximum water elevation reached during the routing process, in order to perform a risk assessment of dam overtopping. A Monte Carlo procedure was developed to compare the probability of occurrence of a flood with the return period linked to the risk of dam overtopping. The procedure is applied to the case study of the Santillana reservoir in Spain. A set of synthetic peak-volume pairs was generated by the fitted copula and synthetic hydrographs were routed through the reservoir. Different reservoir volumes and spillway lengths were considered. Hydrographs with the same risk were represented by a curve in the peak-volume space. These curves were compared to those linked to the probability of occurrence of a flood event, in order to improve the estimation of the Design Flood Hydrograph.
Derivation of RCM-driven potential evapotranspiration for hydrological climate change impact analysis in Great Britain: a comparison of methods and associated uncertainty in future projections
Authors: Prudhomme C. , Williamson J.
Published: January 2013

Abstract. Potential evapotranspiration PET is the water that would be lost by plants through evaporation and transpiration if water was not limited in the soil, and it is commonly used in conceptual hydrological modelling in the calculation of runoff production and hence river discharge. Future changes of PET are likely to be as important as changes in precipitation patterns in determining changes in river flows. However PET is not calculated routinely by climate models so it must be derived independently when the impact of climate change on river flow is to be assessed. This paper compares PET estimates from twelve equations of different complexity, driven by the Hadley Centre's HadRM3-Q0 model outputs representative of 1961–1990, with MORECS PET, a product used as reference PET in Great Britain. The results show that the FAO56 version of the Penman-Monteith equations reproduce best the spatial and seasonal variability of MORECS PET across GB when driven by HadRM3-Q0 estimates of relative humidity, total cloud, wind speed and linearly bias-corrected mean surface temperature. This suggests that potential biases in HadRM3-Q0 climate do not result in significant biases when the physically-based FAO56 equations are used. Percentage changes in PET between the 1961–1990 and 2041–2070 time slices were also calculated for each of the twelve PET equations. Results show a large variation in the magnitude (and sometimes direction) of changes estimated from different PET equations, with Turc, Jensen-Hense and calibrated Blaney-Criddle methods systematically projecting the largest increases across GB for all months and Priestley-Taylor, Makkink and Thornthwaite showing the smallest changes. We recommend the use of the FAO56 equation as when driven by HadRM3-Q0 climate data this best reproduces the reference MORECS PET across Great Britain for the reference period of 1961–1990. Further, the future changes of PET estimated by FAO56 are within the range of uncertainty defined by the ensemble of twelve PET equations. The changes show a clear northwest-southeast gradient of PET increase with largest (smallest) changes in the northwest in January (July and October) respectively. However, the range in magnitude of PET changes due to the choice of PET method shown in this study for Great Britain suggests that PET uncetainty is perhaps one of the greatest challenges facing the assessment of climate change impact on hydrology.
Fuzzy committees of specialised rainfall-runoff models: further enhancements
Authors: Kayastha N. , Ye J. , Fenicia F. , Solomatine D. P.
Published: January 2013

Abstract. Often a single hydrological model cannot capture the details of a complex rainfall-runoff relationship, and a possibility here is building specialised models to be responsible for a particular aspect of this relationship and combining them forming a committee model. This study extends earlier work of using fuzzy committees to combine hydrological models calibrated for different hydrological regimes – by considering the suitability of the different weighting function for objective functions and different class of membership functions used to combine the local models and compare them with global optimal models.
Quantifying soil complexity using network models of soil porous structure
Authors: Samec M. , Santiago A. , Cárdenas J. P. , Benito R. M. , Tarquis A. M. , Mooney S. J. , Korošak D.
Published: January 2013

Abstract. This paper describes an investigation into the properties of spatially embedded complex networks representing the porous architecture of soil systems. We suggest an approach to quantify the complexity of soil pore structure based on the node-node link correlation properties of the networks. We show that the complexity depends on the strength of spatial embedding of the network and that this is related to the transition from a non-compact to compact phase of the network.
NEMO on the shelf: assessment of the Iberia-Biscay-Ireland configuration
Authors: Maraldi C. , Chanut J. , Levier B. , Ayoub N. , De Mey P. , Reffray G. , Lyard F. , Cailleau S. , Drévillon M. , Fanjul E. A. , Sotillo M. G. , Marsaleix P.
Published: January 2013

Abstract. The Iberia-Biscay-Ireland (IBI) system serves one of the 7 MyOcean "Monitoring and Forecasting Centres". A high resolution simulation covering the IBI region is set-up over July 2007–February 2009. The NEMO (Nucleus for European Modelling of the Ocean) model is used with a 1/36° horizontal resolution and 50 z-levels in the vertical. New developments have been incorporated in NEMO to make it suitable to open- as well as coastal-ocean modelling. In this paper, we pursue three main objectives: (1) give an overview of the model configuration used for the simulations; (2) give a broad-brush account of one particular aspect of this work, namely consistency verification; this type of validation is conducted upstream of the implementation of the system before it is used for production and routinely validated; it is meant to guide model development in identifying gross deficiencies in the modelling of several key physical processes; (3) show that such a regional modelling system has potential as a complement to patchy observations (an integrated approach) to give information on non-observed physical quantities and to provide links between observations by identifying broader-scale patterns and processes. We concentrate on the year 2008. We first provide domain-wide consistency verification results in terms of barotropic tides, transports, sea surface temperature and stratification. We then focus on two dynamical sub-regions: the Celtic shelves and the Bay of Biscay slope and deep regions. The model-data consistency is checked for variables and processes such as tidal currents, tidal fronts, internal tides, residual elevation. We also examine the representation in the model of a seasonal pattern of the Bay of Biscay circulation: the warm extension of the Iberian Poleward Current along the northern Spanish coast (Navidad event) in winter 2007–2008.
Quantification of magma ascent rate through rockfall monitoring at the growing/collapsing lava dome of Volcán de Colima, Mexico
Authors: Mueller S. B. , Varley N. R. , Kueppers U. , Lesage P. , Reyes Davila G. Á. , Dingwell D. B.
Published: January 2013

Abstract. The most recent eruptive phase of Volcán de Colima, Mexico, started in 1998 and was characterized by episodic dome growth with a variable effusion rate, interrupted intermittently by explosive eruptions. Between November 2009 and June 2011, growth at the dome was limited to a lobe on the western side where it had previously started overflowing the crater rim, leading to the generation of rockfall events. This meant that no significant increase in dome volume was perceivable and the rate of magma ascent, a crucial parameter for volcano monitoring and hazard assessment, could no longer be quantified via measurements of the dome's dimensions. Here, we present alternative approaches to quantify the magma ascent rate. We estimate the volume of individual rockfalls through the detailed analysis of sets of photographs (before and after individual rockfall events). The relationship between volume and infrared images of the freshly exposed dome surface and the seismic signals related to the rockfall events was then investigated. Larger events exhibited a correlation between the previously estimated volume of a rockfall and the surface temperature of the freshly exposed dome surface as well as the mean temperature of rockfall masses distributed over the slope. We showed that for larger events, the volume of the rockfall correlates with the maximum temperature at the newly formed cliff as well as the seismic energy. By calibrating the seismic signals using the volumes estimated from photographs, the count of rockfalls over a certain period was used to estimate the magma extrusion flux for the period investigated. Over the course of the measurement period, significant changes were observed in number of rockfalls, rockfall volume and hence averaged extrusion rate. The extrusion rate was not constant: it increased from 0.008 m3 s−1 to 0.02 m3 s−1 during 2010 and dropped down to 0.008 m3 s−1 again in March 2011. In June 2011, magma extrusion had come to a halt. The methodology presented represents a reliable tool to constrain the growth rate of domes that are repeatedly affected by partial collapses. There is a good correlation between thermal and seismic energies and rockfall volume. Thus it is possible to calibrate the seismic records associated with the rockfalls (a continuous monitoring tool) to improve both volcano monitoring at volcanoes with active dome growth and hazard management associated with rockfalls specifically.
Climatic drivers of seasonal glacier mass balances: an analysis of 6 decades at Glacier de Sarennes (French Alps)
Authors: Thibert E. , Eckert N. , Vincent C.
Published: January 2013

Abstract. Refined temporal signals extracted from a winter and summer mass balance series recorded at Glacier de Sarennes (French Alps) using variance decomposition are related to local meteorological data and large-scale North Atlantic Oscillation (NAO) anomalies in terms of interannual variability, trends of the low-frequency signals, and breaks in the time series. The winter balance has increased by +23% since 1976 due to more precipitation in early and late winter. The summer balance has decreased since 1982 due to a 43% increase in snow and ice melt. A 24-day lengthening of the ablation period – mainly due to longer ice ablation – is the main component in the overall increase in ablation. In addition, the last 25 yr have seen increases in ablation rates of 14 and 10% for snow and ice, respectively. A simple degree-day analysis can account for both the snow/ice melt rate rise and the lengthening of the ablation period as a function of higher air temperatures. From the same analysis, the equilibrium-line altitude of this 45° N latitude south-facing glacier has a sensitivity to temperature of +93 m °C−1 around its mean elevation of 3100 m a.s.l. over 6 decades. The sensitivity of summer balance to temperature is −0.62 m w.e. yr−1 °C−1 for a typical 125-day-long ablation season. Finally, the correlation of winter and summer mass balance terms with NAO anomalies is investigated. Singularly, highest values are obtained between winter NAO anomalies and summer balance. Winter NAO anomalies and winter balance and precipitation are almost disconnected. However, these results strongly depend on how the NAO signal is smoothed, so that the link between Sarennes mass balance seasonal terms and NAO signal remains tenuous and hard to interpret.
Radio and Facebook: The relationship between broadcast and social media software in the U.S., Germany, and Singapore
Authors: Freeman Bradley Carl , Klapczynski Julia , Wood Elliott
Published: January 2013

Since its inception, the Internet has been eyed with both hope and caution by traditional media outlets. For many years, radio looked to the Internet (Web 1.0) to extend their brand and increase awareness for their stations. Enter Facebook (Web 2.0), with its interactive ability to add friends and build an online community. How are radio stations using social media at this early point in the relationship? The results and the strategy to best build the radio/Facebook relationship are not uniform and the jury is still out on exactly how social media can benefit a station’s bottom line.
Online social networking skills: The social affordances approach to digital inequality
Authors: Hsieh Yuli Patrick
Published: January 2013

This paper sets out to develop a theoretical framework for examining implications of digital media uses for digital inequality in the domain of social interaction. First, by drawing on the social affordances perspective, this paper seeks to establish an additional dimension of digital skills, namely, online social networking skills. Furthermore, to explore the implications of interactional ICT use for digital inequality, this paper theorizes how people’s online social networking skills may condition their uses of various digital media for communication (i.e. communication multiplexity) and proposes two propositions for future empirical examination.
New records of pyrenocarpous lichenized fungi from Bulgaria
Authors: Shivarov Veselin V. , Stoykov Dimitar Y.
Published: January 2013

Five pyrenocarpous species of lichenized fungi, Acrocordia salweyi, Staurothele hymenogonia, Verrucaria praetermissa, V. viridula and Wahlenbergiella striatula, are reported for the first time from Bulgaria. Detailed descriptions, illustrations, and comments are provided.
Conocybe hausknechtii, a new species of sect. Pilosellae from the Western Caucasus, Russia
Authors: Malysheva Ekaterina F.
Published: January 2013

A new species, Conocybe hausknechtii, from the Western Caucasus, Russia is proposed here with detailed descriptions and illustrations.