Land-surface parameter optimisation using data assimilation techniques: The adJULES system V1.0

This is the final version of the article. Available from the European Geosciences Union (EGU) via the DOI in this record.Land-surface models (LSMs) are crucial components of the Earth system models (ESMs) that are used to make coupled climate-carbon cycle projections for the 21st century. The Joint UK Land Environment Simulator (JULES) is the land-surface model used in the climate and weather forecast models of the UK Met Office. JULES is also extensively used offline as a land-surface impacts tool, forced with climatologies into the future. In this study, JULES is automatically differentiated with respect to JULES parameters using commercial software from FastOpt, resulting in an analytical gradient, or adjoint, of the model. Using this adjoint, the adJULES parameter estimation system has been developed to search for locally optimum parameters by calibrating against observations. This paper describes adJULES in a data assimilation framework and demonstrates its ability to improve the model-data fit using eddy-covariance measurements of gross primary production (GPP) and latent heat (LE) fluxes. adJULES also has the ability to calibrate over multiple sites simultaneously. This feature is used to define new optimised parameter values for the five plant functional types (PFTs) in JULES. The optimised PFT-specific parameters improve the performance of JULES at over 85% of the sites used in the study, at both the calibration and evaluation stages. The new improved parameters for JULES are presented along with the associated uncertainties for each parameter.This work was supported by the UK Natural Environment Research Council (NERC) through the National Centre for Earth Observation (NCEO). This study used eddy-covariance data acquired by the FLUXNET community and in particular by the following networks: AmeriFlux (US Department of Energy, Biological and Environmental Research, Terrestrial Carbon Program (DE-FG02-04ER63917 and DE-FG02-04ER63911)), AfriFlux, AsiaFlux, CarboAfrica, CarboEuropeIP, CarboItaly, CarboMont, ChinaFlux, Fluxnet-Canada (supported by CFCAS, NSERC, BIOCAP, Environment Canada, and NRCan), GreenGrass, KoFlux, LBA, NECC, OzFlux, TCOSSiberia, USCCC. Support for eddy-covariance data harmonisation was provided by CarboEuropeIP, FAO-GTOS-TCO, iLEAPS, Max Planck Institute for Biogeochemistry, National Science Foundation, University of Tuscia, Université Laval and Environment Canada and US Department of Energy and the database development and technical support from Berkeley Water Center, Lawrence Berkeley National Laboratory, Microsoft Research eScience, Oak Ridge National Laboratory, University of California – Berkeley, University of Virginia. The authors are grateful to T. Kaminski and R. Giering from FastOpt for their contribution to the development of the adjoint model, and to M. Groenendijk, A. Harper, and the UK Met Office for processing and sharing their data. The authors are particularly grateful to two anonymous referees for their thoughtful and constructive reviews, which greatly improved this manuscript

Culture-negative bivalvular endocarditis with myocardial destruction in a patient with systemic lupus erythematosus: a case report

Culture-negative endocarditis has long been associated with systemic lupus erythematosus, but is usually asymptomatic or involves a single valve. We present a patient with destructive culture-negative endocarditis that remains without a microbial etiology despite an exhaustive workup using advanced diagnostic techniques in a patient with systemic lupus erythematosus

Borrelia recurrentis employs a novel multifunctional surface protein with anti-complement, anti-opsonic and invasive potential to escape innate immunity

Borrelia recurrentis, the etiologic agent of louse-borne relapsing fever in humans, has evolved strategies, including antigenic variation, to evade immune defence, thereby causing severe diseases with high mortality rates. Here we identify for the first time a multifunctional surface lipoprotein of B. recurrentis, termed HcpA, and demonstrate that it binds human complement regulators, Factor H, CFHR-1, and simultaneously, the host protease plasminogen. Cell surface bound factor H was found to retain its activity and to confer resistance to complement attack. Moreover, ectopic expression of HcpA in a B. burgdorferi B313 strain, deficient in Factor H binding proteins, protected the transformed spirochetes from complement-mediated killing. Furthermore, HcpA-bound plasminogen/plasmin endows B. recurrentis with the potential to resist opsonization and to degrade extracellular matrix components. Together, the present study underscores the high virulence potential of B. recurrentis. The elucidation of the molecular basis underlying the versatile strategies of B. recurrentis to escape innate immunity and to persist in human tissues, including the brain, may help to understand the pathological processes underlying louse-borne relapsing fever

Multispacer Sequence Typing Relapsing Fever Borreliae in Africa

In Africa, relapsing fevers are caused by four cultured species: Borrelia crocidurae, Borrelia duttonii, Borrelia hispanica and Borrelia recurrentis. These borreliae are transmitted by the bite of Ornithodoros soft ticks except for B. recurrentis which is transmitted by louse Pediculus humanus. They cause potentially undifferentiated fever infection and co-infection with malaria could also occur. The exact prevalence of each Borrelia is unknown and overlaps between B. duttonii and B. crocidurae have been reported. The lack of tools for genotyping these borreliae limits knowledge concerning their epidemiology. We developed multispacer sequence typing (MST) and applied it to blood specimens infected by B. recurrentis (30 specimens), B. duttonii (18 specimens) and B. crocidurae (13 specimens), delineating these 60 strains and the 3 type strains into 13 species-specific spacer types. B. crocidurae strains were classified into 8 spacer types, B. duttonii into 3 spacer types and B. recurrentis into 2 spacer types. These findings provide the proof-of-concept that that MST is a reliable tool for identification and genotyping relapsing fever borreliae in Africa

Likely Correlation between Sources of Information and Acceptability of A/H1N1 Swine-Origin Influenza Virus Vaccine in Marseille, France

BACKGROUND: In France, there was a reluctance to accept vaccination against the A/H1N1 pandemic influenza virus despite government recommendation and investment in the vaccine programme. METHODS AND FINDINGS: We examined the willingness of different populations to accept A/H1N1 vaccination (i) in a French hospital among 3315 employees immunized either by in-house medical personnel or mobile teams of MDs and (ii) in a shelter housing 250 homeless persons. Google was used to assess the volume of enquiries concerning incidence of influenza. We analyzed the information on vaccination provided by Google, the website of the major French newspapers, and PubMed. Two trust Surveys were used to assess public opinion on the trustworthiness of people in different professions. Paramedics were significantly more reluctant to accept immunisation than qualified medical staff. Acceptance was significantly increased when recommended directly by MDs. Anecdotal cases of directly observed severe infections were followed by enhanced acceptance of paramedical staff. Scientific literature was significantly more in favour of vaccination than Google and French newspaper websites. In the case of the newspaper websites, information correlated with their recognised political reputations, although they would presumably claim independence from political bias. The Trust Surveys showed that politicians were highly dis-trusted in contrast with doctors and pharmacists who were considered much more trustworthy. CONCLUSIONS: The low uptake of the vaccine could reflect failure to convey high quality medical information and advice relating to the benefits of being vaccinated. We believe that the media and internet contributed to this problem by raising concerns within the general population and that failure to involve GPs in the control programme may have been a mistake. GPs are highly regarded by the public and can provide face-to-face professional advice and information. The top-down strategy of vaccine programme management and information delivered by the Ministry of Health could have aggravated the problem, because the general population does not always trust politicians

The Genome of Borrelia recurrentis, the Agent of Deadly Louse-Borne Relapsing Fever, Is a Degraded Subset of Tick-Borne Borrelia duttonii

In an effort to understand how a tick-borne pathogen adapts to the body louse, we sequenced and compared the genomes of the recurrent fever agents Borrelia recurrentis and B. duttonii. The 1,242,163–1,574,910-bp fragmented genomes of B. recurrentis and B. duttonii contain a unique 23-kb linear plasmid. This linear plasmid exhibits a large polyT track within the promoter region of an intact variable large protein gene and a telomere resolvase that is unique to Borrelia. The genome content is characterized by several repeat families, including antigenic lipoproteins. B. recurrentis exhibited a 20.4% genome size reduction and appeared to be a strain of B. duttonii, with a decaying genome, possibly due to the accumulation of genomic errors induced by the loss of recA and mutS. Accompanying this were increases in the number of impaired genes and a reduction in coding capacity, including surface-exposed lipoproteins and putative virulence factors. Analysis of the reconstructed ancestral sequence compared to B. duttonii and B. recurrentis was consistent with the accelerated evolution observed in B. recurrentis. Vector specialization of louse-borne pathogens responsible for major epidemics was associated with rapid genome reduction. The correlation between gene loss and increased virulence of B. recurrentis parallels that of Rickettsia prowazekii, with both species being genomic subsets of less-virulent strains

Absence of convincing evidence of Coxiella burnetii infection in Chile: a cross-sectional serosurvey among healthy adults in four different regions

International audienceBackground: Coxiella burnetii is an important zoonotic pathogen of global distribution. Still, in most parts of South America including Chile, systematic epidemiological data are lacking. The presented study aims to determine the seroprevalence of Coxiella burnetii antibodies in healthy adults of four different regions in Chile. Methods: A cross-sectional study was performed, which included healthy adults living in rural and urban areas of four cities located in different regions in northern, central, and southern Chile. In urban sectors, households were chosen by double stratified random sampling, while in rural areas convenience sampling was performed. Serum specimens were taken and screened for the presence of IgG antibodies against C. burnetii phase II antigen using a commercial ELISA kit. Positive and indeterminate results were confirmed by a reference laboratory using indirect immunofluorescence assay (IFA). Results: A total of 1112 individuals were included. Of those, 8 were positive by ELISA, but only one sample was confirmed using IFA. Statistical analysis for population freedom from disease revealed a high probability that C. burnetii was absent in our study population. Conclusion: Our work provides the first epidemiological data on human Q fever in Chile indicating either a very low endemicity or the absence of this pathogen in the studied areas