Soil Borne Human Diseases

Soils are home to a remarkable array of biodiversity with some estimates stating that 25% of the Earth’s species find their home in the soil. Of these organisms, the vast majority are not of any threat to human health, but rather function to provide numerous ecosystem services which emerge through the multitude of complex interactions between organisms within the soil and even with the soil itself. These ecosystem services range from those which are vital for maintaining life on Earth, such as the formation of soil, the cycling of nutrient with the result of maintaining soil fertility, and filtering of water (MEA 2005), as well as provision of useful compounds such as antibiotics, the majority of which have been isolated from soil organisms. However, soils also contain microorganisms which are capable of causing diseases in humans, either as opportunistic pathogens which take advantage of susceptible individuals such as those who are immuno-compromised, as well as obligate pathogens which require infecting humans in order to complete their life-cycles, but which are capable of surviving within the soil for extended periods of time before infecting humans who come into contact with contaminated soil. This report aims to give an overview of soil borne diseases of humans, including information from the WHO and ECDC on infection and mortality rates within the EU27, and providing a discussion of factors which may affect the incidence of such diseases such as land management practices and the use of antibiotics in livestock before moving on to highlight areas of future research which are needed to further investigate this important and yet understudied area.JRC.H.7-Land management and natural hazard

Biochar Application to Soils - A Critical Scientific Review of Effects on Soil Properties, Processes and Functions

Biochar application to soils is being considered as a means to sequester carbon (C) while concurrently improving soil functions. This report reviews the evidence for potential effects of biochar incorporation into soils on soil properties and processes with implications for agronomic and environmental functions. Further to this, while beyond the main scope of this report, an overview of the main environmental and occupational health issues associated to biochar production and handling, and the socio-economic implications is given. Extrapolation of reported results must be done with caution, owing to the relatively small number of studies reported in the primary literature, when compared to possible instigation of biochar application to soils on a national or European scale . To try and bridge the gap between small scale, controlled experiments and large scale implementation of biochar application to a range of soil types across a range of different climates, a statistical meta-analysis was undertaken. A full search of the scientific literature led to a compilation of studies used for a meta-analysis of the effects of biochar application to soils and plant productivity. Results showed a small overall, but statistically significant, positive effect of biochar application to soils on plant productivity. The greatest positive effects were seen on acidic free-draining soils with other soil types, specifically calcarosols showing no significant effect (either positive or negative). This suggests that one of the main mechanisms behind the reported positive effects of biochar application to soils on plant productivity may be a liming effect although further research is needed to confirm this hypothesis. There is currently a lack of data concerning the effects of biochar application to soils on other soil functions. This means that although these are qualitatively and comprehensively discussed in this report, a robust meta-analysis on such effects is not possible currently. Effects that are expected (both positive and negative) include nutrient leaching to ground/surface waters, soil water retention, soil water repellency, N2O and CH4 emissions, albedo and soil biological activity although insufficient data are available at present to accurately quantify any of these effects or to report a consensus on their direction (either positive or negative). Preliminary evidence has also been reported concerning a possible priming effect whereby accelerated decomposition of soil organic matter occurs upon biochar addition to soil. This has the potential to both harm crop productivity in the long term due to loss of soil organic matter, as well as releasing more CO2 into the atmosphere as increased quantities of soil organic matter is respired from the soil. This is an area which requires urgent further research and is discussed in more detail in this report.JRC.DDG.H.7-Land management and natural hazard

Small-molecule modulators of Hedgehog signaling: identification and characterization of Smoothened agonists and antagonists

BACKGROUND: The Hedgehog (Hh) signaling pathway is vital to animal development as it mediates the differentiation of multiple cell types during embryogenesis. In adults, Hh signaling can be activated to facilitate tissue maintenance and repair. Moreover, stimulation of the Hh pathway has shown therapeutic efficacy in models of neuropathy. The underlying mechanisms of Hh signal transduction remain obscure, however: little is known about the communication between the pathway suppressor Patched (Ptc), a multipass transmembrane protein that directly binds Hh, and the pathway activator Smoothened (Smo), a protein that is related to G-protein-coupled receptors and is capable of constitutive activation in the absence of Ptc. RESULTS: We have identified and characterized a synthetic non-peptidyl small molecule, Hh-Ag, that acts as an agonist of the Hh pathway. This Hh agonist promotes cell-type-specific proliferation and concentration-dependent differentiation in vitro, while in utero it rescues aspects of the Hh-signaling defect in Sonic hedgehog-null, but not Smo-null, mouse embryos. Biochemical studies with Hh-Ag, the Hh-signaling antagonist cyclopamine, and a novel Hh-signaling inhibitor Cur61414, reveal that the action of all these compounds is independent of Hh-protein ligand and of the Hh receptor Ptc, as each binds directly to Smo. CONCLUSIONS: Smo can have its activity modulated directly by synthetic small molecules. These studies raise the possibility that Hh signaling may be regulated by endogenous small molecules in vivo and provide potent compounds with which to test the therapeutic value of activating the Hh-signaling pathway in the treatment of traumatic and chronic degenerative conditions

Comparison of Small- and Large-Footprint Lidar Characterization of Tropical Forest Aboveground Structure and Biomass: A Case Study From Central Gabon

NASA's Global Ecosystem Dynamic Investigation (GEDI) mission has been designed to measure forest structure using lidar waveforms to sample the earth's vegetation while in orbit aboard the International Space Station. In this paper, we used airborne large-footprint (LF) lidar measurements to simulate GEDI observations from which we retrieved ground elevation, vegetation height, and aboveground biomass (AGB). GEDI-like product accuracy was then assessed by comparing them to similar products derived from airborne small-footprint (SF) lidar measurements. The study focused on tropical forests and used data collected during the NASA and European Space Agency (ESA) AfriSAR ground and airborne campaigns in the Lope National Park in Central Gabon. The measurements covered a gradient of successional stages of forest development with different height, canopy density, and topography. The comparison of the two sensors shows that LF lidar waveforms and simulated waveforms from SF lidar are equivalent in their ability to estimate ground elevation (RMSE = 0.5 m, bias = 0.29 m) and maximum forest height (RMSE = 2.99 m, bias = 0.24 m) over the study area. The difference in the AGB estimated from both lidar instruments at the 1-ha spatial scale is small over the entire study area (RMSE = 6.34 Mg·ha-1, bias = 11.27 Mg·ha-1) and the bias is attributed to the impact of ground slopes greater than 10–20° on the LF lidar measurements of forest height. Our results support the ability of GEDILF lidar to measure the complex structure of humid tropical forests and provide AGB estimates comparable to SF-derived ones

Exploring the relation between remotely sensed vertical canopy structure and tree species diversity in Gabon

Mapping tree species diversity is increasingly important in the face of environmental change and biodiversity conservation. We explore a potential way of mapping this diversity by relating forest structure to tree species diversity in Gabon. First, we test the relation between canopy height, as a proxy for niche volume, and tree species diversity. Then, we test the relation between vertical canopy structure, as a proxy for vertical niche occupation, and tree species diversity. We use large footprint full-waveform airborne lidar data collected across four study sites in Gabon (Lopé, Mabounié, Mondah, and Rabi) in combination with in situ estimates of species richness (S) and Shannon diversity (H′). Linear models using canopy height explained 44% and 43% of the variation in S and H′ at the 0.25 ha resolution. Linear models using canopy height and the plant area volume density profile explained 71% of this variation. We demonstrate applications of these models by mapping S and H′ in Mondah using a simulated GEDI-TanDEM-X fusion height product, across the four sites using wall-to-wall airborne lidar data products, and across and between the study sites using ICESat lidar waveforms. The modeling results are encouraging in the context of developing pan-tropical structure diversity models applicable to data from current and upcoming spaceborne remote sensing missions

The Role of Forest Elephants in Shaping Tropical Forest-Savanna Coexistence

Forest edges that border savanna are dynamic features of tropical landscapes. Although the role of fire in determining edge dynamics has been relatively well explored, the role of mega-herbivores, specifically elephants, has not received as much attention. We investigated the role of forest elephants in shaping forest edges of the forest–savanna mosaic in Lopé National Park, Gabon. Using forty camera traps, we collected 1.2 million images between May 2016 and June 2017. These images were classified by over 10,000 volunteers through an online citizen science platform. These data were combined with a 33-year phenology dataset on elephant-favoured fruiting tree species, and field measurements of elephant browsing preferences and damage. Our results showed a strong relationship between forest elephant density at the forest edge and fruit availability. When fruit availability was high, elephant density at the edge reached values nearly double the highest densities ever reported in any other part of the landscape (7.5 elephants km−2 in this study vs the previous highest estimate of 4 elephants km−2). The highest elephant densities occurred at the end of the dry season, but even outside of this high density period elephant density at the forest edge (2.4 elephants km−2) was more than double what other studies estimate for forest interiors with low human hunting pressure (1 elephant km−2). We found forest elephants to be selective browsers, but their browsing was non-destructive (in contrast to savanna elephants) and had little effect on tree size demography. Elephant paths acted as firebreaks during savanna burning, making them inadvertent protectors of the fire-sensitive forest and contributing to the stabilising feedbacks that allow forest and savanna to coexist in tropical landscapes

Cobalt-based molecular electrocatalysis of nitrile reduction: evolving sustainability beyond hydrogen

Two new cobalt bis-iminopyridines, [Co(DDP)(H2O)2](NO3)2 (1, DDP = cis-[1,3-bis(2-pyridinylenamine)] cyclohexane) and [Co(cis-DDOP)(NO3)](NO3) (2, cis-DDOP = cis-3,5-bis[(2- Pyridinyleneamin]-trans-hydroxycyclohexane) electrocatalyse the 4-proton, 4-electron reduction of acetonitrile to ethylamine. For 1, this reduction occurs in preference to reduction of protons to H2. A coordinating hydroxyl proton relay in 2 reduces the yield of ethylamine and biases the catalytic system back towards H2

The NASA AfriSAR campaign: Airborne SAR and lidar measurements of tropical forest structure and biomass in support of current and future space missions

International audienceIn 2015 and 2016, the AfriSAR campaign was carried out as a collaborative effort among international space and National Park agencies (ESA, NASA, ONERA, DLR, ANPN and AGEOS) in support of the upcoming ESA BIOMASS, NASA-ISRO Synthetic Aperture Radar (NISAR) and NASA Global Ecosystem Dynamics Initiative (GEDI) missions. The NASA contribution to the campaign was conducted in 2016 with the NASA LVIS (Land Vegetation and Ice Sensor) Lidar, the NASA L-band UAVSAR (Uninhabited Aerial Vehicle Synthetic Aperture Radar). A central motivation for the AfriSAR deployment was the common AGBD estimation requirement for the three future spaceborne missions, the lack of sufficient airborne and ground calibration data covering the full range of ABGD in tropical forest systems, and the intercomparison and fusion of the technologies. During the campaign, over 7000 km2 of waveform Lidar data from LVIS and 30,000 km2 of UAVSAR data were collected over 10 key sites and transects. In addition, field measurements of forest structure and biomass were collected in sixteen 1-hectare sized plots. The campaign produced gridded Lidar canopy structure products, gridded aboveground biomass and associated uncertainties, Lidar based vegetation canopy cover profile products, Polarimetric Interferometric SAR and Tomographic SAR products and field measurements. Our results showcase the types of data products and scientific results expected from the spaceborne Lidar and SAR missions; we also expect that the AfriSAR campaign data will facilitate further analysis and use of waveform lidar and multiple baseline polarimetric SAR datasets for carbon cycle, biodiversity, water resources and more applications by the greater scientific community

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Percutaneous Coronary Intervention Versus Medical Therapy for Chronic Total Occlusion of Coronary Arteries:A Systematic Review and Meta-Analysis

PURPOSE OF REVIEW: Chronic total occlusion (CTO) of the coronary arteries is a significant clinical problem and has traditionally been treated by medical therapy or coronary artery bypass grafting. Recent studies have examined percutaneous coronary intervention (PCI) as an alternative option. RECENT FINDINGS: This systematic review and meta-analysis compared medical therapy to PCI for treating CTOs. PubMed and Embase were searched from their inception to March 2019 for studies that compared medical therapy and PCI for clinical outcomes in patients with CTOs. Quality of the included studies was assessed by Newcastle-Ottawa scale. The results were pooled by DerSimonian and Laird random- or fixed-effect models as appropriate. Heterogeneity between studies and publication bias was evaluated by I2 index and Egger's regression, respectively. Of the 703 entries screened, 17 studies were included in the final analysis. This comprised 11,493 participants. Compared to PCI, medical therapy including randomized and observational studies was significantly associated with higher risk of all-cause mortality (risk ratio (RR) 1.99, 95% CI 1.38-2.86), cardiac mortality (RR 2.36 (1.97-2.84)), and major adverse cardiac event (RR 1.25 (1.03-1.51)). However, no difference in the rate of myocardial infarction and repeat revascularization procedures was observed between the two groups. Univariate meta-regression demonstrated multiple covariates as independent moderating factors for myocardial infarction and repeat revascularization but not cardiac death and all-cause mortality. However, when only randomized studies were included, there was no difference in overall mortality or cardiac death. In CTO, when considering randomized and observational studies, medical therapy might be associated with a higher risk of mortality and myocardial infarction compared to PCI treatment