The impact of grazing cattle on soil physical properties and nutrient concentrations in overland flow from pasture, Part B

This report has been prepared as part of the Environmental Research Technological Development and Innovation Programme 2000–2006. The programme is financed by the Irish Government under the National Development Plan 2000–2006.End of project reportThe loss of nutrients from agricultural land to water bodies is a serious concern in many countries. To gain information on the contribution of grazing animals to diffuse nutrient losses from pasture areas to water, this study looked at the impact of cattle on nutrient concentrations in overland flow and on soil hydrology (bulk density, macroporosity and resistance to penetration). Rainfall simulations to produce overland flow were conducted and soil physical measurements were taken on experimental plots assigned to one of two treatments: 1) cattle had unrestricted access to the plot; 2) cattle could graze the plot but they could neither walk on the plot area nor deposit excrements on it. Areas to which the cattle had free access were characterised by 57%-83% lower macroporosity, by 8%-17% higher bulk density and by 27%-50% higher resistance to penetration than areas from which the cattle were excluded. The nutrients in overland flow from grassland that were affected by the presence of grazing animals were mainly the particulate nitrogen, the organic phosphorus and the potassium concentrations. Overall, the presence of cattle had a longer lasting effect on the soil hydrological parameters measured than on the nutrient concentrations in overland flow.Environmental Protection Agenc

Agriculture, meteorology and water quality in Ireland: a regional evaluation of pressures and pathways of nutrient loss to water

peer-reviewedThe main environmental impact of Irish agriculture on surface and ground water quality is the potential transfer of nutrients to water. Soil water dynamics mediate the transport of nutrients to water, and these dynamics in turn depend on agro-meteorological conditions, which show large variations between regions, seasons and years. In this paper we quantify and map the spatio-temporal variability of agro-meteorological factors that control nutrient pressures and pathways of nutrient loss. Subsequently, we evaluate their impact on the water quality of Irish rivers. For nitrogen, pressure and pathways factors coincide in eastern and southern areas, which is reflected in higher nitrate levels of the rivers in these regions. For phosphorus, pathway factors are most pronounced in north-western parts of the country. In south-eastern parts, high pressure factors result in reduced biological water quality. These regional differences require that farm practices be customised to reflect the local risk of nutrient loss to water. Where pathways for phosphorus loss are present almost year-round—as is the case in most of the north-western part of the country—build-up of pressures should be prevented, or ameliorated where already high. In south-eastern areas, spatio-temporal coincidence of nutrient pressures and pathways should be prevented, which poses challenges to grassland management

The impact of the grazing animal on phosphorus, nitrogen, potassium and suspended solids loss from grazed pastures, Part A

Teagasc wishes to acknowledge the support of the Environmental Research Technological Development and Innovation (ERTDI) Programme under the Productive Sector Operational Programme which was financed by the Irish Government under the National Development Plan 2000-2006.End of project reportIn Ireland 90% of the 4.2 million ha of farmland is grassland. Phosphorus deficiency limited grassland production in Ireland and this was corrected by chemical fertiliser use in the 1960s and 1970s. The increased inputs of fertilisers led to increased intensification of grassland with a doubling of grass yield and of grazing animal numbers, from about 3 million to over 6 million livestock units. There is little information on relative contribution of increased chemical fertiliser use compared to increased grazing animal numbers on phosphorus loss to water. The main objective of this study was to obtain information on nutrient loss, particularly phosphorus, in overland flow from cut and grazed grassland plots, with a range of soil test phosphorus levels over three years and implications.Environmental Protection Agenc

Pathways for nutrient loss to water with emphasis on phosphorus

Teagasc wishes to acknowledge the support of the Environmental Research Technological Development and Innovation (ERTDI) Programme under the Productive Sector Operational Programme which was financed by the Irish Government under the National Development Plan 2000-2006.End of project reportThe main objective of this project was to study phosphorus (P) loss from agricultural land under a range of conditions in Ireland, to quantify the main factors influencing losses and make recommendations on ways to reduce these losses. This report is a synthesis of the main conclusions and recommendations from the results of the studies. The final reports from the individual sub-projects in this project are available from the EPA (www.epa.ie).Environmental Protection Agenc

Quantification of phosphorus loss from soil to water.

End of Project ReportThe methods, results and discussion of the project are in five separate sections, 4.1) Phosphorus (P) export from agricultural grassland with overland flow and drainage water (Johnstown Castle); 4.2) Phosphorus export from farm in Dripsey catchment, Co. Cork (NMP); 4.3) Hydrometeorological aspects of farm in Dripsey Catchment (NMP); 4.4) Phosphorus desorption from Irish soils; 4.5) National phosphorus model. Most of the field and laboratory studies were carried out at Johnstown Castle, at UCC and the field site in the Dripsey catchment. The main aim of the project was to quantify the loss of P from soil to water where point source contributions from farmyards were not high. This involved the construction of hydrologically isolated field sites where the quantity of overland flow and the P concentrations for different runoff events from the fields could be measured. In addition, 90 soil samples representative of Irish soils were collected and analysed for the different factors influencing soil adsorption and desorption of P. These results, in addition to catchment data, were used as a first attempt at developing a model that could be used to help predict P loss from soil to water at a catchment scale. The study in the Dripsey was on a farm where water flow and P levels at two points in a stream were measured. The hydrometeorology at this site was also studied. At Johnstown Castle, three overland flow sites, of the order of one hectare each, and one subsurface flow site were studied for P loss to water.Environmental Protection Agency

Cushing's Syndrome and Fetal Features Resurgence in Adrenal Cortex–Specific Prkar1a Knockout Mice

Carney complex (CNC) is an inherited neoplasia syndrome with endocrine overactivity. Its most frequent endocrine manifestation is primary pigmented nodular adrenocortical disease (PPNAD), a bilateral adrenocortical hyperplasia causing pituitary-independent Cushing's syndrome. Inactivating mutations in PRKAR1A, a gene encoding the type 1 α-regulatory subunit (R1α) of the cAMP–dependent protein kinase (PKA) have been found in 80% of CNC patients with Cushing's syndrome. To demonstrate the implication of R1α loss in the initiation and development of PPNAD, we generated mice lacking Prkar1a specifically in the adrenal cortex (AdKO). AdKO mice develop pituitary-independent Cushing's syndrome with increased PKA activity. This leads to autonomous steroidogenic genes expression and deregulated adreno-cortical cells differentiation, increased proliferation and resistance to apoptosis. Unexpectedly, R1α loss results in improper maintenance and centrifugal expansion of cortisol-producing fetal adrenocortical cells with concomitant regression of adult cortex. Our data provide the first in vivo evidence that loss of R1α is sufficient to induce autonomous adrenal hyper-activity and bilateral hyperplasia, both observed in human PPNAD. Furthermore, this model demonstrates that deregulated PKA activity favors the emergence of a new cell population potentially arising from the fetal adrenal, giving new insight into the mechanisms leading to PPNAD

Genetic Determination and Linkage Mapping of Plasmodium falciparum Malaria Related Traits in Senegal

Plasmodium falciparum malaria episodes may vary considerably in their severity and clinical manifestations. There is good evidence that host genetic factors contribute to this variability. To date, most genetic studies aiming at the identification of these genes have used a case/control study design for severe malaria, exploring specific candidate genes. Here, we performed a family-based genetic study of falciparum malaria related phenotypes in two independent longitudinal survey cohorts, as a first step towards the identification of genes and mechanisms involved in the outcome of infection. We studied two Senegalese villages, Dielmo and Ndiop that differ in ethnicity, malaria transmission and endemicity. We performed genome-scan linkage analysis of several malaria-related phenotypes both during clinical attacks and asymptomatic infection. We show evidence for a strong genetic contribution to both the number of clinical falciparum malaria attacks and the asymptomatic parasite density. The asymptomatic parasite density showed linkage to chromosome 5q31 (LOD = 2.26, empirical p = 0.0014, Dielmo), confirming previous findings in other studies. Suggestive linkage values were also obtained at three additional chromosome regions: the number of clinical malaria attacks on chromosome 5p15 (LOD = 2.57, empirical p = 0.001, Dielmo) and 13q13 (LOD = 2.37, empirical p = 0.0014 Dielmo), and the maximum parasite density during asymptomatic infection on chromosome 12q21 (LOD = 3.1, empirical p<10−4, Ndiop). While regions of linkage show little overlap with genes known to be involved in severe malaria, the four regions appear to overlap with regions linked to asthma or atopy related traits, suggesting that common immune related pathways may be involved

Frontotemporal dementia and its subtypes: a genome-wide association study

SummaryBackground Frontotemporal dementia (FTD) is a complex disorder characterised by a broad range of clinical manifestations, differential pathological signatures, and genetic variability. Mutations in three genes—MAPT, GRN, and C9orf72—have been associated with FTD. We sought to identify novel genetic risk loci associated with the disorder. Methods We did a two-stage genome-wide association study on clinical FTD, analysing samples from 3526 patients with {FTD} and 9402 healthy controls. To reduce genetic heterogeneity, all participants were of European ancestry. In the discovery phase (samples from 2154 patients with {FTD} and 4308 controls), we did separate association analyses for each {FTD} subtype (behavioural variant FTD, semantic dementia, progressive non-fluent aphasia, and {FTD} overlapping with motor neuron disease FTD-MND), followed by a meta-analysis of the entire dataset. We carried forward replication of the novel suggestive loci in an independent sample series (samples from 1372 patients and 5094 controls) and then did joint phase and brain expression and methylation quantitative trait loci analyses for the associated (p&lt;5 × 10−8) single-nucleotide polymorphisms. Findings We identified novel associations exceeding the genome-wide significance threshold (p&lt;5 × 10−8). Combined (joint) analyses of discovery and replication phases showed genome-wide significant association at 6p21.3, \{HLA\} locus (immune system), for rs9268877 (p=1·05 × 10−8; odds ratio=1·204 95% \{CI\} 1·11–1·30), rs9268856 (p=5·51 × 10−9; 0·809 0·76–0·86) and rs1980493 (p value=1·57 × 10−8, 0·775 0·69–0·86) in the entire cohort. We also identified a potential novel locus at 11q14, encompassing RAB38/CTSC (the transcripts of which are related to lysosomal biology), for the behavioural \{FTD\} subtype for which joint analyses showed suggestive association for rs302668 (p=2·44 × 10−7; 0·814 0·71–0·92). Analysis of expression and methylation quantitative trait loci data suggested that these loci might affect expression and methylation in cis. Interpretation Our findings suggest that immune system processes (link to 6p21.3) and possibly lysosomal and autophagy pathways (link to 11q14) are potentially involved in FTD. Our findings need to be replicated to better define the association of the newly identified loci with disease and to shed light on the pathomechanisms contributing to FTD. Funding The National Institute of Neurological Disorders and Stroke and National Institute on Aging, the Wellcome/MRC Centre on Parkinson's disease, Alzheimer's Research UK, and Texas Tech University Health Sciences Center

Identification of heavy-flavour jets with the CMS detector in pp collisions at 13 TeV

Many measurements and searches for physics beyond the standard model at the LHC rely on the efficient identification of heavy-flavour jets, i.e. jets originating from bottom or charm quarks. In this paper, the discriminating variables and the algorithms used for heavy-flavour jet identification during the first years of operation of the CMS experiment in proton-proton collisions at a centre-of-mass energy of 13 TeV, are presented. Heavy-flavour jet identification algorithms have been improved compared to those used previously at centre-of-mass energies of 7 and 8 TeV. For jets with transverse momenta in the range expected in simulated $\mathrm{t}\overline{\mathrm{t}}$ events, these new developments result in an efficiency of 68% for the correct identification of a b jet for a probability of 1% of misidentifying a light-flavour jet. The improvement in relative efficiency at this misidentification probability is about 15%, compared to previous CMS algorithms. In addition, for the first time algorithms have been developed to identify jets containing two b hadrons in Lorentz-boosted event topologies, as well as to tag c jets. The large data sample recorded in 2016 at a centre-of-mass energy of 13 TeV has also allowed the development of new methods to measure the efficiency and misidentification probability of heavy-flavour jet identification algorithms. The heavy-flavour jet identification efficiency is measured with a precision of a few per cent at moderate jet transverse momenta (between 30 and 300 GeV) and about 5% at the highest jet transverse momenta (between 500 and 1000 GeV)

Particle-flow reconstruction and global event description with the CMS detector

The CMS apparatus was identified, a few years before the start of the LHC operation at CERN, to feature properties well suited to particle-flow (PF) reconstruction: a highly-segmented tracker, a fine-grained electromagnetic calorimeter, a hermetic hadron calorimeter, a strong magnetic field, and an excellent muon spectrometer. A fully-fledged PF reconstruction algorithm tuned to the CMS detector was therefore developed and has been consistently used in physics analyses for the first time at a hadron collider. For each collision, the comprehensive list of final-state particles identified and reconstructed by the algorithm provides a global event description that leads to unprecedented CMS performance for jet and hadronic tau decay reconstruction, missing transverse momentum determination, and electron and muon identification. This approach also allows particles from pileup interactions to be identified and enables efficient pileup mitigation methods. The data collected by CMS at a centre-of-mass energy of 8 TeV show excellent agreement with the simulation and confirm the superior PF performance at least up to an average of 20 pileup interactions