How integrative modelling can break down disciplinary silos

This paper has been published in a peer-reviewed journal as: Kragt, M.E., Robson, B.J. & Macleod, C.J.A. (2013) Modellers’ roles in structuring integrative research projects. Environmental Modelling & Software, 39(1): 322-330. DOI: 10.1016/j.envsoft.2012.06.015Environmental modelling, Interdisciplinary research, Transdisciplinarity, Integration, Research Methods/ Statistical Methods, Q57, Y80, Z19,

Web technologies for environmental big data

Recent evolutions in computing science and web technology provide the environmental community with continuously expanding resources for data collection and analysis that pose unprecedented challenges to the design of analysis methods, workflows, and interaction with data sets. In the light of the recent UK Research Council funded Environmental Virtual Observatory pilot project, this paper gives an overview of currently available implementations related to web-based technologies for processing large and heterogeneous datasets and discuss their relevance within the context of environmental data processing, simulation and prediction. We found that, the processing of the simple datasets used in the pilot proved to be relatively straightforward using a combination of R, RPy2, PyWPS and PostgreSQL. However, the use of NoSQL databases and more versatile frameworks such as OGC standard based implementations may provide a wider and more flexible set of features that particularly facilitate working with larger volumes and more heterogeneous data sources

Woody plant encroachment into grasslands leads to accelerated erosion of previously stable organic carbon from dryland soils

Journal ArticleDrylands worldwide are experiencing rapid and extensive environmental change, concomitant with the encroachment of woody vegetation into grasslands. Woody encroachment leads to changes in both the structure and function of dryland ecosystems and has been shown to result in accelerated soil erosion and loss of soil nutrients. Covering 40% of the terrestrial land surface, dryland environments are of global importance, both as a habitat and a soil carbon store. Relationships between environmental change, soil erosion, and the carbon cycle are uncertain. There is a clear need to further our understanding of dryland vegetation change and impacts on carbon dynamics. Here two grass-to-woody ecotones that occur across large areas of the southwestern United States are investigated. This study takes a multidisciplinary approach, combining ecohydrological monitoring of structure and function and a dual-proxy biogeochemical tracing approach using the unique natural biochemical signatures of the vegetation. Results show that following woody encroachment, not only do these drylands lose significantly more soil and organic carbon via erosion but that this includes significant amounts of legacy organic carbon which would previously have been stable under grass cover. Results suggest that these dryland soils may not act as a stable organic carbon pool, following encroachment and that accelerated erosion of carbon, driven by vegetation change, has important implications for carbon dynamics.University of ExeterRothamsted Research North Wyk

Intensive management in grasslands causes diffuse water pollution at the farm scale

Arable land use is generally assumed to be the largest contributor to agricultural diffuse pollution. This study adds to the growing evidence that conventional temperate intensively managed lowland grasslands contribute significantly to soil erosion and diffuse pollution rates. This is the first grassland study to monitor hydrological characteristics and multiple pollutant fluxes (suspended sediment [SS] and the macronutrients: total oxidized nitrogen-N [TONN], total phosphorus [TP], and total carbon [TC]) at high temporal resolution (monitoring up to every 15 min) over 1 yr. Monitoring was conducted across three fields (6.5-7.5 ha) on the North Wyke Farm Platform, UK. The estimated annual erosion rates (up to 527.4 kg ha-1), TP losses (up to 0.9 kg ha-1), and TC losses (up to 179 kg ha-1) were similar to or exceeded the losses reported for other grassland, mixed land-use, and arable sites. Annual yields of TONN (up to 3 kg ha-1) were less than arable land-use fluxes and earlier grassland N studies, an important result as the study site is situated within a Nitrate Vulnerable Zone. The high-resolution monitoring allowed detailed "system's functioning" understanding of hydrological processes, mobilization- transport pathways of individual pollutants, and the changes of the relative importance of diffuse pollutants through flow conditions and time. Suspended sediment and TP concentrations frequently exceeded water quality guidelines recommended by the European Freshwater Fisheries Directive (25 mg L-1) and the European Water Framework Directive (0.04 mg soluble reactive P L-1), suggesting that intensively managed grasslands pose a significant threat to receiving surface waters. Such sediment and nutrient losses from intensively managed grasslands should be acknowledged in land management guidelines and advice for future compliance with surface water quality standards.NERC-Case PhD awardUK Biotechnology and Biological Sciences Research Counci

Understanding spatial variability of soil properties: a key step in establishing field- to farm-scale agro-ecosystem experiments

PublishedNo abstract is available for this article.NERCBBSR

Learning how to model ecosystem trade-offs at the farm scale

Paper from: International Environmental Modelling and Software Society (iEMSs) 2010 International Congress on Environmental Modelling and Software Modelling for Environment’s Sake, Fifth Biennial Meeting, Ottawa, Canada David A. Swayne, Wanhong Yang, A. A. Voinov, A. Rizzoli, T. Filatova (Eds.) http://www.iemss.org/iemss2010/index.php?n=Main.ProceedingsThe full conference proceedings are available from: http://www.iemss.org/iemss2010/The ecosystem service framework provides a forum for scientists from a range of disciplines to communicate and work together alongside other key stakeholders. However to be effective, place-based comparison of the tradeoffs of ecosystem services need further development. These place-based comparisons are vital in agricultural systems due to the increasing global demand for food production, coupled with the realization that this should be achieved with minimal negative impact on the environment. The farm is the logical unit of management in agricultural systems and hence there is a need for ecosystem tradeoff assessments at the farm scale. We have carried out a literature review of thetradeoffs in the delivery of ecosystem services from intensively managed temperate grassland systems. Building on this work, we are now setting up a farm scale experiment to examine the tradeoffs, identified from the refereed literature, as requiring further investigation due to either limited or conflicting evidence. To facilitate an improved understanding of these tradeoffs we need to learn how to model them, based on previous and current modelling frameworks and coupled with improved knowledge of international best practice. Fundamentally, this requires a dialogue between modellers and field scientist

Data summarizing monitoring and evaluation for three European environmental policies in 9 cases across Europe

Subject area: Environmental policy. More specific subject area: Monitoring; evaluation; European Policy; Water Framework Directive; Natura 2000; Agri-Environment Schemes. Type of data: Tables and text. How data was acquired: Review and analysis of any publicly-available information on monitoring programs. Data format: Summarized, analyzed. Experimental factors: In 2017 the authors searched for publicly available about monitoring programs associated with 3 policy areas: the Water Framework Directive, Natura 2000 and Agri-Environment Schemes under the Common Agricultural Policy. Authors from each organization searched for information about monitoring in the country or region of the organization where they are based: Catalonia (Spain), Estonia, Finland, Flanders (Belgium), Hungary, Romania, Slovakia, Scotland (UK), Sweden. Internet searches of grey and academic literature were used: some authors also contacted policy contacts for advice about where this information could be found, but did not use any information that was not already publicly available. Experimental features: Bibliographic information on the information sources was recorded (see reference list below), and each author team searched for and summarized information about monitoring and evaluation according to a standard template (see below). Data source location: Catalonia (Spain), Estonia, Finland, Flanders (Belgium), Hungary, Romania, Slovakia, Scotland (UK), Sweden. Data accessibility: All of the data are within this article. Related research article: Companion paper to: Waylen, K.A.; Blackstock, K.L.; van Hulst. F.; Damian, C.; Horváth, F.; Johnson, R.; Kanka, R.; Külvik, M.; Macleod, C.; Meissner, C.; Oprina-Pavelescu, M.; Pino, J.; Primmer, E.; Rîșnoveanu, G.; Šatalová, B.; Silander, J.; Špulerová, J.; Suškevičs, M.; Van Uytvanck, J. 2019. Policy-driven monitoring and evaluation: does it support adaptive management of socio-ecological systems? Science of the Total Environment, 662: 373–384 [2].Value of the data • The data provide the first overview of monitoring and evaluation (M&E) practices carried out by a selection European member states and regions, under 3 European environmental policies (the Water Framework Directive, the Natura 2000 network of protected areas, and Agri-Environment Schemes under the Common Agricultural Policy). • The data permit comparison across cases as well as across policies, and so provide a baseline for comparative studies. • The source of information used to describe monitoring in each case are provided, thus providing a baseline for researchers seeking more in-depth analyses.The data presented in this DiB article provide an overview of Monitoring and Evaluation (M&E) carried out for 3 European environmental policies (the Water Framework Directive, the Natura 2000 network of protected areas, and Agri-Environment Schemes implemented under the Common Agricultural Policy), as implemented in 9 cases (Catalonia (Spain), Estonia, Finland, Flanders (Belgium), Hungary, Romania, Slovakia, Scotland (UK), Sweden). These data are derived from reports and documents about monitoring programs that were publicly-available online in 2017. The literature on M&E to support adaptive management structured the issues that have been extracted and summarized. The data is related to the research article entitled “Policy-driven monitoring and evaluation: does it support adaptive management of socio-ecological systems?” [Stem et al., 2005]. The information provides a first overview of monitoring and evaluation that has been implemented in response to key European environmental policies. It provides a structured overview that permits a comparison of cases and policies and can assist other scholars and practitioners working on monitoring and evaluation

Policy-driven monitoring and evaluation : Does it support adaptive management of socio-ecological systems?

Inadequate Monitoring and Evaluation (M&E) is often thought to hinder adaptive management of socio-ecological systems. A key influence on environmental management practices are environmental policies: however, their consequences for M&E practices have not been well-examined. We examine three policy areas - the Water Framework Directive, the Natura 2000 Directives, and the Agri-Environment Schemes of the Common Agricultural Policy - whose statutory requirements influence how the environment is managed and monitored across Europe. We use a comparative approach to examine what is monitored, how monitoring is carried out, and how results are used to update management, based on publicly available documentation across nine regional and national cases. The requirements and guidelines of these policies have provided significant impetus for monitoring: however, we find this policy-driven M&E usually does not match the ideals of what is needed to inform adaptive management. There is a tendency to focus on understanding state and trends rather than tracking the effect of interventions; a focus on specific biotic and abiotic indicators at the expense of understanding system functions and processes, especially social components; and limited attention to how context affects systems, though this is sometimes considered via secondary data. The resulting data are sometimes publicly-accessible, but it is rarely clear if and how these influence decisions at any level, whether this be in the original policy itself or at the level of measures such as site management plans. Adjustments to policy-driven M&E could better enable learning for adaptive management, by reconsidering what supports a balanced understanding of socio-ecological systems and decision-making. Useful strategies include making more use of secondary data, and more transparency in data-sharing and decision-making. Several countries and policy areas already offer useful examples. Such changes are essential given the influence of policy, and the urgency of enabling adaptive management to safeguard socio-ecological systems. Highlights • Policy strongly influences Monitoring & Evaluation (M&E) of socio-ecological systems. • We examine M&E of 3 major European policies in 9 regional and national cases. • Policy-driven M&E is imperfect versus ideals of M&E to support adaptive management. • Attention needed to systems, social issues, sharing data, and sharing intended uses. • Examples from across Europe and different policies offer ideas for improvement

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Multiancestry analysis of the HLA locus in Alzheimer’s and Parkinson’s diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s disease (PD) and Alzheimer’s disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues