Modeling Subdiffusion Using Reaction Diffusion Systems

In many types of media, and in particular within living cells or within their membranes, diffusing species do not follow Fick's laws, but instead show transient subdiffusive behavior. Formulating spatiotemporal models that take this behavior into account is a delicate matter, as one is faced with the choice of resorting either to fractional calculus or to microscopic descriptions. In this article, we provide an alternative designed to be easier to tackle analytically and numerically than the existing approaches. Specifically, starting from the Continuous Time Random Walk model, we construct linear reaction diffusion systems that can be used as components within such a model, and which capture the defining properties of subdiffusion. We show how to impose physically relevant parameters, and prove stability and mass conservation. While applications to cellular biology are our main motivation, our approach is abstract, and should thus be applicable to any situation where anomalous subdiffusion is observed

Belowground DNA-based techniques: untangling the network of plant root interactions

Contains fulltext : 91591.pdf (publisher's version ) (Closed access)7 p

Coalbed Methane Development in Indonesia: Design and Economic Analysis of Upstream Petroleum Fiscal Policy

Due to increasing demand for natural gas in Indonesia, the Government now promotes exploration for coalbed methane (CBM). Currently, Indonesia has 453 trillion cubic feet (TCF) of CBM reserves. However, CBM development in the country is still in the exploration phase, with significant under-investment. To attract investors, a tailored Production Sharing Contracts (PSC) regime is required. Based on a combination of Factor Analysis (FA), Discounted Cash Flows (DCF) and Parameter Sensitivity Analysis, the research explores an optimal scenario of a company’s share of revenue that optimised CBM development contracts. We find that a combination of 5 years straight line depreciation (SLD), 5% First Tranche Petroleum (FTP), 78% Contractor Share (CS) and 35% income tax best spreads the risk of CBM development and exploitation between the government and the contractor. This combination is a more suitable PSC regime for developing CBM in an early stage of the industry. Therefore, the Government must cede some taxes during exploration to incentivise CBM development. Three PSCs regimes are thus required to fully develop and exploit CBM, including exploration, transitional and exploitation phase PSCs which better match contractor risks and returns and ensure reasonable certainty of contractor cost recovery

Plant diversity and root traits benefit physical properties key to soil function in grasslands

Plant diversity loss impairs ecosystem functioning, including important effects on soil. Most studies that have explored plant diversity effects belowground, however, have largely focused on biological processes. As such, our understanding of how plant diversity impacts the soil physical environment remains limited, despite the fundamental role soil physical structure plays in ensuring soil function and ecosystem service provision. Here, in both a glasshouse and a long-term field study, we show that high plant diversity in grassland systems increases soil aggregate stability, a vital structural property of soil, and that root traits play a major role in determining diversity effects. We also reveal that the presence of particular plant species within mixed communities affects an even wider range of soil physical processes, including hydrology and soil strength regimes. Our results indicate that alongside well-documented effects on ecosystem functioning, plant diversity and root traits also benefit essential soil physical properties

Effect of four plant species on soil 15N-access and herbage yield in temporary agricultural grasslands

Positive plant diversity-productivity relationships have been reported for experimental semi-natural grasslands (Cardinale et al. 2006; Hector et al. 1999; Tilman et al. 1996) as well as temporary agricultural grasslands (Frankow-Lindberg et al. 2009; Kirwan et al. 2007; Nyfeler et al. 2009; Picasso et al. 2008). Generally, these relationships are explained, on the one hand, by niche differentiation and facilitation (Hector et al. 2002; Tilman et al. 2002) and, on the other hand, by greater probability of including a highly productive plant species in high diversity plots (Huston 1997). Both explanations accept that diversity is significant because species differ in characteristics, such as root architecture, nutrient acquisition and water use efficiency, to name a few, resulting in composition and diversity being important for improved productivity and resource use (Naeem et al. 1994; Tilman et al. 2002). Plant diversity is generally low in temporary agricultural grasslands grown for ruminant fodder production. Grass in pure stands is common, but requires high nitrogen (N) inputs. In terms of N input, two-species grass-legume mixtures are more sustainable than grass in pure stands and consequently dominate low N input grasslands (Crews and Peoples 2004; Nyfeler et al. 2009; Nyfeler et al. 2011). In temperate grasslands, N is often the limiting factor for productivity (Whitehead 1995). Plant available soil N is generally concentrated in the upper soil layers, but may leach to deeper layers, especially in grasslands that include legumes (Scherer-Lorenzen et al. 2003) and under conditions with surplus precipitation (Thorup-Kristensen 2006). To improve soil N use efficiency in temporary grasslands, we propose the addition of deep-rooting plant species to a mixture of perennial ryegrass and white clover, which are the most widespread forage plant species in temporary grasslands in a temperate climate (Moore 2003). Perennial ryegrass and white clover possess relatively shallow root systems (Kutschera and Lichtenegger 1982; Kutschera and Lichtenegger 1992) with effective rooting depths of <0.7 m on a silt loamy site (Pollock and Mead 2008). Grassland species, such as lucerne and chicory, grow their tap-roots into deep soil layers and exploit soil nutrients and water in soil layers that the commonly grown shallow-rooting grassland species cannot reach (Braun et al. 2010; Skinner 2008). Chicory grown as a catch crop after barley reduced the inorganic soil N down to 2.5 m depth during the growing season, while perennial ryegrass affected the inorganic soil N only down to 1 m depth (Thorup-Kristensen 2006). Further, on a Wakanui silt loam in New Zealand chicory extracted water down to 1.9 m and lucerne down to 2.3 m soil depth, which resulted in greater herbage yields compared with a perennial ryegrass-white clover mixture, especially for dryland plots (Brown et al. 2005). There is little information on both the ability of deep- and shallow-rooting grassland species to access soil N from different vertical soil layers and the relation of soil N-access and herbage yield in temporary agricultural grasslands. Therefore, the objective of the present work was to test the hypotheses 1) that a mixture comprising both shallow- and deep-rooting plant species has greater herbage yields than a shallow-rooting binary mixture and pure stands, 2) that deep-rooting plant species (chicory and lucerne) are superior in accessing soil N from 1.2 m soil depth compared with shallow-rooting plant species, 3) that shallow-rooting plant species (perennial ryegrass and white clover) are superior in accessing soil N from 0.4 m soil depth compared with deep-rooting plant species, 4) that a mixture of deep- and shallow-rooting plant species has greater access to soil N from three soil layers compared with a shallow-rooting two-species mixture and that 5) the leguminous grassland plants, lucerne and white clover, have a strong impact on grassland N acquisition, because of their ability to derive N from the soil and the atmosphere

Stroke Reduction in Elderly Patients With Atrial Fibrillation Through Utilization of an Anticoagulation Toolkit in the Primary Care Setting

Patients, especially those older than 65-years-old, do not receive adequate assessment or management of atrial fibrillation, resulting in higher ischemic stroke rates and worse outcomes related to strokes. Oral anticoagulation is recommended indefinitely for patients with atrial fibrillation and a moderate to high risk of stroke; yet this population is not receiving oral anticoagulation consistently. Factors such as overexaggerated bleeding risk in the elderly, the lack of head-to-head studies comparing anticoagulants, cost, patient compliance, safety, lab monitoring, and reversal agents convolute the process of prescribing anticoagulation for atrial fibrillation. Variations exist with assessing bleeding risk and stroke risk for every patient through reliable tools such as HAS-BLED and CHA2DS2-VASc scores, respectively, and translating these scores into practice. Due to these inconsistencies and the lack of a comprehensive, universal guideline for assessment and management of atrial fibrillation, this topic was selected for a capstone project. A retrospective chart review was completed on 100 patients to assess the current practice of diagnosing atrial fibrillation and treating with anticoagulation in the primary care setting. Through utilization of two rounds of the Delphi method, expert opinion, and the recommendations of national and international guidelines, an evidence-based anticoagulation toolkit was created and modified to guide primary care providers on improving diagnosis of atrial fibrillation and enhanced initiation and maintenance of oral anticoagulation to reduce the incidence of stroke in elderly patients with atrial fibrillation. The Anticoagulation for Atrial Fibrillation Toolkit is a four-step, simplified guideline to guide providers on improved diagnosis and treatment of AF; it is supported by four algorithms: CHA2DS-VASc score, HAS-BLED score, comparison of anticoagulants, and patient specific factors influencing selection of anticoagulant. Additionally, this toolkit offers in one document a summary of additional information and resources for providers to improve the overall management of atrial fibrillation. The chart reviews demonstrated gaps between evidence and practice, predominantly a lack of utilization of CHA2DS2 VASc and HAS-BLED scores to assess for stroke and bleeding risk, respectively, in patients with atrial fibrillation, poor continued monitoring of AF in the primary care setting, a disconnect between the treatment plan and providers, and the absence of consistently diagnosing an irregular pulse as AF through an EKG. Round 1 of the Delphi survey assessed providers’ comfort level and expertise with prescribing anticoagulants and diagnosing and managing AF and Round 2 evaluated the anticoagulation toolkit and how its incorporation could influence practice. Results from Round 1 were utilized to revise the evidence-based anticoagulation toolkit; data analysis concluded 70% consensus was achieved on at least 6 of the 10 questions. Even without 70% consensus, the researcher incorporated provider expertise, suggestions, and requests into the anticoagulation toolkit. In Round 2, data analysis of greater than 70% consensus suggested the Anticoagulation for Atrial Fibrillation Toolkit was evidence based, user-friendly, promoted safety and efficacy of anticoagulation, and could positively impact practice; however, the toolkit was too extensive and lengthy. A thorough evaluation concluded this capstone project successfully addressed the following problem statement: In adult patients with atrial fibrillation older than 65 years old and a moderate to high risk of stroke, how effective is an anticoagulation toolkit in guiding primary care providers on (a) diagnosing atrial fibrillation and (b) initiating and maintaining oral anticoagulation safely, to reduce the incidence of ischemic stroke? The comprehensive literature review not only provided extensive background information on atrial fibrillation and anticoagulation but also highlighted key references to first compare evidence to practice (analyze patient chart reviews) and then utilize these identified gaps to translate evidence into practice (create the anticoagulation toolkit). Furthermore, the PARIHS framework and RE-AIM model evaluated the ability to effectively facilitate the results from this research project into practice. Additionally, this capstone project met all five criteria of the EC as PIE model, concluding this was a successful Doctor of Nursing Practice capstone project. A future extension of this project suggests evaluation of patient outcomes with AF, predominantly stroke incidence, subsequent to implementation of this toolkit in the primary care setting

Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity

There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil-borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below-ground environment has generally been treated as a ‘black box’ in biodiversity experiments, leaving these fungi unidentified. * Using next generation sequencing and pathogenicity assays, we analysed the community composition of root-associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil-borne fungi, plant diversity and productivity. * Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species-specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity. * Our work provides strong evidence for host specificity and negative density-dependent effects of root-associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity-ecosystem functioning relationships