Modelling diverse root density dynamics and deep nitrogen uptake — a simple approach

We present a 2-D model for simulation of root density and plant nitrogen (N) uptake for crops grown in agricultural systems, based on a modification of the root density equation originally proposed by Gerwitz and Page in J Appl Ecol 11:773–781, (1974). A root system form parameter was introduced to describe the distribution of root length vertically and horizontally in the soil profile. The form parameter can vary from 0 where root density is evenly distributed through the soil profile, to 8 where practically all roots are found near the surface. The root model has other components describing root features, such as specific root length and plant N uptake kinetics. The same approach is used to distribute root length horizontally, allowing simulation of root growth and plant N uptake in row crops. The rooting depth penetration rate and depth distribution of root density were found to be the most important parameters controlling crop N uptake from deeper soil layers. The validity of the root distribution model was tested with field data for white cabbage, red beet, and leek. The model was able to simulate very different root distributions, but it was not able to simulate increasing root density with depth as seen in the experimental results for white cabbage. The model was able to simulate N depletion in different soil layers in two field studies. One included vegetable crops with very different rooting depths and the other compared effects of spring wheat and winter wheat. In both experiments variation in spring soil N availability and depth distribution was varied by the use of cover crops. This shows the model sensitivity to the form parameter value and the ability of the model to reproduce N depletion in soil layers. This work shows that the relatively simple root model developed, driven by degree days and simulated crop growth, can be used to simulate crop soil N uptake and depletion appropriately in low N input crop production systems, with a requirement of few measured parameters

Temporal proteomic analysis of HIV infection reveals remodelling of the host phosphoproteome by lentiviral Vif variants

Viruses manipulate host factors to enhance their replication and evade cellular restriction. We used multiplex tandem mass tag (TMT)-based whole cell proteomics to perform a comprehensive time course analysis of >6500 viral and cellular proteins during HIV infection. To enable specific functional predictions, we categorized cellular proteins regulated by HIV according to their patterns of temporal expression. We focussed on proteins depleted with similar kinetics to APOBEC3C, and found the viral accessory protein Vif to be necessary and sufficient for CUL5-dependent proteasomal degradation of all members of the B56 family of regulatory subunits of the key cellular phosphatase PP2A (PPP2R5A-E). Quantitative phosphoproteomic analysis of HIV-infected cells confirmed Vif-dependent hyperphosphorylation of >200 cellular proteins, particularly substrates of the aurora kinases. The ability of Vif to target PPP2R5 subunits is found in primate and non-primate lentiviral lineages, and remodeling of the cellular phosphoproteome is therefore a second ancient and conserved Vif function.This work was supported by a Wellcome Trust PRF (101835/Z/13/Z) to PJL and RTF to NJM (093964/Z/10/Z), NHSBT and the NIHR Cambridge BRC, a Wellcome Trust Strategic Award to CIMR, and the Addenbrooke’s Charitable Trust

Oxygen uptake and denitrification in soil aggregates

A mathematical model of oxygen uptake by bacteria in agricultural soils is presented with the goal of predicting anaerobic regions in which denitrification occurs. In an environment with a plentiful supply of oxygen, microorganisms consume oxygen through normal respiration. When the local oxygen concentration falls below a threshold level, denitrification may take place leading to the release of nitrous oxide, a potent agent for global warming. A two-dimensional model is presented in which one or more circular soil aggregates are located at a distance below the ground-level at which the prevailing oxygen concentration is prescribed. The level of denitrification is estimated by computing the area of any anaerobic cores which may develop in the interior of the aggregates. The oxygen distribution throughout the model soil is calculated first for an aggregated soil for which the ratio of the oxygen diffusivities between an aggregate and its surround is small via an asymptotic analysis. Second, the case of a non-aggregated soil featuring one or more microbial hotspots, for which the diffusion ratio is arbitrary, is examined numerically using the boundary-element method. Calculations with multiple aggregates demonstrate a sheltering effect whereby some aggregates receive less oxygen than their neighbours. In the case of an infinite regular triangular network representing an aggregated soil, it is shown that there is an optimal inter-aggregate spacing which minimises the total anaerobic core area

Mycobacterium tuberculosis cords within lymphatic endothelial cells to evade host immunity

The ability of Mycobacterium tuberculosis to form serpentine cords is intrinsically related to its virulence, but specifically how M. tuberculosis cording contributes to pathogenesis remains obscure. Here, we show that several M. tuberculosis clinical isolates form intracellular cords in primary human lymphatic endothelial cells (hLECs) in vitro and in the lymph nodes of patients with tuberculosis. We identified via RNA-Seq a transcriptional program that activated, in infected-hLECs, cell survival and cytosolic surveillance of pathogens pathways. Consistent with this, cytosolic access was required for intracellular M. tuberculosis cording. Mycobacteria lacking ESX-1 type VII secretion system or phthiocerol dimycocerosates expression, which failed to access the cytosol, were indeed unable to form cords within hLECs. Finally, we show that M. tuberculosis cording is a size-dependent mechanism used by the pathogen to avoid its recognition by cytosolic sensors and evade either resting or IFN-γ–induced hLEC immunity. These results explain the long-standing association between M. tuberculosis cording and virulence and how virulent mycobacteria use intracellular cording as strategy to successfully adapt and persist in the lymphatic tracts

Boundary Interactions of Rough non-Gaussian Surfaces

Surface topography is important as it influences contact load-carrying capacity and operational efficiency through generated friction, as well as wear. As a result, a plethora of machining processes and surface finishing techniques have been developed. These processes yield topographies, which are often non-Gaussian, with roughness parameters that alter hierarchically according to their interaction heights. They are also subject to change through processes of rapid initial running-in wear as well as any subsequent gradual wear and embedding. The stochastic nature of the topography makes for complexity of contact mechanics of rough surfaces, which was first addressed by the pioneering work of Greenwood and Williamson, which among other issues is commemorated by this contribution. It is shown that their seminal contribution, based on idealised Gaussian topography and mean representation of asperity geometry should be extended for practical applications where surfaces are often non-Gaussian, requiring the inclusion of surface-specific data which also evolve through process of wear. The paper highlights a process dealing with practical engineering surfaces from laboratory-based testing using a sliding tribometer to accelerated fired engine testing for high performance applications of cross-hatched honed cylinder liners. Such an approach has not hitherto been reported in literature

Myths and Facts About Static Application Security Testing Tools: An Action Research at Telenor Digital

It is claimed that integrating agile and security in practice is challenging. There is the notion that security is a heavy process, requires expertise, and consumes developers’ time. These contrast with the agile vision. Regardless of these challenges, it is important for organizations to address security within their agile processes since critical assets must be protected against attacks. One way is to integrate tools that could help to identify security weaknesses during implementation and suggest methods to refactor them. We used quantitative and qualitative approaches to investigate the efficiency of the tools and what they mean to the actual users (i.e. developers) at Telenor Digital. Our findings, although not surprising, show that several barriers exist both in terms of tool’s performance and developers’ perceptions. We suggest practical ways for improvement.publishedVersio

Crack-Like Processes Governing the Onset of Frictional Slip

We perform real-time measurements of the net contact area between two blocks of like material at the onset of frictional slip. We show that the process of interface detachment, which immediately precedes the inception of frictional sliding, is governed by three different types of detachment fronts. These crack-like detachment fronts differ by both their propagation velocities and by the amount of net contact surface reduction caused by their passage. The most rapid fronts propagate at intersonic velocities but generate a negligible reduction in contact area across the interface. Sub-Rayleigh fronts are crack-like modes which propagate at velocities up to the Rayleigh wave speed, VR, and give rise to an approximate 10% reduction in net contact area. The most efficient contact area reduction (~20%) is precipitated by the passage of slow detachment fronts. These fronts propagate at anomalously slow velocities, which are over an order of magnitude lower than VR yet orders of magnitude higher than other characteristic velocity scales such as either slip or loading velocities. Slow fronts are generated, in conjunction with intersonic fronts, by the sudden arrest of sub-Rayleigh fronts. No overall sliding of the interface occurs until either of the slower two fronts traverses the entire interface, and motion at the leading edge of the interface is initiated. Slip at the trailing edge of the interface accompanies the motion of both the slow and sub-Rayleigh fronts. We might expect these modes to be important in both fault nucleation and earthquake dynamics.Comment: 19 page, 5 figures, to appear in International Journal of Fractur

Infarct Size Following Treatment With Second‐ Versus Third‐Generation P2Y₁₂ Antagonists in Patients With Multivessel Coronary Disease at ST‐Segment Elevation Myocardial Infarction in the CvLPRIT Study

Background-Third-generation P2Y12 antagonists (prasugrel and ticagrelor) are recommended in guidelines on ST-segment elevation myocardial infarction. Mechanisms translating their more potent antiplatelet activity into improved clinical outcomes versus the second-generation P2Y12 antagonist clopidogrel are unclear. The aim of this post hoc analysis of the Complete Versus Lesion-Only PRImary PCI Trial-CMR (CvLPRIT-CMR) substudy was to assess whether prasugrel and ticagrelor were associated with reduced infarct size compared with clopidogrel in patients undergoing primary percutaneous coronary intervention. Methods and Results-CvLPRIT-CMR was a multicenter, prospective, randomized, open-label, blinded end point trial in 203 STsegment elevation myocardial infarction patients with multivessel disease undergoing primary percutaneous coronary intervention with either infarct-related artery-only or complete revascularization. P2Y12 inhibitors were administered according to local guidelines. The primary end point of infarct size on cardiovascular magnetic resonance was not significantly different between the randomized groups. P2Y12 antagonist administration was not randomized. Patients receiving clopidogrel (n=70) compared with those treated with either prasugrel or ticagrelor (n=133) were older (67.8±12 versus 61.5±10 years, P < 0.001), more frequently had hypertension (49% versus 29%, P=0.007), and tended to have longer symptom-to-revascularization time (234 versus 177 minutes, P=0.05). Infarct size (median 16.1% [quartiles 1-3, 10.5-27.7%] versus 12.1% [quartiles 1-3, 4.8-20.7%] of left ventricular mass, P=0.013) and microvascular obstruction incidence (65.7% versus 48.9%, P=0.022) were significantly greater in patients receiving clopidogrel. Infarct size remained significantly different after adjustment for important covariates using both generalized linear models (P=0.048) and propensity score matching (P=0.025). Conclusions-In this analysis of CvLPRIT-CMR, third-generation P2Y12 antagonists were associated with smaller infarct size and lower microvascular obstruction incidence versus the second-generation P2Y12 antagonist clopidogrel for ST-segment elevation myocardial infarction