Extinctions of aculeate pollinators in Britain and the role of large-scale agricultural changes

Pollinators are fundamental to maintaining both biodiversity and agricultural productivity, but habitat destruction, loss of flower resources, and increased use of pesticides are causing declines in their abundance and diversity. Using historical records we assessed the rate of extinction of bee and flower-visiting wasp species in Britain, from the mid 19th century to the present. The most rapid phase of extinction appears to be related to changes in agricultural policy and practice beginning in the 1920s, before the agricultural intensification prompted by the Second World War, often cited as the most important driver of biodiversity loss in Britain. Slowing of the extinction rate from the 1960s onwards may be due to prior loss of the most sensitive species and/or effective conservation programs

Biodiversity and decomposition in experimental grassland ecosystems

We examined the impact of biodiversity on litter decomposition in an experiment that manipulated plant species richness. Using biomass originating from the experimental species richness gradient and from a species used as a common substrate, we measured rates of decomposition in litterbags in two locations: in situ in the experiment plots and in an adjacent common garden. This allowed us to separate the effects of litter quality and decomposition location on decomposition. We found that plant species richness had a significant, but minor negative effect on the quality (nitrogen concentration) of the biomass. Neither litter type nor location had a consistent effect on the rate of carbon and nitrogen loss over a 1-year period. Thus, the increased productivity and corresponding lower soil available nitrogen levels observed in high diversity plots do not lead to faster litter decomposition or faster nitrogen turnover. This supports the hypothesis that increased productivity corresponding with higher species richness results in increased litter production, higher standing litter pools and a negative feedback on productivity, because of an increased standing nitrogen pool in the litter

The Role of Litter Quality Feedbacks in Terrestrial Nitrogen and Phosphorus Cycling

Many studies in ecosystem ecology argue for strong control of litter quality over nitrogen (N) cycling. We developed a model for temperate grasslands to test the importance of litter quality in decomposition for N and phosphorus (P) cycling based on the following premises. First, terrestrial N and P cycling differ fundamentally because N is a structural component of the soil organic matter (SOM), whereas P is not. Secondly, SOM has a much lower C:N ratio than litter inputs. Thirdly, litter decomposition follows an exponential decay with 20% of the original litter mass turning into SOM. Fourth, litter N concentration shows an exponential increase during decomposition, whereas P does not change and is released proportionally to the litter mass. Based on these premises we constructed a model which shows that 0.75% N is a critical initial litter concentration at which concentration all N is immobilized and no N is released from the litter. Thus at 0.75% N of the litter all net N mineralization is through SOM decomposition and not through litter decomposition. Phosphorus, in contrast, is primarily released in the early stages of litter decomposition. Empirical tests of these model predictions support the applicability of the model to temperate grassland ecosystems. This model predicts that N mineralization from SOM is much more important than mineralization from litter and that plant litter quality differences alone cannot explain ecosystem N cycling patterns. Phosphorus, in contrast, does cycle largely through litter decomposition, and plant litter quality differences are the dominant factor in determining ecosystem P cycling feedbacks

Estimating Survival in Patients with Operable Skeletal Metastases: An Application of a Bayesian Belief Network

BACKGROUND: Accurate estimations of life expectancy are important in the management of patients with metastatic cancer affecting the extremities, and help set patient, family, and physician expectations. Clinically, the decision whether to operate on patients with skeletal metastases, as well as the choice of surgical procedure, are predicated on an individual patient's estimated survival. Currently, there are no reliable methods for estimating survival in this patient population. Bayesian classification, which includes bayesian belief network (BBN) modeling, is a statistical method that explores conditional, probabilistic relationships between variables to estimate the likelihood of an outcome using observed data. Thus, BBN models are being used with increasing frequency in a variety of diagnoses to codify complex clinical data into prognostic models. The purpose of this study was to determine the feasibility of developing bayesian classifiers to estimate survival in patients undergoing surgery for metastases of the axial and appendicular skeleton. METHODS: We searched an institution-owned patient management database for all patients who underwent surgery for skeletal metastases between 1999 and 2003. We then developed and trained a machine-learned BBN model to estimate survival in months using candidate features based on historical data. Ten-fold cross-validation and receiver operating characteristic (ROC) curve analysis were performed to evaluate the BNN model's accuracy and robustness. RESULTS: A total of 189 consecutive patients were included. First-degree predictors of survival differed between the 3-month and 12-month models. Following cross validation, the area under the ROC curve was 0.85 (95% CI: 0.80-0.93) for 3-month probability of survival and 0.83 (95% CI: 0.77-0.90) for 12-month probability of survival. CONCLUSIONS: A robust, accurate, probabilistic naïve BBN model was successfully developed using observed clinical data to estimate individualized survival in patients with operable skeletal metastases. This method warrants further development and must be externally validated in other patient populations

How does flow in a pipe become turbulent?

The transition to turbulence in pipe flow does not follow the scenario familiar from Rayleigh-Benard or Taylor-Couette flow since the laminar profile is stable against infinitesimal perturbations for all Reynolds numbers. Moreover, even when the flow speed is high enough and the perturbation sufficiently strong such that turbulent flow is established, it can return to the laminar state without any indication of the imminent decay. In this parameter range, the lifetimes of perturbations show a sensitive dependence on initial conditions and an exponential distribution. The turbulence seems to be supported by three-dimensional travelling waves which appear transiently in the flow field. The boundary between laminar and turbulent dynamics is formed by the stable manifold of an invariant chaotic state. We will also discuss the relation between observations in short, periodically continued domains, and the dynamics in fully extended puffs.Comment: for the proceedings of statphys 2

Surgery of non-spinal skeletal metastases in renal cell carcinoma

Background and purpose - Surgery for metastases of renal cell carcinoma has increased in the last decade. It carries a risk of massive blood loss, as tumors are hypervascular and the surgery is often extensive. Preoperative embolization is believed to facilitate surgery. We evaluated the effect of preoperative embolization and resection margin on intraoperative blood loss, operation time, and survival in non-spinal skeletal metastases of renal cell carcinoma. Patients and methods - This retrospective study involved 144 patients, 56 of which were treated preoperatively with embolization. The primary outcome was intraoperative blood loss. We also identified factors affecting operating time and survival. Results - We did not find statistically significant effects on intraoperative blood loss of preoperative embolization of skeletal non-spinal metastases. Pelvic localization and large tumor size increased intraoperative blood loss. Marginal resection compared to intralesional resection, nephrectomy, level of hemoglobin, and solitary metastases were associated with better survival. Interpretation - Tumor size, but not embolization, was an independent factor for intraoperative blood loss. Marginal resection rather than intralesional resection should be the gold standard treatment for skeletal metastases in non-spinal renal cell carcinoma, especially in the case of a solitary lesion, as this improved the overall survival.Peer reviewe

Large differences in carbohydrate degradation and transport potential among lichen fungal symbionts.

Lichen symbioses are thought to be stabilized by the transfer of fixed carbon from a photosynthesizing symbiont to a fungus. In other fungal symbioses, carbohydrate subsidies correlate with reductions in plant cell wall-degrading enzymes, but whether this is true of lichen fungal symbionts (LFSs) is unknown. Here, we predict genes encoding carbohydrate-active enzymes (CAZymes) and sugar transporters in 46 genomes from the Lecanoromycetes, the largest extant clade of LFSs. All LFSs possess a robust CAZyme arsenal including enzymes acting on cellulose and hemicellulose, confirmed by experimental assays. However, the number of genes and predicted functions of CAZymes vary widely, with some fungal symbionts possessing arsenals on par with well-known saprotrophic fungi. These results suggest that stable fungal association with a phototroph does not in itself result in fungal CAZyme loss, and lends support to long-standing hypotheses that some lichens may augment fixed CO2 with carbon from external sources

Order-of-magnitude speedup for steady states and traveling waves via Stokes preconditioning in Channelflow and Openpipeflow

Steady states and traveling waves play a fundamental role in understanding hydrodynamic problems. Even when unstable, these states provide the bifurcation-theoretic explanation for the origin of the observed states. In turbulent wall-bounded shear flows, these states have been hypothesized to be saddle points organizing the trajectories within a chaotic attractor. These states must be computed with Newton's method or one of its generalizations, since time-integration cannot converge to unstable equilibria. The bottleneck is the solution of linear systems involving the Jacobian of the Navier-Stokes or Boussinesq equations. Originally such computations were carried out by constructing and directly inverting the Jacobian, but this is unfeasible for the matrices arising from three-dimensional hydrodynamic configurations in large domains. A popular method is to seek states that are invariant under numerical time integration. Surprisingly, equilibria may also be found by seeking flows that are invariant under a single very large Backwards-Euler Forwards-Euler timestep. We show that this method, called Stokes preconditioning, is 10 to 50 times faster at computing steady states in plane Couette flow and traveling waves in pipe flow. Moreover, it can be carried out using Channelflow (by Gibson) and Openpipeflow (by Willis) without any changes to these popular spectral codes. We explain the convergence rate as a function of the integration period and Reynolds number by computing the full spectra of the operators corresponding to the Jacobians of both methods.Comment: in Computational Modelling of Bifurcations and Instabilities in Fluid Dynamics, ed. Alexander Gelfgat (Springer, 2018