Saprolegnia diclina IIIA and S. parasitica employ different infection strategies when colonizing eggs of Atlantic salmon, Salmo salar L.

Acknowledgements The work has been funded by the European Commission through the EU Marie Curie ITN project SAPRO (238550) (MMS, AW). We would also like to acknowledge support from the BBSRC and the University of Aberdeen (PvW) and Landcatch and AquaGen for providing salmon eggs. Elin Rolen's assistance with sequencing of the strains is highly appreciated.Peer reviewedPublisher PD

Morphing Ensemble Kalman Filters

A new type of ensemble filter is proposed, which combines an ensemble Kalman filter (EnKF) with the ideas of morphing and registration from image processing. This results in filters suitable for nonlinear problems whose solutions exhibit moving coherent features, such as thin interfaces in wildfire modeling. The ensemble members are represented as the composition of one common state with a spatial transformation, called registration mapping, plus a residual. A fully automatic registration method is used that requires only gridded data, so the features in the model state do not need to be identified by the user. The morphing EnKF operates on a transformed state consisting of the registration mapping and the residual. Essentially, the morphing EnKF uses intermediate states obtained by morphing instead of linear combinations of the states.Comment: 17 pages, 7 figures. Added DDDAS references to the introductio

A high efficiency, low background detector for measuring pair-decay branches in nuclear decay

We describe a high efficiency detector for measuring electron-positron pair transitions in nuclei. The device was built to be insensitive to gamma rays and to accommodate high overall event rates. The design was optimized for total pair kinetic energies up to about 7 MeV.Comment: Accepted for publication by Nucl. Inst. & Meth. in Phys. Res. A (NIM A

Evaluating Data Assimilation Algorithms

Data assimilation leads naturally to a Bayesian formulation in which the posterior probability distribution of the system state, given the observations, plays a central conceptual role. The aim of this paper is to use this Bayesian posterior probability distribution as a gold standard against which to evaluate various commonly used data assimilation algorithms. A key aspect of geophysical data assimilation is the high dimensionality and low predictability of the computational model. With this in mind, yet with the goal of allowing an explicit and accurate computation of the posterior distribution, we study the 2D Navier-Stokes equations in a periodic geometry. We compute the posterior probability distribution by state-of-the-art statistical sampling techniques. The commonly used algorithms that we evaluate against this accurate gold standard, as quantified by comparing the relative error in reproducing its moments, are 4DVAR and a variety of sequential filtering approximations based on 3DVAR and on extended and ensemble Kalman filters. The primary conclusions are that: (i) with appropriate parameter choices, approximate filters can perform well in reproducing the mean of the desired probability distribution; (ii) however they typically perform poorly when attempting to reproduce the covariance; (iii) this poor performance is compounded by the need to modify the covariance, in order to induce stability. Thus, whilst filters can be a useful tool in predicting mean behavior, they should be viewed with caution as predictors of uncertainty. These conclusions are intrinsic to the algorithms and will not change if the model complexity is increased, for example by employing a smaller viscosity, or by using a detailed NWP model

On dimension reduction in Gaussian filters

A priori dimension reduction is a widely adopted technique for reducing the computational complexity of stationary inverse problems. In this setting, the solution of an inverse problem is parameterized by a low-dimensional basis that is often obtained from the truncated Karhunen-Loeve expansion of the prior distribution. For high-dimensional inverse problems equipped with smoothing priors, this technique can lead to drastic reductions in parameter dimension and significant computational savings. In this paper, we extend the concept of a priori dimension reduction to non-stationary inverse problems, in which the goal is to sequentially infer the state of a dynamical system. Our approach proceeds in an offline-online fashion. We first identify a low-dimensional subspace in the state space before solving the inverse problem (the offline phase), using either the method of "snapshots" or regularized covariance estimation. Then this subspace is used to reduce the computational complexity of various filtering algorithms - including the Kalman filter, extended Kalman filter, and ensemble Kalman filter - within a novel subspace-constrained Bayesian prediction-and-update procedure (the online phase). We demonstrate the performance of our new dimension reduction approach on various numerical examples. In some test cases, our approach reduces the dimensionality of the original problem by orders of magnitude and yields up to two orders of magnitude in computational savings

A prospective multicentre study in Sweden and Norway of mental distress and psychiatric morbidity in head and neck cancer patients

A Swedish/Norwegian head and neck cancer study was designed to assess prospectively the levels of mental distress and psychiatric morbidity in a heterogeneous sample of newly diagnosed head and neck cancer patients. A total of 357 patients were included. The mean age was 63 years, and 72% were males. The patients were asked to answer the HAD scale (the Hospital Anxiety and Depression scale) six times during 1 year. The number of possible or probable cases of anxiety or depression disorder was calculated according to standardized cut-offs. Approximately one-third of the patients scored as a possible or probable case of a major mood disorder at each measurement point during the study year. There were new cases of anxiety or depression at each time point. The anxiety level was highest at diagnosis, while depression was most common during treatment. Females were more anxious than males at diagnosis, and patients under 65 years of age scored higher than those over 65. Patients with lower performance status and more advanced disease reported higher levels of mental distress and more often scored as a probable or possible cases of psychiatric disorder. Our psychometric analyses supported the two-dimensional structure and stability of the HAD scale. The HAD scale seems to be the method of choice for getting valid information about the probability of mood disorder in head and neck cancer populations. The prevalence of psychiatric morbidity found in this study emphasizes the importance of improved diagnosis and treatment

Impact of HPV-associated p16-expression on radiotherapy outcome in advanced oropharynx and non-oropharynx cancer

AbstractBackground and purposeHPV is found in head and neck cancer from all sites with a higher prevalence in oropharynx cancer (OPC) compared to non-OPC. HPV/p16-status has a significant impact on radiotherapy (RT) outcome in advanced OPC, but less is known about the influence in non-OPC. We analyzed HPV-associated p16-expression in a cohort of patients with stage III–IV pharynx and larynx cancer treated with primary, curatively intended (chemo-)RT, aiming to test the hypothesis that the impact of HPV/p16 also extends to tumors of non-oropharyngeal origin.Material and methods1294 patients enrolled in previously conducted DAHANCA-trials between 1992 and 2012 were identified. Tumors were evaluated by p16-immunohistochemistry and classified as positive in case of staining in >70% of tumors cells.ResultsThirty-eight percent (490/1294) of the tumors were p16-positive with a significantly higher frequency in OPC (425/815) than in non-OPC (65/479), p<.0001. In OPC p16-positivity significantly improved loco-regional control (LRC) (adjusted HR [95% CI]: 0.43 [0.32–0.57]), event-free survival (EFS) (HR 0.44 [0.35–0.56]), and overall survival (OS) (HR: 0.38 [0.29–0.49]), respectively, compared with p16-negativity. In non-OPC no prognostic impact of p16-status was found for either endpoint: LRC (HR: 1.13 [0.75–1.70]), EFS (HR: 1.06 [0.76–1.47]), and OS (HR: 0.82 [0.59–1.16]).ConclusionsThe independent influence of HPV-associated p16-expression in advanced OPC treated with primary RT was confirmed. However, RT-outcome in the group of non-OPC did not differ by tumor p16-status, indicating that the prognostic impact may be restricted to OPC only

Femoral artery thrombosis after internal fixation of a transverse acetabular fracture in a patient with osteogenesis imperfecta type I

Osteogenesis imperfecta is a genetic disorder characterized by increased susceptibility to fractures and vascular injuries due to connective tissue fragility. In this case report, we present a patient with osteogenesis imperfecta type I who sustained a transverse fracture of the right acetabulum while transferring from bed to chair. The fracture was repaired through an ilioinguinal approach. During the surgery, an iatrogenic injury to the femoral artery and vein occurred. This intraoperative complication was salvaged by immediate vascular repair. We discuss the possible causes of iatrogenic vascular injuries in patients with osteogenesis imperfecta. Orthopaedic surgeons should be aware of this potentially devastating complication in this particular patient cohort

DADA: data assimilation for the detection and attribution of weather and climate-related events

A new nudging method for data assimilation, delay‐coordinate nudging, is presented. Delay‐coordinate nudging makes explicit use of present and past observations in the formulation of the forcing driving the model evolution at each time step. Numerical experiments with a low‐order chaotic system show that the new method systematically outperforms standard nudging in different model and observational scenarios, also when using an unoptimized formulation of the delay‐nudging coefficients. A connection between the optimal delay and the dominant Lyapunov exponent of the dynamics is found based on heuristic arguments and is confirmed by the numerical results, providing a guideline for the practical implementation of the algorithm. Delay‐coordinate nudging preserves the easiness of implementation, the intuitive functioning and the reduced computational cost of the standard nudging, making it a potential alternative especially in the field of seasonal‐to‐decadal predictions with large Earth system models that limit the use of more sophisticated data assimilation procedures

Variation in beliefs about 'fracking' between the UK and US

In decision-making on the politically-contentious issue of unconventional gas development, the UK Government and European Commission are attempting to learn from the US experience. Although economic, environmental, and health impacts and regulatory contexts have been compared cross-nationally, public perceptions and their antecedents have not. We conducted similar online panel surveys of national samples of UK and US residents simultaneously in September 2014 to compare public perceptions and beliefs affecting such perceptions. The US sample was more likely to associate positive impacts with development (i.e., production of clean energy, cheap energy, and advancing national energy security). The UK sample was more likely to associate negative impacts (i.e., water contamination, higher carbon emissions, and earthquakes). Multivariate analyses reveal divergence cross-nationally in the relationship between beliefs about impacts and support/opposition – especially for beliefs about energy security. People who associated shale gas development with increased energy security in the UK were over three times more likely to support development than people in the US with this same belief. We conclude with implications for policy and communication, discussing communication approaches that could be successful cross-nationally and policy foci to which the UK might need to afford more attention in its continually evolving regulatory environment