Fungus Flora of Panicum virgatum L.

The pathogenic fungi collected on Panicum virgatum in Iowa included Elsinoe sp., Phyllachora graminis, Colletotrichum graminicola, Selenophoma donacis, Puccinia panici, Tilletia maclagani, and Uromyces graminicola. Those which were saprophytic or of doubtful pathogenicity included Ophiobolus herpotrichus, Leptosphaeria microscopica, Mycosphaerella recutita, Phaeoseptoria elymi, and Phaeoseptoria festucae. Reported for the first time on Panicum virgatum are Elsinoe sp., Ophiobolus herpotrichus, Leptosphaeria microscopica, Mycosphaerella recutita, Phaeoseptoria elymi, and P. festucae. This is the initial report of Colletotrichum graminicola and Selenophoma donacis in Iowa on this host

Concentration ratios for chemical analogues of key nuclides for different vegetation types at the Olkiluoto site

Olkiluoto Island on the western coast of Finland has been selected as a repository site for spent nuclear fuel in Finland. This study aimed at identifying differences in concentration ratios (CR), and their distributions, for the elements analysed on soil and vegetation samples taken on the island (Al, B, Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Ni, P, S, Zn). Many of the elements can be considered to be chemically analogous to radionuclides that, potentially, can be released from the repository. Differences between the soil and vegetation in different tree age, tree species and site fertility classes typical of the forest ecosystems in Olkiluoto were investigated. Lognormal distributions were fitted to the different groupings of the CR data calculated on the basis of the results from 94 sampling plots. In most cases no significant differences were found between the different groupings for a specific element when the 95% confidence intervals were applied. According to the results based on real site data for CRs in forest ecosystems on Olkiluoto, it appears that the current CR-based approach to radionuclide modelling in forest ecosystems is problematic due to the large variation in parameter values and in their practical definition

A TV-Gaussian prior for infinite-dimensional Bayesian inverse problems and its numerical implementations

Many scientific and engineering problems require to perform Bayesian inferences in function spaces, in which the unknowns are of infinite dimension. In such problems, choosing an appropriate prior distribution is an important task. In particular we consider problems where the function to infer is subject to sharp jumps which render the commonly used Gaussian measures unsuitable. On the other hand, the so-called total variation (TV) prior can only be defined in a finite dimensional setting, and does not lead to a well-defined posterior measure in function spaces. In this work we present a TV-Gaussian (TG) prior to address such problems, where the TV term is used to detect sharp jumps of the function, and the Gaussian distribution is used as a reference measure so that it results in a well-defined posterior measure in the function space. We also present an efficient Markov Chain Monte Carlo (MCMC) algorithm to draw samples from the posterior distribution of the TG prior. With numerical examples we demonstrate the performance of the TG prior and the efficiency of the proposed MCMC algorithm

Fast Gibbs sampling for high-dimensional Bayesian inversion

Solving ill-posed inverse problems by Bayesian inference has recently attracted considerable attention. Compared to deterministic approaches, the probabilistic representation of the solution by the posterior distribution can be exploited to explore and quantify its uncertainties. In applications where the inverse solution is subject to further analysis procedures, this can be a significant advantage. Alongside theoretical progress, various new computational techniques allow to sample very high dimensional posterior distributions: In [Lucka2012], a Markov chain Monte Carlo (MCMC) posterior sampler was developed for linear inverse problems with $\ell_1$-type priors. In this article, we extend this single component Gibbs-type sampler to a wide range of priors used in Bayesian inversion, such as general $\ell_p^q$ priors with additional hard constraints. Besides a fast computation of the conditional, single component densities in an explicit, parameterized form, a fast, robust and exact sampling from these one-dimensional densities is key to obtain an efficient algorithm. We demonstrate that a generalization of slice sampling can utilize their specific structure for this task and illustrate the performance of the resulting slice-within-Gibbs samplers by different computed examples. These new samplers allow us to perform sample-based Bayesian inference in high-dimensional scenarios with certain priors for the first time, including the inversion of computed tomography (CT) data with the popular isotropic total variation (TV) prior.Comment: submitted to "Inverse Problems

Free digital image analysis software helps to resolve equivocal scores in HER2 immunohistochemistry

Evaluation of human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) is subject to interobserver variation and lack of reproducibility. Digital image analysis (DIA) has been shown to improve the consistency and accuracy of the evaluation and its use is encouraged in current testing guidelines. We studied whether digital image analysis using a free software application (ImmunoMembrane) can assist in interpreting HER2 IHC in equivocal 2+ cases. We also compared digital photomicrographs with whole-slide images (WSI) as material for ImmunoMembrane DIA. We stained 750 surgical resection specimens of invasive breast cancers immunohistochemically for HER2 and analysed staining with ImmunoMembrane. The ImmunoMembrane DIA scores were compared with the originally responsible pathologists' visual scores, a researcher's visual scores and in situ hybridisation (ISH) results. The originally responsible pathologists reported 9.1 % positive 3+ IHC scores, for the researcher this was 8.4 % and for ImmunoMembrane 9.5 %. Equivocal 2+ scores were 34 % for the pathologists, 43.7 % for the researcher and 10.1 % for ImmunoMembrane. Negative 0/1+ scores were 57.6 % for the pathologists, 46.8 % for the researcher and 80.8 % for ImmunoMembrane. There were six false positive cases, which were classified as 3+ by ImmunoMembrane and negative by ISH. Six cases were false negative defined as 0/1+ by IHC and positive by ISH. ImmunoMembrane DIA using digital photomicrographs and WSI showed almost perfect agreement. In conclusion, digital image analysis by ImmunoMembrane can help to resolve a majority of equivocal 2+ cases in HER2 IHC, which reduces the need for ISH testing.Peer reviewe

Metabolic changes in summer active and anuric hibernating free-ranging brown bears (ursus arctos)

The brown bear (Ursus arctos) hibernates for 5 to 6 months each winter and during this time ingests no food or water and remains anuric and inactive. Despite these extreme conditions, bears do not develop azotemia and preserve their muscle and bone strength. To date most renal studies have been limited to small numbers of bears, often in captive environments. Sixteen free-ranging bears were darted and had blood drawn both during hibernation in winter and summer. Samples were collected for measurement of creatinine and urea, markers of inflammation, the calcium-phosphate axis, and nutritional parameters including amino acids. In winter the bear serum creatinine increased 2.5 fold despite a 2-fold decrease in urea, indicating a remarkable ability to recycle urea nitrogen during hibernation. During hibernation serum calcium remained constant despite a decrease in serum phosphate and a rise in FGF23 levels. Despite prolonged inactivity and reduced renal function, inflammation does not ensue and bears seem to have enhanced antioxidant defense mechanisms during hibernation. Nutrition parameters showed high fat stores, preserved amino acids and mild hyperglycemia during hibernation. While total, essential, non-essential and branched chain amino acids concentrations do not change during hibernation anorexia, changes in individual amino acids ornithine, citrulline and arginine indicate an active, although reduced urea cycle and nitrogen recycling to proteins. Serum uric acid and serum fructose levels were elevated in summer and changes between seasons were positively correlated. Further studies to understand how bears can prevent the development of uremia despite minimal renal function during hibernation could provide new therapeutic avenues for the treatment of human kidney disease

A modelling framework for the assessment of the impacts of alternative policy and management options on the sustainability of Finnish agrifood systems

Recently, a new project focussing on integrated assessment modelling of agrifood systems (IAM-Tools) has been launched at MTT Agrifood Research Finland to gather, evaluate, refine and develop these component models and to link tem in an IAM framework for Finnish conditions

Large-scale Graphitic Thin Films Synthesized on Ni and Transferred to Insulators: Structural and Electronic Properties

We present a comprehensive study of the structural and electronic properties of ultrathin films containing graphene layers synthesized by chemical vapor deposition (CVD) based surface segregation on polycrystalline Ni foils then transferred onto insulating SiO2/Si substrates. Films of size up to several mm's have been synthesized. Structural characterizations by atomic force microscopy (AFM), scanning tunneling microscopy (STM), cross-sectional transmission electron microscopy (XTEM) and Raman spectroscopy confirm that such large scale graphitic thin films (GTF) contain both thick graphite regions and thin regions of few layer graphene. The films also contain many wrinkles, with sharply-bent tips and dislocations revealed by XTEM, yielding insights on the growth and buckling processes of the GTF. Measurements on mm-scale back-gated transistor devices fabricated from the transferred GTF show ambipolar field effect with resistance modulation ~50% and carrier mobilities reaching ~2000 cm^2/Vs. We also demonstrate quantum transport of carriers with phase coherence length over 0.2 $\mu$m from the observation of 2D weak localization in low temperature magneto-transport measurements. Our results show that despite the non-uniformity and surface roughness, such large-scale, flexible thin films can have electronic properties promising for device applications.Comment: This version (as published) contains additional data, such as cross sectional TEM image