Sareomycetes cl. nov. : A new proposal for placement of the resinicolous genus Sarea (Ascomycota, Pezizomycotina)

Resinicolous fungi constitute a heterogeneous assemblage of fungi that live on fresh and solidified plant resins. The genus Sarea includes, according to current knowledge, two species, S. resinae and S. difformis. In contrast to other resinicolous discomycetes, which are placed in genera also including non-resinicolous species, Sarea species only ever fruit on resin. The taxonomic classification of Sarea has proven to be difficult and currently the genus, provisionally and based only on morphological features, has been assigned to the Trapeliales (Lecanoromycetes). In contrast, molecular studies have noted a possible affinity to the Leotiomycetes. Here we review the taxonomic placement of Sarea using sequence data from seven phylogenetically informative DNA regions including ribosomal (ITS, nucSSU, mtSSU, nucLSU) and protein-coding (rpb1, rpb2, mcm7) regions. We combined available and new sequence data with sequences from major Pezizomycotina classes, especially Lecanoromycetes and Leotiomycetes, and assembled three different taxon samplings in order to place the genus Sarea within the Pezizomycotina. Based on our data, none of the applied phylogenetic approaches (Bayesian Inference, Maximum Likelihood and Maximum Parsimony) supported the placement of Sarea in the Trapeliales or any other order in the Lecanoromycetes. A placement of Sarea within the Leotiomycetes is similarly unsupported. Based on our data, Sarea forms an isolated and highly supported phylogenetic lineage within the "Leotiomyceta". From the results of our multilocus phylogenetic analyses we propose here a new class, order, and family, Sareomycetes, Sareales and Sareaceae in the Ascomycota to accommodate the genus Sarea. The genetic variability within the newly proposed class suggests that it is a larger group that requires further infrageneric classification.Peer reviewe

Erosion-Corrosion in Pipe Flows of Particle-Laden Liquids

The transmission of particle-bearing liquids in pipes has motivated continuing research into erosion mechanisms and the distribution of erosion rates over wetted surfaces. This chapter covers these initiatives with particular reference to erosion-corrosion modelling within bends and straight sections of cylindrical pipes manufactured in a variety of materials and transporting a variety of liquids. Erosion-corrosion modelling techniques such as submerged slurry jets and rotating cylinder electrodes have been used to study factors influencing material degradation. Improvements in computational fluid dynamics (CFD), such as the development of a moving deforming mesh (MDM) have improved the accuracy of CFD models in predicting pipe wall erosion rates. Combined discrete phase tracking approaches such as the CFD-DPM-DEM (discrete phase-discrete element model) have helped improve computational efficiency. Wall impact erosion models are calibrated using laboratory scale tests. Validation of CFD models using full-scale test data is rare, meaning their accuracy is still largely unreported. Material testing has helped to identify the resilience of prospective pipeline materials to erosion-corrosion, while modifications to internal geometry and pipe section have shown potential to improve erosion-corrosion resistance

Dynamical System Approach to Cosmological Models with a Varying Speed of Light

Methods of dynamical systems have been used to study homogeneous and isotropic cosmological models with a varying speed of light (VSL). We propose two methods of reduction of dynamics to the form of planar Hamiltonian dynamical systems for models with a time dependent equation of state. The solutions are analyzed on two-dimensional phase space in the variables $(x, \dot{x})$ where $x$ is a function of a scale factor $a$. Then we show how the horizon problem may be solved on some evolutional paths. It is shown that the models with negative curvature overcome the horizon and flatness problems. The presented method of reduction can be adopted to the analysis of dynamics of the universe with the general form of the equation of state $p=\gamma(a)\epsilon$. This is demonstrated using as an example the dynamics of VSL models filled with a non-interacting fluid. We demonstrate a new type of evolution near the initial singularity caused by a varying speed of light. The singularity-free oscillating universes are also admitted for positive cosmological constant. We consider a quantum VSL FRW closed model with radiation and show that the highest tunnelling rate occurs for a constant velocity of light if $c(a) \propto a^n$ and $-1 < n \le 0$. It is also proved that the considered class of models is structurally unstable for the case of $n < 0$.Comment: 18 pages, 5 figures, RevTeX4; final version to appear in PR

Variable-Speed-of-Light Cosmology from Brane World Scenario

We argue that the four-dimensional universe on the TeV brane of the Randall-Sundrum scenario takes the bimetric structure of Clayton and Moffat, with gravitons traveling faster than photons instead, while the radion varies with time. We show that such brane world bimetric model can thereby solve the flatness and the cosmological constant problems, provided the speed of a graviton decreases to the present day value rapidly enough. The resolution of other cosmological problems such as the horizon problem and the monopole problem requires supplementation by inflation, which may be achieved by the radion field provided the radion potential satisfies the slow-roll approximation.Comment: 18 pages, LaTeX, revised version to appear in Phys. Rev.

Semi-automatic standardized analysis method to objectively evaluate near-infrared fluorescent dyes in image-guided surgery

Significance: Near-infrared fluorescence imaging still lacks a standardized, objective method to evaluate fluorescent dye efficacy in oncological surgical applications. This results in difficulties in translation between preclinical to clinical studies with fluorescent dyes and in the reproduction of results between studies, which in turn hampers further clinical translation of novel fluorescent dyes. Aim: Our aim is to develop and evaluate a semi-automatic standardized method to objectively assess fluorescent signals in resected tissue. Approach: A standardized imaging procedure was designed and quantitative analysis methods were developed to evaluate non-targeted and tumor-targeted fluorescent dyes. The developed analysis methods included manual selection of region of interest (ROI) on white light images, automated fluorescence signal ROI selection, and automatic quantitative image analysis. The proposed analysis method was then compared with a conventional analysis method, where fluorescence signal ROIs were manually selected on fluorescence images. Dice similarity coefficients and intraclass correlation coefficients were calculated to determine the inter- and intraobserver variabilities of the ROI selections and the determined signal- and tumor-to-background ratios. Results: The proposed non-targeted fluorescent dyes analysis method showed statistically significantly improved variabilities after application on indocyanine green specimens. For specimens with the targeted dye SGM-101, the variability of the background ROI selection was statistically significantly improved by implementing the proposed method. Conclusion: Semi-automatic methods for standardized quantitative analysis of fluorescence images were successfully developed and showed promising results to further improve the reproducibility and standardization of clinical studies evaluating fluorescent dyes.</p

Semi-automatic standardized analysis method to objectively evaluate near-infrared fluorescent dyes in image-guided surgery

Significance: Near-infrared fluorescence imaging still lacks a standardized, objective method to evaluate fluorescent dye efficacy in oncological surgical applications. This results in difficulties in translation between preclinical to clinical studies with fluorescent dyes and in the reproduction of results between studies, which in turn hampers further clinical translation of novel fluorescent dyes. Aim: Our aim is to develop and evaluate a semi-automatic standardized method to objectively assess fluorescent signals in resected tissue. Approach: A standardized imaging procedure was designed and quantitative analysis methods were developed to evaluate non-targeted and tumor-targeted fluorescent dyes. The developed analysis methods included manual selection of region of interest (ROI) on white light images, automated fluorescence signal ROI selection, and automatic quantitative image analysis. The proposed analysis method was then compared with a conventional analysis method, where fluorescence signal ROIs were manually selected on fluorescence images. Dice similarity coefficients and intraclass correlation coefficients were calculated to determine the inter- and intraobserver variabilities of the ROI selections and the determined signal- and tumor-to-background ratios. Results: The proposed non-targeted fluorescent dyes analysis method showed statistically significantly improved variabilities after application on indocyanine green specimens. For specimens with the targeted dye SGM-101, the variability of the background ROI selection was statistically significantly improved by implementing the proposed method. Conclusion: Semi-automatic methods for standardized quantitative analysis of fluorescence images were successfully developed and showed promising results to further improve the reproducibility and standardization of clinical studies evaluating fluorescent dyes.</p

Stromal targets for fluorescent-guided oncologic surgery

Pre-operative imaging techniques are essential for tumor detection and diagnosis, but offer limited help during surgery. Recently, the applicability of imaging during oncologic surgery has been recognized, using near-infrared fluorescent dyes conjugated to targeting antibodies, peptides, or other vehicles. Image-guided oncologic surgery (IGOS) assists the surgeFon to distinguish tumor from normal tissue during operation, and can aid in recognizing vital structures. IGOS relies on an optimized combination of a dedicated fluorescent camera system and specific probes for targeting. IGOS probes for clinical use are not widely available yet, but numerous pre-clinical studies have been published and clinical trials are being established or prepared. Most of the investigated probes are based on antibodies or peptides against proteins on the membranes of malignant cells, whereas others are directed against stromal cells. Targeting stroma cells for IGOS has several advantages. Besides the high stromal content in more aggressive tumor types, the stroma is often primarily located at the periphery/invasive front of the tumor, which makes stromal targets particularly suited for imaging purposes. Moreover, because stroma up-regulation is a physiological reaction, most proteins to be targeted on these cells are “universal” and not derived from a specific genetic variation, as is the case with many upregulated proteins on malignant cancer cells

Raman scattering studies of spin, charge, and lattice dynamics in Ca_{2-x}Sr_{x}RuO_{4} (0 =< x < 0.2)

We use Raman scattering to study spin, charge, and lattice dynamics in various phases of Ca_{2-x}Sr_{x}RuO_{4}. With increasing substitution of Ca by Sr in the range 0 =< x < 0.2, we observe (1) evidence for an increase of the electron-phonon interaction strength, (2) an increased temperature-dependence of the two-magnon energy and linewidth in the antiferromagnetic insulating phase, and (3) evidence for charge gap development, and hysteresis associated with the structural phase change, both of which are indicative of a first-order metal-insulator transition (T_{MI}) and a coexistence of metallic and insulating components for T < T_{MI}

Constraining fundamental constants of physics with quasar absorption line systems

We summarize the attempts by our group and others to derive constraints on variations of fundamental constants over cosmic time using quasar absorption lines. Most upper limits reside in the range 0.5-1.5x10-5 at the 3sigma level over a redshift range of approximately 0.5-2.5 for the fine-structure constant, alpha, the proton-to-electron mass ratio, mu, and a combination of the proton gyromagnetic factor and the two previous constants, gp(alpha^2/mu)^nu, for only one claimed variation of alpha. It is therefore very important to perform new measurements to improve the sensitivity of the numerous methods to at least <0.1x10-5 which should be possible in the next few years. Future instrumentations on ELTs in the optical and/or ALMA, EVLA and SKA pathfinders in the radio will undoutedly boost this field by allowing to reach much better signal-to-noise ratios at higher spectral resolution and to perform measurements on molecules in the ISM of high redshift galaxies.Comment: 11 pages, 3 figure