Atypical status of bovine spongiform encephalopathy in Poland: a molecular typing study

The aim of this study was to analyze molecular features of protease-resistant prion protein (PrPres) in Western blots of BSE cases diagnosed in Poland with respect to a possible atypical status. Confirmed cases were analyzed by Western blotting with several monoclonal antibodies directed at N-terminal and core epitopes of prion protein (PrP). Most cases showed the classical glycoprofile characterized by the dominance of the di- over the monoglycosylated PrPres band, yielding di-/mono- ratios well above 2 and by reactivity with antibodies having their epitopes in bovine PrP region 110-242 (C-type cases). Surprisingly, seven cases of BSE were atypical. Six were classified as L-type based on a slightly lower molecular mass (M-r) of the non- glycosylated band with respect to C-types and a conspicuously low di-/mono- ratio of glycosylated PrPres bands approaching unity. One case was classified as H-type because of a higher M-r of PrPres bands on the blot when compared with C-type cases. A characteristic epitope of H-type PrPres occurred in the 101-110 region of PrP for which only antibody 12B2 had a sufficient affinity. The occurrence of atypical cases only in animals 9 years of age and older raises questions about the mechanisms of prion diseases and the origin of BSE

Spin-Orbit-Induced Kondo Size Effect in Thin Films with 5/2-spin Impurities

Recently, for spin $S=5/2$ impurities quite different size dependence of the Kondo contribution to the resistivity was found experimentally than for S=2. Therefore previous calculation about the effect of the spin-orbit-induced magnetic anisotropy on the Kondo amplitude of the resistivity is extended to the case of $S=5/2$ impurity spin which differs from the integer spin case as the ground state is degenerated. In this case the Kondo contribution remains finite when the sample size goes to zero and the thickness dependence in the Kondo resistivity is much weaker for Cu(Mn). The behavior of the Kondo coefficient as a function of the thickness depends on the Kondo temperature, that is somewhat stronger for larger $T_K$. Comparing our results with a recent experiment in thin Cu(Mn) films, we find a good agreement.Comment: 8 pages, ReVTeX + 4 figures (Postscript

Experimental Controlled-NOT Logic Gate for Single Photons in the Coincidence Basis

We report a proof-of-principle demonstration of a probabilistic controlled-NOT gate for single photons. Single-photon control and target qubits were mixed with a single ancilla photon in a device constructed using only linear optical elements. The successful operation of the controlled-NOT gate relied on post-selected three-photon interference effects which required the detection of the photons in the output modes.Comment: 4 pages, 4 figures; minor change

Processing of agricultural apple fruit waste into sugar rich feedstocks for the catalytic production of 5-HMF over a Sn Amberlyst-15 resin catalyst

In this study we considered processes of treatment of agricultural apple waste which is normally discarded. We show the effect of various pre-treatment procedures on the final catalytic performance to produce 5-HMF from this real world biomass waste. Our study of the various potential pre-treatment steps, and their effect on the catalytic performance, provides valuable new insights which can be used for the development of new processes for the localised small scale valorization of agricultural fruit waste. The apple waste is aimed to be converted into a sugar rich feedstock stream for the catalytic conversion to 5-hydroxymethyl furfural (5-HMF) at low temperatures (∼120 °C). Filters with varying pore sizes were studied for the filtration of apple pomace after milling the rotten apples in order to reduce the solids content. The tested filters varied in pore sizes of 0.2 μm, 2 μm and 54 μm. The effect of heating, acid or base treatment of the apple slurry was evaluated for increasing the speed of filtration. The highest flow rate was obtained for the filter with 54 μm pores. The sugar rich filtrates were investigated in the catalytic conversion to 5-HMF over an easy-to-manufacture Sn exchanged resin (Amberlyst-15) catalyst. Results showed that filtrates obtained over a 2 μm filter lead to the highest 5-HMF yields (18 %) without extra additives. Adjustment of the reaction mixtures to pH 7 resulted in a lower catalytic activity. 5-HMF is proposed to be extracted from the aqueous layer by using an organic liquid layer (methyl isobutyl ketone, MIBK). In order to increase the diffusion of 5-HMF to the MIBK layer the addition of salts to the reaction mixture was investigated. This leads to lower catalytic activity, possibly due to catalyst deactivation. Our results showed that a relatively wide pore filter (54 μm) provides the fastest apple processing method and a filtrate reacting to the highest 5-HMF yield in catalytic conversion of the sugar rich product stream obtained from agricultural waste apples

Rings and rigidity transitions in network glasses

Three elastic phases of covalent networks, (I) floppy, (II) isostatically rigid and (III) stressed-rigid have now been identified in glasses at specific degrees of cross-linking (or chemical composition) both in theory and experiments. Here we use size-increasing cluster combinatorics and constraint counting algorithms to study analytically possible consequences of self-organization. In the presence of small rings that can be locally I, II or III, we obtain two transitions instead of the previously reported single percolative transition at the mean coordination number $\bar r=2.4$, one from a floppy to an isostatic rigid phase, and a second one from an isostatic to a stressed rigid phase. The width of the intermediate phase $~ \bar r$ and the order of the phase transitions depend on the nature of medium range order (relative ring fractions). We compare the results to the Group IV chalcogenides, such as Ge-Se and Si-Se, for which evidence of an intermediate phase has been obtained, and for which estimates of ring fractions can be made from structures of high T crystalline phases.Comment: 29 pages, revtex, 7 eps figure

Application of Pulsed Field Gel Electrophoresis to Determine γ-ray-induced Double-strand Breaks in Yeast Chromosomal Molecules

The frequency of DNA double-strand breaks (dsb) was determined in yeast cells exposed to γ-rays under anoxic conditions. Genomic DNA of treated cells was separated by pulsed field gel electrophoresis, and two different approaches for the evaluation of the gels were employed: (1) The DNA mass distribution profile obtained by electrophoresis was compared to computed profiles, and the number of DSB per unit length was then derived in terms of a fitting procedure; (2) hybridization of selected chromosomes was performed, and a comparison of the hybridization signals in treated and untreated samples was then used to derive the frequency of dsb

The Tug1 locus is essential for male fertility

Background: Several long noncoding RNAs (lncRNAs) have been shown to function as central components of molecular machines that play fundamental roles in biology. While the number of annotated lncRNAs in mammalian genomes has greatly expanded, their functions remain largely uncharacterized. This is compounded by the fact that identifying lncRNA loci that have robust and reproducible phenotypes when mutated has been a challenge. Results: We previously generated a cohort of 20 lncRNA loci knockout mice. Here, we extend our initial study and provide a more detailed analysis of the highly conserved lncRNA locus, Taurine Upregulated Gene 1 (Tug1). We report that Tug1 knockout male mice are sterile with complete penetrance due to a low sperm count and abnormal sperm morphology. Having identified a lncRNA loci with a robust phenotype, we wanted to determine which, if any, potential elements contained in the Tug1 genomic region (DNA, RNA, protein, or the act of transcription) have activity. Using engineered mouse models and cell-based assays, we provide evidence that the Tug1 locus harbors three distinct regulatory activities - two noncoding and one coding: (i) a cis DNA repressor that regulates many neighboring genes, (ii) a lncRNA that can regulate genes by a trans-based function, and finally (iii) Tug1 encodes an evolutionary conserved peptide that when overexpressed impacts mitochondrial membrane potential. Conclusions: Our results reveal an essential role for the Tug1 locus in male fertility and uncover three distinct regulatory activities in the Tug1 locus, thus highlighting the complexity present at lncRNA loci

Atomic X-ray Spectroscopy of Accreting Black Holes

Current astrophysical research suggests that the most persistently luminous objects in the Universe are powered by the flow of matter through accretion disks onto black holes. Accretion disk systems are observed to emit copious radiation across the electromagnetic spectrum, each energy band providing access to rather distinct regimes of physical conditions and geometric scale. X-ray emission probes the innermost regions of the accretion disk, where relativistic effects prevail. While this has been known for decades, it also has been acknowledged that inferring physical conditions in the relativistic regime from the behavior of the X-ray continuum is problematic and not satisfactorily constraining. With the discovery in the 1990s of iron X-ray lines bearing signatures of relativistic distortion came the hope that such emission would more firmly constrain models of disk accretion near black holes, as well as provide observational criteria by which to test general relativity in the strong field limit. Here we provide an introduction to this phenomenon. While the presentation is intended to be primarily tutorial in nature, we aim also to acquaint the reader with trends in current research. To achieve these ends, we present the basic applications of general relativity that pertain to X-ray spectroscopic observations of black hole accretion disk systems, focusing on the Schwarzschild and Kerr solutions to the Einstein field equations. To this we add treatments of the fundamental concepts associated with the theoretical and modeling aspects of accretion disks, as well as relevant topics from observational and theoretical X-ray spectroscopy.Comment: 63 pages, 21 figures, Einstein Centennial Review Article, Canadian Journal of Physics, in pres

Decomposition of operator semigroups on W*-algebras

We consider semigroups of operators on a W$^*$-algebra and prove, under appropriate assumptions, the existence of a Jacobs-DeLeeuw-Glicksberg type decomposition. This decomposition splits the algebra into a "stable" and "reversible" part with respect to the semigroup and yields, among others, a structural approach to the Perron-Frobenius spectral theory for completely positive operators on W$^*$-algebras.Comment: referee's comments incorporated. To appear in Semigroup Foru