Alterations in Gastric Microbiota After H. Pylori Eradication and in Different Histological Stages of Gastric Carcinogenesis

The role of bacteria other than Helicobacter pylori (HP) in the stomach remains elusive. We characterized the gastric microbiota in individuals with different histological stages of gastric carcinogenesis and after receiving HP eradication therapy. Endoscopic gastric biopsies were obtained from subjects with HP gastritis, gastric intestinal metaplasia (IM), gastric cancer (GC) and HP negative controls. Gastric microbiota was characterized by Illumina MiSeq platform targeting the 16 S rDNA. Apart from dominant H. pylori, we observed other Proteobacteria including Haemophilus, Serratia, Neisseria and Stenotrophomonas as the major components of the human gastric microbiota. Although samples were largely converged according to the relative abundance of HP, a clear separation of GC and other samples was recovered. Whilst there was a strong inverse association between HP relative abundance and bacterial diversity, this association was weak in GC samples which tended to have lower bacterial diversity compared with other samples with similar HP levels. Eradication of HP resulted in an increase in bacterial diversity and restoration of the relative abundance of other bacteria to levels similar to individuals without HP. In conclusion, HP colonization results in alterations of gastric microbiota and reduction in bacterial diversity, which could be restored by antibiotic treatment.published_or_final_versio

Multisymplectic Geometry and Multisymplectic Preissman Scheme for the KP Equation

The multisymplectic structure of the KP equation is obtained directly from the variational principal. Using the covariant De Donder-Weyl Hamilton function theories, we reformulate the KP equation to the multisymplectic form which proposed by Bridges. From the multisymplectic equation, we can derive a multisymplectic numerical scheme of the KP equation which can be simplified to multisymplectic forty-five points scheme.Comment: 17 papges, 8 figure

The Quantum Nature of a Nuclear Phase Transition

In their ground states, atomic nuclei are quantum Fermi liquids. At finite temperatures and low densities, these nuclei may undergo a phase change similar to, but substantially different from, a classical liquid gas phase transition. As in the classical case, temperature is the control parameter while density and pressure are the conjugate variables. At variance with the classical case, in the nucleus the difference between the proton and neutron concentrations acts as an additional order parameter, for which the symmetry potential is the conjugate variable. Different ratios of the neutron to proton concentrations lead to different critical points for the phase transition. This is analogous to the phase transitions occurring in $^{4}$He-$^{3}$He liquid mixtures. We present experimental results which reveal the N/Z dependence of the phase transition and discuss possible implications of these observations in terms of the Landau Free Energy description of critical phenomena.Comment: 5 pages, 4 figure

Magnetic Properties of the t-J Model in the Dynamical Mean-Field Theory

We present a theory for the spin correlation function of the t-J model in the framework of the dynamical mean-field theory. Using this mapping between the lattice and a local model we are able to obtain an intuitive expression for the non-local spin susceptibility, with the corresponding local correlation function as input. The latter is calculated by means of local Goldstone diagrams following closely the procedures developed and successfully applied for the (single impurity) Anderson model.We present a systematic study of the magnetic susceptibility and compare our results with those of a Hubbard model at large U. Similarities and differences are pointed out and the magnetic phase diagram of the t-J model is discussed.Comment: 28 pages LaTeX, postscript figures as compressed and uuencoded file included fil

Continuum radiative transfer Modeling of Sagittarius B2

We present results from radiative transfer modeling of the continuum emission towards Sagittarius B2 (hereafter Sgr B2). We have developed a radiative transfer framework – Pandora – that employs RADMC-3D (Dullemond 2012) for a self-consistent determination of the dust temperature. With this pipeline, we have set-up a single model that consistently reproduces the thermal dust and free-free continuum emission of Sgr B2 spanning four orders of magnitude in spatial scales (0.02–45 pc) and two orders of magnitude in frequency (20–4000 GHz)

Rigid spin-labeled nucleoside Ç: a nonperturbing EPR probe of nucleic acid conformation

Rigid spin-labeled nucleoside Ç, an analog of deoxycytidine that base-pairs with deoxyguanosine, was incorporated into DNA oligomers by chemical synthesis. Thermal denaturation experiments and circular dichroism (CD) measurements showed that Ç has a negligible effect on DNA duplex stability and conformation. Nucleoside Ç was incorporated into several positions within single-stranded DNA oligomers that can adopt two hairpin conformations of similar energy, each of which contains a four-base loop. The relative mobility of nucleotides in the alternating C/G hairpin loops, 5′-d(GCGC) and 5′-d(CGCG), was determined by electron paramagnetic resonance (EPR) spectroscopy. The most mobile nucleotide in the loop is the second one from the 5′-end, followed by the third, first and fourth nucleotides, consistent with previous NMR studies of DNA hairpin loops of different sequences. The EPR hairpin data were also corroborated by fluorescence spectroscopy using oligomers containing reduced Ç (Çf), which is fluorescent. Furthermore, EPR spectra of duplex DNAs that contained Ç at the end of the helix showed features that indicated dipolar coupling between two spins. These data are consistent with end-to-end duplex stacking in solution, which was only observed when G was paired to Ç, but not when Ç was paired with A, C or T

Transient dust in warm debris disks - Detection of Fe-rich olivine grains

(Abridged) Debris disks trace remnant reservoirs of leftover planetesimals in planetary systems. A handful of "warm" debris disks have been discovered in the last years, where emission in excess starts in the mid-infrared. An interesting subset within these warm debris disks are those where emission features are detected in mid-IR spectra, which points towards the presence of warm micron-sized dust grains. Given the ages of the host stars, the presence of these grains is puzzling, and questions their origin and survival in time. This study focuses on determining the mineralogy of the dust around 7 debris disks with evidence for warm dust, based on Spitzer/IRS spectroscopic data, in order to provide new insights into the origin of the dust grains. We present a new radiative transfer code dedicated to SED modeling of optically thin disks. We make use of this code on the SEDs of seven warm debris disks, in combination with recent laboratory experiments on dust optical properties. We find that most, if not all, debris disks in our sample are experiencing a transient phase, suggesting a production of small dust grains on relatively short timescales. From a mineralogical point of view, we find that enstatite grains have small abundances compared to crystalline olivine grains. The main result of our study is that we find evidences for Fe-rich crystalline olivine grains (Fe / [Mg + Fe] ~ 0.2) for several debris disks. This finding contrasts with studies of gas-rich protoplanetary disks. The presence of Fe-rich olivine grains, and the overall differences between the mineralogy of dust in Class II disks compared to debris disks suggest that the transient crystalline dust is of a new generation. We discuss possible crystallization routes to explain our results, and comment on the mechanisms that may be responsible for the production of small dust grains

A novel approach to phylogenetic tree construction using stochastic optimization and clustering

BACKGROUND: The problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational biology. RESULTS: A new phylogenetic tree construction method from a given set of objects (proteins, species, etc.) is presented. As an extension of ant colony optimization, this method proposes an adaptive phylogenetic clustering algorithm based on a digraph to find a tree structure that defines the ancestral relationships among the given objects. CONCLUSION: Our phylogenetic tree construction method is tested to compare its results with that of the genetic algorithm (GA). Experimental results show that our algorithm converges much faster and also achieves higher quality than GA