1,798 research outputs found

    Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes

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    Abstract. Background: Myelodysplastic Syndromes (MDSS) are pre-leukemic disorders with increasing incident rates worldwide, but very limited treatment options. Little is known about small regulatory RNAs and how they contribute to pathogenesis, progression and transcriptome changes in MDS. Methods. Patients' primary marrow cells were screened for short RNAs (RNA-seq) using next generation sequencing. Exon arrays from the same cells were used to profile gene expression and additional measures on 98 patients obtained. Integrative bioinformatics algorithms were proposed, and pathway and ontology analysis performed. Results: In low-grade MDS, observations implied extensive post-transcriptional regulation via microRNAs (miRNA) and the recently discovered Piwi interacting RNAs (piRNA). Large expression differences were found for MDS-associated and novel miRNAs, including 48 sequences matching to miRNA star (miRNA*) motifs. The detected species were predicted to regulate disease stage specific molecular functions and pathways, including apoptosis and response to DNA damage. In high-grade MDS, results suggested extensive post-translation editing via transfer RNAs (tRNAs), providing a potential link for reduced apoptosis, a hallmark for this disease stage. Bioinformatics analysis confirmed important regulatory roles for MDS linked miRNAs and TFs, and strengthened the biological significance of miRNA*. The "RNA polymerase II promoters" were identified as the tightest controlled biological function. We suggest their control by a miRNA dominated feedback loop, which might be linked to the dramatically different miRNA amounts seen between low and high-grade MDS. Discussion. The presented results provide novel findings that build a basis of further investigations of diagnostic biomarkers, targeted therapies and studies on MDS pathogenesis. © 2011 Beck et al; licensee BioMed Central Ltd

    Big bang simulation in superfluid 3He-B -- Vortex nucleation in neutron-irradiated superflow

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    We report the observation of vortex formation upon the absorption of a thermal neutron in a rotating container of superfluid 3^3He-B. The nuclear reaction n + 3^3He = p + 3^3H + 0.76MeV heats a cigar shaped region of the superfluid into the normal phase. The subsequent cooling of this region back through the superfluid transition results in the nucleation of quantized vortices. Depending on the superflow velocity, sufficiently large vortex rings grow under the influence of the Magnus force and escape into the container volume where they are detected individually with nuclear magnetic resonance. The larger the superflow velocity the smaller the rings which can expand. Thus it is possible to obtain information about the morphology of the initial defect network. We suggest that the nucleation of vortices during the rapid cool-down into the superfluid phase is similar to the formation of defects during cosmological phase transitions in the early universe.Comment: 4 pages, LaTeX file, 4 figures are available at ftp://boojum.hut.fi/pub/publications/lowtemp/LTL-95009.p

    Direct observation of incommensurate magnetism in Hubbard chains

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    The interplay between magnetism and doping is at the origin of exotic strongly correlated electronic phases and can lead to novel forms of magnetic ordering. One example is the emergence of incommensurate spin-density waves with a wave vector that does not match the reciprocal lattice. In one dimension this effect is a hallmark of Luttinger liquid theory, which also describes the low energy physics of the Hubbard model. Here we use a quantum simulator based on ultracold fermions in an optical lattice to directly observe such incommensurate spin correlations in doped and spin-imbalanced Hubbard chains using fully spin and density resolved quantum gas microscopy. Doping is found to induce a linear change of the spin-density wave vector in excellent agreement with Luttinger theory predictions. For non-zero polarization we observe a decrease of the wave vector with magnetization as expected from the Heisenberg model in a magnetic field. We trace the microscopic origin of these incommensurate correlations to holes, doublons and excess spins which act as delocalized domain walls for the antiferromagnetic order. Finally, when inducing interchain coupling we observe fundamentally different spin correlations around doublons indicating the formation of a magnetic polaron

    Note on Bonus Relations for N=8 Supergravity Tree Amplitudes

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    We study the application of non-trivial relations between gravity tree amplitudes, the bonus relations, to all tree-level amplitudes in N=8 supergravity. We show that the relations can be used to simplify explicit formulae of supergravity tree amplitudes, by reducing the known form as a sum of (n-2)! permutations obtained by solving on-shell recursion relations, to a new form as a (n-3)!-permutation sum. We demonstrate the simplification by explicit calculations of the next-to-maximally helicity violating (NMHV) and next-to-next-to-maximally helicity violating (N^2MHV) amplitudes, and provide a general pattern of bonus coefficients for all tree-level amplitudes.Comment: 21 pages, 9 figures; v2, minor changes, references adde
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