Algorithms for 3D rigidity analysis and a first order percolation transition

A fast computer algorithm, the pebble game, has been used successfully to study rigidity percolation on 2D elastic networks, as well as on a special class of 3D networks, the bond-bending networks. Application of the pebble game approach to general 3D networks has been hindered by the fact that the underlying mathematical theory is, strictly speaking, invalid in this case. We construct an approximate pebble game algorithm for general 3D networks, as well as a slower but exact algorithm, the relaxation algorithm, that we use for testing the new pebble game. Based on the results of these tests and additional considerations, we argue that in the particular case of randomly diluted central-force networks on BCC and FCC lattices, the pebble game is essentially exact. Using the pebble game, we observe an extremely sharp jump in the largest rigid cluster size in bond-diluted central-force networks in 3D, with the percolating cluster appearing and taking up most of the network after a single bond addition. This strongly suggests a first order rigidity percolation transition, which is in contrast to the second order transitions found previously for the 2D central-force and 3D bond-bending networks. While a first order rigidity transition has been observed for Bethe lattices and networks with ``chemical order'', this is the first time it has been seen for a regular randomly diluted network. In the case of site dilution, the transition is also first order for BCC, but results for FCC suggest a second order transition. Even in bond-diluted lattices, while the transition appears massively first order in the order parameter (the percolating cluster size), it is continuous in the elastic moduli. This, and the apparent non-universality, make this phase transition highly unusual.Comment: 28 pages, 19 figure

Self-organization with equilibration: a model for the intermediate phase in rigidity percolation

Recent experimental results for covalent glasses suggest the existence of an intermediate phase attributed to the self-organization of the glass network resulting from the tendency to minimize its internal stress. However, the exact nature of this experimentally measured phase remains unclear. We modify a previously proposed model of self-organization by generating a uniform sampling of stress-free networks. In our model, studied on a diluted triangular lattice, an unusual intermediate phase appears, in which both rigid and floppy networks have a chance to occur, a result also observed in a related model on a Bethe lattice by Barre et al. [Phys. Rev. Lett. 94, 208701 (2005)]. Our results for the bond-configurational entropy of self-organized networks, which turns out to be only about 2% lower than that of random networks, suggest that a self-organized intermediate phase could be common in systems near the rigidity percolation threshold.Comment: 9 pages, 6 figure

Study of impact on helicopter blade

This article presents a study of damage in structures that are similar to helicopter blade sections, subjected to an impact. These complex composite structures were impacted by a steel ball of 125 g at impact speed ranging from 30 to 130 m/s. This led to properly highlight the kinematics of the impact and to define the sequence of the damage’s mechanisms. An explicit FE model is also presented. The damage modelling of the roving is performed through a scale change. It allows a good representation of observed experimental behaviour. As the mesh density is low, it can be used for the modelling of a real structure

Predictability of large future changes in a competitive evolving population

The dynamical evolution of many economic, sociological, biological and physical systems tends to be dominated by a relatively small number of unexpected, large changes (`extreme events'). We study the large, internal changes produced in a generic multi-agent population competing for a limited resource, and find that the level of predictability actually increases prior to a large change. These large changes hence arise as a predictable consequence of information encoded in the system's global state.Comment: 10 pages, 3 figure

Comparative Genomics of Leuconostoc carnosum

Leuconostoc carnosum is a known colonizer of meat-related food matrices. It reaches remarkably high loads during the shelf life in packaged meat products and plays a role in spoilage, although preservative effects have been proposed for some strains. In this study, the draft genomes of 17 strains of L. carnosum (i.e., all the strains that have been sequenced so far) were compared to decipher their metabolic and functional potential and to determine their role in food transformations. Genome comparison and pathway reconstruction indicated that L. carnosum is a compact group of closely related heterofermentative bacteria sharing most of the metabolic features. Adaptation to a nitrogen-rich environment, such as meat, is evidenced by 23 peptidase genes identified in the core genome and by the autotrophy for nitrogen compounds including several amino acids, vitamins, and cofactors. Genes encoding the decarboxylases yielding biogenic amines were not present. All the strains harbored 1–4 of 32 different plasmids, bearing functions associated to proteins hydrolysis, transport of amino acids and oligopeptides, exopolysaccharides, and various resistances (e.g., to environmental stresses, bacteriophages, and heavy metals). Functions associated to bacteriocin synthesis, secretion, and immunity were also found in plasmids. While genes for lactococcin were found in most plasmids, only three harbored the genes for leucocin B, a class IIa antilisterial bacteriocin. Determinants of antibiotic resistances were absent in both plasmids and chromosomes

MicroRNA expression is altered in an ovalbumin-induced asthma model and targeting miR-155 with antagomirs reveals cellular specificity

©2015 Plank et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source arecredited. MicroRNAs are post-transcriptional regulators of gene expression that are differentially regulated during development and in inflammatory diseases. A role for miRNAs in allergic asthma is emerging and further investigation is required to determine whether they may serve as potential therapeutic targets. We profiled miRNA expression in murine lungs from an ovalbumin-induced allergic airways disease model, and compared expression to animals receiving dexamethasone treatment and non-allergic controls. Our analysis identified 29 miRNAs that were significantly altered during allergic inflammation. Target prediction analysis revealed novel genes with altered expression in allergic airways disease and suggests synergistic miRNA regulation of target mRNAs. To assess the impacts of one induced miRNA on pathology, we targeted miR-155-5p using a specific antagomir. Antagomir administration successfully reduced miR-155-5p expression with high specificity, but failed to alter the disease phenotype. Interestingly, further investigation revealed that antagomir delivery has variable efficacy across different immune cell types, effectively targeting myeloid cell populations, but exhibiting poor uptake in lymphocytes. Our findings demonstrate that antagomir-based targeting of miRNA function in the lung is highly specific, but highlights cell-specificity as a key limitation to be considered for antagomir-based strategies as therapeutics

Defining the Incremental Utility of Prostate Multiparametric Magnetic Resonance Imaging at Standard and Specialized Read in Predicting Extracapsular Extension of Prostate Cancer

AbstractMultiparametric magnetic resonance imaging (mpMRI) is increasingly used in staging early prostate cancer (PCa) but remains heavily reader-dependent. We aim to define the incremental utility of mpMRI over clinical parameters in determining the pathologic extracapsular extension (pECE) of PCa interpreted in a standard radiologic setting and when further over-read by a specialized reader. We retrospectively reviewed 120 men with clinically localized PCa undergoing mpMRI and radical prostatectomy. We obtained radiologic prediction of pECE from standard radiologic reports (standard read) and by a specialized reader blinded to clinical and pathologic findings (specialized read). We determined the incremental benefit of standard read and specialized read by sequential addition to a baseline clinical parameters-only logistic regression model predicting pECE. The sensitivity and specificity of standard read were 77% and 44%, respectively, whereas those of specialized read were 86% and 81%. The positive likelihood ratio was 1.7 at baseline, 1.7 adding standard read, and 6.5 adding specialized read. The negative likelihood ratio was 0.6 at baseline, 0.5 adding standard read, and 0.1 adding specialized read. Standard read modestly improved prediction of pECE, whereas specialized read improved it moderately.Patient summaryThe incremental benefit of mpMRI over clinical information is small but increases to moderate with a specialized second opinion. This second opinion may be useful when considering active surveillance, nerve-sparing surgery, or focal therapy

Phage Display Approaches for the Isolation of Monoclonal Antibodies Against Dengue Virus Envelope Domain III from Human and Mouse Derived Libraries

Domain III of the dengue virus envelope protein (EDIII, aa295-395) has an immunoglobulin fold and is the proposed receptor-binding domain of the virus. Previous studies have shown that monoclonal antibodies against EDIII can be neutralizing and have therapeutic potential. Here, cloned Fab-phage libraries of human and mouse origin were screened for DENV specific antibodies. Firstly, bacterially expressed EDIII or whole virus particles were used as bait in biopanning against a large naïve human Fab-phage library (>10 billion independent clones). Multiple panning strategies were employed, and in excess of 1000 clones were screened, but all of the antibodies identified bound the envelope in regions outside EDIII suggesting EDIII antibodies are virtually absent from the naïve human repertoire. Next, a chimeric Fab-phage library was constructed from a panel of EDIII specific mouse hybridomas by pooling the VH and VL chain sequences from the hybridomas and cloning these into the pComb3X phagemid vector with human CH and CL encoding sequences. Biopanning against EDIII identified a unique antibody (C9) that cross-reacts with EDIII from DENV1-3 and, in the IgG format, binds and neutralizes DENV2 in cell-based assays. Sequence analysis and saturation mutagenesis of complementary determining regions (CDR) in the C9 light chain suggest an antigen recognition model in which the LCDR3 is a key determinant of EDIII specificity, while modifications in LCDR1 and LCDR2 affect DENV serotype cross-reactivity. Overall, this study supports the current prevailing opinion that neutralizing anti-EDIII monoclonal antibodies can be readily generated in murine systems, but in humans the anti-DENV immune response is directed away from domain III

Highly multimode memory in a crystal

We experimentally demonstrate the storage of 1060 temporal modes onto a thulium-doped crystal using an atomic frequency comb (AFC). The comb covers 0.93 GHz defining the storage bandwidth. As compared to previous AFC preparation methods (pulse sequences i.e. amplitude modulation), we only use frequency modulation to produce the desired optical pumping spectrum. To ensure an accurate spectrally selective optical pumping, the frequency modulated laser is self-locked on the atomic comb. Our approach is general and should be applicable to a wide range of rare-earth doped material in the context of multimode quantum memory

Nodeless superconductivity in the noncentrosymmetric ThIrSi compound

The ThIrSi superconductor, with $T_c = 6.5$ K, is expected to show unusual features in view of its noncentrosymmetric structure and the presence of heavy elements featuring a sizable spin-orbit coupling. Here, we report a comprehensive study of its electronic properties by means of local-probe techniques: muon-spin rotation and relaxation ({\textmu}SR) and nuclear magnetic resonance (NMR). Both the superfluid density $\rho_\mathrm{sc}(T)$ (determined via transverse-field {\textmu}SR) and the spin-lattice relaxation rate $T_1^{-1}(T)$ (determined via NMR) suggest a nodeless superconductivity. Furthermore, the absence of spontaneous magnetic fields below $T_c$, as evinced from zero-field {\textmu}SR measurements, indicates a preserved time-reversal symmetry in the superconducting state of ThIrSi. Temperature-dependent upper critical fields as well as field-dependent superconducting muon-spin relaxations suggest the presence of multiple superconducting gaps in ThIrSi.Comment: 8 pages, 8 figure