An efficient quantum circuit analyser on qubits and qudits

This paper presents a highly efficient decomposition scheme and its associated Mathematica notebook for the analysis of complicated quantum circuits comprised of single/multiple qubit and qudit quantum gates. In particular, this scheme reduces the evaluation of multiple unitary gate operations with many conditionals to just two matrix additions, regardless of the number of conditionals or gate dimensions. This improves significantly the capability of a quantum circuit analyser implemented in a classical computer. This is also the first efficient quantum circuit analyser to include qudit quantum logic gates

Using segmented regression analysis of interrupted time series data to assess colonoscopy quality outcomes of a web-enhanced implementation toolkit to support evidence-based practices for bowel preparation: A study protocol

BACKGROUND: While there is convincing evidence on interventions to improve bowel preparation for patients, the evidence on how to implement these evidence-based practices (EBPs) in outpatient colonoscopy settings is less certain. The Strategies to Improve Colonoscopy (STIC) study compares the effect of two implementation strategies, physician education alone versus physician education plus an implementation toolkit for staff, on adoption of three EBPs (split-dosing of bowel preparation, low-literacy education, teach-back) to improve pre-procedure and intra-procedure quality measures. The implementation toolkit contains a staff education module, website containing tools to support staff in delivering EBPs, tailored patient education materials, and brief consultation with staff to determine how the EBPs can be integrated into the existing workflow. Given adaptations to the implementation plan and intentional flexibility in the delivery of the EBPs, we utilize a pragmatic study to balance external validity with demonstrating effectiveness of the implementation strategies. METHODS/DESIGN: Participants will include all outpatient colonoscopy physicians, staff, and patients from a convenience sample of six endoscopy settings. Aim #1 will explore the relative effect of two strategies to implement patient-level EBPs on adoption and clinical quality outcomes. We will assess the change in level and trends of clinical quality outcomes (i.e., adequacy of bowel preparation, adenoma detection) using segmented regression analysis of interrupted time series data with two groups (intervention and delayed start). Aim #2 will examine the influence of organizational readiness to change on EBP implementation. We use a PRECIS diagram to reflect the extent to which each indicator of the study was pragmatic versus explanatory, revealing a largely pragmatic study. DISCUSSION: Implementation challenges have already motivated several adaptations to the original plan, reflecting the nature of implementation in real-world healthcare settings. The pragmatic study responds to the evolving needs of its healthcare partners and allows for flexibility in intervention delivery, thereby informing clinical decision-making in real-world settings. The current study will provide information about what works (intervention effectiveness), for whom it works (influence of Medicaid versus other insurance), in which contexts it works (setting characteristics that influence implementation), and how it works best (comparison of implementation strategies). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13012-015-0276-3) contains supplementary material, which is available to authorized users

Conservation of context-dependent splicing activity in distant Muscleblind homologs

The Muscleblind (MBL) protein family is a deeply conserved family of RNA binding proteins that regulate alternative splicing, alternative polyadenylation, RNA stability and RNA localization. Their inactivation due to sequestration by expanded CUG repeats causes symptoms in the neuromuscular disease myotonic dystrophy. MBL zinc fingers are the most highly conserved portion of these proteins, and directly interact with RNA. We identified putative MBL homologs in Ciona intestinalis and Trichoplax adhaerens, and investigated their ability, as well as that of MBL homologs from human/mouse, fly and worm, to regulate alternative splicing. We found that all homologs can regulate alternative splicing in mouse cells, with some regulating over 100 events. The cis-elements through which each homolog exerts its splicing activities are likely to be highly similar to mammalian Muscleblind-like proteins (MBNLs), as suggested by motif analyses and the ability of expanded CUG repeats to inactivate homolog-mediated splicing. While regulation of specific target exons by MBL/MBNL has not been broadly conserved across these species, genes enriched for MBL/MBNL binding sites in their introns may play roles in cell adhesion, ion transport and axon guidance, among other biological pathways, suggesting a specific, conserved role for these proteins across a broad range of metazoan species.National Institutes of Health (U.S.) (DP5 OD017865

Quantum states and intertwining phases in kagome materials

In solid materials, nontrivial topological states, electron correlations, and magnetism are central ingredients for realizing quantum properties, including unconventional superconductivity, charge and spin density waves, and quantum spin liquids. The Kagome lattice, made up of connected triangles and hexagons, can host these three ingredients simultaneously and has proven to be a fertile platform for studying diverse quantum phenomena including those stemming from the interplay of these ingredients. In this review, we introduce the fundamental properties of the Kagome lattice as well as discuss the complex observed phenomena seen in several emergent material systems such as the intertwining of charge order and superconductivity in some Kagome metals, modulation of magnetism and topology in some Kagome magnets, and symmetry breaking with Mott physics in the breathing Kagome insulators. We also highlight many open questions in the field as well as future research directions of Kagome systems

Immunochemical characterization of polysaccharide antigens from six clinical strains of Enterococci

BACKGROUND: Enterococci have become major nosocomial pathogens due to their intrinsic and acquired resistance to a broad spectrum of antibiotics. Their increasing drug resistance prompts us to search for prominent antigens to develop vaccines against enterococci. Given the success of polysaccharide-based vaccines against various bacterial pathogens, we isolated and characterized the immunochemical properties of polysaccharide antigens from five strains of Enterococcus faecalis and one strain of vancomycin-resistant E. faecium. RESULTS: We cultured large batches of each strain, isolated sufficient quantities of polysaccharides, analyzed their chemical structures, and compared their antigenic specificity. Three classes of polysaccharides were isolated from each strain, including a polyglucan, a teichoic acid, and a heteroglycan composed of rhamnose, glucose, galactose, mannosamine, and glucosamine. The polyglucans from all six strains are identical and appear to be dextran. Yields of the teichoic acids were generally low. The most abundant polysaccharides are the heteroglycans. The six heteroglycans are structurally different as evidenced by NMR spectroscopy. They also differ in their antigenic specificities as revealed by competitive ELISA. The heteroglycans are not immunogenic by themselves but conjugation to protein carriers significantly enhanced their ability to induce antibodies. CONCLUSION: The six clinical strains of enterococci express abundant, strain-specific cell-surface heteroglycans. These polysaccharides may provide a molecular basis for serological typing of enterococcal strains and antigens for the development of vaccines against multi-drug resistant enterococci

Paradoxical protection from atherosclerosis and thrombosis in a mouse model of sickle cell disease

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98139/1/bjh12342.pd

RANKL Employs Distinct Binding Modes to Engage RANK and the Osteoprotegerin Decoy Receptor

SummaryOsteoprotegerin (OPG) and receptor activator of nuclear factor κB (RANK) are members of the tumor necrosis factor receptor (TNFR) superfamily that regulate osteoclast formation and function by competing for RANK ligand (RANKL). RANKL promotes osteoclast development through RANK activation, while OPG inhibits this process by sequestering RANKL. For comparison, we solved crystal structures of RANKL with RANK and RANKL with OPG. Complementary biochemical and functional studies reveal that the monomeric cytokine-binding region of OPG binds RANKL with ∼500-fold higher affinity than RANK and inhibits RANKL-stimulated osteoclastogenesis ∼150 times more effectively, in part because the binding cleft of RANKL makes unique contacts with OPG. Several side chains as well as the C-D and D-E loops of RANKL occupy different orientations when bound to OPG versus RANK. High affinity OPG binding requires a 90s loop Phe residue that is mutated in juvenile Paget’s disease. These results suggest cytokine plasticity may help to fine-tune specific tumor necrosis factor (TNF)-family cytokine/receptor pair selectivity

Fluctuations and differential contraction during regeneration of Hydra vulgaris tissue toroids

We studied regenerating bilayered tissue toroids dissected from Hydra vulgaris polyps and relate our macroscopic observations to the dynamics of force-generating mesoscopic cytoskeletal structures. Tissue fragments undergo a specific toroid-spheroid folding process leading to complete regeneration towards a new organism. The time scale of folding is too fast for biochemical signalling or morphogenetic gradients which forced us to assume purely mechanical self-organization. The initial pattern selection dynamics was studied by embedding toroids into hydro-gels allowing us to observe the deformation modes over longer periods of time. We found increasing mechanical fluctuations which break the toroidal symmetry and discuss the evolution of their power spectra for various gel stiffnesses. Our observations are related to single cell studies which explain the mechanical feasibility of the folding process. In addition, we observed switching of cells from a tissue bound to a migrating state after folding failure as well as in tissue injury. We found a supra-cellular actin ring assembled along the toroid's inner edge. Its contraction can lead to the observed folding dynamics as we could confirm by finite element simulations. This actin ring in the inner cell layer is assembled by myosin- driven length fluctuations of supra-cellular {\alpha}-actin structures (myonemes) in the outer cell-layer.Comment: 19 pages and 8 figures, submitted to New Journal of Physic

The Functional Nasal Anatomy of the Pike, <i>Esox lucius</i> L.

Olfactory flow in fishes is a little-explored area of fundamental and applied importance. We investigated olfactory flow in the pike, Esox lucius, because it has an apparently simple and rigid nasal region. We characterised olfactory flow by dye visualisation and computational fluid dynamics, using models derived from X-ray micro-computed tomography scans of two preserved specimens. An external current induced a flow of water through the nasal chamber at physiologically relevant Reynolds numbers (200 – 300). We attribute this externally-induced flow to: the location of the incurrent nostril in a region of high static pressure; the nasal bridge deflecting external flow into the nasal chamber; an excurrent nostril normal to external flow; and viscous entrainment. A vortex in the incurrent nostril may be instrumental in viscous entrainment. Flow was dispersed over the olfactory sensory surface when it impacted on the floor of the nasal chamber. Dispersal may be assisted by: the radial array of nasal folds; a complementary interaction between a posterior nasal fold and the ventral surface of the nasal bridge; and the incurrent vortex. The boundary layer could delay considerably (up to ~ 3 s) odorant transport from the external environment to the nasal region. The drag incurred by olfactory flow was almost the same as the drag incurred by models in which the nasal region had been replaced by a smooth surface. The boundary layer does not detach from the nasal region. We conclude that the nasal bridge and the incurrent vortex are pivotal to olfaction in the pike