Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation

BACKGROUND: Overlapping transcripts in antisense orientation have the potential to form double-stranded RNA (dsRNA), a substrate for a number of different RNA-modification pathways. One prominent route for dsRNA is its breakdown by Dicer enzyme complexes into small RNAs, a pathway that is widely exploited by RNA interference technology to inactivate defined genes in transgenic lines. The significance of this pathway for endogenous gene regulation remains unclear. RESULTS: We have examined transcription data for overlapping gene pairs in Arabidopsis thaliana. On the basis of an analysis of transcripts with coding regions, we find the majority of overlapping gene pairs to be convergently overlapping pairs (COPs), with the potential for dsRNA formation. In all tissues, COP transcripts are present at a higher frequency compared to the overall gene pool. The probability that both the sense and antisense copy of a COP are co-transcribed matches the theoretical value for coexpression under the assumption that the expression of one partner does not affect the expression of the other. Among COPs, we observe an over-representation of spliced (intron-containing) genes (90%) and of genes with alternatively spliced transcripts. For loci where antisense transcripts overlap with sense transcript introns, we also find a significant bias in favor of alternative splicing and variation of polyadenylation. CONCLUSION: The results argue against a predominant RNA degradation effect induced by dsRNA formation. Instead, our data support alternative roles for dsRNAs. They suggest that at least for a subgroup of COPs, antisense expression may induce alternative splicing or polyadenylation

Trace element and isotope constraints on crustal anatexis by upwelling mantle melts in the North Atlantic Igneous Province: an example form the Isle of Rum, NW Scotland

Sr and Nd isotope ratios, together with lithophile trace elements, have been measured in a representative set of igneous rocks and Lewisian gneisses from the Isle of Rum in order to unravel the petrogenesis of the felsic rocks that erupted in the early stages of Palaeogene magmatism in the North Atlantic Igneous Province (NAIP). The Rum rhyodacites appear to be the products of large amounts of melting of Lewisian amphibolite gneiss. The Sr and Nd isotopic composition of the magmas can be explained without invoking an additional granulitic crustal component. Concentrations of the trace element Cs in the rhyodacites strongly suggests that the gneiss parent rock had experienced Cs and Rb loss prior to Palaeogene times, possibly during a Caledonian event. This depletion caused heterogeneity with respect to 87Sr/86Sr in the crustal source of silicic melts. Other igneous rock types on Rum (dacites, early gabbros) are mixtures of crustalmelts and and primarymantle melts. Forward Rare Earth Element modelling shows that late stage picritic melts on Rum are close analogues for the parent melts of the Rum Layered Suite, and for the mantle melts that caused crustal anatexis of the Lewisian gneiss. These primary mantle melts have close affinities to Mid-Oceanic Ridge Basalts (MORB), whose trace element content varies from slightly depleted to slightly enriched. Crustal anatexis is a common process in the rift-to-drift evolution during continental break-up and the formation of Volcanic Rifted Margins systems. The ‘early felsic–later mafic’ volcanic rock associations from Rum are compared to similar associations recovered from the now-drowned seaward-dipping wedges on the shelf of SE Greenland and on the Vøring Plateau (Norwegian Sea). These three regions show geochemical differences that result from variations in the regional crustal composition and the depth at which crustal anatexis took place

Carbenicillin-induced coagulopathy

In high dosage, carbenicillin may interfere with the conversion of fibrinogen to fibrin and result in a haemorrhagic diathesis. The effect is dose-dependent and requires a high concentration of carbenicillin in plasma. Such a level may be attained in renal failure unless the dose of the drug is appropriately reduced. In such situations the screening coagulation tests may be prolonged and this should alert one to the development of a haemorrhagic diathesis due to the drug.S. Afr. Med. J., 48, 457 (1974)

Toward Common Data Elements for International Research in Long-term Care Homes: Advancing Person-Centered Care

To support person-centered, residential long-term care internationally, a consortium of researchers in medicine, nursing, behavioral, and social sciences from 21 geographically and economically diverse countries have launched the WE-THRIVE consortium to develop a common data infrastructure. WE-THRIVE aims to identify measurement domains that are internationally relevant, including in low-, middle-, and high-income countries, prioritize concepts to operationalize domains, and specify a set of data elements to measure concepts that can be used across studies for data sharing and comparisons. This article reports findings from consortium meetings at the 2016 meeting of the Gerontological Society of America and the 2017 meeting of the International Association of Gerontology and Geriatrics, to identify domains and prioritize concepts, following best practices to identify common data elements (CDEs) that were developed through the US National Institutes of Health/National Institute of Nursing Research's CDEs initiative. Four domains were identified, including organizational context, workforce and staffing, person-centered care, and care outcomes. Using a nominal group process, WE-THRIVE prioritized 21 concepts across the 4 domains. Several concepts showed similarity to existing measurement structures, whereas others differed. Conceptual similarity (convergence; eg, concepts in the care outcomes domain of functional level and harm-free care) provides further support of the critical foundational work in LTC measurement endorsed and implemented by regulatory bodies. Different concepts (divergence; eg, concepts in the person-centered care domain of knowing the person and what matters most to the person) highlights current gaps in measurement efforts and is consistent with WE-THRIVE's focus on supporting resilience and thriving for residents, family, and staff. In alignment with the World Health Organization's call for comparative measurement work for health systems change, WE-THRIVE's work to date highlights the benefits of engaging with diverse LTC researchers, including those in low-, middle-, and high-income countries, to develop a measurement infrastructure that integrates the aspirations of person-centered LTC

Characterizing the entanglement of symmetric many-particle spin-1/2 systems

Analyzing the properties of entanglement in many-particle spin-1/2 systems is generally difficult because the system's Hilbert space grows exponentially with the number of constituent particles, $N$. Fortunately, it is still possible to investigate many-particle entanglement when the state of the system possesses sufficient symmetry. In this paper, we present a practical method for efficiently computing various bipartite entanglement measures for states in the symmetric subspace and perform these calculations for $N\sim 10^3$. By considering all possible bipartite splits, we construct a picture of the multiscale entanglement in large symmetric systems. In particular, we characterize dynamically generated spin-squeezed states by comparing them to known reference states (e.g., GHZ and Dicke states) and new families of states with near-maximal bipartite entropy. We quantify the trade-off between the degree of entanglement and its robustness to particle loss, emphasizing that substantial entanglement need not be fragile.Comment: Updated version reflects changes made in January 200

Geometric Strategy for the Optimal Quantum Search

We explore quantum search from the geometric viewpoint of a complex projective space $CP$, a space of rays. First, we show that the optimal quantum search can be geometrically identified with the shortest path along the geodesic joining a target state, an element of the computational basis, and such an initial state as overlaps equally, up to phases, with all the elements of the computational basis. Second, we calculate the entanglement through the algorithm for any number of qubits $n$ as the minimum Fubini-Study distance to the submanifold formed by separable states in Segre embedding, and find that entanglement is used almost maximally for large $n$. The computational time seems to be optimized by the dynamics as the geodesic, running across entangled states away from the submanifold of separable states, rather than the amount of entanglement itself.Comment: revtex, 10 pages, 7 eps figures, uses psfrag packag

Ab initio study of ferroelectric domain walls in PbTiO3

We have investigated the atomistic structure of the 180-degree and 90-degree domain boundaries in the ferroelectric perovskite compound PbTiO3 using a first-principles ultrasoft-pseudopotential approach. For each case we have computed the position, thickness and creation energy of the domain walls, and an estimate of the barrier height for their motion has been obtained. We find both kinds of domain walls to be very narrow with a similar width of the order of one to two lattice constants. The energy of the 90-dergree domain wall is calculated to be 35 mJ/m^2, about a factor of four lower than the energy of its 180-degree counterpart, and only a miniscule barrier for its motion is found. As a surprising feature we detected a small offset of 0.15-0.2 eV in the electrostatic potential across the 90-degree domain wall.Comment: 12 pages, with 9 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/bm_dw/index.htm

Recommended Common Data Elements for International Research in Long-Term Care Homes: Exploring the Workforce and Staffing Concepts of Staff Retention and Turnover

The aim of this review is to develop a common data element for the concept of staff retention and turnover within the domain of workforce and staffing. This domain is one of four core domains identified by the WE-THRIVE (Worldwide Elements to Harmonize Research in Long-Term Care Living Environments) group in an effort to establish an international, person-centered long-term care research infrastructure. A rapid review identified different measurement methods to assess either turnover or retention at facility level or intention to leave or stay at the individual staff level. The selection of a recommended measurement was guided by the WE-THRIVE group’s focus on capacity rather than deficits, the expected availability of internationally comparable data, and the goal to provide a short, ecologically viable measurement. We therefore recommend to measure staff’s intention to stay with a single item, at the individual staff level. This element, we argue, is an indicator of staff stability, which is important for reduced organizational cost and improved productivity, positive work environment, and better resident–staff relationships and quality of care

Tilt order parameters, polarity and inversion phenomena in smectic liquid crystals

The order parameters for the phenomenological description of the smectic-{\it A} to smectic-{\it C} phase transition are formulated on the basis of molecular symmetry and structure. It is shown that, unless the long molecular axis is an axis of two-fold or higher rotational symmetry, the ordering of the molecules in the smectic-{\it C} phase gives rise to more than one tilt order parameter and to one or more polar order parameters. The latter describe the indigenous polarity of the smectic-{\it C} phase, which is not related to molecular chirality but underlies the appearance of spontaneous polarisation in chiral smectics. A phenomenological theory of the phase transition is formulated by means of a Landau expansion in two tilt order parameters (primary and secondary) and an indigenous polarity order parameter. The coupling among these order parameters determines the possibility of sign inversions in the temperature dependence of the spontaneous polarisation and of the helical pitch observed experimentally for some chiral smectic-{\it $C^{\ast}$} materials. The molecular interpretation of the inversion phenomena is examined in the light of the new formulation.Comment: 12 pages, 5 figures, RevTe

A first-principles study of oxygen vacancy pinning of domain walls in PbTiO3

We have investigated the interaction of oxygen vacancies and 180-degree domain walls in tetragonal PbTiO3 using density-functional theory. Our calculations indicate that the vacancies do have a lower formation energy in the domain wall than in the bulk, thereby confirming the tendency of these defects to migrate to, and pin, the domain walls. The pinning energies are reported for each of the three possible orientations of the original Ti-O-Ti bonds, and attempts to model the results with simple continuum models are discussed.Comment: 8 pages, with 3 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/lh_dw/index.htm