Efficient chaining of seeds in ordered trees

We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. For the chaining problem with a set of m constant size seeds, we describe an algorithm with complexity O(m2 log(m)) in time and O(m2) in space

Ce and U speciation in wasteforms for thermal treatment of plutonium bearing wastes, probed by L3 edge XANES

X-ray absorption spectroscopy was applied to understand the speciation of elements relevant to the immobilisation and disposal of radioactive plutonium bearing wastes, utilizing Ce as a Pu surrogate. Ce L3 XANES (X-ray Absorption Near Edge Structure) characterisation of a crystallised glass material produced by cold crucible plasma vitrification, at demonstration scale, evidenced incorporation as Ce3+ within the glass phase, providing an important validation of laboratory scale studies. U and Ce L3 XANES investigation of brannerite ceramics, U0.9Ce0.1Ti2O6, synthesized under oxidizing, neutral and reducing conditions, established the charge compensation mechanism as incorporation of Ce3+ through formation of U5+ and/or U6+ In each of these examples, X-ray Absorption Spectroscopy has provided a pivotal understanding of element speciation in relation to the mechanism of incorporation within the host wasteform intended for geological disposal

Replica Symmetry Breaking in Attractor Neural Network Models

The phenomenon of replica symmetry breaking is investigated for the retrieval phases of Hopfield-type network models. The basic calculation is done for the generalized version of the standard model introduced by Horner [1] and by Perez-Vicente and Amit [2] which can exhibit low mean levels of neural activity. For a mean activity $\bar a =1/2$ the Hopfield model is recovered. In this case, surprisingly enough, we cannot confirm the well known one step replica symmetry breaking (1RSB) result for the storage capacity which was presented by Crisanti, Amit and Gutfreund [3] (\alpha_c^{\hbox{\mf 1RSB}}\simeq 0.144). Rather, we find that 1RSB- and 2RSB-Ans\"atze yield only slightly increased capacities as compared to the replica symmetric value (\alpha_c^{\hbox{\mf 1RSB}}\simeq 0.138\,186 and \alpha_c^{\hbox{\mf 2RSB}}\simeq 0.138\,187 compared to \alpha_c^{\hbox{\mf RS}}\simeq 0.137\,905), significantly smaller also than the value \alpha_c^{\hbox{\mf sim}} = 0.145\pm 0.009 reported from simulation studies. These values still lie within the recently discovered reentrant phase [4]. We conjecture that in the infinite Parisi-scheme the reentrant behaviour disappears as is the case in the SK-spin-glass model (Parisi--Toulouse-hypothesis). The same qualitative results are obtained in the low activity range.Comment: Latex file, 20 pages, 8 Figures available from the authors upon request, HD-TVP-94-

Comprehensive Geriatric Assessment in hospital and hospital-at-home settings: a mixed-methods study

Background: The Comprehensive Geriatric Assessment (CGA) is a multidisciplinary process that determines a frail older person’s medical, functional, psychological and social capability to ensure that they have a co-ordinated plan for treatment and follow-up. Objectives: To improve our understanding of the effectiveness, cost-effectiveness and implementation of the CGA across hospital and hospital-at-home settings. Methods: We used a variety of methods. We updated a Cochrane review of randomised trials of the CGA in hospital for older people aged ≥ 65 years, conducted a national survey of community CGA, analysed data from three health boards using propensity score matching (PSM) and regression analysis, conducted a qualitative study and used a modified Delphi method. Results: We included 29 trials recruiting 13,766 participants in the Cochrane review of the CGA. Older people admitted to hospital who receive the CGA are more likely to be living at home at 3–12 months’ follow-up [relative risk (RR) 1.06, 95% confidence interval (CI) 1.01 to 1.10] (high certainty). The probability that the CGA would be cost-effective at a £20,000 ceiling ratio for quality-adjusted life-years (QALYs), life-years (LYs) and LYs living at home was 0.50, 0.89, and 0.47, respectively (low-certainty evidence). After PSM and regression analysis comparing CGA hospital with CGA hospital at home, we found that the health-care cost (from admission to 6 months after discharge) in site 1 was lower in hospital at home (ratio of means 0.82, 95% CI 0.76 to 0.89), in site 2 there was little difference (ratio of means 1.00, 95% CI 0.92 to 1.09) and in site 3 it was higher (ratio of means 1.15, 95% CI 0.99 to 1.33). Six months after discharge (excluding the index admission), the ratio of means cost in site 1 was 1.27 (95% CI 1.14 to 1.41), in site 2 was 1.09 (95% CI 0.95 to 1.24) and in site 3 was 1.70 (95% CI 1.40 to 2.07). At 6 months’ follow-up (excluding the index admission), there may be an increased risk of mortality (adjusted) in the three hospital-at-home cohorts (site 1: RR 1.09, 95% CI 1.00 to 1.19; site 2: RR 1.29, 95% CI 1.15 to 1.44; site 3: RR 1.27, 95% CI 1.06 to 1.54). The qualitative research indicates the importance of relational aspects of health care, incorporating caregivers’ knowledge in care planning, and a lack of clarity about the end of an episode of health care. Core components that should be included in CGA focus on functional, physical and mental well-being, medication review and a caregiver’s ability to care. Limitations: The risk of residual confounding limits the certainty of the findings from the PSM analysis; a second major limitation is that the research plan did not include an investigation of social care or primary care. Conclusions: The CGA is an effective way to organise health care for older people in hospital and may lead to a small increase in costs. There may be an increase in cost and the risk of mortality in the population who received the CGA hospital at home compared with those who received the CGA in hospital; randomised evidence is required to confirm or refute this. Caregiver involvement in the CGA process could be strengthened. Funding: The National Institute for Health Research Health Services and Delivery Research programme

Finite dimensional corrections to mean field in a short-range p-spin glassy model

In this work we discuss a short range version of the $p$-spin model. The model is provided with a parameter that allows to control the crossover with the mean field behaviour. We detect a discrepancy between the perturbative approach and numerical simulation. We attribute it to non-perturbative effects due to the finite probability that each particular realization of the disorder allows for the formation of regions where the system is less frustrated and locally freezes at a higher temperature.Comment: 18 pages, 5 figures, submitted to Phys Rev

Ramsar Wetlands of International Importance–improving conservation outcomes

The Ramsar Convention (or the Convention on Wetlands), signed in 1971, was one of the first international conservation agreements, promoting global wise use of wetlands. It has three primary objectives: national designation and management of wetlands of international importance; general wise use of wetlands; and international cooperation. We examined lessons learnt for improving wetland conservation after Ramsar’s nearly five decades of operation. The number of wetlands in the Ramsar Site Network has grown over time (2,391 Ramsar Sites, 2.5 million km2, as at 2020-06-09) but unevenly around the world, with decreasing rate of growth in recent decades. Ramsar Sites are concentrated in countries with a high Gross Domestic Product and human pressure (e.g., western Europe) but, in contrast, Ramsar Sites with the largest wetland extent are in central-west Africa and South America. We identified three key challenges for improving effectiveness of the Ramsar Site Network: increasing number of sites and wetland area, improved representation (functional, geographical and biological); and effective management and reporting. Increasing the number of sites and area in the Ramsar network could benefit from targets, implemented at national scales. Knowledge of representativeness is inadequate, requiring analyses of functional ecotypes, geographical and biological representativeness. Finally, most countries have inadequate management planning and reporting on the ecological character of their Ramsar Sites, requiring more focused attention on a vision and objectives, with regular reporting of key indicators to guide management. There are increasing opportunities to rigorously track ecological character, utilizing new tools and available indicators (e.g., remote sensing). It is critical that the world protect its wetlands, with an effective Ramsar Convention or the Convention on Wetlands at the core

A Model for the Stray Light Contamination of the UVCS Instrument on SOHO

We present a detailed model of stray-light suppression in the spectrometer channels of the Ultraviolet Coronagraph Spectrometer (UVCS) on the SOHO spacecraft. The control of diffracted and scattered stray light from the bright solar disk is one of the most important tasks of a coronagraph. We compute the fractions of light that diffract past the UVCS external occulter and non-specularly pass into the spectrometer slit. The diffracted component of the stray light depends on the finite aperture of the primary mirror and on its figure. The amount of non-specular scattering depends mainly on the micro-roughness of the mirror. For reasonable choices of these quantities, the modeled stray-light fraction agrees well with measurements of stray light made both in the laboratory and during the UVCS mission. The models were constructed for the bright H I Lyman alpha emission line, but they are applicable to other spectral lines as well.Comment: 19 pages, 5 figures, Solar Physics, in pres

Statistical mechanics of image restoration and error-correcting codes

We develop a statistical-mechanical formulation for image restoration and error-correcting codes. These problems are shown to be equivalent to the Ising spin glass with ferromagnetic bias under random external fields. We prove that the quality of restoration/decoding is maximized at a specific set of parameter values determined by the source and channel properties. For image restoration in mean-field system a line of optimal performance is shown to exist in the parameter space. These results are illustrated by solving exactly the infinite-range model. The solutions enable us to determine how precisely one should estimate unknown parameters. Monte Carlo simulations are carried out to see how far the conclusions from the infinite-range model are applicable to the more realistic two-dimensional case in image restoration.Comment: 20 pages, 9 figures, ReVTe

All-Optical Broadband Excitation of the Motional State of Trapped Ions

We have developed a novel all-optical broadband scheme for exciting, amplifying and measuring the secular motion of ions in a radio frequency trap. Oscillation induced by optical excitation has been coherently amplified to precisely control and measure the ion's secular motion. Requiring only laser line-of-sight, we have shown that the ion's oscillation amplitude can be precisely controlled. Our excitation scheme can generate coherent motion which is robust against variations in the secular frequency. Therefore, our scheme is ideal to excite the desired level of oscillatory motion under conditions where the secular frequency is evolving in time. Measuring the oscillation amplitude through Doppler velocimetry, we have characterized the experimental parameters and compared them with a molecular dynamics simulation which provides a complete description of the system.Comment: 8 pages, 10 figure

Checkpoint inhibition reduces the threshold for Drug-Specific T-Cell priming and increases the incidence of sulfasalazine hypersensitivity

An emerging clinical issue associated with immune-oncology agents is the collateral effects on the tolerability of concomitant medications. One report of this phenomenon was the increased incidence of hypersensitivity reactions observed in patients receiving concurrent immune checkpoint inhibitors (ICIs) and sulfasalazine (SLZ). Thus, the aim of this study was to characterize the T cells involved in the pathogenesis of such reactions, and recapitulate the effects of inhibitory checkpoint blockade on de-novo priming responses to compounds within in vitro platforms. A regulatory competent human dendritic cell/T-cell coculture assay was used to model the effects of ICIs on de novo nitroso sulfamethoxazole- and sulfapyridine (SP) (the sulfonamide component of SLZ) hydroxylamine-specific priming responses. The role of T cells in the pathogenesis of the observed reactions was explored in 3 patients through phenotypic characterization of SP/sulfapyridine hydroxylamine (SPHA)-responsive T-cell clones (TCC), and assessment of cross-reactivity and pathways of T-cell activation. Augmentation of the frequency of responding drug-specific T cells and intensity of the T-cell response was observed with PD-1/PD-L1 blockade. Monoclonal populations of SP- and SPHA-responsive T cells were isolated from all 3 patients. A core secretory effector molecule profile (IFN-γ, IL-13, granzyme B, and perforin) was identified for SP and SPHA-responsive TCC, which proceeded through Pi and hapten mechanisms, respectively. Data presented herein provides evidence that drug-responsive T cells are effectors of hypersensitivity reactions observed in oncology patients administered ICIs and SLZ. Perturbation of drug-specific T-cell priming is a plausible explanation for clinical observations of how an increased incidence of these adverse events is occurring